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Textbook Bioinformatics and Biomedical Engineering 5Th International Work Conference Iwbbio 2017 Granada Spain April 26 28 2017 Proceedings Part I 1St Edition Ignacio Rojas Ebook All Chapter PDF
Textbook Bioinformatics and Biomedical Engineering 5Th International Work Conference Iwbbio 2017 Granada Spain April 26 28 2017 Proceedings Part I 1St Edition Ignacio Rojas Ebook All Chapter PDF
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Bioinformatics and
Biomedical Engineering
5th International Work-Conference, IWBBIO 2017
Granada, Spain, April 26–28, 2017
Proceedings, Part I
123
Lecture Notes in Bioinformatics 10208
Bioinformatics and
Biomedical Engineering
5th International Work-Conference, IWBBIO 2017
Granada, Spain, April 26–28, 2017
Proceedings, Part I
123
Editors
Ignacio Rojas Francisco Ortuño
Universidad de Granada Universidad de Granada
Granada Granada
Spain Spain
We are proud to present the set of final accepted full papers for the third edition of the
IWBBIO conference “International Work-Conference on Bioinformatics and
Biomedical Engineering” held in Granada (Spain) during April 26–28, 2017.
The IWBBIO 2017 (International Work-Conference on Bioinformatics and
Biomedical Engineering) seeks to provide a discussion forum for scientists, engineers,
educators, and students about the latest ideas and realizations in the foundations,
theory, models, and applications for interdisciplinary and multidisciplinary research
encompassing the disciplines of computer science, mathematics, statistics, biology,
bioinformatics, and biomedicine.
The aim of IWBBIO is to create a friendly environment that could lead to the
establishment or strengthening of scientific collaborations and exchanges among
attendees, and, therefore, IWBBIO 2017 solicited high-quality original research papers
(including significant work in progress) on any aspect of bioinformatics, biomedicine,
and biomedical engineering.
The following topics were especially encouraged: new computational techniques
and methods in machine learning; data mining; text analysis; pattern recognition; data
integration; genomics and evolution; next-generation sequencing data; protein and
RNA structure; protein function and proteomics; medical informatics and translational
bioinformatics; computational systems biology; modelling and simulation and their
application in the life science domain, biomedicine, and biomedical engineering. The
list of topics in the successive call for papers also evolved, resulting in the following
list for the present edition:
1. Computational proteomics. Analysis of protein–protein interactions. Protein
structure modelling. Analysis of protein functionality. Quantitative proteomics and
PTMs. Clinical proteomics. Protein annotation. Data mining in proteomics.
2. Next-generation sequencing and sequence analysis. De novo sequencing,
re-sequencing, and assembly. Expression estimation. Alternative splicing discovery.
Pathway analysis. Chip-seq and RNA-Seq analysis. Metagenomics. SNPs
prediction.
3. High performance in bioinformatics. Parallelization for biomedical analysis.
Biomedical and biological databases. Data mining and biological text processing.
Large-scale biomedical data integration. Biological and medical ontologies. Novel
architecture and technologies (GPU, P2P, Grid etc.) for bioinformatics.
4. Biomedicine. Biomedical Computing. Personalized medicine. Nanomedicine.
Medical education. Collaborative medicine. Biomedical signal analysis. Biomedi-
cine in industry and society. Electrotherapy and radiotherapy.
5. Biomedical engineering. Computer-assisted surgery. Therapeutic engineering.
Interactive 3D modelling. Clinical engineering. Telemedicine. Biosensors and data
acquisition. Intelligent instrumentation. Patient monitoring. Biomedical robotics.
Bio-nanotechnology. Genetic engineering.
VI Preface
• Biomarker discovery
• Integration of image and omics data for systems biology
• Modeling and simulation of dynamical processes
Organizer: Prof. Joel P. Arrais FCTUC – University of Coimbra, Portugal.
