bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region
Authors: Dellicour Simon , Lemey Philippe , Artois Jean , Lam Tommy T , Fusaro Alice , Monne Isabella , Cattoli Giovanni , Kuznetsov Dmitry , Xenarios Ioannis , Dauphin Gwenaelle , Kalpravidh Wantanee , Von Dobschuetz Sophie , Claes Filip , Newman Scott H , Suchard Marc A , Baele Guy , Gilbert Marius 
Published: November 2019

Abstract

Motivation
The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative.

Results
We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities.

Availability and implementation
Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10.

Supplementary information
Supplementary data are available at Bioinformatics online.
Social context alters retreat- and nest-site selection in a globally invasive gecko, Hemidactylus frenatus
Authors: Muller Benjamin J , Andrews Robin M , Schwarzkopf Lin , Pike David A 
Published: November 2019

AbstractMicrohabitat orientation and structure and the presence of conspecifics may strongly influence the choice of habitat. We studied how these variables influence retreat- and nest-site selection in gravid females of a globally successful invasive species, the Asian house gecko (Hemidactylus frenatus). When provided with various substrates (vertical and horizontal ceramic tiles, vertical and horizontal plywood tiles, horizontal bark over leaf litter, vertical bark over a log, and sand) gravid female geckos preferred to retreat to, and nest in, materials with crevices commonly found in urban habitats. When housed alone, gravid females most frequently retreated to vertical ceramic tile or wooden crevices, and 66.7% nested in vertical ceramic tiles. When housed with two other conspecifics, gravid females most frequently retreated to vertical ceramic tiles, but selected a wider range of nest sites. Overall, gravid geckos housed alone typically nested in the same substrates that they used as diurnal retreats; when housed in groups, however, females oviposited in locations different from those they selected as retreats. Thus, H. frenatus females use a wider range of substrates when conspecifics are present. Invasion success in this species might be driven, in part, by preferences for retreat and nest substrates that are common in human-dominated habitats.
Development and Validation of a Novel Stability-Indicating RP-HPLC Method for Simultaneous Determination of Tezacaftor and Ivacaftor in Fixed Dose Combination
Authors: Singh Narendra , Bansal Parveen , Maithani Mukesh , Chauhan Yashpal 
Published: November 2019

Abstract
A simple and precise novel stability-indicating method for the simultaneous estimation of tezacaftor and ivacaftor in combined tablet dosage form was developed and validated using reversed-phase high-performance liquid chromatography (RP-HPLC). The method is being reported for the first time and includes an estimation of degradation products produced post-stress conditions without any extraction or derivatization. The chromatographic separation of the drugs was achieved with a Symmetry Shield RP18 Column (100 Å, 5 μm, 4.6 mm × 250 mm) using a mixture of buffer, methanol and acetonitrile (42:27:31 v/v/v) as mobile phase. The buffer used in mobile phase contained 35 mM potassium dihydrogen phosphate, and its pH was adjusted to 7.0 ± 0.02 with 20% orthophosphoric acid. The instrument was set at flow rate of 1.2 mL min−1 at ambient temperature and the wavelength of UV-visible detector at 275 nm. The developed method could be suitable for the quantitative determination of these drugs in pharmaceutical preparations and also for quality control in bulk manufacturing. Stress testing was performed to prove the specificity. No interference was observed from its stress degradation products. The statistical analysis was done by using F-test and t-test at 95% confidence level.
A Parsimonious Host Inflammatory Biomarker Signature Predicts Incident Tuberculosis and Mortality in Advanced Human Immunodeficiency Virus
Authors: Manabe Yukari C , Andrade Bruno B , Gupte Nikhil , Leong Samantha , Kintali Manisha , Matoga Mitch , Riviere Cynthia , Samaneka Wadzanai , Lama Javier R , Naidoo Kogieleum , Zhao Yue , Johnson W Evan , Ellner Jerrold J , Hosseinipour Mina C , Bisson Gregory P , Salgame Padmini , Gupta Amita 
Published: November 2019

