Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptation to Prisms: Do Proprioceptive Changes Mediate Adapted Behaviour with Ballistic Arm Movements?

In Experiment I subjects pointed repeatedly at a target viewed through laterally displacing prisms and received terminal visual feedback. In one task the pointing movements were slow (proprioceptively controlled), and in the other they were fast (pre-programmed). In both tasks adaptation proceeded at the same rate and to the same level of performance. Following fast pointing with prisms a large amount of arm-body adaptation was found with slow and fast test movements, while following slow pointing with prisms a large amount of arm-body adaptation was found with slow test movements, but only a small amount with fast test movements. The result suggests that adapted behaviour with preprogrammed movements is not mediated by a proprioceptive change. In Experiment II pointing movements were passive. No arm-body adaptation was found with fast test movements, and, contrary to expectation, only a small amount with slow test movements.
Functional neuroimaging of sex differences in autobiographical memory recall in depression

Background Females are more likely than males to develop major depressive disorder (MDD). The current study used fMRI to compare the neural correlates of autobiographical memory (AM) recall between males and females diagnosed with MDD. AM overgenerality is a persistent cognitive deficit in MDD, the magnitude of which is correlated with depressive severity only in females. Delineating the neurobiological correlates of this deficit may elucidate the nature of sex-differences in the diathesis for developing MDD. Methods Participants included unmedicated males and females diagnosed with MDD (n = 20/group), and an age and sex matched healthy control group. AM recall in response to positive, negative, and neutral cue words was compared with a semantic memory task. Results The behavioral properties of AMs did not differ between MDD males and females. In contrast, main effects of sex on cerebral hemodynamic activity were observed in left dorsolateral prefrontal cortex and parahippocampal gyrus during recall of positive specific memories, and middle prefrontal cortex (mPFC), and precuneus during recall of negative specific memories. Moreover, main effects of diagnosis on regional hemodynamic activity were observed in left ventrolateral prefrontal cortex and mPFC during positive specific memory recall, and dorsal anterior cingulate cortex during negative specific memory recall. Sex × diagnosis interactions were evident in the dorsomedial prefrontal cortex, caudate, and precuneus during positive memory recall, and in the posterior cingulate cortex, insula, precuneus and thalamus during negative specific memory recall. Conclusions The differential hemodynamic changes conceivably may reflect sex-specific cognitive strategies during recall of AMs irrespective of the phenomenological properties of those memories.
Are School Boards aware of the educational quality of their schools?

School boards are expected to monitor and enhance the educational quality of their schools. To know whether and how school boards are able to do so, we first of all need to know whether school boards are aware of the educational quality of their schools in the first place. Taking Dutch school boards in primary education as an exemplary case (N = 332) we developed and tested a path model using structural equation modelling to analyse the extent to which school boards discern educational quality in their schools. The results show that, in general, school boards in primary education believe that they can contribute to enhancing the quality of school education. If the school board and school(s) management stick to their governing and management roles respectively, this positively affects the extent to which the school board is able to identify educational quality in the schools it governs.
Setting Up the JBrowse Genome Browser

JBrowse is a Web‐based tool for visualizing genomic data. Unlike most other Web‐base genome browsers, JBrowse exploits the capabilities of the user's Web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all Internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a Web server, and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a Web site that other users can visit to browse the genomic data. Curr. Protoc. Bioinform. 32:9.13. 1‐9.13. 13. © 2010 by John Wiley & Sons, Inc.
Working for washback: a review of the washback concept in language testing

This article is a literature review which seeks to answer four questions: 1) What is washback? 2) How does washback work? 3) How can we promote positive washback? 4) How can we investigate washback? Building on the 'Washback Hypothesis' proposed by Alderson and Wall, and suggestions from Hughes, the article proposes a model that identifies participants, processes and products which may influence, or be influenced by, washback. Strategies for investigating wash back are also discussed.
Team Turnover and Task Conflict: A Longitudinal Study on the Moderating Effects of Collective Experience

