Miracle-dz/UniFAR-FTUs huggingface dataset:
Green Tea Phenolic Epicatechins Inhibit Hepatitis C Virus Replication via Cycloxygenase-2 and Attenuate Virus-Induced Inflammation

Chronic hepatitis C virus (HCV) infection is the leading risk factor for hepatocellular carcinoma (HCC) and chronic liver disease worldwide. Green tea, in addition to being consumed as a healthy beverage, contains phenolic catechins that have been used as medicinal substances. In the present study, we illustrated that the epicatechin isomers (+)-epicatechin and (−)-epicatechin concentration-dependently inhibited HCV replication at nontoxic concentrations by using in vitro cell-based HCV replicon and JFH-1 infectious systems. In addition to significantly suppressing virus-induced cyclooxygenase-2 (COX-2) expression, our results revealed that the anti-HCV activity of the epicatechin isomers occurred through the down-regulation of COX-2. Furthermore, both the epicatechin isomers additively inhibited HCV replication in combination with either interferon-α or viral enzyme inhibitors [2′-C-methylcytidine (NM-107) or telaprevir]. They also had prominent anti-inflammatory effects by inhibiting the gene expression of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and inducible nitrite oxide synthase as well as the COX-2 in viral protein-expressing hepatoma Huh-7 cells. Collectively, (+)-epicatechin and (−)-epicatechin may serve as therapeutic supplements for treating HCV-related diseases.
Y Chromosomal Variation Tracks the Evolution of Mating Systems in Chimpanzee and Bonobo

The male-specific regions of the Y chromosome (MSY) of the human and the chimpanzee (Pan troglodytes) are fully sequenced. The most striking difference is the dramatic rearrangement of large parts of their respective MSYs. These non-recombining regions include ampliconic gene families that are known to be important for male reproduction,and are consequently under significant selective pressure. However, whether the published Y-chromosomal pattern of ampliconic fertility genes is invariable within P. troglodytes is an open but fundamental question pertinent to discussions of the evolutionary fate of the Y chromosome in different primate mating systems. To solve this question we applied fluorescence in situ hybridisation (FISH) of testis-specific expressed ampliconic fertility genes to metaphase Y chromosomes of 17 chimpanzees derived from 11 wild-born males and 16 bonobos representing seven wild-born males. We show that of eleven P. troglodytes Y-chromosomal lines, ten Y-chromosomal variants were detected based on the number and arrangement of the ampliconic fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y)—a so-far never-described variation of a species' Y chromosome. In marked contrast, no variation was evident among seven Y-chromosomal lines of the bonobo, P. paniscus, the chimpanzee's closest living relative. Although, loss of variation of the Y chromosome in the bonobo by a founder effect or genetic drift cannot be excluded, these contrasting patterns might be explained in the context of the species' markedly different social and mating behaviour. In chimpanzees, multiple males copulate with a receptive female during a short period of visible anogenital swelling, and this may place significant selection on fertility genes. In bonobos, however, female mate choice may make sperm competition redundant (leading to monomorphism of fertility genes), since ovulation in this species is concealed by the prolonged anogenital swelling, and because female bonobos can occupy high-ranking positions in the group and are thus able to determine mate choice more freely.
A More Complete Picture of School Resource Policies

Meta-analytic techniques for summarizing information about the relationship between school resources and student performance are capable only of addressing the narrow and uninteresting hypothesis that resources are never used effectively by schools. The data show clearly that resources are sometimes used effectively, although this happens infrequently and there is no description of the circumstances under which resources are used effectively. This article relates the basic evidence on school effectiveness to the specific application of meta-analytic methods employed by Greenwald, Hedges, and Laine (1996). Their analysis, suffering from the narrowness of the inquiry inherent in their statistical methods, is also based on a very highly selected sample of results that biases their analysis precisely toward their conclusions. As a result, their summary of existing work provides a distorted and misleading view of the potential implications of school resource policies. Both detailed econometric evidence and aggregate performance of U.S. schools point toward serious problems with inefficient use of resources. This evidence in turn suggests that lack of resources is not the largest problem facing schools and that more fundamental reforms are needed in schools.
Come FLY with us: toward understanding fragile X syndrome

