bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term impact of temporary and persistent personality disorder on anxiety and depressive disorders
Authors: Tyrer Peter , Tyrer Helen , Yang Min , Guo Boliang 
Published: January 2016

AbstractBackgroundIt is of interest to know if temporary and persistent personality disorders are associated with different outcomes.MethodA cohort of 210 people with anxiety and depressive disorders was followed up on nine occasions over 12 years. During this study, personality status was assessed at baseline and after 2 years using two methods, one linked to the new International Classification of Diseases 11th Revision (ICD‐11) severity codes. The impact on the symptomatic outcome and social function of temporary (i.e. personality disorder on one occasion only) and persistent personality disorder (personality disorder present on both occasions) was compared.ResultsOf the 162 patients studied we identified four groups (no personality disorder at any time (n = 46), two with temporary personality disorder (baseline only (n = 33) and 2 years only (n = 28), and persistent personality disorder (n = 55). Those with persistent personality disorder had significantly worse outcomes than other groups for self‐rated anxiety symptoms (p = 0.02) and overall social function (p < 0.001), 81% had a current DSM diagnosis at 12 years compared with 52–65% in the other groups (p < 0.03). Significantly, more patients with ICD‐11 moderate or severe personality disorder at baseline had persistent personality disorder than had temporary disorders (p = 0.017).ConclusionPersistent personality disorder is associated with more severe personality dysfunction and has a negative impact on the outcome of common mental disorder and particularly on long‐term social functioning. Copyright © 2016 John Wiley & Sons, Ltd.
Tuning the adsorption and fluorescence properties of aminal‐linked porous organic polymers through N‐heterocyclic group decoration
Authors: Weng Jun‐Ying , Xu Yue‐Ling , Song Wei‐Chao , Zhang Ying‐Hui 
Published: January 2016

ABSTRACTAiming at tuning the adsorption and fluorescence properties of targeted porous organic polymer, four new aminal‐linked porous organic polymers (NAPOPs) were synthesized through the reaction of 1,4‐Bis(4,6‐diamino‐s‐triazin‐2‐yl) benzene (BATB) with four kinds of aldehydes substituted with different N‐heterocyclic groups. Among the polymers, NAPOP‐3 decorated with 5‐phenyl‐tetrazole group shows the largest CO2 adsorption capacity (2.52 mmol g−1 at 273 K and 100 kPa) because of its relative large surface area, while NAPOP‐1 decorated with piperazine groups shows relative large CO2/N2 adsorption selectivity (77 at 273 K and 100 kPa), attributable to its large CO2 adsorption heats and cabined pore (<4 Å). Meanwhile, NAPOP‐1 and −3 exhibit high adsorption rate toward iodine with a high capacity (>240 wt %). In addition, different luminescence emissions were also observed for NAPOPs, indicating different intramolecular charger transfer occurred inside polymer networks. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1724–1730
How mutational epistasis impairs predictability in protein evolution and design
Authors: Miton Charlotte M. , Tokuriki Nobuhiko 
Published: January 2016

AbstractThere has been much debate about the extent to which mutational epistasis, that is, the dependence of the outcome of a mutation on the genetic background, constrains evolutionary trajectories. The degree of unpredictability introduced by epistasis, due to the non‐additivity of functional effects, strongly hinders the strategies developed in protein design and engineering. While many studies have addressed this issue through systematic characterization of evolutionary trajectories within individual enzymes, the field lacks a consensus view on this matter. In this work, we performed a comprehensive analysis of epistasis by analyzing the mutational effects from nine adaptive trajectories toward new enzymatic functions. We quantified epistasis by comparing the effect of mutations occurring between two genetic backgrounds: the starting enzyme (for example, wild type) and the intermediate variant on which the mutation occurred during the trajectory. We found that most trajectories exhibit positive epistasis, in which the mutational effect is more beneficial when it occurs later in the evolutionary trajectory. Approximately half (49%) of functional mutations were neutral or negative on the wild‐type background, but became beneficial at a later stage in the trajectory, indicating that these functional mutations were not predictable from the initial starting point. While some cases of strong epistasis were associated with direct interaction between residues, many others were caused by long‐range indirect interactions between mutations. Our work highlights the prevalence of epistasis in enzyme adaptive evolution, in particular positive epistasis, and suggests the necessity of incorporating mutational epistasis in protein engineering and design to create highly efficient catalysts.
Using a second‐order differential model to fit data without baselines in protein isothermal chemical denaturation
Authors: Tang Chuanning , Lew Scott , He Dacheng 
Published: January 2016

