bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Silicon–Hydrogen Exchange Reaction: Catalytic Kinetic Resolution of 2-Substituted Cyclic Ketones
Authors: List Benjamin , Zhou Hui , Zhang Pinglu 
Published: October 2021

AbstractWe have recently reported the strong and confined, chiral acid-catalyzed asymmetric ‘silicon−hydrogen exchange reaction’. One aspect of this transformation is that it enables access to enantiopure enol silanes in a tautomerizing σ-bond metathesis, via deprotosilylation of ketones with allyl silanes as the silicon source. However, until today, this reaction has not been applied to racemic, 2-substituted, cyclic ketones. We show here that these important substrates readily undergo a highly enantioselective kinetic resolution furnishing the corresponding kinetically preferred enol silanes. Mechanistic studies suggest the fascinating possibility of advancing the process to a dynamic kinetic resolution.
Leadership election reform in the British Labour party: democratisation or power struggle?
Authors: Niendorf Tim 
Published: October 2021

AbstractThis article examines the impact of reforms on the outcome of Labour party leadership contests since the premiership of Tony Blair. From a theoretical perspective, these reforms are characterised by a tension between a general trend towards increasing “democratisation” of political parties and the power interests of intra-party actors. While there have been significant changes to both the nomination stage and the final ballot, the impact of these changes has to be strongly qualified. Instead of a major “democratisation” through targeted and deliberate reform measures, simple shifts in the power structure between strategic actors are more prominent among reform effects. Meanwhile, the trend towards “democratisation” in relation to the final ballot stage was largely driven by the massive membership surge since 2015, as well as low-key reform measures unconnected to handing ordinary party members more influence over the election process.
Metrics of Sexual Behavior Stigma Among Cisgender Men Who Have Sex With Men in 9 Cities Across the United States
Authors: Wiginton John Mark , Murray Sarah M , Augustinavicius Jura , Maksut Jessica L , Anderson Bridget J , Sey Kwa , Ma Yingbo , Flynn Colin P , German Danielle , Higgins Emily , Menza Timothy W , Orellana E Roberto , Flynn Anna B , Al-Tayyib Alia , Kienzle Jennifer , Shields Garrett , Lopez Zaida , Wermuth Paige , Baral Stefan D 
Published: October 2021

Abstract
Men who have sex with men (MSM) in the United States are stigmatized for their same-sex practices, which can lead to risky sexual behavior, potentiating risk for human immunodeficiency virus (HIV) infection. Improved measurement is necessary for accurately reporting and mitigating sexual behavior stigma. We added 13 sexual behavior stigma items to local surveys administered in 2017 at 9 sites in the Centers for Disease Control and Prevention’s National HIV Behavioral Surveillance system, which uses venue-based, time-sampling procedures to survey cisgender MSM in US Census Metropolitan Statistical Areas. We performed exploratory factor analytical procedures on site-specific (Baltimore, Maryland; Denver, Colorado; Detroit, Michigan; Houston, Texas; Nassau-Suffolk, New York; Portland, Oregon; Los Angeles, California; San Diego, California; and Virginia Beach-Norfolk, Virginia) and pooled responses to the survey items. A 3-factor solution—“stigma from family” (α = 0.70), “anticipated health-care stigma” (α = 0.75), and “general social stigma” (α = 0.66)—best fitted the pooled data and was the best-fitting solution across sites. Findings demonstrate that MSM across the United States experience sexual behavior stigma similarly. The results reflect the programmatic utility of enhanced stigma measurement, including tracking trends in stigma over time, making regional comparisons of stigma burden, and supporting evaluation of stigma-mitigation interventions among MSM across the United States.
Increased Excess Pressure After Creation of an Arteriovenous Fistula in End-Stage Renal Disease
Authors: Paré Mathilde , Goupil Rémi , Fortier Catherine , Mac-Way Fabrice , Madore François , Hametner Bernhard , Wassertheurer Siegfried , Schultz Martin G , Sharman James E , Agharazii Mohsen 
Published: October 2021

