bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Predisposition to Sporadic Congenital Hearing Loss in a Pediatric Population
Authors: Jung Jinsei , Lee Joon Suk , Cho Kyeong Jee , Yu Seyoung , Yoon Joo-Heon , Yung Gee Heon , Choi Jae Young 
Published: April 2017

AbstractDiscriminating between inherited and non-inherited sporadic hearing loss is challenging. Here, we attempted to delineate genetic inheritance in simplex cases of severe-to-profound congenital hearing loss in Korean children. Variations in SLC26A4 and GJB2 in 28 children with bilateral severe-to-profound non-syndromic hearing loss (NSHL) without familial history were analyzed using Sanger sequencing. Genetic analysis of individuals without mutations in SLC26A4 and GJB2 was performed by whole exome sequencing (WES). Bi-allelic mutations in SLC26A4 and GJB2 were identified in 12 and 3 subjects, respectively. Of the 13 individuals without mutations in SLC26A4 and GJB2, 2 and 1 carried compound heterozygous mutations in MYO15A and CDH23, respectively. Thus, 64.3% (18/28) of individuals with NSHL were determined to be genetically predisposed. Individuals with sporadic severe-to-profound NSHL were found to mostly exhibit an autosomal recessive inheritance pattern. Novel causative candidate genes for NSHL were identified by analysis of WES data of 10 families without mutations in known causative genes. Bi-allelic mutations predisposing to NSHL were identified in 64.3% of subjects with sporadic severe-to-profound NSHL. Given that several causative genes for NSHL are still unidentified, genetic inheritance of sporadic congenital hearing loss could be more common than that indicated by our results.
Five lipoxygenase hypomethylation mediates the homocysteine effect on Alzheimer’s phenotype
Authors: Li Jian-Guo , Barrero Carlos , Merali Salim , Praticò Domenico 
Published: April 2017

AbstractEnvironmental and genetic risk factors are implicated in the pathogenesis of Alzheimer’s disease (AD). However, how they interact and influence its pathogenesis remains to be investigated. High level of homocysteine (Hcy) is an AD risk factor and associates with an up-regulation of the ALOX5 gene. In the current paper we investigated whether this activation is responsible for the Hcy effect on the AD phenotype and the mechanisms involved. Triple transgenic mice were randomized to receive regular chow diet, a diet deficient in folate and B vitamins (Diet), which results in high Hcy, or the Diet plus zileuton, a specific ALOX5 inhibitor, for 7 months. Compared with controls, Diet-fed mice had a significant increase in Hcy levels, memory and learning deficits, up-regulation of the ALOX5 pathway, increased Aβ levels, tau phosphorylation, and synaptic pathology, which were absent in mice treated with zileuton. In vivo and vitro studies demonstrated that the mechanism responsible was the hypomethylation of the ALOX5 promoter. Our findings demonstrate that the up-regulation of the ALOX5 is responsible for the Hcy-dependent worsening of the AD phenotype in a relevant mouse model of the disease. The discovery of this previously unknown cross-talk between these two pathways could afford novel therapeutic opportunities for treating or halting AD.
Early traditional Chinese medicine bundle therapy for the prevention of sepsis acute gastrointestinal injury in elderly patients with severe sepsis
Authors: Wang Yifei , Zhang Yunhua , Jiang Ronglin 
Published: April 2017

