bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Analysis of Atomic Protein-Ligand Interactions in the PDB
Authors: de Freitas Renato Ferreira , Schapira Matthieu 
Published: May 2017

ABSTRACTAs the protein databank (PDB) recently passed the cap of 123,456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11,016 unique structures of small-molecule ligands bound to proteins – 6,444 of which have experimental binding affinity - representing 750,873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C–H…O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
No compelling evidence that more physically attractive young adult women have higher estradiol or progesterone
Authors: Jones Benedict C , Hahn Amanda C , Fisher Claire I , Wang Hongyi , Kandrik Michal , Lao Junpeng , Han Chengyang , Lee Anthony J , Holzleitner Iris J , DeBruine Lisa M 
Published: May 2017

AbstractPutative associations between sex hormones and attractive physical characteristics in women are central to many theories of human physical attractiveness and mate choice. Although such theories have become very influential, evidence that physically attractive and unattractive women have different hormonal profiles is equivocal. Consequently, we investigated hypothesized relationships between salivary estradiol and progesterone and two aspects of women’s physical attractiveness that are commonly assumed to be correlated with levels of these hormones: facial attractiveness (N=249) and waist-to-hip ratio (N=247). Our analyses revealed no compelling evidence that women with more attractive faces or lower (i.e., more attractive) waist-to-hip ratios had higher levels of estradiol or progesterone. One analysis did suggest that women with more attractive waist-to-hip ratios had significantly higher progesterone, but the relationship was weak and the relationship not significant in other analyses. These results do not support the influential hypothesis that between-women differences in physical attractiveness are related to estradiol and/or progesterone.
Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment
Authors: Gaddy Thomas D. , Arnheim Alyssa D. , Finley Stacey D. 
Published: May 2017

AbstractTumors exploit angiogenesis, the formation of new blood vessels from pre-existing vasculature, in order to obtain nutrients required for continued growth and proliferation. Targeting factors that regulate angiogenesis, including the potent promoter vascular endothelial growth factor (VEGF), is therefore an attractive strategy for inhibiting tumor growth. Computational modeling can be used to identify tumor-specific properties that influence the response to anti-angiogenic strategies. Here, we build on our previous systems biology model of VEGF transport and kinetics in tumor-bearing mice to include a tumor compartment whose volume depends on the “angiogenic signal” produced when VEGF binds to its receptors on tumor endothelial cells. We trained and validated the model using publishedin vivomeasurements of xenograft tumor volume, producing a model that accurately predicts the tumor’s response to anti-angiogenic treatment. We applied the model to investigate how tumor growth kinetics influence the response to anti-angiogenic treatment targeting VEGF. Based on multivariate regression analysis, we found that certain intrinsic kinetic parameters that characterize the growth of tumors could successfully predict response to anti-VEGF treatment, the reduction in tumor volume. Lastly, we use the trained model to predict the response to anti-VEGF therapy for tumors expressing different levels of VEGF receptors. The model predicts that certain tumors are more sensitive to treatment than others, and the response to treatment shows a nonlinear dependence on the VEGF receptor expression. Overall, this model is a useful tool for predicting how tumors will respond to anti-VEGF treatment, and it complements pre-clinicalin vivomouse studies.
Adaptation in a fibronectin binding autolysin ofStaphylococcus saprophyticus
Authors: Mortimer Tatum D. , Annis Douglas S. , O’Neill Mary B. , Bohr Lindsey L. , Smith Tracy M. , Poinar Hendrik N. , Mosher Deane F. , Pepperell Caitlin S. 
Published: May 2017

