DCBIOSTEC 2014 Abstracts

Short Papers
Short Papers
Paper Nr: 5
Title:

Genome Sequences as Media Files - Towards Effective, Efficient, and functional Compression of Genomic Data
Authors:

Tom Paridaens, Wesley De Neve, Peter Lambert and Rik Van De Walle
Abstract: In the past decade, the cost of sequencing a human genome has evolved from millions of dollars to a few thousand dollars. As a result of this exponential drop in cost, the amount of sequencing data is increasing exponentially. Given that storage capacity per dollar doubles roughly every 18 months, the storage of genomic data is becoming a big problem. Therefore, research is performed on improving compression ratio. Unfortunately, functionality such as random access and compressed-domain analysis are often neglected. Therefore, genomic data files have to be transmitted and decompressed completely before any analysis or editing can be done, even if the researcher is only interested in one specific gene. In this paper, we describe our view on how we can introduce techniques that are widely used in the world of media file compression and management into the world of genomic data. With these techniques we aim to lower network load by more efficient transmission techniques, to lower processing load by more efficient (compressed-domain) analysis of genomic data, to provide configurable compression tools and to provide privacy protection through encryption and DRM.
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Paper Nr: 6
Title:

Enhanced Bone Healing Through Mechanical Stimulation by Implanted Piezoelectric Actuators
Authors:

Natacha Rosa, Fernão D. Magalhães, Ricardo Simões and António Torres Marques
Abstract: Tibia fractures are one of the most frequent injuries of the musculoskeletal system. Although, in the last decades, fracture treatment has improved considerably, complications, like delayed union and non-unions with an incidence rate up to 13 %, still occur. The healing time is an important parameter with direct implications on the patient’s physical and emotional wellbeing and it also represents an additional cost to the health care system. The main goal of this research work is to develop an actuator device that through piezoelectric mechanical stimulation is capable of accelerating in a controlled manner, the bone physiological fracture-healing process and leads to a reconstructed fracture that approximates normal anatomy. Considering the risks of overload on the healed tissue and inspired by the potential benefits of the very low bone-stimulus during quiet standing, we decided to complement the commonly used external fixator healing technique with a short period, low-magnitude (<5 µɛ), high-frequency (20 to 60 Hz ) local stimulation, using a small sized piezoelectric actuator in contact with the bone fracture. The low amplitudes of the signals created by the actuator appear to be well below those which may cause risk to the regenerate tissue. We do believe that if the natural healing process is not compromised by the presence of the piezoelectric actuator – for example due to a toxicity reaction - and if ideal biological (i.e. in terms of traumatized tissue revascularization and the inflammatory process) and mechanical conditions for repair are created accelerated fracture healing may be achieved. Hence, facilitating an early rehabilitation and avoiding an additional costly surgical intervention.
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Paper Nr: 8
Title:

Silent Speech for Human-Computer Interaction
Authors:

João Freitas, António Teixeira and Miguel Sales Dias
Abstract: A Silent Speech Interface (SSI) performs Automatic Speech Recognition (ASR) in the absence of an intelligible acoustic signal and can be used as a human-computer interface modality in high-background-noise environments such as living rooms, or in aiding speech-impaired individuals such as elderly persons. By acquiring data from elements of the human speech production process – from glottal and articulators activity, their neural pathways or the central nervous system – an SSI produces an alternative digital representation of speech, which can be recognized and interpreted as data, synthesized directly or routed into a communications network. Nowadays, conventional ASR systems rely only on acoustic information, making them susceptible to problems like environmental noise, privacy, information disclosure and also excluding users with speech impairments. To tackle this problem in the context of ASR for Human-Computer Interaction, we propose a novel SSI based on multiple modalities in European Portuguese (EP), a language for which no SSI has yet been developed. After a state-of-the-art assessment, we have selected less-invasive modalities - Vision, Surface Electromyography and Ultrasound – in order to obtain a more complete representation of the human speech production model. Our aim is now to develop a multimodal SSI prototype adapted to EP and evaluate its usability in real-world scenarios.
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Paper Nr: 10
Title:

Biomechanical Analysis of Orthodontic Appliances Through 3D Computer Aided Engineering
Authors:

