Miracle-dz/UniFAR-FTUs huggingface dataset:
Big Data and Biomedical Informatics: A Challenging Opportunity

Summary Big data are receiving an increasing attention in biomedicine and healthcare. It is therefore important to understand the reason why big data are assuming a crucial role for the biomedical informatics community. The capability of handling big data is becoming an enabler to carry out unprecedented research studies and to implement new models of healthcare delivery. Therefore, it is first necessary to deeply understand the four elements that constitute big data, namely Volume, Variety, Velocity, and Veracity, and their meaning in practice. Then, it is mandatory to understand where big data are present, and where they can be beneficially collected. There are research fields, such as translational bioinformatics, which need to rely on big data technologies to withstand the shock wave of data that is generated every day. Other areas, ranging from epidemiology to clinical care, can benefit from the exploitation of the large amounts of data that are nowadays available, from personal monitoring to primary care. However, building big data-enabled systems carries on relevant implications in terms of reproducibility of research studies and management of privacy and data access; proper actions should be taken to deal with these issues. An interesting consequence of the big data scenario is the availability of new software, methods, and tools, such as map-reduce, cloud computing, and concept drift machine learning algorithms, which will not only contribute to big data research, but may be beneficial in many biomedical informatics applications. The way forward with the big data opportunity will require properly applied engineering principles to design studies and applications, to avoid preconceptions or over-enthusiasms, to fully exploit the available technologies, and to improve data processing and data management regulations.
Agent-based personal article citation assistant

Scientific researchers usually need to deal with a large number of scientific and technical articles. A handy toolkit to facilitate retrieval and identification of these articles is vital. This paper presents an agent-based personal article citation assistant (APACA). As an autonomous agent, it provides extensive and efficient assistance for users to identify most related citations in a local article repository in collaboration and interaction with other distributed personal citation assistants. Furthermore, this paper proposes an article ontology and an optimised Bayesian network method to infer the most relevant article annotation in the local article ontology using a given keywords set K.
Clinical patterns and pathophysiology of hypermotor seizures: an ictal SPECT study

Hypermotor seizures (HMS) can include different forms of hypermotor behaviour due to various mechanisms associated with generation of ictal automatisms. Despite the varied location of seizure onset, similar semiologic features during seizures may exist. Ictal single-photon emission tomography (SPECT) apparently reflects not only the origin of epileptic discharge but also the spread to adjacent cortical areas. Taking this benefit of SPECT studies into account, preoperative SPECT results from 13 patients with HMS who underwent epilepsy surgery were analysed. The radioisotope 99mTc-ECD was injected in all patients within five seconds after seizure onset. Group analysis was performed with statistical parametric mapping (SPM) of paired ictal-interictal SPECTs in order to identify regions of significant ictal hyperperfusion. Hyperperfused regions with a corrected cluster-level significance p-value of <0.002 were considered significant. Seizure onset at implanted subdural electrodes was defined as the epileptic focus in 12 of 13 patients. Two patterns were recognized: HMS-1 with marked agitation and HMS-2 with mild agitation. Ictal hyperperfusion images revealed significant hyperperfusion in the anterior cingulate cortex, orbito-frontal gyrus, lentiform nucleus, midbrain and pons. These hyperperfused areas represent the symptomatogenic zone which was different from the epileptogenic zone, asconfirmedby the favourable outcomes after surgical resection. The present findings suggest that a network, including frontal and possibly extrafrontal brainstem and limbic structures, is involved in the genesis of the complex epileptic manifestations of HMS. Moreover, ictal SPECT analysed by SPM is a useful method for studying the neural networks of different types of seizures.
Methodological Approach for Optogenetic Manipulation of Neonatal Neuronal Networks

Coordinated patterns of electrical activity are critical for the functional maturation of neuronal networks, yet their interrogation has proven difficult in the developing brain. Optogenetic manipulations strongly contributed to the mechanistic understanding of network activation in the adult brain, but difficulties to specifically and reliably express opsins at neonatal age hampered similar interrogation of developing circuits. Here, we introduce a protocol that enables to control the activity of specific neuronal populations by light, starting from early postnatal development. We show that brain area-, layer- and cell type-specific expression of opsins by in utero electroporation (IUE), as exemplified for the medial prefrontal cortex (PFC) and hippocampus (HP), permits the manipulation of neuronal activity in vitro and in vivo. Both individual and population responses to different patterns of light stimulation are monitored by extracellular multi-site recordings in the medial PFC of neonatal mice. The expression of opsins via IUE provides a flexible approach to disentangle the cellular mechanism underlying early rhythmic network activity, and to elucidate the role of early neuronal activity for brain maturation, as well as its contribution to neurodevelopmental disorders.
Rehabilitation in Spine and Spinal Cord Trauma

