Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach

Millions of transcript sequences have become available for characterizing the transcriptome of human and mouse. Transcript databases have been extensively mined for extracting alternative splicing information within the same species; but they also represent a potentially valuable resource for the discovery of alternative splice variants in another species. In this study, we have performed analysis of alternative splicing patterns for 7,475 pairs of human and mouse genes. We found that cross-species transcript analysis could accomplish the same level of sensitivity in detecting constitutive splice patterns as EST resource from the same species. In contrast, identifying alternative splice patterns in human genes, mouse transcripts achieved only 50% of the sensitivity of human EST and 70% of the sensitivity of human mRNA. While identifying alternative splice patterns in mouse genes, human transcripts are 38% more sensitive than mouse mRNA, and reach 60% of the sensitivity of mouse EST. Furthermore, using the cross-species approach, we predicted novel alternative splice patterns for 42% of human genes and 51% of mouse genes. Splice site motif analysis suggests that the majority of predicted novel splice patterns are expressed in human. EST-based frequency analysis shows that novel splice patterns are expressed at lower frequency than alternative splice patterns present in the transcript data from both species, possibly explaining why they remain undetected in the transcript data of the same species.
Chemokines and Chemokine Receptors in Multiple Sclerosis

Multiple sclerosis is an autoimmune disease with classical traits of demyelination, axonal damage, and neurodegeneration. The migration of autoimmune T cells and macrophages from blood to central nervous system as well as the destruction of blood brain barrier are thought to be the major processes in the development of this disease. Chemokines, which are small peptide mediators, can attract pathogenic cells to the sites of inflammation. Each helper T cell subset expresses different chemokine receptors so as to exert their different functions in the pathogenesis of MS. Recently published results have shown that the levels of some chemokines and chemokine receptors are increased in blood and cerebrospinal fluid of MS patients. This review describes the advanced researches on the role of chemokines and chemokine receptors in the development of MS and discusses the potential therapy of this disease targeting the chemokine network.
Exploring the predictors of quitting tobacco usage among patients attending a private dental institution--a survey from Jodhpur, India.

BACKGROUND Burden of tobacco epidemic has swiftly moved to developing countries making the exploration of predictors of quitting tobacco usage extremely important. AIM To assess the willingness to quit tobacco use and to ascertain the predictors of quitting tobacco as well as tobacco dependency by employing Fagerstrom scale. METHODS The study consisted of 252 subjects visiting the Public Health Dentistry department in a Dental institution JDCGH (Jodhpur Dental College General Hospital), Rajasthan, India. Data on demographic information, tobacco usage and quitting, information on reasons for quitting like; self-concepts, social concerns, legal issues, and health concern was collected by interview schedule method. RESULTS Overall 76% of the study participants were planning to quit. Demographic variables like age, marital status and religion were significant predictors of planning to quit tobacco usage (p ≤ 0.05). Significant relationship was observed on Fagerstrom Scale with place of residence, type of tobacco use and frequency of tobacco use (p ≤ 0.05). The most frequent cited reason for quitting tobacco usage was spitting and ash dropping which was embarrassing in-front of others (75.65%) and least reported reason was future health concerns (33.16%). CONCLUSIONS Most of the respondents had favourable attitude towards quitting tobacco usage and social concern was the main predictor of quitting tobacco usage. Less reported reasons like legal issues and health concerns have to be explored in depth. The present study highlights the need for more researches exploring the predictors of quitting tobacco usage in India and further nationwide study.
Biased project status reports: A survey of IS professionals

This paper summarizes an empirical investigation that explored biased project reporting by Information Systems (IS) professionals. The study is based on a survey of 91 professionals who were involved with system implementations in various governmental agencies. Our investigation assessed the impact of project importance, control, structure, and size on biasing behaviors. To formulate the research hypotheses for our study, we adopted a Message Exchange Perspective. The results reveal that IS professionals are more likely to bias their project status communications when working in projects that are (1) large, (2) important, and (3) lack controls. The practical and research implications of our findings are discussed.
Incidence of diabetes mellitus in a population‐based cohort of persons with chronic hepatitis B virus infection

