Miracle-dz/UniFAR-FTUs huggingface dataset:
A Decision Support Model for Uncertainty Reasoning in Safety and Security Tasks

Performing safety and security tasks requires the continuous gathering and interpretation of information about objects to detect and predict events of interest. Especially, reasoning about objects' identities and intentions is crucial, but requires making use of heterogeneous information inherent with uncertainty. This makes such tasks very challenging for human operators and decision support systems are clearly needed. In this paper, we present a generic probabilistic logic model for the systematic representation and uncertainty reasoning about the identity and intentions of monitored objects. We apply the model to the area of maritime safety and security after incorporating domain specific knowledge. Experiments with simulated and real-world vessel data demonstrate the model's capabilities to draw conclusions about objects using uncertain information. The first-order probabilistic logic we use shows to be a very powerful tool to deal with dynamic amounts of information and objects. To our knowledge it is one of the few real-world applications of probabilistic logic.
Evolution of a Novel Muscle Design in Sea Urchins (Echinodermata: Echinoidea)

The sea urchin (Echinodermata: Echinoidea) masticatory apparatus, or Aristotle's lantern, is a complex structure composed of numerous hard and soft components. The lantern is powered by various paired and unpaired muscle groups. We describe how one set of these muscles, the lantern protractor muscles, has evolved a specialized morphology. This morphology is characterized by the formation of adaxially-facing lobes perpendicular to the main orientation of the muscle, giving the protractor a frilled aspect in horizontal section. Histological and ultrastructural analyses show that the microstructure of frilled muscles is largely identical to that of conventional, flat muscles. Measurements of muscle dimensions in equally-sized specimens demonstrate that the frilled muscle design, in comparison to that of the flat muscle type, considerably increases muscle volume as well as the muscle's surface directed towards the interradial cavity, a compartment of the peripharyngeal coelom. Scanning electron microscopical observations reveal that the insertions of frilled and flat protractor muscles result in characteristic muscle scars on the stereom, reflecting the shapes of individual muscles. Our comparative study of 49 derived “regular” echinoid species using magnetic resonance imaging (MRI) shows that frilled protractor muscles are found only in taxa belonging to the families Toxopneustidae, Echinometridae, and Strongylocentrotidae. The onset of lobe formation during ontogenesis varies between species of these three families. Because frilled protractor muscles are best observed in situ, the application of a non-invasive imaging technique was crucial for the unequivocal identification of this morphological character on a large scale. Although it is currently possible only to speculate on the functional advantages which the frilled muscle morphology might confer, our study forms the anatomical and evolutionary framework for future analyses of this unusual muscle design among sea urchins.
An Approach for Predicting Essential Genes Using Multiple Homology Mapping and Machine Learning Algorithms

Investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. In this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. We focused on 25 bacteria which have characterized essential genes. The predictions yielded the highest area under receiver operating characteristic (ROC) curve (AUC) of 0.9716 through tenfold cross-validation test. Proper features were utilized to construct models to make predictions in distantly related bacteria. The accuracy of predictions was evaluated via the consistency of predictions and known essential genes of target species. The highest AUC of 0.9552 and average AUC of 0.8314 were achieved when making predictions across organisms. An independent dataset from Synechococcus elongatus, which was released recently, was obtained for further assessment of the performance of our model. The AUC score of predictions is 0.7855, which is higher than other methods. This research presents that features obtained by homology mapping uniquely can achieve quite great or even better results than those integrated features. Meanwhile, the work indicates that machine learning-based method can assign more efficient weight coefficients than using empirical formula based on biological knowledge.
Individuals who are homozygous for the 2282del4 and R501X filaggrin null mutations do not always develop dermatitis and complete long‐term remission is possible

Background About 8–10% of the general population in Europe carry a null mutation in the filaggrin gene which is associated with early onset of atopic dermatitis as well as persistence into adulthood. No studies have investigated whether individuals with the homozygous filaggrin null genotype always develop dermatitis.
Requirement of the Pseudomonas aeruginosa tonB Gene for High-Affinity Iron Acquisition and Infection

