bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculating complex‐valued P‐wave first‐arrival traveltimes in attenuative vertical transversely isotropic media with an irregular surface
Authors: Wang Mengxiu , Chen Jingyi , Zhao Zhencong , Hu Wenyi 
Published: October 2020

ABSTRACTThe complex‐valued first‐arrival traveltime can be used to describe the properties of both velocity and attenuation as seismic waves propagate in attenuative elastic media. The real part of the complex‐valued traveltime corresponds to phase arrival and the imaginary part is associated with the amplitude decay due to energy absorption. The eikonal equation for attenuative vertical transversely isotropic media discretized with rectangular grids has been proven effective and precise to calculate the complex‐valued traveltime, but less accurate and efficient for irregular models. By using the perturbation method, the complex‐valued eikonal equation can be decomposed into two real‐valued equations, namely the zeroth‐ and first‐order traveltime governing equations. Here, we first present the topography‐dependent zeroth‐ and first‐order governing equations for attenuative VTI media, which are obtained by using the coordinate transformation from the Cartesian coordinates to the curvilinear coordinates. Then, we apply the Lax–Friedrichs sweeping method for solving the topography‐dependent traveltime governing equations in order to approximate the viscosity solutions, namely the real and imaginary parts of the complex‐valued traveltime. Several numerical tests demonstrate that the proposed scheme is efficient and accurate in calculating the complex‐valued P‐wave first‐arrival traveltime in attenuative VTI media with an irregular surface.
VdNop12, containing two tandem RNA recognition motif domains, is a crucial factor for pathogenicity and cold adaption in Verticillium dahliae
Authors: Zhang Jun , Cui Weiye , Abdul Haseeb Hafiz , Guo Wei 
Published: October 2020

SummaryPrevious studies have reported the ability of fungi to overwinter in soil or on crop debris under different environmental conditions, but how fungi adapt to chilling is still largely unknown. In this study, we have identified and characterized the RNA binding protein (RBP) (VdNop12) by screening an Agrobacterium tumefaciens‐mediated transformation‐mediated insertional mutational library of Verticillium dahliae. We determined that this protein was essential to the pathogen for virulence on cotton plants. VdNop12 contains two tandem RNA recognition motif domains, and its orthologs are widely distributed in filamentous fungi. Mutants produced by disruption of VdNop12 showed defects in vegetative growth, conidiation and cell wall integrity. The mutant also showed an increase in sensitivity to low temperature, as compared to the wildtype and complementation strains. Yeast complementation assay showed that VdNop12 could functionally restore the growth phenotype of ΔScNop12 mutant of Saccharomyces cerevisiae at 15°C. We demonstrated that the VdNop12 is localized in the nucleus, and its loss resulted in the downregulated expression of several genes related to cAMP‐PKA and MAPK pathways in V. dahliae. Our results demonstrated a crucial role of RBPs in the regulation of morphology, cold adaption, and pathogenic development in V. dahliae.
BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries
Authors: Fontes João T. , Vieira Pedro E. , Ekrem Torbjørn , Soares Pedro , Costa Filipe O. 
Published: October 2020

AbstractBiodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species‐level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R‐based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites
Authors: Ottman Noora , Barrientos‐Somarribas Mauricio , Fyhrquist Nanna , Alexander Helen , Wisgrill Lukas , Olah Peter , Tsoka Sophia , Greco Dario , Levi‐Schaffer Francesca , Soumelis Vassili , Schröder Jens M. , Kere Juha , Nestle Frank O. , Barker Jonathan , Ranki Annamari , Lauerma Antti , Homey Bernhard , Andersson Björn , Alenius Harri 
Published: October 2020