To investigate the effect of hepatitis B virus (HBV) infection on the development of diabetes mellitus (DM), we compared DM incidence and characteristics of Alaska Native persons with and without HBV infection. From 1990 to 2010, there were 52 incident DM cases among 1309 persons with infection vs 4557 DM cases among 85 698 persons without infection (log‐rank test, P = 0.20). Compared to infected persons without DM, those with DM were significantly older (57.0 vs 47.4 years, P < 0.001) and had higher body mass index (34.5 vs 28.4 kg/m2, P < 0.001). Genotype, immune active disease and the presence of cirrhosis were not associated with DM. In this population‐based cohort with over 20 years of follow‐up, there was no effect of HBV infection on DM development.
Capturing Dynamics of Biased Attention: Are New Attention Variability Measures the Way Forward?

Background New indices, calculated on data from the widely used Dot Probe Task, were recently proposed to capture variability in biased attention allocation. We observed that it remains unclear which data pattern is meant to be indicative of dynamic bias and thus to be captured by these indices. Moreover, we hypothesized that the new indices are sensitive to SD differences at the response time (RT) level in the absence of bias. Method Randomly generated datasets were analyzed to assess properties of the Attention Bias Variability (ABV) and Trial Level Bias Score (TL-BS) indices. Sensitivity to creating differences in 1) RT standard deviation, 2) mean RT, and 3) bias magnitude were assessed. In addition, two possible definitions of dynamic attention bias were explored by creating differences in 4) frequency of bias switching, and 5) bias magnitude in the presence of constant switching. Results ABV and TL-BS indices were found highly sensitive to increasing SD at the response time level, insensitive to increasing bias, linearly sensitive to increasing bias magnitude in the presence of bias switches, and non-linearly sensitive to increasing the frequency of bias switches. The ABV index was also found responsive to increasing mean response times in the absence of bias. Conclusion Recently proposed DPT derived variability indices cannot uncouple measurement error from bias variability. Significant group differences may be observed even if there is no bias present in any individual dataset. This renders the new indices in their current form unfit for empirical purposes. Our discussion focuses on fostering debate and ideas for new research to validate the potentially very important notion of biased attention being dynamic.
EVALUATION OF ANTIFERTILITY EFFECTS OF AQUEOUS EXTRACT OF PHYLLANTHUS AMARUS IN MALE WISTAR RATS

The present study was aimed at evaluating the antifertility effect of phyllanthus amarus extract in male wistar rats. The body and organ weights, cauda epididymal sperm parameters, serum levels of male reproductive hormones and fructose were assessed. Daily oral doses of the extract were administered to each animal in three different test groups for 28 consecutive days. Results show significant (p<0.05) dose dependent decrease in the levels of testosterone, leuteinising hormone, sperm motility, sperm count and sperm viability of the treated animals when compared with the control; while follicle stimulating hormone significantly (p<0.05) increased dose dependently. These findings suggest that the aqueous crude extract of phyllanthus amarus has anti-fertility activity.
Acute toxicity of chemically and mechanically dispersed crude oil to juvenile sea bass (Dicentrarchus labrax): Absence of synergistic effects between oil and dispersants

The goal of the present experiment was to assess the relative acute toxicities of mechanically and chemically dispersed oil (crude Arabian Light) in controlled conditions. Juvenile sea bass (Dicentrarchus labrax) were exposed to 4 commercial formulations of dispersants (Corexit EC9500A, Dasic Slickgone NS, Finasol OSR 52, Inipol IP 90), to mechanically dispersed oil, and to the corresponding chemical dispersions. Acute toxicity was evaluated at 24 h, 48 h, 72 h, and 96 h through the determination of 10%, 50%, and 90% lethal concentrations calculated from measured total petroleum hydrocarbon (TPH) concentrations; Kaplan–Meyer mortality analyses were based on nominal concentrations. Animals were exposed to the dissolved fraction of the oil and to the oil droplets (ranging from 14.0 μm to 42.3 μm for the chemical dispersions). Kaplan–Meyer analyses demonstrated an increased mortality in the case of chemical dispersions. This difference can be attributed mainly to differences in TPH, because the chemical lethal concentrations were not reduced compared with mechanical lethal concentrations (except after 24 h of exposure). The ratios of lethal concentrations of mechanical dispersions to the different chemical dispersions were calculated to allow direct comparisons of the relative toxicities of the dispersions. The results ranged from 0.27 to 3.59, with a mean ratio close to 1 (0.92). These results demonstrate an absence of synergistic effect between oil and chemical dispersants in an operational context. Environ Toxicol Chem 2015;34:1543–1551. © 2015 SETAC
Evaluating a social skills training protocol in a private setting: Outcomes and issues

