bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of Free Flaps for Traumatic Wounds of the Lower Extremity: Have Advances in Perioperative Care Changed the Treatment Algorithm?
Authors: Patterson Charles W. , Stalder Mark W. , Richardson William , Steele Thomas , Wise M. Whitten , St Hilaire Hugo 
Published: May 2019

Abstract
Background Despite the landmark study by Godina 30 years ago, opinions still vary within the literature about the management of complex traumatic wounds in the lower extremity. We present a large series of lower extremity reconstructions with vascularized free tissue and examine the perioperative factors that influenced the success of these cases.
Methods We reviewed 88 patients with free flap reconstruction of traumatic lower extremity wounds over 8 years. Primary outcomes were flap infections, flap loss, total flap-specific complications, and total recipient site complications. Independent variables specific to perioperative care including time to flap coverage, injury classification, exposed or infected hardware, prior osteomyelitis, use of wound vacuum-assisted closure (VAC) therapy, and concurrent polytrauma were investigated to establish their influence on primary outcomes. Each independent variable was assessed using Chi-square or Fisher's exact test and was included in a logistic regression analysis to establish significance.
Results Of the 88 patients, 8 had flap loss, 8 had flap infections, and a total of 23 had primary adverse outcomes. Timing of the reconstruction, VAC use, injury classification, prior hardware or wound status, or presence of polytrauma had no statistically significant impact on the primary outcomes. Injury classification/severity on total recipient site complications (p = 0.051) and flap-specific complications (p = 0.073) trended toward significance; however, subgroup analysis did not achieve significance. Logistic regression of any recipient site complication including all independent variables similarly showed no significance.
Conclusion Although the original study by Godina suggests early coverage is critical to optimize outcomes, in the modern era of advanced wound care, our study adds to a growing body of evidence that supports the de-emphasis of the 72-hour reconstruction interval. Our current management is focused on more effectively coordinating efficient peritraumatic and perioperative care on an individualized basis in the often very complicated polytrauma patient.
Role of Oropharyngeal Administration of Colostrum in Very Low Birth Weight Infants for Reducing Necrotizing Enterocolitis: A Randomized Controlled Trial
Authors: Sharma Deepak , Kaur Amandeep , Farahbakhsh Nazanin , Agarwal Sunil 
Published: May 2019

Objective This study aimed to study the role of oropharyngeal administration of colostrum (OAC) in very-low-birth-weight infants for reducing necrotizing enterocolitis (NEC).
Study Design In this randomized controlled trial, 117 infants were enrolled, 59 were randomized to OAC group and 58 to routine care group. Infants with birth weight ≤ 1,250 g and/or gestational age ≤ 30 weeks were enrolled. Infants in OAC group received maternal colostrum (0.2 mL), 0.1 mL on either side, after 24 hours of postnatal life and were given every 2 hour for the next 72 hours irrespective of the enteral feeding status of the neonate. The primary outcome of the study was the incidence of NEC (stage 2 or 3).
Results Baseline characteristics were comparable between the two groups. There was no significant reduction in the incidence of NEC in OAC group (0 [0%] vs. 3 [7.1%]; p = 0.11). There was significant reduction of 7 days of hospital stay in OAC group (34.2 ± 5.7 vs. 41.5 ± 6.7 days; p = 0.04).The incidence of early-onset sepsis, late-onset sepsis, blood culture positive sepsis, and ventilator-associated pneumonia were comparable between the two groups.
Conclusion OAC is safe and reduces the duration of hospital stay.
Does a Care Bundle Reduce Racial Disparities in Postcesarean Surgical Site Infections?
Authors: Kawakita Tetsuya , Umans Jason G. 
Published: May 2019