Team turnover can be harmful to a team in many ways. This study examined whether a team’s collective experience (team organizational tenure) attenuates the association between team turnover and task conflict changes. Differing from prior research, our study used a longitudinal design to assess the effects of team turnover, accounting for the competence of those leaving the team. We built on context-emergent turnover theory and tested a random coefficient growth model by utilizing data from 74 health-care teams. We found support for the hypothesized interaction: The more collective experience the team had, the less likely it was that team turnover associated with increases in task conflict. We discuss implications for theory and practice.
Accurate and efficient query clustering via top ranked search results

To make the search engine more user-friendly, commercial search engines commonly develop applications to provide suggestion or recommendation for every posed query. Clustering semantically similar queries acts as an essential prerequisite to function well in those applications. However, clustering queries effectively is quite challenging, since they are usually short, incomplete and ambiguous. Existing prevalent clustering methods, such as K-Means or DBSCAN cannot guarantee good performance in such a highly dimensional environment. Through analyzing users’ click-through query logs, hierarchical agglomerative clustering gives good results but is computationally quite expensive. This paper identifies a novel feature for clustering search queries based on a key insight – queries’ top ranked search results can themselves be used to quantify query similarity. After investigating such feature, we propose a new similarity metric for comparing those diverse queries. This facilitates us to develop two very efficient and accurate algorithms integrated in query clustering. We conduct comprehensive experiments to compare the accuracy of our approach against the known baselines along two dimensions: 1) quantifying the cohesion/separation of clustered queries, and 2) justifying the results by real-world Internet users. The experimental results demonstrate that our two algorithms and the similarity metric can generate more accurate results within a significantly shorter time.
Mutations that permit efficient replication of hepatitis C virus RNA in Huh-7 cells prevent productive replication in chimpanzees

The development of a subgenomic replicon derived from the hepatitis C virus (HCV) strain Con1 enabled the study of viral RNA replication in Huh-7 cells. The level of replication of replicons, as well as full-length Con1 genomes, increased significantly by a combination of two adaptive mutations in NS3 (E1202G and T1280I) and a single mutation in NS5A (S2197P). However, these cell culture-adaptive mutations influenced in vivo infectivity. After intrahepatic transfection of chimpanzees, the wild-type Con1 genome was infectious and produced viral titers similar to those produced by other infectious HCV clones. Repeated independent transfections with RNA transcripts of a Con1 genome containing the three adaptive mutations failed to achieve active HCV infection. Furthermore, although a chimpanzee transfected with RNA transcripts of a Con1 genome with only the NS5A mutation became infected, this mutation was detected only in virus genomes recovered from serum at day 4; viruses recovered at day 7 had a reversion back to the original Con1 sequence. Our study demonstrates that mutations that are adaptive for replication of HCV in cell culture may be highly attenuating in vivo.
Side chain oxidized oxysterols in cerebrospinal fluid and the integrity of blood-brain and blood-cerebrospinal fluid barriers Published, JLR Papers in Press, February 1, 2003. DOI 10.1194/jlr.M200434-JLR200

