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Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties

Single amino acid variations (SAVs) potentially alter biological functions, including causing diseases or natural differences between individuals. Identifying the relationship between a SAV and certain disease provides the starting point for understanding the underlying mechanisms of specific associations, and can help further prevention and diagnosis of inherited disease.We ...

Multilocus genotyping of Giardia duodenalis in captive non-human primates in Sichuan and Guizhou provinces, Southwestern China

Xuehan Liu and Lei Deng for giving advice on sample collection. We sincerely thank Tao Wang from University of Melbourne for comment on the draft manuscript. Author Contributions Peng. Data curation ... : Zhijun Zhong, Yinan Tian, Wei Li. Methodology: Zhijun Zhong, Yinan Tian, Wei Li, Lei Deng, Yi Geng. Project administration: Guangneng Peng. Software: Zhijun Zhong, Yinan Tian, Wei Li, Lei Deng, Liuhong

Molecular characterization and multi-locus genotypes of Enterocytozoon bieneusi from captive red kangaroos (Macropus Rfus) in Jiangsu province, China

comment on the draft manuscript. Author Contributions Conceptualization: Zhijun Zhong, Lei Deng, Guangneng Peng. Data curation: Zhijun Zhong, Yinan Tian, Yuan Song. Formal analysis: Zhijun Zhong, Zhihua ... Ren, Xiaoping Ma. Investigation: Zhijun Zhong, Junxian Li, Xiaobin Gu, Changliang He, Yi Geng. Methodology: Zhijun Zhong, Yinan Tian, Lei Deng. Software: Zhijun Zhong, Yinan Tian, Changliang He

Multilocus genotyping of Enterocytozoon bieneusi derived from nonhuman primates in southwest China

Enterocytozoon bieneusi has been increasingly reported in non-human primates (NHPs) in recent years, and this has garnered attention. However, reports of E. bieneusi infections in NHPs are limited worldwide. To appreciate the genetic diversity and assess the zoonotic potential during the transmission of human microsporidiosis, we examined a total of 369 fecal samples from NHPs and ...

Presence of zoonotic Cryptosporidium scrofarum, Giardia duodenalis assemblage A and Enterocytozoon bieneusi genotypes in captive Eurasian wild boars (Sus scrofa) in China: potential for zoonotic transmission

Background Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi are the main causal pathogens of gastrointestinal disease. However, there are limited reports about the prevalence of these organisms in captive Eurasian wild boars worldwide. Therefore, we examined the occurrence and identified the species/assemblages/genotypes of these pathogens in captive Eurasian ...

Correction: First Report of the Human-Pathogenic Enterocytozoon bieneusi from Red-Bellied Tree Squirrels (Callosciurus erythraeus) in Sichuan, China

Xuehan Liu Zhijun Zhong Na Xie Shuangshuang Lei Jianqiu Yu Hualin Fu Hongwei Chen Huailiang Xu Yanchun Hu Guangneng Peng The first four authors, Lei Deng, Wei Li, Xingming Yu and Chao Gong, should be

Multi-locus genotypes of Enterocytozoon bieneusi in captive Asiatic black bears in southwestern China: High genetic diversity, broad host range, and zoonotic potential

Enterocytozoon bieneusi is an obligate eukaryotic intracellular parasite that infects a wide variety of vertebrate and invertebrate hosts. Although considerable research has been conducted on this organism, relatively little information is available on the occurrence of E. bieneusi in captive Asiatic black bears. The present study was performed to determine the prevalence, genetic ...

PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility

Background Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibility prediction in recent years, the performance is far from ...

First Report of the Human-Pathogenic Enterocytozoon bieneusi from Red-Bellied Tree Squirrels (Callosciurus erythraeus) in Sichuan, China

Enterocytozoon bieneusi is a common opportunistic pathogen causing diarrhea and enteric disease in a variety of animal hosts. Although it has been reported in many animals, there is no published information available on the occurrence of E. bieneusi in red-bellied tree squirrels. To understand the occurrence, genetic diversity, and zoonotic potential of E. bieneusi in red-bellied ...

The Characters of Dry Soil Layer on the Loess Plateau in China and Their Influencing Factors

A dry soil layer (DSL) is a common soil desiccation phenomenon that generally forms at a particular depth in the soil profile because of climatic factors and poor land management, and this phenomenon can influence the water cycle and has been observed on the Loess Plateau of China and other similar regions around the world. Therefore, an investigation of the DSL formation depth ...

