Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward optimal fragment generations for ab initio protein structure assembly

Fragment assembly using structural motifs excised from other solved proteins has shown to be an efficient method for ab initio protein‐structure prediction. However, how to construct accurate fragments, how to derive optimal restraints from fragments, and what the best fragment length is are the basic issues yet to be systematically examined. In this work, we developed a gapless‐threading method to generate position‐specific structure fragments. Distance profiles and torsion angle pairs are then derived from the fragments by statistical consistency analysis, which achieved comparable accuracy with the machine‐learning‐based methods although the fragments were taken from unrelated proteins. When measured by both accuracies of the derived distance profiles and torsion angle pairs, we come to a consistent conclusion that the optimal fragment length for structural assembly is around 10, and at least 100 fragments at each location are needed to achieve optimal structure assembly. The distant profiles and torsion angle pairs as derived by the fragments have been successfully used in QUARK for ab initio protein structure assembly and are provided by the QUARK online server at http://zhanglab.ccmb. med.umich. edu/QUARK/. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Mental health of college students and their non-college-attending peers: results from the National Epidemiologic Study on Alcohol and Related Conditions.

CONTEXT Although young adulthood is often characterized by rapid intellectual and social development, college-aged individuals are also commonly exposed to circumstances that place them at risk for psychiatric disorders. OBJECTIVES To assess the 12-month prevalence of psychiatric disorders, sociodemographic correlates, and rates of treatment among individuals attending college and their non-college-attending peers in the United States. DESIGN, SETTING, AND PARTICIPANTS Face-to-face interviews were conducted in the 2001-2002 National Epidemiologic Survey on Alcohol and Related Conditions (N = 43,093). Analyses were done for the subsample of college-aged individuals, defined as those aged 19 to 25 years who were both attending (n = 2188) and not attending (n = 2904) college in the previous year. MAIN OUTCOME MEASURES Sociodemographic correlates and prevalence of 12-month DSM-IV psychiatric disorders, substance use, and treatment seeking among college-attending individuals and their non-college-attending peers. RESULTS Almost half of college-aged individuals had a psychiatric disorder in the past year. The overall rate of psychiatric disorders was not different between college-attending individuals and their non-college-attending peers. The unadjusted risk of alcohol use disorders was significantly greater for college students than for their non-college-attending peers (odds ratio = 1.25; 95% confidence interval, 1.04-1.50), although not after adjusting for background sociodemographic characteristics (adjusted odds ratio = 1.19; 95% confidence interval, 0.98-1.44). College students were significantly less likely (unadjusted and adjusted) to have a diagnosis of drug use disorder or nicotine dependence or to have used tobacco than their non-college-attending peers. Bipolar disorder was less common in individuals attending college. College students were significantly less likely to receive past-year treatment for alcohol or drug use disorders than their non-college-attending peers. CONCLUSIONS Psychiatric disorders, particularly alcohol use disorders, are common in the college-aged population. Although treatment rates varied across disorders, overall fewer than 25% of individuals with a mental disorder sought treatment in the year prior to the survey. These findings underscore the importance of treatment and prevention interventions among college-aged individuals.
Screening for lung cancer: a review of the current literature.

STUDY OBJECTIVES To review the available data on the early detection of lung cancer, with a focus on three technologies: chest x-ray (CXR), sputum cytology, and low-dose CT (LDCT) scanning. DESIGN, SETTING, PARTICIPANTS Review of published clinical studies of early detection technologies. The best available evidence on each topic was selected for analysis. Randomized trials were used to evaluate CXR and sputum cytology. Cohort studies, as well as studies providing evidence regarding rates of overdiagnosis and efficacy of initial treatment, were considered in evaluation of LDCT. Study design and results were summarized in evidence tables. Statistical analyses of combined data were not performed. MEASUREMENT AND RESULTS Five randomized trials of CXR with or without sputum cytology have been conducted, each which reports disease-specific mortality as well as other end points. None of these studies provide support for the use of either CXR or sputum cytology for the early detection of lung cancer in asymptomatic individuals. Eight completed and ongoing trials of LDCT were identified. All of these studies report the frequency and stage distribution of lung cancers found during initial ("prevalence") screening, and several studies also report rates of detection at the time of annual follow-up. No outcome data on survival or treatment are available. A number of studies support the hypothesis of "overdiagnosis"--that some lung cancers detected by LDCT may behave in an indolent manner. CONCLUSIONS The use of either CXR or sputum cytology for the early detection of lung cancer is not supported by the published evidence. The evidence for LDCT appears promising, in that the technology typically identifies lung cancer at an early stage, although corollary studies suggest that these findings in isolation may be misleading. Further high-quality research is needed to better define the role of LDCT in the evaluation of asymptomatic high-risk individuals.
DISSOCIATIVE IDENTITY DISORDER: A CLINICAL INVESTIGATION OF 20 CASES IN TURKEY

