Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Yoga in Chronic Obstructive Pulmonary Disease

Yoga is adjunctively utilized outside the United States in the treatment of a variety of diseases, including chronic obstructive pulmonary disease (COPD), but there are no studies assessing its adjunctive efficacy in the United States. We prospectively evaluated the effects of yoga training on the quality of life (QOL) and the parameters of lung function in patients with COPD. Thirty-three patients with documented COPD, per Global Initiative for Obstructive Lung Disease criteria, were recruited. All patients received standard COPD care. The QOL was assessed by the St. George Respiratory questionnaire. Standard spirometry and maximum inspiratory (maximal inspiratory pressure) and expiratory pressure (maximal expiratory pressure) were measured. Patients were taught selected yoga exercises including breathing exercises, meditation, and yoga postures for 1 hour, thrice a week for 6 weeks by a certified yoga therapist. The quality of life and lung function were again assessed at the end of 6 weeks. Twenty-two patients completed the study. Differences in preyoga versus postyoga scores were evaluated using paired t-tests. Statistically significant improvements (P < 0.05) were observed for the St. George Respiratory questionnaire [95% confidence interval (CI) 43.13–58.47], vital capacity (95% CI 2.53–7.65), maximal inspiratory pressure (95% CI 6.62–23.64), and maximal expiratory pressure (95% CI 1.63–13.81). Yoga when practiced by patients with COPD results in improvement in the QOL and lung function on a short-term basis. Additional research is needed to confirm these findings in a randomized controlled trial and in the longer term.
Human Judgements of Control: The Interaction of the Current Contingency and Previous Controllability

Two experiments were carried out to determine the effects of the learned helplessness treatment on judgement of control over a outcome. In the first experiment judgements were found to be sensitive to the actual level of response-outcome contingency. When the contingency level was high, this sensitivity was also influenced by pretreatment, in that a prior uncontrollable experience gave rise to lower judgements than both a controllable one and no experience at all. The latter pretreatments produced the most accurate judgements. In the second experiment the judgements after an uncontrollable task were found to be insensitive to a previous controllable or uncontrollable pretreatment. The results are discussed in terms of contingency-learning models.
GRAPEVINE FANLEAF VIRUS: STILL A MAJOR THREAT TO THE GRAPEVINE INDUSTRY

SUMMARY Grapevine fanleaf virus (GFLV) is responsible for fanleaf degeneration, which is one of the most severe virus diseases of grapevines worldwide. GFLV causes substantial crop losses, reduces fruit quality and shortens the longevity of grapevines in the vineyard. GFLV is transmitted specifically from grapevine to grapevine by the ectoparasitic nematode Xiphinema index, and belongs to the genus Nepovirus in the family Comoviridae. Since the discovery of the nematode vector in the late 1950’s and the identification of GFLV as the agent responsible for fanleaf degeneration in the early 1960’s, a wealth of information has been accumulated on its transmission, biological properties and serological characteristics, as well as on the structure and expression of the GFLV genome. Although dissemination of the virus through propagation material has been drastically reduced over the past two decades by implementing rigorous certification schemes and establishing quarantine facilities, effective strategies are still needed to control GFLV in naturally infected vineyards. Recently, significant progress has been made on the elucidation of the function(s) of most GFLV proteins, in particular those involved in critical steps of the virus multiplication cycle, including RNA replication, cell-to-cell movement, and transmission by X. index. New insights have also been gained into the population structure and genomic variability among isolates from naturally infected vineyards, which have opened new avenues for designing alternative strategies to control this destructive virus. This review article offers a comprehensive overview of the most significant advances made over the past 15 years on GFLV and discusses novel control strategies for one of the major threats to the grapevine industry worldwide.
Collagen triple helix repeat containing 1 is overexpressed in hepatocellular carcinoma and promotes cell proliferation and motility

