bluuebunny/crossref_metadata_2025_split huggingface dataset:
Notes about the macroscopic fluctuating theory
Authors: Garrido P L 
Published: February 2021

Abstract
The macroscopic fluctuating theory developed during the last 30 years is applied to generic systems described by continuum fields ϕ(x, t) that evolve by a Langevin equation that locally either conserves or does not conserve the field. This paper aims to review well-known basic concepts and results from a pedagogical point of view by following a general framework in a practical and self-consistent way. From the probability of a path, we study the general properties of the system’s stationary state. In particular, we focus on the study of the quasipotential that defines the stationary distribution at the small noise limit. To discriminate between equilibrium and non-equilibrium stationary states, the system’s adjoint dynamics are defined as the system’s time-reversal Markov process. The equilibrium is then defined as the unique stationary state that is dynamically time-reversible, and therefore its adjoint dynamics are equal to those of the original one. This property is confronted with the macroscopic reversibility that occurs when the most probable path to create a fluctuation from the stationary state is equal to the time-reversed path that relaxes it. The lack of this symmetry implies a nonequilibrium stationary state; however, the converse is not true. Finally, we extensively study the two-body correlations at the stationary state. We derive some generic properties at various situations, including a discussion about the equivalence of ensembles in nonequilibrium systems.
Point Defects in InGaN/GaN Core–Shell Nanorods: Role of the Regrowth Interface
Authors: Loeto K , Kusch G , Coulon P-M , Fairclough SM , Boulbar E Le , Girgel I , Shields PA , Oliver RA 
Published: February 2021

Abstract
Core-shell nanorod based light-emitting diodes (LEDs) with their exposed non-polar surfaces have the potential to overcome the limitations of planar LEDs by circumventing the quantum confined stark effect. In this experiment, InGaN/GaN core-shell nanorods were fabricated by a combination of top-down etching and bottom-up regrowth using metal-organic vapour phase epitaxy. When viewing the nanorods along their long axis, monochromatic cathodoluminescence maps taken at the GaN near-band-edge emission energy (3.39 eV) reveal a ring-like region of lower emission intensity. The diameter of this ring is found to be 530 (±20)nm corresponding to the ∼510 nm diameter nickel etch masks used to produce the initial GaN nanopillars. Thus, the dark ring corresponds to the regrowth interface. To understand the origin of the ring, scanning transmission electron microscopy (STEM) and cathodoluminescence (CL) hyperspectral mapping at 10K were performed. STEM imaging reveals the absence of extended defects in the nanorods and indeed near the regrowth interface. Monochromatic CL maps recorded at 10K show that the ring remains dark for monochromatic maps taken at the GaN near-band-edge emission energy (3.47 eV) but is bright when considering the donor-acceptor pair emission energy (3.27 eV). This peculiar anticorrelation indicates that the dark ring originates from an agglomeration of point defects associated with donor-acceptor pair emission. The point defects are incorporated and buried at the GaN regrowth interface from the chemical and/or physical damage induced by etching and lower the radiative recombination rate; limiting the radiative efficiency close to the regrowth interface.
Identification of the gene encoding 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase in Burkholderia sp. HME13
Authors: Muramatsu Hisashi , Maguchi Hiroki , Harada Taisuke , Kashiwagi Takehiro , Kim Chul-Sa , Kato Shin-ichiro , Nagata Shinji 
Published: February 2021

ABSTRACT
Here, we report the identification of the gene encoding a novel enzyme, 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase, in Burkholderia sp. HME13. The enzyme converts 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid and H2O to 3-(2,5-dioxoimidazolidin-4-yl) propionic acid and H2S. Amino acid sequence analysis of the enzyme indicates that it belongs to the DUF917 protein family, which consists of proteins of unknown function.
Quantitative Radiomic Features as New Biomarkers for Alzheimer’s Disease: An Amyloid PET Study
Authors: Ding Yanhui , Zhao Kun , Che Tongtong , Du Kai , Sun Hongzan , Liu Shu , Zheng Yuanjie , Li Shuyu , Liu Bing , Liu Yong ,   Alzheimer’s Disease Neuroimaging Initiative
Published: February 2021

