bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tipping points and multiple drivers in changing aquatic ecosystems: A review of experimental studies
Authors: Carrier‐Belleau Charlotte , Pascal Ludovic , Nozais Christian , Archambault Philippe 
Published: November 2021

AbstractNatural ecosystems are experiencing unprecedented rates of change due to anthropogenic activities and global change, leading to either gradual changes in a given response or tipping points. While the tipping point concept has been tested in an array of habitats since the 1960s, the spatiotemporal superposition of multiple drivers in different ecosystems needs to be considered when investigating the response of species, communities, populations, and ecosystems along environmental gradients. Here, we (1) develop a historical and current perspective of tipping point studies in terrestrial, freshwater, and marine ecological systems; (2) portray the research effort in different freshwater and marine habitats; and (3) explore the results of experimental studies focusing on tipping points measured at the individual, communities, ecosystem level, as well as ecosystem functions and services in a context of single and multiple stressors. The number of studies mentioning the concept of tipping points increases every year, but very few studies have specific objective to identify them. Even fewer studies consider how the addition of another stressor into an ecosystem may alter a tipping point. In addition, many studies investigated multiple responses, but only one‐fourth (7 out of 28) of them concentrate their effort on multiple biological or ecological levels of complexity. This review allowed us to identify shortcomings in this research field and propose ways to make this ecological concept anew.
Weakly binary expansions of dense meet‐trees
Authors: Mennuni Rosario 
Published: November 2021

AbstractWe compute the domination monoid in the theory of dense meet‐trees. In order to show that this monoid is well‐defined, we prove weak binarity of and, more generally, of certain expansions of it by binary relations on sets of open cones, a special case being the theory from [7]. We then describe the domination monoids of such expansions in terms of those of the expanding relations.
Comparison of swab types for collection and analysis of microorganisms
Authors: Wise Natalie M. , Wagner Sarah J. , Worst Travis J. , Sprague Jon E. , Oechsle Crystal M. 
Published: November 2021

AbstractThe human microbiome has begun to emerge as a potential forensic tool, with varied applications ranging from unique identification to investigative leads that link individuals and/or locations. The relative abundance of the combined DNA of the microbiome, compared to human nuclear DNA, may expand potential sources of biological evidence, especially in cases with transfer or low‐copy number DNA samples. This work sought to determine the optimal swab type for the collection and analysis of microorganisms. A bacterium (Proteus mirabilis) was deposited by pipette onto four swab types (cotton, flocked, dental applicators, and dissolvable), and extraction and real‐time PCR quantitation of the bacterial DNA were performed, which allowed for absolute microbial DNA recovery and comparison of yields across the four sampling substrates. Flocked swabs had the highest yield (~1240 ng) compared to the cotton swabs (~184 ng), dental applicators (~533 ng), and dissolvable swabs (~430 ng). The collection efficiency was further evaluated for cotton and flocked swabs using dried microbial samples spotted onto non‐porous surfaces (treated wood, glass, plastic, and tile). Flocked swabs performed consistently better across wood, glass, and tile, but showed decreased recovery from plastic. The cotton swabs failed in the recovery of P. mirabilis DNA across all surfaces. Knowing the appropriate sampling substrate will be useful as others continue to investigate the use of the microbiome as a forensics tool.
ON‐rep‐seq as a rapid and cost‐effective alternative to whole‐genome sequencing for species‐level identification and strain‐level discrimination of Listeria monocytogenes contamination in a salmon processing plant
Authors: Thomassen Gunn Merethe Bjørge , Krych Lukasz , Knøchel Susanne , Mehli Lisbeth 
Published: November 2021

AbstractIdentification, source tracking, and surveillance of food pathogens are crucial factors for the food‐producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species‐specific detection by PCR to sequencing‐based methods, whole‐genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost‐effective, and more user‐friendly methods. A newly developed method, ON‐rep‐seq, combines the classical rep‐PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON‐rep‐seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain‐level discriminatory power of ON‐rep‐seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n = 15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON‐rep‐seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON‐rep‐seq may serve as a primary screening method alternative to WGS for identification and strain‐level differentiation for surveillance of potential pathogens in a food‐producing environment.
MicroRNA‐519d‐3p antagonizes osteosarcoma resistance against cisplatin by targeting PD‐L1
Authors: Wang Jing , Zhang Zhenjun , Qiu Chuang , Wang Jiashi 
Published: November 2021

