bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of early life antibiotic use on atopic and metabolic disorders
Authors: Bejaoui Semeh , Poulsen Michael 
Published: October 2020

Abstract

Background and objectives
The impact of antibiotics use early in life on later-in-life morbidities has received substantial attention as explanations for atopic and metabolic disorders with a surge as modern lifestyle diseases. The objective of this study was to perform meta-analyses to determine if antibiotics administration during the first 2 years of infant life is associated with increased risks of atopic or metabolic disorders later in life.

Methodology
We screened more than 100 English-language prospective and retrospective studies published between January 2002 and March 2020 and assessed study quality using the Newcastle–Ottawa scale. We performed overall and subgroup meta-analyses on 31 high-quality comparable studies on atopic and 23 on metabolic disorders, involving more than 3.5 million children.

Results
Antibiotic exposure prenatally and during the first 2 years of life significantly impacts the risk of developing atopic and metabolic disorders. Exposure during the first 6 months of life appears most critical, consistent with this being the time when the microbiome is most susceptible to irreversible perturbations. The presence of dose−response associations and stronger impacts of broad- than narrow-spectrum antibiotics further point to effects being mediated by microbiota-induced changes.

Conclusions and implications
Our findings support that antibiotics use is a mismatch to modernity that can negatively affect the symbiotic associations we rely on for proper immune function and metabolism. Improving our understanding of these associations, the underlying proximate mechanisms and the impact of antibiotics use on future human−symbiont evolution will be important to improve human health.

Lay Summary
The use of antibiotics in infancy has been suggested to increase the risks of atopic and metabolic disorders later in life. Through meta-analyses of more than 100 studies of &gt;3.5 million children, we confirm these risks, and show that patterns are consistent with effects being due to microbiota-driven changes.
Supplemental selenium source on gut health: insights on fecal microbiome and fermentation products of growing puppies
Authors: Pereira Ana Margarida , Pinna Carlo , Biagi Giacomo , Stefanelli Claudio , Maia Margarida R G , Matos Elisabete , Segundo Marcela A , Fonseca António J M , Cabrita Ana Rita J 
Published: October 2020

ABSTRACT
Selenium is an essential trace element that can modulate the gut microbiome with an impact on host health. The present study aimed to evaluate the effects of organic (selenium-enriched yeast) vs inorganic (sodium selenite) selenium source on fecal end-fermentation products and gut microbiome of puppies from 20 to 52 weeks of age. Alpha and beta diversity of the gut bacterial community were affected by age but not by gender or selenium source. The relative abundance of taxa was differently affected by age, and the DNA concentration of all selected bacterial groups increased with age, although total volatile fatty acids (VFA), acetate, propionate, caproate and lactate concentrations decreased. Organic selenium was associated with a higher concentration of total VFA, propionate and butyrate, a higher number of DNA copies of Lactobacillus, and a trend to lower DNA copies of Escherichia coli. Effects on fecal microbiome during growth differed with selenium source. Females had higher fecal end-fermentation products related to protein degradation, whereas males had higher DNA concentration of Bifidobacterium. Organic selenium might be beneficial over inorganic for dog food supplementation due to the positive modulation of the gut microbiome observed in puppies.
Stump removal and tree species composition promote a bacterial microbiome that may be beneficial in the suppression of root disease
Authors: Modi Dixi , Simard Suzanne , Lavkulich Les , Hamelin Richard C , Grayston Sue J 
Published: October 2020

ABSTRACT
Stumping is an effective forest management practice for reducing the incidence of Armillaria root-rot in regenerating trees, but its impact on the soil bacterial community has not been ascertained. This study investigated the long-term impact of stumping and tree species composition in a 48-year-old trial at Skimikin, British Columbia, on the relative abundance, diversity and taxonomic composition of bacterial communities by sequencing the v4 region of 16S rRNA gene using the Illumina Miseq platform. A total of 108 samples were collected from the forest floor (fermented (F) and humus (H) layers) and mineral soil (A (0–10 cm) and B (10–20 cm) horizons) of 36 plots (half each stumped or unstumped) that were planted with pure stands and admixtures of Douglas-fir, western redcedar and paper birch. Bacterial α-diversity in the B horizon declined with stumping whereas β-diversity was affected both by tree species and stumping treatments, with fir and birch supporting distinct bacterial communities. All horizons of stumped plots of birch and its admixtures were significantly enriched with potential plant growth-promoting bacteria. In conclusion, stumping along with planting birch alone or in admixture with other species promotes a bacterial microbiome that appears beneficial in the suppression of root disease.
Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts
Authors: Santos-Garcia Diego , Mestre-Rincon Natividad , Ouvrard David , Zchori-Fein Einat , Morin Shai 
Published: October 2020

