Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Haplotype analysis reveals a possible founder effect of RET mutation R 114 H for Hirschsprung ' s disease in the Chinese population

Background: Hirschsprung’s disease (HSCR) is a congenital disorder associated with the lack of intramural ganglion cells in the myenteric and sub-mucosal plexuses along varying segments of the gastrointestinal tract. The RET gene is the major gene implicated in this gastrointestinal disease. A highly recurrent mutation in RET (RET) has recently been identified in ,6–7% of the Chinese HSCR patients which, to date, has not been found in Caucasian patients or controls nor in Chinese controls. Due to the high frequency of RET in this population, we sought to investigate whether this mutation may be a founder HSCR mutation in the Chinese population. Methodology and Principal Findings: To test whether all RET were originated from a single mutational event, we predicted the approximate age of RET by applying a Bayesian method to RET SNPs genotyped in 430 Chinese HSCR patients (of whom 25 individuals had the mutation) to be between 4–23 generations old depending on growth rate. We reasoned that if RET was a founder mutation then those with the mutation would share a haplotype on which the mutation resides. Including SNPs spanning 509.31 kb across RET from a recently obtained 500 K genome-wide dataset for a subset of 181 patients (14 RET patients), we applied haplotype estimation methods to determine whether there were any segments shared between patients with RET that are not present in those without the mutation or controls. Analysis yielded a 250.2 kb (51 SNP) shared segment over the RET gene (and downstream) in only those patients with the mutation with no similar segments found among other patients. Conclusions: This suggests that RET is a founder mutation for HSCR in the Chinese population. Citation: Cornes BK, Tang CS, Leon TYY, Hui KJWS, So M-T, et al. (2010) Haplotype Analysis Reveals a Possible Founder Effect of RET Mutation R114H for Hirschsprung’s Disease in the Chinese Population. PLoS ONE 5(6): e10918. doi:10.1371/journal.pone. 0010918 Editor: Amanda Ewart Toland, Ohio State University Medical Center, United States of America Received November 2, 2009; Accepted April 1, 2010; Published June 2, 2010 Copyright: 2010 Cornes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by research grants from the Hong Kong Research Grants Council (765407M and 775907M to MMGB and PT respectively) and the University of Hong Kong Seed Funding Programme for Basic Research to MMGB (200611159028). Support was also obtained from the University of Hong Kong Strategic Research Theme of Genomics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mmgarcia@hkucc.hku. hk
Pathological dissociation and neuropsychological functioning in borderline personality disorder

Objective: Transient, stress‐related severe dissociative symptoms or paranoid ideation is one of the criteria defining the borderline personality disorder (BPD). Examinations of the neuropsychological correlates of BPD reveal various findings. The purpose of this study was to investigate the association between dissociation and neuropsychological functioning in patients with BPD.
Micromagnetic Model Analysis of Planar-Type Write Head Field Response and Dependence on Pole Tip, Return Yoke, and Shield Structure

We used a micromagnetic model to investigate the high-frequency (1-5 GHz) response, peak recording field strength, recording field gradient, and adjacent track erasure (ATE) field for various main pole tip, shield, and return yoke structures in planar type heads. The effect of the pole tip area at the air-bearing surface (ABS) and the return yoke structure is also discussed. It was found that the pole tip and shield arrangement had a major effect on the peak recording field strength, recording field gradient, and ATE field, i.e., the trailing and side shields work to reduce the undesired field, however, they also slow the head field response due to the interaction between the main pole tip and the shield. The field responses are also dependent on the main pole tip-shield structures and pole tip structures. The return yoke thickness and area were important determinants of response speed and peak field.
An audio-visual 3D virtual articulation system for visual speech synthesis

A 3D visible articulation system which utilizes audio-visual data to accurately simulate the 3D articulatory motion is developed in this paper. The 3D articulatory shapes are reconstructed from Magnetic Resonance Images (MRI). In order to synthesize accurate audio-visual results, articulatory parametric models are further developed and the Electromagnetic Articulography (EMA) data with synchronized audio information is utilized to simulate articulation animation. Meanwhile, the collisions between the tongue and other articulators are considered for avoiding physically impossible results. Besides evaluating the results by a widely used distance-based method, which is applied to several key points on the articulatory surface, we develop a shape-based evaluation method to calculate the shape accuracy of the deformable articulator (tongue) in each frame of articulation. The experimental results suggest that our method can simulate articulatory animation accurately, and the developed system performs well on realism and expressiveness aspects according to the evaluation.
Imaging RNA and dynamic protein segments with low-resolution virus crystallography: experimental design, data processing and implications of electron density maps.