This study describes the presentation and clinical features of dissociative identity disorder (DID) in Turkey. The first twenty consecutive patients in a dissociative disorders program of a university clinic in Turkey who met the DSM-HI--R criteria for multiple personality disorder (MPD) and DSM-IV criteria for DID were assessed with clinical interviews, a structured evaluation form consisting of 126 items, and the Dissociative Experiences Scale. Eighteen of the patients were women in their twenties. The median number of alternate personalities was four. Eighty five percent of the patients complained severe headache. All of the patients had at least one Schneiderian first- r symptom. Childhood traumas were reported in 85% of the cases. The mean DES score was 47.2. These results are remarkably similar to findings from North America and Western Europe, suggesting the validity of DID across cultures.
Serum Levels of NT-ProBNP as an Early Cardiac Marker of Carbon Monoxide Poisoning

Acute carbon monoxide (CO) poisoning may cause cardiotoxicity. The natriuretic peptides, including atrial natriuretic peptide, brain natriuretic peptide (BNP), N-BNP, and NT-proBNP (N-terminal pro brain natriuretic peptide), are endogenous cardiac hormones that may be secreted upon myocardial stress. The aim of this study was to assess the plasma NT-proBNP level in acute CO poisoning and to compare it with healthy control. After approval by the ethical committee, 15 healthy controls and 15 patients admitted to the Gaziantep University Hospital (Gaziantep, Turkey) between January 2005 and July 2005 with the diagnosis of carbon monoxide poisoning were studied. Echocardiography was performed to all patients. Serum NT-proBNP, creatine kinase (CK), creatine kinase-MB (CK-MB), and troponin-T were also analyzed, along with the carboxyhemoglobin (COHb) level. The correlation between serum NT-proBNP and COHb level was investigated. Electrocardiography (ECG) was performed to all patients and healthy controls, and the results were compared. Differences in troponin, CK, and CK-MB levels were not statistically significant between groups (p > 0.05). The level of NT-proBNP and COHb were found to be increased in the study group. There was a positive correlation between the COHb and the NT-proBNP (r = 0.829, p < 0.01), and between the COHb and the CK (r = 0.394, p < 0.01). There was no difference between groups in other parameters, all of which were within normal range. Thus, in this sudy we showed that the plasma NT-proBNP level may contribute to the early diagnosis of cardiotoxicity in patients with carbon monoxide poisoning.
On the Semantic Development Of English High-frequency Verbs Among Chinese Students

The exploration of the semantic development of English high-frequency verbs is of much significance in the teaching and learning of English vocabulary. Following a cross-sectional approach, this study centers on the meaning and collocation knowledge of six high-frequency English verbs among Chinese students at three different language proficiency levels. Findings are that a plateau phenomenon occurs in the semantic development when students' language proficiency moves from the intermediate to the advanced level and that the acquisition of the major sense is better than that of others.
Disease Burden, Characteristics, and Outcomes of Methicillin-Resistant Staphylococcus aureus Bloodstream Infection in Hong Kong

