bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytocytokines function as immunological modulators of plant immunity
Authors: Hou Shuguo , Liu Derui , He Ping 
Published: September 2021

AbstractPlant plasma membrane-resident immune receptors regulate plant immunity by recognizing microbe-associated molecular patterns (MAMPs), damage-associated molecular patterns (DAMPs), and phytocytokines. Phytocytokines are plant endogenous peptides, which are usually produced in the cytosol and released into the apoplast when plant encounters pathogen infections. Phytocytokines regulate plant immunity through activating an overlapping signaling pathway with MAMPs/DAMPs with some unique features. Here, we highlight the current understanding of phytocytokine production, perception and functions in plant immunity, and discuss how plants and pathogens manipulate phytocytokine signaling for their own benefits during the plant-pathogen warfare.
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling
Authors: Li Yanyan , Zhou Honghong , Chen Xiaomin , Zheng Yu , Kang Quan , Hao Di , Zhang Lili , Song Tingrui , Luo Huaxia , Hao Yajing , Chen Runsheng , Zhang Peng , He Shunmin 
Published: September 2021

Abstract
Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.
Outcomes and associated factors among patients undergone emergency laparotomy: A retrospective study
Authors: Oumer Keder Essa , Ahmed Seid Adem , Tawuye Hailu Yimer , Ferede Yonas Admasu 
Published: September 2021

ABSTRACT

Introduction:
Emergency laparotomy patients are different in pathology and surgical urgency. Mortality rates following emergency laparotomy ranges from 13% to 18% which is five times greater than high-risk elective surgery. In addition, major complication rates are as high as 50%. Limited data is available in our country regarding outcomes of emergency laparotomy. This study aimed to assess outcome of emergency laparotomy.

Objective:
To determine outcomes and associated factors among patients undergone emergency laparotomy.

Methods:
A four years institutional based retrospective observational study was conducted for patients who undergone emergency laparotomy from January 2016 to January 2020.A total of 518 patient charts were enrolled in this study. All consecutive patient charts during the study period were included. Data was entered and analyzed using SPSS version 20. Descriptive statistics, cross-tabs and logistic regression analysis were performed to identify the association between dependant and independent variables. The strength of the association was presented using adjusted odds ratio with 95% confidence interval and p-value≤0.05 was considered as statistically significant with mortality.

Results:
Mortality rate was 42 (8.1%) and 70(13.5%) patients were developed complication which needed surgical intervention under general anesthesia. The mean length of hospital stay was 8 ± 5.9 days. Patients age ≥65 (AOR = 9.6, CI = 3.4–27.1), ASA status of ≥III (AOR = 7.4, CI = 1.9–29.3), presence of preoperative sepsis (AOR = 6.7,(95% CI: 2.0–22.6) and intraoperative use of vasopressor (AOR = 10.5,(95% CI: 3.8–29.5) were significantly associated with mortality of emergency laparotomy patients.

Conclusion:
Emergency laparotomy possesses high mortality. Preoperative resuscitation and sepsis management may improve outcome following emergency laparotomy.

Highlights
The Voices of European Law: Legislators, Judges and Law Professors
Authors: Dyevre Arthur , Glavina Monika , Ovádek Michal 
Published: September 2021

AbstractEuropean Union legislators, CJEU judges and EU law scholars have produced streams of texts which determine both what EU law is and how it is perceived. We explore what these distinct “voices” tell us about the EU’s legal and policy priorities using a mega corpus compiling more than 200,000 legislative acts, 55,000 court rulings and opinions, and 4,000 articles from a leading EU law journal. Applying an unsupervised machine learning technique known as probabilistic topic modelling, we find that economic integration remains the focus of EU law, but that scholars tend to emphasize rights issues more and ignore certain topics, such as farming regulations, almost entirely. The relationship among these partly interdependent, partly autonomous voices, we suggest, can be conceptualized in terms of co-evolution. Legislation influences issue attention on the CJEU, which, in turn, influences what law professors choose to write about.
Racing the Clock: Using Response Time as a Proxy for Attentiveness on Self-Administered Surveys
Authors: Read Blair , Wolters Lukas , Berinsky Adam J. 
Published: September 2021

