Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing and Understanding Women Empowerment through Personality Traits

As women represent half of the population of India, Women Empowerment is one of the most focused issues in the present world. We can see easily that in villages as well as in cities women contributing equally, still they are unable to get equal position in society alike man, specifically in the developing countries. Women Empowerment is a widely used but rarely defined word due to its multiplicity and widespread uses. That is the reason why it is a striking area of research. Researcher at various point of time and in different contexts, have highlighted that Income and Education is a well-built factors that is affecting women empowerment. Research highlighted five components i.e. women's sense of self-worth; right to determine choices; right to access to opportunities and resources and right to have live their life in her own way, ability to be a icon of social change, as strong indicator of Women Empowerment. All Such indicators symbolize personality traits like openness to experience and extroversion. Thus the present paper has been framed to analyse women’s empowerment in India on the basis of different personality traits. Based on the finding, various suggestions have been made.
Importance of carotenoid structure in radical-scavenging reactions

The rate of (parallel) reaction between carotenoids and phenoxyl radical to yield (i) carotenoid/phenoxyl adducts and (ii) carotenoid radical cations (in effect regenerating the phenol by reduction) has been found to increase for an increasing number of (coplanar) conjugated double bonds in the carotenoid and to decrease in the presence of hydroxy and especially keto groups. The reactions to yield the carotenoid radical have half-lives of tenths of milliseconds, and when studied by transient visible and near-infrared absorption spectroscopy using nanosecond laser flash photolysis for radical generation, the relative rates in di-tert-butyl peroxide/benzene (7/3, v/v) at 20 °C were lycopene (1.66), β-carotene (1), zeaxanthin (0.79), lutein (0.70), and echinenone (0.68), while canthaxanthin and β-apo-8‘-carotenal hardly reacted and astaxanthin not at all. When formed, the carotenoid radicals are rather stable (second-order decay on a millisecond time scale). The lower the energy of the near-infrared transiti.
Morphology, benomyl resistance and pathogenicity to wheat and rye of isolates of Pseudocercosporella herpotrichoides

Seventy-one isolates of Pseudocercosporella herpotrichoides, a non-random sample obtained from cereal crops in Britain between 1981 and 1983, were classified as either sensitive or resistant to 2 mg/l benomyl. In agar culture, isolates were of two distinct morphological types, described as ‘fast-even’ and ‘slow-feathery’. Pathogenicity to wheat and rye seedlings was determined for 21 fast-even and 32 slow-feathery isolates. Fast-even isolates were much more pathogenic to wheat than to rye; nearly all slow-feathery isolates were about equally pathogenic to wheat and rye. Thus, in morphology and pathogenicity, irrespective of sensitivity to benomyl, fast-even isolates conformed to the published descriptions of W-types, while slow-feathery isolates conformed to the descriptions of R-types. Sensitivity to 2 mg/l benomyl was determined for 97 isolates, including W-types and R-types, collected between 1956 and 1983, mainly from England but including some from nine other countries. Only 16 isolates were resistant; three were fast-even and 13 were slow-feathery. All were collected in England since 1981, suggesting that resistance has been rare until recently. Resistance was not a feature of R-type isolates collected before 1981. The increase in the proportion of resistant isolates since 1981 appears to have coincided with an increase in the proportion of R-type isolates.
Atyidae and Palaemonidae (Crustacea: Decapoda: Caridea) of Bocas del Toro, Panama

The present contribution is a preliminary report on the freshwater caridean fauna of Bocas del Toro province, northeastern Panama, based on field collections carried out during a Shrimp Taxonomy Workshop at the STRI station in Bocas del Toro in August 2008. A total of eight species from two families, Atyidae and Palaemonidae, were collected at 17 different collection sites in the rivers, streams and ponds on several islands of the Bocas del Toro archipelago and the adjacent mainland. The species reported herein are Atya scabra (Leach, 1815), Jonga serrei (Bouvier, 1909), Micratya poeyi (Guerin-Meneville, 1855), Potimirim glabra (Kingsley, 1878), P. potimirim (Muller, 1881) (Atyidae), Palaemon pandaliformis (Stimpson, 1871), Macrobrachium acanthurus (Wiegmann, 1836) and M. crenulatum Holthuis, 1950 (Palaemonidae). The record of J. serrei is the first for Panama, and M. poeyi and P. glabra the first for Bocas del Toro province.
Jdmbs: An R Package for Monte Carlo Option Pricing Algorithms for Jump Diffusion Models with Correlational Companies

