Miracle-dz/UniFAR-FTUs huggingface dataset:
Astrocyte Dysfunction Induced by Alcohol in Females but Not Males

Chronic alcohol abuse is associated with brain damage in a sex‐specific fashion, but the mechanisms involved are poorly described and remain controversial. Previous results have suggested that astrocyte gene expression is influenced by ethanol intoxication and during abstinence in vivo. Here, bioinformatic analysis of astrocyte‐enriched ethanol‐regulated genes in vivo revealed ubiquitin pathways as an ethanol target, but with sexually dimorphic cytokine signaling and changes associated with brain aging in females and not males. Consistent with this result, astrocyte activation was observed after exposure in female but not male animals, with reduced S100β levels in the anterior cingulate cortex and increased GFAP+ cells in the hippocampus. In primary culture, the direct effects of chronic ethanol exposure followed by recovery on sex‐specific astrocyte function were examined. Male astrocyte responses were consistent with astrocyte deactivation with reduced GFAP expression during ethanol exposure. In contrast, female astrocytes exhibited increased expression of Tnf, reduced expression of the neuroprotective cytokine Tgfb1, disrupted bioenergetics and reduced excitatory amino acid uptake following exposure or recovery. These results indicate widespread astrocyte dysfunction in ethanol‐exposed females and suggest a mechanism that may underlie increased vulnerability to ethanol‐induced neurotoxicity in females.
Automated Tagging for the Retrieval of Software Resources in Grid and Cloud Infrastructures

A key challenge for Grid and Cloud infrastructures is to make their services easily accessible and attractive to end-users. In this paper we introduce tagging capabilities to the Miner soft system, a powerful tool for software search and discovery in order to help end-users locate application software suitable to their needs. Miner soft is now able to predict and automatically assign tags to software resources it indexes. In order to achieve this, we model the problem of tag prediction as a multi-label classification problem. Using data extracted from production-quality Grid and Cloud computing infrastructures, we evaluate an important number of multi-label classifiers and discuss which one and with what settings is the most appropriate for use in the particular problem.
Authorship Attribution of Android Apps

Since the first computer virus hit the Advanced Research Projects Agency Network (ARPANET) in the early 1970s, the security community interest revolved around ways to expose the identities of malware writers. Knowledge of the adversarial identities promised additional leverage to security experts in their ongoing battle against those perpetrators. At the dawn of computing era, when malware writers and malicious software were characterized by the lack of experience and relative simplicity, the task of uncovering the identities of virus writers was more or less straightforward. Manual analysis of source code often revealed personal, identifiable information embedded by authors themselves. But these times have long gone. Modern day's malware writers extensively use numerous malware code generators to mass produce new variants and employ advanced obfuscation techniques to hide their identities. As a result the work of security experts trying to uncover the identities of malware writers became significantly more challenging and time consuming. To gain insight into the identity of an adversary, we turn our attention to authorship attribution research, which offers a broad spectrum of techniques for identifying an author of a document, based on the analysis of an author's writing style. Equipped with these methods, we explore attribution of Android binaries and the role of features related to the development process on the determination of Android binary authorship. Within this context, we propose an incremental approach to perform authorship attribution of Android apps. First to a set of known authors and then the generation of new profiles for unknown apps. We assess the effectiveness of our approach on several sets of malicious and legitimate Android binaries produced by actual developers, as opposed to using artificially created authors' data. We achieve 97.5% accuracy on these authors» data. We further evaluate our approach on more than 131,000 apps collected from various sources including 10 different markets around the globe.
Edinburgh Research Explorer Expression of Barhl2 and its relationship with Pax6 expression in the forebrain of the mouse embryo