– SS6: Omics of Space Travelled Microbes – Bioinformatics and Biomedical
Aspects
The National Research Council (NRC) Committee for the Decadal Survey on
Biological and Physical Sciences in Space reported that “microbial species that are
uncommon, or that have significantly increased or decreased in number, can be
studied in a “microbial observatory” on the International Space Station (ISS).” As
part of the microbial observatory effort the NRC decadal survey committee sug-
gested that NASA should: “(a) capitalize on the technological maturity, low cost,
and speed of genomic analyses and the rapid generation time of microbes to monitor
the evolution of microbial genomic changes in response to the selective pressures
present in the spaceflight environment; (b) study changes in microbial populations
from the skin and feces of the astronauts, plant and plant growth media, and
environmental samples taken from surfaces and the atmosphere of the ISS; and
(c) establish an experimental program targeted at understanding the influence of the
spaceflight environment on defined microbial populations.”
The proposed session discusses state-of-the-art molecular techniques, bioinfor-
matics tools, and their benefit in answering the astronauts and others who live in
closed systems.
Organizer: Dr. Kasthuri Venkateswaran, Senior Research Scientist, California
Institute of Technology, Jet Propulsion Laboratory, Biotechnology and Planetary
Protection Group, Pasadena, CA
– SS7: Data-Driven Biology – New Tools, Techniques, and Resources
Advances in sequencing techniques have accelerated data generation at diverse
regulatory levels in an unprecedented way. The challenge now is to integrate these
data to understand regulation at a systems level. As the sequencing technologies
evolve, new tools and resources follow, revealing new aspects of complex bio-
logical systems.
This special session brings together experts from computational biology and
machine learning to present recent advances in the development of new tools and
resources using next-generation sequencing data including novel emerging fields
such as single-cell transcriptomics. The session features an invited speaker and
three/four short talks. To promote emerging leaders of the field, we select invited
speakers who have gained their independence in recent years.
Organizer: Dr. Joshi Anagha, Division of Developmental Biology at the Roslin
Institute, University of Edinburgh
– SS8: Smart Sensor and Sensor-Network Architectures
There is a significant demand for tools and services supporting rehabilitation,
well-being and healthy life styles while reducing the level of intrusiveness as well as
increasing real-time available and reliable results. For example, self-monitoring
X Preface
• All ages, while focusing on younger people, who can be involved more easily
but are less addressed in the literature
• All diseases, while focusing on chronic illness and severe disabilities (e.g.,
muscle dystrophies and atrophies)
The contributions should show advances in at least one of the following areas:
• Adaptability to users with all kinds of problems (e.g., possibility to configure the
limbs used to play or playing with facial movements, wheelchair and standing
modes, coping with muscle weaknesses etc.)
• Implementation of gaming techniques and special motivators
• Physical or mental exercises, aimed at rehabilitation or daily practice
• Understanding the users, awareness of their level of motivation, fatigue or
progress and react accordingly
Organizer: Dr. Martina Eckert, Associate Professor at University of Madrid,
Spain.
– SS12: Modelling of Glucose Dynamics for Diabetes
Diabetes is the eighth most common cause of death, while its treatment relies on
technology to process continuously measured glucose levels.
Organizer: Dr. Tomas Koutny, Faculty of Applied Sciences, University of West
Bohemia
– SS13: Biological Network Analysis in Multi-omics Data Integration
In many biological applications, multiple data types may be produced to determine
the genetics, epigenetics, and microbiome affecting gene regulation and metabo-
lism. Although producing multiple data types should provide a more complete
description of the processes under study due to multiple factors such as study design
(synchronization of data production, number of samples, varying conditions), the
analysis may leave more unfulfilled promises than synergy expected from the
wealth of data.
In this session, some of the following challenges are addressed:
• How to conduct meaningful meta-analysis on historical data.
• How to use biological knowledge (represented in reproducible and interoperable
manner) in the analysis of large and sparse data sets more effectively.
• How to fill the gap between hypothesis-driven mechanistic studies, e.g.,
applying modelling to very well studied biochemical processes and data-driven
hypothesis-free approaches. How omics data can help.
• Beyond meta-transcriptomics and metagenomics: integration and interpretation
of microbiome and host data.
We would like to bring together communities concerned with these topics to pre-
sent state-of-the-art and current cutting-edge developments, preferably work under
construction or published within the past year.