ABSTRACTBACKGROUNDReservoir-wave analysis (RWA) separates the arterial waveform into reservoir and excess pressure (XSP) components, where XSP is analogous to flow and related to left ventricular workload. RWA provides more detailed information about the arterial tree than traditional blood pressure (BP) parameters. In end-stage renal disease (ESRD), we have previously shown that XSP is associated with increased mortality and is higher in patients with arteriovenous fistula (AVF). In this study, we examined whether XSP increases after creation of an AVF in ESRD.METHODSBefore and after a mean of 3.9 ± 1.2 months following creation of AVF, carotid pressure waves were recorded using arterial tonometry. XSP and its integral (XSPI) were derived using RWA through pressure wave analysis alone. Aortic stiffness was assessed by carotid–femoral pulse wave velocity (CF-PWV).RESURLTSIn 38 patients (63% male, age 59 ± 15 years), after AVF creation, brachial diastolic BP decreased (79 ± 10 vs. 72 ± 12 mm Hg, P = 0.002), but the reduction in systolic BP, was not statistically significant (133 ± 20 vs. 127 ± 26 mm Hg, P = 0.137). However, carotid XSP (14 [12–19] to 17 [12–22] mm Hg, P = 0.031) and XSPI increased significantly (275 [212–335] to 334 [241–439] kPa∙s, P = 0.015), despite a reduction in CF-PWV (13 ± 3.6 vs. 12 ± 3.5 m/s, P = 0.025).CONCLUSIONSCreation of an AVF resulted in increased XSP in this population, despite improvement in diastolic BP and aortic stiffness. These findings underline the complex hemodynamic impact of AVF on the cardiovascular system.
Predictive Ability of Pressure-Corrected Arterial Stiffness Indices: Comparison of Pulse Wave Velocity, Cardio-Ankle Vascular Index (CAVI), and CAVI0
Authors: Spronck Bart , Obeid Mary Jo , Paravathaneni Mahati , Gadela Naga Vaishnavi , Singh Gurpreet , Magro Caroline A , Kulkarni Varsha , Kondaveety Soumya , Gade Keerthi Chandrika , Bhuva Rushik , Kulick-Soper Colin M , Sanchez Nicolas , Akers Scott , Chirinos Julio A 
Published: October 2021

Abstract

BACKGROUND
Pulse wave velocity (PWV) is blood pressure (BP) dependent, leading to the development of the BP-corrected metrics cardio-ankle vascular index (CAVI) and CAVI0. We aimed to assess risk prediction by heart-to-ankle PWV (haPWV), CAVI, and CAVI0 in a US population.

METHODS
We included 154 subjects (94.8% male; 47.7% African American) with and without heart failure (HF). Left and right haPWV, CAVI, and CAVI0 were measured with the VaSera 1500N device. We prospectively followed participants for a mean of 2.56 years for the composite endpoint death or HF-related hospital admission (DHFA).

RESULTS
Left and right haPWV, CAVI, and CAVI0 values did not differ significantly. In unadjusted analyses, haPWV (left standardized hazard ratio [HR] = 1.51, P = 0.007; right HR = 1.66, P = 0.003), CAVI (left HR = 1.45, P = 0.012; right HR = 1.58, P = 0.006), and CAVI0 (left HR = 1.39, P = 0.022; right HR = 1.44, P = 0.014) significantly predicted DHFA. Predictive ability showed a decreasing trend from haPWV to CAVI to CAVI0; in line with the increasing amount of BP correction in these metrics. In Cox models, right-sided metrics showed a trend toward stronger predictive ability than left-sided metrics. After adjustment for baseline HF status, the Meta-Analysis Global Group in Chronic Heart Failure (MAGGIC) risk score, and systolic BP, right haPWV (HR = 1.58, P = 0.025) and CAVI (HR = 1.44, P = 0.044), but no other stiffness metrics, remained predictive.

