Miracle-dz/UniFAR-FTUs huggingface dataset:
Symbolic representation of optic nerve head cup presents difference in patients with Primary Open Angle Glaucoma

The aim of this study was to semantically represent the shape feature of the surface of the optic nerve cupping, that cannot be represented by a single number, using Symbolic Aggregate Approximation (SAX). For this purpose, 114 reports of the Heidelberg Retina Tomograph (HRT) from clinical studies of the Laboratory of Research and Applications in Ophthalmology of Aristotle Univ. Thessaloniki, corresponding to 97 normal subjects and 97 patients with Primary Open Angle Glaucoma (POAG) classified by glaucoma experts after full clinical examination, were used. These reports were exported as TIFF images including the results from HRT analysis. By use of an in-house MATLAB application, optic cup contour was unwrapped with respect to the centroid of the cup surface and thus the 2-d shape of the cup surface contour was transformed to 1-d data series. The min symbolic distance distance(mindist) of the 1-d data series was then calculated for each pair of reports and the results were arranged into three groups Glaucoma-Glaucoma, Normal-Normal and Glaucoma-Normal (GG,NN,GN) depending on the initial classification of the reports. Comparing the means of mindist between the 3 groups, statistically significant differences were found (ANOVA, p<.05). Statistically significant difference among the three distributions of the mindist was confirmed by non parametric Independent-Samples Kruskal-Wallis Test (p<.001). These findings suggest that the symbolic representation of the optic cup surface could be used to unveil features of the phenotype of glaucoma that cannot be spotted by the currently measured quantitative stereometric parameters.
Hepatitis C-Associated Mixed Cryoglobulinemic Vasculitis Induces Differential Gene Expression in Peripheral Mononuclear Cells

This study examines the distinct gene expression profile of peripheral blood mononuclear cells from patients with chronic hepatitis C infection and mixed cryoglobulinemic (MC) vasculitis. Our DNA microarray analysis indicates that hepatitis C virus (HCV)-associated MC vasculitis is characterized by compromised neutrophil function, impaired chemotaxis, and increased interferon-stimulated gene (ISG) expression, contributing to overall MC pathogenesis and end-organ damage. Increased ISG expression is suggestive of an enhanced endogenous interferon gene signature. PBMC depletion assays demonstrate that this increased expression is likely due to an activation of monocytes and not a direct result of B cell expansion. Notably, this monocyte activation of ISG expression in HCV-associated MC vasculitis suggests a poor predictor status of interferon-based treatment. Further analysis of PBMC gene expression profiles before and after in vivo B cell depletion therapy is critical to completely understanding the mechanisms of MC vasculitis pathogenesis.
Regulation of the Functions of Natural Cytotoxicity Receptors by Interactions with Diverse Ligands and Alterations in Splice Variant Expression

The natural cytotoxicity receptor (NCR) family is constituted by NKp46, NKp44, and NKp30 in humans, which are expressed mainly on natural killer (NK) cells and are encoded by the ncr1, ncr2, and ncr3 genes, respectively. NCRs have classically been defined as activating receptors that trigger cytotoxicity and cytokine responses by NK cells upon engaging with ligands on tumor cells. Several new findings, however, have challenged this model and identified alternative mechanisms regulating the function of NCRs. Recent reports indicate that ligand matters, since the interaction of NKp44 with distinct ligands on target cells can either activate or inhibit NK cells. Also, the NCRs have been found to interact with distinct specificities to various heparan sulfate glycosaminoglycans, which are complex polysaccharides found in extracellular matrix or on cell surface heparan sulfate proteoglycans (HSPGs). The NCRs can engage with HSPGs in trans as a co-ligand on the target cells or in cis on the NK cell surface to regulate receptor–ligand interactions and NK cell activation. A number of splice variants of ncr2 and ncr3 have also been identified, and a predominant expression of certain variants results in inhibitory signaling through NKp44 and NKp30. Several recent studies have found that the selective expression of some of these inhibitory splice variants can significantly influence outcome in the contexts of cancer, infection, and pregnancy. These findings establish that NCR functions are more diverse than originally thought, and better understanding of their splice variant expression profiles and ligand interactions are needed to establish their functional regulation in the context of human health.
Venezuelan Equine Encephalitis Virus Capsid Implicated in Infection-Induced Cell Cycle Delay in vitro

