Miracle-dz/UniFAR-FTUs huggingface dataset:
Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east–west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour‐joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.
Transcriptional profiling reveals divergent roles of PPAR and PPAR / in regulation of gene expression in mouse liver

Sanderson LM, Boekschoten MV, Desvergne B, Müller M, Kersten S. Transcriptional profiling reveals divergent roles of PPAR and PPAR / in regulation of gene expression in mouse liver. Physiol Genomics 41: 42–52, 2010. First published December 15, 2009; doi:10.1152/physiolgenomics.00127. 2009. —Little is known about the role of the transcription factor peroxisome proliferator-activated receptor (PPAR) / in liver. Here we set out to better elucidate the function of PPAR / in liver by comparing the effect of PPAR and PPAR / deletion using whole genome transcriptional profiling and analysis of plasma and liver metabolites. In fed state, the number of genes altered by PPAR and PPAR / deletion was similar, whereas in fasted state the effect of PPAR deletion was much more pronounced, consistent with the pattern of gene expression of PPAR and PPAR / . Minor overlap was found between PPAR and PPAR / -dependent gene regulation in liver. Pathways upregulated by PPAR / deletion were connected to innate immunity and inflammation. Pathways downregulated by PPAR / deletion included lipoprotein metabolism and various pathways related to glucose utilization, which correlated with elevated plasma glucose and triglycerides and reduced plasma cholesterol in PPAR / / mice. Downregulated genes that may underlie these metabolic alterations included Pklr, Fbp1, Apoa4, Vldlr, Lipg, and Pcsk9, which may represent novel PPAR / target genes. In contrast to PPAR / mice, no changes in plasma free fatty acid, plasma -hydroxybutyrate, liver triglycerides, and liver glycogen were observed in PPAR / / mice. Our data indicate that PPAR / governs glucose utilization and lipoprotein metabolism and has an important anti-inflammatory role in liver. Overall, our analysis reveals divergent roles of PPAR and PPAR / in regulation of gene expression in mouse liver.
FR121196, a potential antidementia drug, ameliorates the impaired memory of rat in the Morris water maze.

We investigated the effects of FR121196 N-(4-acetyl-1-piperazinyl)-4-fluorobenzenesulfonamide on the performance of rats in the Morris water maze using a two-trial-per-day regimen. Escape latency to find the platform was significantly prolonged in young rats subjected to scopolamine (1 mg/kg) treatment or to nucleus basalis magnocellularis (NBM) or fimbria-fornix (FF) lesioning compared with the respective control animals. Similar memory deficit was observed in aged rats (24-26 months old) compared with young rats. Daily treatment with FR121196 (0.1-1.0 mg/kg i.p.) ameliorated all the memory deficits except in the FF-lesioned rats, whereas physostigmine (0.032-0.32 mg/kg) ameliorated the memory deficits in scopolamine-treated rats but not in the NBM-lesioned, FF-lesioned or aged rats. Methamphetamine (0.32-3.2 mg/kg) hardly ameliorated the memory deficits and, rather, aggravated those in the scopolamine-treated, NBM-lesioned and aged rats. Neurochemical analysis of the brain showed that dopamine, norepinephrine and serotonin levels were significantly reduced in the hippocampus of the FF-lesioned rats compared with the sham control, and a significant reduction of dopamine level in the cortex was also observed in the aged rats compared with young rats. None of these parameters were changed after NBM lesioning. We concluded that FR121196 ameliorates the memory deficits of rats with cholinergic dysfunction through the action on the hippocampal monoaminergic (possibly serotonergic) neurons.
Computation of 2D and 3D eddy currents in moving conductors of electromagnetic retarders

The AV-A formulation is applied to problems where motion is the source of eddy currents. The Lorentz gauge is used to ensure uniqueness of the solution and leads to a two-step computation procedure: A is computed first, followed by V on moving regions only. A stable and accurate solution of A is obtained through implementation of a Petrov-Galerkin method. Numerical results of 2D and 3D problems are included. >
Evolutionary Emergence of a Novel Splice Variant with an Opposite Effect on the Cell Cycle

ABSTRACT Alternative splicing contributes greatly to the diversification of mammalian proteomes, but the molecular basis for the evolutionary emergence of splice variants remains poorly understood. We have recently found a novel class of splicing regulatory elements between the polypyrimidine tract (Py) and 3′ AG (REPA) at intron ends in many human genes, including the multifunctional PRMT5 (for protein arginine methyltransferase 5) gene. The PRMT5 element is comprised of two G tracts that arise in most mammals and accompany significant exon skipping in human transcripts. The G tracts inhibit splicing by recruiting heterogeneous nuclear ribonucleoprotein (hnRNP) H and F (H/F) to reduce U2AF65 binding to the Py, causing exon skipping. The resulting novel shorter variant PRMT5S exhibits a histone H4R3 methylation effect similar to that seen with the original longer PRMT5L isoform but exhibits a distinct localization and preferential control of critical genes for cell cycle arrest at interphase in comparison to PRMT5L. This report thus provides a molecular mechanism for the evolutionary emergence of a novel splice variant with an opposite function in a fundamental cell process. The presence of REPA elements in a large group of genes implies their wider impact on different cellular processes for increased protein diversity in humans.
Black cohosh improves objective sleep in postmenopausal women with sleep disturbance