ABSTRACT To investigate the contribution of the TonB protein to high-affinity iron acquisition in Pseudomonas aeruginosa, we constructed tonB-inactivated mutants from strain PAO1 and its derivative deficient in producing the siderophores pyoverdin and pyochelin. The tonB mutants could not grow in a free-iron-restricted medium prepared by apotransferrin addition, even though the medium was supplemented with each purified siderophore or with a heme source (hemoglobin or hemin). The tonBinactivation was shown to make P. aeruginosa unable to acquire iron from the transferrin with either siderophore. Introduction of a plasmid carrying the intact tonB gene restored growth of the tonB mutant of PAO1 in the free-iron-restricted medium without any supplements and restored growth of thetonB mutant of the siderophore-deficient derivative in the medium supplemented with pyoverdin, pyochelin, hemoglobin, or hemin. In addition, animal experiments showed that, in contrast to PAO1, thetonB mutant of PAO1 could not grow in vivo, such as in the muscles and lungs of immunosuppressed mice, and could not kill any of the animals. The in vivo growth ability and lethal virulence were also restored by introduction of the tonB-carrying plasmid in the tonB mutant. These results indicate clearly that the intact tonB gene—and, therefore, the TonB protein encoded by it—is essential for iron acquisition mediated by pyoverdin and pyochelin and via heme uptake in P. aeruginosa and suggest that the TonB-dependent iron acquisition may be essential for P. aeruginosa to infect the animal host.
Epidemiology of nosocomial fungal infections

This paper briefly reviews the current knowledge of the epidemiology and modes of transmission of nosocomial fungal infections and some of the therapeutic options for treating these diseases. In the mid-1980s, many institutions reported that fungi were common pathogens in nosocomial infections. Most, if not all, hospitals care for patients at risk for nosocomial fungal infections. The proportion in all nosocomial infections reportedly caused by Candida spp. increased from 2% in 1980 to 5% in 1986 to 1989. Numerous studies have identified common risk factors for acquiring these infections, most of which are very common among hospitalized patients; some factors act primarily by inducing immunosuppression (e.g., corticosteroids, chemotherapy, malnutrition, malignancy, and neutropenia), while others primarily provide a route of infection (e.g., extensive burns, indwelling catheter), and some act in combination. Non-albicans Candida spp. , including fluconazole-resistant C. krusei and Torulopsis (C.) glabrata, have become more common pathogens. Newer molecular typing techniques can assist in the determination of a common source of infection caused by several fungal pathogens. Continued epidemiologic and laboratory research is needed to better characterize these pathogens and allow for improved diagnostic and therapeutic strategies.
SoftMAC: Layer 2.5 Collaborative MAC for Multimedia Support in Multihop Wireless Networks

In this paper, we present the challenges in supporting multimedia, in particular, VoIP services over multihop wireless networks using commercial IEEE 802.11 MAC DCF hardware, and propose a novel software solution, called Layer 2.5 SoftMAC. Our proposed SoftMAC resides between the IEEE 802.11 MAC layer and the IP layer to coordinate the real-time (RT) multimedia and best-effort (BE) data packet transmission among neighboring nodes in a multihop wireless network. To effectively ensure acceptable VoIP services, channel busy time and collision rate need to be well controlled below appropriate levels. Targeted at this, our SoftMAC architecture employs three key mechanisms: 1) distributed admission control for regulating the load of RT traffic, 2) rate control for minimizing the impact of BT traffic on RT one, and 3) nonpreemptive priority queuing for providing high priority service to VoIP traffic. To evaluate the efficacy of these mechanisms, extensive simulations are conducted using the network simulator NS2. We also implement our proposed SoftMAC as a Windows network driver interlace specification (NDIS) driver and build a multihop wireless network testbed with 32 wireless nodes equipped with IEEE 802.11 a/b/g combo cards. Our evaluation and testing results demonstrate the effectiveness of our proposed software solution. Our proposed collaborative SoftMAC framework can also provide good support for A/V streaming in home networks where the network consists of hybrid WLAN (wireless LAN) and Ethernet
Dynamics of the fast solar tachocline. II. Migrating field

We present detailed numerical calculations of the fast solar tachocline based on the assumption that the dynamo field dominates over the dynamics of the tachocline. In the present paper of the series, we focus on three shortfalls of the earlier models. First, instead of the simple oscillating dipole poloidal field we study the more general magnetic field structures reminiscent of the butterfly diagram. The migrating field is prescribed as the observed axisymmetric radial magnetic field (Stenflo 1988, 1994). Our results are in good agreement with our analytical estimate and our previous works in Forgacs-Dajka & Petrovay (2001, 2002), but the polar dip in isorotational surfaces is strongly reduced in this case. On the other hand, a more realistic model should have a magnetic diffusivity decreasing significantly inside the radiative interior, so we also explore the effect of diffusivity and magnetic Prandtl number varying with depth. We found that the downwards decreasing magnetic diffusivity and Prandtl number have no significant effect on the solution, although the temporal variation of the tachocline thickness has decreased.
Spatiotemporal Smoothing as a Basis for Facial Tissue Tracking in Thermal Imaging

Accurate tracking of facial tissue in thermal infrared imaging is challenging because it is affected not only by positional but also physiological (functional) changes. This paper presents a particle filter tracker driven by a probabilistic template function with both spatial and temporal smoothing components, which is capable of adapting to abrupt positional and physiological changes. The method was tested on tracking facial regions of subjects under varying physiological and environmental conditions in 25 thermal clips. It demonstrated robustness and accuracy, outperforming other strategies. This new method promises improved performance in a number of biomedical applications that involve physiological measurements on the face, such as unobtrusive sleep and stress studies.
yMGV: a cross-species expression data mining tool