Objective To examine the effect of a care bundle on racial disparities in surgical site infections (SSIs).
Study Design This was a retrospective cohort study of women undergoing cesarean delivery at ≥23 weeks' gestation. The care bundle included routine antibiotics (both cefazolin and azithromycin), chlorhexidine skin preparation, clippers, vaginal cleansing, placental removal by cord traction, subcutaneous tissue closure, suture skin closure, dressing removal in 24 to 48 hours, and postoperative chlorhexidine soap. Our primary outcome was SSI (superficial incisional, deep incisional, and organ/space) occurring up to 6 weeks. Adjusted odds ratios (aOR) with 95% confidence intervals (95% CI) were calculated, adjusting for predefined covariates.
Results Of 2,696 women, 1,947 were black (1,014 in the preimplementation period and 933 in the postimplementation period) and 749 were nonblack (370 in the preimplementation period and 379 in the postimplementation period). Regardless of race, women in the postimplementation period had lower rates of SSI compared with those in the preimplementation period (black: 2.9 vs. 5.2%, aOR: 0.53 [95% CI: 0.33–0.85]; nonblack: 1.1 vs. 3.5%, aOR: 0.28 [95% CI: 0.09–0.89]). There was no interaction by race (p for interaction = 0.94).
Conclusion The care bundle decreased SSI in both black and nonblack women but did not reduce racial disparities.
Bone resorption and body reorganization during maturation induce maternal transfer of toxic metals in anguillid eels
Authors: Freese Marko , Rizzo Larissa Yokota , Pohlmann Jan-Dag , Marohn Lasse , Witten Paul Eckhard , Gremse Felix , Rütten Stephan , Güvener Nihan , Michael Sabrina , Wysujack Klaus , Lammers Twan , Kiessling Fabian , Hollert Henner , Hanel Reinhold , Brinkmann Markus 
Published: May 2019

Significance
Body reorganization in eels during gametogenesis can induce undesired side effects with possible pathological significance. This study provides analytical evidence for the maternal transfer of toxic metals from soft and hard tissues to the ovaries of mature females. By illustrating the metabolic fluxes and fate of mobilized minerals and metals in the fishes’ bodies during sexual development, we have identified a previously unreported aspect of anthropogenic impact on endangered anguillid eels. Furthermore, our findings suggest a physiologically connected interplay of energy metabolism and bone resorption in the reproductive strategy of eels. Consequently, we propose the eel as an interesting model organism for investigating the physiological pathways connecting lipid metabolism and mineral retention, known also to affect the health state of humans.
Dated language phylogenies shed light on the ancestry of Sino-Tibetan
Authors: Sagart Laurent , Jacques Guillaume , Lai Yunfan , Ryder Robin J. , Thouzeau Valentin , Greenhill Simon J. , List Johann-Mattis 
Published: May 2019

SignificanceGiven its size and geographical extension, Sino-Tibetan is of the highest importance for understanding the prehistory of East Asia, and of neighboring language families. Based on a dataset of 50 Sino-Tibetan languages, we infer phylogenies that date the origin of the language family to around 7200 B.P., linking the origin of the language family with the late Cishan and the early Yangshao cultures.
Distinct differences in the nanoscale behaviors of the twist–bend liquid crystal phase of a flexible linear trimer and homologous dimer
Authors: Tuchband Michael R. , Paterson Daniel A. , Salamończyk Mirosław , Norman Victoria A. , Scarbrough Alyssa N. , Forsyth Ewan , Garcia Edgardo , Wang Cheng , Storey John M. D. , Walba David M. , Sprunt Samuel , Jákli Antal , Zhu Chenhui , Imrie Corrie T. , Clark Noel A. 
Published: May 2019

SignificanceThe twist–bend (TB) liquid crystal phase is the newest nematic phase, having only been identified in 2011. Still, there are many outstanding mysteries about the nature of its nanoscale organization and behavior. We elucidate how the number of monomer units in a linear TB oligomer influences the structure of its nanoscale helix, an important TB phase structure–property relationship. While a TB dimer exhibits a temperature-dependent variation of its helix pitch, the analogous trimer features a temperature-independent helix pitch considerably shorter than that of the dimer and other known TB materials. This study illuminates the scope of possible variations that manifest in the TB phase and represents a substantial step in controlling its nanoscale behavior for technological applications.
Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization
Authors: Wang Chong , Lu Tian , Emanuel George , Babcock Hazen P. , Zhuang Xiaowei 
Published: May 2019

