Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping frontal-limbic correlates of orienting to change detection

Orienting responses are elicited by salient stimuli, and may be indexed by skin conductance responses. Concurrent functional magnetic resonance imaging and skin conductance response recording was used to identify neural correlates of orienting to abrupt sensory change (infrequent high pitch oddball ‘target’ tones embedded in frequent lower pitch ‘standard’ tones) in 16 healthy participants. ‘With skin conductance response’ responses to targets were distinguished by preferentially greater activity in the amygdala and ventral medial and lateral frontal cortical regions. By contrast, ‘without skin conductance response’ responses elicited distinctive activity in the dorsal lateral frontal cortex and supramarginal gyrus. These findings suggest that orienting to unexpected sensory change elicits a network for appraising salience and novelty, whereas, in the absence of orienting, a parallel network for sensory and context evaluation is preferentially engaged.
DirectFix: Looking for Simple Program Repairs

Recent advances in program repair techniques have raised the possibility of patching bugs automatically. For an automatically generated patch to be accepted by developers, it should not only resolve the bug but also satisfy certain human-related factors including readability and comprehensibility. In this paper, we focus on the simplicity of patches (the size of changes). We present a novel semantics-based repair method that generates the simplest patch such that the program structure of the buggy program is maximally preserved. To take into account the simplicity of repairs in an efficient way (i.e., Without explicitly enumerating each repair candidate for each fault location), our method fuses fault localization and repair generation into one step. We do so by leveraging partial Max SAT constraint solving and component-based program synthesis. We compare our prototype implementation, Direct Fix, with the state-of-the-art semantics-based repair tool Sem Fix, that performs fault localization before repair generation. In our experiments with SIR programs and GNU Coreutils, Direct Fix generates repairs that are simpler than those generated by Sem Fix. Since both Direct Fix and Sem Fix are test-driven repair tools, they can introduce regressions for other tests which do not drive the repair. We found that Direct Fix causes substantially less regression errors than Sem Fix.
Comparative study for inference of hidden classes in stochastic block models

Inference of hidden classes in stochastic block models is a classical problem with important applications. Most commonly used methods for this problem involve naïve mean field approaches or heuristic spectral methods. Recently, belief propagation was proposed for this problem. In this contribution we perform a comparative study between the three methods on synthetically created networks. We show that belief propagation shows much better performance when compared to naïve mean field and spectral approaches. This applies to accuracy, computational efficiency and the tendency to overfit the data.
End-range mobilization techniques in adhesive capsulitis of the shoulder joint: A multiple-subject case report.

BACKGROUND AND PURPOSE The purpose of this case report is to describe the use of end-range mobilization techniques in the management of patients with adhesive capsulitis. CASE DESCRIPTION Four men and 3 women (mean age=50.2 years, SD=6.0, range=41-65) with adhesive capsulitis of the glenohumeral joint (mean disease duration=8.4 months, SD=3.3, range=3-12) were treated with end-range mobilization techniques, twice a week for 3 months. Indexes of pain, joint mobility, and function were measured by the same observer before treatment, after 3 months of treatment, and at the time of a 9-month follow-up. In addition, arthrographic assessment of joint capacity (ie, the amount of fluid the joint can contain) and measurement of range of motion of glenohumeral abduction on a plain radiograph were conducted initially and after 3 months of treatment. OUTCOMES After 3 months of treatment, there were increases in active range of motion. Mean abduction increased from 91 degrees (SD=16, range=70-120) to 151 degrees (SD=22, range=110-170), mean flexion in the sagittal plane increased from 113 degrees (SD=17, range=90-145) to 147 degrees (SD=18, range=115-175), and mean lateral rotation increased from 13 degrees (SD=13, range=0-40) to 31 degrees (SD=11, range=15-50). There were also increases in passive range of motion: Mean abduction increased from 96 degrees (SD=18, range=70-125) to 159 degrees (SD=24, range 110-180), mean flexion in the sagittal plane increased from 120 degrees (SD=16, range=95-145) to 154 degrees (SD=19, range=120-180), and mean lateral rotation increased from 21 degrees (SD=11, range=10-45) to 41 degrees (SD=8, range=35-55). The mean capacity of the glenohumeral joint capsule (its ability to contain fluid) increased from 10 cc (SD=3, range=6-15) to 15 cc (SD=3, range=10-20). Four patients rated their improvement in shoulder function as excellent, 2 patients rated it as good, and 1 patient rated it as moderate. All patients maintained their gain in joint mobility at the 9-month follow-up. DISCUSSION There seems to be a role for intensive mobilization techniques in the treatment of adhesive capsulitis. Controlled studies regarding the effectiveness of end-range mobilization techniques in the treatment of adhesive capsulitis are warranted.
DySign: dynamic fingerprinting for the automatic detection of android malware

