Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis of functional genomic annotations and sequencing data to identify rare causal variants via hierarchical modeling

Identifying the small number of rare causal variants contributing to disease has been a major focus of investigation in recent years, but represents a formidable statistical challenge due to the rare frequencies with which these variants are observed. In this commentary we draw attention to a formal statistical framework, namely hierarchical modeling, to combine functional genomic annotations with sequencing data with the objective of enhancing our ability to identify rare causal variants. Using simulations we show that in all configurations studied, the hierarchical modeling approach has superior discriminatory ability compared to a recently proposed aggregate measure of deleteriousness, the Combined Annotation-Dependent Depletion (CADD) score, supporting our premise that aggregate functional genomic measures can more accurately identify causal variants when used in conjunction with sequencing data through a hierarchical modeling approach.
Fine Analysis of Genetic Diversity of the tpr Gene Family among Treponemal Species, Subspecies and Strains

Background The pathogenic non-cultivable treponemes include three subspecies of Treponema pallidum (pallidum, pertenue, endemicum), T. carateum, T. paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme (Simian isolate). These treponemes are morphologically indistinguishable and antigenically and genetically highly similar, yet cross-immunity is variable or non-existent. Although all of these organisms cause chronic, multistage skin and systemic disease, they have historically been classified by mode of transmission, clinical presentations and host ranges. Whole genome studies underscore the high degree of sequence identity among species, subspecies and strains, pinpointing a limited number of genomic regions for variation. Many of these “hot spots” include members of the tpr gene family, composed of 12 paralogs encoding candidate virulence factors. We hypothesize that the distinct clinical presentations, host specificity, and variable cross-immunity might reside on virulence factors such as the tpr genes. Methodology/Principal Findings Sequence analysis of 11 tpr loci (excluding tprK) from 12 strains demonstrated an impressive heterogeneity, including SNPs, indels, chimeric genes, truncated gene products and large deletions. Comparative analyses of sequences and 3D models of predicted proteins in Subfamily I highlight the striking co-localization of discrete variable regions with predicted surface-exposed loops. A hallmark of Subfamily II is the presence of chimeric genes in the tprG and J loci. Diversity in Subfamily III is limited to tprA and tprL. Conclusions/Significance An impressive sequence variability was found in tpr sequences among the Treponema isolates examined in this study, with most of the variation being consistent within subspecies or species, or between syphilis vs. non-syphilis strains. Variability was seen in the pallidum subspecies, which can be divided into 5 genogroups. These findings support a genetic basis for the classification of these organisms into their respective subspecies and species. Future functional studies will determine whether the identified genetic differences relate to cross-immunity, clinical differences, or host ranges.
Description of Rotation-Invariant Textures using Local Binary Pattern Features

classification is one of the most interesting research topics in the field of computer vision. This paper aims at classifying static as well as dynamic textures (DT). Uniform Local binary pattern (LBP) is a combination of structural and statistical analysis model for classification of both static and dynamic textures. The LBP Histogram Fourier (LBP-HF) uses Fast Fourier Transform (FFT) for calculating global rotation invariant of LBP histogram for static texture classification. For dynamic texture classification, LBP-TOP method is used, which computes LBP from three orthogonal planes. It combines both motion and appearance together for classification. The results show that, LBP-HF outperforms uniform LBP as well as basic rotation invariant LBP method for static-textures and LBP-TOP gives higher accuracy for dynamic-textures.
Zambian Crisis BehaviorRhodesia's Unilateral Declaration of Independence

This study of the behavior of Zambia's decision makers, confronted with the implications of Rhodesia's unilateral declaration of independence in November 1965, forms part of Michael Brecher's International Crisis Behavior Project and employs (with adaptations) his ICB framework. This article analyzes by period the critical situation Zambia faced, particularly as a result of its historical legacy of almost total dependency on Rhodesia for energy supplies and access to the sea for its copper exports. Next, it seeks to measure, by means of a content analysis of official statements, changes in crisis-induced stress over time in terms of the basic elements in Brecher's operational definition of a crisis. The paper then dissects the decision-making process with respect to one decision in one phase of the crisis in terms of the coping mechanisms employed. On the basis of this, certain tentative conclusions on Zambian crisis behavior are outlined. Finally, the attempt is made to set the Zambian case in the perspective of the wider ICB Project and of African foreign policy studies generally.
Evolution of T1 black holes in patients with multiple sclerosis imaged monthly for 4 years.

