bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pro-angiogenic Ginsenosides F1 and Rh1 Inhibit Vascular Leakage by Modulating NR4A1
Authors: Kang Ji In , Choi Yoonjung , Cui Chang-Hau , Lee Daeyoup , Kim Sun Chang , Kim Ho Min 
Published: March 2019

AbstractVascular endothelial growth factor (VEGF) plays a key role in angiogenesis, but VEGF-induced angiogenesis is often accompanied by a vascular permeability response. Ginsenosides are triterpenoid saponins from the well-known medicinal plant, ginseng, and have been considered a candidate for modulating angiogenesis. Here, we systemically investigated the effects of 10 different ginsenosides on human umbilical vein endothelial cells and newly identified that two PPT-type ginsenosides, F1 and Rh1 induce the migration and proliferation of endothelial cells. Interestingly, RNA transcriptome analysis showed that gene regulation induced by VEGF in endothelial cells is distinct from that of ginsenoside F1 and Rh1. In addition, F1 and Rh1 significantly inhibited vascular leakage both in vitro and in vivo, which are induced by vascular endothelial growth factor. Furthermore, comparative transcriptome analysis revealed that these effects of F1 and Rh1 on vascular leakage restoration are mainly caused by changes in VEGF-mediated TNFα signaling via NFκB, particularly by the suppression of expression and transcriptional activity of NR4A1 by F1 and Rh1, even in the presence of VEGF. These findings demonstrate that ginsenosides F1 and Rh1 can be a promising herbal remedy for vessel normalization in ischemic disease and cancer and that NR4A1 is the key target.
Wing morphology predicts geographic range size in vespertilionid bats
Authors: Luo Bo , Santana Sharlene E. , Pang Yulan , Wang Man , Xiao Yanhong , Feng Jiang 
Published: March 2019

AbstractWhy some species are widespread across continents while others are confined geographically remains an open question in ecology and biogeography. Previous research has attempted to explain interspecific variation in geographic range size based on differences in dispersal ability. However, the relationship between dispersal ability and geographic range size remains uncertain, particularly in mammals. The goal of this study is to test whether geographic range size can be predicted by dispersal capacity among vespertilionid bats within a phylogenetic comparative framework. We integrated a large dataset on range area, longitudinal extent, wing morphology (a proxy for dispersal ability), migratory habit, and biogeographic realm across 126 vespertilionid bat species. We used phylogenetic regressions to disentangle the associations between these predictor factors and species range size while controlling for the effects of migration and biogeographic realm. Our analyses revealed that bat species with higher wing loading exhibit larger distribution ranges than those with lower wing loading, and that the size of geographic ranges was associated with wing aspect ratio in bats. These results highlight the relationship between wing morphology and range size in flying mammals, and suggest a role of dispersal capacity in shaping species’ geographic distributions.
Shotgun Proteomics of Human Dentin with Different Prefractionation Methods
Authors: Widbiller Matthias , Schweikl Helmut , Bruckmann Astrid , Rosendahl Andreas , Hochmuth Eduard , Lindner Sophia R. , Buchalla Wolfgang , Galler Kerstin M. 
Published: March 2019

AbstractHuman dentin is not only a composite material of a collagenous matrix and mineral to provide strength and elasticity to teeth, but also a precious reservoir full of bioactive proteins. They are released after demineralization caused by bacterial acids in carious lesions, by decalcifying irrigants or dental materials and they modulate tissue responses in the underlying dental pulp. This work describes a first-time analysis of the proteome of human dentin using a shotgun proteomic approach that combines three different protein fractionation methods. Dentin matrix proteins were extracted by EDTA and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), OFFGEL isoelectric focusing (IEF) or strong cation exchange chromatography (SCX). Liquid chromatography tandem mass spectrometry (LC-MS/MS) identified 813 human proteins with high confidence, however, isoelectric focusing turned out to be the most beneficial prefractionation method. All Proteins were categorized based on the PANTHER system and representation analysis revealed 31 classes and subclasses to be overrepresented. The acquired knowledge provides a comprehensive insight into the number of proteins in human dentin as well as their physiological and pathological functions. Thus, the data presented paves the way to the analysis of specific functions of dentin matrix proteins in vivo and their potential in tissue engineering approaches to regenerate dental pulp.
Impacts of single nucleotide polymorphisms in three microRNAs (miR-146a, miR-196a2 and miR-499) on the susceptibility to cervical cancer among Indian women
Authors: Thakur Nisha , Singhal Pallavi , Mehrotra Ravi , Bharadwaj Mausumi 
Published: March 2019