The astonishing spread of Android OS, not only in smart phones and tablets but also in IoT devices, makes this operating system a very tempting target for malware threats. Indeed, the latter are expanding at a similar rate. In this respect, malware fingerprints, whether based on cryptographic or fuzzyhashing, are the first defense line against such attacks. Fuzzyhashing fingerprints are suitable for capturing malware static features. Moreover, they are more resilient to small changes in the actual static content of malware files. On the other hand, dynamic analysis is another technique for malware detection that uses emulation environments to extract behavioral features of Android malware. However, to the best of our knowledge, there is no such fingerprinting technique that leverages dynamic analysis and would act as the first defense against Android malware attacks. In this paper, we address the following question: could we generate effective fingerprints for Android malware through dynamic analysis? To this end, we propose DySign, a novel technique for fingerprinting Android malware’s dynamic behaviors. This is achieved through the generation of a digest from the dynamic analysis of a malware sample with respect to existing known malware. It is important to mention that: (i) DySign fingerprints are approximates of the observed behaviors during dynamic analysis so as to achieve resiliency to small changes in the behaviors of future malware variants; (ii) Fingerprint computation is agnostic to the analyzed malware sample or family. DySign leverages state-of-the-art Natural Language Processing (NLP) techniques to generate the aforementioned fingerprints, which are then leveraged to build an enhanced Android malware detection system with family attribution. The evaluation of the proposed system on both real-life malware and benign apps demonstrates a good detection performance with high scalability.
Characterization of infectious molecular clones of simian immunodeficiency virus (SIVmac) and human immunodeficiency virus type 2: persistent infection of rhesus monkeys with molecularly cloned SIVmac

Infection of macaque monkeys with simian immunodeficiency virus (SIV) is probably the best animal model currently available for studying acquired immunodeficiency syndrome. In this report, we describe three infectious molecular clones of SIVmac and one of human immunodeficiency virus type 2 (HIV-2) and their use in the study of cell and species specificity, animal infection, and the relationship of gene sequence to function. Replication of the cloned viruses in different cell lines varied dramatically. Some human CD4+ cell lines (HUT 78 and MT-4) supported the replication of SIVmac and HIV-2, while others (CEM and Jurkat-T) supported the replication of HIV-2 but not SIVmac. Growth of cloned virus in macaque lymphocytes in vitro was predictive of macaque infection in vivo. Macaque lymphocytes supported the replication of SIVmac239 and SIVmac251 but not SIVmac142 or HIV-2ROD. Using virus recovery and antibody response as criteria for infection, macaques that received cloned SIVmac251 and SIVmac239 became infected, while macaques receiving cloned SIVmac142 and HIV-2ROD did not become infected. Nucleotide sequences from the envelope region of all four cloned viruses demonstrated that there is considerable flexibility in the location of the translational termination (stop) signal. These infectious molecular clones will be very useful for future studies directed at the molecular basis for persistence, pathogenicity, tropism, and cell and species specificity.
Impact of the landslide for a Relationship between Rainfall Condition and Land Cover in North Vietnam