Although several therapeutic options are available for hepatocellular carcinoma (HCC), the outcome is still very poor. One reason is the complexity of signal transduction in the pathogenesis of HCC. The aim of this study was to identify new HCC-related genes and to investigate the functions of these genes in the pathogenesis and progression of HCC. Whole genomes of 15 surgically resected HCC specimens were examined for copy number alterations with comparative genomic hybridization. Gene expression was compared between HCC and normal liver tissues. The roles of the new genes in the progression of HCC were studied using cultured cell lines. Copy number gain in chromosome 8q was detected in 53% of HCC tissues examined. The gene that coded for collagen triple helix repeat containing 1 (CTHRC1), located at chromosome 8q22.3, was overexpressed in HCC compared with normal or liver cirrhosis tissues and identified as a new HCC-related gene. CTHRC1 deletion with short hairpin RNA significantly reduced proliferation, migration and invasion of HepG2 and Huh7 cells. In addition, mRNA of integrins β-2 and β-3 was downregulated, with deletion of CTHRC1 in these cells. Immunohistochemical staining on resected HCC tissues showing positive staining areas for CTHRC1 was significantly greater in poorly-differentiated HCC compared with well-differentiated HCC. Moreover, some cases showed strong staining for CTHRC1 in invasive areas of HCC. CTHRC1 has the potential to be a new biomarker for the aggressive HCC, and to be a new therapeutic target in treating HCC.
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Multicellular animals use a three-part molecular toolkit to mediate phospho-tyrosine signaling: Tyrosine kinases (TyrK), protein tyrosine phosphatases (PTP), and Src Homology 2 (SH2) domains function, respectively, as “writers,” “erasers,” and “readers” of phospho-tyrosine modifications. How did this system of three components evolve, given their interdependent function? Here, we examine the usage of these components in 41 eukaryotic genomes, including the newly sequenced genome of the choanoflagellate, Monosiga brevicollis, the closest known unicellular relative to metazoans. This analysis indicates that SH2 and PTP domains likely evolved earliest—a handful of these domains are found in premetazoan eukaryotes lacking tyrosine kinases, most likely to deal with limited tyrosine phosphorylation cross-catalyzed by promiscuous Ser/Thr kinases. Modern TyrK proteins, however, are only observed in two lineages, metazoans and choanoflagellates. These two lineages show a dramatic coexpansion of all three domain families. Concurrent expansion of the three domain families is consistent with a stepwise evolutionary model in which preexisting SH2 and PTP domains were of limited utility until the appearance of the TyrK domain in the last common ancestor of metazoans and choanoflagellates. The emergence of the full three-component signaling system, with its dramatically increased encoding potential, may have contributed to the advent of metazoan multicellularity.
Parallel tracking of all soccer players by integrating detected positions in multiple view images

Soccer, one of the popular sports around the world, is often broadcasted on TV, and various researches have done on soccer scene images such as strategy analysis, scene recovery, automatic indexing of soccer scenes, and automatic intelligent sports casting. As robust player tracking is fundamental to those researches, there is a demand for an automatic player tracking system using soccer imaging data. We propose a method of tracking soccer players using multiple views. Tracking is done by integrating the tracking data from all cameras, using the geometrical relationship between cameras called homography. Integrating information from all cameras enables stable tracking on the scene, where the tracking by a single camera often fails in the case of occlusion.
Structure and functional characterization of the atypical human kinase haspin

The protein kinase haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3). Its protein sequence is only weakly homologous to other protein kinases and lacks the highly conserved motifs normally required for kinase activity. Here we report structures of human haspin in complex with ATP and the inhibitor iodotubercidin. These structures reveal a constitutively active kinase conformation, stabilized by haspin-specific inserts. Haspin also has a highly atypical activation segment well adapted for specific recognition of the basic histone tail. Despite the lack of a DFG motif, ATP binding to haspin is similar to that in classical kinases; however, the ATP γ-phosphate forms hydrogen bonds with the conserved catalytic loop residues Asp-649 and His-651, and a His651Ala haspin mutant is inactive, suggesting a direct role for the catalytic loop in ATP recognition. Enzyme kinetic data show that haspin phosphorylates substrate peptides through a rapid equilibrium random mechanism. A detailed analysis of histone modifications in the neighborhood of H3T3 reveals that increasing methylation at Lys-4 (H3K4) strongly decreases substrate recognition, suggesting a key role of H3K4 methylation in the regulation of haspin activity.
An ontology for bioinformatics applications

MOTIVATION An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results. RESULTS This paper provides an overview of an ontology [the Transparent Access to Multiple Biological Information Sources (TAMBIS) ontology or TaO] that describes a wide range of bioinformatics concepts. The present paper describes the mechanisms used for delivering the ontology and discusses the ontology's design and organization, which are crucial for maintaining the coherence of a large collection of concepts and their relationships. AVAILABILITY The TAMBIS system, which uses a subset of the TaO described here, is accessible over the Web via http://img.cs. man.ac. uk/tambis (although in the first instance, we will use a password mechanism to limit the load on our server). The complete model is also available on the Web at the above URL.
The effect of dyslexia on information retrieval: A pilot study

Purpose – The purpose of this paper is to resolve a gap in the knowledge of how people with dyslexia interact with information retrieval (IR) systems, specifically an understanding of their information‐searching behaviour.Design/methodology/approach – The dyslexia cognitive profile is used to design a logging system, recording the difference between two sets of participants: dyslexic and control users. A standard Okapi interface is used – together with two standard TREC topics – in order to record the information searching behaviour of these users.Findings – Using the log data, the differences in information‐searching behaviour of control and dyslexic users, i.e. in the way the two groups interact with Okapi, are established and it also established that qualitative information collected (such as experience etc.) may not be able to account for these differences. Evidence from query variables was unable to distinguish between groups, but differences on topic for the same variables were recorded. Users who v.
Expression patterns of focal adhesion associated proteins in the developing retina

