EDITORIAL BOARD
EDITOR-IN-CHIEF
Professor IRENA ROTERMAN-KONIECZNA
Medical College  Jagiellonian University, Krakow, st. Lazarza 16
HONORARY ADVISOR
Professor RYSZARD TADEUSIEWICZ
AGH  University of Science and Technology
Professor JAN TRĄBKA
Medical College  Jagiellonian University
MANAGING EDITORS
BIOCYBERNETICS  Professor PIOTR AUGUSTYNIAK
AGH  University of Science and Technology, Krakow, al. Mickiewicza 30
BIOLOGICAL DISCIPLINES  Professor LESZEK KONIECZNY
Medical College  Jagiellonian University, Krakow, Kopernika 7
MEDICINE  Professor KALINA KAWECKA-JASZCZ
Medical College  Jagiellonian University, Krakow, Pradnicka 80
PHARMACOLOGY  Professor STEFAN CHA
OPICKI
Medical College  Jagiellonian University, Krakow, Grzegórzecka 16
PHYSICS  Professor STANISA
AW MICEK
Faculty of Physics  Jagiellonian University, Krakow, Reymonta 4
MEDICAL INFORMATICS AND COMPUTER SCIENCE  Professor MAREK OGIELA
AGH  University of Science and Technology, Krakow, al. Mickiewicza 30
TELEMEDICINE  Professor ROBERT RUDOWSKI
Medical Academy, Warsaw, Banacha 1a
 Dr SYBILLA STANISA
AWSKA-KLOC
LAW (and contacts with business)  Dr SYBILLA STANISA
AWSKA-KLOC
Law Faculty  Jagiellonian University, Krakow, Kanoniczna 14, Institute of Intellectual Property Law
Law Faculty  Jagiellonian University, Krakow, Kanonicza 4
ASSOCIATE EDITORS
Medical College  Jagiellonian University, Krakow, Kopernika 7e
EDITOR-IN-CHARGE  PIOTR WALECKI
E-LEARNING (project-related)  ANDRZEJ KONONOWICZ
E-LEARNING (general)  WIESA
AW PYRCZAK
DISCUSSION FORUMS  WOJCIECH LASOŃ
ENCRYPTION  KRZYSZTOF SARAPATA
TECHNICAL SUPPORT
Medical College  Jagiellonian University, Krakow, st. Lazarza 16
ZDZISA
AW WIR
NIOWSKI  in charge
WOJCIECH ZIAJKA
ANNA ZAREMBA-R
MIETAŃSKA
PoIish Ministry of Science and Higher Education journaI rating: 4.000
3.000
Sustaining institution: Ministry of Science and Higher Education
Edition: 300 copies
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ISSN 1895-9091 (print version)
ISSN 1896-530X (electronic version)
http://www.bams.cm-uj.krakow.pl
Contents
OPENING PAPER
5 Why and how should a virtual patient be constructed?
Paweł Spólnik
BIOINFORMATICS
9 VoGE  java application for presentation of Never Born Proteins gene structure elements
Monika Piwowar, Ewa Matczyńska, Filip Pomański, Adrian Kośmider, Damian Kość, Michał Swatowski,
Piotr Więcek, Tomasz Szepieniec
15 Unfolding simulation to verify the concept of limited conformational sub-space for early-stage
intermediate
Piotr Kiełkowicz, Irena Roterman
DIGITAL IMAGE ANALISIS
25 Computational Analysis of Prostate Perfusion Images  a Preliminary Report
Jacek Śmietański, Ryszard Tadeusiewicz
E-LEARNING
31 Usage of naive bayes classifi er in decision module of e-learning decision support system
Marcin Chabior, Anna Noga, Magdalena Tkacz
35 E-learning with use of virtual patient in pharmacy education
Krzysztof Nesterowicz, Sebastian Polak
EXPERT SYSTEM
39 Interactive knowledge base for expert system
Anna Noga, Marcin Chabior, Grzegorz Sapota
TELEMATICS
45 Speech perception  toward understanding of consciousness
Jan Trąbka, Piotr Walecki, Wojciech Lasoń, Wiesław Pyrczak, Krzysztof Sarapata
51 Neuroinformatic modelling of oculomotor system
Piotr Walecki
TELEMEDICINE
59 HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition and Storage
System for Knowledge Discovery Tasks within an Electronic Platform for Managing Heart Failure
Patients
Andrzej A. Kononowicz, Katarzyna Styczkiewicz, Bogumiła Bacior, Matko Boa
njak, Rajko Horvat,
Marin Prcela, Dragan Gamberger, Angela Sciacqua, Maria Consuelo Valentini, Kalina Kawecka-Jaszcz,
Gianfranco Parati, Domenico Conforti
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 5 8
WHY AND HOW SHOULD A VIRTUAL PATIENT BE CONSTRUCTED?
PAWEA
SPÓLNIK
Chair of Medical Biochemistry, Jagiellonian University  Collegium Medicum, Kopernika 7,
31-034 Krakow, POLAND
Introduction these solutions (5-8). Government-supported insti-
tutions and projects aimed specifi cally at improving
Graduating with even the highest grade does not the situation in the teaching of medical sciences
necessarily guarantee good preparation for the pro- have been developed (AMEE, Association for Medi-
fession of a doctor. Evidence of this fact may be cal Education in Europe; COMET, Consortium on
found in the apparent failure of students of later Medical Education and Technology; CHEC, Cana-
years and young doctors, even those who are stud- dian Healthcare Education Commons; eViP, Elec-
ying or who graduated from the world s top medical tronic Virtual Patients; WebSP, Web-based Simula-
universities, to successfully carry out one of the dai- tion of Patients).
ly clinical activities, namely, the ward round (1, 2).
The skills required for this activity include not only
the ability to perform differential diagnosis, treat- E-learning and electronic virtual
ment and the ability to perform minor surgeries, but
patients
also the ability to effectively and precisely communi-
cate with patients, and, last but not least, the ability
and readiness to work in teams. As many as 30% The development of the e-learning technology
of patients experience fear connected with medical makes it possible to more effectively prepare fu-
appointments, and do not understand the language ture doctors for work in hospitals. It should be em-
doctors use to communicate with them (3). The av- phasized, however, that the direct doctor-patient
erage doctor s visit in the case of a ward patient interaction is irreplaceable in medical didactics.
is approximately 5 min long. Only 44% of patients The computer technology facilitates the teaching
undergo cursory physical examination. One particu- of differential diagnosis, which forms the essence
lar evaluation of ward round quality revealed that of a doctor s work. Arguably, the biggest advantage
convalescents after myocardial infarction received offered by VPs is that there are no clinical conse-
the appropriate medication (as defi ned by the es- quences of wrong decisions made by students.
tablished guidelines) in fewer than half of all cases Other undeniable advantages include easy ac-
(4). These data suggest that there are flaws within cessibility, a unifi ed grading system, the attractive
the system of medical education. This problem has presentation of the problems, and the possibility of
recently been attracting a lot of attention. Conse- using previously prepared comments. Medical uni-
quently, some new solutions are being incorporated versities in Europe, supported by EU grants, are
in order to better prepare young doctors for medi- developing a program for improving virtual patients
cal practice : problem-based learning, integration (eViP) (9). Developments in computer science are
of clinical disciplines and basic sciences (horizontal making it possible to effi ciently manage the created
and vertical), as well as the application of compu- databases. The elaboration of simple and extended
ter systems in education (e-learning). The creation diagnostic models should only be carried out in the
of databases of virtual patients (VP) is also among frame of close cooperation with doctors.
OPENING PAPER
Why and how should a virtual patient be constructed?
6
Development of VP  from scratch which should fi rst be focused on either ruling out or
confirming potentially fatal conditions. If the student
The elaboration of an original virtual patient from focuses on electrocardiographic symptoms that in-
scratch is not an easy task due to the necessity of dicate myocardial ischemia, the diagnosis and the
exchanging data between existing models, and their treatment may be pursued in the wrong direction,
improvement and adaptation to local conditions. thus putting the patient in danger. The hints from the
However, elaboration from scratch does carry some physical examination and the medical history (the
advantages with it. For example, it makes it pos- type of pain experienced, taking of medication from
sible to create a patient in the reality immediate to the NSAID (Non-steroidal Anti-inflammatory Drug)
the student. A clinician may prepare a case ex post group, as well as the presence or absence of me-
based on experience and archival data, or formu- lena provide data with which the correct diagnosis
late it concurrently, while the diagnostic-therapeutic may be made with high probability. Self-evaluation
process is still taking place. The reality of clinical questions concerning, for example, the molecular
work generally favours the first approach. and pathophysiological mechanisms of ulcer forma-
Among the virtual patients we have elaborated, tion during medication with NSAIDs are somewhat
there is one case which makes students particularly more diffi cult. Commentaries by experts outline the
aware of the frequent problem of upper gastrointes- molecular mechanism of the acetylation of serine
tinal bleeding (to be anatomically precise, bleeding in the cyclooxygenase active site. To complete the
from the proximal segment of the digestive tract to exercise, the student must apply their knowledge
the ligament of Treitz). Around 50-100/100,000 peo- in biochemistry, pharmacology, physiology, and
ple are affl icted with this problem each year. Clini- pathophysiology. In the further stage of the diagnos-
cians often need to decide between a dozen or so tic procedure, questions pertaining to the mecha-
possible diagnoses. This stems from the fact that nism of drugs from the PPI (proton pump inhibitors)
each case is different. The discussed diagnostic group should be addressed. This is where knowl-
problem may be a self-containing state which may edge strictly connected with basic subjects is again
not be detected clinically, or a rapid process leading required. In the presented case, we also emphasize
to hypovolemic shock and death (10, 11). the accurate explanation of the changes observed
through laboratory tests, e.g. the results of an arte-
rial blood gas analysis and the mechanism through
Authoring of virtual patients which the level of urea in the serum of a patient with
gastrointestinal bleeding is elevated. The biological
Let us introduce a 40-year old patient who was mechanisms which are exploited in the application
brought into admissions by an ambulance. He com- of the non-invasive ureatic test are also explained.
plained of pain in the epigastrium and vomiting. In addition, the student is expected to know the dif-
A gastroscopic examination revealed a non-bleed- ferent treatment options for Helicobacter pylori, and
ing prepyloric ulcus, and the CLO-Test was positive. to know how to act if the initial treatment fails. In
A fi nal gastroscopic examination, performed after another case that is being elaborated, we try to in-
the eradication of Helicobacter pylori, indicated sig- troduce a lot of data that combine clinical practice
nificant improvement. The patient was discharged in with basic subjects. For example, when discussing
good general condition. It should not be too hard for a patient with mononucleosis, we pay attention to
the student to solve this case, since at the outset of the mechanism of the virus s interaction with hu-
the task they receive vital hints to help them conduct man cells containing antigen CD 21 (which explains
the differential diagnosis. However, the picture may its predilection towards the cells of the immune
be distorted by other clinical data, such as those system). When interpreting the elevated level of
normally available to the doctor in the initial stage of transaminases, we also present their role and ex-
the diagnosis, i.e. data concerning basic life param- amples of physiological reactions.
eters, ECG results, and X-ray images of the chest, in
both planes. The initially presented data correspond
to those available to the doctor that admitted the Discussion and conclusion
patient first. The medical history taken by the doctor
working in the emergency service did not suffice to Commentaries concerning basic subjects, which
put forward a correct working hypothesis. As part of facilitate the understanding and practical applica-
the standard procedure in the hospital he was ad- tion of traditionally conceived preclinical subjects
mitted to, an ECG examination was carried out, and in a doctor s work, require special preparation. It is
the nurse recorded the patient s life parameters. It is easier to consider these dependencies while taking
with such data and the information from the physical a test, whereas in actual clinical conditions there
examination and the medical history that the stu- is often no time for this, and effective action is ex-
dent is confronted with. One element, the teaching pected immediately. According to some estimates,
which is of critical importance for the work of a doc- only 15% of the knowledge acquired during pre-
tor, especially in ward/night duty conditions, is the clinical education is put into practice in a noticeable
ability to carry out effi cient differential diagnosis, way (12). That is far too little. Well-constructed VP
OPENING PAPER
Why and how should a virtual patient be constructed? 7
Fig. 1. Different algorithms for the management of acute upper gastrointestinal bleeding. (NG, nasogastric; GI, gastrointestinal; PPI,
proton pump inhibitor).
models and the adjustment of the teaching strategy of medical practice do not require taking images that
provide an opportunity to change the misguided might be didactically relevant to be recorded during
opinion students sometimes express, namely that diagnostics. At other times, for reasons beyond the
basic subjects are completely irrelevant to profes- researchers control, the visual documentation is not
sional work. A complex presentation of each prob- sufficient (for example, in the case discussed earlier
lem  in the form of a clinical case discussed by endoscopic images could not be taken during the
expert in various fi elds (in practice  the teaching first gastroscopic examination). It seems that a case
of basic subjects based on clinical cases as well as is the most consistent when using documentation
presenting the basic issues again while discussing for only one patient. However, there are times when
the cases during clinical practice)  appears to be didactic goals make it necessary to use the avail-
one of the ways in which the level of education may able images taken from similar cases, if the original
be improved (5, 6, 8). documentation may not be accessed.
This trend towards integration in teaching may Not only does solving a case teach the student
be introduced horizontally (a joint presentation of the skills necessary to take therapeutic action, but,
the case by teachers of preclinical subjects) and by studying basic subjects, they should assimilate
vertically (in the form of cooperation between teach- knowledge on various pathomechanisms, which in
ers of basic subjects and clinicians) (13). It seems turn would allow them to act in a judicious and well-
like a good idea to have specialists in basic subjects thought-out way, and to anticipate certain phenom-
present the background of molecular abnormalities ena.
in a series of lectures given by clinicians. It appears that the application of e-Learning
The problems faced by a doctor elaborating platforms fi lls the gap between textbook theory and
a case are different guidelines and procedures con- practice. It may also serve to prepare the student
cerning the clinical cases to be developed. The even- to make diagnostic and therapeutic recommenda-
tually administered therapies may have a slightly dif- tions. What should be emphasized, however, is the
ferent course. For example, in cases similar to the role of practice, which must complement the theo-
one discussed earlier, there are different procedures retical background.
in different EU countries. There are countries where
patients with gastrointestinal bleeding are assigned
to surgical wards by default, whereas in other coun-
tries such patients are initially treated by internists References
(Fig. 1). What course is taken is often influenced
by guidelines and hints published by the respec- 1. Nłrgaard K., Ringsted C., Dolmans D.: Valida-
tive specialists associations. Another problem faced tion of a checklist to assess ward round perfor-
when elaborating a case is connected with medical mance in internal medicine, Med. Educ. 2004;
documentation. On some occasions, the principles 38(7): 700-707.
OPENING PAPER
Why and how should a virtual patient be constructed?
8
2. Wray N. P., Friedland J. A., Ashton C. M., Scheu- 8. Harden R. M.: E-learning  caged bird or soar-
rich J., Zollo A. J.: Characteristics of house staff ing eagle?, Med. Teach. 2008; 30(1): 1-4.
work rounds on two academic general medicine 9. Hege I., Kononowicz A., Pfahler M., Adler M.,
services, Med. Educ. 1986; 61: 893-900. Fischer M. R.: Implementation of the MedBiq-
3. Montague M., Hussain S. S. M.: Patient per- uitous standard into the learning system casus,
ceptions of the otolaryngology ward round in Bio-Algorithms and Med-Systems 2009; 5(9):
a teaching hospital, J. Laryngol. Otol. 2006 Apr; 51-55.
120(4): 314. 10. Conn H. F. and others: Current therapy: latest
4. Nikendei C., Kraus B., Schrauth M., Briem S., approved methods of treatment for the practic-
J�nger J.: Ward rounds: how prepared are fu- ing physician, Saunders Elsevier, 2007.
ture doctors?, Med. Teach. 2008; 30(1): 88-91. 11. Herold G., Innere Medizin, 2009.
5. Davis M. H., Harden R. M.: AMEE Medical Edu- 12. Oberle S., Huber S., Tonshoff B., Nawrotzki R.,
cation Guide No. 15: Problem-based learning: Huwendiek S.: Repurposing virtual patients for
a practical guide, Med. Teach. 1999; 21(2): 130- the preclinical years  A pilot study, Bio-Algo-
140. rithms and Med-Systems 2009; 5(9): 79-82.
6. Ellaway R., Masters K.: AMEE Guide 32: e- 13. Integration of basic and clinical sciences 
Learning in medical education Part 1: Learning, AMEE Conference archive 2008, http://www.
teaching and assessment, Med. Teach. 2008; amee.org/index.asp?llm=27
30(5): 455-473.
7. Ellaway R., Poulton T., Fors U., McGee J. B.,
Albright S.: Building a virtual patient commons,
Med. Teach. 2008 30(2): 170-174.
OPENING PAPER
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 9 13
VOGE  JAVA APPLICATION FOR PRESENTATION OF NEVER BORN
PROTEINS GENE STRUCTURE ELEMENTS
MONIKA PIWOWAR1, EWA MATCZYC
SKA1, FILIP POMAC
SKI2, ADRIAN KOŚMIDER2,
DAMIAN KOŚĆ2, MICHAA
SWATOWSKI2, PIOTR WI
CEK2, TOMASZ SZEPIENIEC3
1
Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum,
Sw. Anny 12, 31-008 Krakow, Poland
2
Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4,
Krakow, Poland
3
Academic Computer Center CYFRONET, Nawojki 11, 30-950 Krakow, Poland
Abstract: VoGE application for visualizing gene structure elements in nucleotide sequences is presented in the paper.
Genomic analyzing of genome sequences was continuation of proteomic efforts in the EuChinaGrid project that was oriented
on the structure prediction of never born proteins, but probably with pharmacological application (there were 10**4 protein
sequences generated which were used to create structures of that sequences). Finding of gene traces of never born proteins in
all accessible sequenced genomes was one of the aim. As a results of searching genome materials there were found regions
including protein-coding gene fragments that VoGE (Visualiser of Gene Elements) application presents. Graphical presentation
of particular sequences enable user to see localization of coding NBP sequence and gene element composition in wider
sequence context. Application interface and menu is intuitive so it seems to be easy to use.
Keywords: never born proteins, gene structure elements, gene finding
Introduction elements especially exon. GENSCAN software was used For
identification gene elements [8] (fig. 2). Results were put into
Genomic part of the efforts in Euchina grid was the continua- MySQL database. They are used by VoGE application as
tion of proteomic achievements in folding of never born protein VoGE gets all data from the database.
with pharmacological potential [1, 2]. Because there was assumed that exons can be part of
Motivation for finding never born proteins traces was sus- the query sequences so for viewing localization of coding se-
picion that many proteins not occurring in nature as a real pro- quences there were taken lager length of DNA than query se-
teins can have sequences representation in genetic material. quence (fig. 3).
Such hypothesis suggest that DNA can accumulate information
about proteins or fragments of proteins that may have existed
during ancient time, but now are withdrawn from nature. Materials and methods
Innovation of genomic analysis rely on finding information
about proteins in genomic regions where it theoretically should Genome data:
not be (in case of humane genome it is big amount genetic ma-
terials (about 97%) that does not encode any known proteins). DNA from National Center of Biotechnology Information were
Searching all accessible completely sequenced genetic in- taken for analysis (ftp.ncbi.nih.gov). Entire genetic information
formation to identify stretches of genomic sequence about po- was searched not only humane genome but also other Eu-
tential biological function and results presentation was the aim. karyotes genomes e.g. genomes of animals, plants, fungi and
To obtain it all genetic information was translated to aminoac- Protists genomes and organelles.
ids sequences (DNA AA) in three reading frames. Then DNA
AA were searched by random generated sequences (represent
never born proteins [3, 4]), the same sequences which were Never Proteins data:
used to creation theirs three dimensional structures (fig. 1).
The most interesting in searching DNA AA was identify- Never born proteins were obtained from Roma Tre University
ing never born coding stretches that represent structural gene proteomic group [13].
bioinformatics
VoGE  java application for presentation of Never Born Proteins gene structure elements
10
Fig. 1. DNA Amino Acids  DNA AA. DNA AA created on the basis of translation of genome sequences to aminoacid sequences. FP:
Folding proteins, RS: Random sequences
Fig. 2. VoGE input. Data to VoGE application comes form GENSCAN results. DNA AA: DNA Amino Acids (DNA translated to aminoacid
sequences), FP: Folded proteins, RS: Random sequences; FS: Flanked Sequences
Fig. 3. Gene structural elements in analyzing nucleotide sequences. Block without description shows coding information of never born
protein which traces was found in genome sequences.
bioinformatics
VoGE  java application for presentation of Never Born Proteins gene structure elements 11
Software that ware used: Results
BAST: Program for searching DNA AA database by RS data- Workflow
base was BLAST (http://www.ncbi.nlm.nih.gov/BLAST/) [6].
