bluuebunny/crossref_metadata_2025_split huggingface dataset:
RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain
Authors: Magala Pearl , Klevit Rachel E. , Thomas Wendy E. , Sokurenko Evgeni V. , Stenkamp Ronald E. 
Published: October 2019

AbstractFimH is a bacterial adhesin protein located at the tip of Escherichia coli fimbria that functions to adhere bacteria to host cells. Thus, FimH is a critical factor in bacterial infections such as urinary tract infections and is of interest in drug development. It is also involved in vaccine development and as a model for understanding shear‐enhanced catch bond cell adhesion. To date, over 60 structures have been deposited in the Protein Data Bank showing interactions between FimH and mannose ligands, potential inhibitors, and other fimbrial proteins. In addition to providing insights about ligand recognition and fimbrial assembly, these structures provide insights into conformational changes in the two domains of FimH that are critical for its function. To gain further insights into these structural changes, we have superposed FimH's mannose binding lectin domain in all these structures and categorized the structures into five groups of lectin domain conformers using RMSD as a metric. Many structures also include the pilin domain, which anchors FimH to the fimbriae and regulates the conformation and function of the lectin domain. For these structures, we have also compared the relative orientations of the two domains. These structural analyses enhance our understanding of the conformational changes associated with FimH ligand binding and domain‐domain interactions, including its catch bond behavior through allosteric action of force in bacterial adhesion.
Extension of the Lanczos algorithm for simultaneous computation of multiple targeted singular vector sets
Authors: Ono Kosuke 
Published: October 2019

AbstractThis article discusses an extension of the singular vector (SV) method in the context of an initial perturbation generator for an ensemble prediction system (EPS). In general, multiple SVs targeted at different regions are computed in operational EPSs to extract growing modes with focus on different parts of the EPS domain. However, significant computational cost is associated with running all the procedures of the SV computations multiple times. In this study, the Lanczos algorithm used for SV computation was extended to allow simultaneous computation of multiple targeted SV sets. Algebraic calculations in the algorithm, such as orthonormalizations and eigenvalue problem resolution, are separately implemented for multiple “subdomains” incorporating different targeting areas, and SV sets are computed for individual subdomains. However, forward and backward linearized propagation runs through the whole domain, shared among the SV sets from all the subdomains. As such algebraic operation accounts for a relatively small part of all computation, the computational cost increment brought by the algorithm extension is also small in relation to single SV computations. For verifications, consistency between SVs produced with the original and extended algorithms was examined. Both SV sets spanned the same subspaces with similar linear growth rates, except those derived on subdomain boundaries, where SVs produced using the extended algorithm were truncated by the boundary. To avoid such truncation, it is necessary to set a subdomain large enough to cover the target area and its surrounding region. In this article, some applications of this algorithm in operational situations are suggested. Also, an application of subdomain to the wave‐number space is described.
Genetic characterization of Porcine circovirus type 2 from 2013 to 2018 in Shandong Province, China
Authors: Wang Shuo , Xin Changxun , Wu Xiaoyan , Shi Jianli , Peng Zhe , Sun Panpan , Wang Yan , Xu Shaojian , Yang Ying , Zhang Fan , Li Jun 
Published: October 2019

AbstractPCV2 belongs to the genus Circovirus, family Circoviridae, who is recognized as the causative agents of postweaning multisystemic wasting syndrome. Since being found to China in 2000, it has caused serious damage to the pig industry. In this study, we downloaded 40 PCV2 genome‐wide sequences uploaded to GenBank from 2013 to 2018 in Shandong Province, including 23 uploaded by our laboratory. Construction of a genome‐wide evolution tree using MEGA V5.0 software. Phylogenetic tree analysis indicated that the genotype of PCV2 in Shandong Province was: three genotypes coexisted (2a, 2b, 2d); among them, PCV2d has become the main genotype in the province due to its number and spread range. Amino acid sequence analysis of different genotypes of ORF2 showed that specific amino acid sites exist in different genotypes, with the most significant range of 81–160; different genotypes of PCV2 can be distinguished at the molecular level. This study found that due to the increase in infections of the PCV2d genotype in recent years, it may replace PCV2b as the dominant base in Shandong.
Effectiveness of combining microcurrent with resistance training in trained males
Authors: Naclerio Fernando , Seijo Marcos , Karsten Bettina , Brooker George , Carbone Leandro , Thirkell Jack , Larumbe-Zabala Eneko 
Published: October 2019

Abstract

Introduction
Microcurrent has been used to promote tissue healing after injury or to hasten muscle remodeling post exercise post exercise.