AbstractAccumulating evidence indicates that a ligand of programmed cell death receptor‐1 (PD‐L1) participates in the progression and recurrence of multiple malignancies, including osteosarcoma. Nevertheless, the role of PD‐L1 in chemoresistance development is not fully understood. In the current study, we aim to clarify the interaction of miR‐519d‐3p and PD‐L1 in the development of cisplatin resistance. Immunohistochemistry, quantitative reverse‐transcription polymerase reaction, and Western blot were used to evaluate PD‐L1 expression. MTT and transwell migration assays were used to measure cell growth and motility, respectively. ENCORI, miRCode, and miRDB databases were recruited to predict candidate miRNAs targeting PD‐L1. The binding sequences of miR‐519d‐3p and PD‐L1 3ʹ untranslated region were identified by dual‐luciferase reporter and RNA immunoprecipitation assays. Flow cytometric analysis was conducted to measure the cycle distribution and cell apoptosis. Metastatic mouse models were generated with cisplatin‐resistant sublines by intravenous injection. We found that PD‐L1 expression was positively correlated to cisplatin resistance and metastasis, whereas miR‐519d‐3p expression was reduced in cisplatin‐resistant specimens and was negatively correlated to cisplatin resistance and metastasis of osteosarcoma. We demonstrated that miR‐519d‐3p overexpression reversed cisplatin resistance, induced G1/S phase arrest and apoptosis. In addition, we proved that miR‐519d‐3p inhibited lung metastasis by establishing cisplatin‐resistant MG63 metastatic xenograft models. The present findings suggest that miR‐519d‐3p/PD‐L1 axis is a novel signaling pathway contributing to cisplatin resistance. Our study provides new clues for curing refractory osteosarcoma beyond immune checkpoint inhibitors.
Effects of Emulsifiers on an In vitro Model of Intestinal Epithelial Tight Junctions and the Transport of Food Allergens
Authors: Khuda Sefat E , Nguyen Ann V. , Sharma Girdhari M. , Alam Mohammad S. , Balan Kannan V. , Williams Kristina M. 
Published: November 2021

ScopeCertain food emulsifiers may interfere with gut barrier function in ways correlating to increased exposure to allergens. Understanding the consequences of interactions between these food ingredients and the intestinal epithelium is important for evaluating allergen dose exposure characteristics.Methods and ResultsThis study challenged Caco‐2 cell monolayers, an in vitro model of human intestinal epithelial tight junctions with synthetic polysorbate‐80 or natural lecithin alone, or in combination with known allergens (egg proteins: ovalbumin, ovomucoid, and ovotransferrin; and a synthetic form of galactose‐alpha‐1,3‐galactose [alpha‐gal], an allergen of increasing concern). For most doses of individual emulsifiers and allergens, >90% cell viability and <15% cytotoxicity are observed; however, toxicity increased at a 0.5% concentration of emulsifiers. At low cytotoxic concentration (0.2%), only polysorbate‐80 treatment reduced monolayer integrity (≈20%) with increased lucifer yellow passage. Dose‐related differences in expression of tight junction‐associated genes and occludin protein are observed with emulsifier treatments. The transport of all tested allergens across the cell monolayers, excluding ovotransferrin, nearly doubled in the presence of 0.2% polysorbate‐80 compared to lecithin and untreated control.ConclusionBy modulating paracellular permeability, polysorbate‐80 may enhance absorption of allergens in a size‐dependent manner.
Branch‐and‐price for energy optimization in multi‐hop wireless sensor networks
Authors: Xu Liding , Haddad Vanier Sonia 
Published: November 2021

AbstractWireless sensor networks (WSNs) are widely deployed to support transmissions of the huge data emitted by heterogeneous connected devices. The quality of service (QoS) and energy requirements in WSNs are dramatically increasing and becoming challenging issues. Integrating network coding, in the data transmission process, leads to reduced energy consumption and improved QoS. In this work, we study the problem of energy efficiency in multi‐hop WSNs, namely wireless unsplittable multi‐commodity flow with network coding (wUMCFC). We propose mixed‐integer programming formulations of the wUMCFC problem, and we implement an open source solver wUMCFC based on the branch‐and‐price algorithm. To the best of our knowledge, this work is the first study of the wUMCFC problem by mathematical programming tools. We perform a computational study on realistic instances with an analysis of the performance of the proposed algorithm. The computational results show the efficiency of the network coding and provide important information for strategic decisions on routing policies and network management
https://github.com/lidingxu/wUMCFC.
Efficient and robust numerical treatment of a gradient‐enhanced damage model at large deformations
Authors: Junker Philipp , Riesselmann Johannes , Balzani Daniel 
Published: November 2021