The past few years have seen an increased number of articles using Drosophila as a model system to study fragile X syndrome. Phenotypic analyses have demonstrated an array of neuronal and behavioral defects similar to the phenotypes reported in mouse models as well as human patients. The availability of both cellular and molecular tools along with the power of genetics makes the tiny fruit fly a premiere model in elucidating the molecular basis of fragile X syndrome. Here, we summarize the advances made in recent years in the characterization of fragile X Drosophila models and the identification of new molecular partners in neural development.
Using frontier points to recover shape, reflectance and illumination

We describe a method to recover the surface reflectance and the 3D shape of a non-Lambertian object as well as illumination, from a collection of images. It is based on the so-called frontier points, which are extracted from the outlines of an object. Frontier points provide 3D locations on the object surface where the surface normal is known. This information is exploited to infer the surface reflectance of the object and the light distribution of the scene both under varying illumination and fixed vantage point, and under varying vantage point and fixed illumination. We also show how to apply frontier points for shape recovery in photometric stereo. The effectiveness of frontier points for recovering reflectance, illumination and shape is confirmed by a number of experiments on both real and synthetic data.
Modeling and analysis of sequential processes that cooperate through buffers

Deterministically synchronized sequential processes (DSSP) are a subclass of Petri nets, well suited for the methodical construction of models of concurrent systems where several agents cooperate through asynchronous message passing, In this paper, DSSP are presented, illustrating their usability in manufacturing systems. They are compared to other more restrictive subclasses of Petri nets used for similar purposes. In spite of being more expressive, DSSP still enjoy many strong analytical results, some of which are derived and illustrated in the paper.
The interaction of waves and a turbulent current: waves propagating against the current

The results of an experimental study of the interaction between waves and a current propagating in the same direction, have been reported by Kemp & Simons (1982). This paper describes the second part of the study, and considers the case of waves propagating against the current. Tests were performed in a laboratory flume with smooth and rough beds, and velocity measurements were made with a directionally sensitive laser anemometer as described in the previous paper. Analysis, including ensemble averaging of velocities and surface elevation, was performed by an on-line computer. Results indicate that the rate of wave attenuation is greatly increased by the addition of an opposing current, and reduced by a following current. Wave profiles remain closely described by Stokes second-order theory; orbital velocities are also found to be in agreement with a second-order wave theory modified to take account of the presence of the current. Certain results described occur regardless of the relative directions of current and wave. Mean velocities in the upper flow increase in the direction of the wave generator for increasing wave height. This suggests that the current is enhancing the wave-induced mass transport. Near the bed the velocity profiles so change that above the rough bed the current is retarded by the wave motion. In the logarithmic layer over the smooth bed velocities are increased with increasing wave height. However, all changes to velocity profiles have to be carefully interpreted, as the sidewall boundary layer decreases in thickness with even the smallest wave superimposed on the current. Turbulence intensities and Reynolds stresses near the rough bed are increased by the presence of the waves, most strongly in a layer two roughness heights above bed level, where fluctuations are periodic and effected by vortices ejected from the roughness troughs. Above this level, and over the smooth bed, turbulence levels are similar to those for the currents alone.
Cyclooxygenases 1 and 2 Differentially Regulate Blood Pressure and Cerebrovascular Responses to Acute and Chronic Intermittent Hypoxia: Implications for Sleep Apnea