AbstractIn vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well‐defined pre‐ and post‐transition baselines to evaluate Gibbs free‐energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre‐ or post‐transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second‐order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline‐related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies.
Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11
Authors: Fowler Melissa L. , McPhail Jacob A. , Jenkins Meredith L. , Masson Glenn R. , Rutaganira Florentine U. , Shokat Kevan M. , Williams Roger L. , Burke John E. 
Published: January 2016

AbstractThe ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X‐ray crystallography has been a powerful approach to understand protein‐protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX‐MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX‐MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX‐MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ‐Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein‐protein complexes, and is an excellent strategy to optimize constructs for high‐resolution structural approaches.
COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming
Authors: Zhang Huiling , Huang Qingsheng , Bei Zhendong , Wei Yanjie , Floudas Christodoulos A. 
Published: January 2016

ABSTRACTIn this article, we present COMSAT, a hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT consists of two modules: COMSAT_SVM which is trained mainly on position–specific scoring matrix features, and COMSAT_MILP which is an ab initio method based on optimization models. Contacts predicted by the SVM model are ranked by SVM confidence scores, and a threshold is trained to improve the reliability of the predicted contacts. For TM proteins with no contacts above the threshold, COMSAT_MILP is used. The proposed hybrid contact prediction scheme was tested on two independent TM protein sets based on the contact definition of 14 Å between Cα‐Cα atoms. First, using a rigorous leave‐one‐protein‐out cross validation on the training set of 90 TM proteins, an accuracy of 66.8%, a coverage of 12.3%, a specificity of 99.3% and a Matthews' correlation coefficient (MCC) of 0.184 were obtained for residue pairs that are at least six amino acids apart. Second, when tested on a test set of 87 TM proteins, the proposed method showed a prediction accuracy of 64.5%, a coverage of 5.3%, a specificity of 99.4% and a MCC of 0.106. COMSAT shows satisfactory results when compared with 12 other state‐of‐the‐art predictors, and is more robust in terms of prediction accuracy as the length and complexity of TM protein increase. COMSAT is freely accessible at http://hpcc.siat.ac.cn/COMSAT/. Proteins 2016; 84:332–348. © 2016 Wiley Periodicals, Inc.
Identification of putative unfolding intermediates of the mutant His‐107‐tyr of human carbonic anhydrase II in a multidimensional property space
Authors: Halder Puspita , Taraphder Srabani 
Published: January 2016

ABSTRACTIn this article, we develop an extensive search procedure of the multi‐dimensional folding energy landscape of a protein. Our aim is to identify different classes of structures that have different aggregation propensities and catalytic activity. Following earlier studies by Daggett et al. [Jong, D. D.; Riley, R.: Alonso, D.O.: Dagett, V. J. Mol. Biol. 2002, 319, 229], a series of high temperature all‐atom classical molecular simulation studies has been carried out to derive a multi‐dimensional property space. Dynamical changes in these properties are then monitored by projecting them along a one‐dimensional reaction coordinate, dmean. We have focused on the application of this method to partition a wide array of conformations of wild type human carbonic anhydrase II (HCA II) and its unstable mutant His‐107‐Tyr along dmean by sampling a 35‐dimensional property space. The resultant partitioning not only reveals the distribution of conformations corresponding to stable structures of HCA II and its mutant, but also allows the monitoring of several partially unfolded and less stable conformations of the mutant. We have investigated the population of these conformations at different stages of unfolding and collected separate sets of structures that are widely separated in the property space. The dynamical diversity of these sets are examined in terms of the loading of their respective first principal component. The partially unfolded structures thus collected are qualitatively mapped on to the experimentally postulated light molten globule (MGL) and molten globule (MG) intermediates with distinct aggregation propensities and catalytic activities. Proteins 2016; 84:726–743. © 2016 Wiley Periodicals, Inc.
Conformation of membrane‐bound proteins revealed by vacuum‐ultraviolet circular‐dichroism and linear‐dichroism spectroscopy
Authors: Matsuo Koichi , Maki Yasuyuki , Namatame Hirofumi , Taniguchi Masaki , Gekko Kunihiko 
Published: January 2016

