bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rigidity theory for biomolecules: concepts, software, and applications
Authors: Hermans Susanne M.A. , Pfleger Christopher , Nutschel Christina , Hanke Christian A. , Gohlke Holger 
Published: April 2017

The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous composition of flexible and rigid regions, which can aid in the understanding of biomolecular stability and long‐ranged information transfer through biomolecules, and yield valuable information for rational drug design and protein engineering. We review fundamental concepts in rigidity theory, ways to represent biomolecules as constraint networks, and methodological and algorithmic developments for analyzing such networks and linking the results to biomolecular function. Software packages for performing rigidity analyses on biomolecules in an efficient, automated way are described, as are rigidity analyses on biomolecules including the ribosome, viruses, or transmembrane proteins. The analyses address questions of allosteric mechanisms, mutation effects on (thermo‐)stability, protein (un‐)folding, and coarse‐graining of biomolecules. We advocate that the application of rigidity theory to biomolecules has matured in such a way that it could be broadly applied as a computational biophysical method to scrutinize biomolecular function from a structure‐based point of view and to complement approaches focused on biomolecular dynamics. We discuss possibilities to improve constraint network representations and to perform large‐scale and prospective studies. WIREs Comput Mol Sci 2017, 7:e1311. doi: 10.1002/wcms.1311This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Computer and Information Science > Computer Algorithms and Programming
Software > Molecular Modeling
Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example
Authors: Luo Ziliang , Wang Meng , Long Yan , Huang Yongju , Shi Lei , Zhang Chunyu , Liu Xiang , Fitt Bruce D. L. , Xiang Jinxia , Mason Annaliese S. , Snowdon Rod J. , Liu Peifa , Meng Jinling , Zou Jun 
Published: April 2017

Abstract

Key message

A comprehensive linkage atlas for seed yield in rapeseed.

Abstract
Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
Perfusion Abnormalities are Frequently Detected by Early CT Perfusion and Predict Unfavourable Outcome Following Severe Traumatic Brain Injury
Authors: Bendinelli Cino , Cooper Shannon , Evans Tiffany , Bivard Andrew , Pacey Dianne , Parson Mark , Balogh Zsolt J. 
Published: April 2017

BackgroundIn patients with severe traumatic brain injury (TBI), early CT perfusion (CTP) provides additional information beyond the non‐contrast CT (NCCT) and may alter clinical management. We hypothesized that this information may prognosticate functional outcome.MethodsFive‐year prospective observational study was performed in a level‐1 trauma centre on consecutive severe TBI patients. CTP (obtained in conjunction with first routine NCCT) was interpreted as: abnormal, area of altered perfusion more extensive than on NCCT, and the presence of ischaemia. Six months Glasgow Outcome Scale‐Extended of four or less was considered an unfavourable outcome. Logistic regression analysis of CTP findings and core variables [preintubation Glasgow Coma Scale (GCS), Rotterdam score, base deficit, age] was conducted using Bayesian model averaging to identify the best predicting model for unfavourable outcome.ResultsFifty patients were investigated with CTP (one excluded for the absence of TBI) [male: 80%, median age: 35 (23–55), prehospital intubation: 7 (14.2%); median GCS: 5 (3–7); median injury severity score: 29 (20–36); median head and neck abbreviated injury scale: 4 (4–5); median days in ICU: 10 (5–15)]. Thirty (50.8%) patients had an unfavourable outcome. GCS was a moderate predictor of unfavourable outcome (AUC = 0.74), while CTP variables showed greater predictive ability (AUC for abnormal CTP = 0.92; AUC for area of altered perfusion more extensive than NCCT = 0.83; AUC for the presence of ischaemia = 0.81).ConclusionFollowing severe TBI, CTP performed at the time of the first follow‐up NCCT, is a non‐invasive and extremely valuable tool for early outcome prediction. The potential impact on management and its cost effectiveness deserves to be evaluated in large‐scale studies.Level of evidence IIIProspective study.
Trends in Economic Homogamy: Changes in Assortative Mating or the Division of Labor in Marriage?
Authors: Gonalons-Pons Pilar , Schwartz Christine R. 
Published: April 2017

Abstract
The growing economic resemblance of spouses has contributed to rising inequality by increasing the number of couples in which there are two high- or two low-earning partners. The dominant explanation for this trend is increased assortative mating. Previous research has primarily relied on cross-sectional data and thus has been unable to disentangle changes in assortative mating from changes in the division of spouses’ paid labor—a potentially key mechanism given the dramatic rise in wives’ labor supply. We use data from the Panel Study of Income Dynamics (PSID) to decompose the increase in the correlation between spouses’ earnings and its contribution to inequality between 1970 and 2013 into parts due to (a) changes in assortative mating, and (b) changes in the division of paid labor. Contrary to what has often been assumed, the rise of economic homogamy and its contribution to inequality is largely attributable to changes in the division of paid labor rather than changes in sorting on earnings or earnings potential. Our findings indicate that the rise of economic homogamy cannot be explained by hypotheses centered on meeting and matching opportunities, and they show where in this process inequality is generated and where it is not.
Cervical Ectropion May Be a Cause of Desquamative Inflammatory Vaginitis
Authors: Mitchell Leia , King Michelle , Brillhart Heather , Goldstein Andrew 
Published: April 2017

