bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody modeling assessment II. Structures and models
Authors: Teplyakov Alexey , Luo Jinquan , Obmolova Galina , Malia Thomas J. , Sweet Raymond , Stanfield Robyn L. , Kodangattil Sreekumar , Almagro Juan Carlos , Gilliland Gary L. 
Published: March 2014

ABSTRACTTo assess the state‐of‐the‐art in antibody structure modeling, a blinded study was conducted. Eleven unpublished Fab crystal structures were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. In the first round, each participant submitted three non‐ranked complete Fv models for each target. In the second round, CDR‐H3 modeling was performed in the context of the correct environment provided by the crystal structures with CDR‐H3 removed. In this report we describe the reference structures and present our assessment of the models. Some of the essential sources of errors in the predictions were traced to the selection of the structure template, both in terms of the CDR canonical structures and VL/VH packing. On top of this, the errors present in the Protein Data Bank structures were sometimes propagated in the current models, which emphasized the need for the curated structural database devoid of errors. Modeling non‐canonical structures, including CDR‐H3, remains the biggest challenge for antibody structure prediction. Proteins 2014; 82:1563–1582. © 2014 Wiley Periodicals, Inc.
Foliations and conjugacy: Anosov structures in the plane
Authors: GROISMAN JORGE , NITECKI ZBIGNIEW 
Published: March 2014

AbstractIn a non-compact setting, the notion of hyperbolicity, together with the associated structure of stable and unstable manifolds (for unbounded orbits), is highly dependent on the choice of metric used to define it. We consider the simplest version of this, the analogue for the plane of Anosov diffeomorphisms, studied earlier by White and Mendes. The two known topological conjugacy classes of such diffeomorphisms are linear hyperbolic automorphisms and translations. We show that if the structure of stable and unstable manifolds is required to be preserved by these conjugacies, the number of distinct equivalence classes of Anosov diffeomorphisms in the plane becomes infinite.
A cross-sectional study to assess the long-term health status of patients with lower respiratory tract infections, including Q fever
Authors: van DAM A. S. G. , van LOENHOUT J. A. F. , PETERS J. B. , RIETVELD A. , PAGET W. J. , AKKERMANS R. P. , OLDE LOOHUIS A. , HAUTVAST J. L. A. , van der VELDEN J. 
Published: March 2014

SUMMARYPatients with a lower respiratory tract infection (LRTI) might be at risk for long-term impaired health status. We assessed whether LRTI patients without Q fever are equally at risk for developing long-term symptoms compared to LRTI patients with Q fever. The study was a cross-sectional cohort design. Long-term health status information of 50 Q fever-positive and 32 Q fever-negative LRTI patients was obtained. Health status was measured by the Nijmegen Clinical Screening Instrument. The most severely affected subdomains of the Q fever-positive group were ‘general quality of life’ (40%) and ‘fatigue’ (40%). The most severely affected subdomains of the Q fever-negative group were ‘fatigue’ (64%) and ‘subjective pulmonary symptoms’ (35%). Health status did not differ significantly between Q fever-positive LRTI patients and Q fever-negative LRTI patients for all subdomains, except for ‘subjective pulmonary symptoms’ (P = 0·048).
Characterization ofSalmonellaEnteritidis strains isolated from poultry and farm environments in Brazil
Authors: CAMPIONI F. , ZOLDAN M. M. , FALCÃO J. P. 
Published: March 2014

SUMMARYSalmonellaEnteritidis is a major causative agent of foodborne outbreaks worldwide. Using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and pulsed-field gel electrophoresis (PFGE), this study assessed the genetic relatedness, the pathogenic potential, and antimicrobial resistance in 60 strains isolated from chickens and the farm environment in Brazil between 2004 and 2010. The resulting concatenated dendrogram of the two methodologies distinguished the strains into two clusters. Some strains isolated from the two sources were indistinguishable. All the strains contained the 13 virulence markers investigated. Forty-four strains were resistant to nalidixic acid. Quinolone resistance presented by many strains suggests that quinolones may have been used to treat chickens. The high prevalence of virulence markers highlights the importance of poultry as vehicles ofS.Enteritidis strains that have the potential to cause disease.
Houses for responsible hedonists: Troppo Architects in the North of Australia, 1980–1990
Authors: Huang Jessica , Radford Antony 
Published: March 2014