This paper aims to evaluate the probability of landslide hazards using a physical model (TRIGRS: Transient Rainfall Infiltration and Grid-Based Region Slope-Stability) for a regional scale considering the variations of a triggering rainfall condition and land-cover under the climate change. There are certain uncertainties raising from the soil properties and soil depth determination, assumption of groundwater, as well as the same root cohesion for all tree cover in the forest-related region. However, the application of TRIGRS model in a regional scale would provide important references for the distribution of landslide prone area regarding scenarios about changes of weather condition and land cover situation. It thus would support local authorities in obtaining more adequate land planning strategies in a river basin to mitigate potential hazard from the slope failure issue.
Antimetastatic role of Smad4 signaling in colorectal cancer.

BACKGROUND & AIMS Transforming growth factor (TGF)-beta signaling occurs through Smads 2/3/4, which translocate to the nucleus to regulate transcription; TGF-beta has tumor-suppressive effects in some tumor models and pro-metastatic effects in others. In patients with colorectal cancer (CRC), mutations or reduced levels of Smad4 have been correlated with reduced survival. However, the function of Smad signaling and the effects of TGF-beta-receptor kinase inhibitors have not been analyzed during CRC metastasis. We investigated the role of TGF-beta/Smad signaling in CRC progression. METHODS We evaluated the role of TGF-beta/Smad signaling on cell proliferation, migration, invasion, tumorigenicity, and metastasis in Smad4-null colon carcinoma cell lines (MC38 and SW620) and in those that transgenically express Smad4. We also determined the effects of a TGF-beta-receptor kinase inhibitor (LY2109761) in CRC tumor progression and metastasis in mice. RESULTS TGF-beta induced migration/invasion, tumorigenicity, and metastasis of Smad4-null MC38 and SW620 cells; incubation with LY2109761 reversed these effects. In mice, LY2109761 blocked metastasis of CRC cells to liver, inducing cancer cell expression of E-cadherin and reducing the expression of the tumorigenic proteins matrix metalloproteinase-9, nm23, urokinase plasminogen activator, and cyclooxygenase-2. Transgenic expression of Smad4 significantly reduced the oncogenic potential of MC38 and SW620 cells; in these transgenic cells, TGF-beta had tumor suppressor, rather than tumorigenic, effects. CONCLUSIONS TGF-beta/Smad signaling suppresses progression and metastasis of CRC cells and tumors in mice. Loss of Smad4 might underlie the functional shift of TGF-beta from a tumor suppressor to a tumor promoter; inhibitors of TGF-beta signaling might be developed as CRC therapeutics.
Prp 22 and spliceosome components regulate chromatin dynamics in germline polyploid cells

During Drosophila oogenesis, the endopolyploid nuclei of germ-line nurse cells undergo a dramatic shift in morphology as oogenesis progresses; the easily-visible chromosomes are initially polytenic during the early stages of oogenesis before they transiently condense into a distinct ‘5-blob’ configuration, with subsequent dispersal into a diffuse state. Mutations in many genes, with diverse cellular functions, can affect the ability of nurse cells to fully decondense their chromatin, resulting in a ‘5-blob arrest’ phenotype that is maintained throughout the later stages of oogenesis. However, the mechanisms and significance of nurse-cell (NC) chromatin dispersal remain poorly understood. Here, we report that a screen for modifiers of the 5-blob phenotype in the germ line isolated the spliceosomal gene peanuts, the Drosophila Prp22. We demonstrate that reduction of spliceosomal activity through loss of peanuts promotes decondensation defects in NC nuclei during midoogenesis. We also show that the Prp38 spliceosomal protein accumulates in the nucleoplasm of nurse cells with impaired peanuts function, suggesting that spliceosomal recycling is impaired. Finally, we reveal that loss of additional spliceosomal proteins impairs the full decondensation of NC chromatin during later stages of oogenesis, suggesting that individual spliceosomal subcomplexes modulate expression of the distinct subset of genes that are required for correct morphology in endopolyploid nurse cells. Citation: Klusza S, Novak A, Figueroa S, Palmer W, Deng W-M (2013) Prp22 and Spliceosome Components Regulate Chromatin Dynamics in Germ-Line Polyploid Cells. PLoS ONE 8(11): e79048. doi:10.1371/journal.pone. 0079048 Editor: Eduardo Moreno, University of Bern, Switzerland Received May 3, 2013; Accepted September 18, 2013; Published November 7, 2013 Copyright: ß 2013 Klusza et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by National Institutes of Health (NIH) grant R01 GM072562 (http://www.nih.gov) and National Science Foundation Grant IOS1052333 (http://www.nsf.gov). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: wumin@bio.fsu. edu ¤a Current address: Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America ¤b Current address: College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom ¤c Current address: College of Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
Pharmacological Properties of ABT-239 [4-(2-{2-[(2R)-2-Methylpyrrolidinyl]ethyl}-benzofuran-5-yl)benzonitrile]: I. Potent and Selective Histamine H3 Receptor Antagonist with Drug-Like Properties