Abstract Objective Sleep problems are prominent after menopause. The aim of our study was to look into the effect of black cohosh on both objective and subjective sleep in early postmenopausal women with sleep complaints. Methods We performed a randomized, double-blind and placebo-controlled research during a 6-month period. Forty-eight postmenopausal women aged 45–60 years with sleep disturbance were enrolled and received daily administration of either black cohosh or placebo. Polysomnography and the Pittsburg Sleep Quality Index (PSQI) were performed at the initiation and termination of the study, as well as the Menopause-specific Quality of Life questionnaire and estradiol and follicle stimulating hormone tests. Liver and renal functions and breast and pelvic ultrasound were set as safety measures, carried out every 3 months. Results Seventy-six women were interviewed, of whom 42 women completed the whole trial. Compared with placebo, black cohosh treatment led to significant polysomnographic changes, including increased sleep efficiency and decreased wake after sleep onset (WASO) duration, and tended to improve PSQI with a medium effect size. On average, 15.8% of WASO duration was reduced in the black cohosh group. Vasomotor and physical domains of life quality were improved compared with placebo. Safety measures did not yield any adverse event assigned to black cohosh. Conclusions In early postmenopausal women with a major sleep complaint, black cohosh effectively improved sleep and might be a safe measure in managing menopausal sleep disturbance.
Hypothermia for Acute Ischemic Stroke: Not Just Another Neuroprotectant

BackgroundBased on empirical experience, hypothermia has long been known to be a potent putative neuroprotectant. Recent insights into the mechanisms of cerebral ischemia and reperfusion suggest reasons why hypothermia may be an ideal modality for extending the time window for thrombolytic stroke therapy. Review SummaryHypothermia protects brain tissue from the effects of ischemia in multiple ways. It retards energy depletion, reduces intracellular acidosis, and lessens the ischemic overdose of excitatory neurotransmitters. This attenuates the influx of intracellular calcium, the herald of subsequent neuronal death. Additionally, hypothermia suppresses synthesis of oxygen free radicals involved in secondary damage associated with reperfusion. It also suppresses the mechanisms related to blood-brain barrier degeneration and postischemic remodeling. Animal and human data shows that deep hypothermia is primarily protective and is used in several cardiothoracic and neurosurgical applications and that mild hypothermia enhances recovery after focal and global ischemic brain injuries. Preliminary data on hypothermia in human stroke also show promising potential.Current methods of instituting hypothermia, including patient selection, temperature and timing, cooling methods, and complications are reviewed in detail. ConclusionsNeuroprotection conferred by mild to moderate hypothermia is likely to undergo phase III clinical trials in various clinical settings. Novel technology promises a broad application even outside intensive care settings. Preliminary studies suggest that mild to moderate hypothermia is a useful adjunct to thrombolytic therapy for stroke. Timing, degree, and duration rules are being developed and methods of cooling further perfected to optimize the safety and efficacy of this promising approach.
Exploring facilitating factors and barriers to the nationwide dissemination of a Dutch school-based weight gain prevention program “ DOiT ” : a study protocol

Institutional addresses 1 EMGO Institute for Health and Care Research and Department of Public and Occupational Health, VU University Medical Center, Amsterdam, The Netherlands. 2 TNO (Netherlands Organisation of Applied Scientific Research) Life Style, Leiden, The Netherlands. 3 EMGO Institute for Health and Care Research and the Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.
Epidemiology and molecular characteristics of norovirus GII.4 Sydney outbreaks in Taiwan, January 2012–December 2013