Abstract
Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts "Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host’s evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella, Aleurolobus, and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe.
Genome Size Versus Genome Assemblies: Are the Genomes Truly Expanded in Polyploid Fungal Symbionts?
Authors: Kooij Pepijn W , Pellicer Jaume 
Published: October 2020

Abstract
Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyze their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e., mean 1C = 44.2 Mb). Given these opportunities and aiming to gain novel insights into the evolution of mutualisms, we focus on comparing the quality of whole genome assemblies for fungus-growing ants cultivars (Hymenoptera: Formicidae: Attini) and a free-living relative. Our analyses reveal that currently available methodologies and pipelines for analyzing whole-genome sequence data need refining. By using different genome assemblers, we show that the genome assembly size depends on what software is used. This, in turn, impacts gene number predictions, with higher gene numbers correlating positively with genome assembly size. Furthermore, the majority of fungal genome size data currently available are based on estimates derived from whole-genome assemblies generated from short-read genome data, rather than from the more accurate technique of flow cytometry. Here, we estimated the haploid genome sizes of three ant fungal symbionts by flow cytometry using the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (1871) as a calibration standard. We found that published genome sizes based on genome assemblies are 2.5- to 3-fold larger than our estimates based on flow cytometry. We, therefore, recommend that flow cytometry is used to precalibrate genome assembly pipelines, to avoid incorrect estimates of genome sizes and ensure robust assemblies.
Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal GenusBotrytis
Authors: Valero-Jiménez Claudio A , Steentjes Maikel B F , Slot Jason C , Shi-Kunne Xiaoqian , Scholten Olga E , van Kan Jan A L 
Published: October 2020

AbstractFungi of the genus Botrytis infect &gt;1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained &lt;100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8–39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.
Racial/Ethnic Differences in Mortality in Late Midlife: Have They Narrowed in Recent Years?
Authors: Doza Adit , Jensen Gail A , Tarraf Wassim 
Published: October 2020

Abstract

Objectives
To examine whether racial/ethnic differences in mortality rates have changed in recent years among adults in late midlife, and if so, how.

Methods
We analyze Health and Retirement Study data on non-Hispanic Whites (Whites), non-Hispanic Blacks (Blacks), and English- and Spanish-speaking Hispanics (Hispanic-English and Hispanic-Spanish), aged 50–64 from 2 periods: 1998–2004 (Period 1, n = 8,920) and 2004–2010 (Period 2, n = 7,224). Using survey-generalized linear regression techniques, we model death-by-end-of-period as a function of race/ethnicity and sequentially adjust for a series of period-specific baseline risk factors including demographics, health status, health insurance, health behaviors, and social networks. Regression decomposition techniques are used to assess the contribution of these factors to observed racial/ethnic differences in mortality rates.

Results
The odds ratio for death (ORD) was not statistically different for Blacks (vs. Whites) in Period 1 but was 33% higher in Period 2 (OR = 1.33; 95% confidence interval [CI] = 1.05–1.69). The adjusted ORD among Hispanic-English (vs. Whites) was not statistically different in both periods. The adjusted ORD among Hispanic-Spanish (vs. Whites) was lower (ORD = 0.36; 95% CI = 0.22–0.59) in Period 1 but indistinguishable in Period 2. In Period 1, 50.1% of the disparity in mortality rates among Blacks was explained by baseline health status, 53.1% was explained by financial factors. In Period 2, 55.8% of the disparity in mortality rates was explained by health status, 40.0% by financial factors, and 16.2% by health insurance status.