Purpose
To compare the effects of resistance training in combination with either, microcurrent or sham treatment, on-body composition and muscular architecture. Additionally, changes in performance and perceived delayed onset muscle soreness (DOMS) were determined.

Methods
Eighteen males (25.7 ± 7.6 years) completed an 8-week resistance training program involving 3 workouts per week (24 total sessions) wearing a microcurrent (MIC, n = 9) or a sham (SH, n = 9) device for 3-h post-workout or in the morning during non-training days. Measurements were conducted at pre and post intervention.

Results
Compared to baseline, both groups increased (p < 0.05) muscle thickness of the elbow flexors (MIC + 2.9 ± 1.4 mm; SH + 3.0 ± 2.4 mm), triceps brachialis (MIC + 4.3 ± 2.8 mm; SH + 2.7 ± 2.6 mm), vastus medialis (MIC + 1.5 ± 1.5 mm; SH + 0.9 ± 0.8 mm) and vastus lateralis (MIC + 6.8 ± 8.0 mm; SH + 3.2 ± 1.8 mm). Although both groups increased (p < 0.01) the pennation angle of vastus lateralis (MIC + 2.90° ± 0.95°; SH + 1.90° ± 1.35°, p < 0.01), the change measured in MIC was higher (p = 0.045) than that observed in SH. Furthermore, only MIC enlarged (p < 0.01) the pennation angle of brachialis (MIC + 1.93 ± 1.51). Both groups improved (p < 0.05) bench press strength and power but only MIC enhanced (p < 0.01) vertical jump height. At post intervention, only MIC decreased (p < 0.05) DOMS at 12-h, 24-h, and 48-h after performing an exercise-induced muscle soreness protocol.

Conclusion
A 3-h daily use of microcurrent maximized muscular architectural changes and attenuated DOMS with no added significant benefits on body composition and performance.
Modeling managed aquifer recharge processes in a highly heterogeneous, semi-confined aquifer system
Authors: Maples Stephen R. , Fogg Graham E. , Maxwell Reed M. 
Published: October 2019

Abstract
Widespread groundwater overdraft in alluvial aquifer systems like the Central Valley (CV) in California, USA, has increased interest in managed aquifer recharge (MAR). Like most clastic sedimentary basins, recharge to the productive semi-confined CV aquifer system remains a challenge due to the presence of nearly ubiquitous, multiple confining units (silt and clay) that limit recharge pathways. Previous studies suggest the presence of interconnected networks of coarse-texture sand and gravel deposits that bypass regional confining units over a small fraction of the CV near the American and Cosumnes rivers. Here, variably saturated infiltration and recharge processes were simulated across a domain that includes high-resolution representation of the heterogeneous alluvial geologic architecture in this area. Results show that recharge potential is highly dependent on subsurface geologic architecture, with a nearly 2 order-of-magnitude range of recharge across the domain. Where interconnected coarse-texture recharge pathways occur, results show that these features can (1) accommodate rapid, high-volume MAR and (2) propagate widespread and rapid pressure responses over multi-kilometer distances in the semi-confined aquifer system. For all MAR simulations, results show that the majority of MAR is accommodated by filling unsaturated-zone (UZ) pore volume. Results also show that coarse-texture UZ facies (where present) accommodate the majority of MAR volume during early time, but fine-texture facies ultimately accommodate the majority of the total MAR volume, even for coarse-dominated sites. These findings highlight the large variability of MAR potential across the landscape and demonstrate the importance of fine-texture facies for accommodating MAR in alluvial aquifer systems.
Constructing freshness: the vitality of wet markets in urban China
Authors: Zhong Shuru , Crang Mike , Zeng Guojun 
Published: October 2019