Troppo Architects was established in Darwin, northern Australia, in 1981. The radical ‘Troppo Style’ of their houses designed in the 1980s blur edges between indoors and outdoors, formality and informality, and enclosure and openness. In this paper a corpus of ten of those houses is examined through the lens of philosopher Warwick Fox's concept of responsive cohesion. This is a unique quality of the relations between the internal components of a ‘thing’ and also between the ‘thing’ and its contexts. The houses are exemplary in demonstrating this quality of mutual and subtle response through the interactions between their form and local environmental and cultural contexts, including the idea of responsible hedonism as a design principle.The research utilises original documents, site visits and interviews with stakeholders, particularly the architects and the residents. The outcomes reveal interlocking links between the dwelling, the place, the values of the architects and their clients, and the global bio-physical world. They show objectives of personal enjoyment of life and environmental responsibility could co-exist in harmony. However, the research also shows how these houses change over time depending on their location and on the attitudes of their owners. They would not work elsewhere, or for clients without a similar attitude to life and the pleasures offered by everyday living close to the variety and stimuli of the outdoors.
Investigating Processes of Nanocrystal Formation and Transformation via Liquid Cell TEM
Authors: Nielsen Michael H. , Li Dongsheng , Zhang Hengzhong , Aloni Shaul , Han T. Yong-Jin , Frandsen Cathrine , Seto Jong , Banfield Jillian F. , Cölfen Helmut , De Yoreo James J. 
Published: March 2014

AbstractRecentex situobservations of crystallization in both natural and synthetic systems indicate that the classical models of nucleation and growth are inaccurate. However,in situobservations that can provide direct evidence for alternative models have been lacking due to the limited temporal and spatial resolution of experimental techniques that can observe dynamic processes in a bulk solution. Here we report results from liquid cell transmission electron microscopy studies of nucleation and growth of Au, CaCO3, and iron oxide nanoparticles. We show how thesein situdata can be used to obtain direct evidence for the mechanisms underlying nanoparticle crystallization as well as dynamic information that provide constraints on important energetic parameters not available throughex situmethods.
New era for mucosal mast cells: their roles in inflammation, allergic immune responses and adjuvant development
Authors: Kurashima Yosuke , Kiyono Hiroshi 
Published: March 2014

AbstractTo achieve immune homeostasis in such a harsh environment as the intestinal mucosa, both active and quiescent immunity operate simultaneously. Disruption of gut immune homeostasis leads to the development of intestinal immune diseases such as colitis and food allergies. Among various intestinal innate immune cells, mast cells (MCs) play critical roles in protective immunity against pathogenic microorganisms, especially at mucosal sites. This suggests the potential for a novel MC-targeting type of vaccine adjuvant. Dysregulated activation of MCs also results in inflammatory responses in mucosal compartments. The regulation of this yin and yang function of MCs remains to be elucidated. In this review, we focus on the roles of mucosal MCs in the regulation of intestinal allergic reaction, inflammation and their potential as a new target for the development of mucosal adjuvants.
Protecting children from taking up smoking: parents’ views on what would help
Authors: Marck K. , Glover M. , Kira A. , McCool J. , Scragg R. , Nosa V. , Bullen C. 
Published: March 2014

Issue addressedThe present study investigated what factors the parents of children in low‐income areas of Auckland, New Zealand, thought could help protect their children from smoking initiation.MethodsParticipants in a large quasi‐experimental trial that tested a community‐, school‐ and family‐based smoking‐initiation intervention were asked in a questionnaire ‘What could we do to help you protect your children from smoke and taking up smoking?’ Free‐text responses were divided into distinct meaning units and categorised independently by two of the researchers.Results1806 participants (70% of parents who returned the questionnaire) completed the question. The majority of respondents (80%) were either Pacific Island or Mori mothers and 25% were current smokers. Five main categories of suggested strategies for a preventing smoking initiation were identified: building children's knowledge of the ill‐effects of smoking; denormalising smoking; reducing access to tobacco; building children's resilience; and health promotion activities. The most common suggestion was to educate children about smoking.ConclusionBuilding children's knowledge of smoking risks was the main strategy parents proposed. There was some support for banning smoking in most public areas and for tougher moves to stop tobacco sales to minors. Few parents suggested innovative or radical strategies, such as banning the sale of tobacco, fining children for smoking or use of competitions.So what?To ensure reductions in smoking initiation for lower socioeconomic and Mori and Pacific Island people, further research a should engage Mori, Pacific Island and lower socioeconomic parents in a process that elicits innovative thinking about culturally a acceptable strategies.
Lacking alignments? The next-generation sequencing mapper segemehl revisited
Authors: Otto Christian , Stadler Peter F. , Hoffmann Steve 
Published: March 2014