Venezuelan equine encephalitis virus (VEEV) is a positive sense, single-stranded RNA virus and member of the New World alphaviruses. It causes a biphasic febrile illness that can be accompanied by central nervous system involvement and moderate morbidity in humans and severe mortality in equines. The virus has a history of weaponization, lacks FDA-approved therapeutics and vaccines in humans, and is considered a select agent. Like other RNA viruses, VEEV replicates in the cytoplasm of infected cells and eventually induces apoptosis. The capsid protein, which contains a nuclear localization and a nuclear export sequence, induces a shutdown of host transcription and nucleocytoplasmic trafficking. Here we show that infection with VEEV causes a dysregulation of cell cycling and a delay in the G0/G1 phase in Vero cells and U87MG astrocytes. Cells infected with VEEV encoding a capsid NLS mutant or treated with the capsid-importin α interaction inhibitor G281-1485 were partially rescued from this cell cycle dysregulation. Pathway analysis of previously published RNA-sequencing data from VEEV infected U87MG astrocytes identified alterations of canonical pathways involving cell cycle, checkpoint regulation, and proliferation. Multiple cyclins including cyclin D1, cyclin A2 and cyclin E2 and other regulators of the cell cycle were downregulated in infected cells in a capsid NLS dependent manner. Loss of Rb phosphorylation, which is a substrate for cyclin/cdk complexes was also observed. These data demonstrate the importance of capsid nuclear localization and/or importin α binding for inducing cell cycle arrest and transcriptional downregulation of key cell cycle regulators.
Career choice in the context of political conflict: the case of Palestinians social workers in Israel

ABSTRACT The helping professions in general and social work in particular pose particular challenges and opportunities for national minority group members. This article adds to the present knowledge in the literature concerning the interaction between career choice in the welfare professions and minority status, by looking at the voices of Palestinian Israeli social workers. The article is based on data gathered through in-depth interviews with 32 Palestinian Israeli social workers, describes the motivations, the process of choosing social work as a profession and the barriers that Palestinian Israeli professionals face in the context of the political, social and economic factors shaping their lives as belonging to a national minority in Israel.
Implicit Affective Rivalry: A Behavioral and fMRI Study Combining Olfactory and Auditory Stimulation

Aversive odors are highly salient stimuli that serve a protective function. Thus, emotional reactions elicited by negative odors may be hardly influenceable. We aim to elucidate if negative mood induced by negative odors can be modulated automatically by positively valenced stimuli. We included 32 healthy participants (16 men) in an fMRI design combining aversive and neutral olfactory stimuli with positive and neutral auditory stimuli to test the influence of aversive olfactory stimuli on subjective emotional state and brain activation when combined with positive and neutral auditory stimuli. The behavioral results show an interaction of negative olfactory stimuli on ratings of disgust, perceived valence of music, and subjective affective state, while positive auditory stimulation did not show this interaction. On a neuronal level, we observed main effects for auditory and olfactory stimulation, which are largely congruent with previous literature. However, the pairing of both stimuli was associated with attenuated brain activity in a set of brain areas (supplementary motor area, temporal pole, superior frontal gyrus) which overlaps with multisensory processing areas and pave the way for automatic emotion regulation. Our behavioral results and the integrated neural patterns provide evidence of predominance of olfaction in processing of affective rivalry from multiple sensory modalities.
Electronic Reprint Biological Crystallography Structure of a Bifunctional Alcohol Dehydrogenase Involved in Bioethanol Generation in Geobacillus Thermoglucosidasius Biological Crystallography Structure of a Bifunctional Alcohol Dehydrogenase Involved in Bioethanol Generation in Geobacillus Thermoglu

Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr. Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure–function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crys-tallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. Bifunctional alcohol/aldehyde dehydrogenase (ADHE) enzymes are found within many fermentative microorganisms. They catalyse the conversion of an acyl-coenzyme A to an alcohol via an aldehyde intermediate; this is coupled to the oxidation of two NADH molecules to maintain the NAD + pool during fermentative metabolism. The structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from the ethanol-producing thermophile Geobacillus thermo-glucosidasius has been determined to 2.5 A ˚ resolution. This is the first structure to be reported for such a domain. In silico modelling has been carried out to generate a homology model of the aldehyde dehydrogenase domain, and this was subsequently docked with the ADH-domain structure to model the structure of the complete ADHE protein. This model suggests, for the first time, a structural mechanism for the formation of the large multimeric assemblies or 'spirosomes' that are observed for this ADHE protein and which have previously been reported for ADHEs from other organisms.
Reorganization of Human Cerebral Cortex: The Range of Changes Following Use and Injury

Animal and human research over the past decades have increasingly detailed the brain’s capacity for reorganization of neural network architecture to adapt to environmental needs. In this article, the authors outline the range of reorganization of human representational cortex, encompassing 1) reconstruction in concurrence with enhanced behaviorally relevant afferent activity (examples include skilled musicians and blind Braille readers); 2) injury-related response dynamics as, for instance, driven by loss of input (examples include stroke, amputation, or in blind individuals); and 3) maladaptive reorganization pushed by the interaction between neuroplastic processes and aberrant environmental requirements (examples include synchronicity of input nurturing focal hand dystonia). These types of neuroplasticity have consequences for both understanding pathological dynamics and therapeutic options. This will be illustrated in examples of motor and language rehabilitation after stroke, the treatment of focal hand dystonia, and concomitants of injury-related reorganization such as phantom limb pain.
Fluorescence Visualization of the Enteric Nervous Network in a Chemically Induced Aganglionosis Model