ABSTRACTKnowledge of the conformations of a water‐soluble protein bound to a membrane is important for understanding the membrane‐interaction mechanisms and the membrane‐mediated functions of the protein. In this study we applied vacuum‐ultraviolet circular‐dichroism (VUVCD) and linear‐dichroism (LD) spectroscopy to analyze the conformations of α‐lactalbumin (LA), thioredoxin (Trx), and β‐lactoglobulin (LG) bound to phosphatidylglycerol liposomes. The VUVCD analysis coupled with a neural‐network analysis showed that these three proteins have characteristic helix‐rich conformations involving several helical segments, of which two amphiphilic or hydrophobic segments take part in interactions with the liposome. The LD analysis predicted the average orientations of these helix segments on the liposome: two amphiphilic helices parallel to the liposome surface for LA, two hydrophobic helices perpendicular to the liposome surface for Trx, and a hydrophobic helix perpendicular to and an amphiphilic helix parallel to the liposome surface for LG. This sequence‐level information about the secondary structures and orientations was used to formulate interaction models of the three proteins at the membrane surface. This study demonstrates the validity of a combination of VUVCD and LD spectroscopy in conformational analyses of membrane‐binding proteins, which are difficult targets for X‐ray crystallography and nuclear magnetic resonance spectroscopy. Proteins 2016; 84:349–359. © 2016 Wiley Periodicals, Inc.
Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2‐oxopantoate provides structural insights into feedback regulation
Authors: Aikawa Yoshiki , Nishitani Yuichi , Tomita Hiroya , Atomi Haruyuki , Miki Kunio 
Published: January 2016

ABSTRACTCoenzyme A (CoA) plays essential roles in a variety of metabolic pathways in all three domains of life. The biosynthesis pathway of CoA is strictly regulated by feedback inhibition. In bacteria and eukaryotes, pantothenate kinase is the target of feedback inhibition by CoA. Recent biochemical studies have identified ketopantoate reductase (KPR), which catalyzes the NAD(P)H‐dependent reduction of 2‐oxopantoate to pantoate, as a target of the feedback inhibition by CoA in archaea. However, the mechanism for recognition of CoA by KPR is still unknown. Here we report the crystal structure of KPR from Thermococcus kodakarensis in complex with CoA and 2‐oxopantoate. CoA occupies the binding site of NAD(P)H, explaining the competitive inhibition by CoA. Our structure reveals a disulfide bond between CoA and Cys84 that indicates an irreversible inhibition upon binding of CoA. The structure also suggests the cooperative binding of CoA and 2‐oxopantoate that triggers a conformational closure and seems to facilitate the disulfide bond formation. Our findings provide novel insights into the mechanism that regulates biosynthesis of CoA in archaea. Proteins 2016; 84:374–382. © 2016 Wiley Periodicals, Inc.
Foliar application of microdoses of sucrose to reduce codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) damage to apple trees
Authors: Arnault Ingrid , Lombarkia Nadia , Joy‐Ondet Sophie , Romet Lionel , Brahim Imene , Meradi Rahma , Nasri Ardjouna , Auger Jacques , Derridj Sylvie 
Published: January 2016

AbstractBACKGROUNDThe effects of foliar applications of microdoses of sucrose to reduce the damage by the codling moth have been reported from nine trials carried in France and Algeria from 2009 to 2014. The activity of sucrose alone was assessed by comparison with an untreated control and some treatments with the Cydia pomonella granulovirus or a chemical insecticide. The addition of sucrose to these different treatments was also investigated.RESULTSThe application of sucrose at 0.01% reduced the means of infested fruits with a value of Abbott's efficacy of 41.0 ± 10.0%. This involved the induction of resistance by antixenosis to insect egg laying. Indeed, it seems that acceptance of egg laying on leaves treated with sucrose was reduced. The addition of sucrose to thiacloprid improved its efficacy (59.5% ± 12.8) by 18.4%. However, the sucrose had no added value when associated with C. pomonella granulovirus treatments.CONCLUSIONFoliar applications of microdoses of sucrose every 20 days in commercial orchards can partially protect against the codling moth. Its addition to thiacloprid increases the efficacy in integrated control strategies, contrary to C. pomonella granulovirus treatments. This work opens a route for the development of new biocontrol strategies. © 2016 Society of Chemical Industry
An invasive‐native mammalian species replacement process captured by camera trap survey random encounter models
Authors: Caravaggi Anthony , Zaccaroni Marco , Riga Francesco , Schai‐Braun Stéphanie C. , Dick Jaimie T.A. , Montgomery W. Ian , Reid Neil 
Published: January 2016

