bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Contamination of Voided Urine Specimen in Women With Pelvic Organ Prolapse
Authors: Soriano Alex , Sansone Stephanie , Arora Ena , Arya Lily , Andy Uduak 
Published: July 2019

Objectives
The primary aim of this study was to determine if urine cultures are more likely to be contaminated in women with pelvic organ prolapse (POP). The secondary aim was to evaluate the test characteristics of a urine dipstick in women with POP.

Methods
A retrospective cohort study was conducted of women who presented to the urogynecology clinic between September 1, 2017, and August 31, 2018. Associations between the presence of POP and contaminated urine culture results were estimated using univariable and multivariable analyses. The sensitivity and specificity of a urine dipstick in women with POP were calculated.

Results
We included 351 women (143 with and 208 without POP). Women with POP were older (65.4 ± 15.8 vs 60.7 ± 11.0 years, P < 0.01), had a lower body mass index (26.6 ± 4.8 vs 29.2 ± 7.7 kg/m2, P < 0.01), and were less likely to have recurrent urinary tract infections (3.5% vs 9.6%, P=0.03). Women with POP were more likely to have a contaminated urine culture than women without POP (55.9% vs 40.9%, P < 0.01). Rates of contaminated urine culture were higher in women with stage 3 and 4 prolapse than in women with stage 2 prolapse (59.6% vs 41.0%, P < 0.01). On multivariate analysis, the odds of contaminated urine culture remained higher in women with POP (odds ratio, 1.89; 95% confidence interval, 1.20–2.99). In women with POP, the sensitivity (23.5%) and positive predictive value (66.7%) of a urine dipstick were poor.

Conclusions
Women with POP are more likely to provide a contaminated urine culture when collecting a midstream urine specimen.
Helmet use is associated with higher Injury Severity Scores in alpine skiers and snowboarders evaluated at a Level I trauma center
Authors: Porter Eleah D. , Trooboff Spencer W. , Haff Madeleine G. , Cooros James C. , Wolffing Andrea B. , Briggs Alexandra , Rhynhart Kurt K. , Crockett Andrew O. 
Published: July 2019

BACKGROUND
There is uncertainty regarding the efficacy of ski helmets in preventing traumatic injury. We investigated the relationship between helmet use, injury types, and injury severity among skiers and snowboarders.

METHODS
The trauma registry at a Northeast American College of Surgeons Level I trauma center was queried by International Classification of Diseases Codes—9th or 10th Revision for skiing and snowboarding injury between 2010 and 2018. The primary exposure was helmet use and primary outcome was severe injury (Injury Severity Score >15). We performed univariate and multivariable logistic regression to assess for injury types and severity associated with helmet use.

RESULTS
Seven hundred twenty-one patients (65% helmeted, 35% unhelmeted) met inclusion criteria. Helmet use doubled during the study period (43% to 81%, p < 0.001), but the rate of any head injury did not significantly change (49% to 43%, p = 0.499). On multivariable regression, helmeted patients were significantly more likely to suffer severe injury (odds ratio [OR], 2.01; 95% confidence interval [CI], 1.30–3.11), intracranial hemorrhage (OR, 1.81; 95% CI, 1.10–2.96), chest injury (OR, 1.66; 95% CI, 1.05–2.61), and/or lumbosacral spine injury (OR, 1.84; 95% CI, 1.04–3.25) than unhelmeted patients. Helmeted patients were half as likely to suffer cervical spine injury (OR, 0.51; 95% CI, 0.30–0.89) and a third as likely to sustain skull fracture and/or scalp laceration (OR, 0.30; 95% CI, 0.14–0.64). More patients who hit a stationary object were helmeted compared with those who fell from standing height onto snow (70% vs. 56% respectively, p < 0.001). After adjustment, hitting a stationary object was the injury mechanism most significantly associated with severe injury (OR, 2.80; 95% CI, 1.79–4.38).

