bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical performance trajectories and mortality among nursing home residents: results of the SENIOR cohort
Authors: Charles Alexia , Detilleux Johann , Buckinx Fanny , Reginster Jean-Yves , Gruslin Bastien , Bruyère Olivier 
Published: February 2020

Abstract

Background
Previous studies have shown that older people can experience a considerable change in their physical performance (PP) over time.

Objectives
To identify PP trajectories and their association with mortality among nursing home residents who were followed up for 3 years.

Design
Three-year longitudinal observational study.

Setting
Subjects of the SENIOR cohort.

Subjects
Six hundred and four nursing home residents with a mean age of 82.9 ± 9.1 years.

Methods
Baseline characteristics and the date of death were collected from the medical records. PP was assessed annually by the short physical performance battery (SPPB) test. Multiple imputations were performed to manage the missing data. PP trajectory groups were estimated using latent growth curve analysis. Cox proportional hazard regression models were applied to examine the risk of mortality according to the PP trajectory groups.

Results
Three PP trajectory groups were identified: slow decline (N = 96), moderate decline (N = 234) and fast decline (N = 274). After adjustments for potential confounding variables and the baseline SPPB scores, the residents in the fast decline and moderate decline trajectory groups had an increased risk of mortality compared to those in the slow decline trajectory group, with hazard ratio values of 1.78 (95% confidence interval [CI] = 1.34–2.26) and 1.37 (95% CI = 1.10–1.66), respectively.

Conclusions
PP trajectories provide value-added information to baseline geriatric assessments and could be used for predicting 3-year mortality among nursing home residents. It may be important to regularly monitor the SPPB score and signal an alert when a fast decline in PP is detected in older people.
Intrapopulation variation in the behavioral responses of dwarf mongooses to anthropogenic noise
Authors: Eastcott Emma , Kern Julie M , Morris-Drake Amy , Radford Andrew N 
Published: February 2020

AbstractAnthropogenic noise is an increasingly widespread pollutant, with a rapidly burgeoning literature demonstrating impacts on humans and other animals. However, most studies have simply considered if there is an effect of noise, examining the overall cohort response. Although substantial evidence exists for intraspecific variation in responses to other anthropogenic disturbances, this possibility has received relatively little experimental attention with respect to noise. Here, we used field-based playbacks with dwarf mongooses (Helogale parvula) to test how traffic noise affects vigilance behavior and to examine potential variation between individuals of different age class, sex, and dominance status. Foragers exhibited a stronger immediate reaction and increased their subsequent vigilance (both that on the ground and as a sentinel) in response to traffic-noise playback compared with ambient-sound playback. Traffic-noise playback also resulted in sentinels conducting longer bouts and being more likely to change post height or location than in ambient-sound playback. Moreover, there was evidence of variation in noise responses with respect to age class and dominance status but not sex. In traffic noise, foraging pups were more likely to flee and were slower to resume foraging than adults; they also tended to increase their vigilance more than adults. Dominants were more likely than subordinates to move post during sentinel bouts conducted in traffic-noise trials. Our findings suggest that the vigilance–foraging trade-off is affected by traffic noise but that individuals differ in how they respond. Future work should, therefore, consider intrapopulation response variation to understand fully the population-wide effects of this global pollutant.
Occupancy spectrum distribution: application for coalescence simulation with generic mergers
Authors: Becheler Arnaud , Knowles L Lacey 
Published: February 2020

Abstract

Motivation
As the density of sampled population increases, especially as studies incorporate aspects of the spatial landscape to study evolutionary processes, efficient simulation of genetic data under the coalescent becomes a primary challenge. Beyond the computational demands, coalescence-based simulation strategies have to be reconsidered because traditional assumptions about the dynamics of coalescing lineages within local populations may be violated (e.g. more than two daughter lineages may coalesce to a parent at low population densities). Specifically, to efficiently assign n lineages to m parents, the order relation between n and m strongly affects the relevant algorithm for the coalescent simulator (e.g. only when n&lt;2m, it is reasonable to assume that two lineages, at most, can be assigned to the same parent). Controlling the details of the simulation model as a function of n and m is then crucial to represent accurately and efficiently the assignment process, but current implementations make it difficult to switch between different types of lineage mergers at run-time or even compile-time.

Results
With the described occupancy spectrum and algorithm that generates the support of the joint probability distribution of the occupancy spectrum; computation is much faster than realizing the whole assignment process under the coalescent. Using general definitions of lineage merges, which also makes the codebase reusable, we implement several variants of coalescent mergers, including an approximation where low probability spectrums are discarded. Comparison of runtimes and performance of the different C++ highly reusable coalescence mergers (binary, multiple, hybrids) are given, and we illustrate their potential utility with example applications.