Background: The transcription factor Barhl2 is an antiproneural transcription factor with roles in neuronal differentiation. The functions of its homologue in Drosophila development are better understood than its functions in mammalian brain development. Existing evidence suggests that its expression in the embryonic forebrain of the mouse is regional and may complement that of another transcription factor that is important for forebrain development, Pax6. The aim of this study is to provide a more detailed description of the Barhl2 expression pattern in the embryonic forebrain than is currently available, to relate its expression domains to those of Pax6 and to examine the effects of Pax6 loss on Barhl2 expression. Results: We found that Barhl2 is expressed in the developing diencephalon from the time of anterior neural tube closure. Its expression initially overlaps that of Pax6 in a central region of the alar diencephalon but over the following days their domains of expression become complementary in most forebrain regions. The exceptions are the thalamus and pretectum, where countergradients of Pax6 and Barhl2 expression are established by embryonic day 12.5, before overall Pax6 levels in these regions decline greatly while Barhl2 levels remain relatively high. We found that Barhl2 expression becomes upregulated in specifically the thalamus and pretectum in Pax6 -null mice. Conclusions: The region-specific expression pattern of Barhl2 makes it likely to be an important player in the development of region-specific differences in embryonic mouse forebrain. Repression of its expression in the thalamus and pretectum by Pax6 may be crucial for allowing proneural factors to promote normal neuronal differentiation in this region.
Acupuncture with Planning Treatment According to Diagnosis: A Trial Study of Protocol and its Effects for Stiff Shoulder

Background: In order to standardize an effective acupuncture therapy for chronic dull pain and stiffness of neck and shoulder, we made a protocol characterized with planning treatment according to diagnosis and examined its availability. Methods and findings: Thirty-two patients were categorized into three groups based on the pathophysiology of Traditional Chinese Medicine: Blood stasis due to Qi stagnancy (Group-1), Deficiency of Liver-blood (Group-2), Yin deficiency of Liver and Kidney (Group-3) according to their subjective symptoms and signs. Acupuncture treatment was performed once a week over a two week period in accordance with the protocol that was arranged to each group. The averaged VAS values after the 3rd therapy in the whole groups decreased significantly (p<0.01) as compared with that of the initial visit before therapy. Investigating each group, the averaged VAS value after the 3rd therapy in Group 1 was significantly (p<0.05) lower than that of the initial visit at baseline. In other groups, although the VAS scores showed a gradual decrease according to the treatment, there was unfortunately no significance in the changes of the VAS. There were no side effects in all the treatment of this study. Conclusions: These results indicate that the present study protocol would be effective in relieving the patient’s subjective symptoms, and it would alternatively provide an effective and safe medical treatment for stiff neck and shoulder, although it should be modified for Groups 2 and 3.
Gender difference in the association between brachial-ankle pulse wave velocity and cardiovascular risk scores

Background/Aims Although brachial-ankle pulse wave velocity (baPWV) has been validated as a novel method to predict the cardiovascular risk in general population, the relevance of baPWV to the traditional risk scores has not been clearly revealed. This study investigated the relationship between baPWV and four different cardiovascular risk-predicting scores in men and women. Methods A total of 539 subjects (58.1 ± 12.2 years, 50.1% men) without cardiovascular disease (CVD) who underwent health examinations including baPWV measurement were retrospectively analyzed. Four cardiovascular risk scores (Framingham risk score [FRS; 1998], Adult Treatment Panel [ATP] III revised FRS [2002], generalized FRS [2008], and American College of Cardiology/American Heart Association [ACC/AHA] CVD risk [2013]) were calculated in each subject. Results In a total population, baPWV was moderately correlated with four cardiovascular risk scores (r = 0.577 for FRS; r = 0.594 for ATP III revised FRS; r = 0.589 for generalized FRS; r = 0.571 for ACC/AHA CVD risk; p < 0.001 for each). These correlations were stronger in women than in men (r = 0.649 vs. 0.451 for FRS; r = 0.719 vs. 0.411 for ATP III revised FRS; r = 0.735 vs. 0.540 for generalized FRS; r = 0.699 vs. 0.552 for ACC/AHA CVD risk; p for gender difference ≤ 0.005 for each). Conclusions In middle-aged and elderly Koreans without CVD, baPWV was identified as having a moderately positive correlation with four different risk scores. The correlation was stronger in women than in men, implying the better performance of baPWV in women for predicting cardiovascular risk of healthy population.
Analysis of Network structures to support scientific collaboration Analyse van netwerkstructuren voor de ondersteuning van wetenschappelijke samenwerking

Previous Research The "Evolution, Complexity and Cognition" group within the Center Leo Apostel has over ten years of experience in using network models to analyze socially distributed knowledge, and thus to support collective information retrieval and problem-solving [Heylighen, 1999]. This approach has been applied mostly to the World-Wide Web and electronic document collections, using the ways users traverse hyperlinks between webpages to find which pages are related to each other [Bollen & Heylighen, 1996; Heylighen & Bollen, 2002]. A more recent application is societal-scale collective decision-making via the network-based delegation of voting powers [Rodriguez & Steinbock, 2004].
A quantitative assessment of using the Kinect for Xbox 360 for respiratory surface motion tracking