We aimed to describe disease burden, characteristics, and outcomes of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection (BSI) in Hong Kong. A retrospective, observational study was conducted in 26 Hong Kong public hospitals between January 2010 and December 2012. The primary outcome measures were 30-day mortality rate and infection-related hospital cost. Of 1133 patients reviewed, 727 (64.17%) were male, 1075 (94.88%) had health care–associated community-onset and 44 (3.88%) had hospital-onset MRSA infection. The mean age of patients was 76 (SD = 15) years, including 172 (15.18%) aged 20 to 59 years and 961 (84.8%) aged ≥60 years. The annual incidence rates in age groups of 20 to 59 years and ≥60 years were 0.96 to 1.148 per 100 000 and 22.7 to 24.8 per 100 000, respectively. The 30-day mortality was 367 (32.39%). Older patients (>79 years), chronic lung disease, and prior hospitalization were associated with increased mortality. The mean cost was US$10 565 (SD = 11 649; US$1 = HK$7.8). MRSA BSI was a significant burden in Hong Kong.
Schistosoma japonicum egg antigens stimulate CD4+ CD25+ T cells and modulate airway inflammation in a murine model of asthma

A number of epidemiological and clinical studies have suggested an inverse association between allergy and helminth infection, such as Schistosomiasis. Therefore, we hypothesize that Schistosoma japonicum egg antigens, a type of native antigen, can induce production of CD4+ CD25+ T cells with regulatory activity, modulating airway inflammation and inhibiting asthma development. The frequency of CD4+ CD25+ T cells was determined by flow cytometry for mice treated with ovalbumin (OVA), CD25+ depletion/OVA, schistosome egg antigens, schistosome egg antigens/OVA and for control mice. The ability of CD25+ T cells from these mice to suppress T‐cell proliferation and cytokine production was investigated both in vivo and in vitro. Results showed that the CD4+ CD25+ T cells of OVA‐treated mice exhibited impaired control of dysregulated mucosal T helper 2 responses compared to the controls (P < 0·05). Depletion of CD25+ cells accelerated OVA‐induced airway inflammation and increased the expression of interleukin (IL)‐5 and IL‐4. Treatment with schistosome egg antigens increased the number and suppressive activity of CD4+ CD25+ T cells, which made IL‐10, but little IL‐4. In a murine model of asthma, S. japonicum egg antigens decreased the expression of Th2 cytokines, relieved antigen‐induced airway inflammation, and inhibited asthma development. Thus, we provided evidence that S. japonicum egg antigens induced the production of CD4+ CD25+ T cells, resulting in constitutive immunosuppressive activity and inhibition of asthma development. These results reveal a novel form of protection against asthma and suggest a mechanistic explanation for the protective effect of helminth infection on the development of allergy.
Selective activation of the ventrolateral prefrontal cortex in the human brain during active retrieval processing

The present study examined the role of the prefrontal cortex in retrieval processing using functional magnetic resonance imaging in human subjects. Ten healthy subjects were scanned while they performed a task that required retrieval of specific aspects of visual information. In order to examine brain activity specifically associated with retrieval, we designed a task that had retrieval and control conditions that were perfectly matched in terms of depth of encoding, decision making and postretrieval monitoring and differed only in terms of whether retrieval was required. In the retrieval condition, based on an instructional cue, the subjects had to retrieve either the particular stimulus that was previously presented or its location. In the control condition, the cue did not instruct retrieval but shared with the instructional cues the function of alerting the subjects of the impending test phase. The comparison of activity between the retrieval and control conditions demonstrated a significant and selective increase in activity related to retrieval processes within the ventrolateral prefrontal cortical region, more specifically within area 47/12. These activity increases were bilateral but stronger in the right hemisphere. The present study by strictly controlling the level of encoding, postretrieval monitoring, and decision making has demonstrated a specific increase in the ventrolateral prefrontal region that could be clearly related to active retrieval processing, i.e. the active selection of particular stored visual representations.
Marital resemblance for obsessive–compulsive, anxious and depressive symptoms in a population-based sample