Roberto Savignano
Abstract: In the field of dental health care, misaligned teeth can cause aesthetic and functional problems for the patients. Different appliances have been developed to correct malocclusions. In the last decades research in the orthodontic field has focused not only on the effectiveness of the appliances on correcting teeth position, but also on the fulfilment of comfort issues during the treatment. For this reason, many new orthodontic appliances have been developed with the aim at being minimally invasive for the patients. In particular clear removable aligners, made of transparent thermoplastic material and then almost invisible, raised a growing interest. Treatments based on clear aligners are composed of a set of thermoformed templates, having different shapes, which are sequentially worn by the patient. Each aligner is shaped a bit different than the real teeth position in the mouth in order to force teeth to move in the correct position. Even if orthodontic treatments based on the use of clear aligners are commonly used in clinical practice there is no technical literature describing how the loads are transferred from the aligner to the teeth. Since both design and production processes involves many clinical and technological skills, the optimisation of aligners features represents one of the most challenging aspects of this kind of orthodontic treatments. In this context, the present research project is focused on the development of a Finite Element Method (FEM) model to be used in the optimisation process of both geometrical and structural attributes of removable aligners.
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Paper Nr: 11
Title:

Autonomous Cardiac Diagnostic based on Synchronized ECG and PCG Signal
Authors:

Z. Bouguila, A. Moukadem, A. Dieterlen, A. Ahmed Benyahia, A. Hajjam, S. Talha and E. Andres
Abstract: Despite considerable advances in medical therapy, heart failure remains a substantial burden of mortality and economic cost. This is tangibly seen by the rising number of healthcare systems that are adopting telemedicine, by the development of industry investments in telemedicine products and involvement of government in project delivery. The main objective of the telemedicine E-care (www.projet-e-care.fr) project is to greatly contribute to the enhancement of the remote patient monitoring, expanding the possibilities for lifesaving care. In this project, oriented for heart failure patients with NYHA (class III) severity, a smart platform is adopted for home monitoring using noninvasive standard sensors and specific cardiac devices (ElectroCardioGram and PhonoCardioGram). This thesis contribution, with our partners, is to enhance the signal processing part for accurate diagnostic. Although ECG and PCG signals play important roles in heart abnormality detection, diagnosis based on this signal individually cannot detect most cases of heart symptoms, like detection of S4 pathological heart sound. Previously in our laboratory, time-frequency methods showed here potential on PCG segmentation and classification; however these methods can suffer from poor energy concentration in time frequency domain. Hence the first theoretical thesis objective is to optimize the energy concentration of Stockwell time-frequency transform. The second objective, based on the first results, is to combine by time-frequency correlation the information contained in PCG and ECG. This original approach will help us extracting features to classify accurately heart disease. All these methods should be validated by an experimented cardiologist during a measure campaign in Strasbourg University Hospital.
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Paper Nr: 12
Title:

The Homologous Recombination Mathematical Model and the Role of miRNAs in ATM/ATR-dependent and BRCA1/BRCA2-dependent DSBs Repair Pathway - Outline of the Project
Authors:

Katarzyna Jonak, Monika Kurpas and Krzysztof Puszyński
Abstract: DNA double strand breaks (DSBs) are known to be one of the most cytotoxic lesions, caused by exposure to ionizing radiation or clastogenic drugs. Maintaining the genomic integrity through DNA repair processes is essential for proper functioning of the organisms. Therefore, it is important to study interactions between different components of DSBs detection modules and repair systems and to model cellular response to the signals from the specific elements of these pathways. Homologous recombination (HR) is one of the repair pathways in eukaryotic cells and is limited to late S phase and G2 phase of cell cycle. We propose a mathematical model that focuses on the interactions between different components of HR. The model includes the effects of the DNA damages on ATM and ATR detection modules and the activation of key proteins involved in HR, such as BRCA1, BRCA2 and Rad51. It describes the connections between HR and checkpoints proteins, as well as the effect of known specific miRNAs responsible for regulation of transcription of the proteins involved in HR pathway. The purpose of the project is to illustrate the processes occurring during DNA repair. The project will allow to understand the interactions between molecules, probably investigate new components of the HR network, and contribute to putting the hypotheses on possible treatment of different diseases at the level of the cellular pathways.
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Paper Nr: 13
Title:

Development and Evaluation of Human-Computer Interface based on Facial Motor Unit Activity
Authors:

Carlos M. M. Queiroz, Slawomir J. Nasuto and Adriano O. Andrade
Abstract: Interfaces that enable human-computer interaction have progressed significantly. In the past decade a lot of effort has been directed to the development and improvement of perceptual interfaces, i.e., interfaces that promote interaction with the computer without the use of conventional keyboard or mouse. This type of interface combines the understanding of natural human capabilities (e.g., communication, motor, cognitive and perceptual skills) with the use of these for interaction with the computer, taking into account the ways in which people naturally interact with each other and with the world. The search for more natural forms of interaction has directed recent research for the study of biological signals that have the potential to encode control strategies adopted by the central nervous system (CNS). In this context, information obtained through the activity of motor units - such as firing rate, waveform of action potentials and recruitment strategy - can be used in the development of human-computer interfaces. Therefore, this research proposes in an unprecedented manner, the development and evaluation of a human-computer interface based on information extracted from motor units (MUs). The interface development will consist of two steps: i) preparation of a flexible sensor array capable of detecting activity of MUs of facial muscles; ii) implementation of tools for signal processing capable of extracting information from MUs and translation of this information into control signals. The evaluation of the interface will consider: i) the quantification of learning related to the use of the interface; ii) the analysis of the correlation between learning and the dynamics of neural oscillation obtained by means of electroencephalographic signals; iii) the comparison of the new proposed interface with the Muscle Academy (Andrade et al., 2012), which is a myoelectric interface recently developed by our research group
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Paper Nr: 14
Title:

Analysis of Glioblastoma’s Peritumoral Brain Zone - Developing of Per-operative Analysis and New Therapeutic Targets
Authors:

Jean-Michel Lemée, Anne Clavreul and Philippe Menei
Abstract: GB is the most frequent and aggressive primary tumor of the central nervous system. The mechanisms of recurrence remain unclear but the infiltration of the peritumoral brain zone by GB cells may be considered as the explanation of the high rate of local recurrences. A better understanding of the characteristics of the PBZ is critical to understand the mechanisms of GB recurrence, optimize the quality of the surgical resection and develop new therapies. During the first part of my PhD, we studied the heterogeneity of the glioblastoma’s peritumoral brain zone (GB-PBZ) using the different techniques used routinely to analyze tumor samples, identifying several alterations specific to the GB-PBZ. Also, we solved a methodological problem with the definition of the best control for brain tumor proteomic analysis. The second part of my PhD will be focused on the development of per-operative analysis of the GB-PBZ to guide the surgical resection of the tumor, and the molecular analysis of the GB-PBZ to develop new therapeutic targets for GB treatment. First, we decided to study two modern techniques of microscopy: the Second Harmonic Imaging Microscopy and the Two Photons-Excited Fluorescence to allow a fast and reproducible per-operative analysis of the GB-PBZ with the aim to optimize the complete resection of the tumor. After the validation of the proteins found in the multimodal analysis of the GB-PBZ, we will assess the expression of these proteins in a cohort of patients from the national clinico-biological collection of GB to assess if these biomarkers can be used as therapeutic targets or as target for vectorized nanotherapies.
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Paper Nr: 16
Title:

Psychophysiological Measurements in Real Working Environments - Wireless EEG Study of the Operators’ Vigilance

Authors:

Pavle Mijović, Ivan Gligorijević, Evanthia Giagloglou, Ivan Mačužićand and Branislav Jeremić
Abstract: The inability of the industry worker to sustain attention during a task can lead to errors in operating, which can cause the material damage as well as human injuries including catastrophic events with fatalities. Therefore, measuring operators’ focus, referred to as vigilance level, while performing everyday monotonous repetitive task, is of the crucial interest. The objective of the proposed research is to pinpoint to routines used to attain close to constant vigilance level of operators in industrial environment. It is proposed to adapt laboratory proven measures of vigilance level to real-life working environment, where an operators' vigilance level is monitored by the comfortable, lightweight and completely mobile wireless EEG sensors. It is within the scope of this research to also develop an algorithm for the on-line monitoring of the operators' vigilance state in order to provide the real-time estimates of its alertness level. This could lead to prevention of the industrial accidents, as they are most of the time caused by the inability of the operators to sustain attention. As the side objective, it is proposed to develop a brain-computer interface (BCI) where operators' would be able to perform safety actions in cases where operating commands are hardly reachable by the operators' hand.
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Paper Nr: 18
Title:

DNA Damage Detection and its Impact on the Cell Cycle
Authors:

Monika Kurpas, Katarzyna Jonak and Krzysztof Puszyński
Abstract: During evolution number of mechanisms that protect cells from damages evolved to prevent their death and lesions transformation to future generations. For efficient repair it is necessary to detect damages quickly and then transfer the signal to other components of cells. This process takes place in a manner specific to the type of lesion. ATR (ataxia telangiectasia mutated and Rad3-related) module is activated by the presence of DNA single stranded breaks (SSBs) in cell, which are caused by resection of various types of lesions or by stalled replication forks. Double strand breaks (DSBs) are detected indirectly by ataxia telangiectasia mutated (ATM). These proteins are involved in the activation of the signaling cascade, as a result of which tumor suppressor p53 is activated and decision about future fate of cells is taken. If the damage is too extensive cell undergoes apoptosis. If damage is repairable, the cell cycle is arrested and damage repair occurs. Current status of DNA is controlled in cell cycle checkpoints. Cell cycle arrest requires signal from the ATM or ATR and Chk1 and Chk2 (checkpoint kinases). At this point, we have created mathematical models of ATR-p53 and ATM-p53 signaling pathways. We plan to combine the developed DNA damage detection pathways and connect them with the cell cycle. Our purpose is to examine the impact of ATM-ATR-p53 path on the cell cycle and examine influence of cell cycle on this path. We also plan to investigate how disabling of selected interactions between molecules may influence the DNA damage response system.
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Paper Nr: 19
Title:

Forests of Latent Tree Models for Genome-Wide Association Studies
Authors:

Phan Duc Thanh
Abstract: In the bio-medical research domain, with the availability of massive amounts of data generated by high-throughput genotyping technologies, genome-wide association studies (GWAS) have become feasible and are now considered as a method of choice for statistically connecting DNA variations and human disorders. Since GWASs are based upon the principle of linkage disequilibrium (LD) at the population level, it is essential be able to effectively model LD in human genome. At the intersection of multiple fields, this thesis aims to study the design and implementation of methods based on Bayesian Networks (BN) in the context of GWASs, for investigating the genetic architecture of complex diseases.
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Paper Nr: 20
Title:

Spectroscopic Characteristics of the Cationic Dye Basic Orange 21 in Leukocytes
Authors:

Z. Eizig, D. T. Major, H. L. Kasdan, E. Afrimzon, N. Zurgil and M. Deutsch
Abstract: Leukocyte staining with the cationic dye, Basic Orange #21 (BO21) can improve leukocyte differential counting, routinely used to assess general health, help diagnose the cause of an abnormal white blood cell count, and/or monitor other diseases and conditions that affect specific leukocytes . The spectroscopic aspects of BO21 and their changes upon interaction with biological molecules within the live cell in general, and various leukocytes (white blood cells) in particular, were examined. Spectroscopic characteristics were studied in bulk solutions under several conditions (pH, viscosity) and various solvents (salts, proteins). Results show negligible changes in absorption spectra under most conditions and solvents. However, Heparin, an anion organic molecule common to a specific type of leukocyte, causes a blue shift of the spectra from 484 nm in its absence to 465 nm when Heparin is present. Next, it was found that in the presence of heparin the emission peak of BO21 was extremely red shifted; from 519 to 550nm for excitation of BO21 at 490nm. Finally, Fluorescence polarization (FP) measurements of BO21 in water yielded, contrary to all expectations, FP ~ 0.450. However, the presence of heparin produced a dramatically lower FP; about 0.200. may be caused either by an electrostatic bond between the cationic-dye and the polyanions (Heparin) or by effective aggregation of the dye cations due to their occupying adjacent sites on the polyanion. Utilizing different small anion molecules and high dye concentration, we concluded that it is not the electrostatic bond which is responsible for the blue spectral shift of the dye, but rather the aggregation of dye ions. We proposed a mechanism using computational chemistry which indicates that parallel setting of the molecular electrical dipoles of BO21, of which the dimers and trimers are composed, is indeed feasible. Surprisingly, the related binding energies are even lower than those calculated for anti-parallel arrangement.
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Paper Nr: 21
Title:

On the Cryopreservation of Individual Cells in Volumes Less than Nano Liter
Authors:

B. Galmidi, Y. Shafran, R. Orvieto, N. Zurgil and M. Deutsch
Abstract: About a million cases of low sperm count related diseases, are treated in one year at IVF labs, using unsuitable procedures and means for cryopreservation of individual spermatozoa. The micro-arrayed donut-shaped chamber (DSC) is a novel device for individual cell cryo-preservation which was developed and produced in the frame of the current work. Each chamber is designed to act as an individual isolated compartment, and to enclose a minimal number of sperm cells. To date, we have promising results with sperm cells that have undergone the freezing-thawing cycle in suspension volume of about 10nl-2 μl. Under the same freezing-thawing procedure, the motility of thawed sperm cells in a 1nl volume or less was unsatisfactory. The series of experiments lead us to suspect that a unique physical mechanism might be the cause for the explored phenomena. Therefore, an analytical-physical research is under way, to understand the microscopic changes in the freezing-thawing process of water, solution and cell suspension (with different geometric shapes), at very small volumes, together with a biology research aimed to understand the effect of these changes on spermatozoa. These will be followed by medical research for the development of applied clinical devices and protocols. We strongly believe that overcoming the abovementioned temporary problems of cryopreservation of individual sperm cells within volumes less than nano liter, using our novel device for cryopreservation, will ensure there is no loss of spermatozoa during the freezing-thawing process.
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