AbstractThis study aimed to study the effect of early traditional Chinese medicine bundle therapy on the prevention of sepsis-associated acute gastrointestinal injury (AGI). This was a multicenter, prospective, observational, non-randomized cohort study of 296 consecutive patients with severe sepsis during 2013/3 and 2014/11; 150 patients received standard treatments (controls) and 146 received traditional Chinese medicine bundle therapy (intervention group) (herbal decoction gavage based on syndrome differentiation, Chinese acupuncture, application of mirabilite, and defecation mixture). D-lactic acid, diamine oxidase, endotoxin, gastrin, motilin, and intra-abdominal pressure were measured. AGI was categorized into four levels. Compared with controls, D-lactic acid, diamine oxidase, endotoxin, gastrin, and intra-abdominal pressure in the intervention group were decreased, and motilin was increased on day 7. AGI incidence in the intervention group was lower than in controls. GIF scores of the intervention AGI II and III groups were lower than in controls. The APACHE II scores of the intervention AGI II, III, and IV groups were lower than in controls. Compared with controls, mechanical ventilation time and ICU stay in the intervention group were shorter, and 28-day overall and AGI-attributed mortality were lower. For elderly patients with severe sepsis, early traditional Chinese medicine bundle therapy could decrease AGI incidence and improve prognosis.
Doping-induced perturbation and percolation in the two-dimensional Anderson lattice
Authors: Wei Lan-ying , Yang Yi-feng 
Published: April 2017

AbstractWe examine the doping effects in the two-dimensional periodic Anderson model using the determinant Quantum Monte Carlo (DQMC) method. We observe bound states around the Kondo hole site and find that the heavy electron states are destroyed at the nearest-neighbor sites. Our results show no clear sign of hybridization oscillation predicted in previous mean-field calculations. We further study the electron transport with increasing doping and as a function of temperature and obtain a critical doping xc ≈ 0.6 that marks a transition from the Kondo insulator regime to the single-ion Kondo regime. The value of xc is in good agreement with the predicted threshold for the site percolation. Our results confirm the percolative nature of the insulator-metal transition widely observed in doped Kondo insulators.
Identified of a novel cis-element regulating the alternative splicing of LcDREB2
Authors: Liu Zhujiang , Yuan Guangxiao , Liu Shu , Jia Junting , Cheng Liqin , Qi Dongmei , Shen Shihua , Peng Xianjun , Liu Gongshe 
Published: April 2017

AbstractAlternative splicing (AS) is an important gene regulation mechanism in plants. Despite the widespread use of AS in plant gene expression regulation, the identification of the cis-elements involved in the AS mechanism is rarely reported in plants. To explore the regulation mechanism of the AS of LcDREB2, a DREB2 ortholog from Sheepgrass (Leymus chinensis), the genomic sequences of LcDREB2 and its homologs in Poaceae were aligned, and six mutations were introduced in the conserved sequence of LcDREB2. By analyzing the distinct transcript patterns of the LcDREB2 mutants in transgenic Oryza sativa, a novel cis-element that affected the AS of LcDREB2 was identified as Exonic Splicing Enhancer 1 (ESE1). In addition, five serine-arginine rich (SR) proteins were confirmed to interact with ESE1 by electrophoretic mobility shift assay (EMSA). To further explore the expression regulation mechanism of the DREB subfamily, phylogenetic analysis of DREB2 paralogous genes was performed. The results strongly supported the hypothesis that AS is conserved in Poaceae plants and that it is an evolutionary strategy for the regulation of the functional expression of genes. The findings and methods of our study will promote a substantial step forward in understanding of the plant AS regulation mechanism.
The presence of microplastics in commercial salts from different countries
Authors: Karami Ali , Golieskardi Abolfazl , Keong Choo Cheng , Larat Vincent , Galloway Tamara S. , Salamatinia Babak 
Published: April 2017

AbstractThe occurrence of microplastics (MPs) in saltwater bodies is relatively well studied, but nothing is known about their presence in most of the commercial salts that are widely consumed by humans across the globe. Here, we extracted MP-like particles larger than 149 μm from 17 salt brands originating from 8 different countries followed by the identification of their polymer composition using micro-Raman spectroscopy. Microplastics were absent in one brand while others contained between 1 to 10 MPs/Kg of salt. Out of the 72 extracted particles, 41.6% were plastic polymers, 23.6% were pigments, 5.50% were amorphous carbon, and 29.1% remained unidentified. The particle size (mean ± SD) was 515 ± 171 μm. The most common plastic polymers were polypropylene (40.0%) and polyethylene (33.3%). Fragments were the primary form of MPs (63.8%) followed by filaments (25.6%) and films (10.6%). According to our results, the low level of anthropogenic particles intake from the salts (maximum 37 particles per individual per annum) warrants negligible health impacts. However, to better understand the health risks associated with salt consumption, further development in extraction protocols are needed to isolate anthropogenic particles smaller than 149 μm.
Triple-cation mixed-halide perovskites: towards efficient, annealing-free and air-stable solar cells enabled by Pb(SCN)2 additive
Authors: Sun Yong , Peng Jiajun , Chen Yani , Yao Yingshan , Liang Ziqi 
Published: April 2017

