bluuebunny/crossref_metadata_2025_split huggingface dataset:
How accurately do force fields represent protein side chain ensembles?
Authors: Petrović Dušan , Wang Xue , Strodel Birgit 
Published: May 2018

AbstractAlthough the protein backbone is the most fundamental part of the structure, the fine‐tuning of side‐chain conformations is important for protein function, for example, in protein‐protein and protein‐ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*‐ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues.
A method for partitioning the information contained in a protein sequence between its structure and function
Authors: Possenti Andrea , Vendruscolo Michele , Camilloni Carlo , Tiana Guido 
Published: May 2018

AbstractProteins employ the information stored in the genetic code and translated into their sequences to carry out well‐defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding. We thus show that the information remaining in the protein sequence after encoding for its structure (the ‘information gap’) is very close to what needed to encode for its function and interactions. Then, by predicting the information gap directly from the protein sequence, we show that it may be possible to use these insights from information theory to discriminate between ordered and disordered proteins, to identify unknown functions, and to optimize artificially‐designed protein sequences.
Herbicide hormesis can act as a driver of resistance evolution in weeds – PSII‐target site resistance in Chenopodium album L. as a case study
Authors: Belz Regina G 
Published: May 2018

AbstractBACKGROUNDHerbicide hormesis may play a role in the evolution of weed resistance by increasing resistance selection. A standard herbicide rate may be subtoxic to resistant plants and make them more fit than untreated plants. If this increase in fitness is ultimately expressed in reproductive traits, resistance genes can accumulate more rapidly and exacerbate resistance evolution by magnifying the selection differential between resistant and sensitive plants. The hypothesis of hormetically enhanced reproductive fitness was studied for a photosystem II (PSII) target‐site resistant (TSR) biotype of Chenopodium album exposed to the triazinone metamitron in comparison with its wild‐type.RESULTSBoth biotypes showed an initial hormetic growth increase at different doses leading to fitness enhancements of between 19% and 61% above untreated plants. However, hormetic effects only resulted in higher fitness at maturity in resistant plants with a maximum stimulation in seed yield of 45% above untreated plants. Applying realistic metamitron rates, reproductive fitness of resistant plants was increased by 15–32%.CONCLUSIONSAgronomically relevant doses of metamitron induced considerable hormesis in a PSII‐TSR C. album genotype leading to enhanced relative fitness through reproductive maturity. This increase in relative fitness suggests an impact on resistance selection and can compensate for the oft‐reported fitness costs of the mutation studied. Field rates of herbicides can, thus, not only select for resistant plants, but also enhance their reproductive fitness. The finding that herbicide hormesis can be eco‐evolutionary important may have important implications for understanding the evolution of herbicide resistance in weeds. © 2018 Society of Chemical Industry
Assessing vulnerability of remittance‐recipient and nonrecipient households in rural communities affected by extreme weather events: Case studies fromSouth‐WestChina andNorth‐EastIndia
Authors: Banerjee Soumyadeep , Black Richard , Mishra Arabinda , Kniveton Dominic 
Published: May 2018

AbstractMigration is one way in which rural households can seek to reduce their vulnerability to climate change. However, migration also carries risks and costs, such that vulnerability may not be reduced. This article constructs an index of rural households' vulnerability to extreme weather events, in order to explore how key components of vulnerability relate to migration. Applied to case studies in China and India, the study finds that the effect of remittances is non‐linear. Although overall, in Assam, few differences were found in the vulnerability of households that did and did not receive remittances, in Yunnan, remittance‐recipient households were found to have less adaptive capacity in response to drought. However, those who had received remittances over longer periods were found to have improved adaptive capacity in both case studies, and in Yunnan, their exposure to such events was also lower. Meanwhile in Assam, longer distance migration was associated with reduced exposure to flooding and with specific forms of adaptation. The vulnerability index developed has capacity to be used in assessments of effects of migration on vulnerability elsewhere.
Economic disadvantages and migrants' subjective well‐being in China: The mediating effects of relative deprivation and neighbourhood deprivation
Authors: Liu Yuqi , Zhang Fangzhu , Liu Ye , Li Zhigang , Wu Fulong 
Published: May 2018

