bluuebunny/crossref_metadata_2025_split huggingface dataset:
New loci and neuronal pathways for resilience to heat stress in cattle
Authors: Cheruiyot Evans K. , Haile-Mariam Mekonnen , Cocks Benjamin G. , MacLeod Iona M. , Xiang Ruidong , Pryce Jennie E. 
Published: August 2021

AbstractWhile understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature–humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand–receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.
Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling
Authors: Tong Jing , Hu Manman , Han Beibei , Ji Yanhai , Wang Baoju , Liang Hao , Liu Mingchi , Wu Zhanhui , Liu Ning 
Published: August 2021

AbstractChinese chive (Allium tuberosum) is widely cultivated around the world for its unique flavor, nutrient, and medicinal values, yet its molecular mechanism on flavor formation and other metabolic pathways remains intangible. The elucidation of these complex processes begins with investigating the expression of the genes of interest, however the appropriate reference genes (RGs) for normalizing the gene expression are still unavailable in A. tuberosum. To fill this lacuna, transcriptome-wide screening was undertaken to identify the most stable genes according to the analysis of their FPKM values. The expression stability of the RGs was further evaluated using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The comprehensive analysis showed that GLY1 and SKP1, instead of two traditionally used RGs (eIF1α and ACT2), were the most stable genes across diverse A. tuberosum tissues, indicating the necessity to carefully validate the stability of RGs prior to their use for normalizations. As indicated by geNorm, the normalizations with at least two RGs could give more accurate results. qRT-PCR experiments were conducted with randomly selected genes, demonstrating that normalization with a combination of GLY1 and SKP1 resulted in reliable normalization results. Our finding represents the first attempt toward establishing a standardized qRT-PCR analysis in this economically important vegetable.
Cultural diversity and wisdom of crowds are mutually beneficial and evolutionarily stable
Authors: de Courson Benoît , Fitouchi Léo , Bouchaud Jean-Philippe , Benzaquen Michael 
Published: August 2021

AbstractThe ability to learn from others (social learning) is often deemed a cause of human species success. But if social learning is indeed more efficient (whether less costly or more accurate) than individual learning, it raises the question of why would anyone engage in individual information seeking, which is a necessary condition for social learning’s efficacy. We propose an evolutionary model solving this paradox, provided agents (i) aim not only at information quality but also vie for audience and prestige, and (ii) do not only value accuracy but also reward originality—allowing them to alleviate herding effects. We find that under some conditions (large enough success rate of informed agents and intermediate taste for popularity), both social learning’s higher accuracy and the taste for original opinions are evolutionarily-stable, within a mutually beneficial division of labour-like equilibrium. When such conditions are not met, the system most often converges towards mutually detrimental equilibria.
Plastic deformation of synthetic quartz nanopillars by nanoindentation for multi-scale and multi-level security artefact metrics
Authors: Ito Shunya , Omori Toshiyuki , Ando Masao , Yamazaki Hiroyuki , Nakagawa Masaru 
Published: August 2021

AbstractIndividual authentication using artefact metrics has received increasing attention, as greater importance has been placed on the security of individual information. These artefact metrics must satisfy the requirements of individuality, measurement stability, durability, and clone resistance, in addition to possessing unique physical features. In this study, we proposed that nanostructures of synthetic quartz (SQ) deposited on an SQ plate may provide sophisticated artefact metrics if morphological changes could be intentionally introduced into the SQ nanostructures at certain positions. We fabricated SQ nanopillars using a mass-production method (ultraviolet nanoimprint lithography) and investigated their mechanical deformation using nanoindentation with a spheroid diamond tip through a loading and unloading cycle. The SQ nanopillars with an aspect ratio of 1 (i.e., diameters D of 100 and 200 nm with corresponding heights H of 100 and 200 nm, respectively) could be plastically deformed without collapsing within a specified pillar-array format at programmed positions. The plastically deformed SQ nanopillar arrays demonstrated multi-scale (sub-millimetre, micrometre, and nanometre) and multi-level (shape, area, diameter, and height) individuality authentication and clone resistance. Because SQ is physically and chemically stable and durable, individuality authentication can be a highly reliable tool on Earth and in space.
Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians
Authors: Sutkowska Agnieszka , Mitka Józef , Warzecha Tomasz , Bunk Jakub , Rutkowska Julia , Bathelt Roman 
Published: August 2021