Single crystal diffraction data were collected from virus crystals in the resolution range of 270 to 14 A using a synchrotron X-ray source and a small-angle scattering instrument adapted for single crystal measurements. Reflections were measured from single crystals of the capsid of the double-stranded DNA bacteriophage HK97 and synthetic Flock House virus-like particles (sFHV). The quality of the low-resolution measurements was confirmed by excellent scaling statistics for both data sets. The sFHV amplitudes between 270 and 90 A resolution were closely similar to independently measured solution scattering data, and to data calculated from the Fourier transform of a uniform density sphere of 315 A diameter. A rotation function computed with the sFHV data between 70 and 20 A resolution was readily interpretable. A uniform density sphere model was used to compute phases for measured amplitudes between 270 and 68 A resolution. The calculated phases were refined and extended to 14 A resolution with real space averaging employing an external mask shape defined by the high-resolution structure. The resulting electron density map displayed regions interpretable as loosely ordered RNA that connected ordered RNA segments seen in a published 3.0 A resolution map. The published high-resolution electron density map lacked data inside 15 A resolution and the interior of the particle in that map appeared hollow. Difference electron density maps corresponding to bulk RNA were computed by subtracting the contribution of the protein shell, based on the available high-resolution atomic model, from either the cryo-electron microscopy density or the low-resolution X-ray density. Features of the RNA were closely similar in the cryo-electron microscopy and X-ray maps, demonstrating the consistency of the two imaging methods. Electron density maps computed at 14 and 6 A resolution with the X-ray amplitudes showed that RNA contributed little to the scattering beyond 14 A resolution.
WORKER ATTITUDES AND THE COST OF PRODUCTION: HYPOTHESIS TESTS IN AN EQUILIBRIUM MODEL

This paper extends the application of neoclassical production theory to include the effects of worker attitudes on productivity and cost of production, using data for the U.S. automobile industry. Behavioral indicators of worker attitudes are imbedded in a standard four-input translog cost function. The coefficients of the imbedded function are determined in estimation of the cost function simultaneously with its share equation. Hypotheses concerning the effects of worker attitude on the cost function are tested, and the properties of the index of worker attitude that emerge from the estimation are examined. Copyright 1990 by Oxford University Press.
Effects of combined low‐dose spironolactone plus vitamin E vs vitamin E monotherapy on insulin resistance, non‐invasive indices of steatosis and fibrosis, and adipokine levels in non‐alcoholic fatty liver disease: a randomized controlled trial

The beneficial effects of mineralocorticoid receptor blockade by spironolactone have been shown in animal models of non‐alcoholic fatty liver disease (NAFLD). The aim of the present 52‐week randomized controlled trial was to compare the effects of low‐dose spironolactone and vitamin E combination with those of vitamin E monotherapy on insulin resistance, non‐invasive indices of hepatic steatosis and fibrosis, liver function tests, circulating adipokines and hormones in patients with histologically confirmed NAFLD. Homeostasis model of assessment of insulin resistance (HOMA‐IR) and non‐invasive indices of steatosis and fibrosis were calculated. Analysis was intention‐to‐treat. NAFLD liver fat score, an index of steatosis, decreased significantly in the combination treatment group (P = .028), but not in the vitamin E group, and the difference for group*time interaction was significant (P = .047). Alanine aminotransferase‐to‐platelet ratio index, an index of fibrosis, did not change. Insulin levels and HOMA‐IR decreased significantly only within the combination group (P = .011 and P = .011, respectively). In conclusion, the combined low‐dose spironolactone plus vitamin E regimen significantly decreased NAFLD liver fat score. Larger‐scale trials are needed to clarify the effect of low‐dose spironolactone on hepatic histology.
The embryonic central nervous system lineages of Drosophila melanogaster. II. Neuroblast lineages derived from the dorsal part of the neuroectoderm.