AbstractOrgano-metal halide perovskites have suffered undesirably from structural and thermal instabilities. Moreover, thermal annealing is often indispensable to the crystallization of perovskites and removal of residual solvents, which is unsuitable for scalable fabrication of flexible solar modules. Herein, we demonstrate the non-thermal annealing fabrication of a novel type of air-stable triple-cation mixed-halide perovskites, FA0.7MA0.2Cs0.1Pb(I5/6Br1/6)3 (FMC) by incorporation of Pb(SCN)2 additive. It is found that adding Pb(SCN)2 functions the same as thermal annealing process by not only improving the crystallinity and optical absorption of perovskites, but also hindering the formation of morphological defects and non-radiative recombination. Furthermore, such Pb(SCN)2-treated FMC unannealed films present micrometer-sized crystal grains and remarkably high moisture stability. Planar solar cells built upon these unannealed films exhibit a high PCE of 14.09% with significantly suppressed hysteresis phenomenon compared to those of thermal annealing. The corresponding room-temperature fabricated flexible solar cell shows an impressive PCE of 10.55%. This work offers a new avenue to low-temperature fabrication of air-stable, flexible and high-efficiency perovskite solar cells.
Screening the active compounds of Phellodendri Amurensis cortex for treating prostate cancer by high-throughput chinmedomics
Authors: Li Xian-Na , Zhang Aihua , Wang Meijia , Sun Hui , Liu Zhidong , Qiu Shi , Zhang Tianlei , Wang Xijun 
Published: April 2017

AbstractScreening the active compounds of herbal medicines is of importance to modern drug discovery. In this work, an integrative strategy was established to discover the effective compounds and their therapeutic targets using Phellodendri Amurensis cortex (PAC) aimed at inhibiting prostate cancer as a case study. We found that PAC could be inhibited the growth of xenograft tumours of prostate cancer. Global constituents and serum metabolites were analysed by UPLC-MS based on the established chinmedomics analysis method, a total of 54 peaks in the spectrum of PAC were characterised in vitro and 38 peaks were characterised in vivo. Among the 38 compounds characterised in vivo, 29 prototype components were absorbed in serum and nine metabolites were identified in vivo. Thirty-four metabolic biomarkers were related to prostate cancer, and PAC could observably reverse these metabolic biomarkers to their normal level and regulate the disturbed metabolic profile to a healthy state. A chinmedomics approach showed that ten absorbed constituents, as effective compounds, were associated with the therapeutic effect of PAC. In combination with bioactivity assays, the action targets were also predicted and discovered. As an illustrative case study, the strategy was successfully applied to high-throughput screening of active compounds from herbal medicine.
Dual inhibiting OCT4 and AKT potently suppresses the propagation of human cancer cells
Authors: Li Wenxin , Zhou Yanwen , Zhang Xiaoqian , Yang Ying , Dan Songsong , Su Tong , She Shiqi , Dong Weilai , Zhao Qingwei , Jia Jia , Yao Hangping , Zheng Min , Kang Bo , Wang Ying-Jie 
Published: April 2017