In 2012, a new norovirus GII.4 variant (GII.4 Sydney) emerged and caused the majority of the acute gastroenteritis outbreaks in Australia, Asia, Europe, and North America. We examined the epidemiologic and molecular virologic characteristics of reported acute gastroenteritis outbreaks determined to be caused by norovirus in Taiwan from January 2012 to December 2013. A total of 253 (45.7%) of 552 reported acute gastroenteritis outbreaks tested positive for norovirus, of which 165 (65.5%) were typed as GII.4 Sydney. GII.4 Sydney outbreaks were reported from all geographic areas of Taiwan and occurred most frequently in schools (35.8%) and long‐term care facilities (24.2%). Person‐to‐person transmission was identified in 116 (70.3%) of the outbreaks. Phylogenetic analyses of full‐length ORF2 of eight specimens indicated that GII.4 Sydney strains detected in Taiwan were closely related to strains detected globally. Continued outbreak surveillance and strain typing are needed to provide information on epidemiologic and virologic trends of novel norovirus strains. J. Med. Virol. 87:1462–1470, 2015. © 2015 Wiley Periodicals, Inc.
Working memory and multidimensional schizotypy: Dissociable influences of the different dimensions

Compromised working memory is considered a core deficit of schizophrenia and a potential endophenotype for the liability to develop schizophrenia. In keeping with this suggestion, working memory has also been found to be disrupted in people with high levels of schizotypy. However, it is unclear whether this disruption is linked to positive, negative, or disorganized symptoms/characteristics. This issue is the focus of the present investigation. The relationship between multidimensional schizotypy and working memory performance was investigated in 289 participants. Working memory was measured using an n-back task with three conditions; 0-back, 1-back, and 2-back. Covarying for the effect of shared variance between the schizotypy dimensions, we found reduced working memory performance in participants who displayed high levels of positive schizotypy and, to some extent, in participants with low levels of negative schizotypy. The results are discussed in terms of Baddeley's (1986) model of working memory and potential underlying neurological mechanisms.
Factors associated with malnutrition in adolescent and adult patients with cystic fibrosis.

OBJECTIVE To determine the prevalence of malnutrition in patients attending an adult cystic fibrosis (CF) program and to investigate the associations of malnutrition with the clinical characteristics of those patients. METHODS This was a cross-sectional study involving patients with clinically stable CF patients (16 years of age or older). The patients underwent clinical assessment, nutritional assessments, pulmonary function tests, and pancreatic function assessment. They also completed a questionnaire regarding diet compliance. On the basis of their nutritional status, the patients were classified divided into three groups: adequate nutrition; at nutritional risk; and malnutrition. RESULTS The study has included 73 patients (mean age, 25.6 ± 7.3 years), 40 of whom (54.8%) were female. The mean body mass index was 21.0 ± 3.0 kg/m2 and the mean FEV1 was 59.7 ± 30.6% of predicted. In this sample of patients, 32 (43.8%), 23 (31.5%), and 18 (24.7%) of the patients were allocated to the adequate nutrition, nutritional risk, and malnutrition groups, respectively. The logistic regression analysis identified three independent factors associated with the risk of malnutrition: Shwachman-Kulczycki score, percent predicted FEV1; and age. CONCLUSIONS Malnutrition remains a common complication in adolescents and adults with CF, despite dietary advice. Malnutrition is associated with age, clinical severity, and lung function impairment.
Essential motions in a fungal lipase with bound substrate, covalently attached inhibitor and product

As an aid to understanding the influence of dynamic fluctuations during esterolytic catalysis, we follow protein flexibility at three different steps along the catalytic pathway from substrate binding to product clearance via a covalently attached inhibitor, which represents a transition‐state mimic. We have applied a classical approach, using molecular dynamics simulations to monitor protein dynamics in the nanosecond regime. We filter out small amplitude fluctuations and focus on the anharmonic contributions to the overall dynamics. This ‘essential dynamics’ analysis reveals different modes of response along the pathway suggesting that binding, catalysis and product clearance occur along different energy surfaces. Motions in the enzyme with a covalently attached ligand are more complex and occur along several eigenvectors. The magnitudes of the fluctuations in these individual subspaces are significantly smaller than those observed for the substrate and product molecules, indicating that the energy surface is shallow and that a relatively large number of conformational substates are accessible. On the other hand, substrate binding and product release occur at distinct modes of the protein flexibility suggesting that these processes occur along rough energy surfaces with only a few minima. Detailed energetic analyses along the trajectories indicated that in all cases binding is dominated by van der Waals interactions. The carboxylate form of the product is stabilized by a tight hydrogen bond network involving in particular Ser82, which may be a potential cause of product inhibition. Considerations such as these should aid the understanding of mechanisms of substrate, inhibitor or product recognition and could become of importance in the design of new substrates or inhibitors for enzymes. Copyright © 2002 John Wiley & Sons, Ltd.
Mechanomyographic and Electromyographic Responses to Unilateral Isometric Training