In Drosophila, central nervous system (CNS) formation starts with the delamination from the neuroectoderm of about 30 neuroblasts (NBs) per hemisegment. They give rise to approximately 350 neurons and 30 glial cells during embryonic development. Understanding the mechanisms leading to cell fate specification and differentiation in the CNS requires the identification of the NB lineages. The embryonic lineages derived from 17 NBs of the ventral part of the neuroectoderm have previously been described (Bossing et al., 1996). Here we present 13 lineages derived from the dorsal part of the neuroectoderm and we assign 12 of them to identified NBs. Together, the 13 lineages comprise approximately 120 neurons and 22 to 27 glial cells which we include in a systematic terminology. Therefore, NBs from the dorsal neuroectoderm produce about 90% of the glial cells in the embryonic ventral ganglion. Two of the NBs give rise to glial progeny exclusively (NB 6-4A, GP) and five to glia as well as neurons (NBs 1-3, 2-5, 5-6, 6-4T, 7-4). These seven NBs are arranged as a group in the most lateral region of the NB layer. The other lineages (NBs 2-4, 3-3, 3-5, 4-3, 4-4, 5-4, clone y) are composed exclusively of neurons (interneurons, motoneurons, or both). Additionally, it has been possible to link the lateral cluster of even-skipped expressing cells (EL) to the lineage of NB 3-3. Along with the previously described clones, the vast majority (more than 90%) of cell lineages in the embryonic ventral nerve cord (thorax, abdomen) are now known. Moreover, previously identified neurons and most glial cells are now linked to certain lineages and, thus, to particular NBs. This complete set of data provides a foundation for the interpretation of mutant phenotypes and for future investigations on cell fate specification and differentiation.
Cardiovascular and economic outcomes after initiation of lipid-lowering therapy with atorvastatin vs simvastatin in an employed population.

OBJECTIVE To compare the risk of cardiovascular-related hospitalization, statin adherence, and direct (medical and drug) and indirect (disability and medically related absenteeism) costs in US employees in whom atorvastatin or simvastatin was newly prescribed. PATIENTS AND METHODS Active employees aged 18 to 64 years with a new atorvastatin or simvastatin prescription were identified from a deidentified claims database for 23 privately insured US companies from January 1, 1999, through December 31, 2006. Employees given atorvastatin were matched to those given simvastatin according to propensity scores based on patient characteristics, index statin dose, preindex cardiovascular events, and wage. Outcomes were compared between matched cohorts during the 2-year postindex period, including the risk of cardiovascular-related hospitalization, adherence to the index statin, use of other lipid-lowering drugs, direct medical costs for third-party payers, and indirect costs to employers. Indirect costs were computed as follows: Disability Payments + Daily Wage x Days of Medically Related Absenteeism. Atorvastatin and simvastatin drug costs were imputed using recent pricing to account for the availability of lower-cost generic simvastatin after the study period. RESULTS Among 13,584 matched pairs, treatment with atorvastatin vs simvastatin was associated with a reduced risk of cardiovascular-related hospitalization, higher adherence, and less use of other lipid-lowering drugs. The increase in statin costs associated with atorvastatin vs simvastatin therapy was almost completely offset by reductions in medical service and indirect costs. CONCLUSION In this study, treatment with atorvastatin compared with simvastatin was associated with a reduced risk of cardiovascular events, reduced indirect costs, and a minimal difference in total costs to employers.
Hepatitis B Virus Genotypes and Lamivudine Resistance Mutations in HIV/Hepatitis B Virus-Coinfected Patients

