bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of the ZrO2–Al2O3 solid solution on the performance of Ni/ZrO2–Al2O3 catalysts for CO2 methanation
Authors: Chang Shuai , Na Wei , Zhang Jiaqi , Lin Lina , Gao Wengui
Published: October 2021

The appropriate addition of Al2O3 to form a ZrO2-Al2O3 solid solution will weaken the Ni-ZrO2 interaction and increase the concentration of basic sites and oxygen vacancies in the catalyst, resulting in better activation of CO2.
Surface adhered fluorescent carbon dots extracted from the harmful diesel soot for sensing Fe(iii) and Hg(ii) ions
Authors: Gunture  , Kaushik Jaidev , Saini Deepika , Singh Ravindra , Dubey Prashant , Sonkar Sumit Kumar
Published: October 2021

A simple cost effective isolation method has been described for the extraction of surface-adhered blue–green fluorescent carbon material from the diesel soot and used them for the selective sensing of Fe(iii) and toxic Hg(ii) metal ions in aqueous medium.
Chalcogenides as photocatalysts
Authors: Rahman Ashmalina , Khan Mohammad Mansoob
Published: October 2021

Chalcogenides and chalcogenide-based heterostructures as photocatalysts.
Identification of a novel DNA aptamer that selectively targets lung cancer serum
Authors: Zhao Yunwang , He Lei , Huang Baihai , Zhang Weidong , Hu Ailing , Li Baolin , Liao Shiqi , Wang Na
Published: October 2021

Lung cancer is the leading cause of cancer-related deaths worldwide.
The electrostatic origins of specific ion effects: quantifying the Hofmeister series for anions
Authors: Gregory Kasimir P. , Wanless Erica J. , Webber Grant B. , Craig Vincent S. J. , Page Alister J.
Published: October 2021

Analysis of ions’ radial charge densities reveals they correlate with many specific ion effects, and provides a new basis to explain and quantify the 130-year-old Hofmeister series for anions.
Combined adaptive neural network and regressor‐based trajectory tracking control of flexible joint robots
Authors: Montoya‐Cháirez Jorge , Moreno‐Valenzuela Javier , Santibáñez Víctor , Carelli Ricardo , Rossomando Fracisco G. , Pérez‐Alcocer Ricardo
Published: October 2021

By relying on the input–output feedback linearization approach, a novel adaptive controller for flexible joint robots is proposed in this work. First, a model‐based controller is developed to get a structure that is useful in the development of the adaptive controller. The adaptive version is developed by using two techniques. To stabilize the output function, an adaptive neural network controller is used, which approximates the non‐linear function that contains the uncertainties. The desired rotor position required by the input–output feedback linearization controller is defined with the structure of a link dynamics adaptive regressor‐based controller. The main reason to adopt the mentioned structure in the definition of the desired rotor link position is to guarantee its differentiability. Real‐time experiment comparisons among the model‐based controller, a model‐based controller with desired compensation, an adaptive controller based on joint torque feedback, and an adaptive neural network‐based controller are carried out. Experimental results support the theory reported in this document and the accuracy of the proposed approach.
Hierarchical speed control for autonomous electric vehicle through deep reinforcement learning and robust control
Authors: Xu Guangfei , He Xiangkun , Chen Meizhou , Miao Hequan , Pang Huanxiao , Wu Jian , Diao Peisong , Wang Wenjun
Published: October 2021

For the speed control system of autonomous electric vehicle (AEV), challenge happens with how to determine an appropriate driving speed to satisfy the dynamic environment while resisting uncertainty and disturbance. Therefore, this paper proposes a robust optimal speed control approach based on hierarchical architecture for AEV through combining deep reinforcement learning (DRL) and robust control. In decision‐making layer, a deep maximum entropy proximal policy optimization (DMEPPO) algorithm is presented to obtain an optimal speed via dynamic environment information, heuristic target entropy and adaptive entropy constraint. In motion control layer, to track the learned optimal speed while resisting uncertainty and disturbance, a robust speed controller is designed by the linear matrix inequality (LMI). Finally, simulation experiment results show that the proposed robust optimal speed control scheme based on hierarchical architecture for AEV is feasible and effective.
Protection of converter dominated MV microgrid using changes in current's phase angle
Authors: Mohanty Rabindra , Chen Peiyuan , Tuan Le Anh
Published: October 2021

