bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenomic and transcriptomic prioritization of candidate obesity-risk regulatory GWAS SNPs
Authors: Zhang Xiao , Li Tianying , Xiao Hong-Mei , Ehrlich Kenneth C. , Shen Hui , Deng Hong-Wen , Ehrlich Melanie 
Published: November 2021

AbstractConcern about rising rates of obesity has prompted searches for its genetic risk determinants in genome-wide association studies (GWAS). Most genetic variants that contribute to the increased risk of a given trait are probably regulatory single nucleotide polymorphisms (SNPs). However, identifying plausible regulatory SNPs is difficult because of their varied locations relative to their target gene and linkage disequilibrium, which makes most GWAS-derived SNPs only proxies for many fewer functional SNPs. We developed a systematic approach to prioritizing GWAS-derived obesity SNPs using detailed epigenomic and transcriptomic analysis in adipose tissue vs. heterologous tissues. From 50 obesity-related GWAS and 121,064 expanded SNPs, we prioritized 47 potential causal regulatory SNPs (Tier-1 SNPs) for 14 gene loci. A detailed examination of seven of these genes revealed that four (CABLES1, PC, PEMT,andFAM13A) had Tier-1 SNPs that might regulate alternative use of transcription start sites resulting in different polypeptides being generated or different amounts of an intronic microRNA gene being expressed.HOXA11and long noncoding RNA geneRP11-392O17.1had Tier-1 SNPs in their 3’ or promoter region, respectively, and strong preferences for expression in subcutaneous vs. visceral adipose tissue.ZBED3-AS1had two intragenic Tier-1 SNPs, each of which might contribute to mediating obesity risk through modulating long-distance chromatin interactions. We conclude that prioritization of regulatory SNP candidates should focus on their surrounding epigenetic features in a trait-relevant tissue. Our approach not only revealed especially credible novel regulatory SNPs, but also helped evaluate previously highlighted obesity GWAS SNPs that were candidates for transcription regulation.
Suppression of a dsRNA-induced plant immunity pathway by viral movement protein
Authors: Huang Caiping , Sede Ana Rocio , Mutterer Jerome , Boutant Emmanuel , Heinlein Manfred 
Published: November 2021

SummaryThe virome of plants is dominated by RNA viruses1and several of these cause devastating diseases in cultivated plants leading to global crop losses2. To infect plants, RNA viruses engage in complex interactions with compatible plant hosts. In cells at the spreading infection front, RNA viruses replicate their genome through double-stranded RNA (dsRNA) intermediates and interact with cellular transport processes to achieve cell-to-cell movement of replicated genome copies through cell wall channels called plasmodesmata (PD)3. In order to propagate, viruses also must overcome host defense responses. In addition to triggering the antiviral RNA silencing response, RNA virus infection also elicits pattern-triggered immunity (PTI)4whereby dsRNA, a hallmark of virus replication, acts as an important elicitor5. This innate antiviral immune response is also triggered when dsRNA is applied externally and does not require sequence homology to the virus5. However, the mechanism by which PTI restricts virus infection is not known. Here, we show that dsRNA inhibits the progression of virus infection by triggering callose deposition at plasmodesmata and the inhibition of transport through these cell-to-cell communication channels. The dsRNA-induced signaling pathway leading to callose deposition is independent of ROS production and thus distinguished from pathways triggered by bacterial and fungal elicitors. The dsRNA-induced host response at plasmodesmata is suppressed by theTobacco mosaic virusmovement protein (MP). Thus, the virus uses MP to inhibit innate dsRNA-induced immunity at plasmodesmata, which could be a general strategy of phytoviruses to overcome plant defenses and spread infection.
Autologous mitochondria transport via transzonal filopodia rejuvenates aged oocytes by UC-MSCs derived granulosa cells-oocyte aggregation
Authors: Tang Shuang , Yang Nannan , Yu Mingxi , Wang Shuo , Hu Xiangdong , Ni Heliang , Cai Wenyang 
Published: November 2021