Background:Differences in subtypes, hepatitis B early antigen (HBeAg)-negative variants, and drug resistance mutations all seem to influence the clinical and therapeutic outcome in patients with chronic hepatitis B virus (HBV) infection. Information available on the prevalence and distribution of distinct HBV variants in HIV-positive patients is scarce. Methods:All HIV-infected patients with persistent serum hepatitis B surface antigen and detectable HBV viremia were identified in a reference HIV clinic located in Madrid, Spain. HBV load, subtypes, precore (PC) and basal core promoter (BCP) variants, and lamivudine (LAM) resistance mutations were analyzed. Results:A total of 81 HBV/HIV-coinfected patients (4.1%) were identified in a population of 1968 HIV-positive patients. Plasma specimens with detectable HBV viremia could be obtained from 62 subjects, and this was the study population that underwent further virologic characterization. HBV genotype distribution was as follows: A (n = 27), D (n = 27), E (n = 1), F (n = 2), and G (n = 3). Two patients had mixed HBV genotypes (A/E and A/F). HBV subtype A was predominant (74%) among patients infected through sexual contact, whereas HBV-D was most frequent (74%) among intravenous drug users (P < 0.001). PC/BCP mutants were more frequent in patients with HBV-D than in those with HBV-A (63% vs. 18%; P < 0.01). Median time on LAM was 40 months; patients with HBV-A tended to show LAM resistance mutations more often (53% vs. 44%) and to develop them earlier (35 vs. 45 months) than patients with HBV-D. The dual L180M + M204V/I mutant was the predominant resistance pattern, although a triple rt173V + 180M + 204V, which acts as a vaccine escape mutant, was found in 1 individual. In the multivariate analysis, patients with LAM resistance mutations were significantly more frequently HBeAg-positive and older than individuals with wild-type HBV. Hepatitis-delta was recognized in 13 (21%) of these 62 HBV viremic patients, with no association with specific HBV variants. Conclusion:Risk transmission group, age, and positive serum HBeAg are the main determinants of distinct HBV virologic variants, including HBV genotypes and LAM-resistant mutants, in HBV/HIV-coinfected patients.
[Cognitive impairment and alcohol and cigarette consumption in Mexican adults older than 65 years].

OBJECTIVE To determine the prevalence of the consumption of alcohol and cigarette smoking and their association with cognitive impairment among older Mexican adults. MATERIAL AND METHODS A total of 4,872 people over 65 years of age included in the sample of the National Mexican Health and Aging Study carried out in 2001 were questioned about their consumption of alcohol and cigarette smoking. For the classification of those subjects with cognitive impairment, the total scale of the different cognitive domains was used. The chi-square, Mann-Whitney U test, and logistical regression were used in order to find associations. RESULTS The prevalence of alcoholism according to CAGE was 2.8% and the prevalence of the consumption of cigarette smoking was 14%. Factors associated with the consumption of alcohol were:age 65-69 (p <0.001), men (RR 3.17, p <0.001), and high level of education (p <0.001). The association between the consumption of alcohol and cognitive impairment (chi2=6.59, p <0.01) was statistically significant. CONCLUSIONS The prevalence of consumption of alcohol and cigarette smoking in older Mexican adults are similar to that reported in other countries; the consumption of alcohol and its association with cognitive impairment was significant.
Nef Alleles from Human Immunodeficiency Virus Type 1-InfectedLong-Term-Nonprogressor Hemophiliacs with or without Late Disease Progression Are Defective in Enhancing Virus Replication and CD4 Down-Regulation

ABSTRACT Infection with human immunodeficiency virus (HIV)-encoding defective nef variants may contribute to a relatively benign course of disease in a minority of long-term nonprogressors (LTNP). We have examined the functions of nef alleles from six individuals belonging to the same cohort of hemophiliacs infected with HIV-1 prior to 1985 and classified as LTNP in 1995. Three out of six individuals have progressed to HIV disease (late progressors [LP]), whereas the three remainders have maintained their LTNP status at least up to 2003. The nef alleles were obtained from both plasma virus and peripheral blood mononuclear cells of all six individuals in 1995 and 1998. The proportion of sequences containing mutations not yielding Nef expression significantly diminished in 1998 versus that in 1995. Several previously defined functional regions of intact nef alleles were highly conserved. However, the major variant obtained in 1998 from plasma RNA of five out of six individuals significantly reduced HIV infectivity/replication and impaired Nef-mediated CD4 but not major histocompatibility complex class I antigen down-modulation from the cell surface. Thus, functional alterations of the nef gene are present in both LP and LTNP, suggesting that Nef defectiveness in vitro is not necessarily associated with the long-term maintenance of LTNP status. Of interest is the fact that isolates from three out of three LP showed a dual CCR5/CXCR4 coreceptor use (R5X4), in contrast to those from LTNP, which were exclusively R5. Thus, in vivo evolution of gp120 Env to CXCR4 use appears to be associated with HIV disease progression in individuals infected with nef-defective viruses.
Preventing black hole attack in mobile ad-hoc networks using Anomaly Detection