AbstractChina's new‐style urbanisation plan has aroused public concern about the well‐being of internal migrants in large cities. Although a large body of literature has documented and explained migrants' economic disadvantages in the host city, only a few studies have attempted to unravel the link between their actual economic conditions and their subjective well‐being (SWB). What is missing in the literature on migrants' well‐being in Chinese cities is a systematic investigation into how both individuals' feeling of relative deprivation and neighbourhood deprivation mediate the relationship between their economic disadvantages and their SWB. To bridge this knowledge gap, this paper examined to what extent and in what ways migrants' actual economic disadvantages affected their SWB in Guangzhou, China, using questionnaire survey data and multilevel linear regressions. More particularly, it explored the pathways through which deprivation (in both absolute and relative terms) at both individual and neighbourhood levels influenced migrants' SWB. Results from the multilevel analysis showed that migrants' absolute economic disadvantages were negatively associated with their SWB. Results from mediation analysis indicated that feeling socio‐economically deprived relative to other people in the host cities and living in deprived neighbourhoods were two important pathways through which migrants' absolute economic disadvantages negatively affected their SWB. Our findings suggest an urgent need to bridge the migrant–local social gap and curb the poverty of migrant neighbourhoods to enhance migrants' SWB.
Plant growth chamber design for subambient pCO2 and δ13C studies
Authors: Hagopian William M. , Schubert Brian A. , Graper Robert A. , Hope Jahren A. 
Published: May 2018

RationaleSubambient pCO2 has persisted across the major Phanerozoic ice ages, including the entire late Cenozoic (ca 30 Ma to present). Stable isotope analysis of plant‐derived organic matter is used to infer changes in pCO2 and climate in the geologic past, but a growth chamber that can precisely control environmental conditions, including pCO2 and δ13C value of CO2 (δ13CCO2) at subambient pCO2, is lacking.MethodsWe designed and built five identical chambers specifically for plant growth under stable subambient pCO2 (ca 100 to 400 ppm) and δ13CCO2 conditions. We tested the pCO2 and δ13CCO2 stability of the chambers both with and without plants, across two 12‐hour daytime experiments and two extended 9‐day experiments. We also compared the temperature and relative humidity conditions among the chambers.ResultsThe average δ13CCO2 value within the five chambers ranged from −18.76 to −19.10‰; the standard deviation never exceeded 0.14‰ across any experiment. This represents better δ13CCO2 stability than that achieved by all previous chamber designs, including superambient pCO2 chambers. Every pCO2 measurement (n = 1225) was within 5% of mean chamber values. The temperature and relative humidity conditions differed by no more than 0.4°C and 1.6%, respectively, across all chambers within each growth experiment.ConclusionsThis growth chamber design extends the range of pCO2 conditions for which plants can be grown for δ13C analysis of their tissues at subambient levels. This new capability allows for careful isolation of environmental effects on plant 13C discrimination across the entire range of pCO2 experienced by terrestrial land plants.
Distributed integral‐type event‐triggered synchronization of multiagent systems
Authors: Zhang Zhiqiang , Wang Long 
Published: May 2018

SummaryThis paper investigates the synchronization problem of generic linear multiagent systems via integral‐type event‐triggered control. Each agent can only utilize the intermittent information of its neighboring agents in the control scheme. Based on the integral‐type event conditions, an event‐triggered control protocol is designed to guarantee the synchronization of multiagent systems, and Zeno behavior is excluded by showing the existence of a positive lower bound on the inter‐event intervals. Then, we propose the integral‐type event‐triggered control algorithms to study the leader‐following synchronization. It is shown that under the control algorithms all the followers track the leader and no Zeno behavior occurs. The effectiveness of the proposed control schemes is demonstrated by simulation examples.
A Recent Perspective on Noncovalently Formed Polymeric Hydrogels
Authors: Xue Kun , Liow Sing Shy , Karim Anis Abdul , Li Zibiao , Loh Xian Jun 
Published: May 2018