ly and the general ability to learn and adapt to the environment. The identification of different intelligences was specific to the kind of information from which they operated. For instance, verbal-propositional intelligence was concerned with vocabulary and text and perceptual-organization intelligence focused on concepts such as patterns, puzzles and missing parts. The social, practical, and personal classes of intelligence included EI. EI must meet three criteria to be considered a standard intelligence: “(a) it must be operationalized as a mental ability, (b) it must meet correlation criterion that indicate it is a unitary ability that represents a new kind of performance relative to earlier measures of intelligence and other personality dispositions, and (c) it must exhibit growth with age” (Mayer et al. 2004, p. 209). On the basis of the Multifactor EI Scale (MEIS; Mayer, Caruso, & Salovey, 1999), and other findings, Mayer et al. (2001) argued EI met the three criteria. Researchers and philosophers argued whether EI had any value or was the latest in a long line of psychological fads (Matthews et al., 2004). Some questioned the concept of EI as a separate intelligence and as a predictor for social sensitivity, academic achievement, and general well being (Barchard, 2003; Matthews et al., 2004; & Waterhouse, 2006). Davies et al. (1998) assessed both standard intelligence and personality in three studies of EI. The purpose of the studies were (a) to examine the empirical status of both self-report and objective indexes, (b) to determine the relation of EI measures to standard
Enhancing Fraction in Glioma and Its Relationship to the Tumoral Vascular Microenvironment: A Dynamic Contrast-Enhanced MR Imaging Study

BACKGROUND AND PURPOSE: EnF is a newly described measure of proportional tumor enhancement derived from DCE-MR imaging. The aim of this study was to assess the relationship between EnF and the more established DCE-MR imaging parameters: Ktrans, ve, and vp. MATERIALS AND METHODS: Forty-two patients with 43 gliomas (16 grade II, 3 grade III, and 24 grade IV) were studied. Imaging included pre- and postcontrast T1-weighted sequences through the lesion and T1-weighted DCE-MR imaging. Parametric maps of EnF, Ktrans, ve, and vp were generated. Voxels were classified as enhancing if the IAUC was positive (EnFIAUC60>0). A threshold of IAUC > 2.5 mmol.s was used to generate EnFIAUC60>2.5. Both measures of EnF were compared with the DCE-MR imaging parameters (Ktrans, ve, and vp). RESULTS: In grade II gliomas, EnFIAUC60>0 and EnFIAUC60>2.5 correlated with vp (R2 = 0.6245, P < .0005; and R2 = 0.4727, P = .003) but not with Ktrans or ve. In grade IV tumors, both EnFIAUC60>0 and EnFIAUC60>2.5 correlated with Ktrans (R2 = 0.3501, P = .001; and R2 = 0.4699, P < .0005) and vp (R2 = 0.1564, P = .01; and R2 = 0.2429, P = .007), but not with ve. Multiple regression analysis showed Ktrans as the only independent correlate of both EnFIAUC60>0 and EnFIAUC60>2.5 for grade IV tumors. CONCLUSIONS: This study suggests that in grade II tumors, EnF reflects vp and varies due to changes in vascular density. In grade IV gliomas, EnF is affected by Ktrans with secondary associated changes in vp.
Comparison of particle sizing techniques in the case of inhalation dry powders.