GENSCAN: Program for identification gene elements  [5] The VoGE graphical user interface enables user to specify his
request by filling special form. While user is waiting for results,
the request with values entered by user is sent to the Java
Technology used for creating application: Servlet, which is running under Tomcat Server (fig. 4).
Servlet process the user request and builds specific SQL
C: Scripts for translating nucleotide sequences to aminoacide query, which is executed against the database. Results are
sequences are created in C programming language. sent back to the Servlet, where they are checked and format-
Java  Java 1.6 was applied for creation graphical inter- ted, so they can be visualized easily. Eventually result data is
face of VoGE by which user can analyzed data. sent to VoGE GUI and presented to the user.
BioPython  a package of freely available Python tools for
computational molecular biology. It helps parsing the BLAST
output files, making it simple and quick. VoGE options
MySQL  a relational database management system. It is
very useful in storing and processing large amounts of data. On the beginning VoGE give window with name of the experi-
Outputs of BLAST and GENESCAN are parsed and stored in ments that should be choose. Kind of experiment defined which
a relational database called GENOMIC. VoGE connects with genomes and with parameters were processing. During next
database through Java Servlet. All needed data is quickly gath- step user can explicitly enter the sequence FASTA name (for
ered and calculated thanks to SQL queries. Results from data- specifying the sequence, which was used for BLAST search-
base are sent back to VoGE, which presents them in a simple ing) and results for this sequence will be presented.
and accessible way.
Fig. 4. Application created in Java technology connects with Tomcat server due to request. Java servlet connects to database, selects
results and sends it back to user.
Fig. 5. Entry query form for choosing experiment results.
bioinformatics
VoGE  java application for presentation of Never Born Proteins gene structure elements
12
Fig. 6. One of the alignments for particular sequence view.
Fig. 7. Summarized results of experiment view.
bioinformatics
VoGE  java application for presentation of Never Born Proteins gene structure elements 13
The other possibility is to define the organism and result related and give information about amount sequences in par-
sequences properties (sequence length, exon number, exon ticular cluster, in the same way like in analysis that were done
score, polyA, etc.) (fig. 5). The list of matching results are re- during genome-wide expression patterns analysis.
turned.
VoGE enable user to see the result alignment sequence
properties (fig. 6). References
All coordinates of the sequence are in the upper frame. The
visualization of gene structure elements are presented below 1. Brylinski M., Jurkowski W., Konieczny L., Roterman I.: Lim-
the coordinates frame. In addition the raw sequence fragment ited conformational space for early-stage protein folding
and detailed information about gene elements are provided. simulation, Bioinformatics, 20, 199-205, 2004.
Summarized data of experiment for particular genomes 2. Brylinski M., Konieczny L., Roterman I.: Fuzzy-oil-drop
and its chromosomes is possible to present by use VoGE (fig. hydrophobic force fi eld  a model to represent late-stage
7). The participation of all gene structure elements in genome folding (in silico) of lysozyme, J Biomol Struct Dyn, 23(5),
and each chromosome can be visualized. 519-528, 2006.
Sequences, pictures and more detailed information can be 3. Chiarabelli C., Vrijbloed J. W., Thomas R. M., Luisi P. L.:
downloaded in cvs file. Investigation of de novo totally random biosequences. Part
I: A general method for in vitro selection of folded domains
from a random polypeptide library displayed on phage,
Conclusion Chem Biodivers, 3, 827-839, 2006.
4. Chiarabelli C., Vrijbloed J. W., De Lucrezia D., Thomas R.
VoGE is application for visualization localization of gene struc- M., Stano P., Polticelli F., Ottone T., Papa E., Luisi P. L.:
ture elements. Data obtained on the basis of searching nucle- Investigation of de novo totally random biosequences. Part
otide sequences (especially whole genome material) translated II: On the folding frequency in a totally random library of de
to the protein language with protein sequences are possessed novo proteins obtained by phage display, Chem Biodivers,
by common known detection method of gene structure ele- 3, 840-859, 2006.
ments (incorporated to the Genscan tool). 5. Burge C. and Karlin S.: Prediction of complete gene struc-
VoGE helps analyse and visualise stretches of genomic re- tures in human genomic DNA, J Mol Biol, 268, 78-94,
gions encoding NBP that can be important in planning expres- 1997.
sion of NBP in vivo. 6. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D.
In the future construction of hierarchical tree of similar se- J.: Basic local alignment search tool, J Mol Biol, Oct 5;
quences is planned as well as statistical analysis of obtained 215(3): 403-10, 1990.
results. It is expected revealing groups of sequences which are
bioinformatics
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 15 23
UNFOLDING SIMULATION TO VERIFY THE CONCEPT OF LIMITED
CONFORMATIONAL SUB-SPACE FOR EARLY-STAGE INTERMEDIATE
1,2
PIOTR KIEA
KOWICZ, 1 IRENA ROTERMAN
1
Department of Bioinformatics and Telemedicine, Collegium Medium  Jagiellonian University,
Lazarza 16, 31-530 Krakow, POLAND
2
Faculty of Physics, Astronomy, Applied Computer Science  Jagiellonian University, Reymonta 4,
30-059 Krakow, POLAND
Abstract: Model introducing the limited conformational sub-space for early-stage intermediate defi nition for protein folding
process presented formerly is verified in respect to the unfolding process treated as reverse process to folding. It was expected
to receive the step-wise unfolded structure keeping the structural alphabet. It is shown that as long as the secondary structure is
present in the gradually unfolded structures, the codes for structural alphabet are changed for relatively low number of residues.
The high temperature molecular dynamics simulations revealed the structures with signifi cantly increased distance versus the
limited conformational sub-space and large change of alphabet codes. The test was performed for ubiquitine in 300K, 350K,
400K, 500K, 700K and 1000K. It suggests that the structural codes found for crystal structures can not be treated rigorously to
be kept during the folding process simulation. Although some tendencies for structural codes changes are observed suggesting
the corrections for the definition of early stage structural forms.
Introduction
500, 700 and 1 000 K) indicates the approach toward the lim-
The multi-step process of protein folding has been recognized ited conformational sub-space assumed to represent the early-
experimentally [1-17]. The introduction of the early-stage inter- stage intermediate conformations.
mediate seems to be necessary [18]. In consequence the defi-
nition of the limited conformational sub-space is expected [18].
In consequence, the multi-step model to simulate the protein Materials and Methods
folding process was introduced [19]. The early-stage [ES] inter-
mediate was defined according to the backbone conformations Data: the protein ubiquitine (PDB  1UBQ) was taken as the
with side chain-side chain interaction excluded. The backbone example. The protein without the SS-bonds and structurally dif-
conformation described by two geometric parameters: V-angle ferentiated (ą-helix  23%, �-structure  34% and RC  43%)
and R-radius of curvature which appeared to be dependent on and of medium size is the very convenient object for simula-
V-angle in form of second degree polynomial. The structures tion procedure. The secondary structure characteristics was
satisfying this equation  assumed to represent the relaxed performed according to the procedure available on the PDB
backbone conformations  revealed the limited conformational webpage [20].
sub-space as the fragment of Ramachandran map. This space
appeared to be of ellipse path linking all secondary structural
forms (ąR-helix, �-structural area and ąL-helix). Additionally it The structural parameters
was proved that the amount of information carried by amino
acid sequence appeared to be balanced with the amount of The solvent accessible area for post-dynamics structures was
information necessary to define the structure of ES intermedi- calculated according to program Surface Racer 5.0 [21].
ate [19]. The number of non-bonding contacts was calculated ac-
The calculations represented in this paper were aimed to cording to the program prepared specially for the project. Pro-
check whether the unfolding process (molecular dynamics sim- gram was written according to standards (parameters) given
ulation of ubiquitine in different temperatures: 300, 350, 400, in [22].
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate
16
The structural codes
The Phi, Psi angles distributed on the Ramachandran map as
they appear in protein moved (according to shortest distance
criterion) toward the ellipse path reveal the probability distribu-
tion characterized by seven maxima. Some of them represent
the secondary structure elements: Code C  ąR-helix, E,F 
�-structural forms, G  ąL-helix. Others (A, B, D) represent the
structures belonging to Random Coil. The detailed presenta-
tion of the structural codes according the ellipse shaped limited
conformational sub-space is given in [23].
The changes of structural codes were estimated accord-
ing to the structural codes as observed in all post-dynamics
structures.
Molecular dynamics simulation:
The AMBER program was used to simulate the molecular dy-
namics. The following temperatures were applied: 300 K, 350
K, 400 K, 500 K, 700 K, 1000 K.
The implicit solvent model for the ff03 force field applying
the standard parameterization for 0.1 M solution with the rigid
positions of hydrogen atoms was used for simulations. The cut-
off distance was taken to be 16 A. Simulations was performed
in three runs: equilibration until the stabilization of the energy
Fig. 1. The ellipse path defi nition: A  the low energy areas on
was achieved; the heating process  50 000 iterations with the
Ramachandran map, B  the relation between V-angle (dihedral
time step 0.002 ps (the total time range 100 ps). The output
angle between two sequential peptide bond planes) and R  re-
data (structure and parameters) was collected every 1 ps.
sultant radius of curvature (in log scale). The structures satisfy-
The starting (equilibration) simulation was continued until
ing the approximation function are distributed as shown in C. The
the stability of temperature and energy was achieved.
approximation to the ellipse path (D). The relation of ellipse path
The heating dynamics was performer for the appropriate
(early-stage conformational sub-space) in relation to low energy
temperature until the stabilization characteristics for the tem-
areas on Ramachandran map (E).
perature was achieved (about 50 000 steps).
The 500 000 steps of effective simulation with the stable
temperature was performed with the time step 0.002 ps, which
was common for all simulations.
Fig. 2. The probability distribution A - along the ellipse path after moving all Phi, Psi angles (found in proteins) toward the ellipse path.
The letter code is attributed to each local maximum. B  the starting point and the direction of the walk along the ellipse is shown.
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate 17
Fig. 3. The stability of the dynamics process. A  stability of temperatures for particular processed and B  stability of total energy of the
molecule  ubiquitin
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate
18
The early-stage conformational
sub-space
The ellipse path assumed to represent the early-stage related
conformational sub-space is shown in Fig. 1. The ellipse-path
was defined according to the analysis of geometric parameters
describing the backbone conformation. The main assumption
is that all structural forms can be treated as helices including
�-structure. These two parameters are as follows: V- angle be-
tween two sequential peptide bond planes and the resultant ra-
dius of curvature which for V angles close to zero takes the low
values and for values close to 180 degs the radius becomes
very large (this is why the logarithmic scale was introduced)
(Fig. 1. B). The �-structure is treated as helix with large value of
radius of curvature. The structures generated according to the
approximated function are shown in Fig. 1 C. The ellipse path
can be distinguished as the well ordered part of the distribution
(Fig. 1.D). The relation of ellipse path to the low energy areas
on the Ramachandran map (Fig. 1.A.) are shown in Fig. 1.E.
The post-dynamics structures were characterized by Phi,
Fig. 4. The distribution of Phi, Psi angles for native form of ubiqui-
Psi angles distribution and the approach toward the ellipse
tine in relation to the ellipse path.
path was calculated in particular.
The equation for ellipse path can be expressed as follows:
Ś =  A cos (t)  B sin (t) Structural alphabet
� = A cos (t)  B sin (t) eq (1)
The probability distribution along the ellipse path after moving
Where t expresses the angular movement along the el- the Phi, Psi angles toward ellipse path is shown in Fig. 2. The
lipse starting from the lower right quarter of the Ramachandran presence of seven maxima with attributed letter codes may be
map. distinguished producing the  structural alphabet .
Fig. 5. The Phi, Psi angles distribution for step-wise unfolding of ubiquitine in respect to ellipse path.
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate 19
Tab. 1. The distance (in degs units) for step-wise unfolding and for crystal structure. The percentage of changed structural codes during
unfolding with the number of stable alphabet codes is given in two columns on right. The last column on right presents the decreasing
number of side chain-side chain interactions
Percentage of Number of structural Number of side
DISTANCE Standard deviation
TEMPERATURE stable structural alphabet codes chain  side chain
(angular scale) of distance
alphabet codes changed interactions
211
300 K 39.44 31.59 63.51% 27
176
350 K 41.18 26.76 60.81% 29
79
400 K 40.70 30.22 41.89% 43
52
500 K 46.81 32.24 36.49% 47
45
700 K 54.91 37.05 33.78% 49
37
1000 K 56.12 33.76 33.78% 49
247
NATIVE  crystal 35.45 23.48 - -
Tab. 2. The changes of structural codes according to the crystal
structure. On the left: number of residues disappearing from par-
Results:
ticular region; on the right: number of total residues moving from
the region under consideration.
The molecular dynamics simulation
STRUCTURAL
A B C D E F G
CODES TEMP
The stabilization of energy and temperature is shown in
A 300 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
Fig. 3.A and Fig. 3.B. respectively. The given results prove the
350 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
stabilization of the protein molecule in dynamics process for
400 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
the period of time 100-1100 ps. These structures averaged are
500 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
taken for the analysis of the unfolding process of ubiquitine.
700 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
The Phi, Psi re-localization for all structural forms (includ- 1 000 K 0/0 0/0 0/0 0/0 0/0 0/0 0/0
ing crystal structure) was characterized by the parameter mea-
B 300 K 0/2 0/2 2/2 0/2 0/2 0/2 0/2
suring the distance versus the nearest point belonging to the 350 K 0/2 0/2 1/2 0/2 0/2 1/2 0/2
400 K 0/2 0/2 2/2 0/2 0/2 0/2 0/2
ellipse path (shortest distance criterion).
500 K 0/2 0/2 0/2 1/2 1/2 0/2 0/2
The distribution of Phi, Psi angles for crystal structure is
700 K 0/2 0/2 1/2 1/2 0/2 0/2 0/2
given in Fig. 4 and for post-dynamics structures in Fig. 5.
1 000 K 0/2 0/2 2/2 0/2 1/2 1/2 0/2
The significantly larger dispersion of the points represent-
C 300 K 0/20 1/20 17/20 2/20 0/20 0/20 0/20
ing the Phi, Psi angles can be seen in respect to the crystal
350 K 0/20 3/20 14/20 2/20 0/20 0/20 1/20
structure Phi, Psi angle distribution. The gradual disappear-
400 K 0/20 1/20 7/20 2/20 5/20 4/20 1/20
ance of points in the regions of secondary structure related
500 K 0/20 2/20 6/20 2/20 7/20 2/20 1/20
positions can be observed.
700 K 0/20 1/20 5/20 2/20 5/20 6/20 1/20
The relative disappearance of secondary structure can be 1 000 K 0/20 3/20 6/20 0/20 4/20 4/20 3/20
seen also in Fig. 6 A and Fig. 6.B. The post-dynamics struc- D 300 K 0/2 0/2 2/2 0/2 0/2 0/2 0/2
350 K 0/2 0/2 1/2 0/2 1/2 0/2 0/2
tures above 450 K do not represent any form of secondary
400 K 0/2 0/2 1/2 1/2 0/2 0/2 0/2
structure although the low representation of secondary struc-
500 K 0/2 0/2 0/2 0/2 1/2 1/2 0/2
ture is seen also in 400 K post-dynamics structure. The quali-
700 K 0/2 1/2 0/2 0/2 1/2 0/2 0/2
tative measurements of these changes are given in Tab. 1.
1 000 K 0/2 0/2 0/2 0/2 1/2 1/2 0/2
The mean distance between Phi, Psi points and nearest point
E 300 K 0/32 1/32 2/32 1/32 22/32 6/32 0/32
belonging to ellipse seems to be relatively stable for structures
350 K 0/32 0/32 1/32 0/32 22/32 9/32 0/32
below 500 K
400 K 0/32 0/32 7/32 3/32 15/32 7/32 0/32
The analysis of Phi, Psi angles distribution suggests that
500 K 0/32 1/32 6/32 3/32 16/32 6/32 0/32
no approach toward the ellipse was observed during unfolding 700 K 0/32 6/32 3/32 1/32 15/32 6/32 1/32
1 000 K 0/32 5/32 4/32 1/32 14/32 5/32 3/32
procedure. The mean distance between the Phi, Psi angle ob-
F 300 K 0/10 2/10 0/10 0/10 5/10 3/10 0/10
served and the nearest point belonging to ellipse path seems
350 K 0/10 0/10 1/10 0.10 3/10 6/10 0/10
to be almost constant for temperatures below 450 K. Te stabil-
400 K 0/10 0/10 2/10 1/10 1/10 6/10 0/10
ity of the distribution versus the ellipse path for this range of
500 K 0/10 0/10 0/10 3/10 2/10 4/10 1/10
temperatures seems to be related to the range of temperature
700 K 0/10 0/10 2/10 0/10 5/10 2/10 1/10
close to physiological temperatures. The stability of mean dis-
1 000 K 0/10 2/10 0/10 0/10 5/10 3/10 0/10
tance (and standard deviation values) suggests the rearrange-
G 300 K 0/8 0/8 2/8 0/8 1/8 0/8 5/8
ment of the structure without any significant changes using the
350 K 0/8 1/8 1/8 0/8 2/8 1/8 3/8
Phi, Psi angles as criterion for structural changes.
400 K 0/8 0/8 3/8 0/8 2/8 1/8 2/8
The post-dynamic structure at 1000 K obviously represent- 500 K 1/8 1/8 1/8 1/8 2/8 1/8 1/8
700 K 0/8 1/8 0/8 0/8 1/8 3/8 3/8
ing the limit case in extremely high temperature is used just for
1 000 K 0/8 1/8 1/8 0/8 3/8 1/8 2/8
comparison with the highest distance versus the ellipse-path,
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Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate
20
Fig. 6. The 3-D presentation of the post-dynamic structures of ubiquitine. The color scale applied shows the scale of Phi, Psi distances.
The red color indicates the increase of distance (higher than 60 degs), the blue color  decrease of distance (higher than 60 deg), green/
yellow  more or less stable (in between).
A  structures with secondary structure preserved
B  structures secondary structure lost
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate 21
Fig. 7. The changes in the post-dynamics structures (increasing temperatures) displayed versus the crystal structure:
A  distance versus ellipse, # of stable structural codes (%), the number of cavities recognized according to own program prepared on
the basis of [21].
B  # of side chain-side chain contacts
C  solvent accessible area (according to Surface Racer [21]
showing to what extent this distance may increase and what The structural alphabet
range of dispersion of distance values is possible for the pro-
tein under consideration. The distribution of Phi, Psi angles along the ellipse path re-
The post-dynamics structures (300, 350, 400 K) represent ceived by the moving the observed Phi, Psi angles toward
the changes occurring slowly. The 500 K post-dynamics struc- the ellipse path (the shortest distance criterion) revealed the
ture reveals significant changes in all parameters (Fig. 7). presence of seven maxima [23]. Each of them attributed by the
The most important parameter, which is the distance be- letter [from A to G] allowed the construction of the structural al-
tween Phi, Psi angles versus the ellipse path is accordant with phabet for ES intermediate. The comparison of post-dynamics
the changes of all other parameters. The interesting is the de- (step-wise unfolding] structures of ubiquitine classified accord-
crease of number of cavities for the post-dynamics structures ing the structural alphabet revealed the fragments of polypep-
above 350 K. tide with different structural stabilization. The fragments of high
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Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate
22
Fig. 8. The stability versus mobility of the codes.  Stable denotes number of letter codes not changed during dynamics, ( TO denotes
the target letter code,  FROM denotes the original letter code. The bars are shown for lower temperatures (<450 K) and upper (> 450 K).
and low stability (the minimum and maximum of changed let- process to folding. The structures: crystal one and all post-
ters per pentatpetide) are listed in Tab. 2. dynamics ones were classified according to letter codes distin-
The observed structural codes changes in post-dynamics guishing the particular Ramachandran areas (final structures)
structures are given in Tab. 2. and in Fig.8. and particular ellipse fragments (early stage structures). It was
The analysis of Tab. 2. and Fig. 8. suggests that the melt- expected that some of structural codes appear stable. Accord-
ing of helix takes place in upper temperature. The stability of C ing to the results shown in Tab. 2. and Fig. 8. there is no recog-
(helix) and E (�-structure) seems to be the highest in relation nizable patter for structural codes changes. The codes C and E
to other codes. No stable B code and very low stability of D seem to be the most stable. The Phi, Psi angles of molten helix
code were observed. move toward the E / F zone and toward the B zone (which is
Generally there is no significant tendency to regular pattern the neighbor structure in the sense of ellipse localization).
of structural changes categorized according to letter codes. The post-dynamic structures are planned to be used as the
starting forms for folding process (energy minimization proce-
dure) to reveal whether any of these structures are able to find
Conclusions: the proper way to recreate its native structural form.