AbstractInternet-based surveys have expanded public opinion data collection at the expense of monitoring respondent attentiveness, potentially compromising data quality. Researchers now have to evaluate attentiveness ex-post. We propose a new proxy for attentiveness—response-time attentiveness clustering (RTAC)—that uses dimension reduction and an unsupervised clustering algorithm to leverage variation in response time between respondents and across questions. We advance the literature theoretically arguing that the existing dichotomous classification of respondents as fast or attentive is insufficient and neglects slow and inattentive respondents. We validate our theoretical classification and empirical strategy against commonly used proxies for survey attentiveness. In contrast to other methods for capturing attentiveness, RTAC allows researchers to collect attentiveness data unobtrusively without sacrificing space on the survey instrument.
Nutrient patterns are associated with discordant apoB and LDL: a population-based analysis
Authors: Mazidi Mohsen , Webb Richard J. , George Elena S. , Shekoohi Niloofar , Lovegrove Julie A. , Davies Ian G. 
Published: September 2021

AbstractIndividuals with discordantly high apoB to LDL-cholesterol levels carry a higher risk of atherosclerotic CVD compared with those with average or discordantly low apoB to LDL-cholesterol. We aimed to determine associations between apoB and LDL-cholesterol discordance in relation to nutrient patterns (NP) using National Health and Nutrition Examination Survey data. Participants were grouped by established LDL-cholesterol and apoB cut-offs (Group 1: low apoB/low LDL-cholesterol, Group 2: low apoB/high LDL-cholesterol, Group 3: high apoB/low LDL-cholesterol, Group 4: high apoB/high LDL-cholesterol). Principle component analysis was used to define NP. Machine learning (ML) and structural equation models were applied to assess associations of nutrient intake with apoB/LDL-cholesterol discordance using the combined effects of apoB and LDL-cholesterol. Three NP explained 63·2 % of variance in nutrient consumption. These consisted of NP1 rich in SFA, carbohydrate and vitamins, NP2 high in fibre, minerals, vitamins and PUFA and NP3 rich in dietary cholesterol, protein and Na. The discordantly high apoB to LDL-cholesterol group had the highest consumption of the NP1 and the lowest consumption of the NP2. ML showed nutrients that had the greatest unfavourable dietary contribution to individuals with discordantly high apoB to LDL-cholesterol were total fat, SFA and thiamine and the greatest favourable contributions were MUFA, folate, fibre and Se. Individuals with discordantly high apoB in relation to LDL-cholesterol had greater adherence to NP1, whereas those with lower levels of apoB, irrespective of LDL-cholesterol, were more likely to consume NP3.
Coronavirus disease 2019 associated mucormycosis meandering its way into the orbit: a pictorial review
Authors: Khullar T , Kumar J , Sindhu D , Garg A , Meher R , Goel R 
Published: September 2021

AbstractBackgroundThere has been a recent deluge of coronavirus disease 2019 associated mucormycosis in our country. It affects the paranasal sinuses; however, it has a rapid extrasinus progression (the orbit being most common), which can be fatal if not detected early. It may meander into the orbit through various foramina without frank bone destruction.MethodsThis paper reviews the various gateways of the spread of coronavirus disease 2019 associated mucormycosis to the orbit, even before advent of bone destruction or ocular symptoms. Plausible pathways of invasion and subtle imaging findings are depicted, to enable an early diagnosis.ResultsRelevant anatomy and imaging examples have been illustrated to familiarise the surgeons with various routes of coronavirus disease 2019 associated mucormycosis spread to the orbit. Emphasis is laid on searching for subtle imaging findings for the detection of early orbital invasion.ConclusionEarly detection and extension of coronavirus disease 2019 associated mucormycosis is facilitated by knowledge of its gateways of spread, which aids the surgeon in prognostication and planning of the surgical approach.
First records of the flat-headed cat Prionailurus planiceps on the Kampar Peninsula, Sumatra, Indonesia
Authors: Powell Chela , Iqbal Muhammad 
Published: September 2021