Availability and implementation
All components are integrated into Quetzal, an open-source C++ library for coalescence available at https://becheler.github.io/pages/quetzal.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants
Authors: López-Rivera Javier A , Pérez-Palma Eduardo , Symonds Joseph , Lindy Amanda S , McKnight Dianalee A , Leu Costin , Zuberi Sameer , Brunklaus Andreas , Møller Rikke S , Lal Dennis 
Published: February 2020

AbstractA large fraction of rare and severe neurodevelopmental disorders are caused by sporadic de novo variants. Epidemiological disease estimates are not available for the vast majority of these de novo monogenic neurodevelopmental disorders because of phenotypic heterogeneity and the absence of large-scale genomic screens. Yet, knowledge of disease incidence is important for clinicians and researchers to guide health policy planning. Here, we adjusted a statistical method based on genetic data to predict, for the first time, the incidences of 101 known de novo variant-associated neurodevelopmental disorders as well as 3106 putative monogenic disorders. Two corroboration analyses supported the validity of the calculated estimates. First, greater predicted gene-disorder incidences positively correlated with larger numbers of pathogenic variants collected from patient variant databases (Kendall’s τ = 0.093, P-value = 6.9 × 10−6). Second, for six of seven (86%) de novo variant associated monogenic disorders for which epidemiological estimates were available (SCN1A, SLC2A1, SALL1, TBX5, KCNQ2, and CDKL5), the predicted incidence estimates matched the reported estimates. We conclude that in the absence of epidemiological data, our catalogue of 3207 incidence estimates for disorders caused by de novo variants can guide patient advocacy groups, clinicians, researchers, and policymakers in strategic decision-making.
Racial/Ethnic Disparities in the Incidences of Bronchiolitis Requiring Hospitalization
Authors: Inagaki Kengo , Blackshear Chad , Burns Paul A , Hobbs Charlotte V 
Published: February 2020

Abstract

Background
Race/ethnicity is currently not considered a risk factor for bronchiolitis, except for indigenous populations in Western countries. A better understanding of the potential impact of race/ethnicity can inform programs, policies, and practices related to bronchiolitis.

Methods
We performed a population-based, longitudinal, observational study using the State Inpatient Database from New York State in the United States. Infants born between 2009 and 2013 at term without comorbidities were followed for the first 2 years of life, up to 2015. We calculated the cumulative incidences among different race/ethnicity groups, and evaluated the risks by developing logistic regression models.

Results
Of 877 465 healthy, term infants, 10 356 infants were hospitalized with bronchiolitis. The overall cumulative incidence was 11.8 per 1000 births. The cumulative incidences in non-Hispanic White, non-Hispanic Black, Hispanic, and Asian infants were 8.6, 15.4, 19.1, and 6.5 per 1000 births, respectively. In a multivariable analysis adjusting for socioeconomic status, the risks remained substantially high among non-Hispanic Black (odds ratio, 1.42; 95% confidence interval [CI], 1.34–1.51) and Hispanic infants (odds ratio, 1.77; 95% CI, 1.67–1.87), whereas being of Asian race was protective (odds ratio, .62; 95% CI, .56–.69).

Conclusions
The risks of bronchiolitis hospitalization in the first 2 years of life were substantially different by race/ethnicity, with Hispanic and Black infants having the highest rates of hospitalization. Further research is needed to develop and implement culturally appropriate public health interventions to reduce racial and ethnic health disparities in bronchiolitis.
The Relationship Between the Human Immunodeficiency Virus-1 Transmission Network and the HIV Care Continuum in Los Angeles County
Authors: Hassan Adiba , De Gruttola Victor , Hu Yunyin W , Sheng Zhijuan , Poortinga Kathleen , Wertheim Joel O 
Published: February 2020

Abstract

Background
Public health action combating human immunodeficiency virus (HIV) includes facilitating navigation through the HIV continuum of care: timely diagnosis followed by linkage to care and initiation of antiretroviral therapy to suppress viral replication. Molecular epidemiology can identify rapidly growing HIV genetic transmission clusters. How progression through the care continuum relates to transmission clusters has not been previously characterized.

Methods
We performed a retrospective study on HIV surveillance data from 5226 adult cases in Los Angeles County diagnosed from 2010 through 2014. Genetic transmission clusters were constructed using HIV-TRACE. Cox proportional hazard models were used to estimate the impact of transmission cluster growth on the time intervals between care continuum events. Gamma frailty models incorporated the effect of heterogeneity associated with genetic transmission clusters.

Results
In contrast to our expectations, there were no differences in time to the care continuum events among individuals in clusters with different growth dynamics. However, upon achieving viral suppression, individuals in high growth clusters were slower to experience viral rebound (hazard ratio 0.83, P = .011) compared with individuals in low growth clusters. Heterogeneity associated with cluster membership in the timing to each event in the care continuum was highly significant (P &lt; .001), with and without adjustment for transmission risk and demographics.