The similar simulation was performed for immunoglobu-
The simulation of molecular dynamics was performed to mimic lin molecule. The approach toward the ellipse was observed
the process of unfolding, which was treated as the reverse there [24]. Immunoglobulin is highly �-structural protein. The
bioinformatics
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate 23
movement of Phi, Psi maximum of concentration on the Ra- 11. Creighton T. E., Kalef E. & Arnon R. (1978) Immunochemi-
machandran map was observed there to identify the approach cal analysis of the conformational properties of intermedi-
of �-structural maxima toward the ą-helix Phi, Psi area on the ates trapped in the folding and unfolding of bovine pancre-
Ramachandran map. The ubiquitine was selected this time to atic trypsin inhibitor. J. Molec. Biol. 123, 129-147.
analyze the behavior of mixed secondary structure protein. The 12. Creighton T. E. (1875) Reactivities of the cysteine residues
gradual increase of the mean distance between ellipse and el- of the reduced pancreatic trypsin inhibitor. J. Molec. Biol.
lipse path is observed accordant to the increased temperature 96, 777-78.
although the structures for temperatures below 450 K seem to 13. Creighton T. E. (1985) The problem of how and why pro-
be change slowly and above 450 K this difference was found teins adopt folded conformations. J. Phys. Chem. 89,
to be larger. 2452-2459.
The ellipse path and structural alphabet was used for pro- 14. Kosen P. A., Creighton T. E. & Blout E. R. (1983) Circular
tein folding simulation using the ellipse path belonging Phi, dichroism spectroscopy of the intermediates that precede
Psi angles to define the starting structure for folding simula- the rate-limiting step of the refolding pathway of bovine
tion [25-27]. The results of unfolding simulation of BPTI was pancreatic trypsin inhibitor. Relationship of conformation
presented and discussed in [28,29]. The movement of Phi, Psi and the refolding pathway. Biochemistry 22, 2433-2440.
angles in that paper was following the ellipse path moving to- 15. Goldenberg D. P. & Creighton T. E. (1985) Energetics of
ward the left-handed helix in the highest temperature simula- protein structure and folding. Biopolymers 24, 167-182.
tion although visual analysis of these results suggests also the 16. Creighton T. E. (1978) Refolding of bovine pancreatic
increase of Phi, Psi distances versus the ellipse path for all trypsin inhibitor modifi ed at methionine-52. J. Molec. Biol.
analyzed temperatures. 119, 507-518.
The general tendency for structural alphabet changes dur- 17. Hollecker M. & Creighton T. E. (1983) Evolutionary conser-
ing unfolding process will be taken under consideration for vation and variation of protein folding pathways. Two pro-
larger number of proteins. tease inhibitor homologues from black mamba venom. J.
Molec. Biol. 168, 409-437.
18. Alonso D. O., Daggett V. (1998) Molecular dynamics simu-
References: lations of hydrophobic collapse of ubiquitin. Protein Sci. 7,
860-874.
1. Creighton T. E. (1977) Conformational restrictions on the 19. Jurkowski W., Brylinski M., Konieczny L., Wiiniowski Z.,
pathway of folding and unfolding of the pancreatic trypsin Roterman I. (2004) Conformational subspace in simulation
inhibitor. J. Molec. Biol. 113, 275-293. of early-stage protein folding. Proteins 55, 115-127.
2. Creighton T. E. & Goldenberg D. P. (1984) Kinetic role of 20. http://www.rcsb.org/pdb/explore/remediatedSequence.
a meta-stable native-like two-disulphide species in the do?structureId=1UBQ].
folding transition of bovine pancreatic trypsin inhibitor. J. 21. http://apps.phar.umich.edu/tsodikovlab/index_files/
Molec. Biol. 179, 497-526. Page756.htm
3. Creighton T. E. (1978) Experimental studies of protein 22. http://www.cs.rutgers.edu/pub/seredin/DomainRewievEng.
folding and unfolding. Prog. Biophys. Molec. Biol. 33, 231- doc
297. 23. Brylinski M., Konieczny L., Czerwonko P., Jurkowski W.,
4. Creighton T. E. (1974) The single-disulphide intermediates Roterman I. (2005) Early-Stage Folding in Proteins (In
in the refolding of reduced pancreatic trypsin inhibitor. J. Silico) Sequence-to-Structure Relation. J. Biomed. Bio-
Molec. Biol. 87, 603-624. technol. 2, 65-79.
5. States D. J., Creighton T. E., Dobson C. M. & Karplus M. 24. Roterman I., Konieczny L. (1995) Geometrical analysis of
(1987) Conformations of intermediates in the folding of the structural changes in immunoglobulin domains transition
pancreatic trypsin inhibitor. J. Molec. Biol. 195, 731-739. from native to molten state. Comput. Chem. 19, 247-252.
6. States D. J., Dobson C. M., Karplus M. & Creighton T. E. 25. Jurkowski W., Brylinski M., Konieczny L., Roterman I.
(1984) A new two-disulphide intermediate in the refolding (2004) Lysozyme folded in silico according to the limited
of reduced bovine pancreatic trypsin inhibitor. J. Molec. conformational sub-space. J. Biomol. Struct. Dyn. 22, 149-
Biol. 174, 411-418. 158.
7. Creighton T. E. (1980) Experimental elucidation of path- 26. Roterman I. (1995) Modelling the optimal simulation path
ways of protein unfolding and refolding. In: Protein Fold- in the peptide chain folding-studies based on geometry of
ing (ed. Jaenicke R.) 427-446. Elsevier/North-Holland Bio- alanine heptapeptide. J. Theor. Biol. 177, 283-288.
medical, Amsterdam. 27. Roterman I. (1995) The geometrical analysis of peptide
8. Creighton T. E. (1977) Effects of urea and guanidine-HCl backbone structure and its local deformations. Biochimie
on the folding and unfolding of pancreatic trypsin inhibitor. 77, 204-216.
J. Molec. Biol. 113, 313-328. 28. Daggett V., Levitt M. (1993) Protein unfolding pathways ex-
9. Creighton T. E. (1980) Role of the environment in the re- plored through molecular dynamics simulations. J. Molec.
folding of reduced pancreatic trypsin inhibitor. J. Molec. Biol. 232, 600-619.
Biol. 144, 521-550. 29. Daggett V., Levitt M. (1992) Molecular dynamics simula-
10. Creighton T. E. (1974) The single-disulphide intermediates tions of helix denaturation. J. Molec. Biol. 223, 1121-1138.
in the refolding of reduced pancreatic trypsin inhibitor. J.
Molec. Biol. 87, 603-624.
bioinformatics
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 25 30
COMPUTATIONAL ANALYSIS OF PROSTATE PERFUSION IMAGES 
A PRELIMINARY REPORT
1
JACEK ŚMIETAC
SKI, 2 RYSZARD TADEUSIEWICZ
1
Institute of Computer Science
Jagiellonian University, ul. A
ojasiewicza 6, 30-438 Kraków, e-mail: jacek.smietanski@ii.uj.edu.pl
2
Department of Automatics
AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Kraków, e-mail: rtad@agh.edu.pl
Abstract: Currently used diagnostic procedures for identifi cation of the prostate cancer (PCa) are insuffi cient. It occurs quite
often that the existing PCa cannot be detected. Therefore scientists search for other methods enabling a better efficacy of
diagnosis. The perfusion computed tomography technique (p-CT), which measures some parameters of blood flow within
diagnosed organs, is supposed to avoid such problems, even in particularly hard cases.
In this paper some methods of automatic analysis of prostate perfusion tomographic images are presented and discussed.
Although the work concentrates only on one image derived from one patient, we can see the complexity and importance of
the task. The proposed algorithms and methods based on the Haralick s co-occurrence matrices seems to be the appropriate
technique to point out the cancerous lesions.
In the further work described algorithms will be tested on a large set of patients. This goal needs close cooperation between
radiologists, pathologist, computer scientists and engineers. The final goal is to develop a professional diagnostic system used
in computer aided prostate diagnosis.
Introduction
Prostate Cancer (PCa) is the second most popular men s can-
cer in Poland and the most popular in West Europe and in the
USA. In 2006 in Poland there was 7154 new registered cases
and 3861 deaths from the PCa [1, 2]. Such high mortality per-
centage is because that malignancy is often diagnosed too
late. Meanwhile the PCa detected in early stage can be suc-
cessfully treated and increase the lifetime of patients or even
lead to cure. This fact causes that the regular comprehensive
diagnosis is very important.. There are many methods which
could help to detect the tumor in early stage, for example the
DRA examination, PSA measure, transrectal ultrasound, and
biopsy (fig. 1) [3, 4, 5]. However the sensitivity and specificity
of those methods are dissatisfying. Conventional computed to-
mography (CT) can help only with detection of metastasis in
Fig. 2. Analyzed perfusion prostate image  blood flow (BF).
advanced PCa. In view of this the need of other, more effective
method, is obvious.
It is supposed that the effectiveness of detecting early PCa
can be improved using the perfusion computed tomography The presumption that this method can be helpful in detect-
(p-CT) method. In this technique some parameters of blood ing early PCa is based on the documented fact that the growth
flow within diagnosed organs are measured. The patient has of cancer needs many nutrients. To secure their supply to can-
injected the bolus and repeated scans of the minor pelvis using cerous lesion, new blood vessels are created in this area [6]. It
the multislice CT scanner. One of the measured parameters is is supposed that this effect (named angiogenesis) is visible on
blood flow (BF) (fig. 2). the p-CT prostate images.
digital image analisis
Computational Analysis of Prostate Perfusion Images  a Preliminary Report
26
Fig. 1. PCa diagnosis: a) per rectum examination (DRE); b) blood examination (PSA measure); c) transrectal ultrasound (TRUS); d)
biopsy; e) additional radiology diagnostic.
Materials and methods Let I : Z2 �" D G = { 1, ..., Ng } (where Z denotes set
of integers) be a two-dimensional discrete image with Ng gray
The p-CT examination was held in the Cracow branch of the levels. For the given image I we define the GLCM:
Oncology Center for a 61 years old patient with suspected PCa
(the PSA level 13,60). The p-CT scans were started about 10 s #{k,l " D : I(k) = i, I (l) = j, || k - l || = d, "(k - l) = �}
P(i, j | d,� ) =
(1)
after administration of 50 ml non-ionic contrast medium (370 #{m, n " D : || m - n || = d, "(m - n) = �}
mgI/ml) at the rate 5 ml/s, and lasted 50 s. The parametric map
was drawn using the CT Perfusion 3 application on the Ad- where: i,j " G  gray levels of points k and l, respectively;
vantage Workstation. The received image is shown on "(k - l) - the angle between vector kl and axe 0X; d  dis-
the fig. 2. The task is to automatically point out the suspi- tance between k and l; �  direction of co-occurrence, #X 
cious regions, with the existence of PCa. power (number of elements) of set X.
The image analysis was held using different methods and
algorithms from the field of image processing and pattern rec- Notation used in the table:
ognition. The most of our algorithms, tested in this work, were
�x = i j) � = j j)
""P(i, , y " "P(i, ,
based on the Haralick s co-occurrence matrices (GLCM) [7]
i j j i
(fig. 3) and 21 coefficients derived from them (tab. 1) [8].
Fig. 3. Example of GLCM: a) source image with 4 gray levels; b) illustration of counting co-occurrences for d=1, �=0�; c) GLCM, d=1,
�=0� (counted co-occurrences are divided by number of all considered pairs of points (here 9); in this example the values were rounded
to two places after comma).
digital image analisis
Computational Analysis of Prostate Perfusion Images  a Preliminary Report 27
� = - �x )2 j) = j - � )2 j)
x "(i "P(i, , � y "( y "P(i, , Table 1. Coefficients of GLCM
ij ji
no. name abbr. value
Px (i) = j) Py ( j) = j)
"P(i, , "P(i, , Px+ (k) = j) , f1 energy
y "P(i,
"P(i, j)2
j i i, j:i+ j=k ENE
f1 =
i, j
Px- y (k) =
"P(i, j) ,
i, j: |i- j|=k - j)log P(i, j)
"P(i,
f2 entropy ENT
f2 =
i, j
HX  entropy Px(i), HY  entropy P y(j),
f3 homogeneity IDM "1+ (i1 j)2 P(i, j)
.
f3 =
HXY1 = - j) log(Px (i)Py ( j)
)
-
"P(i, i, j
i, j
Those coefficients were calculated for each GLCM character-
"(i - j)2 P(i, j)
f4 inertia CON
f4 =
i, j
ized by displacement d in range from 1 to the mask size (de-
scribed below), and angle � with values 0�, 45�, 90� and 135�.
(i - �x ) j - � )
(
y
- P(i, j)
f5 correlation COR "
f5 =
� �
i, j
x y
Second features analysis
)2 P(i, j)
"(i + j - �x - � y
f6 variance VAR
f6 =
i, j
The mentioned above coefficients are the second statistical
)3 P(i, j)
"(i + j - �x - � y
features of the image. Of course it is unlikely that all of them f7 shade SHA
f7 =
i, j
will be useful to differentiate between healthy and cancerous
area. In addition, the more features we calculate the more )4 P(i, j)
"(i + j - �x - � y
f8 prominence PRO
f8 =
i, j
computationally expensive the analysis is. Hence we need to
select only several features with the best ability to distinguish 2Ng
()
f9 sum average SA f9 = i
healthy and suspicious region.
"iP x+ y
i=2
In order to compute those features there were selected re-
2Ng
gions of interest (ROI) within the analyzed image. Each ROI
i i
f10 sum entropy SE - ()log Px+ y ()
"Px+ y
represents a part of it and all ROIs together covers whole pros-
f10 =
i=2
tate area. The values of GLCM and coefficients strongly de-
2Ng
pends on the shape and size of the analyzed ROIs, so we test-
i
f11 sum variance SV - - f9 )2 Px+ y ()
"(i
f11 =
ed regions with different shape and size. In each experiment
i=2
the image was covered by the fixed masks (ROIs). For each of
Ng -1
difference
them GLCM and finally second features were evaluated.
(i)
f12 DA
"iP x- y
f12 =
average
On the example below we used the square mask sized
i=0
40x40 pixels. The mask was moved within the image by ź of
Ng -1
difference
its size (10 pixels). So, to cover the whole image, we used 130
i i
f13 DE - ()log Px- y ()
"Px- y
f13 =
entropy
positions of the mask. For each position we evaluated GLCM i=0
for each displacement from 1 to 39 and for each of the 4 men-
Ng -1
difference
tioned above angles. So we evaluated 425880 coefficients (21
f14 DV - - f1 )2 Px- y (i)
"(i 2
f14 =
variance
i=0
for each of 20280 GLCM matrices). Within image two example
areas (ROI) were selected. The first in the upper-right part of
f2 - HXY1
information
f15 IMC1
the prostate represents the healthy area, and the second 
f15 =
max(H X , HY )
measure
near the lower-left corner covers the cancerous lesion (fig. 4).
� (P(i, j)
)
coefficient of
f16 COV
f16 =
)
variation �(P(i, j)
peak transition
f17 MAX f17 = max(P(i,j))
probability
diagonal
f18 DIAV f18 = �2(P(i,j))
variance
1
diagonal 2
f19 DIAM
ś# ź#
f19 = - j | P(i, j)ś#
"�# 1 | i
moment
2
i, j �# #
1
second diagonal
| i - j | P(i, j)
f20 DSM "
f20 =
2
moment
i, j
triangular
f21 TRS f21 = | P(i,j)  P(j,i) |
symmetry
Fig. 4. The localization of selected ROIs  cancerous area near
the lower-left corner, and the healthy area in the upper-right region.
digital image analisis
Computational Analysis of Prostate Perfusion Images  a Preliminary Report
28
Fig. 5. The entropy (f2) of analyzed image: a) The value of entropy in dependence on parameters d and � for two selected ROIs; green 
healthy area; red  cancerous area; b) Entropy map, d=10, �=0�.
Fig. 6. Inertia (f4): a) Dependence on d and � for selected ROIs; green  healthy area; red  cancerous area b) Inertia map, d=15,
�=45�.
Fig. 7. The infl uence of mask size. Entropy for d=10, �=0�. On fi g.5b mask 40x40. Here: a) 30x30; b) 20x20; c) 10x10 (in this case, in
term of small mask, d=5).
For each ROI the graph illustrating dependence the value The result for some coefficients and parameters are more
of the analyzed coefficient on displacement d and angle � were spectacular (fig. 6) but here the effect of border area occurs.
drawn. For further analysis such d and � were chosen, where The problem will be discussed in next part.
the differences between the healthy and cancerous area were Another aspect to be considered is the size of the ROI
remarkable and they were enough stable (with reference to the (mask). Presented in the above examples size 40x40 pixels is
neighboring parameters). On the graph below (fig. 5) you can about the size of the cancerous area. The example below (fig.
see that entropy could be a good determinant of the cancerous 7) shows that small mask can point out too many local differ-
region (the highest value). ences in texture instead of the key, pathological change.
digital image analisis
Computational Analysis of Prostate Perfusion Images  a Preliminary Report 29
Fig. 8. The infl uence of mask shape. Entropy for d=10, �=0�: a) square mask 30x30; b) horizontal rectangle mask 40x20; c) vertical
rectangle mask 20x40.
Also the direction and shape of the ROI is important. We
observed that texture in healthy area is rather horizontal than
vertical. So, it is recommended to choose the shape in such
a way to enable emphasis of those anisotropy, for example
rectangle higher than wider (fig. 8).
The boundary problem
As mentioned, one of the key problems was to select the prop-
er ROI for the analysis. In the above quoted examples we con-
centrated on the rectangular (squared or not) mask. But the
shape of the prostate is almost oval. That s why the  boundary
problem in the corners occurs  the resulted values depends
on the size and location of outside-prostate area within ROI.
According to previous examples it is worth to see that en-
tropy  indeed higher on the left side of the image, where the Fig. 9. The mask for which the entropy pointed out on the fig. 5b
pathological change is visible  is not the highest exactly in is the highest.
that ROI which covers all prostate points belonging to the can-
cerous area (fig. 9). Also comparing presented earlier graphs
of entropy with the values for two example ROIs (fig. 5a) give To explain this disagreement we must notice that almost
us food of thought. On the figure 5a higher values are for the half of the area indicated on fig. 4 as cancerous region are
healthy mask (green line), while in the second (cancerous, red points outside the prostate. So it is the effect of  boundary
line) values are almost always smaller. problem . During the analysis, the black points, visible on the
Fig. 10. Entropy calculated for different shapes of the mask and different approaches to the outside-prostate area (d=10, �=0�): a) out-
side-prostate area counted (treated as region with no perfusion), rectangular mask; b) outside-prostate area omitted, rectangular mask;
c) outside-prostate area omitted, circle mask.
digital image analisis
Computational Analysis of Prostate Perfusion Images  a Preliminary Report
30
corners of the image were treated as points without observed Although it seems that the p-CT method has a big potential
perfusion, exactly as black pixels within prostate. Now it is ob- to recognize PCa and to point out the cancerous regions, the
vious that this way is unacceptable. To solve this problem, two full verification of the proposed algorithms and evaluation of
alternative methods were proposed: sensitivity and specificity of this diagnostic method needs a lot
Leave out points outside the prostate. In this approach of work and a close cooperation between radiologists, patholo-
matrices calculated for border ROIs are remarkably sparse. It gist, computer scientists and engineers.
could influence on the values of coefficients.
Analyze ROIs with non-rectangular shape, eg. oval or cir-
cle. In this solution some border effects are eliminated but not References
for all cases  if the middle of the circle is almost on the border,
still many analyzed pixels are outside the prostate. Addition- 1. Estimated New Cancer Cases and Deaths by Sex, US, 2008,
ally, the computational cost of selecting a circle mask is higher http://www.cancer.org/docroot/MED/content/downloads/
than a rectangular one. MED_1_1x_CFF2008_Estimate-d_Cancer_Cases_
The next graph (fig. 10) presents entropy for three differ- Deaths_All.asp
ent mask sized 40x40 pixels. We see that the best solution is 2. Krajowy Rejestr Nowotworów, Raporty na podstawie
rectangular mask where the pixels outside the prostate are not danych Centrum Onkologii, http://85.128.14.124/krn
analyzed. 3. Hricak H., Choyke P., Eberhardt S. et al., Imaging Prostate
Cancer. A Multidisciplinary Perspective, Radiology 2007;
243(1): 28-53.