Gastrointestinal motility disorders, severe variants in particular, remain a therapeutic challenge in pediatric surgery. Absence of enteric ganglion cells that originate from neural crest cells is a major cause of dysmotility. However, the limitations of currently available animal models of dysmotility continue to impede the development of new therapeutics. Indeed, the short lifespan and/or poor penetrance of existing genetic models of dysmotility prohibit the functional evaluation of promising approaches, such as stem cell replacement strategy. Here, we induced an aganglionosis model using topical benzalkonium chloride in a P0-Cre/GFP transgenic mouse in which the neural crest lineage is labeled by green fluorescence. Pathological abnormalities and functional changes in the gastrointestinal tract were evaluated 2–8 weeks after chemical injury. Laparotomy combined with fluorescence microscopy allowed direct visualization of the enteric neural network in vivo. Immunohistochemical evaluation further confirmed the irreversible disappearance of ganglion cells, glial cells, and interstitial cell of Cajal. Remaining stool weight and bead expulsion time in particular supported the pathophysiological relevance of this chemically-induced model of aganglionosis. Interestingly, we show that chemical ablation of enteric ganglion cells is associated with a long lifespan. By combining genetic labeling of neural crest derivatives and chemical ablation of enteric ganglion cells, we developed a newly customized model of aganglionosis. Our results indicate that this aganglionosis model exhibits decreased gastrointestinal motility and shows sufficient survival for functional evaluation. This model may prove useful for the development of future therapies against motility disorders.
Activity recognition from sensors using dyadic wavelets and Hidden Markov Model

Advances in sensor and ubiquitous technologies have contributed to the broad scale adoption of pervasive devices. Context or activity recognition from sensor signals is an emerging area that has garnered huge research interest. In this paper, we propose a novel predictive model that utilizes dyadic wavelet transform, vector quantization and Hidden Markov Model (HMM) to predict a high level activity from low level accelerometer sensor signals. Specifically, we analyze and extract important spectral features of the sensor signal by performing multi-resolution wavelet transform. These features are utilized to institute a codebook through the process of vector quantization. An enhance HMM predictive model for activity recognition is built using the codebook and some wavelet feature vectors. We conducted numerous experiments using accelerometer sensor data stemming from android smart phones. Our experiments reveal superior prediction results with a prediction accuracy of up to 96.15%.
Glimpsing through the high-redshift neutral hydrogen fog

We analyse the transmitted flux in a sample of 17 QSOs spectra at 5.74 ≤ z em ( 6.42 to obtain tighter constraints on the volume-averaged neutral hydrogen fraction, xHI, at z ≈ 6. We study separately the narrow transmission windows (peaks) and the wide dark portions (gaps) in the observed absorption spectra. By comparing the statistics of these spectral features with a semi-analytical model of the Lya forest, we conclude that x HI evolves smoothly from 10 -4.4 at z = 5.3 to 10 -4.2 at z = 5.6, with a robust upper limit x H1 11 Myr. The observed widths of the peaks are found to be systematically larger than the simulated ones. Reasons for such discrepancy might reside either in the photoionization equilibrium assumption or in radiative transfer effects.
Population Pharmacokinetics of Liposomal Amphotericin B in Pediatric Patients with Malignant Diseases

ABSTRACT A population pharmacokinetic model of liposomal amphotericin B (L-AmB) in pediatric patients with malignant diseases was developed and evaluated. Blood samples were collected from 39 pediatric oncology patients who received multiple doses of L-AmB with a dose range from 0.8 to 5.9 mg/kg of body weight/day. The patient cohort had an average age of 7 years (range, 0.2 to 17 years) and weighed an average of 28.8 ± 19.8 kg. Population pharmacokinetic analyses were performed with NONMEM software. Pharmacokinetic parameters, interindividual variability (IIV), between-occasion variability (BOV), and intraindividual variability were estimated. The influence of patient characteristics on the pharmacokinetics of L-AmB was explored. The final population pharmacokinetic model was evaluated by using a bootstrap sampling technique. The L-AmB plasma concentration-time data was described by a two-compartment pharmacokinetic model with zero-order input and first-order elimination. The population mean estimates of clearance (CL) and volume of distribution in the central compartment (V1) were 0.44 liters/h and 3.12 liters, respectively, and exhibited IIV (CL, 10%) and significant BOV (CL, 46% and V1, 56%). The covariate models were CL (liters/h) = 0.44 · e0.0152 ·(WT−21) and V1 (liters) = 3.12 · e0.0241 · (WT − 21), where WT is the patient's body weight (kg) centered on the study population cohort median of 21 kg. Model evaluation by the bootstrap procedure indicated that the full pharmacokinetic model was robust and parameter estimates were accurate. In conclusion, the pharmacokinetics of L-AmB in pediatric oncology patients were adequately described by the developed population model. The model has been evaluated and can be used in the design of rational dosing strategies for L-AmB antifungal therapy in this special population.
Runtime Procedure for Energy Savings in Applications with Point-to-Point Communications