CONCLUSIONS
Although conceptually attractive, BP-corrected arterial stiffness metrics do not offer better prediction of DHFA than conventional arterial stiffness metrics, nor do they predict DHFA independently of systolic BP. Our findings support PWV as the primary arterial stiffness metric for outcome prediction.
Criticism on the Border and the Decolonization of Knowledge
Authors: Saldívar Ramón 
Published: October 2021

AbstractStructures of hierarchy and domination are never represented in transborder literature as singular effects of social conditions. Instead, they arise from multiple historical factors. Unlike writings that assume a racial binary, literature on the border does not posit one kind of domination and hierarchy as barriers to creating a just, democratic society. In recent literary works from the transborder regions, the yearning for justice within the layered social systems on the border is central, even while its attainment through social transformation remains an attenuated hope. This essay outlines a paradigm for studying the relations between global and local areas of study, such as those in the transborder regions of the Americas. Invoking models for literary critical work in a globally bordered form, it posits the need for a larger view based on how knowledge is generated and human resources used, while acknowledging the reservoir of knowledge that exists beyond Europe and the US in the Global South. The function of the rebordered criticism described here is to respond to issues raised by African philosopher Achille Mbembe, Latin American sociologist Enrique Dussel and other decolonial thinkers concerning different ways of conceiving the achievement of an antiracist and socially just future.In the face of [the] compromised hopefulness [for justice on the border], what kind of criticism could best [respond to and] … help enact projects of social change?
Remediations in an Emergency
Authors: Coviello Peter 
Published: October 2021

Abstract
This essay argues that configurations of what we have been calling “method” will not save the humanities from the compounding disasters of austerity, and that pretending this is not so makes for an especially airless kind of criticism. It tracks the insalubrious persistence of a critical grammar across the terrain of method polemicizing. “Method Wars,” it argues, have bequeathed to us nothing so much as an intricate machinery for metabolizing variance in approach as antagonism, the better to produce differing inflections of the fairly standard practice of “reading” as innovations of “method” that, through the rupturing force of their departures, might rescue the declining humanities. But the decimation of the humanities is, paradigmatically, a problem of structural disinvestment proper to the Long Downturn—a problem, that is, of political–economic conditions. Whatever their virtues or liabilities, our methods do not remake those conditions, though pretending that they might imparts a doomed glamour to our conceptual labors. Doing without that pretense, the essay contends, enables a larger purchase on the invigoratingly synthesizing critical projects that have flourished across the discipline—projects that are of more use to us in their fractious noncoincidence than their polemical overcoming.
“Financialization” is Giovanni Arrighi’s term for what happens to capitalist systems in the long last moments of their lurch toward collapse. “Method wars,” a friend recently suggested, “are the financialization of academic literary criticism.”
The role of wood anatomical traits in the coexistence of oak species along an environmental gradient
Authors: Arenas-Navarro Maribel , Oyama Ken , García-Oliva Felipe , Torres-Miranda Andrés , de la Riva Enrique G , Terrazas Teresa 
Published: October 2021

AbstractOaks (Quercus) are a dominant woody plant genus in the northern hemisphere, which occupy a wide range of habitats and are ecologically diverse. We analysed the wood anatomical traits, the variables derived and the relative hydraulic conductivity of 21 oak species to identify their performance according to abiotic factors, leaf phenological patterns and phylogenetic restrictions by analysing the interspecific variation along an environmental gradient. First, we determine the causes of anatomical trait variation in the oaks, analysing the functional trade-offs related to distribution along the environmental gradient. We measure the phenotypic plasticity of the anatomical traits to determine the role of environment and geographic distance in the range of phenotypic plasticity. Second, we examined if oaks co-occurred along the environmental gradient. Then we analysed if wood anatomical traits reflect differences among their phylogenetic section, leaf habit and a phylogenetic section/leaf habit category. Last, we tested the phylogenetic signal. Our results showed that vessel diameter, vessel frequency, wood density and relative hydraulic conductivity are the main axes of trait variation in the species analysed among leaf habit categories. The aridity index and seasonal precipitation drive the variation in the analysed traits. Higher environmental distance resulted in a higher relative distance plasticity index among traits. Co-occurrence of oak species with different leaf habits and phylogenetic trajectories may promote complementary resource acquisition. The phylogenetic signal in the oak species studied was low, which implies labile wood traits.
DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data
Authors: Xu Bingxiang , Li Xiaoli , Gao Xiaomeng , Jia Yan , Liu Jing , Li Feifei , Zhang Zhihua 
Published: October 2021