Background Obstructive sleep apnea (OSA) is associated with increased risk of cardiovascular and cerebrovascular disease resulting from intermittent hypoxia (IH)‐induced inflammation. Cyclooxygenase (COX)‐formed prostanoids mediate the inflammatory response, and regulate blood pressure and cerebral blood flow (CBF), but their role in blood pressure and CBF responses to IH is unknown. Therefore, this study's objective was to determine the role of prostanoids in cardiovascular and cerebrovascular responses to IH. Methods and Results Twelve healthy, male participants underwent three, 6‐hour IH exposures. For 4 days before each IH exposure, participants ingested a placebo, indomethacin (nonselective COX inhibitor), or Celebrex® (selective COX‐2 inhibitor) in a double‐blind, randomized, crossover study design. Pre‐ and post‐IH blood pressure, CBF, and urinary prostanoids were assessed. Additionally, blood pressure and urinary prostanoids were assessed in newly diagnosed, untreated OSA patients (n=33). Nonselective COX inhibition increased pre‐IH blood pressure (P≤0.04) and decreased pre‐IH CBF (P=0.04) while neither physiological variable was affected by COX‐2 inhibition (P≥0.90). Post‐IH, MAP was elevated (P≤0.05) and CBF was unchanged with placebo and nonselective COX inhibition. Selective COX‐2 inhibition abrogated the IH‐induced MAP increase (P=0.19), but resulted in lower post‐IH CBF (P=0.01). Prostanoids were unaffected by IH, except prostaglandin E2 was elevated with the placebo (P=0.02). Finally, OSA patients had elevated blood pressure (P≤0.4) and COX‐1 formed thromboxane A2 concentrations (P=0.02). Conclusions COX‐2 and COX‐1 have divergent roles in modulating vascular responses to acute and chronic IH. Moreover, COX‐1 inhibition may mitigate cardiovascular and cerebrovascular morbidity in OSA. Clinical Trial Registration URL: www.clinicaltrials. gov. Unique identifier: NCT01280006
The effect of celery (Apium graveolens) on reproductive parameters in male wistar rat

* Corresponding Author: Tel: +9851138763852 Fax: +9851138763852 DR_ALIghorbani87@yahoo.com Dear editor In recent years, the number of scientific research papers of Iranian scientists has substantially grown in national and international journals that indicates particular attitude of Iranian scientific community to the development of knowledge in different fields. Moreover, improvement of quality of scientific papers is necessary. For this purpose, criticism of published studies is a way to increase the quality of articles and make them clear. In Avicenna Journal of Phytomedicine, volume (5), issue (2), year 2015, an article entitled “Effects of aqueous extract of celery (Apium graveolens L.) leaves on spermatogenesis in healthy male rats” was published and the papers like this should be appreciated. However, the paper has some drawbacks which if not resolve, could be misleading for researchers who tend to use it or do research in its direction. So, with all due respect to the research team, we decided to evaluate the paper ambiguities in order to improve the quality of future articles.
Bioavailability and Brain-Targeting of Geniposide in Gardenia-Borneol Co-Compound by Different Administration Routes in Mice

Both geniposide (Ge) and borneol (Bo) are bioactive substances derived from traditional Chinese medicine. Injections containing co-compound of Gardenia-Borneol are widely used for stroke treatment in China, such as “Xingnaojing” multi-component injection. As more and more adverse reactions (especially drug allergy) were reported, it is urgent to find more effective and safer routes of administration for such kinds of medicines. In this paper, bioavailabilities and brain-target effects of geniposide in Gardenia-Borneol co-compound through different administration routes in mice were investigated. Geniposide concentrations in plasma and in brain of mice were determined by reversed-phase high-performance liquid chromatography. The pharmacokinetics parameters of intranasal (i.n.) and intragastric (i.g.) administration were compared with intravenous (i.v.) administration. The bioavailabilities of Ge were 85.38% and 28.76% for i.n. and i.g. while Tmax were 1 min and 30 min. Cmax were 21.881 ± 5.398, 1.914 ± 0.327 and 42.410 ± 6.268 μg/mL for i.n. , i.g. and i.v. , respectively. The AUC of Ge in brain were 32413.6 ± 4573.9, 6440.1 ± 863.7 and 37270.5 ± 4160.6 ng/g·min for i.n. , i.g. and i.v. , respectively. The drug target indexes (DTI) were 1.02 and 0.60 for i.n. and i.g. The results demonstrated that geniposide could be absorbed promptly and thoroughly by i.n. administration in mice and basically transported into the brain though blood vessel passways.
Optimization of thermostable alkaline protease production from species of Bacillus using rice bran