Conclusions
Individuals within the same transmission cluster have more similar trajectories through the HIV care continuum than those across transmission clusters. These findings suggest molecular epidemiology can assist public health officials in identifying clusters of individuals who may benefit from assistance in navigating the HIV care continuum.
Faecal glucocorticoid metabolites as a measure of adrenocortical activity in polar bears (Ursus maritimus)
Authors: Hein Anna , Palme Rupert , Baumgartner Katrin , von Fersen Lorenzo , Woelfing Benno , Greenwood Alex D , Bechshoft Thea , Siebert Ursula 
Published: February 2020

AbstractAnalysis of faecal glucocorticoid metabolites (FGMs) is frequently applied to assess adrenocortical activity in animal conservation and welfare studies. Faecal sample collection is non-invasive and feasible under field conditions. FGM levels are also less prone to circadian rhythms, episodic fluctuations and short acute stressors than glucocorticoid (GC) levels obtained from other matrices, for example blood or saliva. To investigate the suitability of FGM measurement in polar bears (Ursus maritimus), a species listed as Vulnerable by the IUCN (International Union for Conservation of Nature), a cortisol enzyme immunoassay (EIA) was biologically validated by demonstrating a significant increase in FGMs after five zoo-to-zoo transports. In addition to validating the method, the study also documented an average delay of 7 h until the first occurrence of food colorants in the monitored polar bears, which provides essential information for future studies. After validation, the assay was applied to measure FGM concentrations of five polar bears over a 1-year period. Several pre-defined potentially stressful events were recorded in an event log to measure their effect on FGM concentrations. A mixed model analysis revealed significant increases in FGM concentrations after social tension and environmental changes, whereas season and sex had no significant effect. The study demonstrates that the applied cortisol EIA is suitable for measuring FGM levels in polar bears and that using a carefully validated assay for FGM analysis in combination with a detailed sampling protocol can serve as a valuable tool for evaluating mid- to long-term stress in polar bears. FGM levels can be used to monitor stress in captive polar bears in order to optimize housing conditions but also to elucidate stress responses in wild populations for targeted conservation measures.
The association of long-term outcome and biological sex in patients with acute heart failure from different geographic regions
Authors: Motiejūnaitė Justina , Akiyama Eiichi , Cohen-Solal Alain , Maggioni Aldo Pietro , Mueller Christian , Choi Dong-Ju , Kavoliūnienė Aušra , Čelutkienė Jelena , Parenica Jiri , Lassus Johan , Kajimoto Katsuya , Sato Naoki , Miró Òscar , Peacock W Frank , Matsue Yuya , Voors Adriaan A , Lam Carolyn S P , Ezekowitz Justin A , Ahmed Ali , Fonarow Gregg C , Gayat Etienne , Regitz-Zagrosek Vera , Mebazaa Alexandre 
Published: February 2020

Abstract

Aims
Recent data from national registries suggest that acute heart failure (AHF) outcomes might vary in men and women, however, it is not known whether this observation is universal. The aim of this study was to evaluate the association of biological sex and 1-year all-cause mortality in patients with AHF in various regions of the world.

Methods and results
We analysed several AHF cohorts including GREAT registry (22 523 patients, mostly from Europe and Asia) and OPTIMIZE-HF (26 376 patients from the USA). Clinical characteristics and medication use at discharge were collected. Hazard ratios (HRs) for 1-year mortality according to biological sex were calculated using a Cox proportional hazards regression model with adjustment for baseline characteristics (e.g. age, comorbidities, clinical and laboratory parameters at admission, left ventricular ejection fraction). In the GREAT registry, women had a lower risk of death in the year following AHF [HR 0.86 (0.79–0.94), P &lt; 0.001 after adjustment]. This was mostly driven by northeast Asia [n = 9135, HR 0.76 (0.67–0.87), P &lt; 0.001], while no significant differences were seen in other countries. In the OPTIMIZE-HF registry, women also had a lower risk of 1-year death [HR 0.93 (0.89–0.97), P &lt; 0.001]. In the GREAT registry, women were less often prescribed with a combination of angiotensin-converting enzyme inhibitors and beta-blockers at discharge (50% vs. 57%, P = 0.001).

