bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inactivation of AdeABC and AdeIJK efflux pumps elicits specific nonoverlapping transcriptional and phenotypic responses in Acinetobacter baumannii
Authors: Leus Inga V. , Adamiak Justyna , Trinh Anhthu N. , Smith Richard D. , Smith Lauren , Richardson Sophie , Ernst Robert K. , Zgurskaya Helen I. 
Published: August 2020

AbstractMultidrug resistant (MDR) strains of Acinetobacter baumannii present a serious clinical challenge. The development of antibiotic resistance in this species is enabled by efflux pumps of the Resistance‐Nodulation‐Division (RND) superfamily of proteins creating an efficient permeability barrier for antibiotics. At least three RND pumps, AdeABC, AdeIJK, and AdeFGH are encoded in the A. baumannii genome and are reported to contribute to antibiotic resistance in clinical isolates. In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075. We found that not only the two pumps have nonoverlapping substrate specificities, their inactivation leads to specific nonoverlapping changes in gene expression as determined by RNA sequencing and confirmed by gene knockouts and growth phenotypes. Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK. We identified additional efflux pumps and transcriptional regulators that contribute to MDR phenotype of clinical A. baumannii isolates.
Bottlenose dolphins (Tursiops truncatus) in North Dalmatia, Croatia: Occurrence and demographic parameters
Authors: Pleslić Grgur , Rako‐Gospić Nikolina , Holcer Draško 
Published: August 2020

AbstractThe common bottlenose dolphin (Tursiops truncatus) population along the eastern Adriatic coast is believed to comprise discrete communities, yet many of them are unstudied. This study provides the first description of occurrence and demographic parameters for the community inhabiting waters of North Dalmatia. Dedicated boat‐based surveys conducted in summer months from 2013 to 2017 resulted in 13,896 km of research effort and 284 dolphin sightings from which 336 individuals were identified. Site‐fidelity analysis revealed that 52.1% of encountered marked adults occur in the area regularly or occasionally. No significant difference among years could be found for mean group sizes (5.73–7.46) and group encounter rates (1.159–1.942 groups/100 km). Pollock's Robust Design models estimated annually variable adult apparent survival (0.737–0.986) and constant temporary emigration rate of 0.172. The estimated abundance varied annually from 116 to 138 individuals and showed a negative slope, but a significant trend could not be confirmed. Age‐dependent models estimated first‐year calf survival at 0.875. These results provide a baseline for informed management of two Sites of Community Importance, and a benchmark for future monitoring in North Dalmatian waters, an area under significant anthropogenic pressure.
Functional connectivity in migraineurs with photo‐, phono‐, or osmophobia: A static and dynamic resting‐state functional magnetic resonance imaging study
Authors: Imai Noboru , Moriya Asami , Kitamura Eiji 
Published: August 2020

AbstractBackgroundMigraine attacks are associated with photo‐, phono‐, and osmophobia, which may be caused by different pathophysiological mechanisms because they are not present in all migraineurs.AimHere, we investigated differences in static and dynamic resting‐state functional connectivities between patients with and without photo‐, phono‐, or osmophobia.MethodsSixty‐two women with migraine with/without photo‐, phono‐, or osmophobia underwent 3‐T functional magnetic resonance imaging during the interictal phase. We compared static and dynamic resting‐state functional connectivities using region of interest‐to‐region of interest analysis of 91 cortical, 15 subcortical, and 26 cerebellar areas.ResultsThe static resting‐state functional connectivity analysis showed that patients with photophobia had 18 different significant connectivity pairs, those with phonophobia had 15, and those with osmophobia had significantly higher connectivity between the right cerebellar lobule and brainstem. The dynamic resting‐state functional connectivity analysis showed that patients with photophobia had 16 different significant connectivity pairs, those with phonophobia had eight without main regions, and those with osmophobia had 14. Static and dynamic functional connectivity alterations in patients with phonophobia and osmophobia had no significant overlapping connectivity pairs.ConclusionOur results showed that static and dynamic resting‐state functional connectivities in migraineurs with and without photo‐, phono‐, or osmophobia differed.
Nurses' perception of their role in extracorporeal membrane oxygenation care: A qualitative assessment
Authors: Alshammari Muna A. , Vellolikalam Chitra , Alfeeli Sadeq 
Published: August 2020