A protease producing microorganism was isolated from soil collected from a detergent industry and identified as Bacillus species. Isolate K-30 produced thermostable alkaline protease utilizing rice bran. The optimum conditions for protease activity was 55°C at pH 9 with 4% inoculum in the medium containing 1% rice bran after 96 h of incubation. Beef extract, tryptone and yeast extract were good nitrogen sources while lactose, starch, and sucrose were suitable for enzyme production. The extracellular production of the enzyme, its thermostable nature and compatibility with most commercial detergents are features which suggest its application in the detergent industry.
Monte Carlo Localization: Efficient Position Estimation for Mobile Robots

This paper presents a new algorithm for mobile robot localization, called Monte Carlo Localization (MCL). MCL is a version of Markov localization, a family of probabilistic approaches that have recently been applied with great practical success. However, previous approaches were either computationally cumbersome (such as grid-based approaches that represent the state space by high-resolution 3D grids), or had to resort to extremely coarse-grained resolutions. Our approach is computationally efficient while retaining the ability to represent (almost) arbitrary distributions. MCL applies sampling-based methods for approximating probability distributions, in a way that places computation "where needed. " The number of samples is adapted on-line, thereby invoking large sample sets only when necessary. Empirical results illustrate that MCL yields improved accuracy while requiring an order of magnitude less computation when compared to previous approaches. It is also much easier to implement.
Two Genomes Are Better Than One: Widespread Paleopolyploidy in Plants and Evolutionary Effects

Polyploidy, or whole genome duplication resulting in the doubling of chromosome numbers, is widespread among the flowering plants and is widely believed to play an important role in species evolution and diversification ([Otto and Whitton, 2000][1]; [Wendel, 2000][2]). It was proposed more than 50
TRIM28 regulates the nuclear accumulation and toxicity of both alpha-synuclein and tau

Several neurodegenerative diseases are driven by the toxic gain-of-function of specific proteins within the brain. Elevated levels of alpha-synuclein (α-Syn) appear to drive neurotoxicity in Parkinson's disease (PD); neuronal accumulation of tau is a hallmark of Alzheimer's disease (AD); and their increased levels cause neurodegeneration in humans and model organisms. Despite the clinical differences between AD and PD, several lines of evidence suggest that α-Syn and tau overlap pathologically. The connections between α-Syn and tau led us to ask whether these proteins might be regulated through a shared pathway. We therefore screened for genes that affect post-translational levels of α-Syn and tau. We found that TRIM28 regulates α-Syn and tau levels and that its reduction rescues toxicity in animal models of tau- and α-Syn-mediated degeneration. TRIM28 stabilizes and promotes the nuclear accumulation and toxicity of both proteins. Intersecting screens across comorbid proteinopathies thus reveal shared mechanisms and therapeutic entry points. DOI: http://dx.doi. org/10.7554/eLife.19809. 001
Diminished suppression of the P50 auditory evoked potential in bipolar disorder subjects with a history of psychosis.

OBJECTIVE People with schizophrenia, schizoaffective disorder, and bipolar illness share clinical symptoms, biological findings, and genetic susceptibility. Diminished suppression of the P50 auditory evoked potential is a phenotype used in studies of genetic susceptibility in schizophrenia. In patients with acute mania, this inhibitory deficit has been correlated with severity of clinical symptoms. This study addresses whether diminished P50 auditory evoked potential suppression represents a phenotype associated with psychosis in bipolar illness. METHOD The P50 auditory evoked potential response to paired stimuli was measured in 64 subjects with bipolar illness. The Structured Clinical Interview for DSM-IV and a life chart determined diagnosis. The Beck Depression Inventory, Young Mania Rating Scale, and the Positive and Negative Syndrome Scale measured severity of current illness. Groups were compared with previously collected data from 36 schizophrenia patients and 42 healthy subjects. RESULTS P50 suppression significantly differed between bipolar disorder patients with a lifetime history of psychosis and healthy subjects. P50 suppression in bipolar disorder patients without a history of psychosis did not differ from that of the healthy subjects. Severity of current symptoms did not correlate with P50 suppression. CONCLUSIONS A longitudinal history of psychosis in subjects with bipolar illness was associated with diminished suppression of the P50 auditory evoked potential. This deficit may represent a common physiological mechanism associated with the vulnerability to psychosis in people with bipolar illness as well as in people with schizophrenia.
Time‐dependent response of the global ocean clathrate reservoir to climatic and anthropogenic forcing