AbstractIt is well established that different sites in healthy human skin are colonized by distinct microbial communities due to different physiological conditions. However, few studies have explored microbial heterogeneity between skin sites in diseased skin, such as atopic dermatitis (AD) lesions. To address this issue, we carried out deep analysis of the microbiome and transcriptome in the skin of a large cohort of AD patients and healthy volunteers, comparing two physiologically different sites: upper back and posterior thigh. Microbiome samples and biopsies were obtained from both lesional and nonlesional skin to identify changes related to the disease process. Transcriptome analysis revealed distinct disease‐related gene expression profiles depending on anatomical location, with keratinization dominating the transcriptomic signatures in posterior thigh, and lipid metabolism in the upper back. Moreover, we show that relative abundance of Staphylococcus aureus is associated with disease severity in the posterior thigh, but not in the upper back. Our results suggest that AD may select for similar microbes in different anatomical locations—an "AD‐like microbiome," but distinct microbial dynamics can still be observed when comparing posterior thigh to upper back. This study highlights the importance of considering the variability across skin sites when studying the development of skin inflammation.
A prospective comparison of four methods for preventing pacemaker pocket infections
Authors: Li Yao‐Dong , MaiMaiTiABuDuLa MaiMaiTiMin , Cao Gui‐Qiu , MaiMaiTiAiLi MaiMaiTiMin , Zhou Xian‐Hui , Lu Yan‐Mei , Zhang Jiang‐Hua , Xing Qiang , Wu Chuang‐Ju , Feng Min , Zhang Ge‐Ge , Tang Bao‐Peng 
Published: October 2020

AbstractThis study aims to evaluate four pacemaker pocket cleaning methods for preventing implantation‐related infections. This single‐center trial prospectively randomized 910 patients undergoing first‐time pacemaker implantation or replacement into four pocket cleaning methods: hemocoagulase (group A, n = 228), gentamicin (group B, n = 228), hemocoagulase plus gentamicin (group C, n = 227), and normal saline (group D, n = 227). Before implanting the pacemaker battery, the pockets were cleaned with gauze presoaked in the respective cleaning solutions. Then, these patients were followed up to monitor the occurrence of infections for 1 month after implantation. Twelve implantation‐related infections occurred in 910 patients (1.32%): four patients from group A (1.75%), three patients from group B (1.32%), two patients from group C (0.88%), and three patients from group D (1.32%) (P > .05). Furthermore, two patients developed bloodstream infections (0.22%), and both of these patients were associated with pocket infection (one patient was from group A, while the other patient was from group C, respectively). No cases of infective endocarditis occurred. The differences in the number of infections in these study groups were not statistically significant. The application of hemocoagulase, gentamicin, hemocoagulase plus gentamicin, or normal saline on the presoaked gauze before implantation was equally effective in preventing pocket‐associated infections.
Reasoned action approach and compliance with recommended behaviours to prevent the transmission of the SARS‐CoV‐2 virus in the UK
Authors: Norman Paul , Wilding Sarah , Conner Mark 
Published: October 2020

ObjectivesTo examine associations between demographics, people’s beliefs, and compliance with behaviours recommended by the UK government to prevent the transmission of the SARS‐CoV‐2 virus that causes COVID‐19.DesignA two‐wave online survey conducted one week apart during the national lockdown (April, 2020).MeasuresA sample of 477 UK residents completed baseline measures from the reasoned action approach (experiential attitudes, instrumental attitudes, injunctive norms, descriptive norms, capacity, autonomy, and intention) and perceived susceptibility for each of the following recommended behaviours: limiting leaving home, keeping at least 2 m away from other people when outside and when inside shops, not visiting or meeting friends or other family members, and washing hands when returning home. Self‐reported compliance with each of the recommended behaviours was assessed one week later.ResultsRates of full compliance with the recommended behaviours ranged from 31% (keeping at least 2 m away from other people when inside shops) to 68% (not visiting or meeting friends or other family members). Capacity was a significant predictor of compliance with each of the five recommended behaviours. Increasing age and intentions were also predictive of compliance with three of the behaviours.ConclusionsInterventions to increase compliance with the recommended behaviours to prevent the transmission of the SARS‐CoV‐2 virus, especially those relating to social distancing, need to bolster people’s intentions and perceptions of capacity. This may be achieved through media‐based information campaigns as well as environmental changes to make compliance with such measures easier. Such interventions should particularly target younger adults.
The science and engineering of stem cell‐derived organoids‐examples from hepatic, biliary, and pancreatic tissues
Authors: Ogoke Ogechi , Maloy Mitchell , Parashurama Natesh 
Published: October 2020