Converter interfaced distributed generations in a microgrid feed the modulated current of limited magnitude during fault conditions. The protection design and its operation are thus challenging due to limited fault current which is further reduced by Petersen coil grounding in medium‐voltage (MV) level. This paper aims to address this challenge by developing a current‐only directional relay algorithm for the protection of converter dominated MV microgrid with Petersen coil grounding. The relay's operating principle is based on the sign of the change in phase angle of the fault current with respect to the prefault which indicates the direction of fault. The negative and positive changes in current's phase angle determine the fault in forward and reverse direction, respectively. The tripping decision is derived by comparing the binary output of the relay at both ends of the line segment under protection. This requires a simple, flexible and low bandwidth communication channel. Both theoretical analyses and simulation studies have been performed on a typical distribution grid intended to be operated as microgrid. The proposed protection method is suitable for microgrid having the converters with and without reactive power support. Various operating conditions are evaluated, including bidirectional power flow, high resistance fault, different fault types, loading conditions and signals with noise.
An alternating high‐low impedance common‐mode filter for differential striplines
Authors: Song Tian‐Hao , Wei Xing‐Chang , Gao Richard Xian‐Ke
Published: October 2021

The conventional quarter/half‐wavelength common‐mode filter (CMF) cannot work well for a differential stripline when there is no ground via. A new and effective via‐free CMF design for the differential striplines is proposed in this study. An alternating high‐low impedance structure is developed to increase the coupling between the stripline and the CMF, thus achieving a good filtering effect. A cascaded CMF design is further studied to enhance the stopband without deterioration of the differential signals. Both simulation and measurement results demonstrate the effectiveness of the proposed high‐low impedance CMF. The significant advantage of the proposed CMF is its compactness and simplicity, which has almost no impact on the original layout of differential striplines.
A novel m6A‐related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients
Authors: Xie Shiyang , Wang Yaxuan , Huang Jin , Li Guang
Published: October 2021

Liver hepatocellular carcinoma (LIHC) comprises most cases of liver cancer with a poor prognosis. N6‐methyladenosine (m6A) plays important biological functions in cancers. Thus, the present research was aimed to determine biomarkers of m6A regulators that could effectively predict the prognosis of LIHC patients. Based on the data collected from the Cancer Genome Atlas (TCGA) database, the correlation between the mRNA expression levels and copy number variation (CNV) patterns were determined. Higher mRNA expression resulted from the increasing number of 9 genes. Using the univariate Cox regression analysis, 11 m6A regulators that had close correlations with the LIHC prognosis were identified. In addition, under the support of the multivariate Cox regression models and the least absolute shrinkage and selection operator, a 4‐gene (YTHDF2, IGF2BP3, KIAA1429, and ALKBH5) signature of m6A regulators was constructed. This signature was expected to present a prognostic value in LIHC (log‐rank test p value < 0.0001). The GSE76427 (n = 94) and ICGC‐LIRI‐JP (n = 212) datasets were used to validate the prognostic signature, suggesting strong power to predict patients' prognosis for LIHC. To sum up, genetic alterations in m6A regulatory genes were identified as reliable and effective biomarkers for predicting the prognosis of LIHC patients.
A Metal-Free β-Stereoselective Synthesis of 2-Deoxy-C-arylglycosides: Synthesis of 5-Aza Analogues of Aquayamycin
Authors: Zhang Jianbo , Mei Yuling , Jiang Nan , Yang Yu , Zhang Wan , Qiu Saifeng , Guo Hong
Published: October 2021

A convenient protocol for the β-stereoselective synthesis of 2-deoxy-C-arylglycosides has been developed. This reaction takes place in one step by using I2/Et3SiH to activate a glycosyl acetate to generate a glycosyl iodide intermediate in situ, which is captured by a naphthol; this is followed by a Fries-like O-to-C glycoside rearrangement to afford a β-C-aryl glycoside selectively. The approach is applicable to a wide range of naphthol moieties, and its utility was demonstrated in syntheses of 5-aza analogues of aquayamycin.
The Silicon–Hydrogen Exchange Reaction: Catalytic Kinetic Resolution of 2-Substituted Cyclic Ketones
Authors: List Benjamin , Zhou Hui , Zhang Pinglu
Published: October 2021

