bluuebunny/crossref_metadata_2025 huggingface dataset:
Selection on protein structure, interaction, and sequence
Authors: Chi Peter B. , Liberles David A.
Published: January 2016

Characterizing the probabilities of observing amino acid substitutions at specific sites in a protein over evolutionary time is a major goal in the field of molecular evolution. While purely statistical approaches at different levels of complexity exist, approaches rooted in underlying biological processes are necessary to characterize both the context‐dependence of sequence changes (epistasis) and to extrapolate to sequences not observed in biological databases. To develop such approaches, an understanding of the different selective forces that act on amino acid substitution is necessary. Here, an overview of selection on and corresponding modeling of folding stability, folding specificity, binding affinity and specificity for ligands, the evolution of new binding sites on protein surfaces, protein dynamics, intrinsic disorder, and protein aggregation as well as the interplay with protein expression level (concentration) and biased mutational processes are presented.
Dynamics of the Tec‐family tyrosine kinase SH3 domains
Authors: Roberts Justin M. , Tarafdar Sreya , Joseph Raji E. , Andreotti Amy H. , Smithgall Thomas E. , Engen John R. , Wales Thomas E.
Published: January 2016

The Src Homology 3 (SH3) domain is an important regulatory domain found in many signaling proteins. X‐ray crystallography and NMR structures of SH3 domains are generally conserved but other studies indicate that protein flexibility and dynamics are not. We previously reported that based on hydrogen exchange mass spectrometry (HX MS) studies, there is variable flexibility and dynamics among the SH3 domains of the Src‐family tyrosine kinases and related proteins. Here we have extended our studies to the SH3 domains of the Tec family tyrosine kinases (Itk, Btk, Tec, Txk, Bmx). The SH3 domains of members of this family augment the variety in dynamics observed in previous SH3 domains. Txk and Bmx SH3 were found to be highly dynamic in solution by HX MS and Bmx was unstructured by NMR. Itk and Btk SH3 underwent a clear EX1 cooperative unfolding event, which was localized using pepsin digestion and mass spectrometry after hydrogen exchange labeling. The unfolding was localized to peptide regions that had been previously identified in the Src‐family and related protein SH3 domains, yet the kinetics of unfolding were not. Sequence alignment does not provide an easy explanation for the observed dynamics behavior, yet the similarity of location of EX1 unfolding suggests that higher‐order structural properties may play a role. While the exact reason for such dynamics is not clear, such motions can be exploited in intra‐ and intermolecular binding assays of proteins containing the domains.
InGaP//GaAs//CIGS 3‐junction spectrum‐splitting solar cells with low‐concentration ratio
Authors: Kang Dong‐Won , Takiguchi Yuki , Sichanugrist Porponth , Konagai Makoto
Published: January 2016

In order to achieve high efficiency of solar cells, solar spectrum‐splitting technique was suggested. On the basis of a previous work of a‐Si:H//CIGS splitting solar cells with 22% efficiency, we tried to demonstrate InGaP//CIGS 4‐terminal spectrum‐splitting structure to reinforce top cell performance instead of using the a‐Si:H. After the spectrum‐splitting at 620 nm, the InGaP//CIGS 4‐terminal cells exhibited an efficiency of 27.4%. With an extension up to a 3‐junction by employing a GaAs solar cells as a middle cell, InGaP//GaAs//CIGS spectrum‐splitting solar cells were realized and measured by a new current–voltage measurement system using two optical splitters of which splitting wavelengths correspond to 645 and 875 nm. By applying those configurations, the InGaP//GaAs//CIGS solar cells showed 28.9% efficiency after the splitting, and the final efficiency higher than 31.0% was also demonstrated under relatively low‐concentration ratio about 10 suns. These results indicate that our spectrum‐splitting approach can open promising opportunities to achieve the high efficiency (>30%) with an additional merit of flexible employment of each solar cell without process limitation.
Static and dynamic properties of [hkl] low‐symmetry trilayers
Authors: Celino K. R. , Costa C. H. , Bezerra C. G. , Chesman C.
Published: January 2016

We present a theoretical study about the influence of magneto‐crystalline anisotropies on the static and dynamic magnetic properties of trilayers coupled via bilinear and biquadratic exchange fields for situations in which the systems are grown in unusual [hkl] low‐symmetry directions. We apply a realistic phenomenological model, with a total free magnetic energy that includes Zeeman interaction and magneto‐crystalline anisotropies as well as exchange energy terms. We consider parameters from the literature to illustrate our results for Fe/Cr/Fe systems. In particular, a total of six different magnetic scenarios for the [211] and [321] low‐symmetry growth orientations and three sets of exchange fields were analyzed, and the associated magnetization, magnetoresistance, and spin‐wave frequencies were calculated. Our results show that the combination of magneto‐crystalline symmetries and exchange fields leads to various interesting properties, including different values of the saturation field for the magnetization and magnetoresistance curves. Regarding the spin‐wave modes, we observed the presence of Goldstone modes, associated with second‐order phase transitions, resulting from the competition between the Zeeman and biquadratic energies.
Influence of Processing Conditions on the Performance of Cu2ZnSnS4 Nanocrystal Solar Cells
Authors: Kida Tetsuya , Horita Keisuke , Suehiro Satoshi , Yuasa Masayosh , Quitain Armando T. , Tanaka Tooru , Fujita Katsuhiko , Ishiwata Yoichi , Shimanoe Kengo
Published: January 2016