SignificanceIn this work, we developed an imaging-based pooled-library CRISPR screening approach that provides readouts of both phenotype and genotype of individual cells by high-resolution, high-content imaging. This approach promises to substantially expand the phenotype space accessible to pooled genetic screening by allowing the probing of complex cellular phenotypes, such as cell morphology and subcellular organization of different molecular species, as well as their dynamics. Applying this approach to screen for genetic factors involved in nuclear RNA localization, we identified both positive and negative regulators that control lncRNA localization to nuclear speckles.
Metameric
Authors: Tulkens Stéphan , Sandra Dominiek , Daelemans Walter 
Published: May 2019

Abstract
An oft-cited shortcoming of Interactive Activation as a
psychological model of word reading is that it lacks the ability to
simultaneously represent words of different lengths.
We present an implementation of the Interactive Activation
model, which we call Metameric, that can simulate words of different lengths,
and show that there is nothing inherent to Interactive Activation which prevents
it from simultaneously representing multiple word lengths. We provide an
in-depth analysis of which specific factors need to be present, and show that
the inclusion of three specific adjustments, all of which have been published in
various models before, lead to an Interactive Activation model which is fully
capable of representing words of different lengths. Finally, we show that our
implementation is fully capable of representing all words between 2 and 11
letters in length from the English Lexicon Project (31, 416 words) in a single
model. Our implementation is completely open source, heavily optimized, and
includes both command line and graphical user interfaces, but is also agnostic
to specific input data or problems. It can therefore be used to simulate a
myriad of other models, e.g., models of spoken word recognition. The
implementation can be accessed at www.github.com/clips/metameric.
Colophons and Marginal Notes of the Avestan Manuscripts of the Pouladi’s Collection in Yazd
Authors: Gholami Saloumeh , Pouladi Mehraban 
Published: May 2019

About 150 years ago, after Avestan researchers such as Jackson, Browne, and Westergaard had unsuccessfully attempted to discover new manuscripts in Iran, it was assumed that there were few or no Avestan manuscripts remaining in Iran. However, recent research and fieldwork in Iran have resulted in important findings disproving this assumption. Since 2011, more than eighty-five Avestan manuscripts have been discovered in Iran. One of these important discoveries has been Pouladi’s Collection, which was found in February 2016 in a Zoroastrian house in the Priests’ Quarter (Mahalle-ye Dastūrān) in Yazd. This article deals with the secondary life of Avestan manuscripts of Pouladi’s Collection, focusing on colophons and marginal notes.The article makes available a collection of Middle Persian and New Persian colophons and marginal notes, all which have been excerpted, transcribed, and translated for the first time from the Avestan manuscripts of Pouladi’s Collection, copied mostly in the seventeenth and eighteenth centuries. Based on different types of colophons, this contribution establishes a classification of colophons and marginal notes of this collection with regard to formal, contextual, and functional characteristics.
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
Authors: Ma Anjun , Sun Minxuan , McDermaid Adam , Liu Bingqiang , Ma Qin 
Published: May 2019

Abstract

Motivation
Metagenomic and metatranscriptomic analyses can provide an abundance of information related to microbial communities. However, straightforward analysis of this data does not provide optimal results, with a required integration of data types being needed to thoroughly investigate these microbiomes and their environmental interactions.

Results
Here, we present MetaQUBIC, an integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data. Additionally, we used this pipeline to investigate 735 paired DNA and RNA human gut microbiome samples, resulting in a comprehensive hybrid gene expression matrix of 2.3 million cross-species genes in the 735 human fecal samples and 155 functional enriched gene modules. We believe both the MetaQUBIC pipeline and the generated comprehensive human gut hybrid expression matrix will facilitate further investigations into multiple levels of microbiome studies.

Availability and implementation
The package is freely available at https://github.com/OSU-BMBL/metaqubic.