Study Design. Systematic review. Objective. To define the optimal time for initiation of rehabilitation and review the most clinically relevant outcome measures of upper and lower limb motor function of the rehabilitating spinal cord injured patient, using a systematic review and expert opinion. Summary of Background Data. Comprehensive rehabilitation programs are required for patients after spinal cord injury (SCI) as early as feasible. In a dedicated SCI rehabilitation setting, effective treatment and proper monitoring of spontaneous and rehabilitation-based motor function improvements by means of appropriate, valid, reliable and internationally accepted clinical assessment tools is warranted. Methods. Focused questions on key topics in rehabilitation of the spinal cord injured patient were defined by a panel of spine trauma surgeons. A keyword literature search for pertinent articles was conducted using multiple databases. Suitable articles were screened and the quality of evidence was graded and tabulated. Based on the evidence and expert opinion, recommendations were composed and rated as strong or weak. Results. The outcome measures literature search yielded a total of 1251 abstracts. Out of these 86 articles were studied in detail. One high quality study was found with 3 articles referring to it. Furthermore, there were 19 moderate quality studies, 39 low quality studies, and 25 very low quality studies. The timing literature search yielded 508 abstracts of which 3 articles focused on the question and were all graded as low quality. Conclusion. For general motor function, assessing the American Spinal Injury Association motor score and the Spinal Cord Independence Measure III is strongly recommended. The American Spinal Injury Association motor score is also useful in assessing upper- and lower-extremity motor function. For ambulatory function, a timed walk test like the 10 m Walk test in combination with the Walking Index for SCI II is strongly recommended. Early rehabilitation, defined as within 30 days of injury, improves outcome and recovery for spinal cord trauma patients.
Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

Abstract Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction–modification (R–M) and CRISPR–Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR–Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR–Cas systems by lowering the affinity of the Cascade and Cas9–crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR–Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
Experiments and Analysis of Collapse Behaviour of Composite Domes under Axial Compression

Composite domes made of short, randomly oriented glass fiber mats with polyester resin were subjected to axial compression in an Instron machine, in both empty and foam filled conditions. The domes were of different sizes and their generator was a parabola. The mechanics of deformation and the energy absorbing characteristics of the shells were studied, and their load compression curves are presented. The effect of foam filling on the response of the domes is discussed. Based on the experimental observations analytical expressions were formulated to find the average crush load and total strain energy by considering the energy absorbed in different mechanisms involved in the crushing process. The results thus obtained were compared with experimental results and these match well. Some conical shells made of the same material, height and diameter as those of domes were also subjected to axial compression, and their behavior is compared with those of the corresponding domes.
A Verifiable and Correct-by-Construction Controller for Robot Functional Levels

Autonomous robots are complex systems that require the interaction and cooperation between numerous heterogeneous software components. In recent times, robots are being increasingly used for complex and safety-critical tasks, such as exploring Mars and assisting/replacing humans. Consequently, robots are becoming critical systems that must meet safety properties, in particular, logical, temporal and real-time constraints. To this end, we present an evolution of the LAAS architecture for autonomous systems, in particular its GenoM tool. This evolution relies on the BIP component-based design framework, which has been successfully used in other domains such as embedded systems. We show how we integrate BIP into our existing methodology for developing the lowest (functional) level of robots. Particularly, we discuss the componentization of the functional level, the synthesis of an execution controller for it, and how we verify whether the resulting functional level conforms to properties such as deadlock-freedom. We also show through experimentation that the verification is feasible and usable for complex, real world robotic systems, and that the BIP-based functional levels resulting from our new methodology are, despite an overhead during execution, still practical on real world robotic platforms. Our approach has been fully implemented in the LAAS architecture, and the implementation has been used in several experiments on a real robot.
A double-emulsion microfluidic platform for in vitro green fluorescent protein expression

Microfluidic droplet technology has gained popularity due to the advantages over conventional emulsion techniques and capabilities for a wide range of applications. In this paper, the development of a simple microfluidic-based double-emulsion system is reported. Such a system could be potentially used for in vitro protein synthesis. The system involves a two-step process to make water-in-oil-in-water (W/O/W) emulsions. A PMMA microchip is used for the formation of water-in-oil (W/O) single-emulsion droplets. Then, the single-emulsion droplets are transported to a PDMS/glass microchip to make the W/O/W double-emulsion droplets. The system was first characterized by detecting fluorescein sodium salt as a model dye in the internal aqueous droplets using laser-induced fluorescence. The effect of the flow rates of the internal aqueous phase and outer continuous aqueous phase on the formation of the double-emulsion droplets is investigated to provide information for system optimization. On-chip storage of double-emulsion droplets is also investigated to allow for protein synthesis from a PCR-generated DNA template using either commercial in vitro transcription and translation kits or crude Escherichia coli S30 extracts. In vitro expression of the green fluorescent protein is successfully demonstrated in this system.
Deadly Attraction – Attentional Bias toward Preferred Cigarette Brand in Smokers