Quaternary Cu2ZnSnS4 is a promising solar cell material because of its narrow band gap, high light absorption coefficient, and low cost. It is known that the composition of Cu2ZnSnS4 largely influences the solar cell performance. Here, to study the composition dependent properties of Cu2ZnSnS4 NCs as a solar cell material, we synthesized oleylamine‐capped Cu2ZnSnS4 NCs with different compositions by a one‐pot solution process, and fabricated solar cells with a ITO/ZnO/CdS/Cu2ZnSnS4/Au structure, and photoelectrochemical cells. A photovoltaic device using Cu2ZnSnS4 NCs with Cu/ (Zn + Sn)=0.87 showed the best performance among the devices tested. To improve the performance, the NC film fabrication processes were modified. We found that ligand stripping with BF3:OEt2 and the subsequent annealing at 250 °C in N2 improved the power conversion efficiency from 0.06 to 0.14 %, most likely due to efficient stripping of surface insulating organic layers. The photocurrent response of a photoelectrochemical cell using the Cu2ZnSnS4 NCs deposited on a ITO substrate was also improved by the modified NC film fabrication processes.
Interchromophore [2+2]photocycloaddition vs. intrachromophore C‐N photocyclization in bis–styrylbenzoquinoline dyad
Authors: Budyka Mikhail F. , Gavrishova Tatiana N. , Potashova Natalia I.
Published: January 2016

Photophysical and photochemical properties of a novel bichromophoric dyad (EE‐D), where two 3‐styrylbenzo[f]quinoline chromophoric groups (trans‐isomers) are connected by an ortho‐xylylene group, in comparison with the model compound trans‐3‐(3‐methoxystyryl)benzo[f]quinoline (E‐MSBQ), are investigated. The main photochemical reaction of the E‐MSBQ is trans → cis photoisomerization with subsequent intrachromophoric C−N photocyclization and oxidation to a derivative of 12b‐azonia‐benzo[c]chrysene (ABC). In contrast to the E‐MSBQ, upon irradiation of the EE‐D, in addition to photoisomerization, interchromophoric [2+2]photocycloaddition takes place and results in formation of a cyclobutane (CB) derivative. Due to reversibility of photoisomerization, under irradiation, both the E‐MSBQ and the EE‐D can be completely transformed to the ABC and CB derivatives, respectively. DFT calculations taking into account dispersion interactions (hybrid functional M06‐2X) allow explanation of the effective stereospecific [2+2]photocycloaddition in the dyad EE‐D by π‐stacking that orients two SBQ groups head‐to‐head and promotes formation of a single CB isomer.
Synthesis of Mono‐Imido Tungsten Complexes Directly from WCl6
Authors: George Sheby Mary , Han Jeong Hwan , Park Bo Keun , Kim Chang Gyoun , Jang Hongseok , Lee Kangyong , Yim Sangjun , Lee Sang‐ick , Kim Myongwoon , Chung Taek‐Mo
Published: January 2016

A new series of tungsten complexes were prepared using WCl6, N‐tert‐butyltrimethylsilylamine, and amide ligands as potential precursors for WNx thin film deposition. The complexes [W(NtBu)(NMe2)4] (2), [W(NtBu)(MeNCH2CH2NMe)2] (3), [W(NtBu)(MeNCH2CH2CH2NMe)2] (4), [W(NtBu)(iPrNCH2CH2NiPr)2] (5), and [W(NtBu)(tBuNCH2CH2NtBu)2] (6) were prepared by a two‐step process. First, the controlled reaction between WCl6 and N‐tert‐butyltrimethylsilylamine afforded the complex [W(NtBu)Cl4(py)] (1) from which the substitution of chloride ions with the corresponding amide ligands gave complexes 2–6. Single crystal X‐ray crystallography showed that complex 1 crystalized in the triclinic space group P‐1 with an octahedral structure. Among complexes 2–6, complexes 4 and 5 exhibited good volatility and stability.
β‐Meso Covalently linked AzaBODIPY‐Pd(II) Dipyrrin Conjugate
Authors: Kumar Ankit , Kumar Sunit , Chatterjee Tamal , Ravikanth Mangalampalli
Published: January 2016

The first example of azaBODIPY‐metal dipyrrin conjugate such as covalently linked azaBODIPY‐Pd(II) dipyrrin conjugate where the meso‐carbon of Pd(II) dipyrrin moiety was linked to β‐pyrrole carbon of azaBODIPY moiety was synthesized over sequence of facile steps under simple reaction conditions. The compound azaBODIPY‐Pd(II) dipyrrin conjugate is freely soluble in common organic solvents and characterized by HR‐MS, 1D & 2D NMR, X‐ray crystallography, absorption, fluorescence and electrochemical techniques. The X‐ray structure revealed that the azaBODIPY and Pd(II) dipyrrin moieties are almost orthogonal to each other with a dihedral angle of 80°. The spectral and electrochemical studies supported weak interaction between azaBODIPY and Pd(II) dipyrrin moieties in conjugate and marginally influences each other's electronic properties.
Gold‐NHC complexes as potent bioactive compounds
Authors: Al‐Majid Abdullah M. , Yousuf Sammer , Choudhary M. Iqbal , Nahra Fady , Nolan Steven P.
Published: January 2016

