bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances on plant–pathogen interactions from molecular toward systems biology perspectives
Authors: Peyraud Rémi , Dubiella Ullrich , Barbacci Adelin , Genin Stéphane , Raffaele Sylvain , Roby Dominique 
Published: November 2016

SummaryIn the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen‐secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant–pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant–pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade‐offs between immunity and growth and in silico plant–pathogen co‐evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future.
Tortoise (Reptilia, Testudinidae) radiations in Southern Africa from the Eocene to the present
Authors: Hofmeyr Margaretha D. , Vamberger Melita , Branch William , Schleicher Alfred , Daniels Savel R. 
Published: November 2016

Africa, inclusive of the West Indian Ocean islands, harbours 11 of the world's 16 extant testudinid genera. Fossil records indicate that testudinids originated in Asia and dispersed first to North America and Europe (Early Eocene) and later to Africa (Late Eocene). We used mitochondrial (1870 bp) and nuclear (1416 bp) DNA sequence data to assess whether molecular data support the late cladogenesis of Southern African testudinid lineages. Our results revealed strong support for the monophyly of a clade consisting of Kinixys, the two Malagasy genera and four Southern African genera (Psammobates, Stigmochelys, Homopus and Chersina). Kinixys diverged from this clade in the Late Palaeocene, suggesting that testudinids occupied Africa at an earlier date than indicated by fossil records. The Southern African tortoises consist of three, strongly supported clades: Psammobates + Stigmochelys; the five‐toed Homopus + Chersina; and the four‐toed Homopus. Due to the paraphyly of Homopus, we propose the taxonomic resurrection of Chersobius for the five‐toed Homopus species (boulengeri, signatus and solus). Cladogenesis at the genus level occurred mainly in the Eocene, with Chersina and Chersobius diverging in the Oligocene. The latter divergence coincided with species‐level radiations within Homopus (areolatus and femoralis) and Psammobates (oculifer, geometricus and tentorius). Our phylogeny could not resolve relationships within Psammobates, indicating rapid speciation between the Late Oligocene and Early Miocene. The Chersobius species were the last to diverge in the Early to Mid‐Miocene. By the Mid‐Miocene, P. tentorius started to differentiate into four lineages instead of the three recognized subspecies: P. t. tentorius, P. t. trimeni and two P. t. verroxii subclades occurring north and south of the Orange River, respectively. Terminal radiations in several taxa suggest the existence of cryptic species and a more diverse tortoise fauna than currently recognized. Factors contributing to this diversity may include the early origin of African testudinids and climatic fluctuations over a heterogeneous landscape.
Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera, Nymphalidae) in the evolving Andes
Authors: Nattier Romain , Capdevielle‐Dulac Claire , Cassildé Catherine , Couloux Arnaud , Cruaud Corinne , Lachaume Gilbert , Lamas Gerardo , Silvain Jean‐François , Blandin Patrick 
Published: November 2016

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.
Understanding the delayed prescribing of antibiotics for respiratory tract infection in primary care: a qualitative analysis
Authors: Ryves R , Eyles C , Moore M , McDermott L , Little P , Leydon G M 
Published: November 2016

ObjectiveTo identify general practitioner (GP) views and understanding on the use of delayed prescribing in primary care.DesignQualitative semistructured telephone interview study.SettingPrimary care general practices in England.Participants32 GPs from identified high-prescribing and low-prescribing general practices in England.MethodSemistructured telephone interviews were conducted with GPs identified from practices within clinical commissioning groups with the highest and lowest prescribing rates in England. A thematic analysis of the data was conducted to generate themes.ResultsAll GPs had a good understanding of respiratory tract infection (RTI) management and how the delayed prescribing approach could be used in primary care. However, GPs highlighted factors that were influential as to whether delayed prescribing was successfully carried out during the consultation. These included the increase in evidence of antimicrobial resistance, and GPs' prior experiences of using delayed prescribing during the consultation. The patient–practitioner relationship could also influence treatment outcomes for RTI, and a lack of an agreed prescribing strategy within and between practices was considered to be of significance to GPs. Participants expressed that a lack of feedback on prescribing data at an individual and practice level made it difficult to know if delayed prescribing strategies were successful in reducing unnecessary consumption. GPs agreed that coherent and uniform training and guidelines would be of some benefit to ensure consistent prescribing throughout the UK.ConclusionsDelayed prescribing is encouraged in primary care, but is not always implemented successfully. Greater uniformity within and between practices in the UK is needed to operationalise delayed prescribing, as well as providing feedback on the uptake of antibiotics. Finally, GPs may need further guidance on how to answer the concerns of patients without interpreting these questions as a demand for antibiotics, as well as educating the patient about antimicrobial resistance and supporting a good patient–practitioner relationship.
Social networks of men who have sex with men and their implications for HIV/STI interventions: results from a cross-sectional study using respondent-driven sampling in a large and a small city in Tanzania
Authors: Ross Michael W , Larsson Markus , Jacobson Jerry , Nyoni Joyce , Agardh Anette 
Published: November 2016