AbstractChemically crosslinked covalent hydrogels form a permanent and often strong network, and have been extensively used so far in drug delivery and tissue engineering. However, it is more difficult to induce dynamic and highly tunable changes in these hydrogels. Noncovalently formed hydrogels show promise as inherently reversible systems with an ability to change in response to dynamic environments, and have garnered strong interest recently. In this Personal Account, we elucidate a few key attractive properties of noncovalent hydrogels and describe recent developments in hydrogels crosslinked using various different noncovalent interactions. These hydrogels offer huge control for modulating material properties and could be more relevant mimics for biological systems.
Microscopic techniques for analysis of ceramic fuel cells
Authors: Jouttijärvi Sami , Asghar Muhammad Imran , Lund Peter D. 
Published: May 2018

Ceramic fuel cells, such as solid oxide fuel cells, convert the chemical energy of a fuel directly to electricity. To make these to a commercial success, several challenges need to be solved such as lowering the operating temperature and improving long‐term stability. Since ceramic fuel cells are complex nanolevel structures, it is crucial to understand how the actual nanostructure of the cell is linked to its macroscopic performance. This paper reviews how different microscopic techniques have been used to obtain information of the fuel cell structure in both two‐dimensional and three‐dimensional and how this information have been used to solve problems related to the cell performance. Finally, the paper proposes how recent development in the field of microscopy could be applied to fuel cell studies.This article is categorized under:

Fuel Cells and Hydrogen > Science and Materials
A critical review of modern approaches for multidimensional energy poverty measurement
Authors: Pelz Setu , Pachauri Shonali , Groh Sebastian 
Published: May 2018

Recent efforts to measure energy poverty more comprehensively attempt to redress the shortcomings of binary metrics that remain in common use. However, significant challenges remain both with the construction of the new measurement frameworks and their application. The paper presents an analysis of recent multidimensional measurement approaches and applications to draw inferences on the implications of applying these for the measurement of energy access and in informing policies aimed at improving it. The assessment suggests that despite progress having been made in capturing the multidimensional nature of energy poverty, the new measures are currently too complex to operationalize at the global level and too prescriptive to gain acceptance in diverse national contexts. Further efforts are thus required to consolidate and simplify the new frameworks for global tracking purposes, and to adapt and modify these to specific country contexts to inform national policy and planning. A subset of key energy poverty dimensions and uniform set of indicators need to be shortlisted for the purposes of global comparisons, while specific national tracking efforts can apply dimensions and thresholds most suited to accurately capture energy poverty and its drivers in a given context.This article is categorized under:Energy Policy and Planning > Economics and PolicyEnergy and Development > Economics and PolicyEnergy Infrastructure > Economics and Policy
Entangled scent of a charge
Authors: Asorey M. , Balachandran A. P. , Lizzi F. , Marmo G. 
Published: May 2018

AbstractWe argue that the ground state of a field theory, in the presence of charged particles, becomes an entangled state involving an infinity of soft photons. The quantum fieldvacuumis altered by the passage of a uniformly moving charge, leaving in its wake a different dressed ground state. In this sense a charged particle leaves its electromagneticscenteven after passing by. Unlike in classical electrodynamics the effect of the charge remains even at infinite time. The calculation is done in detail for the ground state of a spacetime wedge, although the results are more general. This agrees in spirit with recent results over the infrared aspects of field theory, although the technical details are different. These considerations open the possibility that the information carried by quantum fields, being nonlocal, does not disappear beyond the horizon of black holes.
Analysis of Potential Alterations Affecting SETBP1 as a Novel Contributing Mechanism to Inhibit PP2A in Colorectal Cancer Patients
Authors: Torrejón Blanca , Cristóbal Ion , Caramés Cristina , Prieto‐Potín Iván , Chamizo Cristina , Santos Andrea , Sanz‐Alvarez Marta , Serna‐Blasco Roberto , Luque Melania , Madoz‐Gúrpide Juan , Rojo Federico , García‐Foncillas Jesús 
Published: May 2018