AbstractMitochondria transfer can rescue oocyte aging-related infertility. However, heterologous techniques are suspended due to heteroplasmy. Regarding autologous approaches, the donor source and manipulating procedures require further optimization. Here we propose a strategy using umbilical cord mesenchymal stem cells (UC-MSCs) as mitochondria donor cells and employing intercellular mitochondria transport as the transfer method. We cryopreserved UC-MSCs of the female pup. When the female aged, its UC-MSCs were induced into granulosa cells (iGCs). The zona-weakened GV oocytes were aggregated with autologous iGCs into iGC-oocyte complexes. After cultivation in GDF9-containing media, mitochondria migrated from iGCs into the GV oocyte via transzonal filopodia. The maturation rate, quality, and developmental potential of these oocytes were substantially increased. Furthermore, the birth rate after embryo transfer has been improved. This approach utilized noninvasive procedures to collect mitochondria donor cells and optimized mitochondria transfer manipulations, so may represent a promising advance towards the improvement of aging-related infertility.
Underlying factors that influence the acceptance of COVID-19 vaccine in a country with a high vaccination rate
Authors: Toro-Ascuy Daniela , Cifuentes-Muñoz Nicolás , Avaria Andrea , Pereira-Montecinos Camila , Cruzat Gilena , Zorondo-Rodriguez Francisco , Fuenzalida Loreto F 
Published: November 2021

AbstractControl of the COVID-19 pandemic largely depends on the effectiveness of the vaccination. Several factors including vaccine hesitancy can affect the vaccination process. Understanding the factors that underlie the willingness to accept vaccination brings pivotal information to control the pandemic. We analyzed the association between the willingness level to accept the COVID-19 vaccine, and vaccine determinants amidst the Chilean vaccination process. Individual-level survey data was collected from nationally representative samples of 744 respondents, and multivariate regression models used to estimate the association between outcome and explanatory variables. We found that trust in the COVID-19 vaccine, scientists, and medical professionals increased the willingness to: accept the vaccine, a booster dose, annual vaccination, and children vaccination. Our results are critical to understand the acceptance of COVID-19 vaccines in the context of a country with one of the world’s highest vaccination rates. We provide information for decision-making, policy design and communication of vaccination programs.
Cross-border transmissions of delta substrain AY.29 during Olympic and Paralympic Games
Authors: Koyama Takahiko , Tokumasu Reitaro , Katayama Kotoe , Saito Ayumu , Kudo Michiharu , Imoto Seiya 
Published: November 2021

AbstractTokyo Olympic and Paralympic Games, postponed for COVID-19 pandemic, were finally held in summer of 2021. Just before the games, alpha variant was being replaced with more contagious delta variant (B.1.617.2). AY.4 substrain AY.29, which harbors two additional characteristic mutations of 5239C>T (NSP3 Y840Y) and 5514T>C (NSP3 V932A), emerged in Japan and became the dominant strain in Tokyo by the time of the Olympic Games. As of October 18, 98 AY.29 samples are identified in 16 countries outside of Japan. Phylogenetic analysis and ancestral searches identified 46 distinct introductions of AY.29 strains into those 16 countries. United States has 44 samples with 10 distinct introductions, and United Kingdom has 13 distinct AY.29 strains introduced in 16 samples. Other countries or regions with multiple introductions of AY.29 are Canada, Germany, South Korea, and Hong Kong while Italy, France, Spain, Sweden, Belgium, Peru, Australia, New Zealand, and Indonesia have only one distinct strain introduced. There exists no unambiguous evidence that Olympic and Paralympic Games induced cross-border transmission of the delta substrain AY.29. Since most of unvaccinated countries are also under sampled for genome analysis with longer lead time for data sharing, it will take longer to capture the whole picture of cross-border transmissions of AY.29.
Association between maternal depression and the nutritional status of children under five-years-old in Peru: An analysis of the Demographic and Health Survey 2014-2017
Authors: Villagaray-Pacheco Nicole , Villacorta-Landeo Pamela , Mejía-Guerrero Leslie , Virú-Loza Manuel A. , Soto-Becerra Percy 
Published: November 2021