Conclusion 4. Roscigno M., Scattoni V., Bertini R. et al., Diagnosis of
prostate cancer. State of the art, Minerva Urol Nefrol 2004;
In this paper it was shown that it is possible to select such pa- 56(2): 123-145.
rameters of perfusion prostate image, which are deterministic 5. Simon H. (ed.), Prostate Cancer, [in:] Lifespan s A 
and independent from personal assessment. Some algorithms Z Health Information Library 2006, http://www.lifespan.org/
which enable a fast, automatic and correct selection of cancer- adam/indepthreports/10/000033.html
ous regions were presented and discussed. The results assure 6. Miles K. A., Functional computed tomography in oncology,
us that the p-CT technique may be very useful in early prostate European Journal of Cancer 2002; 38: 2079-2084.
cancer diagnosis and it is worth to continue the exploration of 7. Haralick R. M., Shanmugam K., Dinstein I., Textural fea-
this field. tures for image classifi cation, IEEE Transactions on Sys-
In the Oncology Center in Cracow the p-CT method is be- tems, Man and Cybernetics 1973; 3: 610-621.
ing used to examine other patients. Thanks to that it will be 8. Walker R. F., Adaptive multi-scale texture analysis with ap-
possible to verify the usefulness of the proposed algorithm. In plication to automated cytology, University of Queensland
the further work the researches will be also expanded to other 1997.
perfusion parameters in order to determine the effectiveness
of each one.
COMPUTER SCIENCE �! DIAGNOSTICS
�!�!
ENGINERING �! RADIOLOGY
digital image analisis
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 31 34
USAGE OF NAIVE BAYES CLASSIFIER IN DECISION MODULE OF
E-LEARNING DECISION SUPPORT SYSTEM
MARCIN CHABIOR, ANNA NOGA, MAGDALENA TKACZ
University of Silesia
Faculty of Computer and Materials Science
Institute of Computer Science
Abstract.This article describes adopted, within the scope of one of e-learning system creation, a method of diagnosis generation
based on defi ned symptoms with the use of the Bayes naive algorithm. It is intended for Medical Faculties students, inference
module shall facilitate determination of probability of the influence of individual symptoms on diagnosis. Practical application of
such approach presented in the article gives the possibility of distant verification of student s knowledge taking into account not
only diagnosis, but also will facilitate gaining skills of appearance materiality determination of symptoms in relation to diagnosed
affection. For the testing purposes of adopted assumptions the hundred element database has been applied depending on
spine affection in discopathy form and factors, which can affect the origin of the affection  obesity and hard physical work.
The operation of the Bayes algorithm has been presented within the scope of infl uence evaluation of enumerated factors on
affection origin.
Keywords: Bayesian network, na�ve Bayes estimation, elearning, decision support systems, medical e-diagnosis.
Introduction tional probability. For each knot at known values of a distribu-
tion of parents probability is recorded. Conditional distribution
Initial assumptions of e-learning system planned to be devel- is presented in the form of Conditional Probability Tables (CPT)
oped in Medical University of Silesia in Katowice resulted in in- which includes a distribution of conditional probability for Zi and
depth study in forming a concept of the system. Successively for each combination of parents value (Figure 1).
with clearly defined computer scientists a certain assumptions
has been formed for all modules at the same time. But the sec-
ond thought about module intended for online diagnosis bas-
ing on symptoms (concerning the method of determining the
influence of a certain symptoms in final diagnosis of a patient,
which a decision-based module in the decision support sys-
tem) appeared.
Searching the solution for that problem, we decided to use
the Bayes naive estimation. As opposed to quantitative ap-
proach which is basic form of probability estimation where pop-
ulation parameters are constants and randomness depends on
data, the Bayes approach is based on other assumptions. In
the Bayes statistics, parameters are considered to be random
variable, however data are treated as fixed constant [1].
The Bayes network is a consistent representation of total
distribution of a random variable which applies (in the process
of compression), a part of marginal and conditional indepen-
dence between variables [2]. The Bayes network is defined as
acyclic direction graph, where knots represents variables and Figure 1 Example of Bayesian Network with CPT tables
edges  direct reason dependence. The syntax of the Bayes
network is as follows  for each random variable graph knots
are formed, graph edges constitute connections and reflect the The Bayes analysis requires so called  a priori distribu-
dependence between variables and the distribution of condi- tion which is the first distribution of , where represents
e-learning
Usage of naive bayes classifier in decision module of e-learning decision support system
32
parameters of unknown distribution. With this distribution the disc of a spine (discopathy) basing on existing learning set of
expert knowledge on distribution is modeled. The qualifica- connections between variable discopathy and two descriptive
tion of individual probabilities of influence about definite val- variables. Discopathy variable can has two possible values 
ues the parameters usually in case the possible medicines is. truth and false, assuming the following notation:
It required therefore experts knowledge which was provided B means overweight = true
for in project of application. Possible it is as the application on means overweight = false
entry of value of initial probabilities parameters and in case F means physical work = true
of lack of suitable experts knowledge will make possible au- means physical work = false
tomatic their the adjustment across use the of mean value R means the possibility of discopathy appearance = true
(attributing to every of parameters the same value of prob- means the possibility of discopathy appearance = false
ability). Taking under attention fact, that application will serve we can describe dependences with the formula:
students teaching, mentioned solution gives the possibility of
opinion of pertinence put by student of value of probabilities. In (5)
other words, possibility of checking how student be able to ac-
curately diseases from sickness individual definite symptoms. Here the method of maximal a posteriori has been used.
Lack of expert knowledge does not impose the need to change It is a method of a posteriori distribution estimation (estimator
this method because it is possible to assume non-information MAP  Maximum a Posteriori method). The search of esti-
a priori distribution which allows to assign the same probabili- mator with the method of maximal a posteriori consist of seek-
ties for all parameter values. The amount of data in analyzed ing such value , which will maximize the function .
data set usually has significant influence on assumed solutions Using formula on distribution a posteriori we obtain the follow-
of a priori distribution which causes its modification. In this way ing:
we obtain a posteriori distribution where X represents
the whole data set. Distribution a posteriori is expressed with
the formula: (6)
where X represent the whole data set.
(1) Use only two variables is explanatory large simplifying but
it allow to analysis step by step of issue in present article. In
where is a likelihood function reality the number of variables having the influence on occur-
is a priori distribution rence the diseases, can be considerably larger but the pattern
is marginal distribution of analytic conduct stays the same.
The Bayes theorem for simple events presents as follows
 let A and B will be events in testing space. Than conditional Results
probability P(A|B) can be described in the following way:
The next step has been to determine which variables value
discopathy (true or false) has greater probability value to dis-
(2) tinguish the estimator CMAP for the variable. For this purpose
the first step was to find marginal and conditional series of
Analogously probabilities. Results of estimated probabilities a posteriori are
presented in the Table 1.
The next step was to found total conditional probability
(3) in a form . Estimation results are presented in the
Table 2.
And after this simple mapping we obtain: Having the knowledge of total conditional probability, the
evaluation of estimator MAP of discopathia variable was pos-
sible for all four variables combination: overweight and physi-
(4) cal work with formula (5). Because the result for each possible
combination has been false, it did not correlated with expecta-
Which finally is the Bayes theorem for simple events. tions it was necessary to estimate the quotient of aposteriori
chances  which reflect the level in support of the benefit of
every possible classification. The quotient of a chance in case
The problem of a posteriori has been estimated in the following way:
In the first phase of the our approach with the Bayes methods
efficiency testing (in application of concerning the problem of (7)
determining levels of variables interaction on formulated diag-
nosis) two quality explanatory variables has been applied  Where is a specific classification of unknown target
overweight and physical work. The diagnosis problem was variable.
to make appropriate classification of new patients with regard The value of quotient greater than 1 informs, that a pos-
to the possibility of appearing disc prominence of interverterbal teriori distribution gives us a positive classification (true) and
e-learning
Usage of naive bayes classifier in decision module of e-learning decision support system 33
Table 1 Results of estimated probabilities a posteriori
Set size (false) Set size (true) Probability value
Overweight 60 40 0,4
Physical work 48 52 0,52
Discopathy 80 20 0,2
Overweight = true assuming that discopathy = true -13
0,65
Overweight = false assuming that discopathy = true 7-
Overweight = true assuming that discopathy = false -27
0,3375
Overweight = false assuming that discopathy = false 53 -
Physical work = true assuming that discopathy = true -11
0,55
Physical work = false assuming that discopathy = true 9-
Physical work = true assuming that discopathy = false -41
0,5125
Physical work = falsehood assuming that discopathy = false 39
Table 2 Estimation results
Patients having the obesity who perform hard physical work
Patients having the obesity who do not perform physical work
Patients without the obesity who perform hard physical work
Patients without the obesity who do not perform hard work
Table 3 The quatients of a posteriori chance
Patient suffering from overweight and performing hard physical work
Both classifications are supported at the same level
Patient suffering from overweight who do not perform physical work
Justification Discopathy = true with regard to discopathy = false is at the level of 17 %
Patient who does not suffer from overweight and performs hard physical work
Justification Discopathy = true with regard to discopathy = false is at the level of 3,4 %
Patient who does not suffer from overweight and does not perform hard physical work
Justification Discopathy = true with regard to discopathy = false is at the level of 22,7 %
the quotient value lesser than 1 on the contrary  a posteriori sumption about independences of explanatory variables has to
distribution gives us a negative classification (false). The quo- be done here.
tient value equal 1 means that the information from posteriori The two events A and B are independent under condition,
distribution gives the same level at both classification . In the if for some event C: . The as-
case we considered the following results has been obtained sumption of conditional independence can be described with
(Table 3). the following formula,
The considered case (with two explanatory variables with
binary values assumed, as well as variable binary of the tar-
get) does not cause large programming difficulties, because of
uncomplicated mathematic theory usage. Basing on practice,
if there is a possibility of arising of p variables with k values (8)
then we will have a lot of . As the practice shows prob-
abilities which have to be estimated it is the numb. It means
that when we have 20 binary variables (k=2) it is necessary where x1, x2, & , xm are every possibile combination of X de-
to estimate from 2 up to 20 probabilities (1 048 576). The as- scribed factors.
e-learning
Usage of naive bayes classifier in decision module of e-learning decision support system
34
However the notation As we can notice, the results shows that patients suffer-
ing from overweight give positive influence on the probability
of affection origin in a discopathy form. Physical work does not
(9)
presents mentioned tendencies.
is named as the Bayes naive assumption or the Bayes first se-
ries assumption. Conclusion
This approximation facilitates to show complete conditional
distribution from the quantity to the one-dimension The method presented in the article presents clearly the effi-
distribution product requiring probabilities. We obtain ciency of statistical methods application, based on the Bayes
the model of conditional independence which is linear and not theorem. It should be usable for utilization as a part of a deci-
exponential dependent from variables number p. Despite the sion support system, which is able to diagnose with the deter-
fear of reduced model s efficiency, decreasing the number of mination of the fixed probability level of each symptoms Further
parameters is a positive solution and is related to the prob- use of the application will be as one of the module of distant-
lem of diagnostic evaluation based on determined symptoms. learning complex system, and we hope that it will be quite good
For instance, where xi will be Medical symptom and CK cor- method for classical education in diagnosis. The system flex-
respond to various diseases, then the assumption that if a cer- ibility will facilitate the use of the same application regardless
tain person that suffer from CK disease, then the probability of of the Medicine field  where the diagnosis is required together
one symptom dependency (only from CK disease and not from with the determination of the level of its correctness and it can
other symptom) will be faultless. In other words, we are model- be done with classical probability measure.
ing how symptoms appear, given each disease, as having no
interactions (note that this does not mean that we are assum-
ing marginal (unconditional) independence). Bibliography
A practical implementation of such a work are still  in prog- 1. Kłopotek M. A.: Inteligentne Wyszukiwarki Internetowe,
ress . We would like to take into account the possibility of more Akademicka Ofi cyna Wydawnicza EXIT, Warszawa 2001.
than binary variables in the future and in independent way- 2. Ross K. A., Wright C. R. B., Matematyka Dyskretna,
together with the other variable type. Assuming that maximal Wydawnictwo Naukowe PWN, Warszawa 2006.
number of variables is 10 and the number of possible values is 3. Błttcher S. G. Dethlefsen C.: Learning Bayesian Networks
4 than the estimation of values will be need- with R, Proceedings of the 3rd International Workshop on
ed. As the measure of justification, each variable affects the Distributed Statistical Computing, March 20-22, Vienna,
classification decision, the value of chances logarithm a pos- Austria, 2003.
teriori were applied. The quotient is described in the following 7. Larose D. T.: Data Mining Methods and Models, John Wi-
way:: ley & Sons, Hoboken 2006.
8. Moczko J. A.: Wybrane metody analizy danych jakościo-
wych na przykładzie wyników badań kardiologicznych,
(10) StatSoft Polska, Kraków 2008.
9. Hand D., Mannila H., Smyth P.: Principles of Data Mining,
Received results for the tested patent group is presented Massachusets Institute of Technology, Cambridge 2001.
as follows: 10. Friedman N., Linial M., Nachman I., Peer D.: Using Bayes-
ian Networks to Analyze Expression Data, Hebrew Univer-
sity, J. Computational Biology, Vol. 7, No. 3-4, pp. 601-620,
(11) 2000.Kwiatkowska A. M.: Systemy wspomagania decyzji,
Wydawnictwo Naukowe PWN, Warszawa 2007.
(12)
e-learning
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 35 37
E-LEARNING WITH USE OF VIRTUAL PATIENT IN PHARMACY
EDUCATION
KRZYSZTOF NESTEROWICZ, SEBASTIAN POLAK
Unit of Pharmacoepidemiology and Pharmacoeconomics, Faculty of Pharmacy Jagiellonian University
Medical College, Medyczna 9 Street, Kraków 30-688, Poland
contact author: krzysztof.nesterowicz@gmail.com
Abstract: e-learning is an approach to facilitate and enhance learning through, and based on both computer and communications
technology. At first it is necessary to acknowledge an important growth of blended and collaborative learning applications. Many
institutions try to make universal learning modules which promote cooperative methods of work. Other initiatives focus on the
idea of building a common e-learning system.
One of available distance learning techniques in studying pharmacy is a virtual patient application. The practical example of
such educational attitude is presented based on the in-house developed patient case.
Keywords: e-learning, e-education, blended learning, virtual patient
Introduction Today e-education is often connected with traditional learn-
ing. In this way, the first direction of e-learning development
E-learning or e-education is becoming increasingly popular in Europe comes into existence  blended learning [1]. The
and the Internet is laden with the ever growing number of ap- method combines advantages of e-learning with advantages
plications of the subject matter. The European Community is of traditional learning. Main advantages of the e-learning are
fully aware of the importance of these developments and sup- listed below:
ports them in many ways. Today one can pinpoint the direction " differentiation of learning,
of the progress which has so much influence on the European " cost reduction,
investigations. At first it is necessary to acknowledge an impor- " time flexibility,
tant growth of blended and collaborative learning applications. " integrated assessment tools,
Many institutions try to make universal learning modules which " multimedia forms,
promote cooperative methods of work. Other initiatives focus " high interactivity [5].
on the idea of building a common e-learning system [1]. On the other hand, there are undisputable advantages of
E-learning is a term which is commonly used, but does traditional learning, including:
not have a common definition [2]. Most frequently it seems to " direct interpersonal relations,
be used for web-based distance education, with no face-to- " live contact with the tutor,
face interaction. However, also much broader definitions are " exact definite time and place of training,
common. For example, it may include all types of technology " evaluation of knowledge,
enhanced learning, where technology is used to support the " contact with real experiment,
learning process. Although pedagogy is usually not part of the " training of interpersonal abilities [5].
definition, some authors do include it [3]. For example in this One of available distance learning techniques which can
definition, where e-learning is said to be: pedagogy empow- be used during the pharmacy studies is a virtual patient appli-
ered by digital technology [4]. cation. It has become a useful way of teaching pharmaceutical
It cannot be forgotten that e-learning means student-stu- care where students need to challenge with many situations
dent, student-teacher or teacher-teacher interaction. Partici- related to pharmacotherapy of patients with chronic diseases.
pants of an e-learning course should be always aware about By studying with virtual patients students are involved in deci-
results of their education process and their knowledge should sion making procedures.
be evaluated during the course. Therefore uploading some
materials on a website, like lectures or exercises is still not real Simulated patients increase the availability of training op-
e-learning because it lacks the component of interactivity [5]. portunities for pharmacy students, making them less depen-
e-learning
E-learning with use of virtual patient in pharmacy education
36
Picture 1. An example of a decision making tree [8].
e-learning
E-learning with use of virtual patient in pharmacy education 37
dent on actual cases to learn how to handle different situations tions students make creates scenarios that more closely par-
in pharmaceutical care. Unlike real patients, simulated patients allel the reality of pharmaceutical care. Since students must
can be accessed on demand and they can be endlessly re- search online databases and study other resources to gather
playable to allow the user to explore different options and strat- the information needed to make informed decisions about their
egies. They can be structured with narratives that represent patients, the course also builds the data collection skills.
real situations while challenging the user with a wide range of
tasks [6]. Students learn how to handle with some cases which
later they can meet in reality while providing pharmaceutical Decision making tree
care to their own patients.
Nowadays we are to implement in the subject for Pharmacy
students  Practical Pharmacy in a Community Pharmacy ex-
E-education in Poland and abroad ercises with a decision making tree tool to teach pharmaceuti-
cal care. Below there is an example of such decision making
Unfortunately there are still not suitable legal regulations in the tree (Picture 1).
current education system. This is the basic obstacle for the The Virtual Patient Mary Smith asks for a medicine against
development of distance learning in Poland. Nevertheless the cough and says she is not taking other medicines now.
situation has improved recently. Constructing a didactic proc- A participant is granted with one point for each right ques-
ess with the use of the Internet potentially requires the com- tion given before dispensing a medicine (Picture 1).
petent application of both educational regulations and baseline Exercises like that help students to improve their decision
programmes, in schools [1]. making skills which they need to possess during their everyday
The level of technical culture and ability to use computer is work as pharmacists. Besides students learn how to get proper
another barrier. The majority of users confess that their com- information from a patient by asking right questions.
puter activity is limited to simple applications, frequently cre- In the literature teachers sometimes complain that prepar-
ated especially for beginners. ing such materials is very time consuming and require special
In the Faculty of Pharmacy, Medical College, Jagiellonian computer skills. But from the other hand this form of teaching
University in Krakow, Poland there is a course  Practical Phar- is also convenient for educators because it enables to check
macy in a Community Pharmacy where students learn by us- students skills in shorter time comparing to essays or formu-
ing blended learning method. Participants listen to the inter- laries they would need to fill.
view with a patient which is stored in the computer and provide
a patient an adequate pharmaceutical care. During the course
they are provided with some interactive presentations and they References
are allowed to check all medical information in online databas-
es. At the end of the course attendees need to write a final test. 1. Meger Z., E-EUROPE, International Conference on e-lear-
They do it online and receive their results immediately. ning in education, E-Learning  European Trends, 9, War-
This innovative approach challenges students and pro- saw 2006.
motes interactive learning. Student evaluations indicates 2. Dublin L., If You Only Look Under the Street Lamps... Or
achievement the objective of creating a course that more Nine e-Learning Myths, The eLearning Developers Jour-
closely simulates the actual provision of pharmaceutical care. nal, 1-7, 2003.
Pharmaceutical care laboratory courses offer students the 3. http://en.wikipedia.org/wiki/E-Learning
opportunity to learn and practice pharmaceutical care skills in 4. EC, Communication from the Commission: E-Learning 
a controlled environment. These courses usually include in- Designing  Tejas at Niit tomorrow s education, Brussels:
struction in dispensing as well as clinical activities. Typically, European Commission, 2000.
a new patient case is presented in each laboratory section and 5. Nesterowicz K., E-learning in Pharmacy Education, Eu-
no  follow up care of patients from previous laboratory sec- ropean Pharmaceutical Students Association Newsletter,
tions is discussed [7]. Vol. 16, Ed. 3, July 2009.
