bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative modeling of protein‐protein interactions with pyDock for the new docking challenges
Authors: Rosell Mireia , Rodríguez‐Lumbreras Luis A. , Romero‐Durana Miguel , Jiménez‐García Brian , Díaz Lucía , Fernández‐Recio Juan 
Published: November 2019

AbstractThe seventh CAPRI edition imposed new challenges to the modeling of protein‐protein complexes, such as multimeric oligomerization, protein‐peptide, and protein‐oligosaccharide interactions. Many of the proposed targets needed the efficient integration of rigid‐body docking, template‐based modeling, flexible optimization, multiparametric scoring, and experimental restraints. This was especially relevant for the multimolecular assemblies proposed in the CASP12‐CAPRI37 and CASP13‐CAPRI46 joint rounds, which were described and evaluated elsewhere. Focusing on the purely CAPRI targets of this edition (rounds 38‐45), we have participated in all 17 assessed targets (considering heteromeric and homomeric interfaces in T125 as two separate targets) both as predictors and as scorers, by using integrative modeling based on our docking and scoring approaches: pyDock, IRaPPA, and LightDock. In the protein‐protein and protein‐peptide targets, we have also participated with our webserver (pyDockWeb). On these 17 CAPRI targets, we submitted acceptable models (or better) within our top 10 models for 10 targets as predictors, 13 targets as scorers, and 4 targets as servers. In summary, our participation in this CAPRI edition confirmed the capabilities of pyDock for the scoring of docking models, increasingly used within the context of integrative modeling of protein interactions and multimeric assemblies.
Identification of repurposable drugs with beneficial effects on glucose control in type 2 diabetes using machine learning
Authors: Koren Gideon , Nordon Galia , Radinsky Kira , Shalev Varda 
Published: November 2019

AbstractDespite effective medications, rates of uncontrolled glucose levels in type 2 diabetes remain high. We aimed to test the utility of machine learning applied to big data in identifying the potential role of concomitant drugs not taken for diabetes which may contribute to lowering blood glucose. Success in controlling blood glucose was defined as achieving HgA1c levels < 6.5% after 90‐365 days following diagnosis and initiating treatment. Among numerous concomitant drugs taken by type 2 diabetic patients, alpha 1 (α1)‐adrenoceptor antagonist drugs were the only group of medications that significantly improved the success rate of glucose control. Searching the published literature, this effect of α1‐adrenoceptor antagonists has been shown in animal models, where this class of medications appears to induce insulin secretion. In conclusion, machine learning of big data is a novel method to identify effective antidiabetic effects for potential repurposable medications already on the market for other indications. Because these α1‐adrenoceptor antagonists are widely used in men for treating benign prostate hyperplasia (BPH) at age groups exhibiting increased rates of type 2 diabetes, this finding is of potential clinical significance.
Hierarchical Composite of Rose‐Like VS2@S/N‐Doped Carbon with Expanded (001) Planes for Superior Li‐Ion Storage
Authors: Yang Wenjuan , Luo Ningjing , Zheng Cheng , Huang Shuping , Wei Mingdeng 
Published: November 2019

AbstractIn the present work, a hierarchical composite of rose‐like VS2@S/N‐doped carbon (VS2@SNC) with expanded (001) planes is successfully fabricated through a facile synthetic route. Notably, the d‐spacing of (001) planes is expanded to 0.92 nm, which is proved to dramatically reduce the energy barrier for Li+ diffusion in the composite of VS2@SNC by density functional theory calculation. On the other hand, the S/N‐doped carbon in the composite greatly promotes the electrical conductivity and enhances the structural stability. In addition, the hierarchical structure of VS2@SNC facilitates rapid electrolyte diffusion and increases the contact area between the electrode and electrolyte simultaneously. Benefiting from the merits mentioned above, the VS2@SNC electrode exhibits excellent electrochemical properties, such as a large reversible capacity of 971.6 mA h g−1 at 0.2 A g−1, an extremely high rate capability of 772.1 mA h g−1 at 10 A g−1, and a remarkable cycling stability up to 600 cycles at 8 A g−1 with a capacity of 684.5 mA h g−1, making it a promising candidate as an anode material for lithium‐ion batteries.
Designing sustainably agile and resilient organizations
Authors: Holbeche Linda 
Published: November 2019