AbstractThe flat-headed cat Prionailurus planiceps is one of the rarest small felids, with little known about its distribution, population status or habitat requirements, largely because of the few records of the species. We report here 11 detections of this Endangered species, recorded during 4 years of camera-trap surveys in a peat-swamp forest on the Kampar Peninsula, Riau province, Sumatra. These are the first records of this species on the Kampar Peninsula, in an area of c. 1,300 km2 of peat-swamp forest comprising four adjacent Ecosystem Restoration Concession licences. All records were near water bodies (mean distance 351 m) in lowland peat-swamp forest. These findings add to the existing knowledge of the species' distribution in Sumatra and confirm its presence in these peat-swamp forests. To inform species conservation management planning for the Kampar Peninsula, further research on this species is required.
The Babytwins Study Sweden (BATSS): A Multi-Method Infant Twin Study of Genetic and Environmental Factors Influencing Infant Brain and Behavioral Development
Authors: Falck-Ytter Terje , Hamrefors Linnea , Siqueiros Sanches Monica , Portugal Ana Maria , Taylor Mark , Li Danyang , Viktorsson Charlotte , Hardiansyah Irzam , Myers Lynnea , Westberg Lars , Bölte Sven , Tammimies Kristiina , Ronald Angelica 
Published: September 2021

AbstractTwin studies can help us understand the relative contributions of genes and environment to phenotypic trait variation, including attentional and brain activation measures. In terms of applying methodologies such as electroencephalography (EEG) and eye tracking, which are key methods in developmental neuroscience, infant twin studies are almost nonexistent. Here, we describe the Babytwins Study Sweden (BATSS), a multi-method longitudinal twin study of 177 MZ and 134 DZ twin pairs (i.e., 622 individual infants) covering the 5−36 month time period. The study includes EEG, eye tracking and genetics, together with more traditional measures based on in-person testing, direct observation and questionnaires. The results show that interest in participation in research among twin parents is high, despite the comprehensive protocol. DNA analysis from saliva samples was possible in virtually all participants, allowing for both zygosity confirmation and polygenic score analyses. Combining a longitudinal twin design with advanced technologies in developmental cognitive neuroscience and genomics, BATSS represents a new approach in infancy research, which we hope to have impact across multiple disciplines in the coming years.
DNA methylation of the glucocorticoid receptor gene predicts substance use in adolescence: longitudinal data from over 1000 young individuals
Authors: Raffetti Elena , Melas Philippe Anastasios , Landgren Anton Jonatan , Andersson Filip , Forsell Yvonne , Lavebratt Catharina , Galanti Maria Rosaria 
Published: September 2021

AbstractEarly life stress has been linked to increased methylation of the Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1) gene, which codes for the glucocorticoid receptor. Moreover, early life stress has been associated with substance use initiation at a younger age, a risk factor for developing substance use disorders. However, no studies to date have investigated whether NR3C1 methylation can predict substance use in young individuals. This study included adolescents 13–14 years of age that reported no history of substance use at baseline, (N = 1041; males = 46%). Participants contributed saliva DNA samples and were followed in middle adolescence as part of KUPOL, a prospective cohort study of 7th-grade students in Sweden. Outcome variables were self-reports of (i) recent use, (ii) lifetime use, and (iii) use duration of (a) alcohol, (b) tobacco products, (c) cannabis, or (d) any substance. Outcomes were measured annually for three consecutive years. The predictor variable was DNA methylation at the exon 1 F locus of NR3C1. Risk and rate ratios were calculated as measures of association, with or without adjustment for internalizing symptoms and parental psychiatric disorders. For a subset of individuals (N = 320), there were also morning and afternoon salivary cortisol measurements available that were analyzed in relation to NR3C1 methylation levels. Baseline NR3C1 hypermethylation associated with future self-reports of recent use and use duration of any substance, before and after adjustment for potential confounders. The overall estimates were attenuated when considering lifetime use. Sex-stratified analyses revealed the strongest association for cigarette use in males. Cortisol analyses revealed associations between NR3C1 methylation and morning cortisol levels. Findings from this study suggest that saliva NR3C1 hypermethylation can predict substance use in middle adolescence. Additional longitudinal studies are warranted to confirm these findings.
Histone deacetylase HDAC4 participates in the pathological process of myocardial ischemia-reperfusion injury via MEKK1/JNK pathway by binding to miR-206
Authors: Li Qingman , Zhu Lijie , Niu Fangqing , Li Qingmin , Wang Che , Yang Honghui , Gao Chuanyu 
Published: September 2021