The authors of the above course have created several vir- 6. http://en.wikipedia.org/wiki/Virtual_patient
tual patients whose responses to care vary based on students 7. Hussein G., Kawahara N., Adaptive and Longitudinal Phar-
input and recommendations. For example, if a wrong drug or maceutical Care Instruction Using an Interactive Voice
dose is recommended, an adverse event may occur; if patient Response/Text-to-Speech System, Am. J. Pharm. Educ.,
counseling is not provided, an error in administration may 70(2): 37, April 15, 2006.
be encountered; if patient compliance is not evaluated; drug 8. Nesterowicz K., Short communication, International Con-
levels may be unexpectedly altered. The application of virtual ference on Virtual Patient, Kraków, Poland, June 5-6,
patients who change in ways appropriate to the recommenda- 2009.
e-learning
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 39 43
INTERACTIVE KNOWLEDGE BASE FOR EXPERT SYSTEM
ANNA NOGA, MARCIN CHABIOR, GRZEGORZ SAPOTA
The Silesian University
IT and Science Department
Summary: In this article the project of interactive knowledge enabling the record of disease symptoms is presented by doctors
to prepare learning set for expert system based on self-organizing networks. Knowledge base will enable the formulation of
a diagnosis of disease changes caused by a discopathy and degenerative changes of the backbone.
The SpineMedical system can be also used for education purposes for doctor and Medicine faculty students. It enables to
complete database by doctors who formulate a diagnosis while examining patients. The SpineMedical system was equipped
with the possibility of faulty records filtering. In the article results of expert system operation which diagnoses patient morbidity
was presented.
Keywords: Knowledge modelling, expert system, discopathy
Introduction degenerative changes the neurology symptoms defects can
occur this is a dysesthesia in various places of lower limbs,
The SpineMedical program is formed with the cooperation of weakening of foot, lower leg muscles and pareses of lower leg
the Silesian University in Katowice and the Silesian Medicine nerves where the most often is paresis of peoneral nerve and
University. in the final stage a paralysis of peoneral nerve. However, in
The purpose of the application is to facilitate the commu- advanced discopathy disorders of urinary bladder constrictor
nication, team work as well as processing, archiving and files muscles, anus or virility and libido disorders can occur.
creation. The SpineMedical gathers data on discopathy and
degenerative changes of the backbone for quality and quantity
diagnosis of patients affection. Description of interactive program
The backbone is a central anatomical structure of a human
operation
being and diseases are currently one of major health problems
because they hinder normal living, family living, work, rest and
many other daily activities. The SpineMedical is an application which is computer scientist
Familiar backbone pain last increased significantly. The education system which is intended for doctors and students
fact that more and more children and youth has similar prob- and covers the diagnostics in discopathy and backbone s de-
lems is considered. generative changes. This application allows to patient s  con-
The discopathy can be divided into two morbidities. In the versation to formulate a diagnosis with administer method and
first phase the discopathy were treated as needed and in the a choice from the list of proposed questions. The program is
later phase of the disease the diagnostic imaging were used based on database which can be updated, viewed and cor-
that is examination of magnetic resonance type and computer- rected. A doctor has a possibility to complete data with records
assisted tomography as well. Unfortunately, a diagnosis in the connected with new cases and has a possibility of free modifi-
disease advanced stage is connected with the operation this is cation of base s resources (Fig. 1).
nucleus removal [5, 6]. Application operation is based on dialogue windows. When
Intervertebral disc disease can appear in cervical, thoracic the application is activated the user chooses basic identifica-
and lumbar section. The Discopathy symptoms in initial stage tion data like the following: age, sex, growth, weight (Fig 2.)
manifest in thoracic-lumbar section pain. It can appear pain ra- or load data in case of first visit in a database. When data are
diation to one or both lower limbs (hips, genua, lower legs or loaded the program classifies a person in proper weight group
feet), paraesthesia. Despite a sick person can have the impres- (underweight, appropriate weight, overweight).
sion of increased tension of backbone muscles, limitation in this In the following step a patient chooses a type of pain (spo-
section movement caused by pain. The following symptoms of radic, transient, continuous, hard, low, moderate) and indicates
a disease are neurology deficits. In case of more advanced the place of pain appearance (cervical, thoracic, lumbar sec-
expert system
Interactive knowledge base for expert system
40
Description of Data Classification
features processing
Knowledge
database
modelling
Estimations
diagnosis
Fig. 1. Pictorial operation of the SpineMedical application
Fig. 2. The window presenting basic identification data
Fig. 3. The decision module of Spine Medical program
expert system
Interactive knowledge base for expert system 41
tion) what defines the number of a disc. Afterwards, he gives the neural networks were used because they facilitate to apply
probable reason of pain (injury, lifting heavy weights, seden- sophisticated modeling technique which can proceed complex
tary work, vibrations, fall, osteoporosis) [9]. functions mapping. Neural networks enable forming of nonlin-
In the following phase of loading data to the application ear model in easy way as well as allow to a control of complex
a patient determines symptom connections with the disease. multidimensionality problem and with the use of other methods
Final step of data loading is the quality and quantity diagnosis it hinders modeling trials of nonlinear functions having large
of patient s affection (Fig. 3). number of independent variables.
Neural networks are used to associate many factors and
as identifying tool and predicating on this basis other factors
Expert system construction and characteristics. These factors can be for example weak-
ening of foot muscles and foot paraesthesia as well. Neural
The SpineMedical application is equipped with a module ena- expert system consists of few neural networks where each in-
bling data filtration and expert system intended for a definition tends for formulation of other diagnosis. Neural networks were
of affection type. performed on the basis of multidimensional perceptron where
The purpose of data filtration module consist in verification input data included the following parameters: pain type, iden-
of identification data in the first stage of application operation. tification data, section of pain appearance, sections disc, pain
Filtration module divides records into false and probably true reasons. The purpose of the network is determining quality di-
ones. agnosis of patient s affection [4, 8].
The classification of incorrect and uncertain records has Utilizing data set obtained with doctor s diagnosis the pro-
been realised by means of decision trees. cess of learning and neural networks testing was applied. For
Decision trees are one of the most popular techniques used the purposes of evaluation and anticipation of disease type
for data analysis. The advantages of the described technique based on experimental results it was necessary to prepare ex-
are: the possibilities of creating the trees using the algorith- planatory data set and the algorithm which will allow to detect
mic techniques  divide and do ; the perfect protection against rules describing mutual connections [1].
disturbance of data; the possibilities if using this technique to Many factors like the quality of collecting data, a method of
select and extract the features. The following coefficients have testing, initial data processing. The most important thing is the
been used to create a decision tree highest quality. These characteristics can have linear or nonlin-
" Age ear type, this is normal expansion, but from time to time exist
" Weight features of exponential or logarithmic data dispersion to some
" Height dimension. Such features provide lots of information after per-
" Sex forming transformation which are reverse to those observed in
" The type of pain some dimension [2]. That is why data transformation is carried
" The place of occurrence out to level large disproportions between these values in the
" Accompanying symptoms dimension.
On the basis of the introduced data the system generates Data standardization aims to put values within the limit [0;1]
decisions, which give the possibility to classify properly the in- after transformation process. For this purpose, at assumptions
troduced records.
At the moment of loading faulty data the application dis-
x = min x
min i
i
plays information window with data incompatibility. (1.1)
In the application the expert system based on neural net-
works was applied (Fig 4.). Expert system is a part of knowl- x = max xi
max
i
edge where loaded or inserted data, in the following steps, are (1.2)
rules and facts. In this work, to determine the affection type
Fig. 4. Neural network construction
expert system
Interactive knowledge base for expert system
42
mapping for each characteristic is performed where i varies of such neurons despite the fact that they are suitable and can

from 1 to n: be the reason of the model over-learning. The increase and

xi x reduction of model s structure in learning process causes the

min
,
x
i= x x situation that a model can be increased and reduced as need-
max min
(1.3) ed with part of the structure elimination or replacement with
smaller one. The algorithm of proper verification of neurons
It is necessary to remember that at the moment we deal should be defined to increase and reduce network architec-
with faulty values considering some characteristics the result ture by proper selection of learning model s complexity to the
can show that they are outside of some characteristic and model s data loading. With the assumption that density func-
this can be the reason of pressing standardized value of the tion and described neurons of hidden layer are similar, how-
characteristic which can include lots of significant information. ever significance coefficients of neurons of hidden value are
In such a case it is necessary to apply a standardization and defined as the ration of weight amount to the weight variation
a cut. With the use of cut standardization of values x min and [7]. The relation favor only strong weights this is such which
x max selects from the set S= { x1, x2, & x n} after rejecting S k% have significant influence. Defined coefficients are written with
the lowest and highest values where k takes values from 5 to the formula:
2
10.
wi
Selection of existent characteristics among all dimensions Si = (1.7)
w
i
of input data has significant influence on learning and final lev-
el of generalization. There is a lot of methods for characteris- We can eliminate only such neurons where significance
tics selection and they vary with ways of quantity selection and coefficients are the lowest and are written with the formula:
2
the characteristics sequence in the analysis. Data comprising
wi
Li = min Si = min
list of exemplary attributes declared as proper solutions are
w
i i
i
named as training set [3]. (1.8)
While network learning under the supervision we deal with Equation 1.8 can be reduced to the other form:
2
two phases. In the first phase this is learning and the second
wi
one is the knowledge recovery. Prepared attributes sets de- Li = min Si = min (1.9)
[ ]ii
Pw
i i
termine all inputs and also outputs required in the input data
presentation. Current output signal of the network was com- For the purpose of 1.9 dependences one must use ex-
pared with input signal and after processing the whole subset panded Kalman filter as the estimator of model s parameters
of learning samples we correct weight which connects network to determine dwi variance with covariance matrix Pn, which is
neurons was corrected. In other words, correlation aims at re- as follows:
ducing of error measure of network operation. Unfortunately,
Pw Pwv
[]
applied methods of weighting disintegration or their elimination P = (2.0)
Pwv Pv
give positive results. It should be mentioned that even with
small weights small error can be obtained. It is, thus important where PW is a covariance matrix between weight and PWV this
to determine so called significance parameter which allows to is covariance matrix between weight and other parameters but
weighting elimination testing where significance coefficients PV is a covariance matrix between other parameters. Decision
are the lowest and do not cause much changes in error func- on neurons elimination brings to the criterion:
tions. Error function was estimated by the Taylor series [7].
Li 2
< Xi, (2.1)
R
y
E
3
( )T 1 2E
E = * w + wT * * w + O( w2 )
where x2 is the chi-aquare distribution with trust level equal
n, u
w 2
w2
to u%
(1.4)
R = R + dT Pn-1d
n n
(2.2)
y n
2E
Where forms Hessian H.
w2
If the criterion is met the neuron which obtained the lowest
In case weights are in the minimum of function error we significance coefficient should be eliminated.
omit first term of the sum on the right side of equation and the
third summand which results in equation reduction to the fol-
lowing form: Evaluation of the efficiency of expert
m system operation
1
2
"
E = Hii wi
(1.5)
2
i
When the i weight is eliminated we obtain wi= dwi and this To increase the efficiency of the expert system in estimating
can indicate significance coefficients of the Si for each weight the type of illness it needs an enormous database. The base,
2 which is used to study the neural network consists of hundreds
Si = Hiiwi
(1.6) of records introduced by the doctors who co-operated with the
However, while learning the situation can happen where authors. Additionally, on the basis of experts (doctors ) knowl-
some weight or neurons stop to play important roles. Such cir- edge and experience the record set has been generated. This
cumstances cause that the model must proceed in adaptation set has been used to test the system.
expert system
Interactive knowledge base for expert system 43
In the table 1 presented the comparison of the efficiency of doctors in formulation a diagnosis based on provided data. The
expert system operation including diagnoses formulated by the SpineMedical application is intended for doctors and medicine
experienced doctor. students and patients as well. In the future the application can
have larger scope of application for example for the purpose
Table 1. Efficiency of network operation of analyzing and medical imaging processing like X-rays and
computer tomography images enabling to more accurate de-
Sensitivity Specificity Precision
termination of diseases changes in the backbone.
Doctor 88% 92% 89%
Network 80% 82% 82%
Networks and
Bibliography
92% 95% 92%
a doctor
1. Osowski S.: Sieci neuronowe do przetwarzania informacji,
Comparing the efficiency of neuron network operation Ofi cyna Wydawnicza Politechniki Warszawskiej, Warsza-
and doctor s diagnosis we can notice that networks deal with wa 2000.
quality evaluation of a patient. It can be noticed that differ- 2. Cottrell M., Girard B., Girard Y., Mangeas M., Muller C.:
ence between doctor s diagnosis and expert system diagnosis Neural modeling for time series: a statistical stepwise
amounts to few percents. Better result can be obtained if the method for weight elimination, IEEE Transaction on Neural
doctor in the initial phase of the diagnosis uses expert system Networks IEEE Transaction on Neural Networks, 1995.
to formulate own diagnosis. 3. Cichosz P.: Systemy uczące się, Wydawnictwa Naukowo-
Techniczne, Warszawa 2000.
4. Tadeusiewicz R., Lula P.: Wprowadzenie do sieci neurono-
Summary wych, StatSoft & C.H.Beck, Kraków 2001.
5. Rąpała K.: Zespoły bólowe kręgosłupa. Zagadnienia wy-
Today s advanced progress can be observed not only in tech- brane, Warszawa 2004.
niques but also in science and medicine. Current database 6. Stodolny J.: Choroba przeciążeniowa kręgosłupa, Kielce
have gigabytes of data and include hidden information of sig- 2004.
nificant value. This fast increase in size of database caused 7. Le Cun Y., Denker J., Solla S., Kauffman M.: Optimal brain
limitations in analysis and interpretation of collected data. It is damage: Advances in Neural Information Processing Sys-
harder now to analyze efficiently big amount of data and re- tems 2, San Mateo 1990.
sults of various tests determining the patient health. 8. Duch W., Korbicz J., Rutkowski L., Tadeusiewicz R.: Sieci
That is why, expert systems based on computer science neuronowe, Akademicka Ofi cyna Wydawnicza EXIT, War-
technique are formed and become helpful for doctors as can szawa 2000.
use appreciable sets of current and archive databases as well 9. Bubnicki Z.: Wstęp do systemów ekspertowych, Wydaw-
as present deviations of proper values. Computer science ap- nictwo Naukowe PWN, Warszawa 1990.
plications are designed and are more often applied tool for
expert system
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 45 49
SPEECH PERCEPTION  TOWARD UNDERSTANDING OF
CONSCIOUSNESS
JAN TR
BKA, PIOTR WALECKI, WOJCIECH LASOC
, WIESA
AW PYRCZAK,
KRZYSZTOF SARAPATA
Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kopernika 7,
31-034 Krakow
Abstract. This paper presents a project executing within the framework of COST Action BM0605: Consciousness: A Trans-
disciplinary, Integrated Approach. The research is centred on neurophysiological experiments to image brain function in
diseases in which the phenomenon of consciousness plays an important role. The fundamental problem studied in this project
will be an investigation of the relation between consciousness and speech perception. The study will be conducted using
electroencephalographic methods on subjects with Auditory Processing Disorders.
Keywords: speech perception, consciousness, Auditory Processing Disorders, event-related potential
Introduction both of phonological capabilities such as auditory memory vol-
ume and sequence and temporal discrimination and of other
The problem of consciousness is regarded as one of the fun- behavioural phenomenon that are responsible for central audi-
damental problems in contemporary science. Understanding tory processing such as sound localization and lateralization,
the mechanisms which contribute to the creation of states of sound differentiation, auditory pattern recognition, temporal as-
consciousness such as perception, sensation, cognition and pects of hearing (discrimination, masking, integration, organi-
action requires a highly-specialized and interdisciplinary ap- zation), the capacity to distinguish competing acoustic signals
proach which combines research and discoveries from various and the capacity to recognize degraded acoustic signals.
branches of science (ranging from neuroscience and artificial The results of the study are relevant for the development
intelligence to philosophy and psychology), from various exper- of effective therapeutic strategies for patients diagnosed with
imental methods (such as behavioural observation, brain activ- APD. In addition to medical intervention (pharmacotherapy,
ity imaging or simulations and numerical methods) and from surgical procedures) these strategies will include auditory
research of various populations (both animal and human). reception training (e.g. computer games which strengthen or
The project description presented in this article pertains modify temporal concentration disorders in children), compen-
to research carried out by Working Group 3 (WG3) within satory techniques (strengthening receptive reactions and im-
the framework of COST Action BM0605  Consciousness: provement of capacities such as auditory discrimination and
A Transdisciplinary, Integrated Approach. The research is cen- analysis, phoneme synthesis, auditory memory, hearing in
tred on neurophysiological experiments to image brain func- noise, temporal processing) and cognitive training (teaching
tion in diseases in which the phenomenon of consciousness how to actively monitor and autoregulate one s ability to under-
plays an important role. The fundamental problem studied in stand the speech, linguistic and metalinguistic training).
this project will be an investigation of the relation between con- The results of the study also contribute to the formulation of
sciousness and speech perception. The study will be conduct- a widely accepted definition of APD, to the creation of a battery
ed using electroencephalographic methods on subjects with of tests for the diagnosis of this disorder and to the develop-
Auditory Processing Disorders (APD). ment of therapy guidelines. A measurable effect of this project
APD is characterised by an inability to learn from auditory which is related directly to COST Action BM0605 is the increase
stimuli and a difficulty in understanding speech in the follow- of knowledge about the relation between speech perception
ing conditions: a) around normal auditory thresholds, b) in poor and consciousness. The application in this research of objective
acoustic conditions, c) distorted or unclear speech. tests to measure specific physiological parameters will allow us
The studies are based upon an analysis of elicited exog- to study processes related to conscious data processing and of
enous and endogenous potentials. Measurements are made their influence on particular cognitive process disorders.
telematics
Speech perception  toward understanding of consciousness
46
Neuropsychological characterization of Cognitive event-related potential
APD patients  audiological tests and (CERP) assessment in APD patients
evoked potentials analysis
The second stage of the study takes advantage of cognitive
During the first stage of the study the characteristics and degree event-related potential (CERP) advanced mathematical meth-
of severity of APD in the studied patients will be determined. ods (see Fig. 1). Relation to APD is analysed and we determine
Research methods employed during this stage are: interview, the roles of cognitive components, such as the P300 wave,
observation of behavioural responses to auditory stimuli, au- which are related to concentration, of components related to
diological tests: audiometry (cortical audiometry, evoked re- semantic analysis such as the N400 wave and of selective at-
sponse audiometry, pure tone liminal audiometry, supraliminal tention indicators such as the late Contingent Negative Varia-
tonal audiometry, speech audiometry, vocal audiometry), tem- tion (CNV) wave. The Mismatch Negativity (MMN) wave is also
poral process assessment tests, localization and lateralization analysed. This expresses automatic brain activity connected to
assessment tests, monaural low-redundancy speech compre- the perception of a difference between a distinguished auditory
hension, comprehension of binaurally separated stimuli, binau- stimulus and a series of preceding identical standard auditory
ral audition interaction, and speech-language pathology tests. stimuli.