Abstract
Growing evidence indicates that amyloid-beta (Aβ) accumulation is one of the most common neurobiological biomarkers in Alzheimer’s disease (AD). The primary aim of this study was to explore whether the radiomic features of Aβ positron emission tomography (PET) images are used as predictors and provide a neurobiological foundation for AD. The radiomics features of Aβ PET imaging of each brain region of the Brainnetome Atlas were computed for classification and prediction using a support vector machine model. The results showed that the area under the receiver operating characteristic curve (AUC) was 0.93 for distinguishing AD (N = 291) from normal control (NC; N = 334). Additionally, the AUC was 0.83 for the prediction of mild cognitive impairment (MCI) converting (N = 88) (vs. no conversion, N = 100) to AD. In the MCI and AD groups, the systemic analysis demonstrated that the classification outputs were significantly associated with clinical measures (apolipoprotein E genotype, polygenic risk scores, polygenic hazard scores, cerebrospinal fluid Aβ, and Tau, cognitive ability score, the conversion time for progressive MCI subjects and cognitive changes). These findings provide evidence that the radiomic features of Aβ PET images can serve as new biomarkers for clinical applications in AD/MCI, further providing evidence for predicting whether MCI subjects will convert to AD.
Serological Profiling of Group A Streptococcus Infections in Acute Rheumatic Fever
Authors: Lorenz Natalie , Ho Timothy K C , McGregor Reuben , Davies Mark R , Williamson Deborah A , Gurney Jason K , Smeesters Pierre R , Baker Michael G , Moreland Nicole J 
Published: February 2021

Abstract
Rheumatic fever is a serious post-infectious sequela of group A Streptococcus (GAS). Prior GAS exposures were mapped in sera using a large panel of M-type specific peptides. Rheumatic fever patients had serological evidence of significantly more GAS exposures than matched controls suggesting immune priming by repeat infections contributes to pathogenesis.
The Impact of the Auckland Cellulitis Pathway on Length of Hospital Stay, Mortality Readmission Rate, and Antibiotic Stewardship
Authors: Ritchie Stephen R , Cutfield Tim , Lee Arier , Walter Hannah , Gow Robert , Gammie Todd , Punnoose Christy , Nagarkar Suyog , Thomas Mark G 
Published: February 2021

Abstract

Background
The Dundee classification of cellulitis severity, previously shown to predict disease outcomes, provides an opportunity to improve the management of patients with cellulitis.

Methods
We developed and implemented a pathway to guide the management of adults with cellulitis based on their Dundee severity class, and measured its effect on patient outcomes. We compared the outcomes in patients admitted to Auckland City Hospital (ACH) between July 2014 and July 2015 (the baseline cohort) with those in patients admitted between June 2017 and June 2018 (the intervention cohort).

Results
The median length of stay was shorter in the intervention cohort (0.7 days, interquartile range (IQR) 0.1 to 3.0 days) than in the baseline cohort (1.8 days, IQR 0.1 to 4.4 days; P &lt; .001). The 30-day mortality rate declined from 1.8% (19/1092) in the baseline cohort to 0.7% (10/1362; P = .02) in the intervention cohort. The 30-day cellulitis readmission rate increased from 6% in the baseline cohort to 11% (P &lt; .001) in the intervention cohort. Adherence to the ACH cellulitis antibiotic guideline improved from 38% to 48% (P &lt; .01) and was independently associated with reduced length of stay.

Conclusions
The implementation of the Auckland cellulitis pathway, readily generalizable to other settings, improved the outcomes in patients with cellulitis, and resulted in an annual saving of approximately 1000 bed days.
Influenza vaccination: a ‘shot’ at INVESTing in cardiovascular health
Authors: Bhatt Ankeet S , Vardeny Orly , Udell Jacob A , Joseph Jacob , Kim KyungMann , Solomon Scott D 
Published: February 2021