The side chain oxidized oxysterol 24S-hydroxycholesterol (24-OH-chol) is formed almost exclusively in the brain, and there is a continuous passage of this oxysterol through the circulation to the liver. 27-Hydroxycholesterol (27-OH-chol) is produced in most organs and is also taken up by the liver. The 27-OH-chol-24-OH-chol ratio is about 0.1 in the brain and about 2 in the circulation. This ratio was found to be about 0.4 in cerebrospinal fluid (CSF) of asymptomatic patients, consistent with a major contribution from the circulation in the case of 27-OH-chol. In accordance with this, we demonstrated a significant flux of deuterium labeled 27-OH-chol from plasma to the CSF in a healthy volunteer. Patients with a defective blood-brain barrier were found to have markedly increased absolute levels (up to 10-fold) of both 27-OH-chol and 24-OH-chol in CSF, with a ratio between the two sterols reaching up to 2. There was a significant positive correlation between the levels of both oxysterols in CSF and the albuminCSF-albuminplasma ratio. The 27-OH-cholCSF-24-OH-cholCSF ratio was found to be about normal in patients with active multiple sclerosis and significantly increased in patients with meningitis, polyneuropathy, or hemorrhages. Results are discussed in relation to the possible use of 24-OH-cholCSF as a surrogate marker of central nervous system demyelination and/or neuronal death.
Plasmid-Mediated Resistance to Thrombin-Induced Platelet Microbicidal Protein in Staphylococci: Role of theqacA Locus

ABSTRACT Thrombin-induced platelet microbicidal protein 1 (tPMP-1) is a small, cationic peptide released from rabbit platelets following thrombin stimulation. In vitro resistance to this peptide among strains of Staphylococcus aureus correlates with the survival advantage of such strains at sites of endothelial damage in humans as well as in experimental endovascular infections. The mechanisms involved in the phenotypic resistance of S. aureus to tPMP-1 are not fully delineated. The plasmid-encoded staphylococcal gene qacA mediates multidrug resistance to multiple organic cations via a proton motive force-dependent efflux pump. We studied whether the qacA gene might also confer resistance to cationic tPMP-1. Staphylococcal plasmids encoding qacA were found to confer resistance to tPMP-1 in an otherwise susceptible parental strain. Deletions which removed the region containing theqacA gene in the S. aureus multiresistance plasmid pSK1 abolished tPMP-1 resistance. Resistance to tPMP-1 in theqacA-bearing strains was inoculum independent but peptide concentration dependent, with the level of resistance decreasing at higher peptide concentrations for a given inoculum. There was no apparent cross-resistance in qacA-bearing strains to other endogenous cationic antimicrobial peptides which are structurally distinct from tPMP-1, including human neutrophil defensin 1, protamine, or the staphylococcal lantibiotics pep5 and nisin. These data demonstrate that the staphylococcal multidrug resistance geneqacA also mediates in vitro resistance to cationic tPMP-1.
Debating the Land Question in Africa

In February 2000, twenty years after their victories brought Rhodesia's ruling white regime to the conference table, veterans of Zimbabwe's war of liberation began to occupy some of the large privately owned commercial farms that controlled Zimbabwe's most valuable land. During the next few weeks, thousands of people followed suit: by May, nearly a third of the country's large-scale commercial farms had been seized (New York Times, 27 May 2000; Moyo 1998). Armed with a court order, landowners demanded that the “squatters” be evicted, but the police demurred, and President Mugabe refused to order them to carry out the court's instructions. A few weeks earlier, voters had rejected a proposed constitutional amendment that would have strengthened the President's powers to seize white-owned land, without compensation, for redistribution to land-hungry blacks. Angry over the deteriorating economy, rising levels of corruption, and Zimbabwe's costly involvement in Congo's civil war, a majority of those who voted were unwilling to increase the President's powers, even if they supported the cause of land reform. When the veterans took matters into their own hands, Mugabe lost no time in associating with their cause. He, in turn, was accused by Western governments, the opposition Movement for Democratic Change, and the international press, of sacrificing the rule of law in order to save his own political skin.
AITSO: A Tool for Spatial Optimization Based on Artificial Immune Systems