Abstract
Motivation: Next-generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps of bioinformatic analysis is the mapping of reads to reference genomes.
Results: Here, we present thorough benchmarks of our read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, we introduce the tool lack to rescue unmapped RNA-seq reads which works in conjunction with segemehl and many other frequently used split-read aligners.
Availability: lack is distributed together with segemehl and freely available at www.bioinf.uni-leipzig.de/Software/segemehl/ .
Contact: steve@bioinf.uni-leipzig.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Medieval Universities, Legal Institutions, and the Commercial Revolution *
Authors: Cantoni Davide , Yuchtman Noam 
Published: March 2014

AbstractWe present new data documenting medieval Europe’s Commercial Revolution using information on the establishment of markets in Germany. We use these data to test whether medieval universities played a causal role in expanding economic activity, examining the foundation of Germany’s first universities after 1386 following the papal schism. We find that the trend rate of market establishment breaks upward in 1386 and this break is greatest where the distance to a university shrank most. There is no differential pre-1386 trend associated with the reduction in distance to a university, and there is no break in trend in 1386 where university proximity did not change. These results are robust to estimating a variety of specifications that address concerns about the endogeneity of university location. Universities provided training in newly rediscovered Roman and canon law; students with legal training served in positions that reduced the uncertainty of trade in the Middle Ages. We argue that training in the law, and the consequent development of legal and administrative institutions, was an important channel linking universities and greater economic activity in medieval Germany.
Low‐Protein Formula Slows Weight Gain in Infants of Overweight Mothers
Authors: Inostroza Jaime , Haschke Ferdinand , Steenhout Philippe , Grathwohl Dominik , Nelson Steven E. , Ziegler Ekhard E. 
Published: March 2014

ABSTRACTObjectives:Infant formulas provide more protein than breast milk. High protein intakes, as well as maternal obesity, are risk factors for later obesity. The present study tested whether a formula with lower protein content slows weight gain of infants of overweight mothers (body mass index [BMI] > 25 kg/m2).Methods:In a randomized double‐blind study infants of overweight mothers received from 3 months an experimental (EXPL) formula with 1.65 g of protein/100 kcal (62.8 kcal/100 mL) and containing probiotics, or a control (CTRL) formula with 2.7 g of protein/100 kcal (65.6 kcal/100 mL). Breast‐fed infants were studied concurrently. Primary assessment was between 3 and 6 months, although formulas were fed until 12 months. Biomarkers of protein metabolism (blood urea nitrogen, insulin growth factor‐1, insulinogenic amino acids) were measured.Results:Infants fed the low‐protein EXPL formula gained less weight between 3 and 6 months (−1.77 g/day, P = 0.024) than infants fed the CTRL formula. In the subgroup of infants of mothers with BMI > 30 kg/m2 the difference was −4.21 g/day (P = 0.017). Weight (P = 0.011) and BMI (P = 0.027) of EXPL infants remained lower than that of CTRL infants until 2 years but were similar to that of breast‐fed infants. Blood urea nitrogen, insulin growth factor‐1, and insulinogenic amino acids at 6 months were significantly lower in EXPL compared with CTRL.Conclusions:A low‐protein formula with probiotics slowed weight gain between 3 and 6 months in infants of overweight mothers. Weight gain and biomarkers were more like those of breast‐fed infants.
Women with greater pelvic floor muscle strength have better sexual function
Authors: Martinez Caroline S. , Ferreira Fernanda V. , Castro Antonio A.M. , Gomide Liana B. 
Published: March 2014