CONCLUSION
Helmeted skiers and snowboarders evaluated at a Level I trauma center were more likely to suffer severe injury, including intracranial hemorrhage, as compared with unhelmeted participants. However, they were less likely to sustain skull fractures or cervical spine injuries. Helmeted patients were also more likely to hit a stationary object. Our findings reinforce the importance of safe skiing practices and trauma evaluation after high-impact injury, regardless of helmet use.

LEVEL OF EVIDENCE
Prognostic and epidemiological, level IV.
Emergence of artemisinin-resistantPlasmodium falciparumwithkelch13C580Y mutations on the island of New Guinea
Authors: Miotto Olivo , Sekihara Makoto , Tachibana Shin-Ichiro , Yamauchi Masato , Pearson Richard D , Amato Roberto , Gonçalves Sonia , Mehra Somya , Noviyanti Rintis , Marfurt Jutta , Auburn Sarah , Price Ric N , Mueller Ivo , Ikeda Mie , Mori Toshiyuki , Hirai Makoto , Tavul Livingstone , Hetzel Manuel , Laman Moses , Barry Alyssa , Ringwald Pascal , Ohashi Jun , Hombhanje Francis , Kwiatkowski Dominic P , Mita Toshihiro 
Published: July 2019

AbstractThe rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the kelch13 C580Y mutation is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants’ genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance.
Response to “Expression reduction of biallelically transcribed X-linked genes during the female human preimplantation development”
Authors: Moreira de Mello JC , Vibranovski MD , Pereira LV 
Published: July 2019

ABSTRACTReinius and Sandberg (2019) have recently shown that X-linked balletic gene expression decreases during human preimplantation embryonic development, corroborating their previous hypothesis of X dampening as a mechanism of dosage compensation. Here we demonstrate that their analyses are based on biologically false premises, thus not demonstrating the phenomena of X dampening in humans.
Neurological disorder drug discovery from gene expression with tensor decomposition
Authors: Taguchi Y-h. , Turki Turki 
Published: July 2019

AbstractBackgroundIdentifying effective candidate drug compounds in patients with neurological disorders based on gene expression data is of great importance to the neurology field. By identifying effective candidate drugs to a given neurological disorder, neurologists would (1) reduce the time searching for effective treatments; and (2) gain additional useful information that leads to a better treatment outcome. Although there are many strategies to screen drug candidate in pre-clinical stage, it is not easy to check if candidate drug compounds can be also effective to human.ObjectiveWe tried to propose a strategy to screen genes whose expression is altered in model animal experiments to be compared with gene expressed differentically with drug treatment to human cell lines.MethodsRecently proposed tensor decomposition (TD) based unsupervised feature extraction (FE) is applied to single cell (sc) RNA-seq experiments of Alzheimer’s disease model animal mouse brain.ResultsFour hundreds and one genes are screened as those differentially expressed during Aβaccumulation as age progresses. These genes are significantly overlapped with those expressed differentially with the known drug treatments for three independent data sets: LINCS, DrugMatrix and GEO.ConclusionOur strategy, application of TD based unsupervised FE, is useful one to screen drug candidate compounds using scRNA-seq data set.
A lab-on-a-chip model of glaucoma
Authors: Nafian Fatemeh , Azad Babak Kamali Doust , Yazdani Shahin , Rasaee Mohammad Javad , Daftarian Narsis 
Published: July 2019