Molecular characterization and multilocus genotypes of Enterocytozoon bieneusi among horses in southwestern China

Background Enterocytozoon bieneusi is one of the most prevalent causative species of diarrhea and enteric diseases in various hosts. E. bieneusi has been identified in humans, mammals, birds, rodents and reptiles in China, but few studies have reported E. bieneusi in horses. Therefore, the present study was conducted to assess the prevalence, molecular characteristics and zoonotic ...

Multilocus genotypes and broad host-range of Enterocytozoon bieneusi in captive wildlife at zoological gardens in China

Background Enterocytozoon bieneusi is a common opportunistic pathogen that is widely detected in humans, domestic animals and wildlife, and poses a challenge to public health. The present study was performed to evaluate the prevalence, genotypic diversity and zoonotic potential of E. bieneusi among wildlife at Chengdu and Bifengxia zoological gardens in Sichuan Province, China. ...

Inhibition of MTA1 by ERα contributes to protection hepatocellular carcinoma from tumor proliferation and metastasis

Background Although expression of MTA1 inversely correlates with the nuclear localization of ERα, the effect and molecular mechanism of ERα regulation of MTA1 remain unknown. Methods Quantitative real-time PCR and western blot analyses were used to measure levels of MTA1. The effect on HCC cell proliferation and invasion was assessed by EdU incorporation assays and Transwell, ...

Changes in Soil Carbon and Nitrogen following Land Abandonment of Farmland on the Loess Plateau, China

The revegetation of abandoned farmland significantly influences soil organic C (SOC) and total N (TN). However, the dynamics of both soil OC and N storage following the abandonment of farmland are not well understood. To learn more about soil C and N storages dynamics 30 years after the conversion of farmland to grassland, we measured SOC and TN content in paired grassland and ...

PredHS: a web server for predicting protein–protein interaction hot spots by using structural neighborhood properties

Identifying specific hot spot residues that contribute significantly to the affinity and specificity of protein interactions is a problem of the utmost importance. We present an interactive web server, PredHS, which is based on an effective structure-based hot spot prediction method. The PredHS prediction method integrates many novel structural and energetic features with two types ...

Phosphorescence Monitoring of Hypoxic Microenvironment in Solid-Tumors to Evaluate Chemotherapeutic Effects Using the Hypoxia-Sensitive Iridium (III) Coordination Compound

Objectives To utilize phosphorescence to monitor hypoxic microenvironment in solid-tumors and investigate cancer chemotherapeutic effects in vivo. Methods A hypoxia-sensitive probe named BTP was used to monitor hypoxic microenvironment in solid-tumors. The low-dose metronomic treatment with cisplatin was used in anti-angiogenetic chemotherapeutic programs. The phosphorescence ...

The Association between TGF-β1 Polymorphisms and Radiation Pneumonia in Lung Cancer Patients Treated with Definitive Radiotherapy: A Meta-Analysis

Background Previous studies investigating the association between TGF-β1 polymorphisms and Radiation Pneumonia (RP) risk have provided inconsistent results. The aim of our study was to assess the association between the TGF-β1 genes C509T, G915C and T869C polymorphisms and risk of RP in lung cancer patients treated with definitive radiotherapy. Methods Two investigators ...

Prolyl-4-hydroxylase α subunit 2 promotes breast cancer progression and metastasis by regulating collagen deposition

Background Increased collagen deposition provides physical and biochemical signals to support tumor growth and invasion during breast cancer development. Therefore, inhibition of collagen synthesis and deposition has been considered a strategy to suppress breast cancer progression. Collagen prolyl-4-hydroxylase α subunit 2 (P4HA2), an enzyme hydroxylating proline residues in ...

A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces

Background Hot spots are residues contributing the most of binding free energy yet accounting for a small portion of a protein interface. Experimental approaches to identify hot spots such as alanine scanning mutagenesis are expensive and time-consuming, while computational methods are emerging as effective alternatives to experimental approaches. Results In this study, we propose ...

Whole brain radiotherapy plus simultaneous in-field boost with image guided intensity-modulated radiotherapy for brain metastases of non-small cell lung cancer

Background Whole brain radiotherapy (WBRT) plus sequential focal radiation boost is a commonly used therapeutic strategy for patients with brain metastases. However, recent reports on WBRT plus simultaneous in-field boost (SIB) also showed promising outcomes. The objective of present study is to retrospectively evaluate the efficacy and toxicities of WBRT plus SIB with image guided ...