Background Resemblance between spouses can be due to phenotypic assortment, social homogamy and/or marital interaction. A significant degree of assortment can have consequences for the genetic architecture of a population. We examined the existence and cause(s) of assortment for obsessive–compulsive (OC), anxious and depressive symptoms in a population-based twin-family sample. Method OC, anxious and depressive symptoms were measured in around 1400 twin–spouse pairs and >850 parent pairs. Correlations of twins and their spouse, twin and co-twin's spouse, spouses of both twins and parents of twins were obtained to consider phenotypic assortment versus social homogamy as possible causes of marital resemblance. The association of length of relationship with marital resemblance was also investigated. Finally, we examined whether within-trait or cross-trait processes play a primarily role in marital resemblance. Results Small but significant within-trait correlations of between 0.1 and 0.2 were seen for spouse similarity in OC, anxious and depressive symptoms. Cross-correlations were significant but lower. There was no correlation between length of relationship and marital resemblance. From the pattern of correlations for twin–spouse, co-twin–spouse and spouses of both twins, phenotypic assortment could not be distinguished from social homogamy. Both within- and cross-assortment processes play a role in marital resemblance. Conclusions Small within- and across-trait correlations exist for OC, anxious and depressive symptoms. No evidence for marital interaction was found. Spouse correlations are small, which makes it difficult to distinguish between social homogamy and phenotypic assortment. It is unlikely that correlations of this size will have a large impact on genetic studies.
Yeast cycloheximide-resistant crl mutants are proteasome mutants defective in protein degradation.

In 1988 McCusker and Haber generated a series of mutants which are resistant to the minimum inhibitory concentration of the protein synthesis inhibitor cycloheximide. These cycloheximide-resistant, temperature-sensitive (crl) mutants, in addition, exhibited other pleiotropic phenotypes, e.g., incorrect response to starvation, hypersensitivity against amino acid analogues, and other protein synthesis inhibitors. Temperature sensitivity of one of these mutants, crl3-2, had been found to be suppressed by a mutation, SCL1-1, which resided in an alpha-type subunit of the 20S proteasome. We cloned the CRL3 gene by complementation and found CRL3 to be identical to the SUG1/CIM3 gene coding for a subunit of the 19S cap complex of the 26S proteasome. Another mutation, crl21, revealed to be allelic with the 20S proteasomal gene PRE3. crl3-2 and crl21 mutant cells show significant defects in proteasome-dependent proteolysis, whereas the SCL1-1 suppressor mutation causes partial restoration of crl3-2-induced proteolytic defects. Notably, cycloheximide resistance was also detected for other proteolytically deficient proteasome mutants (pre1-1, pre2-1, pre3-1, pre4-1). Moreover, proteasomal genes were found within genomic sequences of 9 of 13 chromosomal loci to which crl mutations had been mapped. We therefore assume that most if not all crl mutations reside in the proteasome and that phenotypes found are a result of defective protein degradation.
Cross-Layer Design for End-to-End Throughput and Fairness Enhancement in Multi-Channel Wireless Mesh Networks

In this paper, we study joint rate control, routing and scheduling in multi-channel wireless mesh networks (WMNs), which are traditionally known as transport layer, network layer and MAC layer issues respectively. Our objective is to find a rate allocation along with a flow allocation and a transmission schedule for a set of end-to-end communication sessions such that the network throughput is maximized, which is formally defined as the maximum throughput rate allocation (MRA) problem. As simple throughput maximization may result in a severe bias on rate allocation, we take account of fairness based on a simplified max-min fairness model and the proportional fairness models. We define the max-min guaranteed maximum throughput rate allocation (MMRA) problem and proportional fair rate allocation (PRA) problem. We present efficient linear programming (LP) and convex programming (CP) based schemes to solve these problems. Numerical results show that proportional fair rate allocation schemes achieves a good tradeoff between throughput and fairness.
Poverty reduction strategy papers (PRSPs)—fulfilling their potential for children in poverty?