ABSTRACTThe field of organoid engineering promises to revolutionize medicine with wide‐ranging applications of scientific, engineering, and clinical interest, including precision and personalized medicine, gene editing, drug development, disease modelling, cellular therapy, and human development. Organoids are a three‐dimensional (3D) miniature representation of a target organ, are initiated with stem/progenitor cells, and are extremely promising tools with which to model organ function. The biological basis for organoids is that they foster stem cell self‐renewal, differentiation, and self‐organization, recapitulating 3D tissue structure or function better than two‐dimensional (2D) systems. In this review, we first discuss the importance of epithelial organs and the general properties of epithelial cells to provide a context and rationale for organoids of the liver, pancreas, and gall bladder. Next, we develop a general framework to understand self‐organization, tissue hierarchy, and organoid cultivation. For each of these areas, we provide a historical context, and review a wide range of both biological and mathematical perspectives that enhance understanding of organoids. Next, we review existing techniques and progress in hepatobiliary and pancreatic organoid engineering. To do this, we review organoids from primary tissues, cell lines, and stem cells, and introduce engineering studies when applicable. We discuss non‐invasive assessment of organoids, which can reveal the underlying biological mechanisms and enable improved assays for growth, metabolism, and function. Applications of organoids in cell therapy are also discussed. Taken together, we establish a broad scientific foundation for organoids and provide an in‐depth review of hepatic, biliary and pancreatic organoids.
Plasma proteome profiles treatment efficacy of incretin dual agonism in diet‐induced obese female and male mice
Authors: Sachs Stephan , Niu Lili , Geyer Philipp , Jall Sigrid , Kleinert Maximilian , Feuchtinger Annette , Stemmer Kerstin , Brielmeier Markus , Finan Brian , DiMarchi Richard D. , Tschöp Matthias H. , Wewer Albrechtsen Nicolai , Mann Matthias , Müller Timo D. , Hofmann Susanna M. 
Published: October 2020

AbstractAimsUnimolecular peptides targeting the receptors for glucagon‐like peptide‐1 (GLP‐1) and glucose‐dependent insulinotropic polypeptide (GIP) (GLP‐1/GIP co‐agonist) have been shown to outperform each single peptide in the treatment of obesity and cardiometabolic disease in preclinical and clinical trials. By combining physiological treatment endpoints with plasma proteomic profiling (PPP), we aimed to identify biomarkers to advance non‐invasive metabolic monitoring of compound treatment success and exploration of ulterior treatment effects on an individual basis.Materials and methodsWe performed metabolic phenotyping along with PPP in body weight‐matched male and female diet‐induced obese (DIO) mice treated for 21 days with phosphate‐buffered saline, single GIP and GLP‐1 mono‐agonists, or a GLP‐1/GIP co‐agonist.ResultsGLP‐1R/GIPR co‐agonism improved obesity, glucose intolerance, non‐alcoholic fatty liver disease (NAFLD) and dyslipidaemia with superior efficacy in both male and female mice compared with mono‐agonist treatments. PPP revealed broader changes of plasma proteins after GLP‐1/GIP co‐agonist compared with mono‐agonist treatments in both sexes, including established and potential novel biomarkers for systemic inflammation, NAFLD and atherosclerosis. Subtle sex‐specific differences have been observed in metabolic phenotyping and PPP.ConclusionsWe herein show that a recently developed unimolecular GLP‐1/GIP co‐agonist is more efficient in improving metabolic disease than either mono‐agonist in both sexes. PPP led to the identification of a sex‐independent protein panel with the potential to monitor non‐invasively the treatment efficacies on metabolic function of this clinically advancing GLP‐1/GIP co‐agonist.
The incidence of non‐ampullary duodenal cancer in Japan: The first analysis of a national cancer registry
Authors: Yoshida Masao , Yabuuchi Yohei , Kakushima Naomi , Kato Motohiko , Iguchi Mikitaka , Yamamoto Yorimasa , Kanetaka Kengo , Uraoka Toshio , Fujishiro Mitsuhiro , Sho Masayuki ,   Japan Duodenal Cancer Guideline Committee
Published: October 2020