We 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

This 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.
Single-nanometer iron oxide nanoparticles as tissue-permeable MRI contrast agents
Authors: Wei He , Wiśniowska Agata , Fan Jingxuan , Harvey Peter , Li Yuanyuan , Wu Victoria , Hansen Eric C. , Zhang Juanye , Kaul Michael G. , Frey Abigail M , Adam Gerhard , Frenkel Anatoly I. , Bawendi Moungi G. , Jasanoff Alan
Published: October 2021

Significance

This work shows that iron oxide species as small as 1 nm in diameter can exhibit superparamagnetic properties and act as potent contrast agents for MRI. Because of their small size, the resulting particles effectively permeate dense biological tissue and undergo ultrasound-facilitated delivery from the vasculature to the brain. They also exhibit
T
1
-weighted contrast-inducing properties similar to widely used paramagnetic MRI contrast agents but with far higher potency per molecule. Single-nanometer iron oxide agents, therefore, constitute a beneficial basis for the development of molecular imaging probes designed to detect targets in
T
1
-weighted MRI. They might also function as alternatives to widely used gadolinium-based MRI agents in clinical contexts where gadolinium-related toxicity is a concern.
Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard
Authors: Bock Dan G. , Baeckens Simon , Pita-Aquino Jessica N. , Chejanovski Zachary A. , Michaelides Sozos N. , Muralidhar Pavitra , Lapiedra Oriol , Park Sungdae , Menke Douglas B. , Geneva Anthony J. , Losos Jonathan B. , Kolbe Jason J.
Published: October 2021

Significance

Hybridization is common in invasive species and can be important for their success. The connection between hybridization and bioinvasions could result in part because of a disruption in the selection pressures that limit hybridization in the native range. We demonstrate that, in the lizard
Anolis sagrei
, hybridization is rare in native populations, which show frequent evidence of natural selection at a large-effect X chromosome locus. Conversely, little selection at this locus was detected in invasive populations, which do not experience large-scale contemporary gene flow, but instead maintain a mosaic of hybrid ancestries formed during invasive range colonization. Ecological changes during biological invasions can affect hybridization frequency and stability, which can in turn drive the success of invasive taxa.
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

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

BACKGROUND

Reservoir-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.

METHODS

Before 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).

RESURLTS

In 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).

CONCLUSIONS

Creation 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

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

Structures 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

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

Oaks (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

As 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

Cytometry 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

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

Whole 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 implementation

WGA-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 information

Supplementary 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

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

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.
1387 Audit of Pregnancy Status Documentation in Emergency Admissions to A Tertiary Colorectal Surgery Unit
Authors: Anbarasan T
Published: October 2021

Aim

Documenting pregnancy status (PS) is an important component of the medical assessment of all females of reproductive age (FRA), defined as age 16-55 years old when admitted to hospital. This audit aims to determine the rate of documentation of PS amongst FRA admitted to a tertiary colorectal surgical unit via the surgical admissions unit (SAU) or transfer from other departments between 01/10/20 – 13/11/20.

Method

A complete documentation of PS comprises of results of urine or serum (β-hCG) and relevant gynaecological history (i.e., last menstrual period and any contraceptive use) clearly reported in the admission clerk-in. Patients with presenting complaint excluding abdominal pain, current pregnancy, history of hysterectomy or sterilisation procedures were excluded.

Results

During the audit duration, 29 FRA were admitted of which 13 (44.8%) were included for analysis. Of patients included, 4/9 (44.4%) and 1/4 (25.0%) admitted via SAU or transferred from other departments respectively had a past colorectal history. 4 (30.8%) had complete documentation of PS of which, 3 (75.0%) were patients transferred from other departments.

Conclusions

Low rates of documentation of PS especially amongst emergency admissions via SAU, is possibly associated with a narrow differential diagnosis influenced by pre-existing colorectal history. This audit did not look at PS documentation prior to any subsequent surgical intervention. A re-audit following the implementation of a guidance poster in SAU is currently underway.
1394 Operation Notes Performa: The Way to Optimise Hand Trauma Service
Authors: Labib A , Oniska S , Karran L , Moledina J
Published: October 2021

Aim

To assess the effect of the introduction of British Society for Surgery of the Hand (BSSH) guided operation note Performa on the hand trauma service in St. George’s University Hospitals.