AbstractBackgroundPeople with advanced human immunodeficiency virus (HIV) (CD4 &lt; 50) remain at high risk of tuberculosis (TB) or death despite the initiation of antiretroviral therapy (ART). We aimed to identify immunological profiles that were most predictive of incident TB disease and death.MethodsThe REMEMBER randomized clinical trial enrolled 850 participants with HIV (CD4 &lt; 50 cells/µL) at ART initiation to receive either empiric TB treatment or isoniazid preventive therapy (IPT). A case-cohort study (n = 257) stratified by country and treatment arm was performed. Cases were defined as incident TB or all-cause death within 48 weeks after ART initiation. Using multiplexed immunoassay panels and ELISA, 26 biomarkers were assessed in plasma.ResultsIn total, 52 (6.1%) of 850 participants developed TB; 47 (5.5%) died (13 of whom had antecedent TB). Biomarkers associated with incident TB overlapped with those associated with death (interleukin [IL]-1β, IL-6). Biomarker levels declined over time in individuals with incident TB while remaining persistently elevated in those who died. Dividing the cohort into development and validation sets, the final model of 6 biomarkers (CXCL10, IL-1β, IL-10, sCD14, tumor necrosis factor [TNF]-α, and TNF-β) achieved a sensitivity of 0.90 (95% confidence interval [CI]: .87–.94) and a specificity of 0.71(95% CI: .68–.75) with an area under the curve (AUC) of 0.81 (95% CI: .78–.83) for incident TB.ConclusionAmong people with advanced HIV, a parsimonious inflammatory biomarker signature predicted those at highest risk for developing TB despite initiation of ART and TB preventive therapies. The signature may be a promising stratification tool to select patients who may benefit from increased monitoring and novel interventions.Clinical Trials RegistrationNCT01380080
The risk for urinary tract infections with sodium-glucose cotransporter 2 inhibitors: no longer a cause of concern?
Authors: Sarafidis Pantelis A , Ortiz Alberto 
Published: November 2019

Abstract
Sodium–glucose co-transporter-2 (SGLT2) inhibitors improve cardiovascular and renal outcomes in patients with type 2 diabetes, including those with diabetic kidney disease. However, the US Food and Drug Administration and European Medicines Agency warnings about potential adverse effects, such as urosepsis and pyelonephritis, based on post-marketing case reports, may deter physicians from prescribing these drugs. A recent evaluation of two large US-based databases of commercial claims failed to find evidence for an increased risk of urinary tract infection (UTI) or severe UTI in type 2 diabetes patients who were prescribed an SGLT2.
O181 SERUM C-REACTIVE PROTEIN CAN BE AN EARLY PREDICTOR OF LENGHT OF HOSPITAL STAY AFTER MINIMALLY INVASIVE OESOPHAGECTOMY
Authors: Corsi Gabriele , Patel Krashna , Abbassi Omar , Gudkalli Zobia , O’Hara David , Tang Cheuk-Bong , Jayanthi Naga Venkatesh , Zanotti Daniela , Charalabopoulos Alexandros , Lorenzi Bruno 
Published: November 2019

Abstract

Aim
Oesophagectomy is associated with a significant number of potential complications affecting the lenght of the post-operative recovery. Serum C-reactive protein (CRP) is an acute phase protein which has been linked to early detection of post-operative complications, including but not limited to anastomotic leak. The aim of this retrospective study was to investigate the value of CRP elevation in the early post-operative days as a predictor of lenght of Hospital stay after minimally invasive oesophagectomy for cancer.

Background and Methods
The study group included 88 patients undergoing minimally invasive oesophagectomy for cancer from September 2017 to April 2019.
CRP values on post-operative day 1,3,5 and 7 were retrieved and correlated to overall lenght of stay. Post-operative morbidity and mortality were also recorded.