Abstract
Desquamative inflammatory vaginitis is a poorly understood chronic vaginitis with an unknown etiology. Symptoms of desquamative inflammatory vaginitis include copious yellowish discharge, vulvovaginal discomfort, and dyspareunia. Cervical ectropion, the presence of glandular columnar cells on the ectocervix, has not been reported as a cause of desquamative inflammatory vaginitis. Although cervical ectropion can be a normal clinical finding, it has been reported to cause leukorrhea, metrorrhagia, dyspareunia, and vulvovaginal irritation. Patients with cervical ectropion and desquamative inflammatory vaginitis are frequently misdiagnosed with candidiasis or bacterial vaginosis and repeatedly treated without resolution of symptoms. We report the case of a 34-year-old woman with a 4-year history of profuse yellowish discharge and dyspareunia. Upon presentation, her symptoms and laboratory results met the criteria for desquamative inflammatory vaginitis, but the standard treatments did not provide long-lasting relief. As a last resort, cryotherapy (cryosurgery) of her cervix was performed for treatment of her cervical ectropion, which provided complete resolution of her symptoms.
Mitchell L, King M, Brillhart H, Goldstein A. Cervical Ectropion May Be a Cause of Desquamative Inflammatory Vaginitis. Sex Med 2017;5:e212–e214.
The effects of pirfenidone on T helper cells in prevention of intraperitoneal adhesions
Authors: Ozbilgin Kemal , Üner Melis Aylin , Ozkut Mahmud , Hasdemir Pinar Solmaz 
Published: April 2017

AbstractAbdominal surgery is linked with peritoneal adhesions. We investigated that the anti‐fibrotic agent pirfenidone (PFD) has immune modulating activities and evaluated its effects on the function of T helper type 1 (Th1), Th2 and T regulatory (Treg) cells, which may play important roles in peritoneal adhesions. Eighteen female Wistar rats underwent right‐sided parietal peritoneal and right uterine horn adhesion model. Rats were randomized into 3 groups as group 1 (control) (closure of midline abdominal incision without any agent administrations), group 2 (closure of incision after intraperitoneal administration of PFD) and group 3 (closure of incision and only oral administration of PFD for 14 days). Relaparotomy was performed 14 days after the first surgery. Effect of PFD on adhesion formation was assessed on Th1, Th2 and Treg cells counts using Anti‐T‐bet, Anti‐GATA‐3 Anti‐FOXP3 antibodies respectively. Th1 counts were moderate in the control group, and didn't show a significant difference between all groups. Th2 cell counts were very high in the control group, but both intraperitoneal and oral administration of PFD resulted in a significant reduction in Th2 cell counts. Treg cell counts were low in number in the control group. In the intraperitoneal administration of PFD group, Treg cell counts were significantly lower than control group. There was no difference of the Treg cells between control groups and the oral administration of PFD group. PFD has prevention effect on intraperitoneal adhesions. This prevention effect seems to be related with the reduction in the numbers of Th2 and Treg cells.
Lateglacial and early Holocene vegetation development and fluvial system changes in the northern Meuse valley, the Netherlands: a review of palynological data
Authors: Hoek W.Z. , Lammertsma E.I. , Bohncke S.J.P. , Bos J.A.A. , Bunnik F. , Kasse C. , Schokker J. , Westerhoff W. 
Published: April 2017

AbstractThis study provides an overview of existing palynological and chronological data of the northern Meuse valley which have been collected over recent decades. The palynological data were used to make a vegetation reconstruction in time and space for the Lateglacial and early Holocene. The vegetation development is strongly influenced by the rapid climate changes that occurred during this time period. It is shown that the biostratigraphy can be used to provide better age estimates for the abandoned channel fills, which have been dated in most cases using conventional bulk14C dates. Furthermore, the combination with a geomorphological reconstruction based on AHN (actual height model of the Netherlands) lidar data has been used to evaluate the interactions between fluvial terrace formation and vegetation development. It appears that, although the vegetation development is comparable to the general vegetation development in the Netherlands, slight differences occur, in particular of the vegetation composition, presumably linked to the dynamic geomorphological activity in the Meuse valley. Finally, the spatial distribution of sites may give indications for the migration routes of pine (Pinus) and poplar (Populus) during this period of rapid vegetation development over the Last Glacial–Interglacial Transition.
Radiocarbon Age Offset Between Shell and Plant Pairs in the Holocene Sediments Under Hakata Bay, Western Japan
Authors: Nakanishi Toshimichi , Hong Wan , Shimoyama Shoichi , Sato Shin’ichi , Park Gyujun , Lee Jong-Geol 
Published: April 2017