Although high-performance computing has always been about efficient application execution, both energy and power consumption have become critical concerns owing to their effect on operating costs and failure rates of large-scale computing platforms. Modern microprocessors are equipped with the capabilities to reduce their power consumption using techniques such as dynamic voltage and frequency scaling (DVFS) and CPU clock modulation (called throttling). Without careful application, however, DVFS and throttling may cause a significant performance loss due to system overhead. This work presents design considerations for a runtime procedure that dynamically analyzes blocking point-to-point communications, groups them according to the proposed criteria, and applies frequency scaling by analyzing both communication and architectural parameters without penalizing the performance much. Experiments, performed on NAS parallel benchmarks verify the proposed design by exhibiting energy savings of as much as 11% with a performance loss as low as 2%.
“If Rainbows Were Everywhere”: Nonmetropolitan SGM Youth Identify Factors That Make Communities Supportive

ABSTRACT Sexual and gender minority (SGM) youth in nonmetropolitan communities face marginalization due to their SGM identities. Community support may mitigate the negative outcomes associated with marginalization. Using the strengths perspective, this study investigated the factors SGM youth identify as making their communities supportive. Interviews were conducted with SGM youth to explore their perceptions of their community, community climate, and the factors that contribute to making communities supportive to SGM youth. Findings revealed four supportive community factors: supportive people, SGM visibility, SGM resources and education, and SGM-inclusive policies. Implications include creating SGM resources and providing professional training on SGM issues.
Receipt of emotional support among rural South African adults

Abstract As the world undergoes rapid ageing, informal support from friends and relatives is becoming especially important among older adults in middle- and low-income countries, where formalised social protections may be limited. We use new data from a cohort of adults aged 40 and older in rural South Africa to explore how receipt of emotional support differs by gender and marital status. Our findings suggest that women are more likely to get emotional support than men and have more sources of support. Moreover, women are more likely to get emotional support from relatives, whereas men are more likely to get support from friends. In regard to marital status, married people are more likely to get emotional support and have more sources of support than people who are not married. However, separated/divorced and widowed people are more likely to get emotional support from relatives and have more sources of non-spousal support than married people. These findings point towards gaps in informal systems of support, and the particular importance of considering men and unmarried (especially never-married) people when designing policies to offer social protections to older populations.
Dairy Cattle, a Potential Reservoir of Human Campylobacteriosis: Epidemiological and Molecular Characterization of Campylobacter jejuni From Cattle Farms

Campylobacter jejuni is a major foodborne pathogen that is increasingly found worldwide and that is transmitted to humans through meat or dairy products. A detailed understanding of the prevalence and characteristics of C. jejuni in dairy cattle farms, which are likely to become sources of contamination, is imperative and is currently lacking. In this study, a total of 295 dairy cattle farm samples from 15 farms (24 visits) in Korea were collected. C. jejuni prevalence at the farm level was 60% (9/15) and at the animal level was 23.8% (68/266). Using the multivariable generalized estimating equation (GEE) model based on farm-environmental factors, we estimated that a high density of cattle and average environmental temperature (7 days prior to sampling) below 24°C affects the presence and survival of C. jejuni in the farm environment. Cattle isolates, together with C. jejuni from other sources (chicken and human), were genetically characterized based on analysis of 10 virulence and survival genes. A total of 19 virulence profile types were identified, with type 01 carrying eight genes (all except hcp and virB11) being the most prevalent. The prevalence of virB11 and hcp was significantly higher in isolates from cattle than in those from other sources (p < 0.05). Multilocus sequence typing (MLST) of C. jejuni isolates from three different sources mainly clustered in the CC-21 and CC-48. Within the CC-21 and CC-48 clusters, cattle isolates shared an indistinguishable pattern with human isolates according to pulsed-field gel electrophoresis (PFGE) and flaA-restriction fragment length polymorphism (RFLP) typing. This suggests that CC-21 and CC-48 C. jejuni from dairy cattle are genetically related to clinical campylobacteriosis isolates. In conclusion, the farm environment influences the presence and survival of C. jejuni, which may play an important role in cycles of cattle re-infection, and dairy cattle represent potential reservoirs of human campylobacteriosis. Thus, environmental management practices could be implemented on cattle farms to reduce the shedding of C. jejuni from cattle, subsequently reducing the potential risk of the spread of cattle-derived C. jejuni to humans through the food chain.