Method

First cycle was done in October 2019. This included retrospective evaluation of accuracy of documentation for closed hand fracture audit. Reassessment was done in September 2020 after introduction of surgical Performa guided by the latest BSSH guidelines.

Results

27 patients have been included in the first cycle compared with 81 patients in the second cycle. While 82% of first cycle patients underwent operation, only 40% of second cycle patients were treated surgically. Overall documentation has improved by a mean of 40% in all parameters. This includes documentation of discussion of shared decision making regarding conservative and surgical management, documentation of level of competency of the operating surgeon and mobilisation advice given to patients before their first appointment with a hand therapist. This led to improvement in overall patient outcome including rate of infection falling from 14% to 1% and reoperation rate from 23% to 1%.

Conclusions

Op notes Performa is a useful tool in the armamentarium of hand trauma management. It helps junior trainees to memorise critical information to document especially in the ones usually missed like detailed post-operative advice.
1444 Is FBC Being Investigated Within 32 Hours of Surgery in Neck of Femur Fractures?
Authors: Lammin K , Dhingra M , Mishra P , Narayan P , Tenang L A H
Published: October 2021

Introduction

The UK treats approximately 76,000 neck of femur (NOF) fractures annually (NHFD 2018). These patients are known to be frail and dehydrated upon arrival to the emergency department. Surgery can expose patients to substantial blood loss both preoperatively and postoperatively (Foss et al). Furthermore, studies have shown that postoperative anaemia is detrimental in patients who have had hip surgery (Marval et al 2014). Thus, it is imperative to monitor patients’ haemoglobin (Hb) levels immediately after the operation so that optimum treatment can be assured. The current audit standard in our local trust states that all patients must have their full blood count (FBC) within 32 hours post-surgery. As Covid-19 has brought disruption to the NHS, It is important for us to highlight any issues that arise in the monitoring of Hb in the post-operative phase of these NOF patients.

Method

Using retrospective analysis, this study analysed the number of patients having the FBC within 32 hours post-surgery during the pandemic (n = 60) and was compared to a similar cohort pre-pandemic (n = 139).

Results

91% of patients overall had their Hb checked within 32 hours. 92% in the pre-covid group had a Hb check within time compared to 81% in the covid group. The risk ratio calculated was 1.5.

Conclusions

Conclusively, patients in the covid group were 1.5 times more likely to have their FBC checked past 32 hours post-surgery. However, this finding was not significant. Overall, the audit standard was not met.
1454 The Challenges of Consent and COVID-19: Analysis of Documentation of Risk of Hospital Acquired COVID-19 Infection in a District General Hospital
Authors: Davis H , Mishra S , Cooke J
Published: October 2021

Background

The COVID-19 pandemic has been a challenging time for society and raised further challenges for medical practice. It poses a new material risk to any hospital admission or procedure, and consenting practice must modify to accommodate this.

Aim

To assess the documentation of the risk of COVID-19 infection and associated morbidity in consenting practice, using the existing consent form as benchmark, for patient’s undergoing general surgical procedures under general anaesthesia.

Method

Retrospective case-note analysis of 41 general surgical inpatient consent forms and operation notes during April 2020. Data were gathered on multiple points mentioned in Royal College of Surgeons (RCS) guidance. This includes documentation of risk of COVID-19 infection, the patient’s diagnosis, other risk documentation, peri-operative lifestyle advice and likelihood of success.

Results

Of 41 cases, 16 (39%) had risk of chest infection documented. Of these 16, 10 (63%) specified COVID-19 in the risk documentation. Further, morbidity related to COVID-19 was documented in 4 out of 41 (10%) cases identified.

Conclusions

A material risk is classified as anything that poses substantial risk to a patient, and it is vital that they are made aware of this prior to undertaking any form of medical intervention. This study demonstrates deviation from RCS guidance, and the results have been discussed and distributed within the general surgical department. Advice has been communicated regarding improvements required in consenting practice from the clinical lead. We aim to re-audit practice in the coming months.
1458 Compliance of Abdominal X-ray Requesting with iRefer Guidelines in CDDFT
Authors: McGurk R , Ross E , Toward M
Published: October 2021

Aim

100% of Abdominal x-ray (AXR) requests in the trust should be compliant with iRefer guidelines. Therefore, with this audit we hope to evaluate the compliance of our hospitals with said guidelines.