The research tools used in these studies will use otoacoustic This part of the project primarily analyses endogenous po-
emission test (OAE): Spontaneous Otoacoustic Emissions tentials, which are an expression of the cognitive or emotional
(SOAE), Transiently Evoked Otoacoustic Emission (TEOAE) reaction to a stimulus, to a change of its parameters or to an
and Distortion-Product Otoacoustic Emission (DPOAE), and unexpected lack of the stimulus. P3b is the name given to the
exogenous and endogenous components of auditory evoked wave which is most clearly registered in the central-parietal
potentials (AEP): Auditory Brainstem Response (ABR) and leads when two stimuli are discriminated though it is more often
Medial Latency Response (MLR). The possibility of peripheral referred to as the P300 potential because when auditory stimuli
auditory system damage, for example conductive or neurosen- are used, this wave occurs at a latency of about 300-350 ms.
sory damage, is eliminated during this stage (using tympanom- The analysis and study of the connection of this potential
etry and tonal audiometry for frequencies in the range of 250 to with APD is important because it arises in a situation when the
8000 Hz measured in octave intervals). stimulus is unexpected or when it carries new and important in-
The ABR measurement is an important element of the formation. Then, the latency is a measure of the time dedicated
study which consists in a series of neurological responses that to the processing of the stimulus (decoding, recognition, classifi-
successively image the activity of the auditory nerve and of cation) and the amplitude reflects the size of engaged cognitive
the neural fibres and nuclei lying on each level of the auditory structures (the wave itself arises at the moment when the cogni-
pathway. Wave peaks labelled with the Roman numerals from tion problem is solved). Factors which impact the amplitude and
I to VII are analyzed. They reflect bridge-interbrain conduction latency of the P300 wave are: the patient s state of conscious-
in the nerve fibres and provide a good measurement of central ness, the type of task presented to the patient during registration
auditory processing on the level of the brain stem. Numerous of the signal, concentration of attention (motivation to complete
studies have confirmed the diagnostic usefulness of the ABR the task) and meaning of the stimuli for the patient.
test in different groups of patients. The correlations between The semantic potential N400 will also be analysed during
results of the Staggered Spondaic Word Test (SSW) test and the study. This potential only arises when sentences are pre-
MLR disorders have also been established. These studies are sented in which the last word does not fit into the preceding con-
carried out using sensitized speech verbal tests in which cer- text. The signal will be registered while words or sentences are
tain verbal stimuli have been deformed in such a way as to presented aloud. Sensitized speech tests will also be applied in
reduce intelligibility. These include tests of filtered, interrupted this case. The main experimental part has been planned assum-
and time-compressed speech perception, a binaural filtered- ing a tonotopic organization of the first segment of the auditory
speech signal composition test using both low and high-pass pathway (precisely determined map of the preferred stimulus
filters turned on alternatingly or increasingly/decreasingly and frequencies).
dichotic CV and spondaic tests. The basic assumption behind The activity of the primary auditor cortex (A1) which is locat-
these tests is the thesis that a person with healthy audition and ed at the centre of the superior temporal gyrus (Brodmann areas
without central auditory pathway disorders will be able to un- 41 and 42) will be mapped. The registration of the EEG signal
derstand distorted speech, but that if there are disorders then and of elicited potentials, especially cognitive potentials, from
the comprehension will be worsened. Because both central specific brain generators (small areas or centres of the cere-
auditory system factors and peripheral auditory system factors bral cortex such as the primary auditory cortex A1) will require
can influence distorted speech comprehension, an assess- very precise placing of the electrodes and an exact determina-
ment of auditory thresholds (sensitivity to different amplitude tion of their location.
and frequency stimuli) is made before interpreting the results A specialized digitizer (Polhemus) has been employed in
of the central auditory system tests. order to overcome the problem of placing the electrodes on the
patient s head as exactly as possible. Thanks to this device, it
is possible to determine points in three-dimensional Cartesian
space with an accuracy of 0.025 angular degrees. The mea-
surements of the coordinates of the electrodes on the patient s
head will be imported into the EGG signal analysis software.
telematics
Speech perception  toward understanding of consciousness 47
A B
C D
Fig. 1. Megis BESA (Brain Electrical Source Analysis). A. Source waveforms separate the activities in auditory, visual and motor cortex
in a reaction time experiment. B. Averaged frontal spike in top view. Peaks can be automatically analyzed. C. Automated artifact scan 
2D artifact scanning tool for fast decision on bad channels and sweeps prior to averaging. D. EEG review  3D whole-head maps and
hemispheric comparison of density spectral arrays (DSA). Source: www.besa.de
Speech perception model gives only a partial understanding and does not permit one to
reconstruct the signal.
assessment based on invariant signal
The application of short-time Fourier transform allows us
characteristics
to observe the changes in the spectrum over time and thus
During the project speech perception models based on invari- to obtain the frequency-time structure of the course, but the
ant signal characteristics will be verified. Initial speech signal resolution of this method is low and limited by the length of the
processing which includes filtration, suppression, adaptation transformation window. Therefore the signal will be analysed
and phase synchronization will be studied as well as an analy- using wavelet transform (the analysis program will be imple-
sis of the functioning detectors of acoustic properties (turning mented in the MATLAB environment). In this way we will obtain
on, spectral changes, formant frequency and periodicity) and a time resolved spectrum of the signal with a resolution higher
of phonetic characteristics (sonority or nasality). than in the case of short-time Fourier transform. DWT also per-
The last stage of this process is segment analysis and lin- mits time-localization of a sought pattern.
gual search. The research methods employed during this stage The underlying assumption behind this analysis is that
are the short-time Fourier transform (STFT) and Daubechies it is possible to find a relatively invariable relation between
discrete wavelet transform (DWT). The FT calculated for the the course of acoustic signals and the perception of speech
time period of the ERP elicited potentials will show us the sounds which in turn relates to the possibility of obtaining rela-
spectral complexity of the signal. An ERP consists of sup- tively stable patterns of neuronal activity corresponding to spe-
pressed oscillations so knowledge of the spectral components cific acoustic signal patterns.
telematics
Speech perception  toward understanding of consciousness
48
Conclusions International Congress of Electroencephalography and
Clinical Neurophysiology, Rome, Italy, 7-13 Sept. 1961,
The presented project is carried out in the Department of Bioin- Exc. Med. Int. Congr. Ser., No. 37, 182.
formatics and Telemedicine of the Jagiellonian University Med- 2. Chermak G. D., Musiek F. E., Managing central auditory
ical College. The project is a continuation and development processing disorders in children and youth, American Jour-
of European programs COST Action B27: Electric Neuronal nal of Audiology, 1, 1992: 61-65.
Oscillations and Cognition (ENOC) and COST Action BM0601: 3. Cole R., Jakimik L., A model of speech perception, in: Cole
Advanced Methods for the Estimate of Human Brain Activity R. (Ed.), Perception and production of fl uent speech, Erl-
and Conectivity (NeuroMath) which were previously carried out baum, Hillsdale, NJ, 1979, pp. 133-160.
by the same team. 4. Colson K., Robin D., Luschei E., Auditory processing and
The results of the study will have a practical significance sequential pitch and timing changes following frontal oper-
(contribution to the development of improved diagnostic and cular damage, Clinical Aphasiology, 20, 1991: 317-325.
therapeutic techniques for auditory processing disorders) and 5. Craig C. H., Kim B. W., Rhyner P. M., Chirillo T. K. B., Ef-
a theoretical significance (increasing our knowledge about fects of word predictability, child development, and aging
the role of consciousness in speech perception). The study of on time-gated speech recognition performance, Journal of
phenomenon related to speech perception contributes to our Speech and Hearing Research, 36, 1993: 832-841.
understanding of the nature of consciousness and its function. 6. Jaśkowski P., Verleger R., Amplitudes and latencies of single-
Both consciousness disorders and auditory processing are re- trial ERP estimated by maximum likelihood method, IEEE
lated to each other although the essence of this relation has not Transactions on Medical Engineering, 46, 1999: 987-993.
been sufficiently understood yet. The studies in the presented 7. Jaśkowski P., Verleger R., An evaluation of methods for sin-
research project based on measurements of neurophysiologi- gle-trial estimation of P3 latency, Psychophysiology, 37, 2000:
cal parameters will serve to verify speech perception models. 153-162.
This is the approach which is suggested by the organizers of 8. Jerger J., Johnson K., Jerger S., Coker N., Pirozzolo R.,
the COST BM0605 project because with the enormous amount Gray L., Central auditory processing disorder: A case
of speculative approaches to consciousness, there are few ob- study, Journal of the American Academy of Audiology, 2,
jective neurophysiological studies at documenting its role. The 1991: 36-54.
process of speech perception is a particularly crucial mecha- 9. Jirsa R. E., Clontz K. B., Long latency auditory event-relat-
nism because it is connected to consciousness, its origin and ed potentials from children with auditory processing disor-
function. ders, Ear and Hearing, 11, 1990: 222-232.
The application of precise methods of neuronal activity 10. Jirsa R. E., The clinical utility of the P3 AERP in children
measurement and advanced mathematical methods of signal with auditory processing disorders, Journal of Speech and
analysis as well as the use of high-power computing devices Hearing Research, 35, 1992: 903-912.
makes it possible to gain new knowledge which can then be 11. Keith R. W. (Ed.), Central auditory and language disorders
used in effective medical intervention. APD s represent a path- in children, San Diego: College-Hill, 1981.
ological sector which is not sufficiently understood nor treated. 12. Sęk A., Auditory filtering at low frequencies, Archives of
Therefore, the precise determination of a widely accepted defi- Acoustics, 25, 2000: 291-316.
nition of APD and the development of effective diagnostic and 13. Sęk A., Moore B. C. J., Detection of quasitrapezoidal fre-
therapeutic methods is so important. The results of the study quency and amplitude modulation, J. Acoust. Soc. Am.,
will contribute to the development of effective therapeutic strat- 107, 2000: 1598-1604.
egies for patients diagnosed with APD. In addition to medical 14. Sęk A., Moore B. C. J., Testing the concept of a modulation
intervention (pharmacotherapy, surgical procedures) these filter bank: The audibility of component modulation and de-
strategies will include auditory reception training (e.g. comput- tection of phase change in three-component modulators, J.
er games which strengthen or modify temporal concentration Acoust. Soc. Am., 113, 2003: 2801-2811.
disorders in children), compensatory techniques (strengthen- 15. Skrodzka E. B., Sęk A. P., Application of BEM to modeling
ing receptive reactions and improvement of capacities such as loudspeaker s directivity patterns based on its dynamic be-
auditory discrimination and analysis, phoneme synthesis, audi- havior, Archives of Acoustics, 26, 2001: 75-91.
tory memory, hearing in noise, temporal processing) and cogni- 16. Szczuka M., Wojdyłło P., Neuro-wavelet classifiersfor EEG
tive training (teaching how to actively monitor and autoregulate signals based on rough set methods, Neurocomputing, 36,
one s ability to understand speech, linguistic and metalinguistic 2001: 103-122.
training). 17. Trąbka J., et al., EEG Signals Described by the Automatic
This area of research also has particular significance in the Linguistic Analysis, w: Rother M., Zwiener U., Quantitative
context of Poland. Because there so few centres specializing EEG Analysis, Univ. Jena, 1993, 114-117.
in speech perception disorders, this project can contribute to 18. Trąbka J., Przewłocki R., Siuta J., The infl uence of topical
increasing general awareness of this problem and to activate administration of the carboline derivatives on direct cortical
environments dedicated to helping people suffering with APD. response (DCR), Diss. Pharm. Pharmacol., 1969, 6, 515-
522.
19. Trąbka J., Sekuła J., Fenczyn J., Warchołek J., Efekt
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20. Trąbka J., Badania EEG u dzieci z zaburzeniami ortostaty- 28. Trąbka W., Stanuch H., Trąbka J., Automatic analysis of
cznymi, EEG examination in the children with orthostatic the evoked potentials using harmonical functions, XIIIth
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21. Trąbka J., Behavioral and EEG changes caused by the roph., Prague, Czechoslovakia, 1990.
substituted derivatives of the gamma-butyrolacton, Ab- 29. Trąbka W., Trąbka J., Fractal Consciousness, Third IBRO
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of brain hemisphere asymetry, EEG Abstracts 6th Interna- the rat s barrel cortex induced by conditioning stimuli, in:
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BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 51 58
NEUROINFORMATIC MODELLING OF OCULOMOTOR SYSTEM
PIOTR WALECKI
Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kopernika 7,
31-034 Krakow, e-mail: pwalecki@cm-uj.krakow.pl
Abstract. Neuroinformatics is a new branch of science that uses informatics tools to modelling some parts of neural system.
This paper presents several models related to oculomotor system, both educational and research models. Most of the models
presented in this paper are our own work. The educational models created for medical purposes demonstrate interactively the
effects of damage to different neuronal structures and also simulate disorders of eyeball movement dynamics and synchronization
in various diseases. The research models may find application both in clinical tests and in experimental study.
Keywords: oculomotor system, modelling, neuroinformatics
Introduction
a fragment of the nervous system, like the oculomotor system,
Using measurements and modelling of eyeball movement we is so complex, that it would be difficult to model it in its entirety
can very precisely analyse one of the most important neurobio- [18]. Thus, it is usually more advantageous to pick for mod-
logical mechanisms of living beings: sensory-motor integration elling only certain subsystems or neuroanatomic structures
[16]. The oculomotor system possesses a small and well de- which are related to a specific function. In this way, based on
fined set of degrees of freedom in comparison to other motor state-of-art advances in neurophysiology, we aim to model the
systems [1], [2]. Thus it seems to be particularly well suited for functioning of the oculomotor system on the level of cellular
modelling neuronal function. structure [14], [15]. We also have the possibility of modelling
Although human behaviour is characterized by an im- only those characteristics which pertain to a specific function.
mense complexity far beyond that found in other organisms, In choosing the right model, it is important determine for
this behaviour is nevertheless often realized through simple whom and based upon which branch of science the given
sensory-motor systems which have a relatively simple con- model is created. This is due to the fact that, for example,
struction [17]. An analysis of the construction of sensory and a physician requires different information from the model than
motor systems thus contributes to a better understanding of a neurobiologist. A separate group are educational models
the function of more complex structures of the central nervous which place less emphasis on numerical calculations and are
system [15], [18]. more focused on illustratively transmitting specific content.
The knowledge provided to us by an understanding of the Most of the models presented in this work are our own
cooperation of sensory-motor systems in processing sensory models which reflect specific neurophysiological functions
stimuli and behavioural expression finds an application in neu- or neuroanatomic structures under various aspects and with
ropsychology and medical diagnostics [1]. Eyeball movement varying amount of detail. A specific type of model are the edu-
irregularities have been observed in neurological disorders cational models created for medical purposes (see Fig. 1-3).
connected to central nervous system or cranial nerve damage These models interactively and dynamically demonstrate the
[2] as well as in the case of patients suffering from schizo- effects of damage to different neuronal structures and also
phrenia [3], autism [4], Parkinson s disease [5], dyslexia [6] or simulate disorders of eyeball movement dynamics and syn-
ADHD [7]. chronization in various diseases.
Fig. 1 shows a model which simulates palsy of different ex-
traocular muscles and cranial nerves. The adaptation of neuro-
Material and methods logical data [8] from this programme contributed to the creation
of two versions of an eyeball movement disorder simulator.
We presently possess a large set of neurobiological data from Both versions use a widely available open-source program-
experimental studies. Thanks to this we can model the oculo- ming environment (JavaScript, HTML, PHP), thanks to which
motor system with varying degrees of accuracy, distinguishing they are suitable for further development and for running on
a certain function depending on the goal of the study. Even different operating systems.
telematics
Neuroinformatic modelling of oculomotor system
52
Fig. 1. The model used in simulation of palsy of different extraocular muscles and cranial nerves.
Executors of the project: Jakub Baka, Piotr Olchawski. Source: www.neurobiologia.pl.
The model is meant for doctors who, while conducting Modelling of eye movement
medical examinations, encounter oculomotor disorders and
abnormal functioning of the mechanisms responsible for motor Modelling eye movement entails making an analysis of eyeball
control of the eyelid and pupil. The computer system simulates position and of changes in movement velocity in response to
natural eyeball movement (movement is triggered by fixing exterior stimuli or to an interior state. The precision of a model
eyesight on the mouse cursor) by means of an interactive ani- which reflects the real functioning of the oculomotor system has
mated patient. The patient s behaviour has been imaged using particular significance because changes in the values of eye
dynamically changing and interactive models of the face based location parameters occur on a millisecond timescale [2], [14].
on series of photographs which can be freely changed and new Nevertheless, the processing of visual information in the
versions of which can be added. Below the photograph of the cerebral cortex is a very complicated process. Moreover, eye-
face is a panel in which one can choose (separately for each ball movement, especially saccades, are elicited as a result of
eye) from among various types of oculomotor damage. the engagement of many neuronal centres which are tied to
The initial version of the model simulated movement dis- cognitive, motivational and emotional processes and to atten-
orders of the eyes, eyelids and pupils which occur in the case tion and memory mechanisms [15], [16]. Therefore, despite the
of palsy of the following oculomotor muscles. Later, the model large amount of collected neuroanatomical and neurophysi-
was enriched with other types of eyeball movement disorders ological knowledge about the oculomotor system and despite
such as pathologic nystagmus, oscillations (see Fig. 2) and the gigantic calculation capacities of computer systems, no at-
strabismus (see Fig. 3). tempt is made at the moment to create a holistic model of the
telematics
Neuroinformatic modelling of oculomotor system 53
Fig. 2. The model used in simulation of pathologic nystagmus and oscillations.
Executors of the project: Jakub Baka, Piotr Olchawski. Source: www.neurobiologia.pl.
Fig. 3. The model used in simulation of strabismus.
Executors of the project: Jakub Baka, Piotr Olchawski. Source: www.neurobiologia.pl.
telematics
Neuroinformatic modelling of oculomotor system
54
Fig. 4. The model used in processing of the virtual movement of eyes following the mouse cursor into data
about their position on the x- and y-axis and which also calculates their angular velocity at a given moment.
Executor of the project: Jan Paluch. Source: www.informatyka.cm-uj.krakow.pl.
oculomotor system which would faithfully represent the course and y-axis position calculations. The data was collected with
of biological processes [17], [18]. It seems, however, that such the Jazz eye tracker (Ober Consulting LTD.).
an undertaking is to a large extent unnecessary, because Fig. 6 presents a model of saccade generator created in
every model is used only in order to explain certain aspects of Simulink MATLAB that was implemented by Ansgar Koene
a given system in accordance with accepted assumptions and [10]. The model was based on the Model With Distributed Vec-
applied methodology. torial Premotor Bursters Accounts for the Component Stretch-
Fig. 4 shows a model which processes the virtual move- ing of Oblique Saccades [9]. This model uses information form
ment of eyes following the mouse cursor into data about their the most recent discoveries in neurobiology regarding how
position on the x- and y-axis and which also calculates their the saccade generator functions [19]. The initial stage of the
angular velocity at a given moment. In the model, the calcula- model s construction was the creation of a block scheme to de-
tion of the movement dynamics values is explicitly shown. The scribe the dynamics of eyeball movement based on selected
model was programmed in Java language. parameters (change in position and time). Using mathematical
Fig. 5 shows an actual recording of free eyeball move- equations, this model simulates eye movement along a cho-
ments in a studied person along with the eye velocity and x- sen trajectory and precisely describes changes in movement
telematics
Neuroinformatic modelling of oculomotor system 55
Fig. 5. The window of JazzManager program shows an actual recording of free eyeball movements in an examined person along with
the eye velocity and x- and y-axis position calculations. The data was collected with the Jazz eye tracker (Ober Consulting LTD.).
Fig. 6. The model of saccade generator created in Simulink MATLAB that was implemented by Ansgar Koene. Source: [10].
telematics
Neuroinformatic modelling of oculomotor system
56
AB C
Fig. 7. The graphs present results of simulation. The model simulated an eye movement along a chosen trajectory (A) and precisely
described changes in movement velocity (B) and position (C). Source: own research.
Fig. 8. The graphs present an actual recording of saccadic movement. The data was collected with the Jazz eye tracker
(Ober Consulting LTD.). Source: own research.
velocity (see Fig. 7). The model was then tested by comparing the choice of a given modelling method and of how detailed
it to actual measurements of saccade dynamics. The meas- it will be is based on the amount of available neurobiological
urements were made using an eye tracker (see Fig. 8). After data. The less we know about a certain neuronal system, the
calibration it was confirmed that the values calculated in the more we will focus on its function. Sometimes we will com-
simulation correlate to the experimental values. This model will pletely abstract from the real biological construction and treat it
find use both in clinical tests and in experimental research. as a so-called  black box [17]. Such an approach is often used
when modelling psyche or consciousness function [18].
A holistic diagram of neuronal connections has been cre-
Modelling of oculomotor neuronal ated as part of the effort to model the oculomotor system (see
Fig. 9) [2], [20]. The next step will be the construction of an
connections
interactive version of this diagram which will be used for edu-
cational purposes and also in the creation of functional models
By modelling neuronal connections we can display actual bio- of selected neuronal functions and in the simulation of certain
logical structure of the connections, or we can focus only on subsystems which participate in eyeball movement.
the function of a chosen system. However, regardless of which Knowledge about the neurophysiological basis of eyeball
approach we choose, knowledge about the construction and movement is indispensable for a doctor. It also provides impor-
function of the nervous system will be indispensable. Usually tant information for a neuropsychologist by demonstrating the
telematics
Neuroinformatic modelling of oculomotor system 57
Fig. 9. The diagram of oculomotor neuronal pathways. Author: Piotr Walecki. Source of neurobiological data: [20].
telematics
Neuroinformatic modelling of oculomotor system
58
basis of the eye attention mechanism and also for a neurobiol- 8. Hodgson T. L., Tiesman B., Owen A. M., Kennard C., 2002,
ogist by showing the evolutionary organizational structure of Abnormal gaze strategies during problem solving in Parkin-
the various sensory-motor systems [11]. The visual and ocu- son s disease, Neuropsychologia, 40, 411-422.
lomotor systems are an excellent example of sensory-motor 9. Fischer B., Hartnegg K., 2000, Effects of visual training on
integration by means of which sensory signals are transformed saccade control in dyslexia, Perception, 29, 531-542.
into motor output [12]. The difficulty in studying eyeball move- 10. Karatekin C., 2006, Improving antisaccade performance in
ment lies in the dynamics of these movements because these adolescents with Attention-Deficit/Hyperactivity Disorder
events occur on a very short, millisecond timescale [2]. Nev- (ADHD), Experimental Brain Research, 174, 324-341.
ertheless, the use of modern diagnostic equipment such as 11. Lasslo R., Henderson G., and Keltner J., Eye Simula-
devices for measuring eyeball movement and of computers tor version 2.0, UC Davis School of Medicine, http://cim.
for data processing and analysis is contributing an increased ucdavis.edu/EyeRelease/
dedication in this field of research [13]. Eyeball movement di- 12. Quaia C., Optican L. M., 1997, Model With Distributed Vecto-
agnostics are applied not only in medicine but also ever more rial Premotor Bursters Accounts for the Component Stretch-
frequently in industry and in the military where some move- ing of Oblique Saccades, J. Neurophysiol., 78: 1120-1134.
ment characteristics contain key information for the success 13. Ansgar Koene, http://arkoene.googlepages.com/matlab-
and effectiveness of certain actions [14]. scripts
14. Krauzlis R. J., 2005, The Control of Voluntary Eye Move-
ments: New Perspectives, Neuroscientist, 11(2): 124-137.