Black-Scholes model is important to calculate option price in the stock market, and some-times stock prices show jump phenomena. In order to handle it, a variety of jump diffusion models are studied. In this paper, we propose a new jump diffusion model which has correlation coefﬁcients in order to calculate the option prices of related companies together. Its model can treat jump phenomena which happen among companies represented as a directed graph structure. Then, we simulate a implemented model in this package.
Distribution of Dibenzofuran-Degrading Bacteria in Soils Polluted with Different Levels of Polychlorinated Dioxins

Aerobic chemoorganotrophic bacteria in soils polluted with different levels of polychlorinated dioxins (6.8 to 4,600 pg-TEQ g-1 dry weight) were isolated by the quantitative agar-plating method and tested for their ability to degrade dibenzofuran (DF) using DF-overlaid agar and DF-containing liquid media. For comparison, bacteria isolated from river sediments were also tested. Out of the 5,069 strains thus isolated, 23 strains were found to be able to degrade DF, and the majority produced soluble yellow metabolites during the degradation. A higher isolation frequency for DF degraders was obtained with samples containing higher concentrations of polychlorinated dioxins. Most of the DF-degrading isolates were identified as members of the class Actinobacteria, particularly of the genera Nocardioides and Rhodococcus. These results suggest that particular actinobacterial species constitute the major populations of culturable DF-degrading bacteria in dioxin-polluted environments.
Tolerance of Paramysis lacustris and Limnomysis benedeni (Crustacea, Mysida) to sudden salinity changes: implications for ballast water treatment.

In order to draw implications for ballast water management, we tested the tolerance of two Ponto-Caspian mysid species Paramysis lacustris and Limnomysis benedeni to sudden salinity changes. The naturally stenohaline P. lacustris was more susceptible to higher salinities; its mortality rate at 19 PSU was 60%, whereas exposure to 23 PSU was 100% lethal. The euryhaline L. benedeni survived in salinities of up to 19 PSU, but experienced 100% mortality at 34 PSU. The return of both mysid species to fresh water after the 24 h exposure to higher salinities did not prevent further mortality. Considering the rather high short-term salinity tolerance of both species, a salinity of at least 30 PSU should be used as an appropriate biocide.
The SEM-4 Transcription Factor Is Required for Regulation of the Oxidative Stress Response in Caenorhabditis elegans

Oxidative stress causes damage to cells by creating reactive oxygen species (ROS) and the overproduction of ROS have been linked to the onset of premature ageing. We previously found that a brap-2 (BRCA1 associated protein 2) mutant significantly increases the expression of phase II detoxification enzymes in C. elegans. An RNAi suppression screen to identify transcription factors involved in the production of gst-4 mRNA in brap-2 worms identified SEM-4 as a potential candidate. Here, we show that knockdown of sem-4 suppresses the activation of gst-4 caused by the mutation in brap-2. We also demonstrate that sem-4 is required for survival upon exposure to oxidative stress and that SEM-4 is required for expression of the transcription factor SKN-1C. These findings identify a novel role for SEM-4 in ROS detoxification by regulating expression of SKN-1C and the phase II detoxification genes. Article Summary Reactive oxygen species have been implicated as a harmful agent in many age-related diseases as well as an important signaling molecule. The transcription factor SKN-1 in C. elegans is an important regulator of reactive oxygen species levels. Here we show that the transcription factor SEM-4 is required to activate the expression of skn-1c and promote phase II detoxification gene expression. These findings identify a novel role for SEM-4 in regulating reactive oxygen species levels.
Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ

Intrinsically disordered proteins (IDPs) account for a significant fraction of any proteome and are central to numerous cellular functions. Yet how sequences of IDPs code for their conformational dynamics is poorly understood. Here we combined NMR spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to characterize the conformations and dynamics of ChiZ1-64. This IDP is the N-terminal fragment (residues 1-64) of the transmembrane protein ChiZ, a component of the cell division machinery in Mycobacterium tuberculosis. Its N-half contains most of the prolines and all of the anionic residues while the C-half most of the glycines and cationic residues. MD simulations, first validated by SAXS and secondary chemical shift data, found scant α-helices or β-strands but considerable propensity for polyproline II (PPII) torsion angles. Importantly, several blocks of residues (e.g., 11-29) emerge as “correlated segments”, identified by frequent formation of PPII stretches, salt bridges, cation-π interactions, and sidechain-backbone hydrogen bonds. NMR relaxation experiments showed non-uniform transverse relaxation rates (R2s) and nuclear Overhauser enhancements (NOEs) along the sequence (e.g., high R2s and NOEs for residues 11-14 and 23-28). MD simulations further revealed that the extent of segmental correlation is sequence-dependent: segments where internal interactions are more prevalent manifest elevated “collective” motions on the 5-10 ns timescale and suppressed local motions on the sub-ns timescale. Amide proton exchange rates provides corroboration, with residues in the most correlated segment exhibiting the highest protection factors. We propose correlated segment as a defining feature for the conformation and dynamics of IDPs.
Biodegradation of Selected Chlorinated Pesticides Contaminating Lake Maruiut Ecosystem

Water pollution with chlorinated pesticides is one of the most serious environemntal problems due to their highpersistence as a result of the slow biodegradation. Residue levels of organochlorine compounds including (P, P' DDT, y-HCH and DDE) and cyclodiene components (aldrin, endrin) in the water and sediments of Lake Mariut, Alexandria (brackish water) were analyzed and determined by capillary gas chromatography. Bacterial isolates collected from sediments of such lake were identified and investigated for their ability to biodegrade the selected pesticides. Water and sediment samples were collected from six different sites in the main basin of Lake Maruit and also through three successive seasons, summer, autumn and winter 1996-97. Bacterial isolates were identified and subjected to two concentrations: 0.05 and 50 ppm of the investigated pesticides to study the interaction between pesticides and bacteria. Results showed that lindane, aldrin. P,P' DDT and endrine were present in the water and sediments of Lake Mariut at very high levels with residue levels significnatiy higehr in sediments compared to water samples. Seasonal and spatial variation of their distribution in the water and sediments were observed. Biodegradation results showed superior ability of the isolated bacteria to decompose the investigated pesticides with very high efficiency reaching 100% for most of them. Results also revealed selective ability among the tested bacteria for biodegradtion of different pesticides especially at the lowet concentrations.
Joint epitope selection and spacer design for string-of-beads vaccines

Motivation Conceptually, epitope-based vaccine design poses two distinct problems: (1) selecting the best epitopes eliciting the strongest possible immune response, and (2) arranging and linking the selected epitopes through short spacer sequences to string-of-beads vaccines so as to increase the recovery likelihood of each epitope during antigen processing. Current state-of-the-art approaches solve this design problem sequentially. Consequently, such approaches are unable to capture the inter-dependencies between the two design steps, usually emphasizing theoretical immunogenicity over correct vaccine processing and resulting in vaccines with less effective immunogencity. Results In this work, we present a computational approach based on linear programming that solves both design steps simultaneously, allowing to weigh the selection of a set of epitopes that have great immunogenic potential against their assembly into a string-of-beads construct that provides a high chance of recovery. We conducted Monte-Carlo cleavage simulations to show that, indeed, a fixed set of epitopes often cannot be assembled adequately, whereas selecting epitopes to accommodate proper cleavage requirements substantially improves their recovery probability and thus the effective immunogenicity, pathogen, and population coverage of the resulting vaccines by at least two fold. Availability The software and the data analyzed are available at https://github.com/SchubertLab/JessEV
Anxiety enhances pain in a model of osteoarthritis and is associated with altered endogenous opioid function and reduced opioid analgesia