SummaryObjectiveTo evaluate the association between maternal depression and nutritional status of children under 5 years old in Peru.DesignCross-sectional study of the Demographic and Health Survey 2014-2017. Outcomes were mild (height Z-score for age <-2 SD) and moderate/severe (<-3DE) childhood chronic undernutrition and also mild (hemoglobin <11 g/dL) and moderate/severe (hemoglobin <10 g/dL) childhood anemia. Maternal depression was assessed by the questionnaire PHQ-9. Odds ratios and their confidence intervals (CIs) were estimated by multinomial logistic regression models, considering the complex sample design.SettingPeruParticipantsPeruvian women of childbearing age from 15 to 49 years who live with children from 6 to 59 months.ResultsMaternal depression was significantly associated with a higher odds of moderate/severe chronic undernutrition in children aged 6-59 months (OR = 2.67; 95% CI 1.16-6.16).ConclusionsThere was evidence that maternal depression was associated with an increased risk of moderate/severe chronic undernutrition
A blood-based miRNA signature with prognostic value for overall survival in advanced stage non-small cell lung cancer treated with immunotherapy
Authors: Rajakumar Timothy , Horos Rastislav , Jehn Julia , Schenz Judith , Muley Thomas , Pelea Oana , Hofmann Sarah , Kittner Paul , Kahraman Mustafa , Heuvelman Marco , Sikosek Tobias , Feufel Jennifer , Skottke Jasmin , Nötzel Dennis , Hinkfoth Franziska , Tikk Kaja , Daniel-Moreno Alberto , Ceiler Jessika , Mercaldo Nathaniel , Uhle Florian , Uhle Sandra , Weigand Markus A , Elshiaty Mariam , Lusky Fabienne , Schindler Hannah , Ferry Quentin , Sauka-Spengler Tatjana , Wu Qianxin , Rabe Klaus F , Reck Martin , Thomas Michael , Christopoulos Petros , Steinkraus Bruno R 
Published: November 2021

AbstractImmunotherapies have recently gained traction as highly effective therapies in a subset of late-stage cancers. Unfortunately, only a minority of patients experience the remarkable benefits of immunotherapies, whilst others fail to respond or even come to harm through immune related adverse events. For immunotherapies within the PD-1/PD-L1 inhibitor class, patient stratification is currently performed using tumor (tissue-based) PD-L1 expression. However, PD-L1 is an accurate predictor of response in only ∼30% of cases. There is pressing need for more accurate biomarkers for immunotherapy response prediction.We sought to identify peripheral blood biomarkers, predictive of response to immunotherapies against lung cancer, based on whole blood microRNA profiling. Using three well characterized cohorts consisting of a total of 334 stage IV NSCLC patients, we have defined a 5 microRNA risk score (miRisk) that is predictive of overall survival following immunotherapy in training and independent validation (HR 2.40, 95% CI 1.37-4.19; P < 0.01) cohorts. We have traced the signature to a myeloid origin and performed miRNA target prediction to make a direct mechanistic link to the PD-L1 signalling pathway and PD-L1 itself. The miRisk score offers a potential blood-based companion diagnostic for immunotherapy that outperforms tissue-based PD-L1 staining.
Pan-cancer mapping of single T cell profiles reveals a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity
Authors: Jerby-Arnon Livnat , Tooley Katherine , Escobar Giulia , Dandekar Gitanjali , Madi Asaf , Goldschmidt Ella , Lambden Conner , Rozenblatt-Rosen Orit , Anderson Ana C. , Regev Aviv 
Published: November 2021

AbstractUnleashing cytotoxic CD8+ T cells for effective cancer treatment requires understanding T cell states across different tumor microenvironments. Here, we developed an algorithm to recover both shared and tumor type specific programs and used it to analyze a scRNA-seq compendium of 38,852 CD8+ T cells from 141 patients spanning nine different human cancers. We uncovered a pan-cancer T cell dysfunction program that was predictive of clinical responses to immunotherapy and highlighted CXCR6 as a pan-cancer marker of dysfunctional T cells. In mouse models, CXCR6 increased following checkpoint blockade and was repressed by TCF1. Its ligand, CXCL16, was expressed primarily by myeloid cells, and was co-regulated with antigen presentation genes. CXCR6 deletion decreased Tox, CX3CR1, and Bcl2 expression, predisposing dysfunctional PD-1+Tim3+CD8+ T cells to apoptosis, and compromising tumor growth control. Our approach discovered a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity, revealing a new perspective on T cell dysfunction and new opportunities for modulating this cell state.
Examining the impact of external reference prices on seller price image dimensions and purchase intentions in pay what you want (PWYW)
Authors: Rai Shivam , Narwal Preeti 
Published: November 2021