This paper describes a quantitative assessment of the Microsoft Kinect for X-box360TM for potential application in tracking respiratory and body motion in diagnostic imaging and external beam radiotherapy. However, the results can also be used in many other biomedical applications. We consider the performance of the Kinect in controlled conditions and find mm precision at depths of 0.8-1.5m. We also demonstrate the use of the Kinect for monitoring respiratory motion of the anterior surface. To improve the performance of respiratory monitoring, we fit a spline model of the chest surface through the depth data as a method of a marker-less monitoring of a respiratory motion. In addition, a comparison between the Kinect camera with and without zoom lens and a marker-based system was used to evaluate the accuracy of using the Kinect camera as a respiratory tracking system.
Interactions of HIV-1 Inhibitory Peptide T20 with the gp41 N-HR Coiled Coil*

Cellular entry of human immunodeficiency virus type 1 (HIV-1) involves fusion of viral and cellular membranes and is mediated by structural transitions in viral glycoprotein gp41. The antiviral C-peptide T20 targets the gp41 N-terminal heptad repeat region (N-HR), blocking gp41 conformational changes essential for the entry process. To probe the T20 structure-activity relationship, we engineered a molecular mimic of the entire gp41 N-HR coiled coil using the 5-Helix design strategy. T20 bound this artificial protein (denoted 5H-ex) with nanomolar affinity (KD = 30 nm), close to its IC50 concentration (∼3 nm) but much weaker than the affinity of a related inhibitory C-peptide C37 (KD = 0.0007 nm). T20/C37 competitive binding assays confirmed that T20 interacts with the hydrophobic groove on the surface of the N-HR coiled coil outside of a deep pocket region crucial for C37 binding. We used 5H-ex to investigate how the T20 N and C termini contributed to the inhibitor binding activity. Mutating three aromatic residues at the T20 C terminus (WNWF → ANAA) had no effect on affinity, suggesting that these amino acids do not participate in T20 binding to the gp41 N-HR. The results support recent evidence pointing to a different role for these residues in T20 inhibition (Peisajovich, S. G., Gallo, S. A., Blumenthal, R., and Shai, Y. (2003) J. Biol. Chem. 278, 21012–21017; Liu, S. , Jing, W. , Cheung, B. , Lu, H. , Sun, J., Yan, X. , Niu, J., Farmar, J., Wu, S. , and Jiang, S. (2007) J. Biol. Chem. 282, 9612–9620). By contrast, mutations near the T20 N terminus substantially influenced inhibitor binding strength. When Ile was substituted for Thr in the second T20 position, a 40-fold increase in binding affinity was measured (KD = 0.75 nm). The effect of this affinity enhancement on T20 inhibitory potency varied among different viral strains. The original T20 and the higher affinity T20 variant had similar potency against wild type HIV-1. However, the higher affinity T20 variant was significantly more potent against T20-resistant virus. The findings suggest that other factors in addition to binding affinity play a role in limiting T20 potency. As a mimetic of the complete gp41 N-HR coiled coil region, 5H-ex will be a useful tool to further elucidate mechanistic profiles of C-peptide inhibitors.
AFLP Genome Scan to Detect Genetic Structure and Candidate Loci under Selection for Local Adaptation of the Invasive Weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B. K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.
Mycobiome of Cysts of the Soybean Cyst Nematode Under Long Term Crop Rotation