Abstract
The link between viral respiratory infection and non-pulmonary organ-specific injury, including cardiac injury, has become increasingly appreciated during the current coronavirus disease 2019 (COVID-19) pandemic. Even prior to the pandemic, however, the association between acute infection with influenza and elevated cardiovascular risk was evident. The recently published results of the NHLBI-funded INfluenza Vaccine to Effectively Stop CardioThoracic Events and Decompensated (INVESTED) trial, a 5200 patient comparative effectiveness study of high-dose vs. standard-dose influenza vaccine to reduce cardiopulmonary events and mortality in a high-risk cardiovascular population, found no difference between strategies. However, the broader implications of influenza vaccine as a strategy to reduce morbidity in high-risk patients remain extremely important, with randomized controlled trial and observational data supporting vaccination in high-risk patients with cardiovascular disease. Given a favourable risk-benefit profile and widespread availability at generally low cost, we contend that influenza vaccination should remain a centrepiece of cardiovascular risk mitigation and describe the broader context of underutilization of this strategy. Few therapeutics in medicine offer seasonal efficacy from a single administration with generally mild, transient side effects, and exceedingly low rates of serious adverse effects. Infection control measures such as physical distancing, hand washing, and the use of masks during the COVID-19 pandemic have already been associated with substantially curtailed incidence of influenza outbreaks across the globe. Appending annual influenza vaccination to these measures represents an important public health and moral imperative.
Common genetic variants with fetal effects on birth weight are enriched for proximity to genes implicated in rare developmental disorders
Authors: Beaumont Robin N , Mayne Isabelle K , Freathy Rachel M , Wright Caroline F 
Published: February 2021

Abstract
Birth weight is an important factor in newborn survival; both low and high birth weights are associated with adverse later-life health outcomes. Genome-wide association studies (GWAS) have identified 190 loci associated with maternal or fetal effects on birth weight. Knowledge of the underlying causal genes is crucial to understand how these loci influence birth weight and the links between infant and adult morbidity. Numerous monogenic developmental syndromes are associated with birth weights at the extreme ends of the distribution. Genes implicated in those syndromes may provide valuable information to prioritize candidate genes at the GWAS loci. We examined the proximity of genes implicated in developmental disorders (DDs) to birth weight GWAS loci using simulations to test whether they fall disproportionately close to the GWAS loci. We found birth weight GWAS single nucleotide polymorphisms (SNPs) fall closer to such genes than expected both when the DD gene is the nearest gene to the birth weight SNP and also when examining all genes within 258 kb of the SNP. This enrichment was driven by genes causing monogenic DDs with dominant modes of inheritance. We found examples of SNPs in the intron of one gene marking plausible effects via different nearby genes, highlighting the closest gene to the SNP not necessarily being the functionally relevant gene. This is the first application of this approach to birth weight, which has helped identify GWAS loci likely to have direct fetal effects on birth weight, which could not previously be classified as fetal or maternal owing to insufficient statistical power.
Oncostatin M Is a Biomarker of Diagnosis, Worse Disease Prognosis, and Therapeutic Nonresponse in Inflammatory Bowel Disease
Authors: Verstockt Sare , Verstockt Bram , Machiels Kathleen , Vancamelbeke Maaike , Ferrante Marc , Cleynen Isabelle , De Hertogh Gert , Vermeire Séverine 
Published: February 2021

Abstract

Background
Oncostatin M (OSM) has been implicated in the pathogenesis of inflammatory bowel disease (IBD) and as a marker for nonresponsiveness to anti-tumor necrosis factor (TNF) therapy. We further unraveled the potential of OSM and related receptors as markers of diagnosis, prognosis, and therapy response in IBD.

Methods
We collected inflamed mucosal biopsies and serum from patients with Crohn disease (CD) and with ulcerative colitis: (1) newly diagnosed patients who were treatment-naïve, (2) patients initiating anti-TNF or (3) vedolizumab therapy, (4) postoperative patients with CD, and (5) multiple-affected families with IBD including unaffected first-degree relatives (FDRs). We measured the gene expression of mucosal OSM and its receptors OSMR/LIFR and co-receptor IL6ST, and the protein expression of serum OSM. Statistical significance was defined as P &lt; 0.05.

Results
Newly diagnosed patients showed significantly increased mucosal OSM/OSMR compared with control patients, with the highest enrichment for OSM (fold change [FC] &gt;17.9). Likewise, ileal OSM/OSMR were significantly upregulated in postoperative recurrent CD. Serum OSM was increased in newly diagnosed patients and postoperative patients with recurrent CD (FC ≥ 2.6). In families with IBD, higher serum levels were observed in FDRs than in control families (FC = 2.2). Furthermore, elevated colonic OSM/OSMR (but not serum OSM) were associated with the early need for biologic therapy (FC ≥ 1.9), and higher OSM was also predictive of primary nonresponse to both anti-TNF and vedolizumab therapy (FC ≥ 2.4). Immunohistochemistry highlighted mucosal OSM expression in macrophages.