Conclusion
Globally women with AHF have a lower 1-year mortality and less evidenced-based treatment than men. Differences among countries need further investigation. Our findings merit consideration when designing future global clinical trials in AHF.
Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species
Authors: Al Suwayyid Barakat A , Rankine-Wilson Leah , Speers David J , Wise Michael J , Coombs Geoffrey W , Kahler Charlene M 
Published: February 2020

Abstract
Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.
The great Chinese surprise: the rupture with the United States is real and is happening
Authors: Yang Xiangfeng 
Published: February 2020

Abstract
Ample evidence exists that China was caught off guard by the Trump administration's onslaught of punishing acts—the trade war being a prime, but far from the only, example. This article, in addition to contextualizing their earlier optimism about the relations with the United States under President Trump, examines why Chinese leaders and analysts were surprised by the turn of events. It argues that three main factors contributed to the lapse of judgment. First, Chinese officials and analysts grossly misunderstood Donald Trump the individual. By overemphasizing his pragmatism while downplaying his unpredictability, they ended up underprepared for the policies he unleashed. Second, some ingrained Chinese beliefs, manifested in the analogies of the pendulum swing and the ‘bickering couple’, as well as the narrative of the ‘ballast’, lulled officials and scholars into undue optimism about the stability of the broader relationship. Third, analytical and methodological problems as well as political considerations prevented them from fully grasping the strategic shift against China in the US.
Association Between Maternal Human Papillomavirus Infection and Adverse Pregnancy Outcomes: Systematic Review and Meta-Analysis
Authors: Niyibizi Joseph , Zanré Nadège , Mayrand Marie-Hélène , Trottier Helen 
Published: February 2020

AbstractBackgroundExperimental studies provide evidence of the harmful effect of human papillomavirus (HPV) infection on pregnancy, but observational studies are inconclusive. We systematically assessed the association between HPV and adverse pregnancy outcomes.MethodsWe searched electronic databases up to December 1, 2019. We included observational studies on the association between HPV and adverse pregnancy outcomes. We conducted a random-effect meta-analysis for each outcome and assessed heterogeneity between studies.ResultsFrom 3034 citations, we included 38 studies and quantitatively synthesized 36 studies. Human papillomavirus was significantly associated with preterm birth (age-adjusted odds ratio [aOR], 1.50; 95% confidence interval [CI], 1.19–1.88), preterm premature rupture of membranes (aOR, 1.96; 95% CI, 1.11–3.45), premature rupture of membranes (aOR, 1.42; 95% CI, 1.08–1.86), intrauterine growth restriction (aOR, 1.17; 95% CI, 1.01–1.37), low birth weight (aOR, 1.91; 95% CI, 1.33–2.76), and fetal death (aOR, 2.23; 95% CI, 1.14–4.37). No significant association was found for spontaneous abortion (aOR, 1.14; 95% CI, 0.40–3.22) and pregnancy-induced hypertensive disorders (aOR, 1.24; 95% CI, 0.80–1.92). Most of the studies were of moderate or low quality, and substantial between-studies heterogeneity remained unexplained.ConclusionsWe found a consistent and significant association between HPV and preterm birth and preterm premature rupture of membranes. Human papillomavirus may also be associated with intrauterine growth restriction, low birth weight, and fetal death, but findings are limited by suboptimal control of biases.
Frequency of capsid substitutions associated with GS-6207 in vitro resistance in HIV-1 from antiretroviral-naive and -experienced patients
Authors: Marcelin Anne-Geneviève , Charpentier Charlotte , Jary Aude , Perrier Marine , Margot Nicolas , Callebaut Christian , Calvez Vincent , Descamps Diane 
Published: February 2020

Abstract

Background
GS-6207 is a first-in-class HIV capsid inhibitor, targeting several functions of the HIV capsid in the viral cycle, including viral particle assembly, capsid formation and nuclear entry. GS-6207 has demonstrated picomolar potency in vitro, activity confirmed by high potency in a Phase 1 clinical study, with a long-acting antiretroviral profile with potential dosing every 6 months. In vitro resistance selections previously conducted with increasing doses of GS-6207 have identified capsid variants with reduced susceptibility to GS-6207.

Objectives
To study the prevalence of capsid mutations associated with in vitro resistance to GS-6207 in people living with HIV (PLWH).

Methods
Plasma samples from ART-naive or -experienced PLWH, including PI-experienced people, were sequenced and analysed for the presence of capsid variants identified during in vitro resistance selection: L56I, M66I, Q67H, K70N, N74D, N74S and T107N.

Results
Among the samples from the 1500 patients studied, none of the seven GS-6207 resistance mutations identified during in vitro selection experiments was detected, regardless of HIV subtype or PLWH treatment history.

Conclusions
Out of the seven HIV capsid substitutions previously selected in vitro and shown to confer phenotypic resistance to GS-6207, none of these seven mutations was observed in this large dataset, suggesting that neither PLWH with previous PI failure nor PLWH with emergence of PI resistance mutations are anticipated to impact GS-6207 activity in these diverse HIV-infected populations.