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe (Phylum Nematoda), is a major pathogen of soybean. It causes substantial yield losses worldwide and is difficult to control because the cyst protects the eggs which can remain viable for nearly a decade. Crop rotation with non-host crops and use of biocontrol organisms such as fungi and bacteria offer promising approaches, but remain hampered by lack of knowledge of the biology of nematode parasitic organisms. We used a high-throughput metabarcoding approach to characterize fungal communities associated with the SCN cyst, a microenvironment in soil that may harbor both nematode parasites and plant pathogens. SCN cysts were collected from a long-term crop rotation experiment in Southeastern Minnesota at three time points over two growing seasons to characterize diversity of fungi inhabiting cysts and to examine how crop rotation and seasonal variation affects fungal communities. A majority of fungi in cysts belonged to Ascomycota and Basidiomycota, but the presence of several early diverging fungal subphyla thought to be primarily plant and litter associated, including Mortierellomycotina and Glomeromycotina (e.g., arbuscular mycorrhizal fungi), suggests a possible role as nematode egg parasites. Species richness varied by both crop rotation and season and was higher in early years of crop rotation and in fall at the end of the growing season. Crop rotation and season also impacted fungal community composition and identified several classes of fungi, including Eurotiomycetes, Sordariomycetes, and Orbiliomycetes (e.g., nematode trapping fungi), with higher relative abundance in early soybean rotations. The relative abundance of several genera was correlated with increasing years of soybean. Fungal communities also varied by season and were most divergent at midseason. The percentage of OTUs assigned to Mortierellomycotina_cls_Incertae_sedis and Sordariomycetes increased at midseason, while Orbiliomycetes decreased at midseason, and Glomeromycetes increased in fall. Ecological guilds of fungi containing an animal-pathogen lifestyle, as well as potential egg-parasitic taxa previously isolated from parasitized SCN eggs, increased at midseason. The animal pathogen guilds included known (e.g., Pochonia chlamydosporia) and new candidate biocontrol organisms. This research advances knowledge of the ecology of nematophagous fungi in agroecosystems and their use as biocontrol agents of the SCN.
Direct endovascular treatment: an alternative for bridging therapy in anterior circulation large‐vessel occlusion stroke

Whether intravenous thrombolysis prior to endovascular treatment in patients with anterior circulation large‐vessel occlusion (LVO) is indispensable remains unclear. The aim was to retrospectively compare, in a Chinese population, the effectiveness and safety of direct endovascular treatment (DEVT) initiated within 4.5 h after onset with bridging therapy in acute anterior circulation LVO stroke patients.
Early detection of consciousness in patients with acute severe traumatic brain injury

&NA; See Schiff (doi:10.1093/awx209) for a scientific commentary on this article. Patients with acute severe traumatic brain injury may recover consciousness before self‐expression. Without behavioural evidence of consciousness at the bedside, clinicians may render an inaccurate prognosis, increasing the likelihood of withholding life‐sustaining therapies or denying rehabilitative services. Task‐based functional magnetic resonance imaging and electroencephalography techniques have revealed covert consciousness in the chronic setting, but these techniques have not been tested in the intensive care unit. We prospectively enrolled 16 patients admitted to the intensive care unit for acute severe traumatic brain injury to test two hypotheses: (i) in patients who lack behavioural evidence of language expression and comprehension, functional magnetic resonance imaging and electroencephalography detect command‐following during a motor imagery task (i.e. cognitive motor dissociation) and association cortex responses during language and music stimuli (i.e. higher‐order cortex motor dissociation); and (ii) early responses to these paradigms are associated with better 6‐month outcomes on the Glasgow Outcome Scale‐Extended. Patients underwent functional magnetic resonance imaging on post‐injury Day 9.2 ± 5.0 and electroencephalography on Day 9.8 ± 4.6. At the time of imaging, behavioural evaluation with the Coma Recovery Scale‐Revised indicated coma (n = 2), vegetative state (n = 3), minimally conscious state without language (n = 3), minimally conscious state with language (n = 4) or post‐traumatic confusional state (n = 4). Cognitive motor dissociation was identified in four patients, including three whose behavioural diagnosis suggested a vegetative state. Higher‐order cortex motor dissociation was identified in two additional patients. Complete absence of responses to language, music and motor imagery was only observed in coma patients. In patients with behavioural evidence of language function, responses to language and music were more frequently observed than responses to motor imagery (62.5–80% versus 33.3–42.9%). Similarly, in 16 matched healthy subjects, responses to language and music were more frequently observed than responses to motor imagery (87.5–100% versus 68.8–75.0%). Except for one patient who died in the intensive care unit, all patients with cognitive motor dissociation and higher‐order cortex motor dissociation recovered beyond a confusional state by 6 months. However, 6‐month outcomes were not associated with early functional magnetic resonance imaging and electroencephalography responses for the entire cohort. These observations suggest that functional magnetic resonance imaging and electroencephalography can detect command‐following and higher‐order cortical function in patients with acute severe traumatic brain injury. Early detection of covert consciousness and cortical responses in the intensive care unit could alter time‐sensitive decisions about withholding life‐sustaining therapies.