Preface XIII
An additional topic that does not fit the proposed session but that I would love to see
addressed is: How to improve open access to the data that is not next-generation
sequencing (e.g., metabolomics, proteomics, plant phenotyping). For this an active
participation of journal editors would be necessary to discuss opportunities to change
journal publication policies.
Organizer: Dr. Wiktor Jurkowski, Jurkowski Group, Earlham Institute, Norwich
Research Park, UK
– SS14: Oncological Big Data and New Mathematical Tools
Current scientific methods produce various omics data sets covering many cellular
functions. However, these data sets are commonly processed separately owing to
limited ways in how to connect different omics data together for a meaningful
analysis. Moreover, it is currently a problem to integrate such data into mathe-
matical models. We are entering the new era of biological research where the main
problem is not to obtain the data but to process and analyze them. In this regard, a
strong mathematical approach can be very effective (see J. Gunawardena’s essay
“Models in biology: accurate descriptions of our pathetic thinking,” BMC Biology
2014, 12:29).
In this Special Session we focus on big data (omics and biological pathways) related
to oncological research. General biological processes that are relevant to cancer can
also be studied. Mathematical tools basically mean statistical learning (data mining,
inference, prediction), modeling, and simulation. We want to place a special
emphasis on causality. Closely tied to mathematical tools, efficient computational
tools can be considered.
Organizers: Dr. Gregorio Rubio, Instituto de Matematica Multidisciplinar,
Universitat Politecnica de Valencia, Valencia, Spain. Dr. Rafael Villanueva,
Instituto de Matematica Multidisciplinar, Universitat Politecnica de Valencia,
Valencia, Spain.
In this edition of IWBBIO, we were honored to have the following invited speakers:
1. Prof. Roderic Guigo, Coordinator of Bioinformatics and Genomics at Centre de
Regulacio Genomica (CRG). Head of the Computational Biology of RNA Pro-
cessing Group. Universitat Pompeu Fabra, Barcelona, Spain
2. Prof. Joaquin Dopazo, Director of the Computational Genomics Department, Centro
de Investigación Príncipe Felipe- CIPF, Valencia, Spain
3. Prof. Jose Antonio Lorente, Director of Centre for Genomics and Oncological
Research (GENYO). Professor of Legal and Forensic Medicine, University of
Granada, Spain
It is important to note, that for the sake of consistency and readability of the book, the
presented papers are classified under 16 chapters. The organization of the papers is in
two volumes arranged following the topics list included in the call for papers. The first
XIV Preface
Steering Committee
Miguel A. Andrade University of Mainz, Germany
Hesham H. Ali University of Nebraska, USA
Oresti Baños University of Twente, the Netherlands
Alfredo Benso Politecnico di Torino, Italy
Giorgio Buttazzo Superior School Sant’Anna, Italy
Mario Cannataro University Magna Graecia of Catanzaro, Italy
Jose María Carazo Spanish National Center for Biotechnology (CNB), Spain
Jose M. Cecilia Universidad Católica San Antonio de Murcia, Spain
M. Gonzalo Claros University of Malaga, Spain
Joaquin Dopazo Research Center Principe Felipe, Spain
Werner Dubitzky University of Ulster, UK
Afshin Fassihi Universidad Católica San Antonio de Murcia, Spain
Jean-Fred Fontaine University of Mainz, Germany
Humberto Gonzalez University of the Basque Country, Spain
Concettina Guerra College of Computing, Georgia Tech, USA
Andy Jenkinson Karolinska Institute, Sweden
Craig E. Kapfer Reutlingen University, Germany
Narsis Aftab Kiani European Bioinformatics Institute, UK