AbstractThis article proposes that so powerful are the various forces for change in the business environment, in particular technological advances, that organizations must develop their adaptive capability—or agility—if they are to survive and thrive. An agile organization is one that can intelligently and proactively seize opportunities and react to threats and make timely, effective, sustainable changes that generate competitive advantage and give them some leverage in the marketplace or in their ecosystem. Yet scaling up for agility remains difficult, not least because the quest for agility calls into question organizational paradigms of various kinds—strategy, change management, the nature of leadership, and organizational design. The author provides a practitioner perspective on both the difficulties and the possibilities of developing organizational agility and proposes an adaptive approach to organization design and development that may offer a way forward for organizations wishing to become more agile.
A “system dynamics perspective” of bioenergy governance and local, sustainable development
Authors: Cavicchi Bianca 
Published: November 2019

AbstractThis study investigates the governance of bioenergy systems (BESs) and how it influences the bioenergy policy process and local sustainable development. The study compares the BES in Emilia Romagna and Hedmark. At first, bioenergy was expected to mitigate climate change and to tackle the crisis of the primary sectors and related industries. However, bioenergy policies were not equipped to address cross‐sectoral and multilevel issues. Therefore, they failed to secure the local, sustainable development. Critical weaknesses lie in BES governance. Actors' discourses, rules, and power issues form a complex structure that influences the bioenergy policy process and its outcomes. The study relies on systems thinking and system dynamics, and the pathways approach. It uses the system archetypes to investigate the bioenergy policy feedback dynamics and how to leverage local, sustainable development. Results show that power relations and social opposition are critical to a policy change that best secures local, sustainable development.
Chemical activation of the Piezo1 channel drives mesenchymal stem cell migration via inducing ATP release and activation of P2 receptor purinergic signaling
Authors: Mousawi Fatema , Peng Hongsen , Li Jing , Ponnambalam Sreenivasan , Roger Sébastien , Zhao Hucheng , Yang Xuebin , Jiang Lin-Hua 
Published: November 2019

AbstractIn this study, we examined the Ca2+-permeable Piezo1 channel, a newly identified mechanosensing ion channel, in human dental pulp-derived mesenchymal stem cells (MSCs) and hypothesized that activation of the Piezo1 channel regulates MSC migration via inducing ATP release and activation of the P2 receptor purinergic signaling. The Piezo1 mRNA and protein were readily detected in hDP-MSCs from multiple donors and, consistently, brief exposure to Yoda1, the Piezo1 channel-specific activator, elevated intracellular Ca2+ concentration. Yoda1-induced Ca2+ response was inhibited by ruthenium red or GsMTx4, two Piezo1 channel inhibitors, and also by Piezo1-specific siRNA. Brief exposure to Yoda1 also induced ATP release. Persistent exposure to Yoda1 stimulated MSC migration, which was suppressed by Piezo1-specific siRNA, and also prevented by apyrase, an ATP scavenger, or PPADS, a P2 generic antagonist. Furthermore, stimulation of MSC migration induced by Yoda1 as well as ATP was suppressed by PF431396, a PYK2 kinase inhibitor, or U0126, an inhibitor of the mitogen-activated protein kinase MEK/ERK signaling pathway. Collectively, these results suggest that activation of the Piezo1 channel stimulates MSC migration via inducing ATP release and subsequent activation of the P2 receptor purinergic signaling and downstream PYK2 and MEK/ERK signaling pathways, thus revealing novel insights into the molecular and signaling mechanisms regulating MSC migration. Such findings provide useful information for evolving a full understanding of MSC migration and homing and developing strategies to improve MSC-based translational applications.
Evaluating changes in salivary oxytocin and cortisol following positive reinforcement training in two adult male western lowland gorillas (Gorilla gorilla gorilla)
Authors: Leeds Austin , Good Julie , Schook Mandi W. , Dennis Patricia M. , Stoinski Tara S. , Willis Mark A. , Lukas Kristen E. 
Published: November 2019