Abstract
Wet markets, a ‘traditional’ form of food retail, have maintained their popularity in urban China despite the rapid expansion of ‘modern’ supermarket chains. Their continued popularity rests in the freshness of their food. Chinese consumers regard freshness as the most important aspect of food they buy, but what constitutes ‘freshness’ in produce is not simply a given. Freshness is actively produced by a range of actors including wholesalers, vendors as well as consumers. The paper examines what fresh food means to consumers in the Chinese market. It argues that wet markets create a sense of freshness that resonates with this culinary culture through their sensoria, atmosphere, and trust between food vendors and consumers. Together these respond to desires for and reproduce criteria used to evaluate freshness. Within a fragmented food trade system, wet market vendors have an advantage in offering ‘freshness’ through their ability to connect various wholesalers, agencies, and middlemen, and shorten supply chains. The paper is based on participatory observation, a consumer survey and in-depth interviews of various stakeholders in southern China, especially Sanya in Hainan and Guangzhou in Guangdong. This study suggests that this cultural construction of freshness creates a niche for small-scale players and ‘traditional’ markets in an increasingly concentrated global food system.
Rankings or leagues or rankings on leagues? - Ranking in fair reference groups
Authors: Kosztyán Zsolt T. , Banász Zsuzsanna , Csányi Vivien V. , Telcs András 
Published: October 2019

AbstractThere are several well-known rankings of universities and higher education systems. Numerous recent studies question whether it is possible to compare universities and countries of different constitutions. These criticisms stand on solid ground. It is impossible to create a one-dimensional ordering that faithfully compares complex systems such as universities or even higher education systems. We would like to convince the reader that using well-chosen elements of a family of state-of-the-art data mining methods, namely, bi-clustering methods, can provide an informative picture of the relative positions of universities/higher education systems. Bi-clustering methods produce leagues of comparable entities alongside the indicators, which produce a similar grouping of them. Within leagues, partial rankings could be specified and furthermore can serve as a proper basis for benchmarking.
Assessment of natural groundwater physico-chemical properties in major industrial and residential locations of Lagos metropolis
Authors: Popoola Lekan Taofeek , Yusuff Adeyinka Sikiru , Aderibigbe Tajudeen Adejare 
Published: October 2019

Abstract
This study investigated groundwater quality collected from two industrial and residential locations in each of Lagos metropolis. Prescribed standard procedures of American Public Health Association were used to measure physico-chemical parameters of each of the groundwater samples which include pH, EC, DO, TDS, BOD, COD, anions (Cl−, NO3−, SO42−, PO43−) and heavy metals (Cu, Zn, Pb, Mn, Fe, Co, Cd and Cr). From laboratory analysis, measured physico-chemical parameters were within the permissible ranges specified by the WHO and NSDWQ except pH, TDS, EC, Pb, Mn and Fe for groundwater samples from industrial locations and pH, Pb, Mn and Fe for residential locations. Higher concentrations of TDS and EC reported for groundwater samples from industrial locations were attributed to heavy discharge of effluents from industrial treatment plants as well as dissolution of ionic heavy metals from industrial activities of heavy machines. Statistical Pearson’s correlation revealed physico-chemical parameters of water quality to be moderately and strongly correlated with one another at either p  < 0.05 or < 0.01.
Augmenting Intrinsic Fenton-Like Activities of MOF-Derived Catalysts via N-Molecule-Assisted Self-catalyzed Carbonization
Authors: Yang Chengdong , Zhou Mi , He Chao , Gao Yun , Li Shuang , Fan Xin , Lin Yi , Cheng Fei , Zhu Puxin , Cheng Chong 
Published: October 2019

Abstract
To overcome the ever-growing organic pollutions in the water system, abundant efforts have been dedicated to fabricating efficient Fenton-like carbon catalysts. However, the rational design of carbon catalysts with high intrinsic activity remains a long-term goal. Herein, we report a new N-molecule-assisted self-catalytic carbonization process in augmenting the intrinsic Fenton-like activity of metal–organic-framework-derived carbon hybrids. During carbonization, the N-molecules provide alkane/ammonia gases and the formed iron nanocrystals act as the in situ catalysts, which result in the elaborated formation of carbon nanotubes (in situ chemical vapor deposition from alkane/iron catalysts) and micro-/meso-porous structures (ammonia gas etching). The obtained catalysts exhibited with abundant Fe/Fe–Nx/pyridinic-N active species, micro-/meso-porous structures, and conductive carbon nanotubes. Consequently, the catalysts exhibit high efficiency toward the degradation of different organic pollutions, such as bisphenol A, methylene blue, and tetracycline. This study not only creates a new pathway for achieving highly active Fenton-like carbon catalysts but also takes a step toward the customized production of advanced carbon hybrids for diverse energy and environmental applications.
Recent Progress on Zinc-Ion Rechargeable Batteries
Authors: Xu Wangwang , Wang Ying 
Published: October 2019