Mobile ad-hoc networks are prone to a number of security threats. The fact that mobile ad-hoc networks lack fixed infrastructure and use wireless link for communication makes them very susceptible to an adversary's malicious attacks. Black hole attack is one of the severe security threats in ad-hoc networks which can be easily employed by exploiting vulnerability of on-demand routing protocols such as AODV. In this paper, we have proposed a solution based on Intrusion Detection using Anomaly Detection (IDAD) to prevent black hole attacks imposed by both single and multiple black hole nodes. Result of a simulation study proves the particular solution maximizes network performance by minimizing generation of control (routing) packets as well as effectively preventing black hole attacks against mobile ad-hoc networks.
Census and vaccination coverage of owned dog populations in four resource-limited rural communities, Mpumalanga province, South Africa

Dogs (Canis familiaris) are often free-roaming in sub-Saharan African countries. Rabies virus circulates in many of these populations and presents a public health issue. Mass vaccination of dog populations is the recommended method to decrease the number of dog and human rabies cases. We describe and compare four populations of dogs and their vaccination coverage in four different villages (Hluvukani, Athol, Utah and Dixie) in Bushbuckridge Municipality, Mpumalanga province, South Africa. Cross-sectional surveys were conducted in the villages of Athol, Utah and Dixie, while data from a Health and Demographic Surveillance System were used to describe the dog population in Hluvukani village. All households of the villages were visited to obtain information on the number, sex, age and rabies vaccination status of dogs. From May to October 2013, 2969 households were visited in the four villages and 942 owned dogs were reported. The populations were all young and skewed towards males. No differences were observed in the sex and age distributions (puppies 0–3 months excluded) among the villages. Athol had a higher proportion of dog-owning households than Hluvukani and Utah. Vaccination coverages were all above the 20% – 40% threshold required for herd immunity to rabies (38% in Hluvukani, 51% in Athol, 65% in Dixie and 74% in Utah). For the preparation of vaccination campaigns, we recommend the use of the relatively stable dog:human ratio (between 1:12 and 1:16) to estimate the number of dogs per village in Bushbuckridge Municipality.
New Capabilities and Methods of the X-12-ARIMA Seasonal-Adjustment Program

X-12-ARIMA is the Census Bureau's new seasonal-adjustment program. It provides four types of enhancements to X-ll-ARIMA—(1) alternative seasonal, trading-day, and holiday effect adjustment capabilities that include adjustments for effects estimated with user-defined regressors; additional seasonal and trend filter options; and an alternative seasonal-trend-irregular decomposition; (2) new diagnostics of the quality and stability of the adjustments achieved under the options selected; (3) extensive time series modeling and model-selection capabilities for linear regression models with ARIMA errors, with optional robust estimation of coefficients; (4) a new user interface with features to facilitate batch processing large numbers of series.
Jardine Matheson Group's Delisting from the Stock Exchange of Hong Kong: Evidence on International Market Integration/Segmentation

In 1994–1995, Jardine Matheson Group delisted its five major group members from the Stock Exchange of Hong Kong, so that their trading was transferred to Singapore. We document that the trading volume of these five stocks fell after the delisting, and that they became less correlated with the Hong Kong market. We use a multivariate GARCH framework, which also allows us to present the correlations dynamically. We argue that this is evidence in favor of international market segmentation, since the delisting was not associated with a change in the business strategy of the Group.