A great challenge facing geocomputation and spatial analysis is spatial optimization, given that it involves various high-dimensional, nonlinear, and complicated relationships. Many efforts have been made with regard to this specific issue, and the strong ability of artificial immune system algorithms has been proven in previous studies. However, user-friendly professional software is still unavailable, which is a great impediment to the popularity of artificial immune systems. This paper describes a free, universal tool, named AITSO, which is capable of solving various optimization problems. It provides a series of standard application programming interfaces (APIs) which can (1) assist researchers in the development of their own problem-specific application plugins to solve practical problems and (2) allow the implementation of some advanced immune operators into the platform to improve the performance of an algorithm. As an integrated, flexible, and convenient tool, AITSO contributes to knowledge sharing and practical problem solving. It is therefore believed that it will advance the development and popularity of spatial optimization in geocomputation and spatial analysis.
Multi-class semi-supervised SVMs with Positiveness Exclusive Regularization

In this work, we address the problem of multi-class classification problem in semi-supervised setting. A regularized multi-task learning approach is presented to train multiple binary-class Semi-Supervised Support Vector Machines (S3VMs) using the one-vs-rest strategy within a joint framework. A novel type of regularization, namely Positiveness Exclusive Regularization (PER), is introduced to induce the following prior: if an unlabeled sample receives significant positive response from one of the classifiers, it is less likely for this sample to receive positive responses from the other classifiers. That is, we expect an exclusive relationship among different S3VMs for evaluating the same unlabeled sample. We propose to use an ℓ1,2-norm regularizer as an implementation of PER. The objective of our approach is to minimize an empirical risk regularized by a PER term and a manifold regularization term. An efficient Nesterov-type smoothing approximation based method is developed for optimization. Evaluations with comparisons are conducted on several benchmarks for visual classification to demonstrate the advantages of the proposed method.
The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus

Transfer RNA (m1G37) methyltransferase (TrmD) catalyzes methyl‐transfer from S‐adenosyl‐L‐methionine to the N1 atom of G37 in tRNA. In Escherichia coli cells, TrmD methylates tRNA species possessing a G36G37 sequence. It was previously believed that G36 was the positive determinant of TrmD recognition. In the current study, we demonstrate that TrmD from Aquifex aeolicus methylates tRNA transcripts possessing an A36G37 sequence as well as tRNA transcripts possessing a G36G37 sequence. In contrast, tRNA transcripts possessing pyrimidine36G37 were not methylated at all. These substrate specificities were confirmed by an in vitro kinetic assay using 16 tRNA transcripts. The modified nucleoside and the position in yeast tRNAPhe transcript were confirmed by LC/MS. Furthermore, nine truncated tRNA molecules were tested to clarify the additional recognition site. Unexpectedly, A. aeolicus TrmD protein efficiently methylated the micro helix corresponding to the anti‐codon arm. Because the disruption of the anti‐codon stem caused the complete loss of the methyl group acceptance activity, the anti‐codon stem is essential for the recognition. Moreover, the existence of the D‐arm structure inhibited the activity. Recently, it was reported that E. coli TrmD methylates yeast tRNAPhe harboring a sequence A36G37. Thus, recognition of the purine36G37 sequence is probably common to eubacteria TrmD proteins.
The Role of PI3K/Akt/mTOR Signaling in Gastric Carcinoma

The phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway is one of the key signaling pathways induced by various receptor-tyrosine kinases. Accumulating evidence shows that this pathway is an important promoter of cell growth, metabolism, survival, metastasis, and resistance to chemotherapy. Genetic alterations in the PI3K/Akt/mTOR pathway in gastric carcinoma have often been demonstrated. Many kinds of molecular targeting therapies are currently undergoing clinical testing in patients with solid tumors. However, with the exception of the ErbB2-targeting antibody, targeting agents, including PI3K/Akt/mTOR inhibitors, have not been approved for treatment of patients with gastric carcinoma. This review summarizes the current knowledge on PI3K/Akt/mTOR signaling in the pathogenesis of gastric carcinoma and the possible therapeutic targets for gastric carcinoma. Improved knowledge of the PI3K/Akt/mTOR pathway in gastric carcinoma will be useful in understanding the mechanisms of tumor development and for identifying ideal targets of anticancer therapy for gastric carcinoma.
Survival trees for left‐truncated and right‐censored data, with application to time‐varying covariate data