The objectives of this work were (i) to validate electrical zone sensing and laser diffraction for the analysis of primary particle size in the case of inhalation dry powders and (ii) to study the influence of the aggregation state of the powder on the sizing techniques. Free-flowing dry powders were prepared by spray-drying with a combination of albumin, lactose, and dipalmitoylphosphatidylcholine. The replacement of lactose by mannitol, the removal of albumin, and the atomization at high relative humidity all increased powder cohesion. Automated measurements were compared with primary particle sizes collected by light and electron microscopy. The mass mode obtained by electrical zone sensing and the mass median diameter measured by laser diffraction following dispersion with compressed air at a pressure of 3 bar or following suspension in water and ultrasonic dispersion at a power of 60 W for 30 s each provided primary particle sizes close to microscopy measurements. However, these conditions only applied in the case of slightly to moderately aggregated powders. For strongly agglomerated powders, an exact measurement of the size was only collected by laser diffraction in the wet state combined with ultrasonic dispersion. Our study underlies how measurement of primary particle size highly depends on both powder material and proper particle dispersion.
14-3-3 σ Expression Effects G2/M Response to Oxygen and Correlates with Ovarian Cancer Metastasis

Background In vitro cell culture experiments with primary cells have reported that cell proliferation is retarded in the presence of ambient compared to physiological O2 levels. Cancer is primarily a disease of aberrant cell proliferation, therefore, studying cancer cells grown under ambient O2 may be undesirable. To understand better the impact of O2 on the propagation of cancer cells in vitro, we compared the growth potential of a panel of ovarian cancer cell lines under ambient (21%) or physiological (3%) O2. Principal Findings Our observations demonstrate that similar to primary cells, many cancer cells maintain an inherent sensitivity to O2, but some display insensitivity to changes in O2 concentration. Further analysis revealed an association between defective G2/M cell cycle transition regulation and O2 insensitivity resultant from overexpression of 14-3-3 σ. Targeting 14-3-3 σ overexpression with RNAi restored O2 sensitivity in these cell lines. Additionally, we found that metastatic ovarian tumors frequently overexpress 14-3-3 σ, which in conjunction with phosphorylated RB, results in poor prognosis. Conclusions Cancer cells show differential proliferative sensitivity to changes in O2 concentration. Although a direct link between O2 insensitivity and metastasis was not determined, this investigation showed that an O2 insensitive phenotype in cancer cells to correlate with metastatic tumor progression.
Seizure Prediction

There is mounting evidence that seizures are preceded by characteristic changes in the EEG that are detectable minutes before seizure onset. Using novel signal analysis techniques, researchers are beginning to characterize the transition from the interictal to the ictal state in quantitative terms. This research has led to the development of automated seizure prediction algorithms. Active debate persists regarding the interpretation of research results, methods of signal analysis, as well as experimental and statistical methods for testing seizure prediction algorithms. Developments in this field have led to new theories on the mechanism of seizure development and resolution. The ability to predict seizures could lead the way to novel diagnostic and therapeutic methods for the treatment of patients with epilepsy.
A Model Reduction Perspective on Thermal Models for Induction Machine Overload Relays

Full-order thermal models are often used by machine designers to analyze the induction machine thermal behavior. The real-time implementation of such models for the purpose of motor thermal protection is difficult because an extensive knowledge on motors and sufficient computational resource are required. This paper demonstrates that full-order thermal models can be systematically reduced via pole-zero cancellation or Hankel singular-values-based model reduction techniques without additional physical assumptions. As a result, a system of a substantially lower dimension, which has nearly the same response characteristics in the frequency band of interest, is obtained. Both the estimated rotor cage temperature, which is extracted from the voltage and current measurements by a sensorless rotor temperature estimator, and the measured stator winding temperature are used to evaluate the performance of low-order thermal models. Given a certain tolerance for the modeling error, a reduced low-order thermal model can be used to characterize the thermal dynamics of a small- to medium-sized line-connected induction machine and to provide proper protection against motor overheating.
Control of virus reactivation arrests pulmonary herpesvirus-induced fibrosis in IFN-gamma receptor-deficient mice.