AbstractAs the basal bricks, the dynamics and arrangement of nucleosomes orchestrate the higher architecture of chromatin in a fundamental way, thereby affecting almost all nuclear biology processes. Thanks to its rather simple protocol, assay for transposase-accessible chromatin using sequencing (ATAC)-seq has been rapidly adopted as a major tool for chromatin-accessible profiling at both bulk and single-cell levels; however, to picture the arrangement of nucleosomes per se remains a challenge with ATAC-seq. In the present work, we introduce a novel ATAC-seq analysis toolkit, named decoding nucleosome organization profile based on ATAC-seq data (deNOPA), to predict nucleosome positions. Assessments showed that deNOPA outperformed state-of-the-art tools with ultra-sparse ATAC-seq data, e.g. no more than 0.5 fragment per base pair. The remarkable performance of deNOPA was fueled by the short fragment reads, which compose nearly half of sequenced reads in the ATAC-seq libraries and are commonly discarded by state-of-the-art nucleosome positioning tools. However, we found that the short fragment reads enrich information on nucleosome positions and that the linker regions were predicted by reads from both short and long fragments using Gaussian smoothing. Last, using deNOPA, we showed that the dynamics of nucleosome organization may not directly couple with chromatin accessibility in the cis-regulatory regions when human cells respond to heat shock stimulation. Our deNOPA provides a powerful tool with which to analyze the dynamics of chromatin at nucleosome position level with ultra-sparse ATAC-seq data.
A systematic comparison of novel and existing differential analysis methods for CyTOF data
Authors: Arend Lis , Bernett Judith , Manz Quirin , Klug Melissa , Lazareva Olga , Baumbach Jan , Bongiovanni Dario , List Markus 
Published: October 2021

AbstractCytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell abundance. For differential expression analysis of markers between conditions, only few tools exist. These tools either reduce the data distribution to medians, discarding valuable information, or have underlying assumptions that may not hold for all expression patterns. Here, we systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. We found that methods using median marker expressions compute fast and reliable results when the data are not strongly zero-inflated. Methods using all data detect changes in strongly zero-inflated markers, but partially suffer from overprediction or cannot handle big datasets. We present a new method, CyEMD, based on calculating the earth mover’s distance between expression distributions that can handle strong zero-inflation without being too sensitive. Additionally, we developed CYANUS – CYtometry ANalysis Using Shiny – a user-friendly R Shiny App allowing the user to analyze cytometry data with state-of-the-art tools, including well-performing methods from our comparison. A public web interface is available at https://exbio.wzw.tum.de/cyanus/.
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning
Authors: Zheng Lujing , Liu Zhenhuan , Yang Yang , Shen Hong-Bin 
Published: October 2021

Abstract

Motivation
Reverse engineering of gene regulatory networks (GRNs) has long been an attractive research topic in system biology. Computational prediction of gene regulatory interactions has remained a challenging problem due to the complexity of gene expression and scarce information resources. The high-throughput spatial gene expression data, like in situ hybridization images that exhibit temporal and spatial expression patterns, has provided abundant and reliable information for the inference of GRNs. However, computational tools for analyzing the spatial gene expression data are highly underdeveloped.