Results
The approach was fully minimally invasive in 65 patients (74%) and hybrid in the remaining 23 (26%). The median length of stay was 11 days (IQR, 6-105 days) with overall mortality of 3.4% (n=3). Gastro-intestinal complications occurred in 15 patients (17%). The overall surgical or endoscopic re-intervention rate was 13.6% (n=12).
The median CRP value was 54.8, 167, 143 and 134 mg/L, respectively on day 1,3,5 and 7.
There was a positive correlation between CRP and length of stay on day 1, 3 and 7. A cut-off value of 167 mg/L on day 3 appeared to be a significant predictor of increased lenght of stay (12.8 vs 23.3 days, p=0.008).

Conclusion
CRP levels above 167mg/L on post-operative day 3 were associated with a prolonged lenght of hospital stay in our group of patients. Elevated CRP in the early post-operative period could represent a useful tool to predict lenght of stay after minimally invasive oesophagectomy.
The Effect of Rural Credit on Deforestation: Evidence from the Brazilian Amazon
Authors: Assunção Juliano , Gandour Clarissa , Rocha Romero , Rocha Rudi 
Published: November 2019

Abstract
In 2008, the Brazilian government made the concession of rural credit in the Amazon conditional upon stricter requirements as an attempt to curb forest clearings. This article studies the impact of this innovative policy on deforestation. Difference-in-differences estimations based on a panel of municipalities show that the policy change led to a substantial reduction in deforestation, mostly in municipalities where cattle ranching is the leading economic activity. The results suggest that the mechanism underlying these effects was a restriction in access to rural credit, one of the main support mechanisms for agricultural production in Brazil.
Heterogeneous impacts of cash transfers on farm profitability. Evidence from a randomised study in Lesotho
Authors: Prifti Ervin , Daidone Silvio , Pace Noemi , Davis Benjamin 
Published: November 2019

AbstractWe estimate the average treatment effect (ATE) of cash transfers on farm profitability by exploiting a randomised control trial for the evaluation Lesotho’s biggest transfer program. We also explore impact heterogeneity by unpacking the ATE into group-specific parameters. We estimate conditional average treatment effects to describe how treatment effects vary with selected covariates and quantile treatment effects to illustrate the variability of effects at different outcome levels. We find that the program had sizable impacts on farm profitability, but these impacts are spread unevenly in the population. The program benefited more those with greater productive potential and had strong distributional impacts.
Positive linkage between bacterial social traits reveals that homogeneous rather than specialised behavioral repertoires prevail in natural Pseudomonas communities
Authors: Kramer Jos , López Carrasco Miguel Ángel , Kümmerli Rolf 
Published: November 2019

ABSTRACTBacteria frequently cooperate by sharing secreted metabolites such as enzymes and siderophores. The expression of such ‘public good’ traits can be interdependent, and studies on laboratory systems have shown that trait linkage affects eco-evolutionary dynamics within bacterial communities. Here, we examine whether linkage among social traits occurs in natural habitats by examining investment levels and correlations between five public goods (biosurfactants, biofilm components, proteases, pyoverdines and toxic compounds) in 315 Pseudomonas isolates from soil and freshwater communities. Our phenotypic assays revealed that (i) social trait expression profiles varied dramatically; (ii) correlations between traits were frequent, exclusively positive and sometimes habitat-specific; and (iii) heterogeneous (specialised) trait repertoires were rarer than homogeneous (unspecialised) repertoires. Our results show that most isolates lie on a continuum between a ‘social’ type producing multiple public goods, and an ‘asocial’ type showing low investment into social traits. This segregation could reflect local adaptation to different microhabitats, or emerge from interactions between different social strategies. In the latter case, our findings suggest that the scope for competition among unspecialised isolates exceeds the scope for mutualistic exchange of different public goods between specialised isolates. Overall, our results indicate that complex interdependencies among social traits shape microbial lifestyles in nature.
Veteran Suicide Risk Factors: A National Sample of Nonveteran and Veteran Men Who Died by Suicide
Authors: Wood David S , Wood Bethany M , Watson Aislinn , Sheffield Devan , Hauter Helena 
Published: November 2019