AbstractPositive reinforcement training (PRT) is associated with increases in species‐typical behavior and decreases in stereotypic and abnormal behavior in participating animals. Physiological changes following PRT, for example, increases in oxytocin (OXT) and/or decreases in cortisol (CORT), may facilitate these behavioral changes. This study evaluated salivary OXT and salivary CORT concentrations in two adult male western lowland gorillas (Gorilla gorilla gorilla) following PRT with their primary animal care staff. Following PRT, no change in OXT was observed. CORT decreased in one subject following PRT. Changes in endogenous OXT are related to affiliative interactions and interact with strongly bonded conspecifics. PRT may not activate the oxytocinergic system because PRT is not a species‐specific affiliative interaction and/or animal care staff are not viewed as conspecifics. Regardless, PRT may still be viewed as a positive interaction resulting in stress reduction via a decrease in CORT. Relationships are unique, thus these results only apply to these two gorillas and one animal caregiver. Larger population‐level studies are needed to understand overall trends in human–animal interactions, and ultimately human–animal relationships. Further evaluation of physiological changes following human–animal interactions should be informative for understanding the human–animal relationship in zoos.
Graded quivers, generalized dimer models and toric geometry
Authors: Franco Sebastían , Hasan Azeem 
Published: November 2019

Abstract
The open string sector of the topological B-model on CY (m + 2)-folds is de- scribed by m-graded quivers with superpotentials. This correspondence extends to general m the well known connection between CY (m + 2)-folds and gauge theories on the world- volume of D(5 − 2m)-branes for m = 0, …, 3. We introduce m-dimers, which fully encode the m-graded quivers and their superpotentials, in the case in which the CY (m + 2)-folds are toric. Generalizing the well known m = 1, 2 cases, m-dimers significantly simplify the connection between geometry and m-graded quivers. A key result of this paper is the generalization of the concept of perfect matching, which plays a central role in this map, to arbitrary m. We also introduce a simplified algorithm for the computation of perfect matchings, which generalizes the Kasteleyn matrix approach to any m. We illustrate these new tools with a few infinite families of CY singularities.
Dieback and expansions: species-specific responses during 20 years of amplified warming in the high Alps
Authors: Steinbauer Klaus , Lamprecht Andrea , Semenchuk Philipp , Winkler Manuela , Pauli Harald 
Published: November 2019

AbstractThe largest alpine–nival vegetation permanent plot site in the Alps, the GLORIA mastersite Schrankogel (Tirol, Austria), provided evidence of warming-driven vegetation changes already 10 years after its establishment in 1994. Another decade later, in 2014, substantial compositional changes with increasing ratios of warmth-demanding to cold-adapted species have been found. The current study deals with species-specific responses involved in an ongoing vegetation transformation across the alpine–nival ecotone on Schrankogel by using presence/absence as well as cover data from permanent plots, situated between 2900 and 3400 masl. The number of occupied plots per species remained constant or even increased during the first decade, whereas disappearance events became more frequent during the second one, especially for cold-adapted specialists (subnival–nival species). Remarkably, the latter was accompanied by continued strong losses in cover of all subnival–nival species. These losses were more frequent in plots with a more thermophilous species composition, suggesting an increasing maladaptation of subnival–nival species to warmer habitat conditions and a successive trailing-edge decline. Several species with a distribution centre at lower elevations (alpine–subnival) markedly increased in cover, comparatively more so in colder plots, indicating a leading-edge expansion. Moreover, our findings show an increase in occupied plots and cover of almost all snowbed species, suggesting that areas previously with a too long snowpack period are now becoming suitable snowbed habitats. Vegetation gaps arising from population dieback of cold-adapted species, however, could only be partly filled by advancing species, indicating that species declines have occurred already before the onset of strong competition pressure.
Energy Consumption, Carbon Emissions and Global Warming Potential of Wolfberry Production in Jingtai Oasis, Gansu Province, China
Authors: Wang Yaolin , Ma Quanlin , Li Yingke , Sun Tao , Jin Hujia , Zhao Chuanyan , Milne Eleanor , Easter Mark , Paustian Keith , Yong Hoi Wen Au , McDonagh John 
Published: November 2019