Abstract
Background: Cervical cancer is the second major female cancer in India and constitutes one-fourth of the world’s burden. Human Papilloma Virus (HPV) infection is an essential but insufficient cause for cervical cancer. Genetic variants in microRNAs (miRNAs/miRs) play an important role in the susceptibility of various types of cancers.
Objective: To evaluate the association of Single Nucleotide Polymorphisms (SNPs) in miR-146a (rs2910164), miR-196a2 (rs11614913), and miR-499 (rs3746444), with cervical cancer susceptibility in Indian population.
Methods: Three hundred samples were genotyped by Polymerase chain reaction (PCR)-Restriction fragment length polymorphism (RFLP). Both patients and controls were also screened for the presence of HPV DNA.
Results: In this case–control study, 125 (83.3%) cervical cancer cases were found to be infected with HPV DNA. The frequency of miR-146a C allele was higher in controls than in cases [odds ratio (OR) (95% confidence interval (CI)) = 0.81 (0.57–1.14), P-value = 0.258]. miR-196a2 T allele was found to be associated with the decreased risk of cervical cancer [OR (95% CI) = 0.36 (0.26–0.50), P-value&lt;0.0001]. Approximately 1.22-fold increased risk has been observed in individuals carrying miR-499 TT genotypes [OR (95% CI) = 1.22 (0.63–2.36), P-value = 0.617]. Interaction studies for miR-196a2/miR-499 loci showed that women carrying TT/CC and TT/CT genotypes were less likely to develop cervical cancer than CC/CC combination [P&lt;0.05]. Likewise, miR-146a/miR-196a2 genotypic combinations (CC/TT, CG/TT, GG/TT) followed the similar trend [P&lt;0.05], exhibited the protective effect against cervical cancer with reference to CC/CC group. Combined genotypes of miR-146a/miR-499 [CC/CT, CG/CC, CG/CT, CG/TT, GG/CC, GG/CT, GG/TT] demonstrated a non-significant trend toward higher cervical cancer risk [OR &gt; 1.00, P&gt;0.05].
Conclusion: Polymorphisms in miR-146a, miR-196a2, and miR-499 individually or collectively have the prospective to emerge as biomarkers for cervical cancer.
Inzidentelle Befunde in der onkologischen Staging-CT-Untersuchung
Authors: Meyer Hans-Jonas , Surov Alexey 
Published: March 2019

AbstractIncidental findings are frequently detected in modern cross sectional imaging in up to 73 % of all radiological examinations with an increasing incidence. Especially clinically relevant findings, such as thromboembolisms, inflammation or therapy associated findings can be found in staging examinations of oncological patients. Those findings should be categorized according to their clinical relevance.
Central Nervous System Complications due to Human Herpesvirus 6 Infection in Pediatric Age Group
Authors: Barrea Christophe , Demonceau Nathalie , Loeckx Isabelle , Senterre Jean-Marc , Philippet Pierre 
Published: March 2019

AbstractHuman herpesvirus 6 (HHV-6) has been demonstrated to be a neurotropic virus and has been linked to several neurological complications associated with a wide range of clinical outcomes. Here, we present data from immunocompetent children with a central neurological condition and intrathecal DNA detection of HHV-6 virus. Through these cases, physiopathology, investigations, and outcome of the disease will be described. Finally, specific treatment will be discussed.
Conventional Nanofat and SVF/ADSC-Concentrated Nanofat: A Comparative Study on Improving Photoaging of Nude Mice Skin
Authors: Zheng Hui , Qiu Lihong , Su Yingjun , Yi Chenggang 
Published: March 2019

Abstract

Background
Nanofats could improve photoaging. Stromal vascular fraction (SVF) and adipose-derived stem cells (ADSCs) may play pivotal roles. However, SVFs and ADSCs in nanofats processed by conventional methods cannot be enriched. Some researchers have found that after centrifugation, the SVF/ADSC density increases from top to bottom.