AbstractBackgroundThe functional loss of the tumor suppressor protein phosphatase 2A (PP2A) occurs in a wide variety of human cancers including colorectal cancer (CRC), and SET overexpression has been reported as a key contributing mechanism to inhibit PP2A. Although SET binding protein 1 (SETBP1) overexpression and gain of function mutations have been described in several hematological malignancies as common events that increase the expression levels of the PP2A inhibitor SET, thereby leading to PP2A inactivation, the potential existence of SETBP1 alterations in CRC still remains unexplored.MethodsWe studied the expression profile of SETBP1 by Western blot in a set of CRC cell lines and patient samples. Moreover, we performed co‐immunoprecipitation assays to analyze the formation of the previously reported SETBP1–SET–PP2A inhibitory complex. Furthermore, we evaluated the mutational status of SETBP1 by pyrosequencing assays in a cohort of 55 CRC patients with metastatic disease after the immunohistochemical characterization of SET and p‐PP2A expression in this cohort.ResultsWe found high SETBP1 expression in several CRC lines but only in two of the patients analyzed. In addition, we demonstrated the formation of the SETBP1–SET–PP2A heterotrimeric complex in CRC cells. However, we failed to detect SETBP1 mutations in any of the CRC patient samples included in the study.ConclusionsOur results suggest that SETBP1 expression is mainly similar o lower in colorectal cancer tissue compared to normal colonic mucosa. However, its overexpression is a low prevalent alteration which could contribute to inhibit PP2A in CRC through the formation of a SETBP1–SET–PP2A complex in some CRC patients. Moreover, SETBP1 mutations are, if exist, rare events in CRC patients.
Increased nitroglycerin-mediated vasodilation in migraineurs without aura in the interictal period
Authors: Fujioka Kazumi , Oishi Minoru , Fujioka Akira , Nakayama Tomohiro 
Published: May 2018

AbstractPurposeMigraine is associated with vascular disorders, but the underlying mechanism is unknown. Nitric oxide (NO) sensitivity is believed to play a major role in migraine pathophysiology. We investigated flow-mediated vasodilatation (FMD) and nitroglycerin-mediated vasodilatation (NMD) of the brachial artery by means of a key molecular mediator, NO, in patients with migraine without aura in the interictal period whether the abnormality is found.MethodsA total of 12 patients with migraine without aura and 12 matched healthy controls were enrolled in this study. FMD and NMD were measured in all patients and controls using brachial artery ultrasonography.ResultsThere was no significant difference in brachial artery diameter between migraineurs and nonmigraineurs (3.39 ± 0.68 vs 3.89 ± 0.67 mm, respectively;p = 0.083). A significant difference in FMD was not found between migraineurs and nonmigraineurs (6.94 ± 5.72 vs 6.08 ± 2.98%, respectively;p = 0.651). However, NMD in migraineurs was significant higher than that in nonmigraineurs (21.56 ± 7.36 vs 14.23 ± 7.41%, respectively;p = 0.024).ConclusionWe think that patients with migraine without aura in the interictal period have selective sensitivity in dilator response to nitroglycerin and may have systemic NO sensitivity.
A Topological Approach to Full Belief
Authors: Baltag Alexandru , Bezhanishvili Nick , Özgün Aybüke , Smets Sonja 
Published: May 2018