AbstractThe modeling of damage processes in materials constitutes an ill‐posed mathematical problem which manifests in mesh‐dependent finite element results. The loss of ellipticity of the discrete system of equations is counteracted by regularization schemes of which the gradient enhancement of the strain energy density is often used. In this contribution, we present an extension of the efficient numerical treatment, which has been proposed by Junker et al. in 2019, to materials that are subjected to large deformations. Along with the model derivation, we present a technique for element erosion in the case of severely damaged materials. Efficiency and robustness of our approach is demonstrated by two numerical examples including snapback and springback phenomena.
A study to introduce National Early Warning Scores (NEWS) in care homes: Influence on decision‐making and referral processes
Authors: Hodgson Philip , Greaves Jane , Cook Glenda , Fraser Angela , Bainbridge Lesley 
Published: November 2021

AbstractAimEarly warning scores are commonly used in hospital settings, but little is known about their use in care homes. This study aimed to evaluate the impacts of National Early Warning Scores alongside other measures in this setting.DesignConvergent parallel design.MethodsQuantitative data from 276 care home residents from four care homes were used to analyse the relationship between National Early Warning Scores score, resident outcome and functional daily living (Barthel ADL (Barthel Index for Activities of Daily Living)) and Rockwood (frailty). Interviews with care home staff (N = 13) and care practitioners (N = 4) were used to provide qualitative data.ResultsA statistically significant link between National Early Warning Scores (p = .000) and Barthel ADL (p = .013) score and hospital admissions was found, while links with Rockwood were insignificant (p = .551). Care home staff reported many benefits of National Early Warning Scores, including improved communication, improved decision‐making and role empowerment. Although useful, due to the complexity of the resident population's existing health conditions, National Early Warning Scores alone could not act as a diagnostic tool.
Bullying bystanders and emotional school engagement: The roles of rumination and depression
Authors: Dorio Nicole B. , Demaray Michelle K. , Riffle Logan N. 
Published: November 2021

AbstractIt is important to understand the mechanisms behind student academic engagement, as engagement in school is associated with a host of positive outcomes. As children mature, their peers become more important compared to adults in regard to their emotional engagement in school. Thus, this study sought to examine an aspect of peer relations, bullying‐related behavior, and its associations with emotional engagement in school. Additionally, this study aimed to examine the potential mediating roles of depression and rumination in the association between bystander role behaviors and emotional school engagement. With a diathesis‐stress theoretical foundation, it was hypothesized that low emotional school engagement would result from a combination of witnessing bullying and experiencing rumination and/or depression symptoms. Bystander behavior has been studied significantly less compared to bully‐ and victim‐role behaviors, despite the significant role that bystanders can play in bullying scenarios. There is a gap in the literature regarding how bystanders' behaviors in bullying situations are associated with emotional engagement in school. Further, the role(s) of rumination and depression have not been studied within these associations. The current study utilized structural equation modeling as well as double mediation analyses to investigate the associations between bystander role behaviors (assisting, defending, and outsider behaviors) and emotional engagement in school and to determine if those associations are mediated by rumination and/or depression. From a sample of 847 middle school students (47.1% female), results suggested a significant indirect effect of rumination and depression on emotional school engagement for defending and outsider behaviors, but not assisting behaviors. Additional results and implications will be discussed.
Structural empirical model of personal positive youth development, parenting, and school climate
Authors: Balaguer Álvaro , Benítez Edgar , de la Fuente Jesús , Osorio Alfonso 
Published: November 2021

AbstractThis study tested an empirical model of the relationship between Personal Positive Youth Development (PPYD) and two contextual factors: Positive Parenting (PP), and Perception of the Climate and Functioning of the School (PcfS). The hypothesis tested was that a positive relationship with parents and a positive perception of the school will contribute to the prediction of PPYD. The sample was composed of 1507 adolescents recruited in 10 Spanish schools who were aged between 12 and 18 years and 52% were female. PPYD was evaluated through Dispositional optimism, Self‐competence, and Sense of coherence. PP was evaluated through Affect and communication, Autonomy granting, Humor, and Self‐disclosure. PcfS was evaluated through School climate, School bonds, Clarity of rules and values, and Empowerment. Previous reliability and validity analyses of the constructs were carried out, and correlational analyses and structural predictions were made. The results show that both PP and PcfS were associated with better scores in PPYD. Also, a positive correlation between those two contextual factors was found. Implications for applied research are discussed.
Digital policy in European countries from the perspective of the Digital Economy and Society Index
Authors: Liu Tze‐Chang 
Published: November 2021

AbstractThe concept of digital economy has gained currency in recent years and has caught the attention of policymakers and the public. This study uses the 2017 Digital Economy and Society Index indicators—connectivity, human capital, use of Internet services, integration of digital technology, and digital public services—to determine the digital policy performance of various European countries. It uses the co‐plot method to visualize and classify countries based on their correlations with similar variables. The top‐performing European Union (EU) countries have strong correlations with at least one of these indicators. By ranking these countries in this way, policymakers can ascertain their development levels and make changes to infrastructure, human resources, and regulations to develop their digital economy.
Boosting the analysis of protein interfaces with multiple interface string alignments: Illustration on the spikes of coronaviruses
Authors: Béreux Stéphane , Delmas Bernard , Cazals Frédéric 
Published: November 2021