AbstractAKT serves as an epigenetic modulator that links epigenetic regulation to cell survival and proliferation while the epigenetic mediator OCT4 critically controls stem cell pluripotency and self-renewal. Emerging evidence indicated their complicated interplays in cancer cells and cancer stem cells (CSCs), and inhibiting either one may activate the other. Thus, in this study, we propose a strategy to targeting both factors simultaneously. Firstly, a combination of an OCT4-specific shRNA and the specific AKT inhibitor Akti-1/2 potently suppressed the propagation of human embryonal carcinoma cells, adherent cancer cells and stem-like cancer cells, establishing the proof-of-concept that dual inhibiting OCT4 and AKT can effectively target various cancer cells. Next, we combined Akti-1/2 with metformin, a widely-prescribed drug for treating type 2 diabetes, which was reported to down-regulate OCT4 expression. The metformin + Akti-1/2 combo significantly altered multiple signaling and epigenetic pathways, induced growth arrest and cell death of adherent and stem-like glioblastoma U87 cells, and attenuated their tumorigenicity in vivo. Taken together, we demonstrate here that simultaneously targeting an epigenetic mediator and an epigenetic modulator, by dual inhibiting OCT4 and AKT, can have significantly improved efficacies over single treatment in suppressing the propagation of CSCs as well as the entire bulk of differentiated cancer cells.
Physical Rehabilitation in Minor Traumatic Injury or Concussion
Authors: DeMatteo Carol , Arora Himanshu , Sharma Vivek 
Published: April 2017

AbstractConcussion is a traumatic brain injury and can be caused by sports and non-sports related injuries. Most patients recover completely within days to several weeks; but, some patients continue to experience postconcussion symptoms including but not limited to headache, dizziness and neck pain. The mainstay of treatment for concussion in sports has been physical and cognitive rest until the acute symptoms abates. However, the window period for rest is currently being debated. For patients with persisting symptoms, longer than 1 month, multidisciplinary team approach is advisable. There is emerging evidence for the role of physical therapy as a treatment option in this population, especially for postconcussion symptoms.
Safety of ERCP in patients with liver cirrhosis: a national database study
Authors: Navaneethan Udayakumar , Njei Basile , Zhu Xiang , Kommaraju Kiran , Parsi Mansour , Varadarajulu Shyam 
Published: April 2017

Abstract
Background and aims Given the limited data on the safety of endoscopic retrograde cholangiopancreatography (ERCP) in patients with liver cirrhosis, we attempted to evaluate this question using a large national database.
Methods We conducted a matched case – control study using the 2010 National Inpatient Sample database in which four non-cirrhotic controls were matched randomly for every cirrhotic patient from the same 10-year age group. We compared adverse events and safety of inpatient ERCP between patients with (n = 3228) and without liver cirrhosis (controls, n = 12 912).
Results Of the 3228 cirrhotic patients, 2603 (80.6 %) had decompensated and 625 (19.4 %) had compensated disease. Post-procedure bleeding (2.1 % vs. 1.2 %, P < 0.01) was higher in patients compared to controls. On multivariable analysis, decompensated cirrhosis (adjusted odds ratio [aOR], 2.7; 95 % confidence interval [CI], 2.2 – 3.2), compensated cirrhosis (aOR 2.2; 95 %CI 1.2 – 3.9), therapeutic ERCPs (aOR 1.4; 95 % CI 1.2 – 2.1), and biliary sphincterotomy (aOR 1.6; 95 %CI 1.1 – 2.1) were independently associated with increased risk of post-procedure bleeding. Performing ERCPs in large (aOR 0.5; 95 %CI 0.4 – 0.6) and medium (aOR 0.7; 95 %CI 0.6 – 0.9) sized hospitals was associated with a decreased risk of post-procedure bleeding. Biliary sphincterotomy (aOR 1.7; 95 %CI 1.2 – 2.3) and therapeutic ERCPs (aOR 1.1; 95 %CI 1.1 – 1.3) increased the risk of post-ERCP pancreatitis, and pancreatic stent placement was associated with a decreased risk of post-ERCP pancreatitis (aOR 0.8; 95 %CI 0.7 – 0.9).
Conclusions Cirrhosis (both compensated and decompensated), performing therapeutic ERCPs and biliary sphincterotomy increase the risk of post-procedure bleeding. Performing ERCPs in large and medium sized hospitals may improve outcomes.
The Study on Eco-environmental Issue of Aral Sea from the Perspective of Sustainable Development of Silk Road Economic Belt
Authors: Xu Hanyan 
Published: April 2017