Supplementary information
Supplementary data are available at Bioinformatics online.
deepDR: a network-based deep learning approach toin silicodrug repositioning
Authors: Zeng Xiangxiang , Zhu Siyi , Liu Xiangrong , Zhou Yadi , Nussinov Ruth , Cheng Feixiong 
Published: May 2019

AbstractMotivationTraditional drug discovery and development are often time-consuming and high risk. Repurposing/repositioning of approved drugs offers a relatively low-cost and high-efficiency approach toward rapid development of efficacious treatments. The emergence of large-scale, heterogeneous biological networks has offered unprecedented opportunities for developing in silico drug repositioning approaches. However, capturing highly non-linear, heterogeneous network structures by most existing approaches for drug repositioning has been challenging.ResultsIn this study, we developed a network-based deep-learning approach, termed deepDR, for in silico drug repurposing by integrating 10 networks: one drug–disease, one drug-side-effect, one drug–target and seven drug–drug networks. Specifically, deepDR learns high-level features of drugs from the heterogeneous networks by a multi-modal deep autoencoder. Then the learned low-dimensional representation of drugs together with clinically reported drug–disease pairs are encoded and decoded collectively via a variational autoencoder to infer candidates for approved drugs for which they were not originally approved. We found that deepDR revealed high performance [the area under receiver operating characteristic curve (AUROC) = 0.908], outperforming conventional network-based or machine learning-based approaches. Importantly, deepDR-predicted drug–disease associations were validated by the ClinicalTrials.gov database (AUROC = 0.826) and we showcased several novel deepDR-predicted approved drugs for Alzheimer’s disease (e.g. risperidone and aripiprazole) and Parkinson’s disease (e.g. methylphenidate and pergolide).Availability and implementationSource code and data can be downloaded from https://github.com/ChengF-Lab/deepDRSupplementary informationSupplementary data are available online at Bioinformatics.
Behavioural avoidance of sperm ageing depends on genetic similarity of mates in a monogamous seabird
Authors: Pineaux Maxime , Blanchard Pierrick , Danchin Étienne , Hatch Scott A , Helfenstein Fabrice , Mulard Hervé , White Joël , Leclaire Sarah , Wagner Richard H 
Published: May 2019

Abstract
Inbreeding, i.e. the mating of genetically related individuals, can lead to reduced fitness and is considered to be a major selective force of mate choice. Although inbreeding avoidance has been found in numerous taxa, individuals may face constraints when pairing, leading to mating with suboptimal partners. In such circumstances, individuals that are able to avoid factors exacerbating detrimental effects of inbreeding should be favoured. Using the socially and genetically monogamous black-legged kittiwake (Rissa tridactyla), we explored whether the detrimental effects of inbreeding are exacerbated by sperm ageing (i.e. the post-meiotic senescence of sperm cells, mainly occurring within the female tracts after copulation), and whether they can be mitigated by behavioural tactics. First, by experimentally manipulating the age of the fertilizing sperm, we found that hatching failure due to sperm ageing increased with higher genetic similarity between mates. We then investigated whether more genetically similar pairs exhibited mating behaviours that prevent fertilization by old sperm. The more genetically similar mates were, the less likely they were to copulate early in the reproductive season and the more females performed post-copulatory sperm ejections. By flexibly adapting their behaviour in response to within-pair genetic similarity, kittiwakes may avoid exacerbation of inbreeding costs due to sperm ageing.
Follicle-stimulating hormone and luteinizing hormone increase Ca2+ in the granulosa cells of mouse ovarian follicles†
Authors: Egbert Jeremy R , Fahey Paul G , Reimer Jacob , Owen Corie M , Evsikov Alexei V , Nikolaev Viacheslav O , Griesbeck Oliver , Ray Russell S , Tolias Andreas S , Jaffe Laurinda A 
Published: May 2019