The yeast Microarray Global Viewer (yMGV @ http://transcriptome.ens.fr/ymgv) was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharo myces pombe microarray data sets published in 82 different articles. yMGV couples data mining tools with a user-friendly web interface so that, with a few mouse clicks, one can identify the conditions that affect the expression of a gene or list of genes regulated in a set of experiments. One of the major new features we present here is a set of tools that allows for inter-organism comparisons. This should enable the fission yeast community to take advantage of the large amount of available information on budding yeast transcriptome. New tools and ongoing developments are also presented here.
Chip to wafer copper direct bonding electrical characterization and thermal cycling

Copper direct bonding technology is considered to be one of the most promising approach for matching the miniaturization needs of future 3D integrated high performance circuits (3D-IC). In this study, we discuss the recent achievements in copper direct bonding technology with oxide/copper mixed surface and present the latest electrical and physical characterizations of chip to wafer bonding structures after annealing at 400°C and thermal cycling tests. In addition, electrical performance of chip to wafer bonding on 300mm wafers is also presented. Finally, thermo-mechanical finite element simulations showing the impact of the annealing conditions on the closure of the interface are shown.
Immuno-epidemiologic correlates of pandemic H1N1 surveillance observations: higher antibody and lower cell-mediated immune responses with advanced age.

BACKGROUND Pandemic H1N1 (pH1N1) surveillance data showed lower attack rates but higher risk of severe outcomes with advanced age. We explored immuno-epidemiologic correlates of surveillance findings including humoral and cell-mediated immunity (CMI). METHODS In an age-based design, ∼100 banked/residual sera per 10-year age stratum were assessed by hemagglutination inhibition (HI) and microneutralization (MN) assays for preexisting antibody to pH1N1 and recent seasonal H1N1 and H3N2 strains. In a separate birth cohort design defined by childhood influenza A/subtype priming (1919-1929: H1N1; 1945-1949: H1N1; 1958-1960: H2N2; 1969-1970: H3N2; 1978-1989: H3N2/H1N1), whole blood was collected from up to 50 volunteers per birth cohort. The ratio of Th1(IFN-γ):Th2(IL-10) cytokine responses was evaluated in vitro. RESULTS Antibody to seasonal viruses was highest in school-age children. Cross-reactive HI/MN antibody to pH1N1 was low among participants <70 years of age (yoa; 6%/4% ≥ 40), but seroprevalence increased at 70-79 yoa (27%/6%), increased even more at 80-89 yoa (65%/47%), and was highest at ≥90 yoa (88%/76%). CMI to pH1N1 was evident in all 5 birth cohorts but was lower compared with seasonal strains. There was little differentiation by subtype priming, but the Th1:Th2 ratio for all viruses dropped significantly in the 2 oldest cohorts. CONCLUSIONS Preexisting antibody may have protected the very old from pH1N1 infection, while diminished CMI may have contributed to greater severity once infected. In the young, cross-reactive pH1N1 antibody was mostly absent, while more intact CMI may have protected against severe outcomes.
A Bio-inspired Optimization Technique for Cluster Ensembles Optimization

Several clustering algorithms have been applied to a great variety of problems in different application domains. Each algorithm, however, has its own advantages and limitations, which can result in different solutions for the same problem. In this sense, combining different clustering algorithms (cluster ensembles) is one of the most used approaches, in an attempt to overcome the limitations of each clustering technique. The main aim is to combine multiple partitions generated by different clustering algorithms into a single clustering solution (consensus partition). To date, several approaches have been proposed in literature in order to provide optimization, or continuously improve the solutions found by the cluster ensembles. Therefore, as a contribution to this important subject, this paper presents a new bio-inspired optimization technique to optimize the cluster ensembles. In this proposed technique, the cluster ensembles are heterogeneously created and the initial partitions are combined through a method which uses the Coral Reefs Optimization algorithm, resulting in a consensus partition. In order to evaluate the feasibility of the proposed technique, an empirical analysis will be conducted using 15 different problems and applying two different indexes in order to examine its efficiency and feasibility.
Pearls & Oy-sters: Episodic ataxia type 2

A 38-year-old man presented to our clinic for evaluation of increasingly frequent spells of gait instability, diplopia, vertigo, and dysarthria. These spells began at 12 years of age. Initially, he experienced isolated periods of vertigo without accompanying symptoms. He told no family or friends of his problem at the time. Two years later, the symptoms progressed, manifesting as semistereotyped episodes characterized by a shock-like sensation radiating from his neck down his back followed by binocular diplopia, vertigo, gait instability, mental clouding, and nausea lasting 2–8 hours. Later, he experienced dysarthria during spells. Interictally, he returned to his baseline except for a persistent mild diplopia.
Intra-Transaction Parallelism in the Mapping of an Object Model to a Relational Multi-Processor System