AbstractVeteran suicide is a serious public health problem. Some data suggest that veteran suicide risk profiles differ from those of nonveterans. Records for veteran (n = 21,692) and nonveteran (n = 83,430) men who died by suicide were examined from 17 U.S. states using the National Violent Death Reporting System data. Seventeen precipitating factors were examined and combined through meta-analysis of proportions. Many precipitating factors were found to be less frequent for veterans. A smaller number of factors were found to be higher in the veteran population, including physical health problems. A sizable cumulative effect size (1.02) was observed, suggesting that veteran and nonveteran men show meaningful and substantive differences in their risk profiles—differences that should be considered when planning and implementing suicide prevention and intervention efforts. The conspicuous role of physical health problems among veterans who die by suicide is discussed. The article concludes with specific practice recommendations for social workers.
Highlighting growth regulation processes in fish populations by a simplex simulation approach: application to Merluccius hubbsi stocks in the Southwestern Atlantic
Authors: Semmar Nabil , Vaz-dos-Santos André M 
Published: November 2019

AbstractA new simplex-based simulation approach (Spx) was developed to highlight multidirectional and multi-scale relationships between morphometric variables helping to functionally differentiate biological (fish) groups for better stocks definition and monitoring. Application concerned Merluccius hubbsi sampled in 1968–1972 and 2004 in six Southwestern Atlantic areas. Simulation results highlighted negative trends opposing front to back compartments indicating competition for body biomass distribution. However, top and bottom parts within these compartments were positively correlated indicating cooperative processes in favour of target local growth regulation. Positive and negative trends of growth regulation were also highlighted at lower body scale, notably between smaller components constituting body front compartment. On a geographical scale, average regulation levels of same morphometric variables showed monotonic or alternated variations between successive fish groups. This highlighted target and modulated growth regulations governing biomass distribution in different body parts by geographical-dependent ways. Under dynamical aspect (1968–1972 vs. 2004), growth regulation of mouth tended to increase with time leading to conclude on morphometric responses of M. hubbsi to overfishing pressure. Spx results were confirmed by several traditional approaches which showed less integrative aspect.
Determinants of the population health distribution: an illustration examining body mass index
Authors: Bann David , Fitzsimons Emla , Johnson William 
Published: November 2019

Abstract
Most epidemiological studies examine how risk factors relate to average difference in outcomes (linear regression) or odds of a binary outcome (logistic regression); they do not explicitly examine whether risk factors are associated differentially across the distribution of the health outcome investigated. This paper documents a phenomenon found repeatedly in the minority of epidemiological studies which do this (via quantile regression): associations between a range of established risk factors and body mass index (BMI) are progressively stronger in the upper ends of the BMI distribution. In this paper, we document this finding and provide illustrative evidence of it in the 1958 British birth cohort study. Associations of low childhood socio-economic position, high maternal weight, low childhood general cognition and adult physical inactivity with higher BMI are larger at the upper end of the BMI distribution, on both absolute and relative scales. For example, effect estimates for socio-economic position and childhood cognition were around three times larger at the 90th compared with 10th quantile, while effect estimates for physical inactivity were increasingly larger from the 50th to 90th quantiles, yet null at lower quantiles. We provide potential explanations for these findings and discuss implications. Risk factors may have larger causal effects among those in worse health, and these effects may not be discovered when health is only examined in average terms. In such scenarios, population-based approaches to intervention may have larger benefits than anticipated when assuming equivalent benefit across the population. Further research is needed to understand why effect estimates differ across the BMI outcome distribution and to investigate whether differential effects exist for other physical and mental health outcomes.
Clinical Diagnostic Testing for Human Cytomegalovirus Infections
Authors: Razonable Raymund R , Inoue Naoki , Pinninti Swetha G , Boppana Suresh B , Lazzarotto Tiziana , Gabrielli Liliana , Simonazzi Giuliana , Pellett Philip E , Schmid D Scott 
Published: November 2019