Discussion
Mortality rates among Blacks and Hispanic-Spanish have risen since the mid-1990s. Hispanic-Spanish may be losing their advantageous lower risk of mortality, long known as the “Hispanic Paradox.”
The Effects of Age Stereotypes on Physical and Mental Health Are Mediated by Self-perceptions of Aging
Authors: Brothers Allyson , Kornadt Anna E , Nehrkorn-Bailey Abigail , Wahl Hans-Werner , Diehl Manfred 
Published: October 2020

Abstract

Objectives
Although the evidence linking views on aging (VoA) with aging outcomes is robust, little is known about how different types of VoA may interact to influence such outcomes. Therefore, this study examined two types of VoA, age stereotypes (AS), representing general VoA, and self-perceptions of aging (SPA), representing personal VoA. We operationalized SPA in terms of awareness of age-related change (AARC), distinguishing between gain- and loss-related SPA (e.g., awareness of positive and negative age-related changes, respectively). Based on theoretical reasoning, we hypothesized that AS would be an antecedent of SPA, and that the effect of AS on physical and mental health would be mediated by SPA.

Method
A total of 819 German and U.S. adults aged 40–98 completed a survey on VoA, physical health, and mental health at baseline and 2.5 years later. Structural equation modeling with latent variables was used to examine the effects of Time 1 AS (predictor) and Time 2 gain- and loss-related SPA (mediators) on physical and mental health outcomes.

Results
As hypothesized, AS predicted later SPA. Loss-related SPA mediated the effect of AS on physical health; both gain- and loss-related SPA mediated the effect of AS on mental health.

Discussion
Congruent with theoretical assumptions, our findings provide empirical support for a directional pathway by which AS shape later SPA. We conclude that AS and SPA may affect physical health outcomes more strongly than mental health outcomes. Studies that assess both types of VoA are needed to illuminate the pathways by which VoA influence aging outcomes.
Efficient probabilistic inversion using the rejection sampler—exemplified on airborne EM data
Authors: Hansen Thomas M 
Published: October 2020

SUMMARY
Probabilistic inversion methods, typically based on Markov chain Monte Carlo, exist that allow exploring the full uncertainty of geophysical inverse problems. The use of such methods is though limited by significant computational demands, and non-trivial analysis of the obtained set of dependent models. Here, a novel approach, for sampling the posterior distribution is suggested based on using pre-calculated lookup tables with the extended rejection sampler. The method is (1) fast, (2) generates independent realizations of the posterior, and (3) does not get stuck in local minima. It can be applied to any inverse problem (and sample an approximate posterior distribution) but is most promising applied to problems with informed prior information and/or localized inverse problems. The method is tested on the inversion of airborne electromagnetic data and shows an increase in the computational efficiency of many orders of magnitude as compared to using the extended Metropolis algorithm.
Defending the Spanish Match in early Stuart England
Authors: Turnbull Emma C 
Published: October 2020

Abstract
This article broadens our understanding of the Spanish Match crisis of the early 1620s by analysing pro-marriage contributions to the public debate. It argues that anti-popery was a key feature of the language of pro-match literature, but that, crucially, supporters of the match dissociated Spain from the wider threat of popish tyranny. The article provides a detailed, contextualized reading of three pamphlets. It considers the complex ways that religious and political views interacted to form subtle anti-papal rhetorical strategies, which challenged the dominant anti-papal narrative aligning Spain with Rome. It thus significantly adds to the literature on early Stuart anti-popery.
Lung volume reduction surgery as salvage procedure after previous use of endobronchial valves
Authors: Caviezel Claudio , Guglielmetti Laura-Chiara , Ladan Mateja , Hansen Henrik Jessen , Perch Michael , Schneiter Didier , Weder Walter , Opitz Isabelle , Franzen Daniel 
Published: October 2020

Abstract

OBJECTIVES
Lung volume reduction (LVR) is an efficient and approved treatment for selected emphysema patients. There is some evidence that repeated LVR surgery (LVRS) might be beneficial, but there are no current data on LVRS after unsuccessful bronchoscopic LVR (BLVR) with endobronchial valves (EBVs). We hypothesize good outcome of LVRS after BLVR with valves.

METHODS
In this study, we retrospectively investigated all patients who underwent LVRS between 2015 and 2019 at 2 centres after previous unsuccessful EBV treatment. They were further divided into subgroups with patients who never achieved the intended improvement after BLVR (primary failure) and patients whose benefit was fading over time due to the natural development of emphysema (secondary failure). Patients with severe air leak after BLVR and immediate concomitant LVRS and fistula closure thereafter were analysed separately.

RESULTS
A total of 38 patients were included. Of these, 19 patients had primary failure, 15 secondary failure and 4 were treated as an emergency due to severe air leak. At 3 months after LVRS, forced expiratory volume in 1 s had improved significantly by 12.5% (P = 0.011) and there was no 90-day mortality. Considering subgroups, patients with primary failure after BLVR seem to profit more than those with secondary failure. Patients with severe air leak after BLVR did not profit from fistula closure with concomitant LVRS.