AbstractCamera traps are used to estimate densities or abundances using capture‐recapture and, more recently, random encounter models (REMs). We deploy REMs to describe an invasive‐native species replacement process, and to demonstrate their wider application beyond abundance estimation. The Irish hare Lepus timidus hibernicus is a high priority endemic of conservation concern. It is threatened by an expanding population of nonnative, European hares L. europaeus, an invasive species of global importance. Camera traps were deployed in thirteen 1 km squares, wherein the ratio of invader to native densities were corroborated by night‐driven line transect distance sampling throughout the study area of 1652 km2. Spatial patterns of invasive and native densities between the invader's core and peripheral ranges, and native allopatry, were comparable between methods. Native densities in the peripheral range were comparable to those in native allopatry using REM, or marginally depressed using Distance Sampling. Numbers of the invader were substantially higher than the native in the core range, irrespective of method, with a 5:1 invader‐to‐native ratio indicating species replacement. We also describe a post hoc optimization protocol for REM which will inform subsequent (re‐)surveys, allowing survey effort (camera hours) to be reduced by up to 57% without compromising the width of confidence intervals associated with density estimates. This approach will form the basis of a more cost‐effective means of surveillance and monitoring for both the endemic and invasive species. The European hare undoubtedly represents a significant threat to the endemic Irish hare.
Directed Dedifferentiation Using Partial Reprogramming Induces Invasive Phenotype in Melanoma Cells
Authors: Knappe Nathalie , Novak Daniel , Weina Kasia , Bernhardt Mathias , Reith Maike , Larribere Lionel , Hölzel Michael , Tüting Thomas , Gebhardt Christoffer , Umansky Viktor , Utikal Jochen 
Published: January 2016

Abstract
The combination of cancer-focused studies and research related to nuclear reprogramming has gained increasing importance since both processes—reprogramming towards pluripotency and malignant transformation—share essential features. Studies have revealed that incomplete reprogramming of somatic cells leads to malignant transformation indicating that epigenetic regulation associated with iPSC generation can drive cancer development [J Mol Cell Biol 2011;341–350; Cell 2012;151:1617–1632; Cell 2014;156:663–677]. However, so far it is unclear whether incomplete reprogramming also affects cancer cells and their function. In the context of melanoma, dedifferentiation correlates to therapy resistance in mouse studies and has been documented in melanoma patients [Nature 2012;490:412–416; Clin Cancer Res 2014;20:2498–2499]. Therefore, we sought to investigate directed dedifferentiation using incomplete reprogramming of melanoma cells. Using a murine model we investigated the effects of partial reprogramming on the cellular plasticity of melanoma cells. We demonstrate for the first time that induced partial reprogramming results in a reversible phenotype switch in melanoma cells. Partially reprogrammed cells at day 12 after transgene induction display elevated invasive potential in vitro and increased lung colonization in vivo. Additionally, using global gene expression analysis of partially reprogrammed cells, we identified SNAI3 as a novel invasion-related marker in human melanoma. SNAI3 expression correlates with tumor thickness in primary melanomas and thus, may be of prognostic value. In summary, we show that investigating intermediate states during the process of reprogramming melanoma cells can reveal novel insights into the pathogenesis of melanoma progression. We propose that deeper analysis of partially reprogrammed melanoma cells may contribute to identification of yet unknown signaling pathways that can drive melanoma progression.
Learning in a community of practice: Factors impacting english‐learning students' engagement in scientific argumentation
Authors: González‐Howard María , McNeill Katherine L. 
Published: January 2016

AbstractRecent education reform efforts have included an increasing push for school science to better mirror authentic scientific endeavor, including a focus on science practices. However, despite expectations that all students engage in these language‐rich practices, little prior research has focused on how such opportunities will be created for English‐learning students. This case study uses the conceptual framework of communities of practice to investigate the relationship between English‐learning students' argumentation and their middle school sheltered English immersion (SEI) science classroom community. Considering various aspects of this conceptual framework—including the role of legitimate peripheral participation, as well as the degree to which community members' goals and expectations around the practice of interest align—allowed us to identify classroom characteristics that both hindered and facilitated students' opportunities to engage in argumentation. First, the classroom community, and consequently the presence and quality of argumentative discourse, was influenced by student movement in and out of this classroom, as their English proficiencies improved. The constantly changing class roster made it difficult for newer members to watch, learn, and engage in argumentation with more knowledgeable peers. Furthermore, certain elements of the SEI approach, namely its deductive nature, conflicted with the type of instruction necessary to encourage language use for sensemaking. However, this instructional context also offered English‐learning students with affordances they may not find in other educational settings. Specifically, we found that when students worked in smaller group structures, such as pairs, and they utilized both their native and second language as a linguistic resource for engaging in science discourse, their engagement in argumentation was promoted. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 53: 527–553, 2016