The purpose of this investigation was to examine the effects of unilateral, isometric training of the forearm flexors on strength and the mechanomyographic (MMG) and electromyographic (EMG) responses of the biceps brachii in the trained and untrained limb at three joint angles. Seventeen adult females (mean age ± SD = 21 ± 2 years) were randomly assigned to a control (CTL; N=7) or a training (TRN; N=10) group. The TRN group performed isometric training of the non-dominant forearm flexors on a Cybex II Dynamometer at a joint angle such that the Cybex lever arm was positioned 60° above the horizontal plane. The training consisted of 3 to 5 sets of 8, 6-second repetitions at 80% of maximal voluntary contraction 3 times per week for 8 weeks. The results indicated a significant increase in flexed arm circumference as well as isometric strength in the trained limb at all three joint angles. There were, however, no changes in MMG or EMG amplitude in the trained or untrained limb and no cross-training effect for strength or flexed arm circumference. These findings suggested that the increased strength may have been due to factors associated with hypertrophy, independent of neural adaptations in the biceps brachii. Furthermore, hypertrophy may have had counteractive effects on the MMG signal that could be responsible for the lack of a training-induced change in the MMG amplitude.
Is position "special" in visual attention? Evidence that top-down processes guide visual selection.

The role of spatial position in selective visual processing has been the source of recent debate. Experiments by Tsal and Lavie (1988) and van der Heijden et al. (1996) have been designed to establish the status of position in visual selection. Tsal and Lavie found that observers tend to select letters from a briefly presented array according to position. Using the same paradigm, van der Heijden et al. found that observers tend to select according to colour, except under conditions of low contrast and unrestricted eye movements. The present study attempted to reconcile these findings by exploring the influence of top-down processes (task instructions) while explicitly controlling for eye movements. Experiment 1 demonstrated there was no inherent selection bias for stimuli similar to those used by van der Heijden et al., suggesting that the tendency to select according to colour found by van der Heijden et al. was due to task demands. Experiment 2 further established the role of top-down factors by replicating the results of van der Heijden et al. with our stimuli. Experiment 3 demonstrated that selection can be switched from colour to position by changing the demands of the task. These results suggest that selection may be accounted for by task demands (e.g., instructions) with no priority access for position information.
Biological explanations, realism, ontology, and categories

Extended review of: Processes of Life: Essays in the philosophy of biology John Dupré, Oxford University Press, Oxford, 2012, pp. 350, Price £30.00, CA$57.00, US$55.00, Hardback, ISBN-13: 9780199691982
Soil moisture variability effect on GPR data

In this paper the effect of local variability of soil moisture within the antenna footprint on GPR data is studied. A combination of GprMax3D with GPR full-wave model of Lambot and André (2013) is used for an errorless set of measurements. The GprMax3D simulations are used as real GPR measurements regarding several physical-based configurations. The Greens functions of the simulated data are extracted using calibrations based on GPR full-wave models. The inversion results of horizontal local soil moisture variability focusing on the surface wavelet reflection are compared with the averaged soil moisture values within different antenna footprints which led to the antenna footprint of -9 dB as the best. Finally, the inversion results of the vertical soil moisture variability shows significant effect of shallow soil moisture layering on the GPR-retrieved soil moisture values, which is highly correlated to the antenna height from the ground surface.
QoS-based active dropping mechanism for NGN video streaming optimization

Abstract Video streaming over mobile wireless networks is getting popular in recent years. High video quality relies on large bandwidth provisioning, however, it decreases the number of supported users in wireless networks. Thus, effective bandwidth utilization becomes a crucial issue in wireless network as the bandwidth resource in wireless environment is precious and limited. The NGN quality of service mechanisms should be designed to reduce the impact of traffic burstiness on buffer management. For this reason, we propose an active dropping mechanism to deal with the effective bandwidth utilization in this paper. We use scalable video coding extension of H.264/AVC standard to provide different video quality for users of different levels. In the proposed dropping mechanism, when the network loading exceeds the threshold, the dropping mechanism starts to drop data of the enhancement layers for users of low service level. The dropping probability alters according to the change in network loading. With the dropping mechanism, the base station increases the system capability and users are able to obtain better service quality when the system is under heavy loading. We also design several methods to adjust the threshold value dynamically. By using the proposed mechanism, better quality can be provided when the network is in congestion.
Slackers and Zealots: Civil Service, Policy Discretion, and Bureaucratic Expertise

In this paper we investigate how “civil service” personnel management interacts with bureaucratic discretion to create high capacity, expert bureaucracies populated by policy-motivated agents. We build a model in which bureaucrats may invest in (relationship specific) policy expertise, and may be either policy-motivated or policy-indifferent. We show that under specific conditions on the nature of expertise and bureaucratic discretion over policy choices, merit system protections for job tenure encourage the development of expertise and problem solving capacity in the bureaucracy. In addition, we identify conditions under which typical civil service rules encourage policy-motivated bureaucrats to enter and remain in public service, and policy- indifferent bureaucrats to leave it.