bluuebunny/crossref_metadata_2025_split huggingface dataset:
Replidec - Use naive Bayes classifier to identify virus lifecycle from metagenomics data
Authors: Peng Xue , Ru Jinlong , Mirzaei Mohammadali Khan , Deng Li 
Published: July 2022

AbstractMotivationViruses are the most abundant biological entities on earth. The majority of these entities are bacterial viruses or phages which specifically infect bacteria. Phages can use different replication strategies to invade their hosts including lytic, lysogenic, chronic cycle and pseudolysogeny. While the determination of the replication strategy used by phages is important to explore the phage-bacteria relationships in different ecosystems there are not many tools that can predict this in metagenomic data. In addition, most of the tools available can only predict lytic and lysogenic cycles. To address this issue, we have developed a new software called Replidec to identify three most common phage replication cycles (virulent, temperate, chronic) in viral sequences.ResultsReplidec uses Naive Bayes classifier combined with alignment-based methods to improve the prediction accuracy in metagenomic data. We test Replidec on viral genomes with known replication cycle and simulated metagenomic sequences. Replidec perform relatively good both in isolated genomes (F1 score: 92.29% ± 0.81; mcc: 89.14% ± 1.22) and simulated metagenomic sequences(F1 score: 87.55% ± 2.12; mcc: 88.23% ± 2.55). Moreover, Replidec can also accurately predict the replication cycle in small viral fragments(∼3000bp). In conclusion, Replidec can achieve the best performance in simulated metagenomic data compared to most prediction softwares including BACPHLIP.
Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei
Authors: Fu Janine Y. , Muroski John M. , Arbing Mark A. , Salguero Jessica A. , Wofford Neil Q. , McInerney Michael J. , Gunsalus Robert P. , Loo Joseph A. , Loo Rachel R. Ogorzalek 
Published: July 2022

AbstractSyntrophomonas wolfei is an anaerobic syntrophic microbe that degrades short-chain fatty acids to acetate, hydrogen, and/or formate. This thermodynamically unfavorable process proceeds through a series of reactive acyl-Coenzyme A species (RACS). In other prokaryotic and eukaryotic systems, the production of intrinsically reactive metabolites correlates with acyl-lysine modifications, which have been shown to play a significant role in metabolic processes. Analogous studies with syntrophic bacteria, however, are relatively unexplored and we hypothesize that highly abundant acylations could exist in S. wolfei proteins, corresponding to the RACS derived from degrading fatty acids. Here, by mass spectrometry-based proteomics (LC-MS/MS), we characterize and compare acylome profiles of two S. wolfei subspecies grown on different carbon substrates. Because modified S. wolfei proteins are sufficiently abundant for post-translational modification (PTM) analyses without antibody enrichment, we could identify types of acylations comprehensively, observing six types (acetyl-, butyryl-, 3-hydroxybutyryl-, crotonyl-, valeryl-, hexanyl-lysine), two of which have not been reported in any system previously. All of the acyl-PTMs identified correspond directly to RACS in fatty acid degradation pathways. A total of 369 sites of modification were identified on 237 proteins. Changing the carbon substrate altered the acylation profile. Moreover, structural studies and in vitro acylation assays of a heavily modified enzyme, acetyl-CoA transferase, provided insight on the possible impact of these acyl-protein modifications. Our findings link protein acylation by RACS to shifts in cellular metabolism.
A methodological framework to assess temporal trends and sub-national disparities in healthcare quality metrics using facility surveys, with applications to sick-child care in Kenya, Senegal, and Tanzania
Authors: Allorant Adrien , Fullman Nancy , Leslie Hannah H. , Sarr Moussa , Gueye Daouda Malick , Eliakimu Eliudi , Wakefield Jonathan , Dieleman Joseph L. , Pigott David , Puttkammer Nancy , Reiner Robert C. 
Published: July 2022