T1 black holes (BHs) on MRIs may represent either areas of oedema or axonal loss in patients with multiple sclerosis. BHs begin as contrast enhancing lesions (CELs) and evolve differently from patient to patient, and within the same patient over time. We analysed BHs formation over a 4-year period. Forty-eight monthly MRIs of nine non-treated multiple sclerosis patients were evaluated for numbers of CELs and BHs. A BH was defined as a hypointense lesion on a T1 pre-contrast image that coincided with a region of high signal intensity on the T2-weighted images. A BH was considered as acute (ABH) when it occurred coincidently with the presence of enhancement and as persisting (PBH) when present after the cessation of enhancement. The present study aimed to analyse: (i) the incidence of CELs and new PBHs, and the accumulation of PBHs; (ii) the relationship between the quantity of the CELs in a given month and the likelihood of accumulating PBHs in the subsequent month; and (iii) the relationship between the duration of CELs and PBHs. Pitman's correlation test evaluated the effect of time on either the increase of CELs and new PBHs or the accumulation of PBHs, while a multiple logistic regression analysis evaluated the relationship between progression of time and CELs, and the increase of PBHs in a multivariate model. The relationship between the enhancing lesions duration and the PBHs duration, or the time to revert back to an isointense lesion was analysed using Kaplan-Meier survival models. PBHs accumulated (P < 0.001) in all patients, but the formation of new PBHs increased in four patients (P < or = 0.007) in conjunction with an increase in either the quantity of CELs (P < 0.001, for two patients) or the proportion of CELs turning into PBHs (P < or = 0.02, for two patients). Logistic regression analysis showed that neither progression of time nor the number of CELs in a given month were able to predict the probability of increasing the number of PBHs in the subsequent month in any patient. Out of 397 ABHs, 55.7% evolved to a PBH. The duration of PBHs correlated with the duration of enhancement. PBHs preceded by CELs observable on a single MRI persisted for a shorter time (P < 0.002) than those preceded by CELs visible on > or =2 monthly MRIs. The formation of a new PBH was found to be related to CELs activity; however, duration of PBHs is most likely a consequence of the duration of the enhancement.
The factor analysis of university student's interpersonal relationship

Objective To explore the characteristics of interpersonal relationship and the relationship of dimensions and self-conceptions in university students.Methods We organized "a questionnaire about relationships of undergraduates with peoples" from the view of intercourse objects and extension of undergraduates.The questionnaire contained two dimensionalities:reality relationship and dummy relationship.Then reality relationship included three factors:relationship with teachers,relationship with schoolmates and living relationship.We investigated 313 undergraduates in Guangxi province using this questionnaire and Tennessee self-conceptions questionaire. Results (1) the reality relationship of the testees was all right collectivity,and there was difference between cadres and nor-cadres,and the reality relationship was correlated with self-summation about their ability and contentment about the reality (P0.05);(2) there had notable difference between arts and science undergraduates,and science students'score was higher than those of arts students,the dummy relationship was not correlated with self-conceptions (P0.05);(3) the relationship with schoolmates was correlated with genders,girls were better than boys(P0.05),and the relationship with schoolmates had significantly correlation with self-conceptions(P0.01);(4) the relationship with teachers was not correlated with self-conceptions; (5) the living relationship was significantly positively correlated with social-conception and psychology-conception.Conclusion The condition of university student's relationship is widespread and good,having the community characteristic and individual difference;the exhibition of self-condeptions education in university students may be helpful for better relationship;The dummy relationship differs from the cyberspace relationship,the former has no relation with self-conception.
Antiplatelet Effect of Clopidogrel Can Be Reduced by Calcium-Channel Blockers

Purpose Clopidogrel is metabolized by the hepatic cytochrome P450 (CYP) system into its active thiol metabolite. CYP3A4 is involved in the metabolism of both clopidogrel and dihydropyridine calcium channel blockers (CCBs). A few reports have suggested an inhibitory interaction between CCBs and clopidogrel. Accordingly, the aim of this study was to determine the effect of CCBs on the antiplatelet activity of clopidogrel by serial P2Y12 reaction unit (PRU) measurements. Materials and Methods We assessed changes in antiplatelet activity in patients receiving both clopidogrel and CCBs for at least 2 months prior to enrollment in the study. The antiplatelet activity of clopidogrel was measured by VerifyNow P2Y12 assay in the same patient while medicated with CCBs and at 8 weeks after discontinuation of CCBs. After discontinuation of the CCBs, angiotensin receptor blockers were newly administered to the patients or dosed up for control of blood pressure. Results Thirty patients finished this study. PRU significantly decreased after discontinuation of CCBs (238.1±74.1 vs. 215.0±69.3; p=0.001). Of the 11 patients with high post-treatment platelet reactivity to clopidogrel (PRU≥275), PRU decreased in nine patients, decreasing below the cut-off value in seven of these nine patients after 8 weeks. Decrease in PRU was not related to CYP2C19 genotype. Conclusion CCBs inhibit the antiplatelet activity of clopidogrel.
The effects of attention, stimulus intensity, and individual differences on the average evoked response.