AbstractTo measure chronological changes in the marine reservoir effect in western Japan, 47 marine shells and 35 terrestrial plants from the same horizons in two cores of Holocene sediments were radiocarbon dated by the KIGAM AMS facility. These cores were obtained from the central and northern parts of Hakata Bay using a Geoslicer device. This drilling tool provided us continuous coverage and many samples. In order to determine the species effects on the marine reservoir effect, both filter feeders and a deposit feeder were selected for study. Based on the analysis of lithology, mollusk assemblage, and14C dating, two sedimentary units were determined: the upper bay floor sediment and lower estuarine sediment. Reservoir ages of 280±150 yr (n=17) and 340±140 yr (n=18) were obtained from the central and northern parts of Hakata Bay during 2000 to 10,000 cal BP, respectively. Based on these results, it is clear that a paleoenvironmental change occurred here as a result of sea-level rise during the deglacial period.
Exploring the 14C Bomb Peak with Tree Rings of Tropical Species from the Amazon Forest
Authors: Linares R , Santos H C , Brandes A F N , Barros C F , Lisi C S , Balieiro F C , de Faria S M 
Published: April 2017

AbstractIn this work we explore the radiocarbon (14C) signal as an independent tool to assess the year of formation of individual tree rings of tropical species in northern Brazil. Three different species were analyzed in this work: Dipteryx magnifica, Enterolobium maximum, and Hymenolobium petraeum. The studied samples are from the stem of only one individual of each species, all cut down in 2008 in Porto Trombetas, Pará, Brazil. Individual tree rings were identified based on wood anatomy and they were counted from bark to pith. Several rings were selected for 14C analysis in order to cover the overall shape of the 14C atmospheric bomb peak (after 1955). The 14C content was measured at Laboratory of Radiocarbon, Universidade Federal Fluminense (LAC-UFF). Results are compared with the Southern Hemisphere 14C atmospheric calibration curves. For E. maximum and H. petraeum the 14C signal exhibits an overall good match with the SH zone 3 and suggests annual seasonality in the growth-ring formation. These species offer suitable characteristics for dendrochronology. The D. magnifica shows mismatches in the 14C measurements that are likely a result of difficulties in identifying ring boundaries with certainty. Additional techniques may be helpful to disentangle the origin of this discrepancy.
Why User Comments Affect the Perceived Quality of Journalistic	Content
Authors: Weber Patrick , Prochazka Fabian , Schweiger Wolfgang 
Published: April 2017

Abstract. User comments on news websites are frequently uncivil and are not supported by reasoned argumentation. These characteristics can have negative effects on the perceived quality of the commented-on journalistic content, yet to date, it remains unclear how such effects occur. We propose three mechanisms that assume that the effect of user comments depends on how deliberately and elaborately the quality of the commented-on news item is judged. We conducted an experiment ( N = 633) in which we varied the level of civility and reasoning in the comments accompanying a news article and the brand of the news website on which it was presented. The results showed that a lack of reasoning in the comments decreased the perceived quality of the news item irrespective of brand awareness, but only with high elaboration during judgment. Incivility in the comments decreased the perceived quality of the journalistic content, but only with low elaboration, and only with an unknown news brand. We discuss different psychological mechanisms that can explain this pattern of effects.
HMGA1 amplifies Wnt signalling and expands the intestinal stem cell compartment and Paneth cell niche
Authors: Xian Lingling , Georgess Dan , Huso Tait , Cope Leslie , Belton Amy , Chang Yu-Ting , Kuang Wenyong , Gu Qihua , Zhang Xiaoyan , Senger Stefania , Fasano Alessio , Huso David L. , Ewald Andrew J. , Resar Linda M. S. 
Published: April 2017

AbstractHigh-mobility group A1 (Hmga1) chromatin remodelling proteins are enriched in intestinal stem cells (ISCs), although their function in this setting was unknown. Prior studies showed that Hmga1 drives hyperproliferation, aberrant crypt formation and polyposis in transgenic mice. Here we demonstrate that Hmga1 amplifies Wnt/β-catenin signalling to enhance self-renewal and expand the ISC compartment. Hmga1 upregulates genes encoding both Wnt agonist receptors and downstream Wnt effectors. Hmga1 also helps to ‘build’ an ISC niche by expanding the Paneth cell compartment and directly inducing Sox9, which is required for Paneth cell differentiation. In human intestine, HMGA1 and SOX9 are positively correlated, and both become upregulated in colorectal cancer. Our results define a unique role for Hmga1 in intestinal homeostasis by maintaining the stem cell pool and fostering terminal differentiation to establish an epithelial stem cell niche. This work also suggests that deregulated Hmga1 perturbs this equilibrium during intestinal carcinogenesis.
Mechanism of SOS PR-domain autoinhibition revealed by single-molecule assays on native protein from lysate
Authors: Lee Young Kwang , Low-Nam Shalini T. , Chung Jean K. , Hansen Scott D. , Lam Hiu Yue Monatrice , Alvarez Steven , Groves Jay T. 
Published: April 2017