AbstractDuring the last decade, China's agro-food production has increased rapidly and been accompanied by the challenge of increasing greenhouse gas (GHG) emissions and other environmental pollutants from fertilizers, pesticides, and intensive energy use. Understanding the energy use and environmental impacts of crop production will help identify environmentally damaging hotspots of agro-production, allowing environmental impacts to be assessed and crop management strategies optimized. Conventional farming has been widely employed in wolfberry (Lycium barbarum) cultivation in China, which is an important cash tree crop not only for the rural economy but also from an ecological standpoint. Energy use and global warming potential (GWP) were investigated in a wolfberry production system in the Yellow River irrigated Jingtai region of Gansu. In total, 52 household farms were randomly selected to conduct the investigation using questionnaires. Total energy input and output were 321,800.73 and 166,888.80 MJ ha−1, respectively, in the production system. The highest share of energy inputs was found to be electricity consumption for lifting irrigation water, accounting for 68.52%, followed by chemical fertilizer application (11.37%). Energy use efficiency was 0.52 when considering both fruit and pruned wood. Nonrenewable energy use (88.52%) was far larger than the renewable energy input. The share of GWP of different inputs were 64.52% electricity, 27.72% nitrogen (N) fertilizer, 5.07% phosphate, 2.32% diesel, and 0.37% potassium, respectively. The highest share was related to electricity consumption for irrigation, followed by N fertilizer use. Total GWP in the wolfberry planting system was 26,018.64 kg CO2 eq ha−1 and the share of CO2, N2O, and CH4 were 99.47%, 0.48%, and negligible respectively with CO2 being dominant. Pathways for reducing energy use and GHG emission mitigation include: conversion to low carbon farming to establish a sustainable and cleaner production system with options of raising water use efficiency by adopting a seasonal gradient water pricing system and advanced irrigation techniques; reducing synthetic fertilizer use; and policy support: smallholder farmland transfer (concentration) for scale production, credit (small- and low-interest credit) and tax breaks.
Long‐Term and Oncologic Outcomes of Robotic Versus Laparoscopic Liver Resection for Metastatic Colorectal Cancer: A Multicenter, Propensity Score Matching Analysis
Authors: Beard Rachel E. , Khan Sidrah , Troisi Roberto I. , Montalti Roberto , Vanlander Aude , Fong Yuman , Kingham T. Peter , Boerner Thomas , Berber Eren , Kahramangil Bora , Buell Joseph F. , Martinie John B. , Vrochides Dionisios , Shen Chengli , Molinari Michele , Geller David A. , Tsung Allan 
Published: November 2019

AbstractBackgroundTo assess long‐term oncologic outcomes of robotic‐assisted liver resection (RLR) for colorectal cancer (CRC) metastases as compared to a propensity‐matched cohort of laparoscopic liver resections (LLR). Although safety and short‐term outcomes of RLR have been described and previously compared to LLR, long‐term and oncologic data are lacking.MethodsA retrospective study was performed of all patients who underwent RLR and LLR for CRC metastases at six high‐volume centers in the USA and Europe between 2002 and 2017. Propensity matching was used to match baseline characteristics between the two groups. Data were analyzed with a focus on postoperative and oncologic outcomes, as well as long‐term recurrence and survival.ResultsRLR was performed in 115 patients, and 514 patients underwent LLR. Following propensity matching 115 patients in each cohort were compared. Perioperative outcomes including mortality, morbidity, reoperation, readmission, intensive care requirement, length‐of‐stay and margin status were not statistically different. Both prematching and postmatching analyses demonstrated similar overall survival (OS) and disease‐free survival (DFS) between RLR and LLR at 5 years (61 vs. 60% OS, p = 0.87, and 38 vs. 31% DFS, p = 0.25, prematching; 61 vs. 60% OS, p = 0.78, and 38 vs. 44% DFS, p = 0.62, postmatching).ConclusionsPropensity score matching with a large, multicenter database demonstrates that RLR for colorectal metastases is feasible and safe, with perioperative and long‐term oncologic outcomes and survival that are largely comparable to LLR.
Saint-Venant torsion of non-homogeneous orthotropic circular cylinder
Authors: Ecsedi István , Baksa Attila 
Published: November 2019