Natividad Martinez Reutlingen University, Germany
Marco Masseroli Politechnical University of Milan, Italy
Federico Moran Complutense University of Madrid, Spain
Cristian R. Munteanu University of A Coruña, Spain
Jorge A. Naranjo New York University, Abu Dhabi
Michael Ng Hong Kong Baptist University, SAR China
Jose L. Oliver University of Granada, Spain
Juan Antonio Ortega University of Seville, Spain
Julio Ortega University of Granada, Spain
Alejandro Pazos University of A Coruña, Spain
Javier Perez Florido Genomics and Bioinformatics Platform of Andalusia,
Spain
Violeta I. Pérez Nueno Inria Nancy Grand Est, LORIA, France
Horacio Pérez-Sánchez Universidad Católica San Antonio de Murcia, Spain
Alberto Policriti University of Udine, Italy
Omer F. Rana Cardiff University, UK
M. Francesca Romano Superior School Sant’Anna, Italy
Yvan Saeys VIB - Ghent University, Belgium
Vicky Schneider The Genome Analysis Centre, UK
Ralf Seepold HTWG Konstanz, Germany
XVI Organization
Program Committee
Additional Reviewers
Machine Learning for Critical Care: An Overview and a Sepsis Case Study . . . 15
Alfredo Vellido, Vicent Ribas, Carles Morales, Adolfo Ruiz Sanmartín,
and Juan Carlos Ruiz-Rodríguez
Biomedical Engineering
Elbow Orthosis for Tremor Suppression – A Torque Based Input Case . . . . . 292
Gil Herrnstadt and Carlo Menon
Clustering of Food Intake Images into Food and Non-food Categories . . . . . . 454
Abul Doulah and Edward Sazonov
Feature Extraction Using Deep Learning for Food Type Recognition . . . . . . . 464
Muhammad Farooq and Edward Sazonov
Biomedicine
Secret Life of Tiny Blood Vessels: Lactate, Scaffold and Beyond . . . . . . . . . 591
Vladimir Salmin, Andrey Morgun, Elena Khilazheva, Natalia Pisareva,
Elizaveta Boitsova, Pavel Lavrentiev, Michael Sadovsky,
and Alla Salmina
What Can the Big Data Eco-System and Data Analytics Do for E-Health?
A Smooth Review Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
Sidahmed Benabderrahmane
Computational Genomics
Computational Proteomics
Data Mining the Protein Data Bank to Identify and Characterise Chameleon
Coil Sequences that Form Symmetric Homodimer b-Sheet Interfaces. . . . . . . 118
Johanna Laibe, Melanie Broutin, Aaron Caffrey, Barbara Pierscionek,
and Jean-Christophe Nebel
Kauan sen jälkeen kun muut iltasin ovat vaipuneet unen uumeniin,
valvoo
Anna kamarissaan kauniitten käsitöittensä ääressä.
Ja nyt! —
*****
Lokakuu on lopullaan.
"Sano, sano!" —
"… Antti…"
"Kipeäksikö se on kääntynyt?" —
"Niin sanoo koskevan, — vaan kunhan lepää rauhassa, niin ehkä
se menee ylitse." —
VIII.
Mutta kummalleko — —?
"Sanoin…"
"Anna!"
"Sano!" —
"Kuulithan, että minä kysyn sitä sinulta." Antin kasvot ovat niin
valkoiset, kuin olisi viime yö satanut niihinkin lumen.
"Täytä velvollisuutesi."
"Pikku-Hilmaa kohtaan."
"Et milloinkaan!"
"Ei aivan, — tahdon vielä lisätä sen, että sinun tulee kohdella
hyvin Pikku-Hilmaa, kaiken elinaikanne — elä unhoita sitä!" — Sitten
kääntyy hän menemään. Kylmänä, repivänä virtana kulkee tuuli
autioitten peltojen ylitse. Se pistää ahnaan kielensä jokaiseen
pienimpäänkin soppeen, — ikäänkuin peläten menneen kesän
onnistuneen piiloittamaan niihin muistojansa…
"Isä —" sanoo hän silloin hiljaa ja painaa päänsä ukon syliin. —
*****
"Lähteekös tätikin?" —
"En. Minä olen aina täällä kotimaassa, — täällä Iso-Marttilassa."
—
Uusi oluttehdas.
*****
Tuvan ovi oli auki ja ilta aurinko paistoi vienosti vasta pestylle
lattialle.
"Aj, teelkö sine asukin, sine Eljas poika, joka toi meille se punase
mansika… niin söötti, niin make…" rätysti neiti iloisesti.
"Kiitosta paljo! No mine istu vehen… Ja tuo sine Eljas viel huomen
aamun mansikat minulle. Ilta junalla mine lähde Parisiin, Franskan
maalle. — Tietekö Eljas sen?"