AbstractMonitoring healthcare quality at a subnational resolution is key to identify and resolve geographic inequities and ensure that no sub-population is left behind. Yet, health facility surveys are typically not powered to report reliable estimates at a subnational scale.In this study, we present a framework to fill this gap and jointly analyse publicly available facility survey data, allowing exploration of temporal trends and subnational disparities in healthcare quality metrics. Specifically, our Bayesian hierarchical model includes random effects to account for differences between survey instruments; space-time processes to leverage correlations in space and time; and covariates to incorporate auxiliary information. We apply this framework to Kenya, Senegal, and Tanzania - three countries with at least four rounds of standardized facility surveys each – and estimate the readiness and process quality of sick-child care over time and across subnational areas.These estimates of readiness and process quality of care over time and at a fine spatial resolution show uneven progress in improving facility-based service provision in Kenya, Senegal, and Tanzania. For instance, while national gains in overall readiness of care improved in Tanzania, geographic inequities persisted; in contrast, Senegal, and Kenya experienced stagnation in overall readiness at the national level, but disparities grew across subnational areas. Overall, providers adhered to about one-third of the clinical guidelines for managing sick-child illnesses at the national level. Yet across subnational units, such adherence greatly varied (e.g., 25% to 85% between counties of Kenya in 2020).Our new approach enables identifies precise estimation of changes in the spatial distribution of healthcare quality metrics over time, at a a programmatic spatial resolution, and with accompanying uncertainty estimates. Use of our framework will provide new insights at a policy-relevant spatial resolution for national and regional decision-makers, and international funders.
An iterative gene editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to several potyvirus isolates
Authors: Kuroiwa Kyoka , Danilo Benoit , Perrot Laura , Thenault Christina , Veillet Florian , Delacote Fabien , Duchateau Philippe , Nogué Fabien , Mazier Marianne , Gallois Jean-Luc 
Published: July 2022

AbstractResistance to potyviruses in plants have been largely provided by the selection of natural variant alleles of eukaryotic initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus strains continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base-editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting its functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.
Experimental study of the boosters impact on the rocket aerodynamic characteristics
Authors: Krzysiak Andrzej , Cieśliński Dawid , Placek Robert , Kekus Pawel 
Published: July 2022

Purpose
The purpose of this study is to determine the impact of two parallel boosters fixed to the ILR 33 AMBER 2 K core rocket stage on its aerodynamic characteristics in the subsonic and transonic regimes and for M = 2.3.

Design/methodology/approach
Wind tunnel tests of the rocket model were carried out in a trisonic wind tunnel using a six-component internal balance. Three rocket model configurations were investigated.

Findings
The results of the presented studies showed that the presence of boosters causes a significant increase in the total rocket drag, which depends on both the Mach number and the rocket flight phase. Experimental tests of the rocket model allowed to determine the difference in drag coefficient between active and passive flight versus Mach number. It was found that, in the case of a deviation from the rocket’s flight direction, the aerodynamic coefficients strongly depend on the location of the boosters in relation to the direction of the deviation.

Practical implications
Studies of the rocket model aerodynamic characteristics allow the assessment of the influence of parallel boosters on rocket performance, which is important when the decision of a rocket staging type is taken.

Originality/value
The presented wind tunnel test results of the rocket model equipped with the two parallel boosters are an original contribution to the rocket research results presented in the literature.
Does sustainable board governance drive corporate social responsibility? A structured literature review on European archival research
Authors: Velte Patrick 
Published: July 2022

PurposeThis paper aims to analyze the impact that sustainable board governance has on corporate social responsibility (CSR) on the European capital market because of the current debate of future European regulations on the topic.Design/methodology/approachBased on a legitimacy and stakeholder theoretical framework, the author conducts a structured literature review and includes 86 quantitative peer-reviewed empirical (archival) studies on board gender diversity, sustainability board expertise and sustainability-related executive compensation and their impact on CSR variables.FindingsGender board diversity represents the most important variable in this literature review. The included categories of sustainable board governance positively influence both the total CSR and environmental outputs.Research limitations/implicationsA detailed analysis of sustainable board governance proxies is needed in future archival research to differentiate between symbolic and substantive use of CSR. In view of the current European reform initiatives on sustainable corporate governance in line with the EU Green Deal project, future research should also analyze the interactions between the included sustainable board governance variables and their contributions to CSR.Practical implicationsAs both stakeholder demands’ on CSR outputs and CSR washing have increased since the financial crisis of 2008–2009, firms should be aware of a substantive integration of sustainability within their boards of directors (e.g. because of composition and compensation) to increase their CSR efforts and long-term firm reputation.Originality/valueThis analysis makes useful contributions to prior research by focusing on sustainable board governance as a key determinant of CSR outputs on the European capital market. The European Commission’s future evidence-based regulations [e.g. the corporate sustainability reporting directive (CSRD) and the corporate sustainability due diligence directive (CSDD)] should be promoted.
Do independent directors and big-4 audit firms limit classification shifting: evidence from Indian firms
Authors: Mulchandani Kalyani , Mulchandani Ketan 
Published: July 2022