AbstractHuman-pathogenic bacteria are found in a variety of niches, including free-living, zoonotic, and microbiome environments. Identifying bacterial adaptions that enable invasive disease is an important means of gaining insight into the molecular basis of pathogenesis and understanding pathogen emergence.Staphylococcus saprophyticus, a leading cause of urinary tract infections, can be found in the environment, food, animals, and the human microbiome. We identified a selective sweep in the gene encoding the Aas adhesin, a key virulence factor that binds host fibronectin. We hypothesize that the mutation under selection (aas_2206A>C) facilitates colonization of the urinary tract, an environment where bacteria are subject to strong shearing forces. The mutation appears to have enabled emergence and expansion of a human pathogenic lineage ofS. saprophyticus. These results demonstrate the power of evolutionary genomic approaches in discovering the genetic basis of virulence and emphasize the pleiotropy and adaptability of bacteria occupying diverse niches.ImportanceStaphylococcus saprophyticusis an important cause of urinary tract infections (UTI) in women, which are common, can be severe, and are associated with significant impacts to public health. In addition to being a cause of human UTI,S. saprophyticuscan be found in the environment, in food, and associated with animals. After discovering that UTI strains ofS. saprophyticusare for the most part closely related to each other, we sought to determine whether these strains are specially adapted to cause disease in humans. We found evidence suggesting that a mutation in the geneaasis advantageous in the context of human infection. We hypothesize that the mutation allowsS. saprophyticusto survive better in the human urinary tract. These results show how bacteria found in the environment can evolve to cause disease.
Impact of organizational cultural differences on mergers and acquisitions performance
Authors: Shi Kan , Liu Xiaoqian , Yang Chengjun , Yao Ziping , Liu Dong 
Published: May 2017

PurposeDrawing upon the theory of organizational commitment and relative standing, this study aimed to develop an integrative model to examine how organizational cultural differences impact on mergers and acquisitions (M&A) performance.Design/methodology/approachThe study used regression analysis and moderated path analysis to test the hypothesis with a sample of 103 executives from 49 firms acquired by Chinese state-owned enterprises.FindingsThe paper arrives at the conclusion that the executives’ organizational commitment mediated the association between organizational cultural differences and M&A performance. Besides, the authors also confirmed the moderator role of relative standing.Practical implicationsThe paper suggests ways that can help practitioners better eliminate cultural differences obstacles during the M&A by presenting an integrative framework and showed an actual Chinese case.Originality/valueThis study contributes to the M&A literature by developing an integrative model to explain the complexity between organizational cultural differences and M&A performance with a Chinese executive sample.
Functionally specialised birds respond flexibly to seasonal changes in fruit availability
Authors: Bender Irene M. A. , Kissling W. Daniel , Böhning‐Gaese Katrin , Hensen Isabell , Kühn Ingolf , Wiegand Thorsten , Dehling D. Matthias , Schleuning Matthias 
Published: May 2017

Summary

Interactions between resource and consumer species result in complex ecological networks. The overall structure of these networks is often stable in space and time, but little is known about the temporal stability of the functional roles of consumer species in these networks.

We used a trait‐based approach to investigate whether consumers (frugivorous birds) show similar degrees of functional specialisation on resources (plants) in ecological networks across seasons. We additionally tested whether closely related bird species have similar degrees of functional specialisation and whether birds that are functionally specialised on specific resource types within a season are flexible in switching to other resource types in other seasons.

We analysed four seasonal replicates of two species‐rich plant–frugivore networks from the tropical Andes. To quantify fruit preferences of frugivorous birds, we projected their interactions with plants into a multidimensional plant trait space. To measure functional specialisation of birds, we calculated a species’ functional niche breadth (the extent of seasonal plant trait space utilised by a particular bird) and functional originality (the extent to which a bird species’ fruit preference functionally differs from those of other species in a seasonal network). We additionally calculated functional flexibility, i.e. the ability of bird species to change their fruit preference across seasons in response to variation in plant resources.

Functional specialisation of bird species varied more among species than across seasons, and phylogenetically similar bird species showed similar degrees of functional niche breadth (phylogenetic signal λ = 0·81) and functional originality (λ = 0·89). Additionally, we found that birds with high functional flexibility across seasons had narrow functional niche breadth and high functional originality per season, suggesting that birds that are seasonally specialised on particular resources are most flexible in switching to other fruit resources across seasons.