AbstractThe genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.
Antibiotic-resistant bacteria, antibiotic resistance genes, and antibiotic residues in wastewater from a poultry slaughterhouse after conventional and advanced treatments
Authors: Savin Mykhailo , Alexander Johannes , Bierbaum Gabriele , Hammerl Jens Andre , Hembach Norman , Schwartz Thomas , Schmithausen Ricarda Maria , Sib Esther , Voigt Alexander , Kreyenschmidt Judith 
Published: August 2021

AbstractSlaughterhouse wastewater is considered a reservoir for antibiotic-resistant bacteria and antibiotic residues, which are not sufficiently removed by conventional treatment processes. This study focuses on the occurrence of ESKAPE bacteria (Enterococcus spp., S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.), ESBL (extended-spectrum β-lactamase)-producing E. coli, antibiotic resistance genes (ARGs) and antibiotic residues in wastewater from a poultry slaughterhouse. The efficacy of conventional and advanced treatments (i.e., ozonation) of the in-house wastewater treatment plant regarding their removal was also evaluated. Target culturable bacteria were detected only in the influent and effluent after conventional treatment. High abundances of genes (e.g., blaTEM, blaCTX-M-15, blaCTX-M-32, blaOXA-48, blaCMY and mcr-1) of up to 1.48 × 106 copies/100 mL were detected in raw influent. All of them were already significantly reduced by 1–4.2 log units after conventional treatment. Following ozonation, mcr-1 and blaCTX-M-32 were further reduced below the limit of detection. Antibiotic residues were detected in 55.6% (n = 10/18) of the wastewater samples. Despite the significant reduction through conventional and advanced treatments, effluents still exhibited high concentrations of some ARGs (e.g., sul1, ermB and blaOXA-48), ranging from 1.75 × 102 to 3.44 × 103 copies/100 mL. Thus, a combination of oxidative, adsorptive and membrane-based technologies should be considered.
Agonistic experience during development establishes inter-individual differences in approach-avoidance behaviour of crickets
Authors: Balsam Julia S. , Stevenson Paul A. 
Published: August 2021

AbstractMembers of numerous animal species show consistent inter-individual differences in behaviours, but the forces generating animal “personality” or individuality remain unclear. We show that experiences gathered solely from social conflict can establish consistent differences in the decision of male crickets to approach or avoid a stimulus directed at one antenna. Adults isolated for 48 h from a colony already exhibit behavioural differences. Prior to staging a single dyadic contest, prospective winners approached the stimulus whereas prospective losers turned away, as they did also after fighting. In contrast, adults raised as nymphs with adult males present but isolated from them as last instar nymphs, all showed avoidance. Furthermore, adults raised without prior adult contact, showed no preferred directional response. However, following a single fight, winners from both these groups showed approach and losers avoidance, but this difference lasted only one day. In contrast, after 6 successive wins or defeats, the different directional responses of multiple winners and losers remained consistent for at least 6 days. Correlation analysis revealed examples of consistent inter-individual differences in the direction and magnitude of turning responses, which also correlated with individual aggressiveness and motility. Together our data reveal that social subjugation, or lack thereof, during post-embryonic and early adult development forges individuality and supports the notion of a proactive–reactive syndrome in crickets.
Immunoglobulin subtype-coated bacteria are correlated with the disease activity of inflammatory bowel disease
Authors: Masu Yutaro , Kanazawa Yoshitake , Kakuta Yoichi , Shimoyama Yusuke , Onodera Motoyuki , Naito Takeo , Moroi Rintaro , Kuroha Masatake , Kimura Tomoya , Shiga Hisashi , Kinouchi Yoshitaka , Masamune Atsushi 
Published: August 2021

AbstractImmune response involving various immunoglobulin (Ig) isotypes and subtypes to microbiome is involved in the pathogenesis and disease activity of inflammatory bowel diseases (IBDs). To clarify the presence of Ig-coated bacteria in the intestine and its association with disease activity in ulcerative colitis (UC) and Crohn’s disease (CD), we extracted and classified Ig-coated bacteria from fecal samples of 42 patients with IBD and 12 healthy controls (HCs) using flow cytometry and 16S ribosomal RNA sequence analysis. The percentage of bacteria coated with IgA and IgM was higher in patients with IBD than in HCs, and IgG-coated bacteria were found only in patients with IBD. Moreover, the percentages of bacteria coated with IgG1, IgG2, IgG3, and IgM in UC samples and IgG3, IgG4, and IgM in CD samples were correlated with disease activities. The proportions of Bacteroides ovatus and Streptococcus increased during the active phase of CD. Hence, the detailed analysis of Ig-coated bacteria and Ig subtypes using flow cytometry could aid in developing useful indicators of disease activity and identifying more disease-related bacteria, which could become novel treatment targets for IBDs.
iCOVID: interpretable deep learning framework for early recovery-time prediction of COVID-19 patients
Authors: Wang Jun , Liu Chen , Li Jingwen , Yuan Cheng , Zhang Lichi , Jin Cheng , Xu Jianwei , Wang Yaqi , Wen Yaofeng , Lu Hongbing , Li Biao , Chen Chang , Li Xiangdong , Shen Dinggang , Qian Dahong , Wang Jian 
Published: August 2021