Abstract
Human cytomegalovirus (HCMV) infections are among the most common complications arising in transplant patients, elevating the risk of various complications including loss of graft and death. HCMV infections are also responsible for more congenital infections worldwide than any other agent. Congenital HCMV (cCMV) infections are the leading nongenetic cause of sensorineural hearing loss and a source of significant neurological disabilities in children. While there is overlap in the clinical and laboratory approaches to diagnosis of HCMV infections in these settings, the management, follow-up, treatment, and diagnostic strategies differ considerably. As yet, no country has implemented a universal screening program for cCMV. Here, we summarize the issues, limitations, and application of diagnostic strategies for transplant recipients and congenital infection, including examples of screening programs for congenital HCMV that have been implemented at several centers in Japan, Italy, and the United States.
Impact of oral amoxicillin and amoxicillin/clavulanic acid treatment on bacterial diversity and β-lactam resistance in the canine faecal microbiota
Authors: Espinosa-Gongora Carmen , Jessen Lisbeth Rem , Kieler Ida Nordang , Damborg Peter , Bjørnvad Charlotte Reinhard , Gudeta Dereje Dadi , Pires dos Santos Teresa , Sablier-Gallis Frédérique , Sayah-Jeanne Sakina , Corbel Tanguy , Nevière Agathe , Hugon Perrine , Saint-Lu Nathalie , de Gunzburg Jean , Guardabassi Luca 
Published: November 2019

Abstract

Background
Aminopenicillins with or without a β-lactamase inhibitor are widely used in both human and veterinary medicine. However, little is known about their differential impact on the gut microbiota and development of antimicrobial resistance.

Objectives
To investigate changes in the faecal microbiota of dogs treated with amoxicillin or amoxicillin/clavulanic acid.

Methods
Faeces collected from 42 dogs (21 per treatment group) immediately before, during and 1 week after termination of oral treatment with amoxicillin or amoxicillin/clavulanic acid were analysed by culture and 16S rRNA gene sequence analysis.

Results
In both groups, bacterial counts on ampicillin selective agar revealed an increase in the proportion of ampicillin-resistant Escherichia coli during treatment, and an increased occurrence and proportion of ampicillin-resistant enterococci during and after treatment. 16S rRNA gene analysis showed reductions in microbial richness and diversity during treatment followed by a return to pre-treatment conditions approximately 1 week after cessation of amoxicillin or amoxicillin/clavulanic acid treatment. While no significant differences were observed between the effects of amoxicillin and amoxicillin/clavulanic acid on microbial richness and diversity, treatment with amoxicillin/clavulanic acid reduced the abundance of taxa that are considered part of the beneficial microbiota (such as Roseburia, Dialister and Lachnospiraceae) and enriched Escherichia, although the latter result was not corroborated by phenotypic counts.

Conclusions
Our results suggest a limited effect of clavulanic acid on selection of antimicrobial resistance and microbial richness when administered orally in combination with amoxicillin. However, combination with this β-lactamase inhibitor appears to broaden the spectrum of amoxicillin, with potential negative consequences on gut health.
Wide-angle redshift-space distortions at quasi-linear scales: cross-correlation functions from Zel’dovich approximation
Authors: Taruya Atsushi , Saga Shohei , Breton Michel-Andrès , Rasera Yann , Fujita Tomohiro 
Published: November 2019

ABSTRACT
Redshift-space distortions (RSD) in galaxy redshift surveys generally break both the isotropy and homogeneity of galaxy distribution. While the former aspect is particularly highlighted as a probe of growth of structure induced by gravity, the latter aspect, often quoted as wide-angle RSD but ignored in most of the cases, will become important and critical to account for as increasing the statistical precision in next-generation surveys. However, the impact of wide-angle RSD has been mostly studied using linear perturbation theory. In this paper, employing the Zel’dovich approximation, i.e. first-order Lagrangian perturbation theory for gravitational evolution of matter fluctuations, we present a quasi-linear treatment of wide-angle RSD, and compute the cross-correlation function. The present formalism consistently reproduces linear theory results, and can be easily extended to incorporate relativistic corrections (e.g. gravitational redshift).