Abstract
The increasing demands for environmentally friendly grid-scale electric energy storage devices with high energy density and low cost have stimulated the rapid development of various energy storage systems, due to the environmental pollution and energy crisis caused by traditional energy storage technologies. As one of the new and most promising alternative energy storage technologies, zinc-ion rechargeable batteries have recently received much attention owing to their high abundance of zinc in natural resources, intrinsic safety, and cost effectiveness, when compared with the popular, but unsafe and expensive lithium-ion batteries. In particular, the use of mild aqueous electrolytes in zinc-ion batteries (ZIBs) demonstrates high potential for portable electronic applications and large-scale energy storage systems. Moreover, the development of superior electrolyte operating at either high temperature or subzero condition is crucial for practical applications of ZIBs in harsh environments, such as aerospace, airplanes, or submarines. However, there are still many existing challenges that need to be resolved. This paper presents a timely review on recent progresses and challenges in various cathode materials and electrolytes (aqueous, organic, and solid-state electrolytes) in ZIBs. Design and synthesis of zinc-based anode materials and separators are also briefly discussed.
Association between edible mushroom intake and the prevalence of newly diagnosed non-alcoholic fatty liver disease: results from the Tianjin Chronic Low-Grade Systemic Inflammation and Health Cohort Study in China
Authors: Zhang Shunming , Gu Yeqing , Lu Min , Fu Jingzhu , Zhang Qing , Liu Li , Meng Ge , Yao Zhanxin , Wu Hongmei , Bao Xue , Sun Shaomei , Wang Xing , Zhou Ming , Jia Qiyu , Song Kun , Wu Yuntang , Niu Kaijun 
Published: October 2019

AbstractAnimal studies have suggested that mushroom intake can alleviate non-alcoholic fatty liver disease (NAFLD) due to its anti-inflammatory and antioxidant properties. However, the association between mushroom intake and NAFLD is unknown in humans. We aimed to investigate the association of mushroom intake with NAFLD among Chinese adults. This is a cross-sectional study of 24 236 adults (mean (standard deviation) age: 40·7 (sd 11·9) years; 11 394 men (47·0 %)). Mushroom intake was assessed via a validated FFQ. Newly diagnosed NAFLD was identified based on the results of annual health examinations, including ultrasound findings and a self-reported history of the disease. Multiple logistic models were used to examine the association between mushroom intake and NAFLD. The prevalence of newly diagnosed NAFLD was 19·0 %. Compared with those consuming mushrooms less frequently (≤1 time/week), the fully adjusted OR of newly diagnosed NAFLD were 0·95 (95 % CI 0·86, 1·05) for those consuming 2–3 times/week and 0·76 (95 % CI 0·63, 0·92) for those consuming ≥4 times/week (Pfor trend = 0·01). The inverse association was consistent in subgroups defined by age, sex and BMI. In conclusion, higher mushroom intake was significantly associated with lower prevalence of NAFLD among Chinese adults. Future research is required to understand the causal association between mushroom intake and NAFLD.
Speed Adaptation in Learning from Demonstration through Latent Space Formulation
Authors: Koskinopoulou Maria , Maniadakis Michail , Trahanias Panos 
Published: October 2019