Conclusions
We found that OSM is a diagnostic biomarker in the tissue and serum not only of newly diagnosed patients with IBD and postoperative patients with recurrent CD but also of their FDRs. Higher colonic OSM levels are furthermore associated with poor prognosis and with primary nonresponse to biologic therapies. Therefore, OSM could guide clinical decision-making.
bootComb—an R package to derive confidence intervals for combinations of independent parameter estimates
Authors: Henrion Marc YR 
Published: February 2021

Abstract

Motivation
To address the limits of facility- or study-based estimates, multiple independent parameter estimates may need to be combined. Specific examples include (i) adjusting an incidence rate for healthcare utilisation, (ii) deriving a disease prevalence from a conditional prevalence and the prevalence of the underlying condition, (iii) adjusting a seroprevalence for test sensitivity and specificity. Calculating combined parameter estimates is generally straightforward, but deriving corresponding confidence intervals often is not. bootComb is an R package using parametric bootstrap sampling to derive such intervals.

Implementation
bootComb is a package for the statistical computation environment R.

General features
Apart from a function returning confidence intervals for parameters combined from several independent estimates, bootComb provides auxiliary functions for 6 common distributions (beta, normal, exponential, gamma, Poisson and negative binomial) to derive best-fit distributions for parameters given their reported confidence intervals.

Availability
bootComb is available from the Comprehensive R Archive Network (https://CRAN.R-project.org/package=bootComb).
Mind The Gap! The Role of Political Identity and Attitudes in the Emergence of Belief Gaps
Authors: Saldaña Magdalena , McGregor Shannon , Johnson Tom 
Published: February 2021

Abstract
To more fully understand the belief gap hypothesis, this study examines the effect of political identity, education, and partisan media consumption on the formation of attitudes and false beliefs. Using a two-wave, nationally representative online survey of the U.S., we assess people’s attitudes and beliefs toward climate change, on the one hand, and Syrian refugees, on the other. Building on previous studies, we demonstrate that the effect of one’s political identity on attitudes and false beliefs is contingent upon education, which appears to widen the belief gap in consort with political identity.
Dissecting and modelling the comparative adaptation to water limitation of sorghum and maize: role of transpiration efficiency, transpiration rate and height
Authors: van Oosterom E J , Kulathunga M R D L , Deifel K S , McLean G B , Barrasso C , Wu A , Messina C , Hammer G L 
Published: February 2021

Abstract
Maize is considered less drought-tolerant than sorghum, but sorghum is commonly grown as a short triple dwarf (3dwarf) type, so difference in plant height confounds the species comparison. The objectives of this study were to experimentally determine effects of species and plant height differences on transpiration efficiency (TE) and transpiration rate per unit green leaf area (TGLA) and use findings to explain input parameters in a simulation study on the comparative adaptation of 3dwarf sorghum and maize in environments with contrasting water availability. Maize, tall double dwarf (2dwarf) and short 3dwarf sorghum genotypes were grown in two lysimeter experiments in 2011 in SE Queensland, Australia. Each plant was harvested after anthesis and total transpiration, shoot and root dry mass were measured to estimate TE. Daily TGLA was used to compare transpiration rates. Species and height had limited effect on TE, but significantly affected TGLA. This was associated with differences in biomass allocation. The similar TE but higher TGLA in maize compared with 3dwarf sorghum meant it potentially produces more biomass, consistent with published differences in biomass accumulation and radiation use efficiency (RUE). The simulation study, which used similar TE for maize and 3dwarf sorghum, but captured differences in TGLA through differences in RUE, predicted crossover interactions for grain yield between species and total water use. The greater TGLA of maize decreased grain yield in water-limited environments, but increased yields in well-watered situations. Results highlight that similarity in TE and differences in TGLA can influence comparative adaptation to water limitation.
Genetic Differentiation and Demographic Trajectory of the Insular Formosan and Orii’s Flying Foxes
Authors: Lin Kung-Ping , Chaw Shu-Miaw , Lo Yun-Hwa , Kinjo Teruo , Tung Chien-Yi , Cheng Hsi-Chi , Liu Quintin , Satta Yoko , Izawa Masako , Chen Shiang-Fan , Ko Wen-Ya 
Published: February 2021