The effects of shifting attention toward or away from visual or auditory stimuli of varying intensities were studied using average evoked responses (AERs) in 24 normal human volunteers. Ss were asked to attend to visual or auditory stimuli of four intensities (randomly presented) or to ignore the lights and tones and do mental arithmetic. For visual stimuli, attentional effects were largest at low intensities whereas for auditory stimuli equal effects were shown across intensities. Similar individual rates of increase of AER amplitude with increasing intensity were observed for both visual and auditory stimuli when attentional conditions were controlled. These results suggest that some general intensity processing response is reflected in the AER and that it is important to control attention in AER experiments.
Influence of amino acids on gastric adaptive relaxation (accommodation) in rats as evaluated with a barostat

Aim: The present study aimed to evaluate the effects of selected straight alkyl chain, hydroxylated chain and branched chain amino acids on gastric adaptive relaxation, as these have previously been shown to have differing effects on gastric emptying. Materials and Methods: Gastric adaptive relaxation was evaluated using a barostat in rats under urethane anesthesia. The pressure within the balloon, introduced from the mouth to the stomach, was changed stepwise from 1 to 8 mmHg. The increased volume just after the increase of balloon pressure was defined as distension-induced gastric adaptive relaxation (accommodation). Amino acids were administered orally or intravenously. Results: As compared with control rats administered with distilled water, those rats that were orally administered amino acids having straight alkyl chain and extra hydroxylated alkyl chain, such as glycine and l-serine, had significantly enhanced gastric adaptive relaxation, but administration of l-alanine and l-threonine did not. Branched chain amino acids, such as l-isoleucine, l-leucine and l-valine, also did not significantly influence gastric adaptive relaxation. Glycine and l-serine showed the same efficacy when administered intravenously. Conclusion: Among the amino acids evaluated in the present study, glycine and l-serine significantly enhanced gastric adaptive relaxation, suggesting that short alkyl chain amino acids may enhance gastric adaptive relaxation as compared with the other amino acids. These findings may suggest that glycine and l-serine would be useful in the therapy of functional dyspepsia, especially for early satiety, because the dysfunction of adaptive relaxation is one of the causes of early satiety.
The Effects of the WebQuest Writing Instruction Program on EFL Learners' Writing Performance, Writing Apprehension, and Perception

This study investigated the effects of the WebQuest Writing Instruction (WQWI) program on Taiwanese EFL learners' writing performance, writing apprehension, and perception of web-resource integrated language learning. Participants were students from two junior college classes. One class received traditional classroom writing instruction and the other class, the WQWI program. The results indicated that students in the WQWI class improved their writing performance significantly more than those in the traditional classroom writing class. The WQWI class also experienced significant reduction in writing apprehension; however, no significant difference in reduced apprehension could be found between the two classes. In addition, students had a favorable perception of the WQWI program, recognizing more advantages than disadvantages of language learning through web resources. Nonetheless, no significant correlation could be detected between students' perception and their improved writing performance. Neither was there a significant relationship between students' perception and their reduced writing apprehension. The findings suggested that integrating web resources into EFL writing instruction, using the WebQuest model, was effective for enhancing students' writing performance and provided a positive learning experience.
Should infant girls receive micronutrient supplements?

BACKGROUND We have proposed the hypothesis that the combination of vitamin A supplementation and diphtheria-tetanus-pertussis (DTP) vaccination may be associated with increased mortality in girls. Recent zinc/folic acid (FA) and iron supplementation trials did not find any beneficial effects on mortality. We reviewed the studies for evidence of a negative interaction between zinc/folic acid/iron and DTP vaccination in girls. METHODS Based on the published papers, we calculated age- and sex-specific mortality estimates. No vaccination status data were provided. RESULTS Both zinc/FA and iron seemed to have a sex- and age-differential effect, the effect being less beneficial in the youngest girls who are most likely to have DTP vaccine as their most recent vaccination. CONCLUSIONS Like vitamin A, zinc/FA and iron may not benefit the youngest girls. The question is whether this is inherent in girls or due to an interaction with some environmental factor like DTP.
Expression and function of activin beta A during mouse cardiac cushion tissue formation