AbstractWe developed a glaucoma-on-a-chip (GOC) model to evaluate the viability of retinal ganglion cells (RGCs) against high pressure and the potential effect of neuroprotection. A three-layered chip consisting of interconnecting microchannels and culture wells was designed based on simulation of physical parameters. The chip layers were fabricated from poly-methyl methacrylate sheets. Multiple inlet ports allow culture media and gas into the wells under elevated hydrostatic pressure (EHP). The bottom surface of the wells was modified by air plasma and coated with different membranes to model an extracellular microenvironment. The SH-SY5Y neuroblastoma cell line served as model cells to determine the best supporting membrane which was revealed to be PDL/laminin. Thereafter, the study experiments were performed using RGCs obtained from postnatal 5-7 Wistar rats purified by magnetic assisted cell sorting. Flow cytometry and immunocytochemistry assays demonstrated 70% purification for RGCs. The cultured RGCs were exposed to normal (15 mmHg) or elevated pressure (33 mmHg) for 6, 12, 24, 36 and 48 hours, with and without adding brain-derived neurotrophic factor (BDNF) or a novel BDNF mimetic (RNYK). RGC survival rates were 85, 78, 70, 67 and 61 percent under normal pressure versus 40, 22, 18, 12 and 10 percent under high pressure at 6, 12, 24, 36 and 48 hours, respectively (P <0.0001). BDNF and RNYK treatments induced separately an approximate two-fold decrease in the rate of RGC death under both normal and elevated pressures (p <0.01 to 0.0001). This GOC model recapitulated the effects of elevated pressure during relatively short time periods and demonstrated the neuroprotective effects of BDNF and RNYK.
Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour
Authors: Lovegrove Alison , Wingen Luzie U. , Plummer Amy , Wood Abigail , Passmore Diana , Kosik Ondrej , Freeman Jackie , Mitchell Rowan A.C. , Ulker Mehmet , Tremmel-Bede Karolina , Rakszegi Marianna , Bedő Zoltán , Petterant Marie-Reine , Charmet Gilles , Leverington Waite Michelle , Orford Simon , Burridge Amanda , Pellny Till , Shewry Peter R , Griffiths Simon 
Published: July 2019

AbstractDietary fibre (DF) has multiple health benefits, and wheat products are major sources of DF for human health. However, DF is depleted in white flour, which is most widely consumed, compared to wholegrain. The major type of DF in white wheat flour is the cell wall polysaccharide arabinoxylan (AX). Previous studies have identified the Chinese wheat cultivar Yumai 34 as having unusually high contents of AX in both water-soluble and insoluble forms. We have therefore used populations generated from crosses between Yumai 34 and four other wheat cultivars, three with average contents of AX (Ukrainka, Altigo and Claire) and one also having unusually high AX (Valoris), in order to map QTLs for soluble AX (determined as relative viscosity) of aqueous extracts of wholemeal flours) and total AX (determined by enzyme fingerprinting of white flour). A number of QTL were mapped, but most were only detected in one or two crosses. However, all four crosses showed strong QTLs for high RV/total AX on chromosome 1B, with Yumai 34 being the increasing parent, and a KASP marker for the high AX Yumai 34 allele was validated by analysis of high AX lines derived from Yumai 34 but selected by biochemical analysis. A QTL for RV was mapped on chromosome 6B in Yumai 34 × Valoris, with Valoris being the increasing allele, which was consistent with the observation of transgressive segregation for this trait. The data indicate that breeding can be used to develop wheat with high AX fibre in white flour.
Highly efficient and super-bright neurocircuit tracing using vector mixing-based virus cocktail
Authors: Sun Pei , Jin Sen , Tao Sijue , Wang Junjun , Li Anan , Li Ning , Wu Yang , Kuang Jianxia , Liu Yurong , Wang Lizhao , Lin Huimin , Lv Xiaohua , Liu Xiuli , Peng Jundan , Zhang Siyu , Xu Min , Luo Zhen , He Xiaobin , Xu Tonghui , Li Xiangning , Zeng Shaoqun , Zhang Yu-Hui , Xu Fuqiang 
Published: July 2019