AbstractInsular flying foxes are keystone species in island ecosystems due to their critical roles in plant pollination and seed dispersal. These species are vulnerable to population decline because of their small populations and low reproductive rates. The Formosan flying fox (Pteropus dasymallus formosus) is one of the 5 subspecies of the Ryukyu flying fox. Pteropus dasymallus formosus has suffered from a severe decline and is currently recognized as a critically endangered population in Taiwan. On the contrary, the Orii’s flying fox (Pteropus dasymallus inopinatus) is a relatively stable population inhabiting Okinawa Island. Here, we applied a genomic approach called double digest restriction-site associated DNA sequencing to study these 2 subspecies for a total of 7 individuals. We detected significant genetic structure between the 2 populations. Despite their contrasting contemporary population sizes, both populations harbor very low degrees of genetic diversity. We further inferred their demographic history based on the joint folded site frequency spectrum and revealed that both P. d. formosus and P. d. inopinatus had maintained small population sizes for a long period of time after their divergence. Recently, these populations experienced distinct trajectories of demographic changes. While P. d. formosus suffered from a drastic ~10-fold population decline not long ago, P. d. inopinatus underwent a ~4.5-fold population expansion. Our results suggest separate conservation management for the 2 populations—population recovery is urgently needed for P. d. formosus while long-term monitoring for adverse genetic effects should be considered for P. d. inopinatus.
An urban–rural spotlight: evolution at small spatial scales among urban and rural populations of common ragweed
Authors: Kostanecki Adam , Gorton Amanda J , Moeller David A 
Published: February 2021

Abstract
Urbanization produces similar environmental changes across cities relative to their neighboring rural environments. However, there may be high environmental heterogeneity across an urban–rural gradient. Previous research in Minneapolis, MN, USA, found mixed evidence that urban and rural plant populations of common ragweed have locally adapted and that urban populations exhibit greater among-population divergence in ecologically-important traits. To investigate whether there are parallel patterns of urban–rural trait divergence across different urban areas, we examined trait variation across an urban–rural gradient in a second city, St. Louis, MO, USA. We used growth chamber and greenhouse common environments to investigate variation in six traits within and among 16 populations of common ragweed (eight from each urban and rural area). Urban and rural plants diverged significantly in three of five traits, with rural plants having lower percent germination, greater height and lower leaf dissection index. We also found greater variance in plant height among urban compared to rural populations, potentially driven by heterogeneity in human management practices on urban populations. Patterns of urban-rural trait divergence (e.g. in flowering time) differ substantially from those found previously in the reciprocal transplant experiment in Minneapolis, contradicting the hypothesis of parallel evolution across different metropolitan areas. The results of this study suggest that there is considerable population variation in ecologically-important traits, but that urban populations do not consistently differ from neighboring rural populations.
Characterization of the variability in the O+B eclipsing binary HD 165246
Authors: Johnston C , Aimar N , Abdul-Masih M , Bowman D M , White T R , Hawcroft C , Sana H , Sekaran S , Dsilva K , Tkachenko A , Aerts C 
Published: February 2021

ABSTRACT
O-stars are known to experience a wide range of variability mechanisms originating at both their surface and their near-core regions. Characterization and understanding of this variability and its potential causes are integral for evolutionary calculations. We use a new extensive high-resolution spectroscopic data set to characterize the variability observed in both the spectroscopic and space-based photometric observations of the O+B eclipsing binary HD 165246. We present an updated atmospheric and binary solution for the primary component, involving a high level of microturbulence ($13_{-1.3}^{+1.0}\,$ km s−1) and a mass of $M_1=23.7_{-1.4}^{+1.1}$ M⊙, placing it in a sparsely explored region of the Hertzsprung--Russell diagram. Furthermore, we deduce a rotational frequency of $0.690\pm 0.003\,$d−1 from the combined photometric and line-profile variability, implying that the primary rotates at 40 per cent of its critical Keplerian rotation rate. We discuss the potential explanations for the overall variability observed in this massive binary, and discuss its evolutionary context.