Buffett and Archer (2004) showed a model of the steady state global ocean clathrate reservoir that reproduces drill data and predicts a global methane inventory of about 5000 Gton C. The model inventory is very sensitive to ocean temperature, with factor‐of‐two changes in methane inventory in response to temperature changes of 1.5°C. Here we explore the potential time‐dependent behavior of the clathrate reservoir, assuming simple first‐order rate constants for methane accumulation and meltdown in response to changes in the predicted steady state reservoir. For melting, we divide the reservoir into two parts, one melting catastrophically and the other slowly. Evolution of clathrates through geologic time is very sensitive to the choice of these rate constants. A positive feedback exists during a transient meltdown event, stronger if the catastrophic‐melting fraction is high and its melting timescale is fast. A clathrate reservoir governed by such kinetics would melt down periodically, on a multimillion‐year timescale determined by the rate constant for clathrate accumulation. Ideally, we would like a model that predicts runaway melting in the Paleocene and stability in the Pleistocene. However, the model is most unstable when climate is cold, rather than warm. Opting for stability in the Pleistocene constrains the melting kinetic parameters, leaving one degree of freedom. The grow‐in timescale must be 5 Myr or longer, to get the deglacial δ13C right, but shorter than 10 Myr, in order for clathrates to have built up through geologically recent cooling. The model thus constrained predicts methane fluxes of 200 Gton C or less on deglaciations, but eventual releases of 2000–4000 Gton C in response to a ∼2000 Gton C anthropogenic carbon release. Anthropogenic climate change differs from a deglaciation in that it warms the ocean to temperatures not seen in millions of years.
Prestimulus oscillatory power and connectivity patterns predispose conscious somatosensory perception

Significance Experimental use of near-threshold stimuli is regarded as an important approach to study neural processes leading to conscious access (defined in operational terms as “reportability”). Looking to what extent prestimulus periods contribute to the variability of perceptual states has become increasingly popular, frequently pointing to an increased excitability of relevant sensory regions. Here, we aim to extend this “local” perspective by a network approach. A framework called “Windows to Consciousness” is introduced. We postulate that along with an enhanced excitability, preestablished pathways of information flow are a crucial ingredient, determining whether an upcoming near-threshold stimulus will be consciously perceived. Using magnetoencephalography combined with state-of-the-art source-imaging approaches, we are able to report supportive evidence. Which aspects of our sensory environment enter conscious awareness does not only depend on physical features of the stimulus, but also critically on the so-called current brain state. Results from magnetoencephalography/EEG studies using near-threshold stimuli have consistently pointed to reduced levels of α- (8–12 Hz) power in relevant sensory areas to predict whether a stimulus will be consciously perceived or not. These findings have been mainly interpreted in strictly “local” terms of enhanced excitability of neuronal ensembles in respective cortical regions. The present study aims to introduce a framework that complements this rather local perspective, by stating that the functional connectivity architecture before stimulation will predetermine information flow. Thus, information computed at a local level will be distributed throughout a network, thereby becoming consciously accessible. Data from a previously published experiment on conscious somatosensory near-threshold perception was reanalyzed focusing on the prestimulus period. Analysis of spectral power showed reduced α-power mainly in the contralateral S2 and middle frontal gyrus to precede hits, thus overall supporting the current literature. Furthermore, differences between hits and misses were obtained on global network (graph theoretical) features in the same interval. Most importantly, in accordance with our framework, we could show that the somatosensory cortex is “more efficiently” integrated into a distributed network in the prestimulus period. This finding means that when a relevant sensory stimulus impinges upon the system, it will encounter preestablished pathways for information flow. In this sense, prestimulus functional connectivity patterns form “windows” to conscious perception.