PurposePay what you want (PWYW) is a participative pricing mechanism that permits customers complete freedom to choose prices. PWYW literature reports the influence of external reference price (ERP) on customers' price decisions and payments. The current research examines the influence of ERP presence, salience and understanding at the seller level by analysing customers' perceptions of seller price image dimensions and purchase intentions.Design/methodology/approachStudy 1 tests the impact of ERP presence and salience in controlled lab settings while Study 2 takes this investigation further by including the moderating effect of ERP understanding on seller price image dimensions and purchase intentions in online settings.FindingsResults illustrate the positive impact of ERP presence on all seller price image dimensions excluding the perceived price level. Perceived price fairness mediates the impact of ERP presence on perceived value. ERP salience positively impacts price processability. ERP presence and salience attached to it positively impact customers' purchase intentions through seller price image dimensions.Originality/valueThis is possibly the first paper to investigate the ERP effect on seller price image dimensions in a PWYW context that lacks fixed posted prices.
SCAFFOLDing all abilities into makerspaces: a design framework for universal, accessible and intersectionally inclusive making and learning
Authors: Seo JooYoung , Richard Gabriela T. 
Published: November 2021

PurposeIn response to the underexplored need for holistically inclusive makerspaces for learning, we put propose the “SCAFFOLD” framework, which considers equity, inclusion and accessibility in the design of spaces and activities for socioculturally diverse learners.Design/methodology/approachThis paper proposes a universal design (UD) framework that is intersectionally inclusive for learners with diverse needs in makerspaces and maker activities. This paper provides conjecture mapping to put forth theoretical and empirical arguments for the design of holistically inclusive makerspaces that consider gender equity and cultural inclusivity, as well as accessibility for diverse learners with divergent and unique abilities and dis/abilities.FindingsCombining related literature and three existing UD frameworks (i.e. UD, web accessibility and UD for learning) and prior research on equity and inclusivity in making, this paper proposes the integration of eight principles, which leverage individuals’ diverse abilities to become agentic makers: simplicity, collaboration, accessibility, flexibility, fail-safe, object-oriented, linkability and diversity.Research limitations/implicationsResearchers who have implemented conjecture maps (Leeet al., 2018) have found them to be useful for developing theory and learning designs grounded in research and practice. However, it should be noted that design research is iterative and contextual, and conjecture maps are effective in providing visibility and rigor, but are meant to be flexible and responsive to changes in context (Leeet al., 2018; Sandoval, 2014).Originality/valueThis paper provides practical guidelines and principles for researchers, educators, instructional designers and product developers to assess and redesign makerspaces and activities that are intersectionally and universally inclusive, equitable and accessible.
Molecular dynamics study on the mechanical and tribological properties of polyimide reinforced by lanthana
Authors: Cai Peng , Xu Chengpeng , Zheng Fei , Song Jingfu , Zhao Gai 
Published: November 2021

Purpose
The purpose of this paper is to investigate the effect of lanthana (La2O3) on the mechanical and tribological properties of polyimide (PI).

Design/methodology/approach
The mechanical and tribological properties of PI nanocomposites filled with La2O3 were studied by molecular dynamic simulations to explore the deep mechanisms from an atomic or molecular view.

Findings
The results showed that the hardness of the PI matrix increased after La2O3 modification with a decrease of 72.4% nanoindentation depth. Besides, the friction coefficient of PI decreased by 72.2% after filling La2O3, and the shear deformation was largely reduced under the same conditions. The adsorption effect of La2O3 on the PI molecular, which reduced the atomic relative concentration, velocity, interaction with counterpart Fe layer and the temperature rise in the frictional interface, contributed to the improvement of the mechanical and tribological performance.