Poverty Reduction Strategy Papers (PRSPs) are currently at the centre of development assistance and planning in many countries and donor agencies. As such, they are potentially of enormous significance for children living in poverty. Based on a review of PRSP documents, authors' experiences and other evidence, the paper explores the main policies of economic growth and social sector investment laid out in PRSPs and some likely implications for children's lives and equitable development. It examines how far PRSPs recognize childhood poverty as a priority, and the strategies' often limited commitments to tackle it. The paper reflects on changes in policy planning, budgeting and review processes associated with PRSPs and examines their potential to contribute to effective poverty reduction. It concludes that, to date, changes in these processes are the most significant contribution of PRSPs; while the potential for more effective policy is strong, much work is required by all involved before they are a comprehensive or strategic approach to reducing childhood poverty or securing the wellbeing of future generations. Copyright © 2002 John Wiley & Sons, Ltd.
MP-Draughts: Ordering the Search Tree and Refining the Game Board Representation to Improve a Multi-agent System for Draughts

In this paper the authors present an extension of the automatic player system MP-Draughts (MultiPhase-Draughts): a self-learning multi-agent environment for draughts composed of 26 Multiple Layer Perceptrons (MLPs). The weights of the MLPs are updated by Temporal Differences (TD). The search for the best move is conducted by a search algorithm based on Alpha-Beta pruning, Iterative Deepening and Table Transposition. One of the agents is trained in such a way that it becomes an expert in the initial stages of play and the remaining (25), in endgame stages. The endgame boards used to train the endgame agents are retrieved from an endgame board database and clustered by a Kohonem-SOM Neural Network (NN). The same Kohonem-SOM NN will also be used during the games to select which endgame agent is more suitable to play each time the endgame stage of play is reached. In this paper the authors propose the following modifications to improve the performance of MP-Draughts: first, to change the mapping of the board states such that, instead of indicating the presence or not of certain features, it indicates the number of elements pointed out by each feature, second, to order the search tree of each agent in such a way as to attenuate the innumerous re-evaluations of the same board state inherent to the iterative deepening strategy.
Perceptual assimilation and discrimination of falling, level, and rising lexical tones by native English speakers

Perceptual assimilation model posits that the perceived relation of non-native sounds to native sound categories predicts the discriminability of non-native sounds [1]. This study examines whether the degree of perceived similarity between Vietnamese tones and English intonation patterns predicts the accuracy of tone-contrast discrimination. In a categorization task, ten native English speakers were asked to match falling, level, and rising tone words with five English intonation patterns. Then, in a discrimination task, they were asked to judge the similarity of Vietnamese tones to each other. In the first task, speakers perceived both of the falling and level tones as most similar to the statement intonation ( Right ), and the rising tone as most similar to the question intonation ( Right? ). These cross-language mappings averaged at 74%, 65% and 73% of responses, respectively, suggesting relatively reliable categorization of tones and predicting relatively low discrimination accuracy for the level-falling tone contrast. In the second task, however, level-falling tones were discriminated significantly better than level-rising tones. This suggests that assimilation of tones to different intonation patterns is not the sole predictor of tone discrimination accuracy.
Functional Genetic Analysis of Rhesus Cytomegalovirus: Rh01 Is an Epithelial Cell Tropism Factor

ABSTRACT Rhesus cytomegalovirus (RhCMV) is an emerging model for human cytomegalovirus (HCMV) pathogenesis that facilitates experimental CMV infection of a natural primate host closely related to humans. We have generated a library of RhCMV mutants with lesions in genes whose HCMV orthologues have been characterized as nonessential for replication in human fibroblasts, and we characterized their replication in rhesus fibroblasts and epithelial cells. The RhCMV mutants grew well in fibroblasts, as predicted by earlier studies with HCMV. However, mutations in four genes caused replication defects in rhesus retinal pigment epithelial cells: Rh01 (an HCMV TRL1 orthologue), Rh159 (HCMV UL148), Rh160 (HCMV UL132), and Rh203 (HCMV US22). Growth of the Rh01-deficient mutant was examined in detail. After entry into epithelial cells, the mutant expressed representative viral proteins, accumulated viral DNA, and generated infectious virus, but it failed to spread efficiently. We conclude that Rh01 is a cell tropism determinant that has the potential to dramatically affect virus spread and pathogenesis.