Conclusion 15. Becker W., 1989, The neurobiology of saccadic eye move-
ments (eds Wurtz and Goldberg), Elsevier, Amsterdam.
The modelling of the oculomotor system is significantly con- 16. Hoffman J. E. & Subramaniam B., 1995, The role of visual
tributing to a better understanding of the processes which take attention in saccadic eye movements, Perception and Psy-
place in the nervous system. The oculomotor system models chophysics, 57, 787-795.
presented here develop these ideas on different planes. The 17. Walecki P., 2007, Neurofi zjologia ruchu gałek ocznych
utility of all of the mentioned models are currently being devel- (Neurophysiology of eye movement), Episteme, 4/2007,
oped further and improved. The implementation of the model 159-176.
which simulates eye movement disorders is being applied for 18. Kien J., McCrohan C. R., Winlow W., 1992, Neurobiology
educational purposes in the formation of medical professionals. of Motor Programme Selection, Elsevier Science Pub Co.
Further development of the model with the addition of eyeball 19. Shadmehr R., Wise S. P., 2005, The Computational Neuro-
movement disorders which occur in the case of patients suffer- biology of Reaching and Pointing: A Foundation for Motor
ing, for example, from schizophrenia or Parkinson s disease, Learning, The MIT Press.
is planned. 20. Arbib M. A. (Ed.), Grethe J. S. (Ed.), 2001, Computing the
Brain: A Guide to Neuroinformatics, Academic Press.
21. Moss F. (Ed.), Gielen S. (Ed.), 2001, Neuro-informatics and
References Neural Modelling, North Holland.
22. Scudder C. A., Kaneko C. S., Fuchs A. F., 2002, The brain-
1. Karatekin C., 2007, Eye tracking studies of normative and stem burst generator a modern synthesis, Exp. Brain Res.,
atypical development, Developmental Review 27, 283-348. 142, 439-62.
2. Leigh J., Zee D., 2006, The neurology of eye movements, 23. Becker W., 1989, The neurobiology of saccadic eye move-
Oxford University Press. ments (eds Wurtz and Goldberg), Elsevier, Amsterdam.
3. Jacobsen L. K., Hong W. L., Hommer D. W., Hamburger 24. Karatekin C., 2007, Eye tracking studies of normative and
S. D., Castellanos F. X., Frazier J. A., et al., 1996, Smooth atypical development, Developmental Review 27, 283-
pursuit eye movements in childhood-onset schizophrenia: 348.
Comparison with attention-defi cit hyperactivity disorder and 25. Krauzlis R. J., 2005, The Control of Voluntary Eye Move-
normal controls, Biological Psychiatry, 40, 1144-1154. ments: New Pers 38. pectives, Neuroscientists, 11(2): 124-
4. Holzman P. S., 2000, Eye movements and the search for 137.
the essence of schizophrenia, Brain Research Reviews, 26. Missal M., Heinen S. J., 2004, Supplementary eye fields
31, 350-356. stimulation facilitates anticipatory pursuit, J. Neurophysiol,
5. Broerse A., Crawford T. J., den Boer J. A., 2001, Parsing 92: 1257-62.
cognition in schizophrenia using saccadic eye movements: 27. Schiller P. H., Chou I. H., 1998, The effects of frontal eye
A selective overview, Neuropsychologia, 39, 742-756. fi eld and dorsomedial frontal cortex lesions on visually
6. Avila M. T., Hong E., Moates A., Turano K. A., Thaker G. K., guided eye movements, Nat. Neurosci., 1: 248-53.
2006, Role of anticipation in schizophrenia-related pursuit 28. McPeek R. M., Keller E. L., 2004, Defi cits in saccade tar-
initiation defi cits, Journal of Neurophysiology, 95, 593-601. get selection after inactivation of superior colliculus, Nat.
Levy D., Holzman R., Matthyse S., Mendeil N., 1993, Eye Neurosci. 7: 757-63.
tracking dysfunction and schizophrenia: a critical perspec- 29. Sommer M. A., Tehovnik E.J., 1997, Reversible inactivation
tive, Schizophr. Buli., 19, 3, 461- 536. of macaque frontal eye fi eld, Exp. Brain Res., 116: 229-49.
7. Dalton K. M., Nacewicz B. M., Johnstone T., Schaefer H. 30. Sparks D., Rohrer W. H., Zhang Y., 2000, The role of the
S., Gernsbacher M. A., Goldsmith H. H., et al., 2005, Gaze superior colliculus in saccade initiation: a study of express
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telematics
BIO-ALGORITHMS AND MED-SYSTEMS
JOURNAL EDITED BY MEDICAL COLLEGE  JAGIELLONIAN UNIVERSITY
Vol. 5, No. 10, 2009, pp. 59 69
HEARTFAID S ECRF: LESSONS LEARNT FROM USING A TWO-LEVEL
DATA ACQUISITION AND STORAGE SYSTEM FOR KNOWLEDGE
DISCOVERY TASKS WITHIN AN ELECTRONIC PLATFORM FOR
MANAGING HEART FAILURE PATIENTS
1
ANDRZEJ A. KONONOWICZ, 1 KATARZYNA STYCZKIEWICZ, 1 BOGUMIA
A BACIOR,
2
MATKO BO`
NJAK, 2 RAJKO HORVAT, 2 MARIN PRCELA, 2 DRAGAN GAMBERGER,
3
ANGELA SCIACQUA, 5 MARIA CONSUELO VALENTINI, 1 KALINA KAWECKA-JASZCZ,
4,5
GIANFRANCO PARATI, 6 DOMENICO CONFORTI
1
Jagiellonian University Medical College, Kraków, Poland
2
Rudjer Boskovic Institute, Zagreb, Croatia
3
University  Magna Graecia of Catanzaro, Department of Experimental and Clinical Medicine, Italy
4
University of Milan  Bicocca, Department of Clinical Medicine and Prevention, Milan, Italy
5
Department of Cardiology, S.Luca Hospital, Istituto Auxologico Italiano, Milano, Italy
6
University of Calabria, Department of Electronics, Informatics, Systems (DEIS), Italy
Abstract: Case report forms are important sources of medical knowledge in all clinical studies. Electronic versions of these
forms have several advantages compared to traditional paper-based questionnaires, and they have been adopted in many
contemporary research projects in medicine. This paper presents a framework for creating case report forms designed with
a two-level approach. Data at the generic information model level is stored in EAV (entity-attribute-value) tables and extended
by tables facilitating specification of the questionnaire layout. The second layer (knowledge model) specifies the domain specific
concepts describing the fi eld of application of the questionnaire. This framework has been applied and tested in the frame of
an EU FP6 research project  HEARTFAID  the objective of which was to build a knowledge-based platform supporting the
management of elderly patients suffering from heart failure. Data collected by the electronic case report form (eCRF) was used
in the project s knowledge discovery and decision support tasks. The work presents a new way for effective extraction of the
data necessary for the integration with the knowledge discovery process in a distributed, service oriented framework of the
HEARTFAID platform. It is demonstrated that it is feasible to implement these tasks using the two-level EAV table design.
Keywords: Electronic Data Capture, Remote Data Entry, EAV, Two Layers Modelling, eCRF, Spring Framework
1. Introduction The conventional method of designing database schemes
for questionnaires is to map a form to a single table or a set of
Electronic Data Capture (EDC) techniques have been used in tables in a relational database in which each attribute (ques-
clinical trials for a long time [8]. The first EDC systems (also tion from the form) is stored into an individual column [10, 14].
known under other names e.g. Remote Data Entry (RDE) Sys- Even though this technique works fine for many applications, it
tems) date back to the early 1970s [7]. Since that time a huge has become apparent that this method is not always effective
amount of applications (either academic or commercial) for [14], especially in bio-medical research or electronic health re-
creating, managing and publishing medical on-line forms has cords. This problem pertains to databases with a large, hetero-
been developed. The electronic versions of questionnaires geneous list of fields from which many are optional and can be
seem to have lot of advantages in comparison to their paper- omitted. In such databases new fields are often added, altered
based counterparts [18]. Among the assets of EDC are cost or removed after the database has been deployed, and this
savings, faster dissemination of forms and collection of data, introduces additional complication in its structure. Designing
built-in validation mechanisms, easy maintenance and export such databases with the conventional approach is possible but
to statistical packages. often troublesome and ineffective due to the limitations of tra-
telemedicine
HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition&
60
ditional RDBM systems (e.g. a maximum limit of 255 columns that the eCRF system implements insertion, modification and
in a single database table in some RDBM systems) or to the querying of large forms (containing over 700 attribute values
need to frequently update the database structure. for each patient). The system needed to be well integrated with
An alternative approach is to store records as association the remaining services of the platform.
lists containing (attribute name, attribute value) pairs of vari-
ables [13]. A database that stores information in that form is
called an entity-attribute-value (EAV) database. This storage 2. The HEARTFAID Platform
method by itself is not new since it dates back to at least the
time when the LISP programming language was created. How- Heart failure (HF) occurs when the heart fails to pump enough
ever, its application in relational databases has not yet been blood to meet the metabolic needs of the body s tissues and/
very widespread. Classical EAV-databases contain one large or organs. The prevalence of this pathological condition is
table with just three columns: identifier of the described object, very high  approximately 10 million patients suffering from
identifier of the attribute, value of the attribute. Additionally, dic- HF in Europe. Chronic (C)HF is a disease of older people; the
tionaries are required which contain metadata describing the Framingham study noted a doubling of prevalence with each
attributes applied. advancing decade, reaching a rate ranging from 7% to 10% in
This simple design technique enables a very flexible meth- those aged 80 and older. The mortality of patients with severe
od of space-efficient storage of heterogeneous data. However, HF is also high, approaching 50% in the course of one year in
it should be acknowledged that also this approach is not free NYHA IV1 class patients. However, it is believed that through
from flaws. It is well suited for one object-at-a-time queries in regular monitoring and personalised management of patients
which all information about a single object (e.g. patient) is re- affected by this condition, their survival rate and quality of life
turned, but it is less efficient in complex attribute-centric que- can be significantly improved.
ries [14]. For such situations special frameworks facilitating The role of the HEARTFAID platform is to support physi-
more advanced searches in this model are implemented (as cians and healthcare personnel (e.g. nurses) in managing
e.g. QAV: querying entity-attribute framework [13]), thus em- heart failure patients, while at the same time empowering
powering the user to browse the data more easily. The over- patients to self-monitor their health condition [3, 4]. HEART-
head that is needed to organise the data in an EAV manner is FAID is a web-based platform of services integrating several
often not worth the effort for the simple and static databases diverse modules (Fig. 1). Its basic function is to collect patient-
used in many business applications. The queries are also not related biomedical data from different sources (e.g. mobile and
time-effective, rendering them less suitable for commercial wearable measurement devices or medical imaging systems)
usage. These drawbacks are, however, not as obvious in re- and enable access to previously collated data from electronic
search projects and clinical trials where more emphasis is put health records. Part of the system includes declarative and
on the flexibility of the tool than its efficiency. procedural knowledge taken from evidence-based sources
The EAV model can be considered the first generic layer of such as medical guidelines and carefully selected research pa-
a database. This tier may be used in virtually any field of ap- pers [6, 16]. The users of the platform may securely access the
plication, and can be extended by additional tables supporting data it contains in a standardised manner. The platform gives
more complex data design. An example of a model with such access to data taking into account the different roles and rights
additions is represented by the EAV/CR by Nadkarni et al. [14], of the users. New knowledge can be discovered based on the
which enhances the EAV by structures for the representation data collected on the platform by employing newly developed
of classes and relationships. Other approaches customize the artificial intelligence tools. The system has the potential to sup-
EAV to store clinical forms [5]. The EAV model with its exten- port physicians in making clinical decisions in the workplace
sions represents an information model of the database which also by alerting them if a dangerous situation is detected. All
is domain independent. In a two-level approach to database HEARTFAID services are integrated by an enterprise service
design, a second layer (i.e. the knowledge model), is added bus (ESB). The system utilises a single sign-on mechanism.
on top of the first [11]. This model specifies the domain specific Users interact with the system through a customisable web
concepts describing the field of application of the question- portal. The anticipated results of integrating the platform into
naire. It may consist of terminologies and ontologies related to clinical practice include a reduction in the re-admission of HF
a given specialization field. The values that can be entered into patients to hospital, improvement in the quality of treatment
the information model can be constrained by knowledge model and a decrease in management costs [3, 4].
archetypes [2]  i.e. special templates that specify at runtime A knowledge-based platform like HEARTFAID requires
the way data can be entered. Archetypes may be specified au- various forms of medical data acquired from different sources.
tonomously by subject matter experts (e.g. clinicians) without Data collected from mobile and wearable devices are covered
the need to consult database specialists. A clear separation by the AmI service. The role of the HEARTFAID s electronic
between the first and second level of the database makes the case report form (eCRF) is to handle all data required by clini-
architecture flexible and reusable. cians that need to be inserted manually by the medical person-
The aim of this paper is to report on the information ob- nel. Beyond the scope of the eCRF is the storage of medical
tained while implementing a vast two-level electronic case knowledge in the form of rules or ontologies which are used
report form (eCRF) which was designed for the cardiology for inference in knowledge discovery and decision support sys-
domain. The eCRF is part of a large knowledge-based plat- tems. However, these modules exploit the data collected by the
form called HEARTFAID supporting the management of elderly
heart failure patients, developed in the frame of the EU FP6
1 NYHA  New York Heart Association Functional Classification
research program. It was required by the HEARTFAID project
 A four scale classification of heart failure extent
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition& 61
Fig. 1. General overview of the HEARTFAID services
eCRF. The eCRF is intended to be used by medical personnel support large questionnaires with nested groups of questions,
in the hospital and is not accessible by patients. It plays the based on XML and J2EE technologies, and easy to integrate
role of a specialised electronic health record, collecting heart into the HEARTFAID platform. None of the existing tools we
failure data from a multitude of sources. From a medical (i.e. found for designing web-based questionnaires (e.g. ArchiMed
cardiographic) perspective the eCRF is useful because it gives [5], Form Handler [21], Instant Survey [24], Survey Monkey
easy access to the results of lab tests, to treatment schedules [26], WebEAV [15], Zoomerang [27]), fully met our demands.
and to the prognostic assessment of HF patients. For that reason it was decided to implement the eCRF from
The HEARTFAID eCRF comprises three parts: the base- scratch. Since the number of questions was large (more then
line, additional visits and final evaluation forms. Each of these 700), quite diverse, potentially changeable and the efficiency of
forms is uniquely assigned to a patient and can be filled out the tool was not a critical factor, it was decided to employ a two
only once, with the exception of the additional visit form which level architecture. The idea of a two-level approach emerged
may be repeatedly compiled without limitations. Questions in in electronic health records development [11]. Following this
the eCRF questionnaire may be combined into groups. The ac- approach database structures are divided into two separated
tivation of a group may be triggered in real-time by the input of models: information model and knowledge model. The infor-
a specific value by the user. Question groups may be nested to mation model represents stabile and generic concepts, where-
an unlimited depth. Most of the questions are of simple types: as the knowledge model depicts the dynamics of the problem
Boolean values, text strings, numerical values (integer, real field [11]. In the HEARTFAID s eCRF the information model
numbers) and dates. However, there are also more complex expresses a generic database for storing clinical forms follow-
types of questions which involve, for instance, the selection of ing the EAV paradigm. The classical EAV data model has been
a value from a controlled vocabulary, or the use of a special tool extended to facilitate the usage of complex web-based forms.
to specify a medication and its dosage from a hierarchical list In Fig. 2 the ERD (entity-relationship-diagram) of the informa-
of products (drug class, international name and generic name). tion model underlying the HEARTFAID eCRF is presented.
It is also possible to add new drugs to the list. Some questions The model is generic  i.e. it does not contain any information
are grouped into matrices (tables) of values of simple types. specific to the heart failure domain and can be used in diverse
The forms also contain rules for validating inserted values. multi-centred clinical trials. The EAV model was implemented
in a RDBM system. Basic EAV tables were extended by ad-
ditional tables for storing hierarchical question groups and for
3. Method user management. Similar approach was taken in other EAV
projects (as e.g. in EAV/CR representation by Nadkarni at al
While planning the implementation of the eCRF we looked [14]). The User Center and User tables enable the separa-
for off-the-shelf products that were web-based, available free, tion of patients coming from different research institutions and
open source, flexible enough to add new question types, able to enable access to the data only by entitled users. The Patient
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UserCenter Patient
UserSession User Form
Page
Table Group Question Description
ColumnType Row Type DrugRepository Dict
Cell DrugClass Entry
DrugInt
DrugBrand
Fig. 2. ERD of the information model under laying the HEARTFAID eCRF












Fig. 3. XML archetypes specifying the values that can be inserted into the form
table contains basic patient data. Since the questions are as- the forms. The Drug[X] (X"{Repository,Class,Int,Brand}) and
signed to pages and these pages may contain many levels of Dict tables represent respectively the pharmacological treat-
nested question groups or tables this structure is reflected by ment and values from controlled vocabularies.
the Page, Table and Group entities. The grey-shaded Question The archetypes (second layer of the model) constraining
and Cell tables are classic EAV tables containing a reference the values that can be inserted into the database are specified
to the type of the question, the owning entity (i.e. Page, Group, in XML syntax, compatible with the bean definition syntax of
or Row) and the value. Additionally, these tables contain in- the Spring Application Framework [9]. An example of the speci-
formation about the time of creation and last modification of fication of a question type and its instance is presented in Fig.
the values, version number, as well as the identity of the user 3. The first archetype bean example defines a type represent-
that modified the value. The dashed line between the Question ing a patient s systolic blood pressure taken during a physical
or Cell tables and the Form table is a redundant connection examination. This question has its description in HTML format
added for efficiency reasons to accelerate queries with fields (attribute html), stating that it accepts only integer values (at-
nested deep in many subgroups. The Description table con- tribute type) and a mapping to a concept in the UMLS ontol-
tains textual information needed as additional description in ogy explaining its semantics (attribute cui). The second bean
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition& 63
is an instantiation of the previously mentioned question type XSLT transformation of XML archetypes and data retrieved
(attribute type). The position at which the question is displayed from the database (Fig. 4). The top bar contains the question-
in the question group is specified by the attribute order, and its naire s name, patient id and page number. The pages can be
default value may be specified by the attribute value. The ar- changed either through the list of pages in the table of content
chetypes often also contain lists of questions or subgroups ag- panel in the right part of the form or through the backward and
gregated by group type, or information about question groups forward buttons in the navigation bar. The form is automatically
being activated or deactivated based on specific values of the saved after changing a page or after clicking on the submit but-
questionnaire fields inserted by the user. ton. Activation of the cancel button rejects the last changes and
Both archetype beans (i.e. type declaration bean and exits the form. Question groups are marked by red boxes and
question instantiation bean) are mapped to POJO (plain old activated by trigger questions (e.g. in Fig. 4 the group contain-
java objects) elements and are stored on demand in the eCRF ing the max. ST depression question is activated by setting the
database using the Hibernate Framework [12]. The way the value  yes in the ST depression field). In Fig. 5 a 3x3 question
archetypes are specified enables easy extension of the list of table (matrix) of integers is presented. In addition, above the
constraining rules (e.g. by information about the soft or hard main form a list of detected validation errors is presented.
limits for ranges of accepted values). Communication with the eCRF with the HEARTFAID plat-
form is established through an XML protocol implemented by
one of the partners in the project (SYNAPSIS) including all
4. Results the necessary information of an HL7 message [22] and follow-
ing the transactions suggested by IHE [23]. The HEARTFAID
The eCRF has been implemented in the course of the second middleware implements Patient Demographic Query HL7 V3
year of the HEARTFAID project in the Java 5 programming lan- (PDQ) and Patient Identifier Cross-Reference HL7 V3 (PIX)
guage. The development has been accelerated by the usage profiles. In order to integrate the patient-related data into the
of the Spring Application Framework [9] version 1.2 and Hiber- platform a MPI (Master Patient Index) service is used which
nate 3 [12]. The final knowledge model of the eCRF specified manages patient s demographic information and guarantees
by XML archetypes included 735 question instances of 364 their unique identification in the environment. For instance,
semantic types. Archetypes were created using a general pur- while registering a new patient on the platform, a message
pose XML editor (Altova XMLSpy 2008 [20]). Data were stored is sent from the HEARTFAID portal to the ESB which was
in a MySQL 5.1 RDBM system. A simplified structure of the implemented using the Mule open-source framework [25].
eCRF is presented in the figures included in the Appendices Mule descriptors for routing the information to a MIDA Graph
1 and 2. In order to make the schemes legible, the number of (a workflow engine implemented by SYNAPSIS [19]) are read
fields for each object was limited to a maximum of 10 fields. and transformed into information that is stored in the MPI and
The letters b,a and/or f denote in which eCRF type of form this transmitted as HTTP XML messages to the eCRF service. The
question is located (i.e. baseline, additional form or final visit). eCRF receives the messages, enrols the patient and sends
The forms are presented online as HTML views created with back a confirmation message [19].