PurposeThis study investigates the moderating role of Big-4 audit firms on the association between board independence and classification shifting (CS) in Indian firms.Design/methodology/approachThis study has employed a fixed-effect panel data regression model to analyze the sample data. Board independence is measured by taking the proportion of independent directors on a firm’s board. CS is measured from the core earnings expectation model (McVay, 2006). Principal Score Matching is applied to validate the results.FindingsBased on 6,016 firm-year observations of Indian firms listed on the Bombay Stock Exchange, results show that firms with a higher proportion of independent directors on board are effective in limiting expense CS. Further, firms that Big-4 audit firms audit play a significant role in curbing expense CS. Overall, results also exhibit that Big-4 audit firms significantly influence the association between board independence and CS.Originality/valueThis study is one of its kind to examine the moderating role of Big-4 audit firms between board independence and CS.
Ruderals naturalize, competitors invade: Varying roles of plant adaptive strategies along the invasion continuum
Authors: Guo Kun , Pyšek Petr , Chytrý Milan , Divíšek Jan , Lososová Zdeňka , van Kleunen Mark , Pierce Simon , Guo Wen‐Yong 
Published: July 2022

Abstract

It is increasingly recognized that the factors facilitating plant invasions depend on the stage along the introduction–naturalization–invasion continuum. Adaptative strategies, that is, combinations of functional traits that represent overall fitness in the face of one or more selection pressures, have shown promise in explaining plant invasions. However, whether adaptive strategy patterns change with stages of plant invasion is not yet known.

Using the Pladias Database of the Czech Flora and Vegetation, we explored how Grime's adaptive strategies (competitors, stress‐tolerators, ruderals; CSR) and introduction pathways (deliberate vs. accidental) relate to plant invasion along the introduction–naturalization–invasion continuum.

Phylogenetically corrected ANOVAs showed that naturalized species (referring to non‐invasive naturalized species in this study) were mostly R‐selected, whereas invasive species tended to be C‐selected. The results of phylogenetic regression analysis further confirmed that across the deliberately and accidentally introduced species, R‐ and C‐selection were positively related to naturalization and invasion success respectively. We also found that deliberate introduction was negatively related to naturalization success and grid‐cell occupancy of naturalized species, likely due to the different CSR strategies of deliberately and accidentally introduced aliens.

Our study provides empirical evidence that different adaptive strategies are associated with species that have reached different invasion stages and confirms the usefulness of the CSR strategy framework for understanding plant invasion. This has implications for predicting and preventing potential high‐impact invaders. For example, our results show that naturalized C‐selected species have a higher probability of becoming invasive than naturalized R‐selected species. Therefore, management actions are essential to prevent further introductions and spread of competitors.

Read the free Plain Language Summary for this article on the Journal blog.
The lives of others: Class divisions, network segregation, and attachment to society in Chile
Authors: Otero Gabriel , Volker Beate , Rözer Jesper , Mollenhorst Gerald 
Published: July 2022

AbstractIn this paper, we examine whether social class and class divides in social networks contribute to individuals' attachment to society. We argue that network segregation restricts individuals' social worlds, thereby diminishing societal attachment. Our research site is Chile, a country with relatively low social cohesion and one of the world's highest levels of economic inequality. We use large‐scale representative survey data collected in 2016 for the Chilean urban population aged 18–75 years (n = 2983) and interrelate indicators of well‐established dimensions and sub‐dimensions of societal attachment. Results of our regression analyses show that members of the upper middle class are more attached to society than their fellow citizens from other social strata. In addition, having more social contacts within one's own social class reduces attachment to society. In particular, network homogeneity lessens societal attachment for lower‐ and upper‐class individuals, but not so strongly in the middle class. We conclude that social cohesion in Chilean society would be enhanced not only by more equal opportunities but also by changes to the social settings in which social class segregation is (re)produced.
Fecal calprotectin as a biomarker of microscopic bowel inflammation in patients with spondyloarthritis
Authors: Campos Júlia Faria , Resende Gustavo Gomes , Barbosa Alfredo José Afonso , de Carvalho Silas Castro , Lage Junia Aguiar , Cunha Pedro Ferrari Sales , de Souza Stela Cristina Silva , Ferrari Maria de Lourdes Abreu 
Published: July 2022