Objectives
The authors hypothesized that centrifugation can be used to obtain SVF/ADSC-concentrated nanofats that are superior to conventional nanofats in improving the photoaging of skin.

Methods
After a photoaging model was successfully established in nude mice, the back of each mouse was divided into 4 areas and randomly injected with conventional nanofat, centrifuged nanofat (either the middle or lower layer of centrifuged nanofat), or normal saline. Wrinkles, dermis thickness, dermal collagen content, and elastic fiber morphology were measured and compared at weeks 4 and 8.

Results
Compared with the wrinkles in the physiological saline injection areas, the wrinkles in the areas injected with the 3 nanofats (lower and middle layers of centrifuged nanofat and conventional nanofat) were significantly reduced. All 3 nanofat groups showed increased dermal thickness, increased collagen content, and a more regular distribution of elastic fibers compared with the saline injection areas.

Conclusions
The study established the efficacy of nanofats in improving photoaging by reducing wrinkles and increasing the thickness of dermal collagen, making nanofats a promising novel treatment for photoaging. The SVF/ADSC-concentrated nanofats exhibited the most improvement.
Global Contributions to Aesthetic Surgery Journal Over the Past Decade
Authors: Moore Meredith L Grogan , Van Belle Christopher , Ovalle Fernando , Kitzmiller William John , Gobble Ryan M 
Published: March 2019

Abstract

Background
The Aesthetic Surgery Journal (ASJ) is a world-renowned publication with valuable contributions from around the globe.

Objectives
To better characterize the journal’s evolving representation of global contributions to aesthetic surgery, the authors examined the author affiliations of all articles published in ASJ over the last decade.

Methods
A PubMed search was performed for all journal articles published in ASJ from January 2008 to August 2018. For each article, the first author’s primary affiliation as indexed in MEDLINE was recorded as the source country. Data were tabulated by source country and year. The authorless errata, corrigenda, and Cosmetic Surgery National Data Bank Statistics were excluded from analysis.

Results
A total of 1746 articles were published during this period, contributed from 49 distinct countries. All continents other than Antarctica were represented. Higher income countries where aesthetic surgery is more prevalent produced 87% of published articles. The total number of published articles in ASJ has climbed from 77 annually in 2008 to 318 in 2018 as of August. In 2008, 27.3% of articles were from non-US countries, whereas in 2018 this increased to 43.7%. In particular, Turkey, the United Kingdom, Australia, Brazil, and Italy demonstrate steady increases in contributions over the 10-year period.

Conclusions
Publications in ASJ have increased in number over the past decade, and the journal has become increasingly global in its network of contributing authors. The increased global contribution to the ASJ may enhance readers’ experience both in the United States and in the world beyond.
mirtronDB: a mirtron knowledge base
Authors: Da Fonseca Bruno Henrique Ribeiro , Domingues Douglas Silva , Paschoal Alexandre Rossi 
Published: March 2019

Abstract

Motivation
Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB currently contains a total of 1407 mirtron precursors and 2426 mirtron mature sequences in 18 species.

Results
Through a user-friendly interface, users can now browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource that provides free and user-friendly access to knowledge on mirtron data.

Availability and implementation
MirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/.

Supplementary information
Supplementary data are available at Bioinformatics online.
FoldX 5.0: working with RNA, small molecules and a new graphical interface
Authors: Delgado Javier , Radusky Leandro G , Cianferoni Damiano , Serrano Luis 
Published: March 2019

Abstract

Summary
A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) that were not previously recognized in old versions, has been released. An extended FoldX graphical user interface has also being developed (available as a python plugin for the YASARA molecular viewer) allowing user-friendly parametrization of new custom user molecules encoded using JSON format.