This report describes the evaluation of the biological activities of 13 gold‐NHC complexes. These complexes were evaluated in vitro for their antioxidant properties, α‐glucosidase, thymidine phosphorylase, β‐glucuronidase and xanthine oxidase enzyme inhibition activities. Among the tested complexes, those bearing chloride ligands were found to be potent antioxidant, α‐glucosidase, thymidine phosphorylase, β‐glucuronidase and xanthine oxidase enzyme inhibitors, showing several hundred fold higher activity than the standard drugs. Some of these complexes were found to be potent antileishmanial agents, which were superior to standard antileishmanil drugs. These gold complexes were also evaluated for their in vitro cytotoxic activity against PC‐3 (normal cells), HeLa (cervical cancer), MCF‐3 (breast cancer) and 3T3 (mouse fibroblast) cell lines.
Evaluation of [11C]TAZA for amyloid β plaque imaging in postmortem human Alzheimer's disease brain region and whole body distribution in rodent PET/CT
Authors: Pan Min‐Liang , Mukherjee Meenakshi T. , Patel Himika H. , Patel Bhavin , Constantinescu Cristian C. , Mirbolooki M. Reza , Liang Christopher , Mukherjee Jogeshwar
Published: January 2016

Objective: Alzheimer's disease (AD) is a neurodegenerative disease characterized by Aβ plaques in the brain. The aim of this study was to evaluate the effectiveness of a novel radiotracer, 4‐[11C]methylamino‐4′‐N,N‐dimethylaminoazobenzene ([11C]TAZA), for binding to Aβ plaques in postmortem human brain (AD and normal control (NC)). Methods: Radiosyntheses of [11C]TAZA, related [11C]Dalene (11C‐methylamino‐4′‐dimethylaminostyrylbenzene), and reference [11C]PIB were carried out using [11C]methyltriflate prepared from [11C]CO2 and purified using HPLC. In vitro binding affinities were carried out in human AD brain homogenate with Aβ plaques labeled with [3H]PIB. In vitro autoradiography studies with the three radiotracers were performed on hippocampus of AD and NC brains. PET/CT studies were carried out in normal rats to study brain and whole body distribution. Results: The three radiotracers were produced in high radiochemical yields (>40%) and had specific activities >37 GBq/μmol. TAZA had an affinity, Ki = 0.84 nM and was five times more potent than PIB. [11C]TAZA bound specifically to Aβ plaques present in AD brains with gray matter to white matter ratios >20. [11C]TAZA was displaced by PIB (>90%), suggesting similar binding site for [11C]TAZA and [11C]PIB. [11C]TAZA exhibited slow kinetics of uptake in the rat brain and whole body images showed uptake in interscapular brown adipose tissue (IBAT). Binding in brain and IBAT were affected by preinjection of atomoxetine, a norepinephrine transporter blocker. Conclusion: [11C]TAZA exhibited high binding to Aβ plaques in human AD hippocampus. Rat brain kinetics was slow and peripheral binding to IBAT needs to be further evaluated. Synapse, 2016. © 2016 Wiley Periodicals, Inc. Synapse 70:163–176, 2016. © 2016 Wiley Periodicals, Inc.
TESOL Quarterly Research Guidelines
Authors: Mahboob Ahmar , Paltridge Brian , Phakiti Aek , Wagner Elvis , Starfield Sue , Burns Anne , Jones Rodney H. , De Costa Peter I.
Published: January 2016

This article provides research guidelines for authors intending to submit their manuscripts to TESOL Quarterly. These guidelines include information about the TESOL Quarterly review process, advice on converting a dissertation into a research article, broad introductions to a number of research methods, and a section on research ethics. The research methods discussed here are experimental research, survey research, ethnographic research, discourse analysis, and practitioner research. These are, of course, not the only methods that authors draw on for their submissions to TESOL Quarterly but ones we thought it would be helpful to provide advice on. Each of the sections on research methods includes a broad introduction to the method (or approach), a guide for preparing a manuscript using the particular method or approach, and an analysis of an article published in TESOL Quarterly using that method or approach.
A practitioner's guide to thermal infrared remote sensing of rivers and streams: recent advances, precautions and considerations
Authors: Dugdale Stephen J
Published: January 2016

Stream temperature is a key habitat variable controlling all physical and biological river processes. In light of the threat of climate change to fluvial environments, growing importance is being placed on the need to gain a better understanding of stream temperature dynamics. However, many current or historic stream temperature datasets are of very low spatial resolution. Such in situ measurements are often unable to provide the fine scale information on longitudinal or lateral temperature patterns necessary for understanding links between thermal heterogeneity and fluvial processes. In recent years, attention has therefore turned to the use of thermal infrared (TIR) remote sensing in order to acquire 2D stream temperature data at ecologically meaningful scales. While TIR remote sensing is a relatively mature technology in its own right, its application in fluvial environments is accompanied by a range of limitations and considerations that must be respected in order to ensure the acquisition of reasonable quality data. It is only in recent years that researchers have been started to shift from detailing the technical aspects of TIR imaging of river environments toward describing its application for river management and fundamental fluvial science. We critically review this recent research, demonstrating the utility of TIR for applied river temperature research. We also provide a detailed guide to the practical use of TIR in river environments with a view to further stimulating its use for advancing stream temperature science. WIREs Water 2016, 3:251–268. doi: 10.1002/wat2.1135

This article is categorized under:

Water and Life > Nature of Freshwater Ecosystems

Science of Water > Hydrological Processes

Science of Water > Water Quality
From big data to deep insight in developmental science
Authors: Gilmore Rick O.
Published: January 2016

The use of the term ‘big data’ has grown substantially over the past several decades and is now widespread. In this review, I ask what makes data ‘big’ and what implications the size, density, or complexity of datasets have for the science of human development. A survey of existing datasets illustrates how existing large, complex, multilevel, and multimeasure data can reveal the complexities of developmental processes. At the same time, significant technical, policy, ethics, transparency, cultural, and conceptual issues associated with the use of big data must be addressed. Most big developmental science data are currently hard to find and cumbersome to access, the field lacks a culture of data sharing, and there is no consensus about who owns or should control research data. But, these barriers are dissolving. Developmental researchers are finding new ways to collect, manage, store, share, and enable others to reuse data. This promises a future in which big data can lead to deeper insights about some of the most profound questions in behavioral science. WIREs Cogn Sci 2016, 7:112–126. doi: 10.1002/wcs.1379

This article is categorized under:

Psychology > Development and Aging
Syntheses and Crystal Structures of Copper and Silver Complexes with the Ylide Ph3PCHP(O)PPh2 as Ligand
Authors: Petz Wolfgang , Neumüller Bernhard
Published: January 2016

The reactivity of the hydrolysis product of hexaphenylcarbodiphosphorane, PPh3CHP(O)Ph2, towards different soft Lewis acids, such as CuI and Ag[BF4] are reported. While CuI exclusively binds at the ylidic carbon atom, reaction of the silver cation in CH2Cl2 leads to proton abstraction from the solvent to give the cation [PPh3CH2P(O)Ph2]+. Surprisingly, Ag+ replaces the methyl group of [PPh3CHMeP(O)Ph2]+ to produce a dimeric complex, in which Ag+ is coordinated to C and O forming an eight membered ring. The compounds were characterized by spectroscopic methods and X‐ray diffraction.
Unsupervised self‐care predicts conduct problems: The moderating roles of hostile aggression and gender
Authors: Atherton Olivia E. , Schofield Thomas J. , Sitka Angela , Conger Rand D. , Robins Richard W.
Published: January 2016

Despite widespread speculation about the detrimental effect of unsupervised self‐care on adolescent outcomes, little is known about which children are particularly prone to problem behaviors when left at home without adult supervision. The present research used data from a longitudinal study of 674 Mexican‐origin children residing in the United States to examine the prospective effect of unsupervised self‐care on conduct problems, and the moderating roles of hostile aggression and gender. Results showed that unsupervised self‐care was related to increases over time in conduct problems such as lying, stealing, and bullying. However, unsupervised self‐care only led to conduct problems for boys and for children with an aggressive temperament. The main and interactive effects held for both mother‐reported and observational‐rated hostile aggression and after controlling for potential confounds.
Home monitoring report from a single lead Lumax DX implantable cardioverter defibrillator: New observations in a new system
Authors: Konstantino Yuval , Kleiman Alex , Amit Guy
Published: January 2016

A 56‐year‐old man underwent a single lead Lumax 640 DX implantable cardioverter defibrillator implantation for primary prevention of sudden cardiac death. A DX system consists of a single lead, which provides atrial as well as ventricular electrograms, and enhances atrial arrhythmia detection. Three months after the implantation, high‐frequency episodes were detected on the far field and the atrial channels, but not on the bipolar right ventricular channel; these were classified as atrial tachycardia. In the present report, we discussed the unusual pattern of the artifacts that was related to an electromagnetic interference detected by the novel DX system.
Opioid-induced constipation, use of laxatives, and health-related quality of life
Authors: Christensen Helene Nordahl , Olsson Urban , From Jesper , Breivik Harald
Published: January 2016

Background and aims

Real-life data on laxative use in patients suffering from opioid-induced constipation (OIC) are very limited, and many OIC patients are only using over the counter laxatives to resolve their constipation. Our aim was to describe laxative utilization and quality of life in participants in Norway who ever experienced OIC.

Methods

This was a cross-sectional online survey conducted between 27th of June and 3rd of July 2014 among participants above 18 years with self-reported OIC and who had agreed to receive information from the pharmacy chain (Boots A/S, Norway). The questionnaire comprised a series of multiple choice, close-ended, and free text questions on abdominal symptoms, laxative use and health-related quality of life.

Results

A total of 417 participants met the study eligibility criteria: (1) treated with opioid for a minimum of 4 weeks, (2) actively accepted participation, and (3) confirmed ever experiencing OIC and in addition completed the survey. Among the eligible participants, 86% were females, 85% were younger than 60 years of age, and 57% were currently suffering OIC. More than half of the currently constipated participants were experiencing moderate to very severe abdominal bloating (63%), abdominal pain (55%) and/or pain during bowel movement (50%). Less than every fourth participant (23%) had consulted health care professionals (HCPs) about their constipation. Up to 39% reported that they handled their OIC by self-management, e.g., bought laxative, reduced the dose and/or changed opioid without consulting HCP or pharmacy. Less than half (48%) of the laxative users were satisfied with the laxative they were using to relieve their constipation. The EQ-5D health-related quality of life score was mean (SD): 0.587 (0.272). Although not statistically significant (p = 0.067), there was a tendency of lower quality of life among the participants who were currently constipated compared with those not currently constipated (difference of mean EQ-5D: 0.629-0.555 = 0.074). A significantly lower (p = 0.001) quality of life was found among participants who were dissatisfied with their laxative [mean (SD): 0.424 (0.350)] than among those who were satisfied or neither satisfied nor dissatisfied [mean (SD): 0.628 (0.235) and 0.673 (0.155), respectively].