AbstractMost prior studies focused on developing models for the severity or mortality prediction of COVID-19 patients. However, effective models for recovery-time prediction are still lacking. Here, we present a deep learning solution named iCOVID that can successfully predict the recovery-time of COVID-19 patients based on predefined treatment schemes and heterogeneous multimodal patient information collected within 48 hours after admission. Meanwhile, an interpretable mechanism termed FSR is integrated into iCOVID to reveal the features greatly affecting the prediction of each patient. Data from a total of 3008 patients were collected from three hospitals in Wuhan, China, for large-scale verification. The experiments demonstrate that iCOVID can achieve a time-dependent concordance index of 74.9% (95% CI: 73.6-76.3%) and an average day error of 4.4 days (95% CI: 4.2-4.6 days). Our study reveals that treatment schemes, age, symptoms, comorbidities, and biomarkers are highly related to recovery-time predictions.
Threshold concentration and random collision determine the growth of the huntingtin inclusion from a stable core
Authors: Pei Sen , Swayne Theresa C. , Morris Jeffrey F. , Emtage Lesley 
Published: August 2021

AbstractThe processes underlying formation and growth of unfolded protein inclusions are relevant to neurodegenerative diseases but poorly characterized in living cells. In S. cerevisiae, inclusions formed by mutant huntingtin (mHtt) have some characteristics of biomolecular condensates but the physical nature and growth mechanisms of inclusion bodies remain unclear. We have probed the relationship between concentration and inclusion growth in vivo and find that growth of mHtt inclusions in living cells is triggered at a cytoplasmic threshold concentration, while reduction in cytoplasmic mHtt causes inclusions to shrink. The growth rate is consistent with incorporation of new material through collision and coalescence. A small remnant of the inclusion is relatively long-lasting, suggesting that it contains a core that is structurally distinct, and which may serve to nucleate it. These observations support a model in which aggregative particles are incorporated by random collision into a phase-separated condensate composed of a particle-rich mixture.
Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation
Authors: Yang Yiting , Ye Xidong , Dai Ranran , Li Zhaoqiang , Zhang Yan , Xue Wei , Zhu Yongchang , Feng Delong , Qin Litao , Wang Xin , Lei Bo , Liao Shixiu , Hao Bingtao 
Published: August 2021

AbstractEpstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by reorganizing chromatin and manipulating epigenetics. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation. Here we show that EBNA2 reorganized chromatin topology to form accessible chromatin domains (ACDs) of the host genome by phase separation. The N-terminal region of EBNA2, which is necessary for phase separation, is sufficient to induce ACDs. The C-terminal domain of EBNA2 promotes the acetylation of accessible chromatin regions by recruiting histone acetylase p300 to ACDs. According to these observations, we proposed a model of EBNA2 reorganizing chromatin topology for its acetylation through phase separation to explain the mechanism of EBNA2 hijacking the host genome by controlling its epigenetics.
Investigation of vanadia–alumina catalysts with solid-state NMR spectroscopy and DFT
Authors: Papulovskiy Evgeniy , Shubin Aleksandr A. , Lapina Olga B. 
Published: August 2021

VOx particles on alumina at low vanadium content were theoretically studied, their 51V NMR parameters were predicted, and an ODH reaction was simulated.
Amplatzer occluders for refractory esophago-respiratory fistulas: a case series
Authors: Belle Arthur , Lorut Christine , Lefebvre Aurélie , Ali Einas Abou , Hallit Rachel , Leblanc Sarah , Bordacahar Benoit , Coriat Romain , Roche Nicolas , Chaussade Stanislas , Barret Maximilien 
Published: August 2021