AbstractObjectiveTo investigate the relation between pelvic floor muscle strength and sexual function among women with higher and lower pelvic floor muscle strength.DesignA cross‐sectional study was performed among employees and students of the University.SettingUrogynecology department, Federal University of Pampa, Brazil, carried out between January and July of 2012.PopulationForty women, aged 20–28 years.MethodsForty‐nine women were screened and nine were excluded. Baseline information of the participants was obtained. The Female Sexual Function Index questionnaire was applied and pelvic floor muscle strength was randomly measured by transvaginal palpation according to the Ortiz scale, and by perineometry. Women were allocated into two groups according to muscle strength.Main outcome measuresIndex of sexual function and pelvic floor muscle strengthResultsWomen with stronger pelvic floor muscles scored higher in the following domains: desire, excitement, orgasm and general score of the questionnaire (4.9 ± 0.73 vs. 3.8 ± 0.58; 5.0 ± 0.35 vs. 4.3 ± 0.82; 5.8 ± 0.21 vs. 4.0 ± 1.00 and 32.4 ± 0.77 vs. 27.6 ± 3.29, p < 0.001). There was a moderate correlation between pelvic floor muscle pressure and both sexual satisfaction (r = 0.47, p = 0.03) and lubrication (r = −0.69, p = 0.001) as well as the manual evaluation of pelvic floor muscle strength, graded by the Ortiz and perineometry, which were interrelated (r = 0.65, p = 0.001).ConclusionOur findings suggest that women with stronger pelvic floor muscles have better sexual function.
Does fire induce flowering inBrazilian subtropical grasslands?
Authors: Fidelis Alessandra , Blanco Carolina 
Published: March 2014

AbstractQuestionsWe aimed to analyse the effect of fire on flowering in subtropical grasslands, by addressing the following questions: will fire history affect flowering? If yes, do fire feedbacks influence flowering or is it just the removal of above‐ground biomass? Are there differences in burned and mowed plots?LocationSubtropical grasslands inSouthernBrazil (30°03′S, 51°07′W).MethodsWe established plots in areas with different fire histories: 30 d (30 plots: five replicates), 1 yr (14 replicates), 3 yr (30 plots: five replicates) since the last fire, in experimentally burned and mowed plots (14 replicates each). We counted the number of flowering species, as well as the number of flowering stalks.ResultsGraminoid species flowered in highest numbers 1 yr after fire, whilst forbs had more species flowering just after fire, indicating different reproductive strategies in post‐fire environments. Mowing was not as efficient as fire in stimulating flowering. Finally, the different functional groups showed different flowering responses to time since last fire and to the different types of management.ConclusionsOur results show fire stimulated flowering. Although mowing can be a good alternative for maintaining plant diversity, our study showed that this practice is not as efficient as fire in stimulating flowering. However, fire season should be noted as a limiting factor to the recovery of C3grasses in these subtropical grasslands, and annual burns may be harmful to C4grasses, since they delay their flowering to the next post‐fire growing season.
Reactive oxygen species induce MMP12‐dependent degradation of collagen 5 and fibronectin to promote the motility of human umbilical cord‐derived mesenchymal stem cells
Authors: Yun Seung Pil , Lee Sei‐Jung , Oh Sang Yub , Jung Young Hyun , Ryu Jung Min , Suh Han Na , Kim Mi Ok , Oh Keon Bong , Han Ho Jae 
Published: March 2014