Availability and implementation
http://foldxsuite.crg.eu/
Significance tests for analyzing gene expression data with small sample sizes
Authors: Ullah Insha , Paul Sudhir , Hong Zhenjie , Wang You-Gan 
Published: March 2019

AbstractMotivationUnder two biologically different conditions, we are often interested in identifying differentially expressed genes. It is usually the case that the assumption of equal variances on the two groups is violated for many genes where a large number of them are required to be filtered or ranked. In these cases, exact tests are unavailable and the Welch’s approximate test is most reliable one. The Welch’s test involves two layers of approximations: approximating the distribution of the statistic by a t-distribution, which in turn depends on approximate degrees of freedom. This study attempts to improve upon Welch’s approximate test by avoiding one layer of approximation.ResultsWe introduce a new distribution that generalizes the t-distribution and propose a Monte Carlo based test that uses only one layer of approximation for statistical inferences. Experimental results based on extensive simulation studies show that the Monte Carol based tests enhance the statistical power and performs better than Welch’s t-approximation, especially when the equal variance assumption is not met and the sample size of the sample with a larger variance is smaller. We analyzed two gene-expression datasets, namely the childhood acute lymphoblastic leukemia gene-expression dataset with 22 283 genes and Golden Spike dataset produced by a controlled experiment with 13 966 genes. The new test identified additional genes of interest in both datasets. Some of these genes have been proven to play important roles in medical literature.Availability and implementationR scripts and the R package mcBFtest is available in CRAN and to reproduce all reported results are available at the GitHub repository, https://github.com/iullah1980/MCTcodes.Supplementary informationSupplementary data is available at Bioinformatics online.
Diagnostic Reasoning and Expertise in Health Care
Authors: Patel Vimla L. , Kaufman David R. , Kannampallil Thomas G. 
Published: March 2019

Abstract
The study of diagnostic expertise initially focused on characterizing the reasoning process and, later, on understanding the nature of expert knowledge and its impact on performance, including memory, comprehension, and reasoning. This research demonstrated that medical expertise is not a simple construct, and its development is characterized by non-linear growth in skills and knowledge. Facilitated by new technology, recent research has moved toward real-world studies (or a combination of both laboratory-based and naturalistic studies), with automated and often precise methods of data collection and analysis. Findings from these studies contribute to our knowledge of medical experts’ performance, which often varies as a function of domain complexity as well as the clinician’s ability to recognize and correct medical errors. The role of cognitive science in modeling diagnostic reasoning plays a significant role when building successful systems to support reasoning processes of individual experts, teams, and trainees in real-world settings.
Revenue Losses to State and Federal Government From Opioid-related Employment Reductions
Authors: Segel Joel E. , Shi Yunfeng , Moran John R. , Scanlon Dennis P. 
Published: March 2019

Objective:
The main purpose of this study was to estimate the tax revenue lost by state and federal governments as a result of adverse labor market outcomes attributable to opioid misuse.

Methods:
We pair existing, plausibly causal estimates of the effect of opioid misuse on the decline in the labor force from 2000 to 2016 with a variety of data sources to compute tax revenues lost by state and federal governments using the online TAXSIM calculator.

Results:
We find that between 2000 and 2016, opioid misuse cost state governments $11.8 billion, including $1.7 billion in lost sales tax revenue and $10.1 billion in lost income tax revenue. In addition, the federal government lost $26.0 billion in income tax revenue.

Conclusions:
By omitting lost tax revenue due to labor force exits, prior studies have missed an important component of opioid-related costs borne by state and federal governments.