The high flexibility of functionally specialised bird species to switch seasonally to other resources challenges the view that consumer species rely on functionally similar resources throughout the year. This flexibility of consumer species may be an important, but widely neglected mechanism that could potentially stabilise consumer–resource networks in response to human disturbance and environmental change.
De Novo Advanced Adult‐Onset Offending: New Evidence from a Population of Federal Correctional Clients
Authors: DeLisi Matt , Tahja Katherine N. , Drury Alan J. , Elbert Michael J. , Caropreso Daniel E. , Heinrichs Timothy 
Published: May 2017

AbstractAdult antisocial behavior is almost always predated by delinquency during childhood or adolescence; however, there is also evidence of adult‐onset criminal offending. This study examined this controversial subgroup of offenders using self‐reported and official data from a total population of federal correctional clients selected from the Midwestern United States. Difference of means t‐tests, chi‐square tests, and logistic regression models found that 11.7% of clients had an adult onset of offending and 2.7% of clients (n = 23) had an onset occurring at age 60 years or older. This group—introduced as de novo advanced adult‐onset offenders—had high socioeconomic status, mixed evidence of adverse childhood experiences, and virtually no usage of drugs with the exception of alcohol. These offenders were primarily convicted of social security and white‐collar crimes and evinced remarkably low psychopathology and criminal risk. More research is needed to replicate the phenomenon of de novo advanced adult‐onset offending.
Differences in presentation, progression and rates of arthroplasty between hip and knee osteoarthritis: Observations from an osteoarthritis cohort study‐a clear role for conservative management
Authors: Dabare Chamila , Le Marshall Kim , Leung Albert , Page Carolyn J. , Choong Peter F. , Lim Keith K. 
Published: May 2017

AbstractAimTo describe the natural progression and the rates of arthroplasty of a cohort of hip and knee osteoarthritis (OA) patients.MethodsAn observational study of 247 consecutive patients who attended an OA clinic between May 2008 and August 2009. Follow‐up survey was conducted from July 2014 to December 2014, with the primary end point being joint replacement surgery.ResultsOne hundred and sixty‐seven patients had knee OA and 80 patients had hip OA. When adjusted for other variables (age, gender, body mass index, Kellgren‐Lawrence stage, symptom duration, presence of OA elsewhere and pain score), patients with hip OA demonstrated 86% increased hazard of surgery compared to knee OA patients (95% CI increase of 19% to 193%). At 6 years after initial consultation, 67% of patients with knee OA did not require a knee replacement surgery, while 40% (30, 51) of hip OA patients did not undergo surgery (95% CI: 59–74%). Overall at 6 years, 58% of patients (95% CI: 51–64%) did not undergo joint replacement surgery.ConclusionKnee and hip OA patients appear to behave differently, with hip OA patients more likely to undergo arthroplasty. There is a significant number of both hip OA and knee OA patients who did not require arthroplasty at the end of 6 years, suggesting a major role for conservative therapy.
Interaction between ADH1B*3 and alcohol‐facilitating social environments in alcohol behaviors among college students of african descent
Authors: Desalu Jessica M. , Zaso Michelle J. , Kim Jueun , Belote John M. , Park Aesoon 
Published: May 2017