Fig. 4. User interface of the HEARTFAID eCRF
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition&
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Fig. 5. Question tables and form validation in eCRF HEARTFAID
Fig. 6. The result of reasoning based on the data collected by the eCRF
The eCRF was deployed on the HEARTFAID platform in System (DSS) developed by Rudjer Boskovic Institute in Za-
2007 and since then it has been in constant use. Data from ap- greb (Croatia). Both services require tight integration with the
proximately 100 patients from four clinical centres [Universitą large amount of patient data collected by eCRF, however these
degli studi Magna Graecia, Catanzaro (Italy), Universitą degli services require substantially different data access types. DSS
studi di Milano Bicocca, Milan (Italy), Jagiellonian University is always focussed on one patient while KDS requires informa-
Medical College, Kraków (Poland) and S. Luca Hospital, Isti- tion about all or most of available patient data that has been
tuto Auxologico Italiano, Milan (Italy)] have been collected. collected by the eCRF. Additionally, it must be noted that DSS
The eCRF has been integrated with the HEARTFAID s requires effective access to the most recent information for all
Knowledge Discovery Service (KDS) and Decision Support potentially relevant measurements regardless of when they
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition& 65
were collected and with a clear indication about when the data These functions are available through a HTTP GET in-
was acquired. In contrast to this, actual data collection time is terface. In the following line a command is shown that starts
not relevant for KDS, but it requires access to the data grouped a query involving the getLastValue function http://local-
according to the time of its collection, that data should be or- host:8080/heartfaid/query.html?function=getLastValue&uuid=3
dered by its historical order, and that it is identified by the time 12&sid=physical_exam.weight
interval from previous measurements. Fig. 6 demonstrates After execution the interface searches in the eCRF data-
a typical result from the decision support service while Fig. 7 base for all values of the physical_exam.weight attribute re-
and 8 illustrate the knowledge discovery service. garding the patient with the id 312. The result of the function
A unique property of the currently implemented KDS is that is returned in simple XML syntax. This allows a clear separa-
it integrates knowledge discovery algorithms with direct data- tion of the data collection and query tool located at one centre
base access into one web-based service. This is not a sim- (currently at Jagiellonian University Medical College, Kraków,
ple task due to the complexity of the KD process [16]. The Poland), from the knowledge discovery system located at a re-
HEARTFAID service implements the modern random forest mote centre (currently located at Rudjer Boskovic Institute, Za-
based machine learning algorithm [1] that has been reimple- greb, Croatia).
mented by Rudjer Boskovic Institute. The service has been
built as a series of projects so that every project consists of
different datasets with many tasks that can be performed for Discussion
every dataset. Access to projects, datasets, and tasks is en-
abled though a web interface (Fig. 7). After the generic framework for designing questionnaires
Computationally, the most complex part of the service is had been developed, the process of implementation of the
the construction of the classifier and the preparation of a re- HEARTFAID s eCRF knowledge model by specifying the XML
port (Fig. 8) based on the results of this process. The value archetypes took little time and did not cause any difficulties.
of this newly implemented service is the realisation of direct The structure of the eCRF turned out to be more stable than
access to the data in the eCRF and its automatic transforma- initially anticipated, so the benefit of the flexibility of the archi-
tion into a form that can enter the KD process. Direct access to tecture has not been fully used (with the exception of a few mi-
the relational database containing EAV tables by a traditional nor changes). On the other hand, the drawbacks of decreased
SQL interface is very laborious. This problem can be solved database efficiency in this type of application are hardly notice-
by implementing a special query module for external analytical able. In the production database containing just a few users
services. An interface consisting of four generic functions has and approximately 100 forms installed on a Intel Core 2 Duo
been implemented for the purpose of the knowledge discovery T5450 1,66Ghz,1GB RAM computer, loading a whole form
task. Table 1 contains a description of these functions: from a database took in average 1360 ms, saving a modified
Fig. 7. The main page of the HEARTFAID knowledge discovery service with three current projects:
 platform-test-worsening ,  Iris-test-project , and  platform-demographic
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition&
66
Fig. 8. The result of any KD task is a report. The fi gure presents a report for a two-class domain obtained after constructing a random
forest with 100 trees. The main part of the report is the confusion matrix demonstrating the predictive accuracy measured by cross-
validation on the training set.
form 600 ms, querying the last value of a selected parameter presented in this paper, or to export the data to an external
84 ms. . Thanks to the application of XML technology the in- system with a different data model.
tegration of the eCRF to the platform s enterprise service bus
was easy and fulfilled the requirements of current medical in-
formatics standards. Conclusions
The future plan for the proposed architecture includes
implementation of a graphical editor for the XML archetypes This paper presents a practical implementation of a two-level
and extension of the list of constraints that can be used for database system for a medical research project. The generic
the knowledge model s specification. Tighter integration of layer of this database uses EAV tables which are useful for
the eCRF with knowledge engineering and data mining tools designing large heterogeneous and frequently changeable da-
through the proposed interface also seems to be important. tabase schemas, as are often found in research studies. In this
It is not easy to give definite advice about when to use system a method for implementing the concept of two-level
EAV tables instead of traditional relational database design. architecture in a modern application framework (Spring Frame-
If our highest priority is flexibility, and the number of collected work) has been demonstrated. The fact that the system has
attributes is very large and potentially often changeable, this been in use for almost two years in the HEARTFAID project
suggests that a two-level EAV design should be used. In all and has delivered useful data for other modules like a knowl-
other cases, a more traditional design would probably be more edge discovery module and decision support services proves
advantageous. When designing frameworks with EAV data- the feasibility and the effectiveness of this solution. The sig-
bases for knowledge discovery tasks it is imperative to also nificance of our work consists in the proposal of a new type of
offer a special query module with an interface similar to that direct interface for accessing complex data structures with the
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HEARTFAID s eCRF: Lessons Learnt from Using a Two-Level Data Acquisition& 67
Tab. 1. eCRF interface for knowledge discovery tasks
Function Name Description
getLastValue Returns the last known descriptor value available for the patient. If all values are
unknown the returned value is also unknown.
getAnyValue Returns information concerning all previous visits. For numerical measurements it
returns two values: minimum and maximum while for categorical attributes it returns
most frequent (mode) value. If all values are unknown the returned value is also
unknown.
getDifference Returns the difference between the last available piece of data and the penultimate
piece. If there are not two available entries the value is unknown. For numerical
attributes (e.g. laboratory values) it is the difference (+/- value). For categorical
attributes it is 0 (no change) and 1 (value changes) [or -1 improved, 0 no change,
1 worsening]
getFlattenedTable For categorical values it returns the number of known values and the most frequent
value.
For numerical it returns mean, minimal and maximum value, range, standard deviation
and slope.
output already prepared for artificial intelligence applications. 10. Merzweiler A., Weber R., Garde S., Haux R., Knaup-Gre-
Additionally, it is also clearly stated that this model is not ap- gori P., TERMTrial  terminology-based documentation
propriate for every database, especially not for large commer- systems for cooperative clinical trials, Comput. Meth. Pro-
cial databases, and therefore its adoption needs to be carefully grams Biomed., 78, pp. 11-24, 2005.
considered. 11. Michelsen L., Pedersen S. S., Tilma H. B., Andersen S. K.,
Comparing different approaches to two-level modelling of
electronic health records., Stud. Health Technol. Inform.,
References 116, pp. 113-118, 2005.
12. Minter D., Linwood J., Hibernate From Novice to Profes-
1. Breiman L., Random Forests, Machine Learning 45(1), pp. sional, Apress, 3 edition, 2006.
5-32, 2001. 13. Nadkarni P., QAV: querying entity  attribute  value meta-
2. Bird L., Goodchild A., Tun Z., Experiences with a Two-Level data in a biomedical database, Comput. Meth. Programs
Modelling Approach to Electronic Health Records, Journal Biomed., 53, pp. 93-103, 1997.
of Research and Practice in Information Technology, 35(2), 14. Nadkarni P. et al., Organization of Heterogeneous Scien-
pp. 121-138, 2003. tifi c Data Using the EAV/CR Representation, J. Am. Med.
3. Chiarugi F. et al., Support for the Medical-Clinical Man- Inform. Assoc., 6(6), pp. 478-493, 1999.
agement of Heart Failure within Elderly Population: the 15. Nadkarni P., Brandt C., Marenco L., WebEAV: Automatic
HEARTFAID Platform, Proc. of ITAB, Ioannina, Greece, Metada-driven Generation of Web Interfaces to Entity-At-
26-28 October 2006. tribute-Value Databases, J. Am. Med. Inform. Assoc., 7(4),
4. Conforti D. et al., HEARTFAID: A Knowledge Based Plat- pp. 343-356, 2000.
form for Supporting the Clinical Management of Elderly 16. Prcela M., Gamberger D., Bogunovic N., Developing Fac-
Patients with Heart Failure, The Journal on Information tual Knowledge from Medical Data by Composing Ontol-
Technology in Healthcare, 4(5), pp. 283-300, 2006. ogy Structures, MIPRO 2007, Opatija, Croatia.
5. Duftschmid G., Gall W., Eigenbauer E., Dorda W., Manage- 17. Sonicki Z., Gamberger D., Smuc T., Sonicki D., Kern J.,
ment of data from clinical trials using the ArchiMed system, Data mining server: On-line knowledge induction tool, in:
Med. Inform. Internet, 27(2), pp. 85-98, 2002. Proc. of Medical Informatics Europe, IOS press, pp. 330-
6. Gamberger D., Prcela M., Jović A., `
muc T., Parati G., 334, 2002.
Valentini M., Kawecka-Jaszcz K., Kononowicz A. A., Can- 18. Wyatt J. C., When to Use Web-based Surveys, J. Am.
delieri A., Conforti D., Guido R., Medical Knowledge Rep- Med. Inform. Assoc., 7(4), pp. 426-430, 2000.
resentation Within Heartfaid Platform, Healthinf, Funchal, 19. HEARTFAID Consortium, D28  Integration and Interoper-
Madeira  Portugal, 2008. ability middleware prototype, 2008.
7. Helms R. W., Entering Data from Remote Terminals in Clin- 20. Altova XMLSpy, http://www.altova.com/xml-editor/
ical Centers using IBM s OS/TSO in the Kidney Transplant 21. Form Handler, http://www.formhandler.net
Histocompability Study, Technical Report 007, Chapel Hill, 22. HL7, Health Level 7, http://www.hl7.org
NC University of North Carolina, KTHS Statistics and Data 23. IHE, Integrating the Healthcare Enterprise, http://www.ihe.
Management Center, Department of Biostatistics, 1973. net
8. Helms R. W., Data Quality Issues in Electronic Data Cap- 24. Instant Survey, http://www.instantsurvey.com
ture, Drug Information Journal, 35, pp. 827-837, 2001. 25. Mule, ESB http://www.mulesoft.org/display/COMMUNITY/
9. Johnson R., Hoeller J., Arendsen A., Risberg T., Sam- Home
paleanu C., Professional Java Development with the 26. Survey Monkey, http://www.surveymonkey.com
Spring Framework, John Wiley & Sons, 2005. 27. Zoomerang, http://www.zoomerang.com
telemedicine
Appendix 1  Knowledge model of the HEARTFAID eCRF, Simplified  Part 1 of 2
Anamnesis Rehabilitation Laboratory Assessment
model (f) textfield
blood_pressure_change (a,f) enum[change] ALT (b,a,f) double
required (f) boolean
bradycardia (b) boolean AST (b,a,f) double
time (f) integer
bradycardia_change (a,f) enum[change] blood_samples_for_DNA-RNA (b,a,f) boolean
chest_pain (b) boolean BNP (b,a,f) pmol mg
Chest X-ray
chest_pain_change (a,f) enum[change] creatinine (b,a,f) umol mg
chest_pain_remote (b) boolean cardio-thoracic_ratio (b,a,f) integer creatinine_clearance (b,a,f) double
dyspnoea (b) boolean comment (b,a,f) textarea date (b,a,f) date
dyspnoea_change (a,f) enum[change] date (b,a,f) date glucose (b,a,f) mmol mg
dyspnoea_remote (b) boolean pulmonary_congestion_or_oedema (b,a,f) boolean glycated_hb (b,a,f) double
fatigue (b) boolean hb (b,a,f) double
and 19 more fields and 12 more fields
Quality of Life Questionnaire
date (b,f) date
Physical Examination
minnesota_total_score (b,f) integer
Echocardiography
body_temperature (b,a,f) double
sf36_bodily_pain (b,f) integer
aorta_ascending_aorta_diameter (b,a,f) double
diastolic_blood_pressure (a,f) integer
sf36_general_health (b,f) integer
aorta_root_diameter (b,a,f) double
heart_murmurs (b,a,f) boolean
sf36_mental_component_summary (b,f) integer
contractility_akinesis (b,a,f) boolean
heart_murmurs_apex (b,a,f) boolean
sf36_mental_health (b,f) integer
left_atrium_anteroposterior_diameter (b,a,f) double
heart_murmurs_base (b,a,f) boolean
sf36_physical_component_summary (b,f) integer
left_ventricle_end-diastolic_diameter (b,a,f) double
heart_murmurs_diastolic (b,a,f) boolean
sf36_role_emotional (b,f) integer
left_ventricle_end-diastolic_volume (b,a,f) integer
heart_murmurs_systolic (b,a,f) boolean
sf36_role_physical (b,f) integer
mitral_valve_deceleration_time (b,a,f) integer
heart_sounds (a,f) boolean
sf36_social_functioning (b,f) integer
mitral_valve_emax-amax (b,a,f) double
heart_sounds_bilateral (b,a,f) boolean
and 2 more fields
mitral_valve_mitral_regurgitation (b,a,f) integer
heart_sounds_fourth (b,a,f) boolean
pulmonary_artery_pressure (b,a,f) integer
and 24 more fields
and 16 more fields
Family History
Cardiopulmonary Exercise Testing
primary_cardiomyopathy (b) boolean
AT (b,f) double
24 h Holter Electrocardiography
BP_baseline_DBP (b,f) integer
Beat-to-beat Blood Pressure Monitoring
atria_ fibrillation_flutter (b,a,f) boolean
BP_baseline_SBP (b,f) integer
baseline_finger_BP_SBP (b,f) integer
conduction_abnormalities (b,a,f) boolean
BP_end_DBP (b,f) integer
baseline_finger_HR (b,f) integer
conduction_abnormalities_details (b,a,f) textfield
BP_end_SBP (b,f) integer
comments (b,f) textarea
date (b,a,f) date
BP_peak_ex_DBP (b,f) integer
cuff_size (b,f) enum[cuff_size]
heart_rate_HF (b,a,f) double
BP_peak_ex_SBP (b,f) integer
date (b,f) date
heart_rate_LF (b,a,f) double
data_recorded (b,f) boolean
device (b,f) enum[device]
heart_rate_pNN50 (b,a,f) double
O2_pulse (b,f) double
end_standing_CB_finger_BP_SBP (b,f) integer
heart_rate_rMSSD (b,a,f) double
RQ (b,f) double
end_standing_CB_finger_HR (b,f) integer
heart_rate_SDANN (b,a,f) double
and 10 more fields
finger (b,f) enum[finger]
heart_rate_total_power (b,a,f) double
Additional Visit
hand (b,f) enum[hand]
and 9 more fields
date (a) date
and 13 more fields
next_scheduled_visit_date (a) date
Final Visit Drug Theraphy other_than_chf_reasons_of_visit (a) boolean
required_advice
date (f) double drug_theraphy (b,a,f) drug (a) boolean
required_hospitalization_date (f) double drug_theraphy_change (a) drug required_advice_details (a) boolean
Appendix 2  Knowledge model of the HEARTFAID eCRF  Simplified  Part 2 of 2
Demographic Data Substudy 1 - Inclusion Criteria
Six-minute walking test
birthday (b) date age_gt_65 (b) boolean
BP_baseline_DBP (a) integer
death (a,f) boolean chf (b) enum[diag_chf]
BP_baseline_SBP (a) integer
death_cause (a,f) textfield diastolic_dysfunction (b) boolean
BP_end_DBP (a) integer
death_date (a,f) date ef_lt_40p (b) boolean
BP_end_SBP (a) integer
sex (b) enum[sex]
functional_capacity (b) boolean
date (a) date
status (b) enum[pat_status]
hypertension (b) boolean
HR_baseline (a) integer
idcm (b) boolean
HR_end (a) integer
Cardiovascular Status
ihd (b) boolean
SpO2_baseline (a) integer
aortic_regurgitation (b) boolean
informed_consent (b) boolean
walking_distance (a) integer
aortic_stenosis (b) boolean
sinus_rhythm_presence (b) boolean
Lifestyle Information CABG (b,a,f) boolean
and 2 more fields
cardiovascular_reason_of_death (a,f) boolean
alcohol_use (b) boolean
Substudy 1 - Exclusion Criteria
cerebrovascular_events (b,a,f) boolean
physical_activity (b) enum[ph_activity]
AIDS (b) boolean
changes_in_therapy (a) boolean
smoking (b) boolean
autoimmune_disorders (b) boolean
chf_status_improved (a) boolean
smoking_cessation (a,f) boolean
cardiac_resynchronization_therapy (b) boolean
chf_status_requires_hospitalization (a) boolean
smoking_cessation_date (a,f) date
drug_or_alcohol_abuse (b) boolean
congenital_heart_disease (b) boolean
smoking_duration (b) integer
gfr_lt_30 (b) boolean
congestive_heart_failure (b) boolean
smoking_no_cigarettes (b) integer
hepatic_disease (b) boolean
and 41 more fields
immunosuppressive_therapy (b) boolean
Non Cardiovascular Medical History
12-Lead Electrocardiography
malignancy (b) boolean
anemia (b) boolean
conduction_LBBB (b,a,f) boolean
no_informed_consent (b) boolean
anemia_worsening (a,f) boolean
conduction_PQ (b,a,f) integer
pacemaker (b) boolean
bronchial_asthma (b) boolean
conduction_QRS (b,a,f) integer
and 3 more fields
connective_tissue_diseases (b) boolean
conduction_QT (b,a,f) integer
diabetes (b) boolean
Patient
conduction_RBBB (b,a,f) boolean
diabetes_type (b) enum[type12]
id long
date (b,a,f) date
diseases_not related_to_hf (b) boolean
uuid string
heart_rate (b,a,f) integer
diseases_potentially related_to_hf (b) boolean
initials string
heart_rate_24h_max (b,a,f) integer
endocrine_disorders (b) boolean
usercenter integer
heart_rate_24h_mean (b,a,f) integer
exposure_to_endemic_diseasesy (b) boolean
createTime date
heart_rate_24h_min (b,a,f) integer
and 29 more fields
updateTime date
and 14 more fields
createUser string
updateUser string
1. The original and one Photostat copy of the manuscript should be mailed to: Managing Editor Zdzisław Wisniowski.
Authors are strongly urged to submit a CD containing the manuscript in Word for PCs format along with the hard
copies. Articles already published or those under consideration for publication in other journals or periodicals should
not be submitted.


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