Conclusions

The results suggest a high degree of moderate to very severe abdominal symptoms, a high degree of self-management of opioid-induced constipation, a low degree of satisfaction with laxative, and low health-related quality of life of patients suffering from chronic pain necessitating long-term opioid treatment, subsequent constipation and laxatives use.

Implications

Patients suffering from OIC with low quality of life and remaining symptoms despite use of two or more laxatives are a vulnerable patient group in need of optimized healthcare management, who also might benefit from more specific and innovative therapy.
Convective mass transfer from a submerged drop in a thin falling film
Authors: Landel Julien R. , Thomas A. L. , McEvoy H. , Dalziel Stuart B.
Published: January 2016

We investigate the fluid mechanics of removing a passive tracer contained in small, thin, viscous drops attached to a flat inclined substrate using thin gravity-driven film flows. We focus on the case where the drop cannot be detached either partially or completely from the surface by the mechanical forces exerted by the cleaning fluid on the drop surface. Instead, a convective mass transfer establishes across the drop–film interface and the dilute passive tracer dispersed in the drop diffuses into the film flow, which then transports them away. The Péclet number for the passive tracer in the film phase is very high, whereas the Péclet number in the drop phase varies from $\mathit{Pe}_{d}\approx 10^{-2}$ to $1$. The characteristic transport time in the drop is much larger than in the film. We model the mass transfer of the passive tracer from the bulk of the drop phase into the film phase using an empirical model based on an analogy with Newton’s law of cooling. This simple empirical model is supported by a theoretical model solving the quasi-steady two-dimensional advection–diffusion equation in the film, coupled with a time-dependent one-dimensional diffusion equation in the drop. We find excellent agreement between our experimental data and the two models, which predict an exponential decrease in time of the tracer concentration in the drop. The results are valid for all drop and film Péclet numbers studied. The overall transport characteristic time is related to the drop diffusion time scale, as diffusion within the drop is the limiting process. This result remains valid even for $\mathit{Pe}_{d}\approx 1$. Finally, our theoretical model predicts the well-known relationship between the Sherwood number and the Reynolds number in the case of a well-mixed drop $\mathit{Sh}\propto \mathit{Re}_{L}^{1/3}=({\it\gamma}L^{2}/{\it\nu}_{f})^{1/3}$, based on the drop length $L$, film shear rate ${\it\gamma}$ and film kinematic viscosity ${\it\nu}_{f}$. We show that this relationship is mathematically equivalent to a more physically intuitive relationship $\mathit{Sh}\propto \mathit{Re}_{{\it\delta}}$, based on the diffusive boundary-layer thickness ${\it\delta}$. The model also predicts a correction in the case of a non-uniform drop concentration. The correction depends on $Re_{{\it\delta}}$, the film Schmidt number, the drop aspect ratio and the diffusivity ratio between the two phases. This prediction is in remarkable agreement with experimental data at low drop Péclet number. It continues to agree as $\mathit{Pe}_{d}$ approaches $1$, although the influence of the Reynolds number increases such that $\mathit{Sh}\propto \mathit{Re}_{{\it\delta}}$.
Mechanical Mass-Spring Model for Understanding Globular Motion of Proteins
Authors: Kim J.-I. , Eom K. , Na S.
Published: January 2016

The conformational (structural) change of proteins plays an essential role in their functions. Experiments have been conducted to try to understand the conformational change of proteins, but they have not been successful in providing information on the atomic scale. Simulation methods have been developed to understand the conformational change at an atomic scale in detail. Coarse-grained methods have been developed to calculate protein dynamics with computational efficiency when compared with than all-atom models. A structure-based mass-spring model called the elastic network model (ENM) showed excellent performance in various protein studies. Coarse-grained ENM was modified in various ways to improve the computational efficiency, and consequently to reduce required computational cost for studying the large-scale protein structures. Our previous studies report a modified mass-spring model, which was developed based on condensation method applicable to ENM, and show that the model is able to accurately predict the fluctuation behavior of proteins. We applied this modified mass-spring model to analyze the conformational changes in proteins. We consider two model proteins as an example, where these two proteins exhibit different functions and molecular sizes. It is shown that the modified mass-spring model allows for accurately predicting the pathways of conformation changes for proteins. Our model provides structural insights into the conformation change of proteins related to the biological functions of large protein complexes.
Energy and resilience: The effects of endogenous interdependencies on trade network formation across space among major Japanese firms
Authors: MATOUS PETR , TODO YASUYUKI
Published: January 2016