Policy Implications:
As more states and the federal government contemplate litigation for opioid-related damages, lost tax revenue represents an important cost that could be recouped and allocated to opioid prevention and treatment programs.
MicroRNA-transcriptome networks in whole blood and monocytes of women undergoing preterm labor
Authors: Paquette Alison G. , Shynlova Oksana , Wu Xiaogang , Kibschull Mark , Wang Kai , Price Nathan D. , Lye Stephen J 
Published: March 2019

ABSTRACTPreterm birth is attributed to neonatal morbidity as well as cognitive and physiological challenges. We have previously identified significant differences in mRNA expression in whole blood and monocytes, as well as differences in miRNA concentration in blood plasma, extracellular vesicles (EV) and EV-depleted plasma in women undergoing spontaneous preterm labor (sPTL). The goal of this analysis was to identify differences in miRNA expression within whole blood (WB) and peripheral monocytes (PM) from the same population of women undergoing sPTL compared to nonlaboring controls matched by gestational age. We performed single end small RNA sequencing in whole blood and peripheral monocytes from women undergoing sPTL with active contractions(24-34 weeks of gestation, N=15) matched for gestational age to healthy pregnant non laboring controls (>37 weeks gestation, N=30) who later delivered at term as a part of the Ontario Birth Study (Toronto, Ontario CA). We identified significant differences in expression of 16 miRNAs in PMs and 9 miRNAs in WB in women undergoing sPTL. In PMs, these miRNAs were predicted targets of 541 genes, including 28 previously associated with sPTL. In WB, miRNAs were predicted to target 303 genes, including 9 previously associated with sPTL. These genes were involved in a variety of immune pathways, including interleukin 2 signaling. This study is the first to identify changes in miRNA expression in WB and PMs of women undergoing sPTL. Our results shed light on potential mechanisms by which miRNAs may play a role in mediating systemic inflammatory response in pregnant women that deliver prematurely.
A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays
Authors: Klein Jason , Agarwal Vikram , Inoue Fumitaka , Keith Aidan , Martin Beth , Kircher Martin , Ahituv Nadav , Shendure Jay 
Published: March 2019

ABSTRACTMassively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validatingen massethat enhancer activity is robustly independent of orientation. Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.
Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs
Authors: Lev Itamar , Toker Itai Antoine , Mor Yael , Nitzan Anat , Weintraub Guy , Bhonkar Ornit , Shushan Itay Ben , Seroussi Uri , Claycomb Julie M. , Gingold Hila , Zaidel-Bar Ronen , Rechavi Oded 
Published: March 2019

AbstractInC. elegansnematodes, components of liquid-like germ granules were shown to be required for transgenerational small RNA inheritance. Surprisingly, we show here that mutants with defective germ granules (pptr-1,meg-3/4,pgl-1) can nevertheless inherit potent small RNA-based silencing responses, but some of the mutants lose this ability after many generations of homozygosity. Animals mutated inpptr-1, which is required for stabilization of P granules in the early embryo, display extremely strong heritable RNAi responses, which last for tens of generations, long after the responses in wild type animals peter out. The phenotype of mutants defective in the core germ granules proteins MEG-3 and MEG-4, depends on the genotype of the ancestors: Mutants that derive from maternal lineages that had functional MEG-3 and MEG-4 proteins exhibit enhanced RNAi inheritance for multiple generations. While functional ancestralmeg-3/4alleles correct, and even potentiates the ability of mutant descendants to inherit RNAi, defects in germ granules functions can be memorized as well; Wild type descendants that derive from lineages of mutants show impaired RNAi inheritance for many (>16) generations, although their germ granules are intact. Importantly, while P granules are maternally deposited, wild type progeny derived frommeg-3/4male mutants also show reduced RNAi inheritance. Unlike germ granules, small RNAs are inherited also from the sperm. Moreover, we find that the transgenerational effects that depend on the ancestral germ granules require the argonaute protein HRDE-1, which carries heritable small RNAs in the germline. Indeed, small RNA sequencing reveals imbalanced levels of many endogenous small RNAs in germ granules mutants. Strikingly, we find thathrde-1;meg-3/4triple mutants inherit RNAi, althoughhrde-1was previously thought to be essential for heritable silencing. We propose that germ granules sort and shape the RNA pool, and that small RNA inheritance memorizes this activity for multiple generations.