ObjectiveMen who have sex with men (MSM) in sub-Saharan Africa remain hidden and hard to reach for involvement in HIV and sexually transmitted infection (STI) services. The aim of the current study was to describe MSM social networks in a large and a small Tanzanian city in order to explore their utility for peer-based healthcare interventions.MethodsData were collected through respondent-driven sampling (RDS) in Dar es Salaam (n=197) and in Tanga (n=99) in 2012 and 2013, using 5 and 4 seeds, respectively. All results were adjusted for RDS sampling design.ResultsMean personal network size based on the number of MSM who were reported by the participants, as known to them was 12.0±15.5 in Dar es Salaam and 7.6±8.1 in Tanga. Mean actual RDS network size was 39.4±31.4 in Dar es Salaam and 25.3±9.7 in Tanga. A majority (97%) reported that the person from whom they received the recruitment coupon was a sexual partner, close friend or acquaintance. Homophile in recruitment patterns (selective affiliation) was present for age, gay openness, and HIV status in Dar es Salaam, and for sexual identification in Tanga.ConclusionsThe personal network sizes and existence of contacts between recruiter and referral indicate that it is possible to use peer-driven interventions to reach MSM for HIV/STI interventions in larger and smaller sub-Saharan African cities. The study was reviewed and approved by the University of Texas Health Science Center's Institutional Review Board (HSC-SPH-10-0033) and the Tanzanian National Institute for Medical Research (NIMR/HQ/R.8a/Vol. IX/1088).
Impact of a pharmacist-delivered discharge and follow-up intervention for patients with acute coronary syndromes in Qatar: a study protocol for a randomised controlled trial
Authors: Zidan Amani , Awaisu Ahmed , Kheir Nadir , Mahfoud Ziyad , Kaddoura Rasha , AlYafei Sumaya , El Hajj Maguy Saffouh 
Published: November 2016

IntroductionAcute coronary syndrome (ACS) is one of the leading causes of morbidity and mortality worldwide. Secondary cardiovascular risk reduction therapy (consisting of an aspirin, a β-blocker, an ACE inhibitor or an angiotensin II receptor blocker and a statin) is needed for all patients with ACS. Less than 80% of patients with ACS in Qatar use this combination after discharge. This study is aimed to evaluate the effectiveness of clinical pharmacist-delivered intervention at discharge and tailored follow-up postdischarge on decreasing hospital readmissions, emergency department (ED) visits and mortality among patients with ACS.Methods and analysisA prospective, randomised controlled trial will be conducted at the Heart Hospital in Qatar. Patients are eligible for enrolment if they are at least 18 years of age and are discharged from any non-surgical cardiology service with ACS. Participants will be randomised into 1 of 3 arms: (1) ‘control’ arm which includes patients discharged during weekends or after hours; (2) ‘clinical pharmacist delivered usual care at discharge’ arm which includes patients receiving the usual care at discharge by clinical pharmacists; and (3) ‘clinical pharmacist-delivered structured intervention at discharge and tailored follow-up postdischarge’ arm which includes patients receiving intensive structured discharge interventions in addition to 2 follow-up sessions by intervention clinical pharmacists. Outcomes will be measured by blinded research assistants at 3, 6 and 12 months after discharge and will include: all-cause hospitalisations and cardiac-related hospital readmissions (primary outcome), all-cause mortality including cardiac-related mortality, ED visits including cardiac-related ED visits, adherence to medications and treatment burden. Percentage of readmissions between the 3 arms will be compared on intent-to-treat basis using χ2test with Bonferroni's adjusted pairwise comparisons if needed.Ethics and disseminationThe study was ethically approved by the Qatar University and the Hamad Medical Corporation Institutional Review Boards. The results shall be disseminated in international conferences and peer-reviewed publications.Trials registration numberNCT02648243; pre-results.
Positive predictive value of cardiovascular diagnoses in the Danish National Patient Registry: a validation study
Authors: Sundbøll Jens , Adelborg Kasper , Munch Troels , Frøslev Trine , Sørensen Henrik Toft , Bøtker Hans Erik , Schmidt Morten 
Published: November 2016