The dynamic drivers of interfirm interactions across space have rarely been explored in the context of disaster recovery; therefore, the mechanism through which shocks propagate is unclear. This paper uses stochastic actor-oriented modeling to examine how trade networks among the 500 largest Japanese companies evolved during 2010 and 2011, i.e. before and after the Great East Japan Earthquake to identify sources of vulnerability in the system. In contrast to previous reports on broken supply chains, the network displayed only modest change even in the directly affected areas. Controlling for distance and for firm size, we find that when firms changed their partners, they preferred firms that were popular among other firms, that had partners in common with them and that also bought some products or services from them. These findings concur with a criticism that Japanese firms avoid external actors and exhibit inflexibility in reorganizing their networks in times of need, which contrasts with the non-cliquish network structures observed in high-performing economic sectors. The results also highlight the role of energy firms in disaster resilience. Unlike other large Japanese companies that cluster in major urban centers, energy firms are distributed across Japan. However, despite their peripheral physical locations, energy firms are centrally located in trade networks. Thus, while a disaster in any region may affect some energy firms and lead to large-scale temporary shocks, the entire network is unlikely to be disconnected by any region-specific disaster because of the spatial distribution of the topological network core formed by energy companies.
Interactions between dietary oil treatments and genetic variants modulate fatty acid ethanolamides in plasma and body weight composition
Authors: Pu Shuaihua , Eck Peter , Jenkins David J. A. , Connelly Philip W. , Lamarche Benoît , Kris-Etherton Penny M. , West Sheila G. , Liu Xiaoran , Jones Peter J. H.
Published: January 2016

Fatty acid ethanolamides (FAE), a group of lipid mediators derived from long-chain fatty acids (FA), mediate biological activities including activation of cannabinoid receptors, stimulation of fat oxidation and regulation of satiety. However, how circulating FAE levels are influenced by FA intake in humans remains unclear. The objective of the present study was to investigate the response of six major circulating FAE to various dietary oil treatments in a five-period, cross-over, randomised, double-blind, clinical study in volunteers with abdominal obesity. The treatment oils (60 g/12 552 kJ per d (60 g/3000 kcal per d)) provided for 30 d were as follows: conventional canola oil, high oleic canola oil, high oleic canola oil enriched with DHA, flax/safflower oil blend and corn/safflower oil blend. Two SNP associated with FAE degradation and synthesis were studied. Post-treatment results showed overall that plasma FAE levels were modulated by dietary FA and were positively correlated with corresponding plasma FA levels; minor allele (A) carriers of SNP rs324420 in gene fatty acid amide hydrolase produced higher circulating oleoylethanolamide (OEA) (P=0·0209) and docosahexaenoylethanolamide (DHEA) levels (P=0·0002). In addition, elevated plasma DHEA levels in response to DHA intake tended to be associated with lower plasma OEA levels and an increased gynoid fat mass. In summary, data suggest that the metabolic and physiological responses to dietary FA may be influenced via circulating FAE. Genetic analysis of rs324420 might help identify a sub-population that appears to benefit from increased consumption of DHA and oleic acid.
Appraisals of psychotic experiences: an experimental investigation of symptomatic, remitted and non-need-for-care individuals
Authors: Underwood R. , Kumari V. , Peters E.
Published: January 2016

Background

Appraisals are suggested to play a determining role in the clinical outcome of psychotic experiences (PEs). We used experimental tasks that mimic PEs to investigate appraisals in individuals with PEs with and without a ‘need-for-clinical-care’, and psychosis patients whose symptoms have remitted. We predicted that patients would appraise the tasks as threatening regardless of current symptom level, while non-clinical and control groups would appraise them as non-threatening.

Method

Appraisals following three anomalous experiences-inducing tasks [Telepath, Cards task, Virtual acoustic space paradigm (VASP)] were examined in 71 individuals: symptomatic (n= 18) and remitted (n= 16) psychosis patients; non-clinical group with PEs (n= 16); controls without PEs (n= 21).

Results

As predicted, symptomatic patients endorsed more threatening appraisals for all tasks than non-clinical and control groups, who did not differ from each other. However, remitted patients were less likely to endorse threatening appraisals of the Cards and Telepath than their symptomatic counterparts, although they did not differ in global ratings of how striking, threatening and distressing they found the tasks. Moreover, remitted participants endorsed more threatening appraisals of the Telepath and VASP than non-clinical participants, and of the VASP than controls. Remitted participants also rated all three tasks as globally more threatening than the non-clinical group and controls.

Conclusions

Clinical outcome may not necessarily be driven by the presence of symptoms, with threatening appraisals of PEs representing a key factor. The remitted group's intermediate appraisal scores imply that the relationship between appraisal and clinical outcome is not straightforward, and potential mediating factors need to be determined.
Common and differential alterations of general emotion processing in obsessive-compulsive and social anxiety disorder
Authors: Weidt S. , Lutz J. , Rufer M. , Delsignore A. , Jakob N. J. , Herwig U. , Bruehl A. B.
Published: January 2016

Background

Obsessive compulsive disorder (OCD) and social anxiety disorder (SAD) are characterized by biased perception and processing of potentially threatening stimuli. A hyper-reactivity of the fear-circuit [e.g. amygdala, anterior cingulate (ACC)] has been consistently reported using functional magnetic resonance imaging (fMRI) in SAD in comparison with healthy controls (HCs). Studies investigating the processing of specific emotional stimuli in OCD reported mainly orbitofrontal-striatal abnormalities. The goal of this study was to examine similar/common and differential neurobiological responses in OCD and SAD using unspecific emotional stimuli.

Method

Fifty-four subjects participated: two groups (eachn= 18) of outpatients with a current diagnosis of OCD or SAD, and 18 HCs. All subjects underwent fMRI while anticipating and perceiving unspecific visual stimuli with prior announced emotional valence (e.g. positive).