SUMMARYPerforming actions in a timely manner is an indispensable aspect in everyday human activities. Accordingly, it has to be present in robotic systems if they are going to seamlessly interact with humans. The current work addresses the problem of learning both the spatial and temporal characteristics of human motions from observation. We formulate learning as a mapping between two worlds (the observed and the action ones). This mapping is realized via an abstract intermediate representation termed “Latent Space.” Learned actions can be subsequently invoked in the context of more complex human–robot interaction (HRI) scenarios. Unlike previous learning from demonstration (LfD) methods that cope only with the spatial features of an action, the formulated scheme effectively encompasses spatial and temporal aspects. Learned actions are reproduced under the high-level control of a time-informed task planner. During the implementation of the studied scenarios, temporal and physical constraints may impose speed adaptations in the reproduced actions. The employed latent space representation readily supports such variations, giving rise to novel actions in the temporal domain. Experimental results demonstrate the effectiveness of the proposed scheme in the implementation of HRI scenarios. Finally, a set of well-defined evaluation metrics are introduced to assess the validity of the proposed approach considering the temporal and spatial consistency of the reproduced behaviors.
Punishment and disagreement in the state of nature
Authors: Barrett Jacob 
Published: October 2019

AbstractHobbes believed that the state of nature would be a war of all against all. Locke denied this, but acknowledged that in the absence of government, peace is insecure. In this paper, I analyse both accounts of the state of nature through the lens of classical and experimental game theory, drawing especially on evidence concerning the effects of punishment in public goods games. My analysis suggests that we need government not to keep wicked or relentlessly self-interested individuals in line, but rather to maintain peace among those who disagree about morality.
Ultra-processed foods, incident overweight and obesity, and longitudinal changes in weight and waist circumference: the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)
Authors: Canhada Scheine Leite , Luft Vivian Cristine , Giatti Luana , Duncan Bruce Bartholow , Chor Dora , Fonseca Maria de Jesus M da , Matos Sheila Maria Alvim , Molina Maria del Carmen Bisi , Barreto Sandhi Maria , Levy Renata Bertazzi , Schmidt Maria Inês 
Published: October 2019

AbstractObjective:To evaluate the association of ultra-processed food (UPF) consumption with gains in weight and waist circumference, and incident overweight/obesity, in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) cohort.Design:We applied FFQ at baseline and categorized energy intake by degree of processing using the NOVA classification. Height, weight and waist circumference were measured at baseline and after a mean 3·8-year follow-up. We assessed associations, through Poisson regression with robust variance, of UPF consumption with large weight gain (1·68 kg/year) and large waist gain (2·42 cm/year), both being defined as ≥90th percentile in the cohort, and with incident overweight/obesity.Setting:Brazil.Participants:Civil servants of Brazilian public academic institutions in six cities (n11 827), aged 35–74 years at baseline (2008–2010).Results:UPF provided a mean 24·6 (sd9·6) % of ingested energy. After adjustment for smoking, physical activity, adiposity and other factors, fourth (>30·8 %)v. first (<17·8 %) quartile of UPF consumption was associated (relative risk (95 % CI)) with 27 and 33 % greater risk of large weight and waist gains (1·27 (1·07, 1·50) and 1·33 (1·12, 1·58)), respectively. Similarly, those in the fourth consumption quartile presented 20 % greater risk (1·20 (1·03, 1·40)) of incident overweight/obesity and 2 % greater risk (1·02; (0·85, 1·21)) of incident obesity. Approximately 15 % of cases of large weight and waist gains and of incident overweight/obesity could be attributed to consumption of >17·8 % of energy as UPF.Conclusions:Greater UPF consumption predicts large gains in overall and central adiposity and may contribute to the inexorable rise in obesity seen worldwide.
Genetic and Environmental Influences on Cognitive Abilities in Extreme Poverty
Authors: Hur Yoon-Mi , Bates Timothy 
Published: October 2019

AbstractTo improve global human capital, an understanding of the interplay of endowment across the full range of socioeconomic status (SES) is needed. Relevant data, however, are absent in the nations with the most abject poverty (Tucker-Drob & Bates, 2016), where the lowest heritability and strong effects of SES are predicted. Here we report the first study of biopsychosocial gene–environment interaction in extreme poverty. In a sub-Saharan sample of early teenage twins (N = 3192), we observed substantial (~30–40%) genetic influence on cognitive abilities. Surprisingly, shared environmental influences were similar to those found in adolescents growing in Western affluent countries (25–28%). G × SES moderation was estimated at aˋ = .06 (p = .355). Family chaos did not moderate genetic effects but did moderate shared environment influence. Heritability of cognitive abilities in extreme poverty appears comparable to Western data. Reduced family chaos may be a modifiable factor promoting cognitive development.