AbstractHistone deacetylases (HDACs) and microRNAs (miRs) have been reported to exert pivotal roles on the pathogenesis of myocardial ischemia-reperfusion injury (MIRI). Therefore, the present study was performed to define the underlying role of HDAC4 and miR-206 in the pathological process of MIRI. An IRI rat model was established. The interaction between HDAC4 and the promoter region of miR-206 was determined using ChIP, and that between miR-206 and mitogen-activated protein kinase kinase kinase 1 (MEKK1) was determined using dual luciferase reporter gene assay. After the loss- or gain-of-function assay in cardiomyocytes, western blot analysis, RT-qPCR, TUNEL, and ELISA assay were performed to define the roles of HDAC4, miR-206, and MEKK1. Up-regulation of HDAC4 and down-regulation of miR-206 occurred in rat myocardial tissues and cardiomyocytes in MIRI. HDAC4 down-regulation or miR-206 up-regulation contributed to reduced cell apoptosis and the levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and malondialdehyde (MDA), while elevating the superoxide dismutase (SOD) and glutathione (GSH) contents. Meanwhile, HDAC4 silencing promoted the expression of miR-206, which targeted and negatively regulated MEKK1. Then inhibition of JNK phosphorylation reduced the cardiomyocyte apoptosis to alleviate MIRI. Coherently, HDAC4 silencing could up-regulate the expression of miR-206 to reduce cardiomyocyte apoptosis and inhibit oxidative stress, and exerting a protective effect on MIRI via the MEKK1/JNK pathway.
Production of high-energy Li-ion batteries comprising silicon-containing anodes and insertion-type cathodes
Authors: Eshetu Gebrekidan Gebresilassie , Zhang Heng , Judez Xabier , Adenusi Henry , Armand Michel , Passerini Stefano , Figgemeier Egbert 
Published: September 2021

AbstractRechargeable Li-based battery technologies utilising silicon, silicon-based, and Si-derivative anodes coupled with high-capacity/high-voltage insertion-type cathodes have reaped significant interest from both academic and industrial sectors. This stems from their practically achievable energy density, offering a new avenue towards the mass-market adoption of electric vehicles and renewable energy sources. Nevertheless, such high-energy systems are limited by their complex chemistry and intrinsic drawbacks. From this perspective, we present the progress, current status, prevailing challenges and mitigating strategies of Li-based battery systems comprising silicon-containing anodes and insertion-type cathodes. This is accompanied by an assessment of their potential to meet the targets for evolving volume- and weight-sensitive applications such as electro-mobility.
Identifying and characterizing pesticide use on 9,000 fields of organic agriculture
Authors: Larsen Ashley E. , Claire Powers L. , McComb Sofie 
Published: September 2021