Adhesive interactions between integrin receptors and the extracellular matrix (ECM) are intimately involved in regulating development of a variety of tissues within the organism. In the present study, we have investigated the relationships between β1 integrin receptors and focal adhesion associated proteins during eye development. We used specific antibodies to examine the distribution of β1 integrin ECM receptors and the cytoplasmic focal adhesion associated proteins, talin, vinculin, and paxillin in the developing Xenopus retina. Immunoblot analysis confirmed antibody specificity and indicated that β1 integrins, talin, vinculin, and paxillin were expressed in developing retina and in the retinal‐derived Xenopus XR1 glial cell line. Triple‐labeling immunocytochemistry revealed that talin, vinculin, paxillin, and phosphotyrosine proteins colocalized with β1 integrins at focal adhesions located at the termini of F‐actin filaments in XR1 cells. In the retina, these focal adhesion proteins exhibited developmentally regulated expression patterns during eye morphogenesis. In the embryonic retina, immunoreactivities for focal adhesion proteins were expressed in neuroepithelial cells, and immunoreactivity was especially strong at the interface between the optic vesicle and overlying ectoderm. At later stages, these proteins were expressed throughout all retinal layers with higher levels of expression observed in the plexiform layers, optic fiber layer, and in the region of the inner and outer limiting membrane. Strong immunoreactivities for β1 integrin, paxillin, and phosphotyrosine were expressed in the radially oriented Müller glial cells at later stages of development. These results suggest that focal adhesion‐associated proteins are involved in integrin‐mediated adhesion and signaling and are likely to be essential in regulating retinal morphogenesis. © 2002 Wiley‐Liss, Inc.
The major central endocannabinoid directly acts at GABAA receptors

GABAA receptors are the major ionotropic inhibitory neurotransmitter receptors. The endocannabinoid system is a lipid signaling network that modulates different brain functions. Here we show a direct molecular interaction between the two systems. The endocannabinoid 2-arachidonoyl glycerol (2-AG) potentiates GABAA receptors at low concentrations of GABA. Two residues of the receptor located in the transmembrane segment M4 of β2 confer 2-AG binding. 2-AG acts in a superadditive fashion with the neurosteroid 3α, 21-dihydroxy-5α-pregnan-20-one (THDOC) and modulates δ-subunit–containing receptors, known to be located extrasynaptically and to respond to neurosteroids. 2-AG inhibits motility in CB1/CB2 cannabinoid receptor double-KO, whereas β2-KO mice show hypermotility. The identification of a functional binding site for 2-AG in the GABAA receptor may have far-reaching consequences for the study of locomotion and sedation.
Orthogonal chaotic vector shift keying in digital communications

An orthogonal chaotic vector shift keying digital communication scheme is presented. The main characteristics of the scheme are increased data transmission rates with greatly improved robustness and an increase in security of communications links because of the structure of the scheme and the nature of the message bearer. Compared with some existing schemes, for example, quadrature chaos shift keying (QCSK) reported in the literature, the noise rejection is improved by an increase in the 'inter-symbolic separation'. Furthermore, a new method of characterising non-linear processing elements in complex communication schemes has been presented. Based on this, a simple modelling and evaluation method to determine the bit error rates of these schemes is derived. Various simulated results are presented to demonstrate these achievements.
How do galaxies populate dark matter haloes

For any assumed standard stellar initial mass function, the Sloan Digital Sky Survey (SDSS) gives a precise determination of the abundance of galaxies as a function of their stellar mass over the full stellar mass range 108 M(circle dot) < M(*) < 1012 M(circle dot). Within the concordance Lambda cold dark matter (Lambda CDM) cosmology, the Millennium Simulations give precise halo abundances as a function of mass and redshift for all haloes within which galaxies can form. Under the plausible hypothesis that the stellar mass of a galaxy is an increasing function of the maximum mass ever attained by its halo, these results combine to give halo mass as a function of stellar mass. The result agrees quite well with observational estimates of mean halo mass as a function of stellar mass from stacking analyses of the gravitational lensing signal and the satellite dynamics of SDSS galaxies. For M(*) similar to 5.5 x 1010 M(circle dot), the stellar mass usually assumed for the Milky Way (MW), the implied halo mass is similar to 2 x 1012 M(circle dot), consistent with most recent direct estimates and inferences from the MW/M31 timing argument. The fraction of the baryons associated with each halo which are present as stars in its central galaxy reaches a maximum of 20 per cent at masses somewhat below that of the MW and falls rapidly at both higher and lower masses. These conversion efficiencies are lower than in almost all recent high-resolution simulations of galaxy formation, showing that these are not yet viable models for the formation of typical members of the galaxy population. When inserted in the Millennium-II Simulation, our derived relation between stellar mass and halo mass predicts a stellar mass autocorrelation function in excellent agreement with that measured directly in the SDSS. The implied Tully-Fisher relation also appears consistent with observation, suggesting that galaxy luminosity functions and Tully-Fisher relations can be reproduced simultaneously in a Lambda CDM cosmology.
LipNet: End-to-End Sentence-level Lipreading