Results

Compared to HCs, the combined patient group showed increased activation in amygdala, caudate and prefrontal/orbitofrontal cortex while anticipating unspecific emotional stimuli. Caudate was more active in the combined patient group during perception. A comparison between the OCD and the SAD samples revealed increased amygdala and decreased rostral ACC activation in OCD patients during perception, but no differences in the anticipation phase.

Conclusions

Overall, we could identify common fronto-subcortical hyper-reactivity in OCD and SAD while anticipating and perceiving unspecific emotional stimuli. While differential neurobiological responses between OCD and SAD when processing specific stimuli are evident from the literature, differences were less pronounced using unspecific stimuli. This could indicate a disturbance of emotion regulation common to both OCD and SAD.
How I think Hauerwas thinks about theology
Authors: Larsen Sean
Published: January 2016

This paper highlights two aspects of Stanley Hauerwas's thought: philosophical ethics, which consists of second-order methodological claims; and moral theology, which consists of first-order, local, unsystematic moral descriptions. I show how the philosophical ethics relates to the moral theology by proposing a set of rules that constitute a ‘grammar’ of Hauerwas's thought. These rules are asymmetrical in that later rules presuppose earlier rules but earlier rules do not presuppose later rules. Each rule corresponds to texts that Hauerwas recommends and relies upon. The first rule prioritizes MacIntyre's concept of non-foundational ‘practical wisdom’. The second rule, which draws on Aristotle, Wittgenstein, Anscombe and Kovesi to stress the impossibility of separating agent from act, influences the third rule that ethics is moral description. The fourth rule uses ‘postliberal’ theologians and draws on the liturgy alongside Barth and Yoder, in order to redescribe the shape of Christian life in liberal modernity.
Adolf Schlatter on scripture as Gnadenmittel: remedy for a hypertensive debate?
Authors: Bräutigam Michael
Published: January 2016

Adolf Schlatter (1852–1938) found himself time and again caught in the crossfire between the opposing camps of fundamentalist Pietism and liberal historical-criticism. This article suggests that Schlatter, by avoiding the pitfalls of both extremes, provides a unique way of uniting faith and scientific criticism through his creative reinterpretation of classic attributes of scripture, namely, (1) inspiration as organic and historic-pneumatic, (2) unity as Christocentric, (3) scriptural authority as evoking discipleship, (4) infallibility as relational-volitional, and finally, (5) perspicuity as catholic. In times where there still seems to exist a big gap between ‘evangelical’ and ‘scientific’ approaches to scripture, Schlatter's focus on scripture not only as a means to know God (Erkenntnismittel), but primarily as a means to receive God's grace (Gnadenmittel), remains valuable, helping us to do away with possible misunderstandings and stereotypes and enabling us to recalibrate our perspective on scripture.
Persistence of Ebola virus in various body fluids during convalescence: evidence and implications for disease transmission and control
Authors: CHUGHTAI A. A. , BARNES M. , MACINTYRE C. R.
Published: January 2016

The aim of this study was to review the current evidence regarding the persistence of Ebola virus (EBOV) in various body fluids during convalescence and discuss its implication on disease transmission and control. We conducted a systematic review and searched articles from Medline and EMBASE using key words. We included studies that examined the persistence of EBOV in various body fluids during the convalescent phase. Twelve studies examined the persistence of EBOV in body fluids, with around 800 specimens tested in total. Available evidence suggests that EBOV can persist in some body fluids after clinical recovery and clearance of virus from the blood. EBOV has been isolated from semen, aqueous humor, urine and breast milk 82, 63, 26 and 15 days after onset of illness, respectively. Viral RNA has been detectable in semen (day 272), aqueous humor (day 63), sweat (day 40), urine (day 30), vaginal secretions (day 33), conjunctival fluid (day 22), faeces (day 19) and breast milk (day 17). Given high case fatality and uncertainties around the transmission characteristics, patients should be considered potentially infectious for a period of time after immediate clinical recovery. Patients and their immediate contacts should be informed about these risks. Convalescent patients may need to abstain from sex for at least 9 months or should use condoms until their semen tests are negative. Breastfeeding should be avoided during the convalescent phase. There is a need for more research on persistence, and a uniform approach to infection control guidelines in convalescence.
NLP-driven citation analysis for scientometrics
Authors: JHA RAHUL , JBARA AMJAD-ABU , QAZVINIAN VAHED , RADEV DRAGOMIR R.
Published: January 2016

This paper summarizes ongoing research in Natural-Language-Processing-driven citation analysis and describes experiments and motivating examples of how this work can be used to enhance traditional scientometrics analysis that is based on simply treating citations as a ‘vote’ from the citing paper to cited paper. In particular, we describe our dataset for citation polarity and citation purpose, present experimental results on the automatic detection of these indicators, and demonstrate the use of such annotations for studying research dynamics and scientific summarization. We also look at two complementary problems that show up in Natural-Language-Processing-driven citation analysis for a specific target paper. The first problem is extracting citation context, the implicit citation sentences that do not contain explicit anchors to the target paper. The second problem is extracting reference scope, the target relevant segment of a complicated citing sentence that cites multiple papers. We show how these tasks can be helpful in improving sentiment analysis and citation-based summarization.
Coping strategies and mental health outcomes of conflict-affected persons in the Republic of Georgia
Authors: Saxon L. , Makhashvili N. , Chikovani I. , Seguin M. , McKee M. , Patel V. , Bisson J. , Roberts B.
Published: January 2016

Aims.