ObjectiveThe majority of cardiovascular diagnoses in the Danish National Patient Registry (DNPR) remain to be validated despite extensive use in epidemiological research. We therefore examined the positive predictive value (PPV) of cardiovascular diagnoses in the DNPR.DesignPopulation-based validation study.Setting1 university hospital and 2 regional hospitals in the Central Denmark Region, 2010–2012.ParticipantsFor each cardiovascular diagnosis, up to 100 patients from participating hospitals were randomly sampled during the study period using the DNPR.Main outcome measureUsing medical record review as the reference standard, we examined the PPV for cardiovascular diagnoses in the DNPR, coded according to the International Classification of Diseases, 10th Revision.ResultsA total of 2153 medical records (97% of the total sample) were available for review. The PPVs ranged from 64% to 100%, with a mean PPV of 88%. The PPVs were ≥90% for first-time myocardial infarction, stent thrombosis, stable angina pectoris, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, takotsubo cardiomyopathy, arterial hypertension, atrial fibrillation or flutter, cardiac arrest, mitral valve regurgitation or stenosis, aortic valve regurgitation or stenosis, pericarditis, hypercholesterolaemia, aortic dissection, aortic aneurysm/dilation and arterial claudication. The PPVs were between 80% and 90% for recurrent myocardial infarction, first-time unstable angina pectoris, pulmonary hypertension, bradycardia, ventricular tachycardia/fibrillation, endocarditis, cardiac tumours, first-time venous thromboembolism and between 70% and 80% for first-time and recurrent admission due to heart failure, first-time dilated cardiomyopathy, restrictive cardiomyopathy and recurrent venous thromboembolism. The PPV for first-time myocarditis was 64%. The PPVs were consistent within age, sex, calendar year and hospital categories.ConclusionsThe validity of cardiovascular diagnoses in the DNPR is overall high and sufficient for use in research since 2010.
Post hoc evaluation of a common-sense intervention for asthma management in community pharmacy
Authors: Watkins Kim , Seubert Liza , Schneider Carl R , Clifford Rhonda 
Published: November 2016

ObjectivesThe aim was to evaluate a common-sense, behavioural change intervention to implement clinical guidelines for asthma management in the community pharmacy setting.DesignThe components of the common-sense intervention were described in terms of categories and dimensions using the Intervention Taxonomy (ITAX) and Behaviour Change Techniques (BCTs) using the Behaviour Change Wheel (BCW), Capability, Opportunity and Motivation-Behaviour (COM-B) System and Behaviour Change Techniques Taxonomy (BCTTv1). The retrospective application of these existing tools facilitated evaluation of the mechanism, fidelity, logistics and rationale of the common-sense intervention.InterventionThe initial intervention study was conducted in 336 community pharmacies in the metropolitan area of Perth, Western Australia. Small-group workshops were conducted in 25 pharmacies; 162 received academic detailing and 149 acted as controls. The intervention was designed to improve pharmacy compliance with guidelines for a non-prescription supply of asthma reliever medications.ResultsRetrospective application of ITAX identified mechanisms for the short-acting β agonists intervention including improving knowledge, behavioural skills, problem-solving skills, motivation and self-efficacy. All the logistical elements were considered in the intervention design but the duration and intensity of the intervention was minimal. The intervention was delivered as intended (as a workshop) to 13.4% of participants indicating compromised fidelity and significant adaptation. Retrospective application of the BCW, COM-B system and BCTTv1 identified 9 different behaviour change techniques as the rationale for promoting guideline-based practice change.ConclusionsThere was a sound rationale and clear mechanism for all the components of the intervention but issues related to logistics, adaptability and fidelity might have affected outcomes. Small group workshops could be a useful implementation strategy in community pharmacy, if logistical issues can be overcome and less adaptation occurs. Duration, intensity and reinforcement need consideration for successful wider implementation. Further qualitative evaluations, triangulation of research and evaluations across interventions should be used to provide a greater understanding of unresolved issues.
Physical activity and incident asthma in adults: the HUNT Study, Norway
Authors: Brumpton Ben M , Langhammer Arnulf , Ferreira Manuel A R , Chen Yue , Mai Xiao-Mei 
Published: November 2016

ObjectiveWe aimed to investigate the associations of physical activity and change in physical activity with incident asthma in a cohort of Norwegian adults.DesignWe conducted a prospective cohort study using data on self-reported physical activity from 3 waves of the Nord-Trøndelag Health Study. Physical activity was reported at the first and second surveys (1985–1986 and 1995–1997). Physical activity was defined from the second survey as inactive or active and the active group was further defined as very low, low, moderate and high. Change in physical activity was defined from the first and second surveys.SettingA large population-based health survey in Norway.ParticipantsWe followed 18 894 adults over 11 years who were free from asthma at baseline in 1995–1997.OutcomeIncident asthma was reported in the third survey (2006–2008).ResultsThe cumulative incidence of asthma was 3.6% over the 11 years. The adjusted OR for incident asthma among active participants compared with inactive participants was 0.95 (95% CI 0.69 to 1.34). The adjusted OR for those who were active in the first or second survey versus those who were inactive in both surveys was 0.64 (95% CI 0.34 to 1.38); however, this association was strongly attenuated in sensitivity analysis (OR 0.93, 95% CI 0.38 to 3.09).ConclusionsWe did not observe statistically significant associations of physical activity or change in physical activity with incident asthma in adults over the 11-year follow-up.
Human Pancreatic Cancer Cells Induce a MyD88-Dependent Stromal Response to Promote a Tumor-Tolerant Immune Microenvironment
Authors: Delitto Daniel , Delitto Andrea E. , DiVita Bayli B. , Pham Kien , Han Song , Hartlage Emily R. , Newby Brittney N. , Gerber Michael H. , Behrns Kevin E. , Moldawer Lyle L. , Thomas Ryan M. , George Thomas J. , Brusko Todd M. , Mathews Clayton E. , Liu Chen , Trevino Jose G. , Hughes Steven J. , Wallet Shannon M. 
Published: November 2016