Background and PurposeReactive oxygen species (ROS) are potent regulators of stem cell behaviour; however, their physiological significance as regards MMP‐mediated regulation of the motility of human umbilical cord blood‐derived mesenchymal stem cells (UCB‐MSCs) has not been characterized. In the present study, we investigated the role of hydrogen peroxide (H2O2) and associated signalling pathways in promoting UCB‐MSCs motility.Experimental ApproachThe regulatory effects of H2O2 on the activation of PKC, MAPKs, NF‐κB and β‐catenin were determined. The expressions of MMP and extracellular matrix proteins were examined. Pharmacological inhibitors and gene‐specific siRNA were used to identify the signalling pathways of H2O2 that affect UCB‐MSCs motility. An experimental skin wound‐healing model was used to confirm the functional role of UCB‐MSCs treated with H2O2 in ICR mice.Key ResultsH2O2 increased the motility of UCB‐MSCs by activating PKCα via a calcium influx mechanism. H2O2 activated ERK and p38 MAPK, which are responsible for the distinct activation of transcription factors NF‐κB and β‐catenin. UCB‐MSCs expressed eight MMP genes, but only MMP12 expression was uniquely regulated by NF‐κB and β‐catenin activation. H2O2 increased the MMP12‐dependent degradation of collagen 5 (COL‐5) and fibronectin (FN) associated with UCB‐MSCs motility. Finally, topical transplantation of UCB‐MSCs treated with H2O2 enhanced skin wound healing in mice.Conclusions and ImplicationsH2O2 stimulated UCB‐MSCs motility by increasing MMP12‐dependent degradation of COL‐5 and FN through the activation of NF‐κB and glycogen synthase kinase‐3β/β‐catenin, which is critical for providing a suitable microenvironment for MSCs transplantation and re‐epithelialization of skin wounds in mice.
A study of the molecular mechanism of binding kinetics and long residence times of human CCR5 receptor small molecule allosteric ligands
Authors: Swinney David C , Beavis Paul , Chuang Kai‐Ting , Zheng Yue , Lee Ina , Gee Peter , Deval Jerome , Rotstein David M , Dioszegi Marianna , Ravendran Palani , Zhang Jun , Sankuratri Surya , Kondru Rama , Vauquelin Georges 
Published: March 2014

Background and PurposeThe human CCR5 receptor is a co‐receptor for HIV‐1 infection and a target for anti‐viral therapy. A greater understanding of the binding kinetics of small molecule allosteric ligand interactions with CCR5 will lead to a better understanding of the binding process and may help discover new molecules that avoid resistance.Experimental ApproachUsing [3H] maraviroc as a radioligand, a number of different binding protocols were employed in conjunction with simulations to determine rate constants, kinetic mechanism and mutant kinetic fingerprints for wild‐type and mutant human CCR5 with maraviroc, aplaviroc and vicriviroc.Key ResultsKinetic characterization of maraviroc binding to the wild‐type CCR5 was consistent with a two‐step kinetic mechanism that involved an initial receptor–ligand complex (RA), which transitioned to a more stable complex, R'A, with at least a 13‐fold increase in affinity. The dissociation rate from R'A, k−2, was 1.2 × 10−3 min−1. The maraviroc time‐dependent transition was influenced by F85L, W86A, Y108A, I198A and Y251A mutations of CCR5.Conclusions and ImplicationsThe interaction between maraviroc and CCR5 proceeded according to a multi‐step kinetic mechanism, whereby initial mass action binding and later reorganizations of the initial maraviroc–receptor complex lead to a complex with longer residence time. Site‐directed mutagenesis identified a kinetic fingerprint of residues that affected the binding kinetics, leading to the conclusion that allosteric ligand binding to CCR5 involved the rearrangement of the binding site in a manner specific to each allosteric ligand.
The Social Value of Shareholder Value
Authors: Morck Randall 
Published: March 2014

AbstractManuscript TypePerspectiveResearch Question/IssueCan maximizing shareholder value maximize social value?Research Findings/InsightsIf good corporate governance is defined as maximizing a firm's contribution to overall social welfare, shareholder valuation maximization can achieve this only if capital markets are functionally efficient, a concept quite distinct from the definitions of market efficiency usually found in finance textbooks. Functional efficient capital markets allocate capital to its highest value uses subject to achieving tolerable success toward other social goals, such as equality or environmental standards.Theoretical/Academic ImplicationsPressing top managers to maximize shareholder valuation is of questionable social value if share prices are either informationally inefficient (noisy) or informationally efficient but functionally inefficient (share prices faithfully reflect fundamental values, which depend on political lobbying, gaming complex regulations, etc., more than genuine productivity growth).Practitioner/Policy ImplicationsShareholder valuation, if surrounded by institutions that foster functional efficiency, is a readily observable, legally useful, and socially defensible barometer of corporate governance. The efficacy of corporate governance institutions associated with shareholder value thus depends on the bundle of political economy institutions that promote functional efficiency.