Numerous studies have shown that biases in visual attention might be evoked by affective and personally relevant stimuli, for example addiction-related objects. Despite the fact that addiction is often linked to specific products and systematic purchase behaviors, no studies focused directly on the existence of bias evoked by brands. Smokers are characterized by high levels of brand loyalty and everyday contact with cigarette packaging. Using the incentive-salience mechanism as a theoretical framework, we hypothesized that this group might exhibit a bias toward the preferred cigarette brand. In our study, a group of smokers (N = 40) performed a dot probe task while their eye movements were recorded. In every trial a pair of pictures was presented – each of them showed a single cigarette pack. The visual properties of stimuli were carefully controlled, so branding information was the key factor affecting subjects’ reactions. For each participant, we compared gaze behavior related to the preferred vs. other brands. The analyses revealed no attentional bias in the early, orienting phase of the stimulus processing and strong differences in maintenance and disengagement. Participants spent more time looking at the preferred cigarettes and saccades starting at the preferred brand location had longer latencies. In sum, our data shows that attentional bias toward brands might be found in situations not involving choice or decision making. These results provide important insights into the mechanisms of formation and maintenance of attentional biases to stimuli of personal relevance and might serve as a first step toward developing new attitude measurement techniques.
Influence of structure on soft magnetic properties of Co70Fe5Si15B10 metallic glass ribbons

Purpose: The paper presents a structural, thermal and magnetic characterization of Co-based amorphous samples in as-cast state and after annealing process. Design/methodology/approach: The studies were performed on Co70Fe5Si15B10 metallic glass in form of ribbons with different thickness. The amorphous structure and phase analysis of studied samples after annealing process was examined by X-ray diffraction (XRD). The crystallization behaviour of the studied ribbons was also examined by differential scanning calorimetry (DSC). The fracture morphology of the ribbons after heat treatment was analysed using the scanning electron microscopy (SEM). The soft magnetic properties examination contained relative initial magnetic permeability and magnetic permeability relaxation measurements. Findings: The X-ray diffraction investigations revealed that the tested ribbons with different thickness were amorphous. The two exothermic peaks describing crystallization process of Co70Fe5Si15B10 alloy were observed for all studied samples with different thickness. The heat treatment process of ribbon samples involved crystallization of α-Co(Si), Co2Si phases and cobalt borides at temperature above 773 K. The study of fracture morphology of samples after annealing at 623 K shows mixed fractures with “river” patterns, which are characteristic for glassy materials and some areas of scaly morphology. The initial magnetic permeability decreases in function of the increase of annealing temperature, but a local maximum could be determine at 673 K. Practical implications: The soft magnetic properties of studied metallic glasses can be formed by different sample thickness and applying the appropriate conditions of annealing process. Originality/value: The applied investigation methods are suitable to determine the changes of structure and soft magnetic properties of examined Co-based alloy with function of sample thickness and heat treatment conditions.
Analysis Of Adiabatic Heating In High Strain RateTorsion Tests By An Iterative Method:Application To An Ultrahigh Carbon Steel

An iterative algorithm has been developed to establish the adiabatic heating correction of flow curves for torsion tests of an ultrahigh carbon steel containing 1.3% C. High temperatures (1223 to 1473 K) and high strain rates (2, 5, 10 and 26 s) were used. The curves are corrected in a finite and discrete set of strain data by means of parametric derivatives and integration on the initial curve without correction. The process is repeated until the termination tolerance for the stress is less than 10 MPa. Usually, four iterations are needed to reach this tolerance. The corrections are bounded by the maximum of mechanical energy available to be converted into heat. The corrections are carried out until a true strain e = 4 in order to avoid the effects of flow localization in the material.
Pericardial Fat is Associated With Atrial Conduction: The Framingham Heart Study