We map an object model to a commercial relational multi-processor database system using replication and view materialisation to provide fast retrieval. To speed up complex update operations, we exploit intra-transaction parallelism by breaking such an operation down into shorter relational operations which are executed as parallel subtransactions of the update transaction. To ensure the correctness and recoverability of the operation’s execution, we use multi-level transactions. In addition, we minimise the resulting overhead for the logging of the compensating inverse operation required by the multi-level concept by logging the compensation for non-derived data only. In particular, we concentrate on the novel application of multi-level transaction management to efficiently maintain the replicated data and materialised views. We present a prototype implementation and give a performance evaluation of an exemplary set-oriented update statement.
Pomegranate Fruit as a Rich Source of Biologically Active Compounds

Pomegranate is a widely used plant having medicinal properties. In this review, we have mainly focused on the already published data from our laboratory pertaining to the effect of methanol extract of pericarp of pomegranate (PME) and have compared it with other relevant literatures on Punica. Earlier, we had shown its antiproliferative effect using human breast (MCF-7, MDA MB-231), and endometrial (HEC-1A), cervical (SiHa, HeLa), and ovarian (SKOV3) cancer cell lines, and normal breast fibroblasts (MCF-10A) at concentration of 20–320 μg/mL. The expressions of selected estrogen responsive genes (PR, pS2, and C-Myc) were downregulated by PME. Unlike estradiol, PME did not increase the uterine weight and proliferation in bilaterally ovariectomized Swiss-Albino mice models and its cardioprotective effects were comparable to that of 17β-estradiol. We had further assessed the protective role of PME on skeletal system, using MC3T3-E1 cells. The results indicated that PME (80 μg/mL) significantly increased ALP (Alkaline Phosphatase) activity, supporting its suggested role in modulating osteoblastic cell differentiation. The antiosteoporotic potential of PME was also evaluated in ovariectomized (OVX) rodent model. The results from our studies and from various other studies support the fact that pomegranate fruit is indeed a source of biologically active compounds.
Deterministic replay using processor support and its applications

The processor industry is at an inflection point. In the past, performance was the driving force behind the processor industry. But in the coming many-core era, improving programmability and reliability of the system will be at least as important as improving raw performance. To meet this vision, this thesis presents a processor feature that assists programmers in understanding software failures. Reproducing software failures is a significant challenge. The problem is severe especially for multi-threaded programs because the causes of failure can be non-deterministic in nature. The proposed processor feature continuously logs a program's execution while sacrificing very little performance (1%). If the program crashes, the developer can use the log to debug the failure by deterministically replaying every single instruction executed as part of the failed program's execution. Two key mechanisms enable this deterministic replay feature. One is BugNet, a checkpointing technique, which logs all of the non-deterministic input to a thread by logging the values of load instructions. The other is Strata, a logging primitive for recording shared-memory dependencies in a snoop-based or a directory-based shared-memory multi-processor. The former is sufficient for uni-processor systems and the later is required for multi-processor systems. As a proof-of-concept, this thesis presents a software implementation of BugNet replayer built using the Pin instrumentation tool. To understand the space requirements of the BugNet recorder for debugging, this thesis empirically quantifies how much of a program's execution need to be logged and replayed in order to understand the root cause of a majority of bugs. Finally, to demonstrate the utility of the deterministic replay feature, this thesis presents a software tool built using a deterministic replayer that finds data race bugs in shared-memory multi-threaded programs and automatically prioritizes them. The data race detection tool was built in collaboration with Microsoft. It has been used to find and fix data race bugs in production code, including Windows Vista and Internet Explorer.
The effects of a weighted vest on aggressive and self-injurious behavior in a child with autism

Objective: Analyse the effects of a weighted vest on the aggressive and self-injurious behavior of a young boy with autism. Methods: The effects of the weighted vest were examined during a functional analysis utilizing an ABAB design with an embedded multielement design, in which the participant wore a five pound weighted vest or no vest. Results: The results do not suggest the existence of a functional relationship between the use of a weighted vest and challenging behavior, as the weighted vest had no marked effect on levels of aggression and self-injurious behavior. Conclusions: Weighted vests are a commonly implemented form of sensory integration therapy, frequently used as a treatment for disruptive behaviors associated with autism spectrum disorder [Stephenson J, Carter M. The use of weighted vests with children with autism spectrum disorders and other disabilities. Journal of Autism and Developmental Disabilities 2009;39:105–114]. However, the current findings support previous literature which states that the use of weighted vests does not appear to decrease challenging behavior.