Background and ObjectivesAlthough alcohol‐facilitating social environmental factors, such as alcohol offers and high perceived peer drinking norms, have been extensively studied as determinants of college drinking, their role among college students of African descent remains understudied. Furthermore, gene‐environment interaction research suggests that the effects of alcohol‐facilitating environments may differ as a function of genetic factors. Specifically, the alcohol dehydrogenase gene's ADH1B*3 allele, found almost exclusively in persons of African descent, may modulate the association of risky social environments with alcohol behaviors. The current study examined whether the ADH1B*3 allele attenuated the relationship between alcohol‐facilitating environments (ie, alcohol offers and perceived peer drinking norms) and alcohol behaviors.MethodParticipants were 241 undergraduate students who self‐identified as being of African descent (mean age = 20 years [SD = 4.11]; 66% female).ResultsSignificant interaction effects of ADH1B*3 with alcohol offers were found on alcohol use frequency (incidence rate ratio [IRR] = 1.14) and on drinking consequences (IRR = 1.21). ADH1B*3 also interacted with perceived peer norms on drinking consequences (IRR = 1.41). Carriers of the ADH1B*3 allele drank less frequently and experienced fewer negative consequences than non‐carriers when exposed to lower levels of alcohol offers and perceived peer drinking. In contrast, in high alcohol‐facilitating environments, no protective genetic effect was observed.Discussion and ConclusionThis study demonstrates that ADH1B*3 may protect college students of African descent against alcohol outcomes, although only in low alcohol‐facilitating environments.Scientific SignificanceFindings add to the growing body of knowledge regarding genetic and social determinants of alcohol behaviors among college students of African descent. (Am J Addict 2017;26:349–356)
Reconsidering the Role of Politics in Leaving Religion: The Importance of Affiliation
Authors: Djupe Paul A. , Neiheisel Jacob R. , Sokhey Anand E. 
Published: May 2017

AbstractStudies have pointed to politics as an important force driving people away from religion—the argument is that the dogmatic politics of the Christian Right have alienated liberals and moderates, effectively threatening organized religion in America. We argue that existing explanations are incomplete; a proper reconsideration necessitates distinguishing processes of affiliation (with specific congregations) from identification (with religious traditions). Using three data sets, we find evidence that qualifies and complements existing narratives of religious exit. Evaluations of congregational political fit drive retention decisions. At the same time, opposition to the Christian Right only bears on retention decisions when it is salient in a congregational context, affecting primarily evangelicals and Republicans. These results help us understand the dynamics of the oft‐observed relationship between the Christian Right and deidentification and urge us to adopt a broader, more pluralistic view of the politicization of American religion.
Allergen immunotherapy for allergic rhinoconjunctivitis: A systematic review and meta‐analysis
Authors: Dhami S. , Nurmatov U. , Arasi S. , Khan T. , Asaria M. , Zaman H. , Agarwal Arnav , Netuveli G. , Roberts G. , Pfaar O. , Muraro A. , Ansotegui I. J. , Calderon M. , Cingi C. , Durham S. , van Wijk R. Gerth , Halken S. , Hamelmann E. , Hellings P. , Jacobsen L. , Knol E. , Larenas‐Linnemann D. , Lin S. , Maggina P. , Mösges R. , Oude Elberink H. , Pajno G. , Panwankar R. , Pastorello E. , Penagos M. , Pitsios C. , Rotiroti G. , Timmermans F. , Tsilochristou O. , Varga E.‐M. , Schmidt‐Weber C. , Wilkinson J. , Williams A. , Worm M. , Zhang L. , Sheikh A. 
Published: May 2017

AbstractBackgroundThe European Academy of Allergy and Clinical Immunology (EAACI) is in the process of developing Guidelines on Allergen Immunotherapy (AIT) for Allergic Rhinoconjunctivitis. To inform the development of clinical recommendations, we undertook a systematic review to assess the effectiveness, cost‐effectiveness, and safety of AIT in the management of allergic rhinoconjunctivitis.MethodsWe searched nine international biomedical databases for published, in‐progress, and unpublished evidence. Studies were independently screened by two reviewers against predefined eligibility criteria and critically appraised using established instruments. Our primary outcomes of interest were symptom, medication, and combined symptom and medication scores. Secondary outcomes of interest included cost‐effectiveness and safety. Data were descriptively summarized and then quantitatively synthesized using random‐effects meta‐analyses.ResultsWe identified 5960 studies of which 160 studies satisfied our eligibility criteria. There was a substantial body of evidence demonstrating significant reductions in standardized mean differences (SMD) of symptom (SMD −0.53, 95% CI −0.63, −0.42), medication (SMD −0.37, 95% CI −0.49, −0.26), and combined symptom and medication (SMD −0.49, 95% CI −0.69, −0.30) scores while on treatment that were robust to prespecified sensitivity analyses. There was in comparison a more modest body of evidence on effectiveness post‐discontinuation of AIT, suggesting a benefit in relation to symptom scores.ConclusionsAIT is effective in improving symptom, medication, and combined symptom and medication scores in patients with allergic rhinoconjunctivitis while on treatment, and there is some evidence suggesting that these benefits are maintained in relation to symptom scores after discontinuation of therapy.
A path model of different forms of impulsivity with externalizing and internalizing psychopathology: Towards greater specificity
Authors: Johnson Sheri L. , Tharp Jordan A. , Peckham Andrew D. , Carver Charles S. , Haase Claudia M. 
Published: May 2017