Abstract
Background and study aims Endoscopic management of esophagorespiratory fistulas (ERF) is challenging and currently available options (stents, double pigtail, endoscopic vacuum therapy) are not very effective. We report the feasibility and efficacy of endoscopic placement of Amplatzer cardiovascular occluders for this indication.
Patients and methods This was a single-center, prospective study (June 2019 to September 2020) of all patients with non-malignant ERF persistent after conventional management with esophageal and/or tracheal stents. The primary outcome was the technical feasibility of Amplatzer placement. Secondary outcomes were clinical success defined by effective ERF occlusion and resolution of respiratory symptoms allowing oral food intake.
Results Endoscopic placement of Amplatzer occluders was feasible in 83 % of patients (5/6), with a 50 % (3/6) clinical success rate at 9 months. The mortality rate was 33 % (2/6).
Conclusions An Amplatzer cardiac or vascular occluder is a feasible and safe treatment option for refractory ERF, with a 50 % short-term clinical success.
A deep learning framework for autonomous detection and classification of Crohnʼs disease lesions in the small bowel and colon with capsule endoscopy
Authors: Majtner Tomáš , Brodersen Jacob Broder , Herp Jürgen , Kjeldsen Jens , Halling Morten Lee , Jensen Michael Dam 
Published: August 2021

Abstract
Background and study aims Small bowel ulcerations are efficiently detected with deep learning techniques, whereas the ability to diagnose Crohnʼs disease (CD) in the colon with it is unknown. This study examined the ability of a deep learning framework to detect CD lesions with pan-enteric capsule endoscopy (CE) and classify lesions of different severity.
Patients and methods CEs from patients with suspected or known CD were included in the analysis. Two experienced gastroenterologists classified anonymized images into normal mucosa, non-ulcerated inflammation, aphthous ulceration, ulcer, or fissure/extensive ulceration. An automated framework incorporating multiple ResNet-50 architectures was trained. To improve its robustness and ability to characterize lesions, image processing methods focused on texture enhancement were employed.
Results A total of 7744 images from 38 patients with CD were collected (small bowel 4972, colon 2772) of which 2748 contained at least one ulceration (small bowel 1857, colon 891). With a patient-dependent split of images for training, validation, and testing, ulcerations were diagnosed with a sensitivity, specificity, and diagnostic accuracy of 95.7 % (CI 93.4–97.4), 99.8 % (CI 99.2–100), and 98.4 % (CI 97.6–99.0), respectively. The diagnostic accuracy was 98.5 % (CI 97.5–99.2) for the small bowel and 98.1 % (CI 96.3–99.2) for the colon. Ulcerations of different severities were classified with substantial agreement (κ = 0.72).
Conclusions Our proposed framework is in excellent agreement with the clinical standard, and diagnostic accuracies are equally high for the small bowel and colon. Deep learning approaches have a great potential to help clinicians detect, localize, and determine the severity of CD with pan-enteric CE.
Safety and effectiveness of endoluminal vacuum-assisted closure for esophageal defects: Systematic review and meta-analysis
Authors: Aziz Muhammad , Haghbin Hossein , Sharma Sachit , Weissman Simcha , Saleem Saad , Lee-Smith Wade , Kobeissy Abdallah , Nawras Ali , Alastal Yaseen 
Published: August 2021

Abstract
Background and study aims Esophageal defects (leaks, fistulas, and perforations) are associated with significant morbidity and mortality. Endoluminal vacuum-assisted closure (EVAC) is a novel intervention that entails the use of sponges in the defect along with negative pressure to achieve granulation tissue formation and healing and has been gaining popularity. We performed a systematic review and pooled analysis of available literature to assess the safety and effectiveness of EVAC for esophageal defects.
Patients and methods We queried PubMed/Medline, Embase, Cochrane, and Web of Science through September 25, 2020 to include all pertinent articles highlighting the safety and effectiveness profile of EVAC for esophageal defects. Pooled rates, 95 % confidence intervals (CIs), and heterogeneity (I2
) were assessed for each outcome.
Results A total of 18 studies with 423 patients were included (mean age 64.3 years and males 74.4 %). The technical success for EVAC was 97.1 % (CI: 95.4 %–98.7 %, I2
= 0 %). The clinical success was 89.4 % (CI: 85.6 %–93.1 %, I2
= 36.8 %). The overall all-cause mortality and adverse events (AEs) noted were 7.1 % (CI: 4.7 %–9.5 %, I2
= 0 %) and 13.6 % (CI: 8.0 %–19.1 %, I2
= 68.9 %), respectively. The pooled need for adjuvant therapy was 15.7 % (CI: 9.8 %–21.6 %, I2
= 71.1 %).
Conclusions This systematic review and meta-analysis showed high rates of technical success, clinical success, and low all-cause mortality and AEs using EVAC. Although the technique is a promising alternative, the lack of comparative studies poses a challenge in making definite conclusions regarding use of EVAC compared to other endoscopic modalities, such as clips and stents.