AbstractAimMicroscopic bowel inflammation is present in up to 60% of all patients with spondyloarthritis (SpA) and appears to be associated with more severe joint disease and a higher risk of developing inflammatory bowel disease (IBD). This study aimed to determine the utility of fecal calprotectin (fCAL) in evaluating endoscopic and histological bowel inflammation in SpA patients.MethodsIleocolonoscopies with biopsies and fCAL measurements were performed in 65 patients with SpA.ResultsIn 47 (72.3%) patients, the fCAL levels were higher than 50 μg/g, whereas in 20 (30.7%), these levels were greater than 250 μg/g. A total of 38 (58.5%) patients presented with microscopic bowel inflammation, and 13 (20%) presented with signs of endoscopic inflammation. fCAL levels were significantly higher in patients with microscopic bowel inflammation than in those without inflammatory findings (P < .001); additionally, these levels were slightly higher in patients with endoscopic signs of bowel inflammation (P = .053). A fCAL cutoff value of 96 μg/g predicted histological bowel inflammation with 73% sensitivity and 67% specificity. No statistically significant difference was observed in the fCAL levels between patients who had been treated or not treated with nonsteroidal anti‐inflammatory drugs (NSAIDs).ConclusionOur findings confirm a high prevalence of microscopic bowel inflammation in SpA patients, regardless of the use of NSAIDs. The evaluation of fCAL levels proved to be useful in the identification of microscopic inflammation and could help in the more judicious indication of ileocolonoscopy. These results support the use of fCAL for the evaluation of microscopic bowel inflammation in SpA patients.
How to distinguish thoracic and cervical lymph nodes during minimally invasive esophagectomy
Authors: Zeng Taidui , Chen Maohui , Cai Bingqiang , Zheng Wei , Xu Chi , Xu Guobing , Chen Chun , Zheng Bin 
Published: July 2022

AbstractPurposeIn this article, we aimed to reconstruct the cervical–thoracic junction plane (CTJP) using a three‐dimensional (3D) reconstruction system. Thus, the CTJP can be judged during surgery to better distinguish cervical–thoracic lymph nodes.MethodsWe included patients in Fujian Medical University Union Hospital from December 2019 to March 2020. All patients underwent a thin‐slice and enhanced computed tomography scan of the chest with 3D reconstruction using the IQQA system (EDDA technology) to reconstruct the CTJP, brachiocephalic trunk, right common carotid artery, and right subclavian artery. The distance from the intersection of the right subclavian artery and the CTJP to the origin of the right subclavian artery (ORSA) was measured, and the relationship between this distance and the patient's sex, BMI and height was analyzed.ResultsSeventy‐three patients were enrolled, of whom 12 had ORSA above the CTJP, while 61 had ORSA below the plane. There was a significant difference in age between the two groups (p = 0.04), compared with height, weight and BMI (p > 0.05). In 61 patients with the ORSA below the CTJP, the average distance was 24.7 ± 7.6 mm. The difference between the distance and BMI (p = 0.02) was statistically significant, and it was increased with increasing BMI.ConclusionsThe relationship between the ORSA and CTJP can be clarified through 3D reconstruction. The cervical‐thoracic recurrent laryngeal nerve lymph nodes can be distinguished clearly in minimally invasive esophagectomy, contributing to the accurate N staging of middle‐thoracic esophageal cancer.
The prevalence and significance of gestational cannabis use at an Australian tertiary hospital
Authors: Dunn Mikaela L. , Bradley Clare , Ayonrinde Oyedeji A. , Van Rooyen Derrick M. , Tait Robert J. , White Scott W. , Fisher Petrovia , Sunanda Gargeswari , Mehta Shailender , Ayonrinde Oyekoya T 
Published: July 2022

BackgroundCannabis is one of the most common non‐prescribed psychoactive substances used in pregnancy. The prevalence of gestational cannabis use is increasing.AimThe aim was to examine the prevalence of gestational cannabis use and associated pregnancy and neonate outcomes.Materials and MethodsA retrospective observational study involving pregnant women delivering in 2019 was conducted at a tertiary hospital in Perth, Western Australia. Gestational cannabis and other substance use records were based on maternal self‐report. Pregnancy outcomes included neonatal gestational age, birthweight, birth length, head circumference, resuscitation measures, special care nursery admission, 5‐min Apgar score and initial neonatal feeding method.ResultsAmong 3104 pregnant women (mean age: 31 years), gestational cannabis use was reported by 1.6% (n = 50). Cannabis users were younger, more likely to use other substances and experience mental illness or domestic violence compared with non‐users. Neonates born to cannabis users had a lower mean gestational age, birthweight and birth length compared to those born to non‐cannabis users. Gestational cannabis use (odds ratio (OR) 3.3, 95% confidence interval (CI) 1.6–6.7) and tobacco smoking (OR 2.2, 95% CI 1.5–3.6) were associated with increased odds of a low‐birthweight neonate. Combined cannabis and tobacco use during pregnancy further increased the likelihood of low birthweight (LBW, adjusted OR 3.9, 95% CI 1.6–9.3). Multivariate logistic regression analysis adjusted for maternal sociodemographical characteristics, mental illness, alcohol, tobacco and other substance use demonstrated gestational cannabis use to be independently associated with LBW (OR 2.3, 95% CI 1.1–5.2).ConclusionGestational cannabis use was independently associated with low birthweight, synergistically affected by tobacco smoking.