ObjectivesA growing empirical literature indicates that emotion‐related impulsivity (compared to impulsivity that is unrelated to emotion) is particularly relevant for understanding a broad range of psychopathologies. Recent work, however, has differentiated two forms of emotion‐related impulsivity: A factor termed Pervasive Influence of Feelings captures tendencies for emotions (mostly negative emotions) to quickly shape thoughts, and a factor termed Feelings Trigger Action captures tendencies for positive and negative emotions to quickly and reflexively shape behaviour and speech. This study used path modelling to consider links from emotion‐related and non‐emotion‐related impulsivity to a broad range of psychopathologies.Design and methodsUndergraduates completed self‐report measures of impulsivity, depression, anxiety, aggression, and substance use symptoms.ResultsA path model (N = 261) indicated specificity of these forms of impulsivity. Pervasive Influence of Feelings was related to anxiety and depression, whereas Feelings Trigger Action and non‐emotion‐related impulsivity were related to aggression and substance use.ConclusionsThe findings of this study suggest that emotion‐relevant impulsivity could be a potentially important treatment target for a set of psychopathologies.Practitioner points

Recent work has differentiated two forms of emotion‐related impulsivity.

This study tests a multivariate path model linking emotion‐related and non‐emotion‐related impulsivity with multiple forms of psychopathology.

Impulsive thoughts in response to negative emotions were related to anxiety and depression.

Impulsive actions in response to emotions were related to aggression and substance use, as did non‐emotion‐related impulsivity.

The study was limited by the reliance on self‐report measures of impulsivity and psychopathology.

There is a need for longitudinal work on how these forms of impulsivity predict the onset and course of psychopathology.
Distress, omnipotence, and responsibility beliefs in command hallucinations
Authors: Ellett Lyn , Luzon Olga , Birchwood Max , Abbas Zarina , Harris Abi , Chadwick Paul 
Published: May 2017

ObjectivesCommand hallucinations are considered to be one of the most distressing and disturbing symptoms of schizophrenia. Building on earlier studies, we compare key attributes in the symptomatic, affective, and cognitive profiles of people diagnosed with schizophrenia and hearing voices that do (n = 77) or do not (n = 74) give commands.MethodsThe study employed a cross‐sectional design, in which we assessed voice severity, distress and control (PSYRATs), anxiety and depression (HADS), beliefs about voices (BAVQ‐R), and responsibility beliefs (RIQ). Clinical and demographic variables were also collected.ResultsCommand hallucinations were found to be more distressing and controlling, perceived as more omnipotent and malevolent, linked to higher anxiety and depression, and resisted more than hallucinations without commands. Commanding voices were also associated with higher conviction ratings for being personally responsible for preventing harm.ConclusionsThe findings suggest key differences in the affective and cognitive profiles of people who hear commanding voices, which have important implications for theory and psychological interventions.Practitioner points

Command hallucinations are associated with higher distress, malevolence, and omnipotence.

Command hallucinations are associated with higher responsibility beliefs for preventing harm.

Responsibility beliefs are associated with voice‐related distress.

Future psychological interventions for command hallucinations might benefit from focussing not only on omnipotence, but also on responsibility beliefs, as is done in psychological therapies for obsessive compulsive disorder.

Limitations

The cross‐sectional design does not assess issues of causality.

We did not measure the presence or severity of delusions.