Histamine H3 receptor antagonists are being developed to treat a variety of neurological and cognitive disorders that may be ameliorated by enhancement of central neurotransmitter release. Here, we present the in vitro pharmacological and in vivo pharmacokinetic profiles for the nonimidazole, benzofuran ligand ABT-239 [4-(2-{2-[(2R)-2-methylpyrrolidinyl]ethyl}-benzofuran-5-yl)benzonitrile] and compare it with several previously described imidazole and nonimidazole H3 receptor antagonists. ABT-239 binds to recombinant human and rat H3 receptors with high affinity, with pKi values of 9.4 and 8.9, respectively, and is over 1000-fold selective versus human H1, H2, and H4 histamine receptors. ABT-239 is a potent H3 receptor antagonist at recombinant human and rat receptors, reversing agonist-induced changes in cAMP formation (pKb = 7.9 and 7.6, respectively), guanosine 5′-O-(3-[35S]thio) triphosphate ([35S]GTPγS) binding (pKb = 9.0 and 8.3, respectively), and calcium mobilization (human pKb = 7.9). ABT-239 also competitively reversed histamine-mediated inhibition of [3H]histamine release from rat brain cortical synaptosomes (pKb = 7.7) and agonist-induced inhibition of contractile responses in electric field stimulated guinea pig ileal segments (pA2 = 8.7). Additionally, ABT-239 is a potent inverse agonist, inhibiting constitutive [35S]GTPγS binding at both rat and human H3 receptors with respective pEC50 values of 8.9 and 8.2. ABT-239 demonstrates good pharmacokinetic characteristics in rat, dog, and monkey with t1/2 values ranging from 4 to 29 h, corresponding with clearance values and metabolic turnover in liver microsomes from these species, and good oral bioavailability ranging from 52 to 89%. Thus, ABT-239 is a selective, nonimidazole H3 receptor antagonist/inverse agonist with similar high potency in both human and rat and favorable drug-like properties.
Antigenic specificity of convalescent serum from cattle with haemophilus somnus-induced experimental abortion

The antigens of Haemophilus somnus recognized by convalescent bovine serum were studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting with a protein A-peroxidase conjugate. The same two 76K and 40K antigens were predominant in whole-bacterium preparations and in outer-membrane-enriched, Triton X-100-insoluble fractions. The surface location of these two antigens was confirmed by absorbing antiserum with whole, live bacteria. Absorption with H. somnus removed antibody reactivity for the 76K antigen and reduced reactivity for the 40K antigen. Absorption with Pasteurella multocida, Actinobacillus equuli, or Escherichia coli did not reduce reactivity, and results with Pasteurella haemolytica were equivocal. The two immunodominant antigens detected in this study were conserved in isolates of H. somnus from thromboembolic meningoencephalitis, pneumonia, reproductive failure, or asymptomatic carriers. Convalescent sera from nearly all 17 cattle studied recognized these two antigens. Other antigens were recognized less consistently. Although other antigens may also be involved, the 76K and 40K surface antigens of H. somnus appear to be important candidates for a subunit vaccine or an immunodiagnostic assay.
Functional neuroanatomy of human sleep states after zolpidem and placebo: A H215O‐PET study