AbstractNotwithstanding popular perception, the environmental impacts of organic agriculture, particularly with respect to pesticide use, are not well established. Fueling the impasse is the general lack of data on comparable organic and conventional agricultural fields. We identify the location of ~9,000 organic fields from 2013 to 2019 using field-level crop and pesticide use data, along with state certification data, for Kern County, CA, one of the US’ most valuable crop producing counties. We parse apart how being organic relative to conventional affects decisions to spray pesticides and, if spraying, how much to spray using both raw and yield gap-adjusted pesticide application rates, based on a global meta-analysis. We show the expected probability of spraying any pesticides is reduced by about 30 percentage points for organic relative to conventional fields, across different metrics of pesticide use including overall weight applied and coarse ecotoxicity metrics. We report little difference, on average, in pesticide use for organic and conventional fields that do spray, though observe substantial crop-specific heterogeneity.
Structural determinants and regulation of spontaneous activity in GABAA receptors
Authors: Sexton Craig A. , Penzinger Reka , Mortensen Martin , Bright Damian P. , Smart Trevor G. 
Published: September 2021

AbstractGABAA receptors are vital for controlling neuronal excitability and can display significant levels of constitutive activity that contributes to tonic inhibition. However, the mechanisms underlying spontaneity are poorly understood. Here we demonstrate a strict requirement for β3 subunit incorporation into receptors for spontaneous gating, facilitated by α4, α6 and δ subunits. The crucial molecular determinant involves four amino acids (GKER) in the β3 subunit’s extracellular domain, which interacts with adjacent receptor subunits to promote transition to activated, open channel conformations. Spontaneous activity is further regulated by β3 subunit phosphorylation and by allosteric modulators including neurosteroids and benzodiazepines. Promoting spontaneous activity reduced neuronal excitability, indicating that spontaneous currents will alter neural network activity. This study demonstrates how regional diversity in GABAA receptor isoform, protein kinase activity, and neurosteroid levels, can impact on tonic inhibition through the modulation of spontaneous GABAA receptor gating.
Evidence of two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn
Authors: Han Minyong , Inoue Hisashi , Fang Shiang , John Caolan , Ye Linda , Chan Mun K. , Graf David , Suzuki Takehito , Ghimire Madhav Prasad , Cho Won Joon , Kaxiras Efthimios , Checkelsky Joseph G. 
Published: September 2021

AbstractThe kagome lattice has long been regarded as a theoretical framework that connects lattice geometry to unusual singularities in electronic structure. Transition metal kagome compounds have been recently identified as a promising material platform to investigate the long-sought electronic flat band. Here we report the signature of a two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn by means of planar tunneling spectroscopy. Employing a Schottky heterointerface of FeSn and an n-type semiconductor Nb-doped SrTiO3, we observe an anomalous enhancement in tunneling conductance within a finite energy range of FeSn. Our first-principles calculations show this is consistent with a spin-polarized flat band localized at the ferromagnetic kagome layer at the Schottky interface. The spectroscopic capability to characterize the electronic structure of a kagome compound at a thin film heterointerface will provide a unique opportunity to probe flat band induced phenomena in an energy-resolved fashion with simultaneous electrical tuning of its properties. Furthermore, the exotic surface state discussed herein is expected to manifest as peculiar spin-orbit torque signals in heterostructure-based spintronic devices.
Reprogrammable plasmonic topological insulators with ultrafast control
Authors: You Jian Wei , Ma Qian , Lan Zhihao , Xiao Qiang , Panoiu Nicolae C. , Cui Tie Jun 
Published: September 2021

AbstractTopological photonics has revolutionized our understanding of light propagation, providing a robust way to manipulate light. So far, most of studies in this field are focused on designing a static photonic structure. Developing a dynamic photonic topological platform to switch multiple topological functionalities at ultrafast speed is still a great challenge. Here we theoretically propose and experimentally demonstrate a reprogrammable plasmonic topological insulator, where the topological propagation route can be dynamically changed at nanosecond-level switching time, leading to an experimental demonstration of ultrafast multi-channel optical analog-digital converter. Due to the innovative use of electric switches to implement the programmability of plasmonic topological insulator, each unit cell can be encoded by dynamically controlling its digital plasmonic states while keeping its geometry and material parameters unchanged. Our reprogrammable topological plasmonic platform is fabricated by the printed circuit board technology, making it much more compatible with integrated photoelectric systems. Furthermore, due to its flexible programmability, many photonic topological functionalities can be integrated into this versatile topological platform.