ABSTRACTMapping the detailed cell-type-specific input networks and neuronal projectomes are essential to understand brain function in normal and pathological states. However, several properties of current tracing systems, including labeling sensitivity, trans-synaptic efficiencies, reproducibility among different individuals and different Cre-driver animals, still remained unsatisfactory. Here, we developed MAP-ENVIVIDERS, a recombinase system-dependent vector mixing-based strategy for highly efficient neurocircuit tracing. MAP-ENVIVIDERS enhanced tracing efficiency of input networks across the whole brain, with over 10-fold improvement in diverse previously poor-labeled input brain regions and particularly, up to 70-fold enhancement in brainstem compared with the current standard rabies-virus-mediated systems. MAP-ENVIVIDERS was over 10-fold more sensitive for cell-type-specific labeling than previous strategies, enabling us to capture individual cell-type-specific neurons with extremely complex axonal branches and presynaptic axonal boutons, both about one order of magnitude than previously reported and considered. MAP-ENVIVIDERS provides powerful tools for deconstructing novel input/output circuitry towards functional studies and disorders-related mechanisms.
Heparanase-2 protects from endothelial injury by inhibiting TLR4 signaling
Authors: Kiyan Yulia , Tkachuk Sergey , Kurselis Kestutis , Shushakova Nelli , Stahl Klaus , Dawodu Damilola , Kiyan Roman , Chichkov Boris , Haller Hermann 
Published: July 2019

AbstractObjectiveThe endothelial glycocalyx and the regulation of its shedding are important to vascular health. Endo-β-D-glucuronidase heparanase-1 (HPSE1) is the only enzyme that can shed heparan sulfate. However, the mechanisms are not well understood.Approach and resultsTo investigate HPSE1 and its endogenous inhibitor, heparanase-2 (HPSE2), we used cell culture, lentiviral protein overexpression, a microfluidic chip model of cell culture under shear stress conditions, and lipopolysaccharide (LPS) injections in mice. We show that HPSE1 activity aggravated Toll-like receptor 4 (TLR4)-mediated response of endothelial cells to LPS. On the contrary, HPSE2 overexpression was protective. The microfluidic chip flow model confirmed that HPSE2 prevented heparan sulfate shedding by HPSE1. Furthermore, heparan sulfate did not interfere with cluster of differentiation-14 (CD14)-dependent LPS binding, but instead reduced the presentation of the LPS-CD14 complex to TLR4. HPSE2 reduced LPS-mediated TLR4 activation by LPS, subsequent cell signaling, and cytokine expression. Moreover, HPSE2-overexpressing endothelial cells remained protected against LPS-mediated loss of cell-cell contacts. In vivo, expression of HPSE2 in plasma and kidney medullary capillaries was decreased in mouse sepsis model. We next applied purified HPSE2 in mice and observed decreases in TNFα and IL-6 plasma concentrations after intravenous LPS injections.ConclusionsOur data demonstrate the important role of heparan sulfate and the glycocalyx in endothelial cell activation and suggest a protective role of HPSE2 in microvascular inflammation. HPSE2 offers new options for protection against HPSE1-mediated endothelial damage and preventing microvascular disease.Graphical abstractNon standard abbreviations
Phazolicin – a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way
Authors: Travin Dmitrii Y. , Watson Zoe L. , Metelev Mikhail , Ward Fred R. , Osterman Ilya A. , Khven Irina M. , Khabibullina Nelli F. , Serebryakova Marina , Mergaert Peter , Polikanov Yury S. , Cate Jamie H. D. , Severinov Konstantin 
Published: July 2019

ABSTRACTRibosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly expanding and largely untapped class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display an outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium sp. Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) – an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants belonging to the Rhizobiales. PHZ inhibits prokaryotic translation through the obstruction of the passage of the nascent peptide through the ribosome exit channel. The cryo-EM structure of the Escherichia coli ribosome with bound PHZ revealed that the drug interacts with the 23S rRNA and ribosomal proteins uL4 and uL22 and obstructs the exit tunnel in a way that is distinct from other compounds blocking the exit channel. We show that the sequence of uL4 ribosomal protein loop involved in PHZ binding determines the species-specificity of antibiotic interaction with its target. PHZ and its predicted homologs from other bacterial species expand the known diversity of LAPs and may be used in the future as biocontrol agents for the needs of agriculture.
An integrative ENCODE resource for cancer genomics
Authors: Zhang Jing , Lee Donghoon , Dhiman Vineet , Jiang Peng , Xu Jie , McGillivray Patrick , Yang Hongbo , Liu Jason , Meyerson William , Clarke Declan , Gu Mengting , Li Shantao , Lou Shaoke , Xu Jinrui , Lochovsky Lucas , Ung Matthew , Ma Lijia , Yu Shan , Cao Qin , Harmanci Arif , Yan Koon-Kiu , Sethi Anurag , Gursoy Gamze , Schoenberg Michael Rutenberg , Rozowsky Joel , Warrell Jonathan , Emani Prashant , Yang Yucheng T. , Galeev Timur , Kong Xiangmeng , Liu Shuang , Li Xiaotong , Krishnan Jayanth , Feng Yanlin , Rivera-Mulia Juan Carlos , Adrian Jessica , Broach James R , Bolt Michael , Moran Jennifer , Fitzgerald Dominic , Dileep Vishnu , Liu Tingting , Mei Shenglin , Sasaki Takayo , Trevilla-Garcia Claudia , Wang Su , Wang Yanli , Zang Chongzhi , Wang Daifeng , Klein Robert , Snyder Michael , Gilbert David M. , Yip Kevin , Cheng Chao , Yue Feng , Liu X. Shirley , White Kevin , Gerstein Mark 
Published: July 2019

AbstractENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.
Deformity Index: A semi-reference quality metric of phylogenetic trees based on their clades
Authors: Mahapatra Aritra , Mukherjee Jayanta 
Published: July 2019

abstractMeasuring the correctness of a phylogenetic tree is one of the most fundamental tasks in phylogenetic study. A large number of methods have been proposed to measure the correctness of a tree. Such methods completely depend on the reference tree and they compute the distance between reference the tree and the target tree. But it is very difficult to obtain a precise and an accurate reference tree for a selected dataset. As a result, the existing methods for comparing the phylogenetic trees can behave unexpectedly in various scenarios. In this paper, we introduce a scoring function, called the Deformity Index, to measure the correctness of a tree based on the biological knowledge of the clades. The strength of our proposed method is that it does not consider any reference tree. We have also investigated the range and the distributions of the different modules of Deformity Index. Furthermore, we perform different goodness of fit tests to understand its cumulative distribution. We have also examined in detail the robustness as well as the scalability of our measure by different statistical tests under the Yule and the uniform models. Moreover, we show that our proposed scoring function can overcome the limitations of the conventional methods of tree comparing by experimenting on different biological datasets.
Calculating sample size for identifying cell subpopulation in single-cell RNA-seq experiments
Authors: Kim Kyung In , Youn Ahrim , Bolisetty Mohan , Palucka A. Karolina , George Joshy 
Published: July 2019

SummarySingle-cell RNA sequencing (scRNA-seq) is a rapidly developing technology for studying gene expression at the individual cell level and is often used to identify subpopulations of cells. Although the use of scRNA-seq is steadily increasing in basic and translational research, there is currently no statistical model for calculating the optimal number of cells for use in experiments that seek to identify cell subpopulations. Here, we have developed a statistical method ncells for calculating the number of cells required to detect a rare subpopulation in a homogeneous cell population for the given type I and II error. ncells defines power as the probability of separation of subpopulations which is calculated from three user-defined parameters: the proportion of rare subpopulation, proportion of up-regulated marker genes of the subpopulation, and levels of differential expression of the marker genes. We applied ncells to the scRNA-seq data on dendritic cells and monocytes isolated from healthy blood donor to show its efficacy in calculating the optimal number of cells in identifying a novel subpopulation.