Adults who experienced the 1992 and 2008 armed conflicts in the Republic of Georgia were exposed to multiple traumatic events and stressors over many years. The aim was to investigate what coping strategies are used by conflict-affected persons in Georgia and their association with mental disorders.

Method.

A cross-sectional survey was conducted with 3600 adults, representing internally displaced persons (IDPs) from conflicts in the 1990s (n = 1200) and 2008 (n = 1200) and former IDPs who returned to their homes after the 2008 conflict (n = 1200). Post-traumatic stress disorder, depression, anxiety and coping strategies were measured using the Trauma Screening Questionnaire, Patient Health Questionnaire-9, Generalised Anxiety and adapted version of the Brief Coping Inventory, respectively. Descriptive and multivariate regression analyses were used.

Results.

Coping strategies such as use of humour, emotional support, active coping, acceptance and religion were significantly associated with better mental health outcomes. Coping strategies of behavioural and mental disengagement, denial, venting emotions, substance abuse and gambling were significantly associated with poorer mental health outcomes. The reported use of coping strategies varied significantly between men and women for 8 of the 15 strategies addressed.

Conclusions.

Many conflict-affected persons in Georgia are still suffering mental health problems years after the conflicts. A number of specific coping strategies appear to be associated with better mental health and should be encouraged and supported where possible.
“Work for their prime, the workhouse for their age”: Old Age Pauperism in Victorian England
Authors: Boyer George R.
Published: January 2016

This paper examines the extent of local government support for the elderly, in the form of poor relief, in Victorian England. It presents newly constructed estimates of old age pauperism rates for each of England's ten registration divisions from 1861 to 1908, the year the Old Age Pension Act was adopted. My estimates show that the share of persons aged 65 and older receiving government assistance in the nineteenth century was far larger than most contemporaries, and many historians, believe. The share receiving poor relief declined after 1871, largely as a result of changes in relief administration, but on the eve of the adoption of the Old Age Pension Act more than one in five persons over 65 was in receipt of public assistance. In sum, government support for the elderly is not a post-welfare state phenomenon. Old age pauperism rates differed substantially across registration divisions and in general were higher in southern than in northern England. I present evidence that much of the north-south differential was due to differences in wage rates and employment opportunities and differences in the administration of poor relief, although differences in welfare customs might have played a role.
Quantum algorithms for topological and geometric analysis of data
Authors: Lloyd Seth , Garnerone Silvano , Zanardi Paolo
Published: January 2016

Extracting useful information from large data sets can be a daunting task. Topological methods for analysing data sets provide a powerful technique for extracting such information. Persistent homology is a sophisticated tool for identifying topological features and for determining how such features persist as the data is viewed at different scales. Here we present quantum machine learning algorithms for calculating Betti numbers—the numbers of connected components, holes and voids—in persistent homology, and for finding eigenvectors and eigenvalues of the combinatorial Laplacian. The algorithms provide an exponential speed-up over the best currently known classical algorithms for topological data analysis.
Intracellular repair of oxidation-damaged α-synuclein fails to target C-terminal modification sites
Authors: Binolfi Andres , Limatola Antonio , Verzini Silvia , Kosten Jonas , Theillet Francois-Xavier , May Rose Honor , Bekei Beata , Stuiver Marchel , van Rossum Marleen , Selenko Philipp
Published: January 2016

Cellular oxidative stress serves as a common denominator in many neurodegenerative disorders, including Parkinson’s disease. Here we use in-cell NMR spectroscopy to study the fate of the oxidation-damaged Parkinson’s disease protein alpha-synuclein (α-Syn) in non-neuronal and neuronal mammalian cells. Specifically, we deliver methionine-oxidized, isotope-enriched α-Syn into cultured cells and follow intracellular protein repair by endogenous enzymes at atomic resolution. We show that N-terminal α-Syn methionines Met1 and Met5 are processed in a stepwise manner, with Met5 being exclusively repaired before Met1. By contrast, C-terminal methionines Met116 and Met127 remain oxidized and are not targeted by cellular enzymes. In turn, persisting oxidative damage in the C-terminus of α-Syn diminishes phosphorylation of Tyr125 by Fyn kinase, which ablates the necessary priming event for Ser129 modification by CK1. These results establish that oxidative stress can lead to the accumulation of chemically and functionally altered α-Syn in cells.
Electropolymerization on wireless electrodes towards conducting polymer microfibre networks
Authors: Koizumi Yuki , Shida Naoki , Ohira Masato , Nishiyama Hiroki , Tomita Ikuyoshi , Inagi Shinsuke
Published: January 2016

Conducting polymers can be easily obtained by electrochemical oxidation of aromatic monomers on an electrode surface as a film state. To prepare conducting polymer fibres by electropolymerization, templates such as porous membranes are necessary in the conventional methods. Here we report the electropolymerization of 3,4-ethylenedioxythiophene and its derivatives by alternating current (AC)-bipolar electrolysis. Poly(3,4-ethylenedioxythiophene) (PEDOT) derivatives were found to propagate as a fibre form from the ends of Au wires used as bipolar electrodes (BPEs) parallel to an external electric field, without the use of templates. The effects of applied frequency and of the solvent on the morphology, growth rate and degree of branching of these PEDOT fibres were investigated. In addition, a chain-growth model for the formation of conductive material networks was also demonstrated.