Chronic pain states such as osteoarthritis (OA) are often associated with negative affect, including anxiety and depression. This is, in turn, associated with greater opioid analgesic use, potentially contributing to current and future opioid crises. We utilise an animal model to investigate the neurobiological mechanisms underlying increased opioid use associated with high anxiety and chronic pain. Combining a genetic model of negative affect, the Wistar Kyoto (WKY) rat, and intra-articular injection of monosodium iodoacetate (MIA; 1mg), our model of high anxiety and augmented OA-like pain behaviour mirrors the clinical problem. Effects of morphine (0.5-6mg.kg-1) on pain behaviour and spinal nociceptive neuronal activity were determined in WKY rats, and normo-anxiety Wistar rats, 3 weeks after MIA injection. WKY rats developed augmented OA-like pain, and had blunted inhibitory responses to morphine, when compared to Wistar rats. Potential alterations in endogenous opioid function were probed via systemic blockade of opioid receptors with naloxone (0.1-1mg.kg-1), quantification of circulating levels of β-endorphin, and determination of spinal expression of the mu-opioid receptor (MOR). These studies revealed increased opioidergic tone, and increased spinal desensitization of MORs via the master phosphorylation site at serine residue 375, in this model. We demonstrate attenuated MOR function in the absence of previous exogenous opioid ligand exposure in our model of high anxiety and OA-like pain, which may account for reduced analgesic effect of morphine and provide a potential explanation for increased opioid analgesic intake in high anxiety chronic pain patients. Significance Statement Chronic pain affects large numbers of people, and pain management often relies on poorly effective opioid analgesics, the iatrogenic effects of which are increasingly recognised. The endogenous opioid system - the target for exogenous opioid analgesics - plays key roles in emotional affective states and pain control, but the complex interplay between anxiety, chronic pain, and endogenous opioid system function is challenging to study in people. Here, we have addressed this using a clinically-relevant experimental model. Anxiety-like behaviour was associated with increased chronic arthritis-like pain behaviour, altered opioid receptor function, and reduced efficacy of opioid analgesics. We provide new evidence, which may explain why chronic pain patients with comorbid high anxiety have higher opioid analgesic use.
Joint eQTL mapping and Inference of Gene Regulatory Network Improves Power of Detecting both cis- and trans-eQTLs

Motivation Genetic variations of expression quantitative trait loci (eQTLs) play a critical role in influencing complex traits and diseases development. Two main factors that affect the statistical power of detecting eQTLs are: 1) relatively small size of samples available, and 2) heavy burden of multiple testing due to a very large number of variants to be tested. The later issue is particularly severe when one tries to identify trans-eQTLs that are far away from the genes they influence. If one can exploit co-expressed genes jointly in eQTL-mapping, effective sample size can be increased. Furthermore, using the structure of the gene regulatory network (GRN) may help to identify trans-eQTLs without increasing multiple testing burden. Results In this paper, we employ the structure equation model (SEM) to model both GRN and effect of eQTLs on gene expression, and then develop a novel algorithm, named sparse SEM, for eQTL mapping (SSEMQ) to conduct joint eQTL mapping and GRN inference. The SEM can exploit co-expressed genes jointly in eQTL mapping and also use GRN to determine trans-eQTLs. Computer simulations demonstrate that our SSEMQ significantly outperforms eight existing eQTL mapping methods. SSEMQ is further employed to analyze a real dataset of human breast tissues, yielding a number of cis- and trans-eQTLs. Availability R package ssemQr is available on https://github.com/Ivis4ml/ssemQr.git.
Flexible machine learning prediction of antigen presentation for rare and common HLA-I alleles