AbstractWe introduce multiple interface string alignment (MISA), a visualization tool to display coherently various sequence and structure based statistics at protein–protein interfaces (SSE elements, buried surface area, , B factor values, etc). The amino acids supporting these annotations are obtained from Voronoi interface models. The benefit of MISA is to collate annotated sequences of (homologous) chains found in different biological contexts, that is, bound with different partners or unbound. The aggregated views MISA/SSE, MISA/BSA, MISA/ΔASA, and so forth, make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. As such, they should prove of key relevance for knowledge‐based annotations of protein databases such as the Protein Data Bank. Illustrations are provided on the receptor binding domain of coronaviruses, in complex with their cognate partner or (neutralizing) antibodies. MISA computed with a minimal number of structures complement and enrich findings previously reported. The corresponding package is available from the Structural Bioinformatics Library (http://sbl.inria.frand https://sbl.inria.fr/doc/Multiple_interface_string_alignment-user-manual.html).
Understanding London's summertime cloud cover
Authors: Theeuwes Natalie E. , Boutle Ian A. , Clark Peter A. , Grimmond Sue 
Published: November 2021

AbstractCities are a source of complex land–atmosphere interactions. Spatial differences in the energy balance and enhanced surface roughness interact with the atmosphere to alter clouds and precipitation. Here, we explore how London (UK) alters cloud formation during the spring and summer. The Met Office's high‐resolution operational forecasts predict enhanced cloud cover over the city, as found in observations, but underpredicts the intensity. During low wind speeds, cloud enhancement over the city is strongest and linked to an urban‐induced thermal circulation. These circulations advect moist air from the city edge inwards, transporting it upwards with a large moisture convergence over the urban area. At around 1,000 m above the surface, the turbulent moisture flux takes over the moisture transport to the cloud layer. A relative humidity budget shows the moisture flux in the upper boundary layer to be the largest contribution to the urban–rural differences in relative humidity.
A liquidity crunch in an endogenous growth model with human capital
Authors: Salas Sergio 
Published: November 2021

AbstractThere is by now reasonable evidence that supports the notion of a trend break in the U.S. GDP since the Great Recession. To explain this phenomenon, I construct a version of the Lucas endogenous growth model, amplified with financial frictions and financial disruptions in the firms' sector. I then show how a transitory liquidity crunch is capable, at least qualitatively, of producing a similar pattern of a persistent downward shift in the GDP trend as one could infer happened in the United States since 2008. The main mechanism by which such a result is found relies on workers' decisions on providing labor to firms versus accumulating human capital. I show that a transitory liquidity crunch reduces the demand of labor. Workers anticipating a phase of depressed wages make the decision of accumulating more human capital in the short run, thereby reducing labor supply to firms. In the long run, however, incentivized by a strong recovery, workers decrease human capital accumulation and increase labor supply. Under plausible parameterizations of the model, this situation produces a net effect of a decrease in overall productivity that permanently reduces the trend at which the economy was growing prior to the crisis.
Preparation, Structure, and Properties of Enzymatically‐Hydrolyzed Starch for Slowing Down the Retrogradation of High Starchy Foods
Authors: Xie Jiating , Wei Siwen , Xu Xueming , Xu Dan , Jin Yamei , Yang Na , Wu Fengfeng 
Published: November 2021

AbstractAmylase represents a green and healthy method that can be used to inhibit retrogradation of starch and high starchy foods. In this study, glutinous rice starch is hydrolyzed using α‐amylase or β‐amylase at different dextrose equivalent (DE) values to investigate the effect of enzymatically‐hydrolyzed glutinous rice starch (EGS) on the anti‐retrogradation of rice cakes. The latter's hardness shows that EGS successfully slowed down the retrogradation of rice cakes with this effect being dependent on the type of amylase and DE value. The structure and physicochemical characteristics of different EGS are determined to identify the reasons for their different anti‐retrogradation effects. It is found that with increasing DE values, molecular weight decreased but molecular structural differences increased, with both effects influencing the properties of EGS. Similarly, decreased swelling power and viscosity, and increased solubility affects the texture of rice cakes while decreased retrogradation enthalpy and crystallinity indicates that EGS can retard the retrogradation process. Overall, there are significant differences in structure and physicochemical properties of EGS that are hydrolyzed by α‐amylase or β‐amylase. Since the production of enzymatically‐hydrolyzed starch can be standardized, it is feasible for rice cake and other high starchy foods to become modern industrially‐made convenience foods.