The formation of cardiac cushion tissue, which ultimately contributes to formation of the valves and septa, is dependent on the regional activation of cardiac endothelial cells to undergo an epithelial‐mesenchymal transition. This endothelial transition was correlated with activin βA mRNA expression by Northern and in situ hybridization in both a temporal and spatial manner in developing mouse embryos. Activin βA was the only subunit of the inhibin family detected during the initial phase of endothelial cell transition; activin βB was detected at later stages, and inhibin α was not detectable in the heart. An in vitro assay that has been used to study mesenchymal cell formation in chick was modified for use with mammalian embryos. Conditioned media from embryonic mouse cardiocyte cultures was shown to substitute for the endogenous inductive signal in these assays. The presence of activin βA was demonstrated by Western blot analysis of the cardiocyte conditioned media (CCM). Modified antisense oligonucleotides to activin βA inhibited the endothelial‐mesenchymal transition in the assay system, which was not affected by control oligonucleotides. Adapting the avian culture system for use with mice enabled the use of tissue from mice with a null allele for activin βA. CCM produced from embryos homozygous for the mutant βA allele did not contain activin βA and was used in in vitro assays. CCM lacking activin βA produced fewer mesenchymal cells from cardiac endothelial monolayers than CCM with activin βA. Localized expression of activin βA in the embryonic heart indicates a possible role in the endothelial‐mesenchymal transition. Bioassays in which activin βA expression is blocked or activin βA is absent from the media indicate that activin βA promotes the formation of mesenchymal cells in the endothelial cushions, which are required for normal septation. Dev. Dyn. 1998;212:548–562. © 1998 Wiley‐Liss, Inc.
Evidence-based Intervention with Women Pregnant after Perinatal Loss

Purpose:To test the feasibility and acceptability of a caring-based nurse home visit intervention for women pregnant after perinatal loss (PAL), the goal of which was to provide a safe, supportive environment, normalize the pregnancy after loss, reduce anxiety and depression through stress reduction skills, and facilitate prenatal attachment. Study Design and Methods:This mixed methods study was conducted in two phases: Phase I, to determine the components of the intervention, and Phase II, a randomized trial that used the revised intervention components. Pregnant women with a history of at least one perinatal loss (9 in Phase I and 24 in Phase II) were recruited from obstetrical practices. Phase II sample size was adequate to detect group differences. Background measures of demographics, obstetrical history, and meaning of past losses were collected at baseline. Measured at three points across pregnancy were threat appraisal of pregnancy; and emotional states: anxiety (pregnancy, state, trait), depression, self mastery, prenatal attachment, and satisfaction with social support. The caring-based nurse home visit intervention included activities aimed to reduce anxiety and promote prenatal attachment. The control group were sent pregnancy information booklets that coincided with their gestational age. Qualitative and quantitative evaluations were obtained. Results:In Phase I, 8 women received the intervention; in Phase II, 13 received the intervention and 11 were in the control group. No baseline between-group differences were found. The intervention group had significantly higher satisfaction with social support over time. Women's evaluations were very positive; home visits were rated most liked and helpful. They appreciated a knowledgeable nurse who knew their story, listened, normalized the PAL experience, and was there with nonjudgmental support. Clinical Implications:The intervention is both feasible and acceptable. Most women felt that they could reduce their own anxiety using the tools and skills they were provided. Healthcare providers should consider past history's impact on current pregnancy experiences and incorporate process and content of the intervention into their practice.
Physical long-term health problems and mental comorbidity: evidence from Vietnam

Objective: The mental health of children living in low-income countries remains a neglected research area despite the high burden of disease. This study is one of the first that examines the effects of long-term physical health problems on child mental health disorders in a low-income country and investigates whether this association is modified by the socio-economic status of the child’s family. Methods: Community-based cross-sectional survey of 975 eight-year-old children from 20 sites in Vietnam. Long-term physical health problems were measured by a caregiver report and included conditions such as anaemia, congenital malformation, physical disability and skin problems. Child mental disorders were assessed using the strengths and difficulties questionnaire (SDQ). Generalised estimating equations models were fitted to explore the association between long-term physical health problems and child mental disorders. Results: Vietnamese children who suffer from long-term physical health problems have odds 2:1 times greater than children without long-term physical health problems of having a mental disorder (95% CI 1.2 to 3.6, p = 0.006). No significant interaction with socio-economic status was found. Conclusions: This study showed a high burden of mental disorders among physically ill children, re-enforcing the idea that there is “no health without mental health”. While this association needs to be explored longitudinally, children with long-term health problems may be a visible group for targeted mental-health interventions.
Contribution of Cognitive Abilities and Home Literacy Activities to Hiragana Reading and Spelling Skills in Kindergarten Children

: The contribution of cognitive abilities and home literacy activities to early reading and spelling skills of Japanese Hiragana were investigated in a cross-sectional study of 243 Japanese-speaking upper kindergarten children. They were tested in phonological awareness (nonword repetition and word repetition in reversed order), rapid automatized naming (RAN), visual cognition, receptive vocabulary, and reading and spelling of Hiragana characters. Parents filled in a questionnaire about home literacy activities, frequency of home reading and parent teaching. For reading, the scores of RAN, word repetition in reversed order and nonword repetition significantly predicted the reading score, while home literacy activities showed no significant contribution. For spelling, the scores of RAN, word repetition in reversed order, nonword repetition, figure copying and frequency of parent teaching at home significantly predicted the spelling score. These findings suggest that cognitive abilities are important for reading and spelling acquisition in kindergarten children, but parent teaching may also play a role for early spelling acquisition in Hiragana.