AbstractThe object of this paper is the Saint-Venant torsion of a radially non-homogeneous, hollow and solid circular cylinder made of orthotropic piezoelectric material. The elastic stiffness coefficients, piezoelectric constants and dielectric constants have only radial dependence. This paper gives the solution of the Saint-Venant torsion problem for torsion function, electric potential function, Prandtl’s stress function and electric displacement potential function.
Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)
Authors: Liu Guijia , Dong Linsong , Gu Linlin , Han Zhaofang , Zhang Wenjing , Fang Ming , Wang Zhiyong 
Published: November 2019

AbstractYellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)–informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.
Spoilage and Squatting: A Lockean Argument
Authors: Harding Eloise 
Published: November 2019

AbstractJohn Locke is generally seen as an unequivocal defender of private property. However, taken normatively, certain aspects of his argument leave room for interesting loopholes with relevance to some of today’s social and political crises. This paper focuses largely on the spoilage proviso—in which Locke warns against appropriating more than one can make use of—and its possible application to abandoned buildings and the potential for legitimate productive use to be made of them by people other than the legal owner. Using two case studies in which squatters have actively reversed the dereliction of abandoned buildings, this article aims to build a defence of certain types of squatting based on the limitations Locke has placed on the appropriation and (by some readings) the retention of property.
Comparison of radical-driven technologies applied for paraben mixture degradation: mechanism, biodegradability, toxicity and cost assessment
Authors: Gmurek Marta , Gomes João F. , Martins Rui C. , Quinta-Ferreira Rosa M. 
Published: November 2019

AbstractParabens (esters of p-hydroxybenzoic acid) are xenobiosis belonging to endocrine disruptors and commonly used as a preservative in cosmetics, food, pharmaceutical, and personal care products. Their wide use is leading to their appearance in water and wastewater in the range from ng/L to mg/L. In fact, the toxicity of benzylparaben is comparable to bisphenol A. Therefore, it is important to find not only effective but also ecofriendly methods for their removal from aqueous environment since the traditional wastewater treatment approaches are ineffective. Herein, for the first time, such extended comparison of several radical-driven technologies for paraben mixture degradation is presented. The detailed evaluation included (1) comparison of ozone and hydroxyl peroxide processes; (2) comparison of catalytic and photocatalytic processes (including photocatalytic ozonation); (3) characterisation of catalysts using SEM, XRD, DRS, XPS techniques and BET isotherm; (4) mineralisation, biodegradability and toxicity assessment; and (5) cost assessment. O3, H2O2/Fe2+, H2O2/UVC, O3/H2O2, O3/UVA, O3/H2O2/UVA, UVA/catalyst, O3/catalyst and O3/UVA/catalyst were selected from advanced oxidation processes to degrade parabens as well as to decrease its toxicity towards Aliivibrio fischeri, Corbicula fluminea and Lepidium sativum. Research was focused on the photocatalytic process involving visible light (UVA and natural sunlight) and TiO2 catalysts modified by different metals (Ag, Pt, Pd, Au). Photocatalytic oxidation showed the lowest efficiency, while in combining ozone with catalysis and photocatalysis process, degradation efficiency and toxicity removal were improved. Photocatalytic ozonation slightly improved degradation efficiency but appreciably decreased transferred ozone dose (TOD). Results indicate that the degradation pathway is different, or different transformation products (TPs) could be formed, despite that the hydroxyl radicals are the main oxidant.