AbstractBackground and AimAlthough duodenal cancer is rare, no epidemiological research on this disease has been conducted in Asian countries. We aimed to elucidate the incidence and clinical features of duodenal cancer in Japan using a large‐scale national database.MethodsData of patients with primary duodenal cancer diagnosed from January 1, 2016, to December 31, 2016, were extracted from the Japanese national cancer registry. Excluding malignant neoplasm of the Vater's ampulla, we calculated the incidence among the population as a crude number of patients with duodenal cancer divided by the total Japanese population in 2016. We performed multivariate analyses using logistic regression models to identify risk factors for advanced cancer, defined as metastatic cancer or local invasion to adjacent organs.ResultsData on 3005 patients were included. The incidence of duodenal cancer was 23.7 per 1 000 000 person‐years. In total, 56.4% of cases were detected at the localized stage. In the localized cancer group, endoscopic resection was more frequently performed (48.0%), whereas in the advanced cancer group, surgery and chemotherapy were the major treatment options (39.3% and 41.5%, respectively). Multivariate analyses identified age ≥80 years (odds ratio [OR], 1.489; 95% confidence interval [CI], 1.113–1.992; P = 0.007), incidental detection (OR, 2.325; CI, 1.623–3.331; P < 0.0001), and precise examination for symptomatic patients (OR, 10.561; CI, 7.416–15.042; P < 0.0001) as independent risk factors for advanced cancer.ConclusionsOur study revealed the incidence of duodenal cancer in Japan. However, localized cancer was the major tumor stage at detection, resulting in a high rate of endoscopic resection.
Trichloroacetic acid 35% as a therapeutic line for localized patchy alopecia areata in comparison with intralesional steroids: Clinical and trichoscopic evaluation
Authors: Mahgoub Doaa A. , Dhannoon Tamarah I. , El‐Mesidy Marwa S. 
Published: October 2020

AbstractBackgroundIntralesional corticosteroids (ILCs) is the first‐line therapy for patients older than 10 years having patchy alopecia areata, however some patients do not respond effectively.AimsTo evaluate the efficacy of a chemical peel trichloro acetic acid (TCA 35%) in comparison to ILCs.Patients/MethodsTwenty‐two patients with two patches of alopecia areata were included. Two treatment modalities with ILCs and topical TCA 35% were performed in two randomly selected patches. Three sessions were done, 3 weeks apart and were followed‐up for three months. Evaluation was done using Mac Donald Hull and Norris grading system and by counting trichoscopic parameters in each patch.ResultsBoth ILCs and TCA 35% treated patches showed measurable improvement with no statistically significant difference between the results of the two modalities (p>0.05) at different times of the study. Yellow dots, black dots, exclamation marks and dystrophic hair were all reduced by 100%, 82.0%, 100% and 88.3% in ILCs treated patches and by 70.4%, 69.1%, 100% and 75.0% in TCA treated patches, respectively.ConclusionTopical TCA 35% is an effective and safe treatment for the treatment of AA without serious side effects, despite the slower response when compared to ILCs.
The generalizability of water‐deficit on bacterial community composition; Site‐specific water‐availability predicts the bacterial community associated with coast redwood roots
Authors: Willing Claire E. , Pierroz Grady , Coleman‐Derr Devin , Dawson Todd E. 
Published: October 2020

AbstractExperimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of Actinobacteria, however, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Bacterial cell wall thickness and growth morphology (e.g., filamentous or unicellular) have been proposed as traits that may mediate bacterial responses to environmental drivers. Leveraging a natural gradient of water‐availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (a) that site‐specific water‐availability is an important predictor of bacterial community composition for redwood roots and rhizosphere soils; (b) that there is relative enrichment of Actinobacteria and other monoderm bacterial groups within the redwood microbiome in response to drier conditions; and (c) that bacterial growth morphology is an important predictor of bacteria response to water‐availability, where filamentous taxa will become more dominant at drier sites compared to unicellular bacteria. We find that both α‐ and β‐diversity of redwood bacterial communities is partially explained by water‐availability and that Actinobacterial enrichment is a conserved response of land plants to water‐deficit. Further, we highlight how the trend of Actinobacterial enrichment in the redwood system is largely driven by the Actinomycetales. We propose bacterial growth morphology (filamentous vs. unicellular) as an additional mechanism behind the increase in Actinomycetales with increasing aridity. A trait‐based approach including cell‐wall thickness and growth morphology may explain the distribution of bacterial taxa across environmental gradients and help to predict patterns of bacterial community composition for a wide range of host plants.
Effect of farm management on topsoil organic carbon and aggregate stability in water: A case study from Southwest England, UK
Authors: Collier Sarah M. , Green Sophie M. , Inman Alex , Hopkins David W. , Kendall Hazel , Jahn Molly M. , Dungait Jennifer A. J. 
Published: October 2020

AbstractThere are few reliable data sets to inspire confidence in policymakers that soil organic carbon (SOC) can be measured on farms. We worked with farmers in the Tamar Valley region of southwest England to select sampling sites under similar conditions (soil type, aspect and slope) and management types. Topsoils (2–15 cm) were sampled in autumn 2015, and percentage soil organic matter (%SOM) was determined by loss on ignition and used to calculate %SOC. We also used the stability of macroaggregates in cold water (WSA) (‘soil slaking’) as a measure of ‘soil health’ and investigated its relationship with SOC in the clay‐rich soils. %SOM was significantly different between management types in the order woodland (11.1%) = permanent pasture (9.5%) > ley‐arable rotation (7.7%) = arable (7.3%). This related directly to SOC stocks that were larger in fields under permanent pasture and woodland compared with those under arable or ley‐arable rotation whether corrected for clay content (F = 8.500, p < .0001) or not (F = 8.516, p < .0001). WSA scores were strongly correlated with SOC content whether corrected for clay content (SOCadj R2 = .571, p < .0001) or not (SOCunadj R2 = 0.490, p = .002). Time since tillage controlled SOC stocks and WSA scores, accounting for 75.5% and 51.3% of the total variation, respectively. We conclude that (1) SOC can be reliably measured in farmed soils using accepted protocols and related to land management and (2) WSA scores can be rapidly measured in clay soils and related to SOC stocks and soil management.
Development and Cross-Validation of a Prediction Equation for Estimating Percentage Body Fat From Body Mass Index in Young People With Intellectual Disability
Authors: Bertapelli Fabio , Agiovlasitis Stamatis , Motl Robert W. , Soares Roberto A. , de Barros-Filho Marcos M. , do Amaral-Junior Wilson D. , Guerra-Junior Gil 
Published: October 2020

The purpose of this study was to develop and cross-validate an equation for estimating percentage body fat (%BF) from body mass index and other potential independent variables among young persons with intellectual disability. Participants were 128 persons with intellectual disability (62 women; age 16–24 years) split between development (n = 98) and cross-validation (n = 30) samples. Dual-energy X-ray absorptiometry served as the reference method for %BF. An equation including 1/body mass index and sex (0 = male; 1 = female) was highly accurate in estimating %BF (p < .001; R2 = .82; standard error of estimate  = 5.22%). Mean absolute and root mean square errors were small (3.1% and 3.9%, respectively). A Bland–Altman plot indicated nearly zero mean difference between actual and predicted %BF with modest 95% confidence intervals. The prediction equation was %BF = 56.708 − (729.200 × [1/body mass index]) + (12.134 × sex). Health care professionals may use the prediction equation for monitoring %BF among young people with intellectual disability.