Originality/value
This study reveals the friction and wear mechanism of PI composites filled with rare earth oxide at the nanoscale.
Analyzing the Internet financial market risk management using data mining and deep learning methods
Authors: Feng Ran , Qu Xiaoe 
Published: November 2021

PurposeTo identify and analyze the occurrence of Internet financial market risk, data mining technology is combined with deep learning to process and analyze. The market risk management of the Internet is to improve the management level of Internet financial risk, improve the policy of Internet financial supervision and promote the healthy development of Internet finance.Design/methodology/approachIn this exploration, data mining technology is combined with deep learning to mine the Internet financial data, warn the potential risks in the market and provide targeted risk management measures. Therefore, in this article, to improve the application ability of data mining in dealing with Internet financial risk management, the radial basis function (RBF) neural network algorithm optimized by ant colony optimization (ACO) is proposed.FindingsThe results show that the actual error of the ACO optimized RBF neural network is 0.249, which is 0.149 different from the target error, indicating that the optimized algorithm can make the calculation results more accurate. The fitting results of the RBF neural network and ACO optimized RBF neural network for nonlinear function are compared. Compared with the performance of other algorithms, the error of ACO optimized RBF neural network is 0.249, the running time is 2.212 s, and the number of iterations is 36, which is far less than the actual results of the other two algorithms.Originality/valueThe optimized algorithm has a better spatial mapping and generalization ability and can get higher accuracy in short-term training. Therefore, the ACO optimized RBF neural network algorithm designed in this exploration has a high accuracy for the prediction of Internet financial market risk.
Differential impacts of the US–China trade war and the outbreak of COVID-19 on Chinese air quality
Authors: Shahbaz Muhammad , Sinha Avik , Shah Muhammad Ibrahim 
Published: November 2021

PurposeOver the last couple of years, the Chinese manufacturing sector was affected by the onset of the US–China trade war and the outbreak of coronavirus disease 2019 (COVID-19). In such a scenario air quality in China has encountered a shock, and the impacts of these two incidents are unknown. In this study, the authors analyze the convergence of air quality in China in the presence of multiple structural breaks and how the impacts of these two events are different from each other.Design/methodology/approachIn order to assess the nature of shocks in the presence of multiple structural breaks, unit root tests with multiple structural breaks are employed.FindingsThe results reveal that air quality in China is showing the sign of convergence, and it is consistent across 18 provinces which are worst hit by the outbreak of COVID-19. In the presence of transitory shocks, the impact of COVID-19 outbreak is found to be higher, whereas the impact of the US–China trade war is found to be more persistent. Lastly, the outbreak of COVID-19 has been found to have more impact on pollutants with higher severity of health hazard.Originality/valueTo the best of the authors’ knowledge, this is the first study that contributes to the empirical literature in terms of investigating the convergence of overall air pollution and individual air pollutants taking COVID-19 and the trade war into account.
Tree mortality response to drought‐density interactions suggests opportunities to enhance drought resistance
Authors: Bradford John. B. , Shriver Robert K. , Robles Marcos D. , McCauley Lisa A. , Woolley Travis J. , Andrews Caitlin A. , Crimmins Michael , Bell David M. 
Published: November 2021

AbstractThe future of dry forests around the world is uncertain given predictions that rising temperatures and enhanced aridity will increase drought‐induced tree mortality. Using forest management and ecological restoration to reduce density and competition for water offers one of the few pathways that forests managers can potentially minimize drought‐induced tree mortality. Competition for water during drought leads to elevated tree mortality in dense stands, although the influence of density on heat‐induced stress and the durations of hot or dry conditions that most impact mortality remain unclear.Understanding how competition interacts with hot‐drought stress is essential to recognize how, where and how much reducing density can help sustain dry forests in a rapidly changing world. Here, we integrated repeat measurements of 28,881 ponderosa pine trees across the western US (2000–2017) with soil moisture estimates from a water balance model to examine how annual mortality responds to competition, temperature and soil moisture conditions.Tree mortality responded most strongly to basal area, and was elevated in places with high mean temperatures, unusually hot 7‐year high temperature anomalies, and unusually dry 8‐year low soil moisture anomalies. Mortality was also lower in places that experienced unusually wet 3‐year soil moisture anomalies between measurements. Importantly, we found that basal area interacts with temperature and soil moisture, exacerbating mortality during times of stress imposed by high temperature or low moisture.Synthesis and applications. Our results imply that a 50% reduction in forest basal area could reduce drought‐driven tree mortality by 20%–80%. The largest impacts of density reduction are seen in areas with high current basal area and places that experience high temperatures and/or severe multiyear droughts. These interactions between competition and drought are critical to understand past and future patterns of tree mortality in the context of climate change, and provide information for resource managers seeking to enhance dry forest drought resistance.