Background Obesity is associated with altered atrial electrophysiology and a prominent risk factor for atrial fibrillation. Body mass index, the most widely used adiposity measure, has been related to atrial electrical remodeling. We tested the hypothesis that pericardial fat is independently associated with electrocardiographic measures of atrial conduction. Methods and Results We performed a cross‐sectional analysis of 1946 Framingham Heart Study participants (45% women) to determine the relation between pericardial fat and atrial conduction as measured by P wave indices (PWI): PR interval, P wave duration (P‐duration), P wave amplitude (P‐amplitude), P wave area (P‐area), and P wave terminal force (P‐terminal). We performed sex‐stratified linear regression analyses adjusted for relevant clinical variables and ectopic fat depots. Each 1‐SD increase in pericardial fat was significantly associated with PR interval (β=1.7 ms, P=0.049), P‐duration (β=2.3 ms, P<0.001), and P‐terminal (β=297 μV·ms, P<0.001) among women; and P‐duration (β=1.2 ms, P=0.002), P‐amplitude (β=−2.5 μV, P<0. 001), and P‐terminal (β=160 μV·ms, P=0.002) among men. Among both sexes, pericardial fat was significantly associated with P‐duration in analyses additionally adjusting for visceral fat or intrathoracic fat; a similar but non‐significant trend existed with P‐terminal. Among women, pericardial fat was significantly associated with P wave area after adjustment for visceral and intrathoracic fat. Conclusions Pericardial fat is associated with atrial conduction as quantified by PWI, even with adjustment for extracardiac fat depots. Further studies are warranted to identify the mechanisms through which pericardial fat may modify atrial electrophysiology and promote subsequent risk for arrhythmogenesis.
Validation of Faster Joint Control Strategy for Battery- and Supercapacitor-Based Energy Storage System

Energy storage system (ESS) is generally used to manage the intermittency of the renewable energy sources (RESs). The proper control strategy is needed to effectively maintain the power balance between the RESs, load demand, and ESS. The conventional control strategy for the hybrid energy storage system (HESS) uses the high-/low-pass filter method for system net power decomposition and the ESS power dispatch. In this paper, a new joint control strategy is proposed for photovoltaic-based dc grid system, with battery and supercapacitor (SC) as a HESS. The new joint control strategy utilizes the uncompensated power from the battery system to increase the performance of the overall HESS. The advantages of the proposed control strategy over the conventional control strategy are faster dc-link voltage restoration and effective power sharing between the battery and the SC. The detailed stability analysis of the proposed control strategy is also presented. The effectiveness of the proposed control strategy over the conventional control strategy is validated with the short-term and long-term experimental studies.
The nutrient profile of traditional Lebanese composite dishes: comparison with composite dishes consumed in France

Primary objective: To estimate the overall nutritional quality of traditional Lebanese dishes by calculating their nutrient profile. Methods: Fifty traditional Lebanese composite dishes (LD) were compared with 50 composite dishes consumed in France (FD), based on the SAIN (score of nutritional adequacy of individual foods) and LIM (score of nutrients to be limited) nutrient profiling system. Each dish was attributed to one of four nutrient profiling classes based on their SAIN and LIM values. The dishes’ distributions within the four classes and their content in selected nutrients and ingredient groups were compared. Results: LD had a better nutrient profile than FD (P <0.001). LD were richer in vitamin C and contained less proteins, saturated fatty acids, and sodium. They contained more vegetables and unrefined starches and less cheese and refined starches than FD. Conclusions: Nutrient profiles may help identify those composite dishes whose consumption should be encouraged to promote healthy eating in Lebanon.
Worst-Case Value-At-Risk and Robust Portfolio Optimization: A Conic Programming Approach

Classical formulations of the portfolio optimization problem, such as mean-variance or Value-at-Risk (VaR) approaches, can result in a portfolio extremely sensitive to errors in the data, such as mean and covariance matrix of the returns. In this paper we propose a way to alleviate this problem in a tractable manner. We assume that the distribution of returns is partially known, in the sense that onlybounds on the mean and covariance matrix are available. We define the worst-case Value-at-Risk as the largest VaR attainable, given the partial information on the returns' distribution. We consider the problem of computing and optimizing the worst-case VaR, and we show that these problems can be cast as semidefinite programs. We extend our approach to various other partial information on the distribution, including uncertainty in factor models, support constraints, and relative entropy information.
HeapShield : Library-Based Heap Overflow Protection for Free

While numerous approaches have been proposed to prevent stack overflows, heap overflows remain both a security vulnerability and a frequent source of bugs. Previous approaches to preventing these overflows require source code or can slow programs down by a factor of two or more. We present HeapShield, an approach that prevents all library-based heap overflows at runtime. It works with arbitrary, unaltered binaries. It incurs no space overhead and is efficient, imposing minimal impact on real application performance (2% on average).