&NA; Tree methods (recursive partitioning) are a popular class of nonparametric methods for analyzing data. One extension of the basic tree methodology is the survival tree, which applies recursive partitioning to censored survival data. There are several existing survival tree methods in the literature, which are mainly designed for right‐censored data. We propose two new survival trees for left‐truncated and right‐censored (LTRC) data, which can be seen as a generalization of the traditional survival tree for right‐censored data. Further, we show that such trees can be used to analyze survival data with time‐varying covariates, essentially building a time‐varying covariates survival tree. Implementation of the methods is easy, and simulations and real data analysis results show that the proposed methods work well for LTRC data and survival data with time‐varying covariates, respectively.
Field Evaluation of a Rapid Immunochromatographic Test for Tuberculosis

ABSTRACT Rapid diagnostic tests for tuberculosis (TB) are needed to facilitate early treatment of TB and prevention of Mycobacterium tuberculosis transmission. The ICT Tuberculosis test is a rapid, card-based immunochromatographic test for detection of antibodies directed against M. tuberculosis antigens. The objective of the study was to evaluate the performance of the ICT Tuberculosis test for the diagnosis of active pulmonary TB (PTB) with whole blood, plasma, and serum from patients suspected of having PTB and from asymptomatic controls in a setting with a high prevalence of PTB. Seventy patients suspected of having PTB (and who were later confirmed to have or not to have PTB by use of M. tuberculosis culture as the “gold standard”) and 42 controls were studied. Twenty-one controls were neither vaccinated with Mycobacterium bovis bacillus Calmette-Guérin (BCG) nor tuberculin skin test (TST) positive (group A controls), and 21 controls were TST positive and/or had previously been vaccinated with BCG (group B controls). Study subjects were drawn from one hospital and one primary health care unit in Rio de Janeiro City, Brazil. One version of the test (ICT-1) was evaluated by using whole blood, plasma, and serum samples. Sera obtained for this study were frozen and later tested with a manufacturer-modified version of the test (ICT-2). Among the patients suspected of having PTB, the sensitivities of the ICT-1 with whole blood, serum, and plasma were 83, 65, and 70%, respectively, and the specificities were 46, 67, and 56%, respectively. Among the group A controls, the specificities of ICT-1 with the three specimen types were 95, 100, and 95%, respectively. Among the group B controls, the specificities of ICT-1 with the three specimen types were 71, 86, and 86%, respectively. Among the patients suspected of having PTB, the sensitivity of ICT-2 was 70% and the specificity was 65%. Among the group A controls, the specificity of ICT-2 was 95%, and among the group B controls, the specificity of ICT-2 was 81%. With a 29% observed prevalence of PTB among patients suspected of having PTB, the positive predictive values of the ICT tests ranged from 39 to 50% and the negative predictive values ranged from 82 to 87%. The ICT Tuberculosis tests were not sufficiently predictive to warrant their widespread use as routine diagnostic tests for PTB in this setting. However, further evaluation of these tests in specific epidemiologic settings may be warranted.
An alternative method for predicting attrition from an alcohol treatment programme.

AIMS To test the predictive validity of a vignette methodology based on a Signal Detection model by examining treatment attrition within an alcohol clinic. METHODS Participants were asked to categorize vignettes that described individuals drinking alcohol as problem or nonproblem alcohol use at the beginning of a 4-week intensive course of treatment. These participants were divided retrospectively into two groups: those who completed treatment and those who dropped-out of treatment. A matched post-treatment long-term abstainer group was also tested. RESULTS Signal Detection analyses demonstrated that response bias scores predicted who would drop out of treatment (P = 0.01). CONCLUSIONS The vignette methodology provided useful levels of prediction in an applied clinical setting. It was argued that verbal reports from problem alcohol users may be more usefully conceptualized in terms of sensitivity and response bias than in terms of memory or 'truth'.