AbstractThe guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) plays a critical role in signal transduction by activating Ras. Here we introduce a single-molecule assay in which individual SOS molecules are captured from raw cell lysate using Ras-functionalized supported membrane microarrays. This enables characterization of the full-length SOS protein, which has not previously been studied in reconstitution due to difficulties in purification. Our measurements on the full-length protein reveal a distinct role of the C-terminal proline-rich (PR) domain to obstruct the engagement of allosteric Ras independently of the well-known N-terminal domain autoinhibition. This inhibitory role of the PR domain limits Grb2-independent recruitment of SOS to the membrane through binding of Ras·GTP in the SOS allosteric binding site. More generally, this assay strategy enables characterization of the functional behaviour of GEFs with single-molecule precision but without the need for purification.
Segregation of liquid crystal mixtures in topological defects
Authors: Rahimi Mohammad , Ramezani-Dakhel Hadi , Zhang Rui , Ramirez-Hernandez Abelardo , Abbott Nicholas L. , de Pablo Juan J. 
Published: April 2017

AbstractThe structure and physical properties of liquid crystal (LC) mixtures are a function of composition, and small changes can have pronounced effects on observables, such as phase-transition temperatures. Traditionally, LC mixtures have been assumed to be compositionally homogenous. The results of chemically detailed simulations presented here show that this is not the case; pronounced deviations of the local order from that observed in the bulk at defects and interfaces lead to significant compositional segregation effects. More specifically, two disclination lines are stabilized in this work by introducing into a nematic liquid crystal mixture a cylindrical body that exhibits perpendicular anchoring. It is found that the local composition deviates considerably from that of the bulk at the interface with the cylinder and in the defects, thereby suggesting new assembly and synthetic strategies that may capitalize on the unusual molecular environment provided by liquid crystal mixtures.
Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species
Authors: Ni Fei , Qi Juan , Hao Qunqun , Lyu Bo , Luo Ming-Cheng , Wang Yan , Chen Fengjuan , Wang Shuyun , Zhang Chaozhong , Epstein Lynn , Zhao Xiangyu , Wang Honggang , Zhang Xiansheng , Chen Cuixia , Sun Lanzhen , Fu Daolin 
Published: April 2017

AbstractMale sterility is a valuable trait for plant breeding and hybrid seed production. The dominant male-sterile gene Ms2 in common wheat has facilitated the release of hundreds of breeding lines and cultivars in China. Here, we describe the map-based cloning of the Ms2 gene and show that Ms2 confers male sterility in wheat, barley and Brachypodium. MS2 appears as an orphan gene within the Triticinae and expression of Ms2 in anthers is associated with insertion of a retroelement into the promoter. The cloning of Ms2 has substantial potential to assemble practical pipelines for recurrent selection and hybrid seed production in wheat.
Activin A more prominently regulates muscle mass in primates than does GDF8
Authors: Latres Esther , Mastaitis Jason , Fury Wen , Miloscio Lawrence , Trejos Jesus , Pangilinan Jeffrey , Okamoto Haruka , Cavino Katie , Na Erqian , Papatheodorou Angelos , Willer Tobias , Bai Yu , Hae Kim Jee , Rafique Ashique , Jaspers Stephen , Stitt Trevor , Murphy Andrew J. , Yancopoulos George D. , Gromada Jesper 
Published: April 2017

AbstractGrowth and differentiation factor 8 (GDF8) is a TGF-β superfamily member, and negative regulator of skeletal muscle mass. GDF8 inhibition results in prominent muscle growth in mice, but less impressive hypertrophy in primates, including man. Broad TGF-β inhibition suggests another family member negatively regulates muscle mass, and its blockade enhances muscle growth seen with GDF8-specific inhibition. Here we show that activin A is the long-sought second negative muscle regulator. Activin A specific inhibition, on top of GDF8 inhibition, leads to pronounced muscle hypertrophy and force production in mice and monkeys. Inhibition of these two ligands mimics the hypertrophy seen with broad TGF-β blockers, while avoiding the adverse effects due to inhibition of multiple family members. Altogether, we identify activin A as a second negative regulator of muscle mass, and suggest that inhibition of both ligands provides a preferred therapeutic approach, which maximizes the benefit:risk ratio for muscle diseases in man.