AbstractCancer cells exert mastery over the local tumor-associated stroma (TAS) to configure protective immunity within the tumor microenvironment. The immunomodulatory character of pancreatic lysates of patients with cancer differs from those with pancreatitis. In this study, we evaluated the cross-talk between pancreatic cancer and its TAS in primary human cell culture models. Upon exposure of TAS to pancreatic cancer cell-conditioned media, we documented robust secretion of IL6 and IL8. This TAS response was MyD88-dependent and sufficient to directly suppress both CD4+ and CD8+ T-cell proliferation, inducing Th17 polarization at the expense of Th1. We found that patients possessed a similar shift in circulating effector memory Th17:Th1 ratios compared with healthy controls. The TAS response also directly suppressed CD8+ T-cell–mediated cytotoxicity. Overall, our results demonstrate how TAS contributes to the production of an immunosuppressive tumor microenvironment in pancreatic cancer. Cancer Res; 77(3); 672–83. ©2016 AACR.
CBX4 Suppresses Metastasis via Recruitment of HDAC3 to the Runx2 Promoter in Colorectal Carcinoma
Authors: Wang Xin , Li Liping , Wu Yuanzhong , Zhang Ruhua , Zhang Meifang , Liao Dan , Wang Gang , Qin Ge , Xu Rui-hua , Kang Tiebang 
Published: November 2016

AbstractPolycomb chromobox (CBX) proteins participate in the polycomb repressive complex (PRC1) that mediates epigenetic gene silencing and endows PRC1 with distinct oncogenic or tumor suppressor functions in a cell-type–dependent manner. In this study, we report that inhibition of cell migration, invasion, and metastasis in colorectal carcinoma requires CBX4-mediated repression of Runx2, a key transcription factor that promotes colorectal carcinoma metastasis. CBX4 inversely correlated with Runx2 expression in colorectal carcinoma tissues, and the combination of high CBX4 expression and low Runx2 expression significantly correlated with overall survival, more so than either CBX4 or Runx2 expression alone. Mechanistically, CBX4 maintained recruited histone deacetylase 3 (HDAC3) to the Runx2 promoter, which maintained a deacetylated histone H3K27 state to suppress Runx2 expression. This function of CBX4 was dependent on its interaction with HDAC3, but not on its SUMO E3 ligase, its chromodomain, or the PRC1 complex. Disrupting the CBX4–HDAC3 interaction abolished Runx2 inhibition as well as the inhibition of cell migration and invasion. Collectively, our data show that CBX4 may act as a tumor suppressor in colorectal carcinoma, and strategies that stabilize the interaction of CBX4 with HDAC3 may benefit the colorectal carcinoma patients with metastases. Cancer Res; 76(24); 7277–89. ©2016 AACR.
The Population Tracking Model: A Simple, Scalable Statistical Model for Neural Population Data
Authors: O’Donnell Cian , Gonçalves J. Tiago , Whiteley Nick , Portera-Cailliau Carlos , Sejnowski Terrence J. 
Published: November 2016

Our understanding of neural population coding has been limited by a lack of analysis methods to characterize spiking data from large populations. The biggest challenge comes from the fact that the number of possible network activity patterns scales exponentially with the number of neurons recorded ([Formula: see text]). Here we introduce a new statistical method for characterizing neural population activity that requires semi-independent fitting of only as many parameters as the square of the number of neurons, requiring drastically smaller data sets and minimal computation time. The model works by matching the population rate (the number of neurons synchronously active) and the probability that each individual neuron fires given the population rate. We found that this model can accurately fit synthetic data from up to 1000 neurons. We also found that the model could rapidly decode visual stimuli from neural population data from macaque primary visual cortex about 65 ms after stimulus onset. Finally, we used the model to estimate the entropy of neural population activity in developing mouse somatosensory cortex and, surprisingly, found that it first increases, and then decreases during development. This statistical model opens new options for interrogating neural population data and can bolster the use of modern large-scale in vivo Ca[Formula: see text] and voltage imaging tools.