Abstract
The Aral Sea crisis is the most prominent environmental problem in building Silk Road and Economic Belt, which is mainly induced by extensive exploitation of land resources in Aral Sea basin since the middle of last century. The upstream part of Amu Darya River, as the main water source of Aral Sea, is almost entirely located in Tajikistan, thus, the development and utilization of Tajikistan water resources affect the whole Aral Sea basin. The author puts forward oriented-development of green energy under the overall framework of co-building Silk Road and Economic Belt, developing small hydro-power and dam-free hydro-power stations, standardized implementation of agricultural modernization in Central Asia, through high efficiency and water saving agriculture to achieve “returning water to sea”, to reverse drying trend of Aral Sea, to renovate ecological environment, resulting in simultaneous implementation of agricultural production and Aral Sea governance, simultaneous achievement of agricultural harvest and ecological environment improvement of Aral Sea basin. The article makes a scientific proof of reality and feasibility regarding the proposed methods. Green ecological environment and stable social environment will contribute to the sustainable development of Green Silk Road and Economic belt.…
MISA-web: a web server for microsatellite prediction
Authors: Beier Sebastian , Thiel Thomas , Münch Thomas , Scholz Uwe , Mascher Martin 
Published: April 2017

Abstract

Motivation
Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging.

Results
We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis.

Availability and Implementation
MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code.
ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Authors: Navarro José Fernández , Sjöstrand Joel , Salmén Fredrik , Lundeberg Joakim , Ståhl Patrik L 
Published: April 2017

Abstract

Motivation
In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sections. The spatial resolution adds an extra level of complexity, which requires the development of new tools and algorithms for efficient and accurate data processing.

Results
Here we present a pipeline to automatically and efficiently process RNA-seq data obtained from spatial transcriptomics experiments to generate datasets for downstream analysis.

Availability and implementation
The ST Pipeline is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_pipeline.

Supplementary information
Supplementary data are available at Bioinformatics online.
Elizabethan Absolutism and Tamburlaine’s Tents: Sir Humphrey Gilbert Reads De Republica Anglorum
Authors: Rapple Rory 
Published: April 2017

Abstract
In 1571 Sir Humphrey Gilbert made a speech in the House of Commons that incited denunciation by his fellow MPs. He warned that Elizabeth could, if she so desired, suppress parliament and never summon it again. When this intervention is considered alongside Gilbert’s statements and alleged actions while on campaign in Ireland in the late 1560s, as well as his known activities in England in the early 1570s, it becomes clear that the speech was but one expression of a coherent absolutist political theology. This seems anomalous given our received historiographical knowledge about the range of ideas available in early Elizabethan England. This impression becomes more pointed once we realise Gilbert was taking an explicit stance against the ‘mixed monarchical’ vision of the Elizabethan Constitution proffered by his acquaintance and intellectual interlocutor Sir Thomas Smith in De Republica Anglorum. Clearly Gilbert believed that both England and Ireland were ruled under the dispensation of something akin to what Fortescue termed dominium tantum regale and Bodin would later call monarchie seigneuriale. Gilbert fused this absolutist regalian vision with Machiavellian ethics, implying consistently that a monarch’s actions, by definition, could not defy natural and divine laws: a remarkably proleptic approach to monarchical power both in English and French terms. His anticipation of developments in political thinking and thought as well as his explicit antagonism towards opinions often deemed ‘Monarchical Republican’ in provenance gives rise to questions, both historical and historiographical, about our account of Elizabethan political thinking.
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Authors: Vlastaridis Panayotis , Kyriakidou Pelagia , Chaliotis Anargyros , Van de Peer Yves , Oliver Stephen G , Amoutzias Grigoris D 
Published: April 2017

Abstract

Background
Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast).

Results
In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable.

Conclusions
Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70 % to 95 % of total phosphoproteins, but only 40 % to 60 % of total p-sites.