CONCLUSIONS
LVRS after previous BLVR with EBVs can provide significant clinical improvement with low morbidity, although results might not be as good as after primary LVRS.
“A catalyst for action”: Factors for implementing clinical risk prediction models of infection in home care settings
Authors: Dowding Dawn , Russell David , McDonald Margaret V , Trifilio Marygrace , Song Jiyoun , Brickner Carlin , Shang Jingjing 
Published: October 2020

Abstract

Objective
The study sought to outline how a clinical risk prediction model for identifying patients at risk of infection is perceived by home care nurses, and to inform how the output of the model could be integrated into a clinical workflow.

Materials and Methods
This was a qualitative study using semi-structured interviews with 50 home care nurses. Interviews explored nurses’ perceptions of clinical risk prediction models, their experiences using them in practice, and what elements are important for the implementation of a clinical risk prediction model focusing on infection. Interviews were audio-taped and transcribed, with data evaluated using thematic analysis.

Results
Two themes were derived from the data: (1) informing nursing practice, which outlined how a clinical risk prediction model could inform nurse clinical judgment and be used to modify their care plan interventions, and (2) operationalizing the score, which summarized how the clinical risk prediction model could be incorporated in home care settings.

Discussion
The findings indicate that home care nurses would find a clinical risk prediction model for infection useful, as long as it provided both context around the reasons why a patient was deemed to be at high risk and provided some guidance for action.

Conclusions
It is important to evaluate the potential feasibility and acceptability of a clinical risk prediction model, to inform the intervention design and implementation strategy. The results of this study can provide guidance for the development of the clinical risk prediction tool as an intervention for integration in home care settings.
Coercion at the ICC
Authors: Schack Marc 
Published: October 2020

Abstract
Throughout the history of international criminal justice, it has been the source of fierce debate whether institutions like the International Criminal Court (ICC) can prevent atrocity crimes from being committed by putting coercive judicial pressure on potential rule-breakers. Theories and insights drawn from the domestic literature on criminal justice have shaped much of this debate — based on the assumption that international criminal justice is essentially an internationalized version of domestic criminal justice (what I term the ‘domestic origin’ approach). The present article challenges this perspective by pointing out its shortcomings. It suggests that we should instead — or, at least, additionally — treat these international courts and tribunals as sui generis institutions imbedded in the world of international politics. From this perspective we can therefore draw on rationalist approaches to coercive power within the field of International Relations (IR) to analyse these institutions' coercive capacity. Unlike the domestic origin approach, this would allow researchers to draw on existing work on coercive power focusing on scenarios that play out in the kind of setting (major intra- or interstate conflicts) and involve the types of people (leaders of nations, armies and militias) which courts like the ICC were built to deal with.
Evaluating the Effects of Minimal Risk Natural Products for Control of the Tick, Ixodes scapularis (Acari: Ixodidae)
Authors: Dyer Megan C , Requintina Matthew D , Berger Kathryn A , Puggioni Gavino , Mather Thomas N 
Published: October 2020

Abstract
Knockdown and residual activity of 10 minimal risk natural products (MRNPs), one experimental formulation of nootkatone, and two bifenthrin labels were evaluated against host-seeking nymphal Ixodes scapularis Say using a novel micro-plot product screening system placed in a landscape setting similar to a wooded residential property. The MRNPs evaluated included Tick Stop, EcoPCO EC-X, Met52 EC, CedarCide PCO Choice, EcoEXEMPT IC2, EcoSMART Organic Insecticide, Essentria IC3, privately labeled products 1 and 2 (based on EcoEXEMPT IC2 and sold as a professional pest control application), and Tick Killz. Just the nootkatone and 4 of these 10 products tested (EcoPCO EC-X, Met52 EC, EcoEXEMPT IC2, and Essentria IC3) had statistically significant (P &lt; 0.05) knockdown effects (killed ticks while active in the arenas) when compared to water-only controls, but only 2 of these, EcoPCO EC-X and nootkatone, displayed significant residual tick-killing activity after weathering naturally in the landscape for 2 wk prior to tick application/testing. Moreover, botanical oil-based products with the same active ingredients provided inconsistent results when tested multiple times across study years.