Method

This audit was retrospective with AXRs taken between 23 – 29th of November 2020 being analysed for compliance creating our first loop. On the 1st of December we placed our intervention. This came in the form of educational posters in the four areas that request the majority of AXRs. Following this, a further weeks’ worth of AXRs were assessed for compliance between 2nd – 8th of December 2020.

Results

Between 23-29/11/20 there were 67 AXRs requested. Eight of these were excluded according to our exclusion criteria, leaving a total of 59 AXRs to be assessed. After reviewing the request cards for these AXRs, 17 were non-compliant (28.8%). Following the intervention, AXR requests were re-audited. Between 2-8/12/20 there were 69 AXRs requested. Six were excluded leaving a total of 63 AXRs to be assessed. After review, 22 were non-compliant (34.9%)

Conclusions

In both loops of this audit, the standard of 100% compliance with iRefer guidelines was not met. There was a high percentage of non-compliance in both loops with a rate of 28.8% and 34.9% respectively – a decrease in compliance. One possible reason to account for this was due the changeover of Junior Doctors within the trust on 2/12/20. Our interventional posters were placed in only half of the Trusts hospitals which may also account for the decrease in compliance.
1503 Review of Electronic Theatre Coding System & Documentation of Neurosurgical Activity
Authors: Broomes N , Giamouriadis A
Published: October 2021

Introduction

It was noticed that the current electronic theatre coding system was limited in its reflection of departmental theatre activity and discrepancies in discharge letters compared to the actual operations performed. To prevent this from recurring, a standardised neurosurgical operation note was developed, and an audit of the electronic coding system was undertaken to see if the correct operation matched that of the code listed.

Method

A 6-month retrospective analysis from March to September 2020 was completed using the electronic theatre coding system, patients’ electronic records and the patient handover list.

Results

232 operations performed and only 10.3% of procedures were correctly coded by the current coding system. 11 operations were not on the theatre system although performed in theatres. The current system only coded for 82 procedures and did not show the full range of operations. There was wide variety of operation notes and only 185 operation notes were found on the patients’ electronic record. Frequently the procedure was not clearly identified so juniors relied on the inaccurate electronic code on the theatre list for the patients’ operation hence explaining the problem identified in discharge letters.

Conclusions

A new coding list for the electronic theatre system was created with 228 procedures divided into correct subcategories. A standardised template for operation notes was also developed and implemented so that full neurosurgical departmental activity is reflected, and accurate discharge letters are completed so that complete data collection can be done for audit purposes.
1507 Prospective Audit of Vascular Handover List
Authors: Eves J , Stoner R , Cerneviciute R
Published: October 2021

Introduction

Good handover is paramount for orientating on-call teams coming onto shift and maintaining patient safety. In our tertiary referral centre a pre-prepared list on our shared drive is used to handover vascular patients in the hospital. It was felt that there was insufficient information on the list and that inconsistencies / inaccuracies could compromise patient safety.

Method

We performed a full-cycle prospective audit using GMC/ RCSEng guidance as standards. Our list was audited over a period of 10 days 4/2/20-14/2/20. In addition, a questionnaire was sent around doctors of all grades to highlight areas of improvement and to gather ideas. The second cycle (17/2/20- 27/2/20) was then performed after introduction of a new list, which allowed more comprehensive information to be collected in a shared drive. Junior doctors on the team were briefed, and results collected with a second questionnaire.

Results

The new list showed statistically significant improvements in inclusion of key information as set out in the standards. These included presenting complaint ’92% from 57%,’ Diagnosis ’98% from 89%, clinical history 91% from 35%, significant results 86% from 13% and outstanding tasks 80% from 6.2%. (These were all significant p = 0.001 Mann-Whitney U.) Further information including antibiotics and VTE was included after feedback from department. 85% found the new list easier to navigate and 76% felt it reduced risk to patient safety.

Conclusions

Introduction of a revised handover list in a vascular tertiary referral centre resulted in significant improvements in adherence to RCSEng/ BMA standards and staff perceived benefit to patient safety.