RATIONALE Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic lung disorder of unknown cause. Several studies suggest an association between Epstein-Barr virus pulmonary infection and the development of IPF. OBJECTIVES To determine whether reduction of gamma-herpesvirus reactivation from latency would alter progressive lung fibrogenesis in an animal model of virus-induced pulmonary fibrosis. METHODS IFN-gamma receptor-deficient (IFN-gammaR(-/-)) mice infected intranasally with murine gamma-herpesvirus 68 (MHV68) develop lung fibrosis that progresses for up to at least 180 days after initial infection. Viral replication during the chronic phase of infection was controlled by two methods: the administration of cidofovir, an antiviral drug effective at clearing lytic but not latent virus, and by using a mutant gamma-herpesvirus defective in virus reactivation from latency. MEASUREMENTS AND MAIN RESULTS Ten percent of the asymptomatic MHV68-infected animals that received antiviral treatment beginning on Day 45 postinfection had severe pulmonary fibrosis compared with 40% of the control saline-treated animals. Absence of severe fibrosis was also observed in IFN-gammaR(-/-) mice infected with the defective reactivation mutant MHV68 v-cyclin stop. Decreased fibrosis was associated with lower levels of transforming growth factor-beta, vascular endothelial growth factor, and markers of macrophage alternative activation. When antiviral treatment was administered on Day 60 in symptomatic animals, survival improved from 20 to 80% compared with untreated symptomatic animals, but lung fibrosis persisted in 60% of the mice. CONCLUSIONS MHV68-induced fibrosis is a result of viral lytic replication during chronic lung herpesvirus infection in mice. We speculate that antiviral therapy might help to control lung fibrosis in humans with IPF and associated herpesvirus infection.
19F MRI oximetry: simulation of perfluorocarbon distribution impact

In 19F MRI oximetry, a method used to image tumour hypoxia, perfluorocarbons serve as oxygenation markers. The goal of this study is to evaluate the impact of perfluorocarbon distribution and concentration in 19F MRI oximetry through a computer simulation. The simulation studies the correspondence between 19F measured (pOFNMR2) and actual tissue oxygen tension (pO2) for several tissue perfluorocarbon distributions. For this, a Krogh tissue model is implemented which incorporates the presence of perfluorocarbons in blood and tissue. That is, in tissue the perfluorocarbons are distributed homogeneously according to Gaussian diffusion profiles, or the perfluorocarbons are concentrated in the capillary wall. Using these distributions, the oxygen tension in the simulation volume is calculated. The simulated mean oxygen tension is then compared with pOFNMR2, the 19F MRI-based measure of pO2 and with pO02, pO2 in the absence of perfluorocarbons. The agreement between pOFNMR2 and actual pO2 is influenced by vascular density and perfluorocarbon distribution. The presence of perfluorocarbons generally gives rise to a pO2 increase in tissue. This effect is enhanced when perfluorocarbons are also present in blood. Only the homogeneous perfluorocarbon distribution in tissue with no perfluorocarbons in blood guarantees small deviations of pOFNMR2 from pO2. Hence, perfluorocarbon distribution in tissue and blood has a serious impact on the reliability of 19F MRI-based measures of oxygen tension. In addition, the presence of perfluorocarbons influences the actual oxygen tension. This finding may be of great importance for further development of 19F MRI oximetry.
Sexual behaviors and sexually transmitted infections in a nationally representative sample of women veterans and nonveterans.

BACKGROUND Women veterans are a growing population with unique characteristics and documented health disparities. Few studies have examined their sexual behaviors and rates of sexually transmitted infections (STIs), and none have compared women veterans to nonveterans to identify potential sexual health disparities. METHODS We used data from the 1999-2010 National Health and Nutrition Examination Survey, a nationally representative U.S. survey. We compared lifetime sexual history (age at first intercourse, number of partners), sexual activity in the last year, and STIs between women veterans (n=151) and nonveterans (n=8738), adjusting for age, race/ethnicity, education, marital status, binge drinking, and survey year. RESULTS Compared to nonveterans, women veterans reported a younger age at first intercourse and a greater number of female and male lifetime sexual partners, and they were more likely to have ever had sex with a woman. They were also more likely than nonveterans to have genital herpes and genital warts. CONCLUSIONS Women veterans reported higher rates of sexual activity and STIs than nonveterans. Future research is needed to assess high-risk behaviors and determine what factors may underlie these associations. Providers should ensure thorough screening and intervention services are provided for this growing population.