AbstractStalnaker (Philosophical Studies, 128(1), 169–199 2006) introduced a combined epistemic-doxastic logic that can formally express a strong concept of belief, a concept of belief as ‘subjective certainty’. In this paper, we provide a topological semantics for belief, in particular, for Stalnaker’s notion of belief defined as ‘epistemic possibility of knowledge’, in terms of theclosure of the interior operatoron extremally disconnected spaces. This semantics extends the standard topological interpretation of knowledge (as the interior operator) with a new topological semantics for belief. We prove that the belief logicKD45is sound and complete with respect to the class of extremally disconnected spaces and we compare our approach to a different topological setting in which belief is interpreted in terms of the derived set operator. We also study (static) belief revision as well as belief dynamics by providing a topological semantics for conditional belief and belief update modalities, respectively. Our setting based on extremally disconnected spaces, however, encounters problems when extended with dynamic updates. We then propose a solution consisting in interpreting belief in a similar way based onhereditarily extremally disconnected spaces, and axiomatize the belief logic of hereditarily extremally disconnected spaces. Finally, we provide a complete axiomatization of the logic of conditional belief and knowledge, as well as a complete axiomatization of the corresponding dynamic logic.
Averaging of motion capture recordings for movements’ templates generation
Authors: Hachaj Tomasz , Koptyra Katarzyna , Ogiela Marek R. 
Published: May 2018

AbstractIn this paper we propose, describe and evaluate the novel motion capture (MoCap) data averaging framework. It incorporates hierarchical kinematic model, angle coordinates’ preprocessing methods, that recalculate the original MoCap recording making it applicable for further averaging algorithms, and finally signals averaging processing. We have tested two signal averaging methods namely Kalman Filter (KF) and Dynamic Time Warping barycenter averaging (DBA). The propose methods have been tested on MoCap recordings of elite Karate athlete, multiple champion of Oyama karate knockdown kumite who performed 28 different karate techniques repeated 10 times each. The proposed methods proved to have not only high effectiveness measured with root-mean-square deviation (4.04 ± 5.03 degrees for KF and 5.57 ± 6.27 for DBA) and normalized Dynamic Time Warping distance (0.90 ± 1.58 degrees for KF and 0.93 ± 1.23 for DBA), but also the reconstruction and visualization of those recordings persists all crucial aspects of those complicated actions. The proposed methodology has many important applications in classification, clustering, kinematic analysis and coaching. Our approach generates an averaged full body motion template that can be practically used for example for human actions recognition. In order to prove it we have evaluated templates generated by our method in human action classification tasks using DTW classifier. We have made two experiments. In first leave - one - out cross - validation we have obtained 100% correct recognitions. In second experiment when we classified recordings of one person using templates of another recognition rate 94.2% was obtained.
Personal and perceived public mental‐health stigma as predictors of help‐seeking intentions in adolescents
Authors: Nearchou Finiki A. , Bird Niamh , Costello Audrey , Duggan Sophie , Gilroy Jessica , Long Roisin , McHugh Laura , Hennessy Eilis 
Published: May 2018

ABSTRACTThis study aimed to determine predictors of help‐seeking intentions for symptoms of depression/anxiety and self‐harm in adolescents. It focused on personal and perceived public stigma to gather data of value for the design of anti‐stigma interventions. Participants (n = 722; 368 girls) were recruited from three cohorts of secondary school students in Ireland (mean ages: 1st = 12.9 years; 3rd = 14.9 years; 5th = 16.6 years). Hierarchical regression models indicated that perceived public stigma is a significant unique predictor of help‐seeking intentions for depression [F(4, 717) = 13.4, p < .001] and self‐harm [F(4, 717) = 13.5, p < .001]. This indicates that young people's beliefs about other people's stigma towards mental health problems was a stronger predictor of help‐seeking intentions than their own stigma beliefs. These findings highlight the importance of looking separately at different types of stigma when investigating the role of stigma in predicting help‐seeking intentions.