The recent increase of immunopeptidomic data, obtained by mass spectrometry or binding assays, opens unprecedented possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. We introduce a flexible and easily interpretable peptide presentation prediction method, RBM-MHC. We validate its performance as a predictor of cancer neoantigens and viral epitopes and we use it to reconstruct peptide motifs presented on specific HLA-I molecules. By benchmarking RBM-MHC performance on a wide range of HLA-I alleles, we show its importance to improve prediction accuracy for rarer alleles.
DeepArk: modeling cis-regulatory codes of model species with deep learning

To enable large-scale analyses of regulatory logic in model species, we developed DeepArk (https://DeepArk.princeton.edu), a set of deep learning models of the cis-regulatory codes of four widely-studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus. DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed), and enables the regulatory annotation of understudied model species.
Obtaining leaner deep neural networks for decoding brain functional connectome in a single shot

Neuroscientific knowledge points to the presence of redundancy in the correlations of brain’s functional activity. These redundancies can be removed to mitigate the problem of overfitting when deep neural network (DNN) models are used to classify neuroimaging datasets. We propose an algorithm that removes insignificant nodes of DNNs in a layerwise manner and then adds a subset of correlated features in a single shot. When performing experiments with functional MRI datasets for classifying patients from healthy controls, we were able to obtain simpler and more generalizable DNNs. The obtained DNNs maintained a similar performance as the full network with only around 2% of the initial trainable parameters. Further, we used the trained network to identify salient brain regions and connections from functional connectome for multiple brain disorders. The identified biomarkers were found to closely correspond to previously known disease biomarkers. The proposed methods have cross-modal applications in obtaining leaner DNNs that seem to fit the data better. The corresponding code is available at https://github.com/SCSE-Biomedical-Computing-Group/LEAN_CLIP.
Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse

Background The specification and differentiation of neocortical projection neurons is a complex process under precise molecular regulation; however, little is known about the similarities and differences in cerebral cortex development between human and mouse at single-cell resolution. Results Here, using single-cell RNA-seq (scRNA-seq) data we explore the divergence and conservation of human and mouse cerebral cortex development using 18,446 and 7,610 neocortical cells. Systematic cross-species comparison reveals that the overall transcriptome profile in human cerebral cortex is similar to that in mouse such as cell types and their markers genes. By single-cell trajectories analysis we find human and mouse excitatory neurons have different developmental trajectories of neocortical projection neurons, ligand-receptor interactions and gene expression patterns. Further analysis reveals a refinement of neuron differentiation that occurred in human but not in mouse, suggesting that excitatory neurons in human undergo refined transcriptional states in later development stage. By contrast, for glial cells and inhibitory neurons we detected conserved developmental trajectories in human and mouse. Conclusions Taken together, our study integrates scRNA-seq data of cerebral cortex development in human and mouse, and uncovers distinct developing models in neocortical projection neurons. The earlier activation of cognition -related genes in human may explain the differences in behavior, learning or memory abilities between the two species.
Aberrant Activation of Notch Signaling in Human Breast Cancer

A role for Notch signaling in human breast cancer has been suggested by both the development of adenocarcinomas in the murine mammary gland following pathway activation and the loss of Numb expression, a negative regulator of the Notch pathway, in a large proportion of breast carcinomas. However, it is not clear currently whether Notch signaling is frequently activated in breast tumors, and how it causes cellular transformation. Here, we show accumulation of the intracellular domain of Notch1 and hence increased Notch signaling in a wide variety of human breast carcinomas. In addition, we show that increased RBP-Jkappa-dependent Notch signaling is sufficient to transform normal breast epithelial cells and that the mechanism of transformation is most likely through the suppression of apoptosis. More significantly, we show that attenuation of Notch signaling reverts the transformed phenotype of human breast cancer cell lines, suggesting that inhibition of Notch signaling may be a therapeutic strategy for this disease.
Implications of the Irrelevant Sound Effect on Cognitive Performance – A Developmental Study

4 Introduction.5 Method.11 Participants.11 Design.11 Procedure.11 Materials.12 Results.13 Proportion correct.13 Reaction times.15 Discussion.17 Conclusion.20 References.21 Appendix A.25 Appendix B.25 Selbstständigkeitserklärung. 26