Results
In this study, we develop a new method for identifying gene regulatory interactions from gene expression images, called ConGRI. The method is featured by a contrastive learning scheme and deep Siamese convolutional neural network architecture, which automatically learns high-level feature embeddings for the expression images and then feeds the embeddings to an artificial neural network to determine whether or not the interaction exists. We apply the method to a Drosophila embryogenesis dataset and identify GRNs of eye development and mesoderm development. Experimental results show that ConGRI outperforms previous traditional and deep learning methods by a large margin, which achieves accuracies of 76.7% and 68.7% for the GRNs of early eye development and mesoderm development, respectively. It also reveals some master regulators for Drosophila eye development.

Availabilityand implementation
https://github.com/lugimzheng/ConGRI.

Supplementary information
Supplementary data are available at Bioinformatics online.
WGA-LP: a pipeline for whole genome assembly of contaminated reads
Authors: Rossi N , Colautti A , Iacumin L , Piazza C 
Published: October 2021

AbstractSummaryWhole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads.Availability and implementationWGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/).Supplementary informationSupplementary data are available at Bioinformatics online.
dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA–protein binding
Authors: Shatoff Elan , Bundschuh Ralf 
Published: October 2021

Abstract

Motivation
RNA-binding proteins are fundamental to many cellular processes. Double-stranded RNA-binding proteins (dsRBPs) in particular are crucial for RNA interference, mRNA elongation, A-to-I editing, host defense, splicing and a multitude of other important mechanisms. Since dsRBPs require double-stranded RNA to bind, their binding affinity depends on the competition among all possible secondary structures of the target RNA molecule. Here, we introduce a quantitative model that allows calculation of the effective affinity of dsRBPs to any RNA given a principal affinity and the sequence of the RNA, while fully taking into account the entire secondary structure ensemble of the RNA.

Results
We implement our model within the ViennaRNA folding package while maintaining its O(N3) time complexity. We validate our quantitative model by comparing with experimentally determined binding affinities and stoichiometries for transactivation response element RNA-binding protein (TRBP). We also find that the change in dsRBP binding affinity purely due to the presence of alternative RNA structures can be many orders of magnitude and that the predicted affinity of TRBP for pre-miRNA-like constructs correlates with experimentally measured processing rates.

Availability and implementation
Our modified version of the ViennaRNA package is available for download at http://bioserv.mps.ohio-state.edu/dsRBPBind, is free to use for research and educational purposes, and utilizes simple get/set methods for footprint size, concentration, cooperativity, principal dissociation constant and overlap.
1373 Semi-Elective Trauma Patients Pathway and Medical Clerking Proforma, Closed Loop Audit
Authors: Altell T , Massa E , Edwards M 
Published: October 2021

Abstract

Introduction
Semi-elective Trauma care is a service provided by the Trauma and Orthopaedic department for patients who sustain fractures to the upper and lower limbs requiring surgical intervention, are still ambulatory and can be cared for safely at home until the date of operation.

Aim
To assess patients’ referral pathway and clerking documentation against the Standards for the Clinical Structure and Content of Patient Records, published by the RCSEng.

Method
We performed a closed loop audit on the clerking documentation and the referral pathway for these patients. We collected data retrospectively for three months, assessing the clerking documentation against the guidelines. The data was analysed and presented at our Clinical Governance meeting. We then implemented the Semi-Elective Trauma Pathway and the Medical Clerking Proforma. Afterwards, data was collected prospectively to complete the audit cycle.

Results
A sum of 181 patient were included. Before the use of our changes, only 36% of patients had a complete clerking documentation, with two cases of near misses, and no comprehensive referral pathway for these patients. Post implementation of the Pathway and the Clerking Proforma, 88% of patients had complete clerking documentation, no near misses and 95% of them went properly through the pathway we introduced.

Conclusions
These patients present an important part of any trauma list. This Audit shows that having a comprehensive referral pathway and a clerking proforma will make sure that patients will have full medical history taken and are ready for the operation on the day of surgery and decrease the number of near misses.