Lipreading is the task of decoding text from the movement of a speaker's mouth. Traditional approaches separated the problem into two stages: designing or learning visual features, and prediction. More recent deep lipreading approaches are end-to-end trainable (Wand et al., 2016; Chung & Zisserman, 2016a). However, existing work on models trained end-to-end perform only word classification, rather than sentence-level sequence prediction. Studies have shown that human lipreading performance increases for longer words (Easton & Basala, 1982), indicating the importance of features capturing temporal context in an ambiguous communication channel. Motivated by this observation, we present LipNet, a model that maps a variable-length sequence of video frames to text, making use of spatiotemporal convolutions, a recurrent network, and the connectionist temporal classification loss, trained entirely end-to-end. To the best of our knowledge, LipNet is the first end-to-end sentence-level lipreading model that simultaneously learns spatiotemporal visual features and a sequence model. On the GRID corpus, LipNet achieves 95.2% accuracy in sentence-level, overlapped speaker split task, outperforming experienced human lipreaders and the previous 86.4% word-level state-of-the-art accuracy (Gergen et al., 2016).
Influence and Limitations of Popout in the Selection of Salient Visual Stimuli by Area V4 Neurons

The neural mechanism of bottom-up attention and its relationship to top-down attention are poorly understood. Visual stimuli that differ from others in their component features are salient and tend to draw attention in a bottom-up manner. “Popout” stimuli differ uniformly from surrounding items and are more easily detected than stimuli composed of a conjunction of surrounding features. We compared the responses of single area V4 neurons to popout and conjunction stimuli appearing within the classical receptive field (CRF) and found that their responses are modulated by popout. This selectivity was more robust when larger numbers of surrounding items and multiple features were included in the display, and it was absent when only a few items were presented immediately outside the CRF. In addition, the popout modulation of V4 activity was eliminated when top-down attention was directed to locations outside of the CRFs during saccade preparation, indicating that the salience of popout stimuli is not sufficient to drive selection by V4 neurons. These results demonstrate that neurons in feature-selective cortex are influenced by bottom-up attention, but that this influence is limited by top-down attention.
Encoding of local and global cues in domestic dogs’ spatial working memory

The current study investigated whether domestic dogs encode local and/or global cues in spatial working memory. Seven dogs were trained to use a source of allocentric information (local and/or global cues) to locate an attractive object they saw move and disappear behind one of the three opaque boxes arrayed in front of them. To do so, after the disappearance of the target object and out of the dogs’ knowledge, all sources of allocentric information were simultaneously shifted to a new spatial position and the dogs were forced to follow a U-shaped pathway leading to the hiding box. Out of the seven dogs that were trained in the detour problem, only three dogs learned to use the cues that were moved from trial to trial. On tests, local (boxes and experimenter) and/or global cues (walls of the room) were systematically and drastically shifted to a new position in the testing chamber. Although they easily succeeded the control trials, the three dogs failed to use a specific source of allocentric information when local and global cues were put in conflict. In discussion, we explore several hypotheses to explain why dogs have difficulties to use allocentric cues to locate a hidden object in a detour problem and why they do not differentiate the local and global cues in this particular experimental setting.
Scaling rules for diffusive drug delivery in tumor and normal tissues

Delivery of blood-borne molecules and nanoparticles from the vasculature to cells in the tissue differs dramatically between tumor and normal tissues due to differences in their vascular architectures. Here we show that two simple measures of vascular geometry—δmax and λ—readily obtained from vascular images, capture these differences and link vascular structure to delivery in both tissue types. The longest time needed to bring materials to their destination scales with the square of δmax, the maximum distance in the tissue from the nearest blood vessel, whereas λ, a measure of the shape of the spaces between vessels, determines the rate of delivery for shorter times. Our results are useful for evaluating how new therapeutic agents that inhibit or stimulate vascular growth alter the functional efficiency of the vasculature and more broadly for analysis of diffusion in irregularly shaped domains.