Abstract
In mammalian ovarian follicles, follicle stimulating hormone (FSH) and luteinizing hormone (LH) signal primarily through the G-protein Gs to elevate cAMP, but both of these hormones can also elevate Ca2+ under some conditions. Here, we investigate FSH- and LH-induced Ca2+ signaling in intact follicles of mice expressing genetically encoded Ca2+ sensors, Twitch-2B and GCaMP6s. At a physiological concentration (1 nM), FSH elevates Ca2+ within the granulosa cells of preantral and antral follicles. The Ca2+ rise begins several minutes after FSH application, peaks at ∼10 min, remains above baseline for another ∼10 min, and depends on extracellular Ca2+. However, suppression of the FSH-induced Ca2+ increase by reducing extracellular Ca2+ does not inhibit FSH-induced phosphorylation of MAP kinase, estradiol production, or the acquisition of LH responsiveness. Like FSH, LH also increases Ca2+, when applied to preovulatory follicles. At a physiological concentration (10 nM), LH elicits Ca2+ oscillations in a subset of cells in the outer mural granulosa layer. These oscillations continue for at least 6 h and depend on the activity of Gq family G-proteins. Suppression of the oscillations by Gq inhibition does not inhibit meiotic resumption, but does delay the time to 50% ovulation by about 3 h. In summary, both FSH and LH increase Ca2+ in the granulosa cells of intact follicles, but the functions of these Ca2+ rises are only starting to be identified.
Core–periphery segregation in evolving prisoner’s dilemma networks
Authors: Sohn Yunkyu , Choi Jung-Kyoo , Ahn T K 
Published: May 2019

AbstractDense cooperative networks are an essential element of social capital for prosperous societies. These networks enable individuals to overcome collective action dilemmas by enhancing trust. In many biological and social settings, network structures evolve endogenously as agents exit relationships and build new ones. However, the interplay between game strategy and interaction structure by which evolutionary dynamics leads to self-organization of dense cooperative networks has not been understood. Our prisoner’s dilemma experiments with exit and partner choice options show that core–periphery segregation of cooperators and defectors drives the emergence of cooperation. Cooperators’ Quit-for-Tat and defectors’ Roving strategy lead to a highly asymmetric core and periphery structure. Densely connected to each other at the core, cooperators successfully isolate defectors at the periphery and earn larger payoffs.
Transcriptional dynamics of pluripotent stem cell-derived endothelial cell differentiation revealed by single-cell RNA sequencing
Authors: McCracken Ian R , Taylor Richard S , Kok Fatma O , de la Cuesta Fernando , Dobie Ross , Henderson Beth E P , Mountford Joanne C , Caudrillier Axelle , Henderson Neil C , Ponting Chris P , Baker Andrew H 
Published: May 2019

Abstract

Aims
Pluripotent stem cell-derived endothelial cell products possess therapeutic potential in ischaemic vascular disease. However, the factors that drive endothelial differentiation from pluripotency and cellular specification are largely unknown. The aims of this study were to use single-cell RNA sequencing (scRNA-seq) to map the transcriptional landscape and cellular dynamics of directed differentiation of human embryonic stem cell-derived endothelial cells (hESC-EC) and to compare these cells to mature endothelial cells from diverse vascular beds.

Methods and results
A highly efficient directed 8-day differentiation protocol was used to generate a hESC-derived endothelial cell product (hESC-ECP), in which 66% of cells co-expressed CD31 and CD144. We observed largely homogeneous hESC and mesodermal populations at Days 0 and 4, respectively, followed by a rapid emergence of distinct endothelial and mesenchymal populations. Pseudotime trajectory identified transcriptional signatures of endothelial commitment and maturation during the differentiation process. Concordance in transcriptional signatures was verified by scRNA-seq analysis using both a second hESC line RC11, and an alternative hESC-EC differentiation protocol. In total, 105 727 cells were subjected to scRNA-seq analysis. Global transcriptional comparison revealed a transcriptional architecture of hESC-EC that differs from freshly isolated and cultured human endothelial cells and from organ-specific endothelial cells.

Conclusion
A transcriptional bifurcation into endothelial and mesenchymal lineages was identified, as well as novel transcriptional signatures underpinning commitment and maturation. The transcriptional architecture of hESC-ECP was distinct from mature and foetal human EC.