Changes in the functional organization of the brain during the course of sleep and waking are reflected by different patterns of regional cerebral blood flow (rCBF). To investigate the effect of the hypnotic zolpidem, a benzodiazepine receptor agonist, drug or placebo were administered to eight young, healthy men prior to bedtime. The subjects were sleep‐deprived to promote sleep during the 4‐h recording period in the positron emission tomography scanner. Intravenous injections of labelled water were administered during pre‐drug wakefulness, and during Stage 2, Stage 4 and rapid eye movement (REM) sleep, each injection being followed by an emission scan. Statistical parametric mapping was used to investigate the effects of treatment and sleep states. During sleep (combined Stages 2 and 4, and REM sleep) relative rCBF was lower after zolpidem than after placebo in the basal ganglia and insula, and higher in the parietal cortex. A ‘multiple study’ analysis of REM sleep revealed that rCBF in the anterior cingulum was lower after zolpidem than after placebo, whereas rCBF in the occipital and parietal cortex, parahippocampal gyrus and cerebellum was higher. When the pooled data (drug and placebo) of Stages 2 and 4 were compared with wakefulness, rCBF was lower in prefrontal cortex and insula, and higher in the occipital and parietal cortex. The results indicate that some differences in rCBF from wakefulness to non‐REM sleep are further augmented by zolpidem.
Spatial duty cycle model for Cognitive Radio

Spectrum occupancy modeling in the context of Dynamic Spectrum Access/Cognitive Radio (DSA/CR) constitutes a rather unexplored research area that still requires much more effort. This paper addresses the problem of modeling spectrum occupancy in the spatial domain by proposing a novel theoretical approach that enables modeling the occupancy level perceived at any geographical location based on the knowledge of some simple primary signal parameters. The validity of the theoretical model is verified with extensive empirical measurement results. Some examples of its potential applicability are discussed as well.
Broadband learning for doctors

Has huge potential but needs funding for high quality content B roadband internet has finally come of age. It's changing the way we listen to music and radio, and it means we can watch television on demand. What could broadband internet do for medical education? Early signs suggest that rapid change is underway, led by the learners. In the United States 14% of the credit hours for continuous medical education in 2004 were obtained online, double the figure for two years before.1 In this country BMJ Learning has tapped into this demand, attracting more than 60 000 registered users in less than three years.2 Broadband could offer learners in medicine the next generation of online learning: the prospect of high quality interactive video and audio alongside traditional text and photographs. Audiovisual materials would bring many advantages: they are easy to watch, add realism, and can enable learning of procedural and interpersonal skills. Younger doctors are digital natives and will increasingly expect such materials as the norm. But …
CHANGING CONCEPTS IN PARKINSON DISEASE: MOVING BEYOND THE DECADE OF THE BRAIN

I congratulate Marras and Lang1 on their invited article concerning the changing concepts in Parkinson disease (PD). They provide three alternatives to define PD: 1) a clinical syndrome dominated by levodopa responsive parkinsonism; 2) a neuropathologic entity characterized by degeneration of the substantia nigra and formation of Lewy bodies; or 3) levodopa responsive parkinsonism associated with Lewy bodies. They opt for “an adult onset progressive disorder dominated by parkinsonism responsive to levodopa and commonly associated with motor complications. ”1 The authors had previously termed this “classic parkinsonism. ” I agree with Marras and Lang’s implicit view that clinicians need an accurate, nonspeculative, working definition for what can …