"Tiedän."
"Jaa mut mine sano, at sine anta nyt selkä sen! Ja teke sine töö ja
maka sine öö, — mut parempi ihmisi et sine saa söö…!"
"Itse sinä ihmisiä syöt…", ajatteli Tuomas mutta sanoa ei hän sitä
olisi voinut, siksi oli hän liian arka ja hyväluontoinen. Mutta kotiin
tultuansa oli hän niin kiihdyksissä, että tosiaankin vähällä oli panna
täytäntöön tehtailijan määräyksen selkäsaunasta…
"Kun on niin typerä että ottaa sen harmiksi", vastasi Mari. "Anna
vaan pojan olla rauhassa, sillä siinä asiassa hän ei pienintäkään
pahaa tehnyt! Kun sanoo sen mikä on totta ja oikeata, niin ei ole
mitään syytä perästä päin pahoitella."
"Sillehän se juuri oli sanottava. Tee aina niin Eljas, jos tahdot
miehestä käydä — se on äitisi neuvo!"
*****
"Niin kuuluu. — Vaan tullappa kerran sellainen aika ettei olisi sitä
turmion lientä herroilla eikä talonpojilla… Mitähän ne sitten
kesteissään kulauttelisivat?"
"Talonpoika! Työmies!"
"Minä vaan arvelin", sanoi Mari, "että kun Luoja kerran sanoi:
hallitse! niin voisi se silloin myöskin olla hallittavissa, — sekin."
"Vai akat täällä isäntinä… kyllä siitä lystistä pian loppu tulee…" ja
kohotti nyrkkinsä lyöntiin.
"Voi hyvä Jumala, kun sen piti vielä lapseen sattua!" vaikeroi Mari
polvistuen pienokaisen viereen lattialle. — "Tuo Eljas kulta joutuin
kylmää vettä kaivosta! — Ja te nahjukset menkää katsomaan, ettei
enemmän pahaa tapahdu… Viekää sinne tehtailijan hoviin mokoma
räysääjä — viskelköön sitten kiviään — jos kuin…"
Mutta ilo oli liian aikaista, se sai jälleen väistyä harmaan, raskaan
todellisuuden tieltä. Kun arpi pikku Hilman ohimossa oli parantunut ja
tapaus unhottunut mielistä, solui isänkin elämä takaisin entiselle
ladullensa — ja se oli samaa kuin jokapäiväinen juopottelu.
Odotat! —
Sellaiset puheet soivat Helvin korvissa tyhjääkin tyhjemmältä.
Eivät ne antaneet etsivälle hengelle minkäänlaista kiinnekohtaa,
korkeintaan ne vaan myllersivät painostavan epämääräisyyden
entistäkin epämääräisemmäksi…
Jos hän puhui siitä äidille, hymähti tämä vaan ja sanoi Helvillä
olevan yllin kyllin työtä, jos sitä halusi. — Salin pieni nurkkasohva
kaipasi tyynyä, — samoin isän lepotuoli uutta mattoa, — punaiseen
lampunvarjostimeen olisi ollut poimuteltava uusi petsi — ja
ennenkaikkea isän kirjoituspöydälle ommeltava kynttiläjalan matot.
*****
Syksyinen tuuli, jonka sydämessä on intoa ja siivissä voimaa,
puhalsi kiihkeästi ylitse routaisen, alastoman maan. Se puski päänsä
rajusti seiniä vasten, puisteli puutarhan puita, ikäänkuin
koetellakseen niiden niskojen norjuutta ja koetettuaan turhaan
tunkeutua kaksinkertaisten akkunaruutujen lävitse, malttoi sen
viimein hetkiseksi mielensä ja jättäytyi niiden taakse salaperäisenä
suhajamaan…
Toisinaan, kun Helvi luuli Eeron nukkuvan aikoi hän hiljaa vetäistä
kätensä hänen kädestään, vaan silloin puristautuivat sairaan heikot
sormet yhä lujempaan ja polttavat huulet kuiskasivat hiljaa:
"En jätä."
"Lapsiko?" —
"Viija."
"Kiitoksia." —