AbstractBackgroundRecently, there has been interest in the education of nursing personnel to provide veno‐venous extracorporeal membrane oxygenation in Kuwait. There is need to understand the experience of nurses who take on this new role.AimWe aimed to explore the perspectives of nurses about their role, with a special focus on their competencies and the challenges faced while caring for patients who require extracorporeal membrane oxygenation.MethodsWe used a qualitative descriptive approach, using in‐depth individual interviews. Nineteen nurses working with veno‐venous an extracorporeal membrane oxygenation machine in an adult intensive care unit of a general hospital in Kuwait were included in the study. Interviews were audio‐recorded, transcribed verbatim, and analysed thematically.ResultsThe role of nurses was found to be diverse and challenging and involved engaging in multiple responsibilities. Nurses worked with other health care providers in a team, which facilitated their performance. Nurses viewed themselves as competent to perform their role and attributed their competency mainly to the training received and the experience spent providing extracorporeal membrane oxygenation care. In executing their role, nurses reported encountering significant challenges, including heavy workload, inefficient communication among colleagues, and a lack of an organized/supportive system.ConclusionsThis study suggests that nurses play an integral role in the management of patients on extracorporeal membrane oxygenation. An understanding of their role and their competence, the challenges they face with in the care setting, and providing a supportive environment is essential for transformation in the practice of extracorporeal membrane oxygenation nursing.
PHOTO‐SENSITIVE LEAF ROLLING 1 encodes a polygalacturonase that modifies cell wall structure and drought tolerance in rice
Authors: Zhang Guangheng , Hou Xin , Wang Li , Xu Jing , Chen Jian , Fu Xue , Shen Nianwei , Nian Jinqiang , Jiang Zhuanzhuan , Hu Jiang , Zhu Li , Rao Yuchun , Shi Yafei , Ren Deyong , Dong Guojun , Gao Zhenyu , Guo Longbiao , Qian Qian , Luan Sheng 
Published: August 2020

Summary

The biosynthesis and modification of cell wall composition and structure are controlled by hundreds of enzymes and have a direct consequence on plant growth and development. However, the majority of these enzymes has not been functionally characterised.

Rice mutants with leaf‐rolling phenotypes were screened in a field. Phenotypic analysis under controlled conditions was performed for the selected mutant and the relevant gene was identified by map‐based cloning. Cell wall composition was analysed by glycome profiling assay.

We identified a photo‐sensitive leaf rolling 1 (psl1) mutant with ‘napping’ (midday depression of photosynthesis) phenotype and reduced growth. The PSL1 gene encodes a cell wall‐localised polygalacturonase (PG), a pectin‐degrading enzyme. psl1 with a 260‐bp deletion in its gene displayed leaf rolling in response to high light intensity and/or low humidity. Biochemical assays revealed PG activity of recombinant PSL1 protein. Significant modifications to cell wall composition in the psl1 mutant compared with the wild‐type plants were identified. Such modifications enhanced drought tolerance of the mutant plants by reducing water loss under osmotic stress and drought conditions.

Taken together, PSL1 functions as a PG that modifies cell wall biosynthesis, plant development and drought tolerance in rice.
Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift
Authors: Gabaldón Toni 
Published: August 2020

AbstractEvolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries. However, mounting evidence from comparative genomics indicates that this paradigm is often violated. Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes. Nonvertical evolution might be more restricted in eukaryotes than in prokaryotes, yet it is not negligible and can be common in certain groups. Recognition of such processes brings about the need to incorporate this complexity into our models, as well as to conceptually reframe eukaryotic diversity and evolution. Here, I review the recent work from genomics studies that supports the effects of nonvertical modes of evolution including introgression, hybridization, and horizontal gene transfer in different eukaryotic groups. I then discuss emerging patterns and effects, illustrated by specific examples, that support the conclusion that nonvertical processes are often at the root of important evolutionary transitions and adaptations. I will argue that a paradigm shift is needed to naturally accommodate nonvertical processes in eukaryotic evolution.
Advances in fungal chemical genomics for the discovery of new antifungal agents
Authors: Xue Alice , Robbins Nicole , Cowen Leah E. 
Published: August 2020

AbstractInvasive fungal infections have escalated from a rare curiosity to a major cause of human mortality around the globe. This is in part due to a scarcity in the number of antifungal drugs available to combat mycotic disease, making the discovery of novel bioactive compounds and determining their mode of action of utmost importance. The development and application of chemical genomic assays using the model yeast Saccharomyces cerevisiae has provided powerful methods to identify the mechanism of action of diverse molecules in a living cell. Furthermore, complementary assays are continually being developed in fungal pathogens, most notably Candida albicans and Cryptococcus neoformans, to elucidate compound mechanism of action directly in the pathogen of interest. Collectively, the suite of chemical genetic assays that have been developed in multiple fungal species enables the identification of candidate drug target genes, as well as genes involved in buffering drug target pathways, and genes involved in general cellular responses to small molecules. In this review, we examine current yeast chemical genomic assays and highlight how such resources provide powerful tools that can be utilized to bolster the antifungal pipeline.
Fundamentality in metaphysics and the philosophy of physics. Part II: The philosophy of physics
Authors: Morganti Matteo 
Published: August 2020

AbstractThis is the second part of an overview article on fundamentality in metaphysics and the philosophy of physics. Here, the notion of fundamentality is looked at from the viewpoint of the philosophical analysis of physics and physical theories. The questions are considered (1) whether physics can be regarded as fundamental with respect to other sciences, and in what sense; (2) what the label ‘fundamental physics’ should exactly be taken to mean; (3) on what grounds a particular physical theory should be considered fundamental; (4) what should be regarded as fundamental according to particular theories of physics; and (5) what indications come from contemporary physics concerning the fundamental structure of reality.
Creaming among Caseworkers: Effects of Client Competence and Client Motivation on Caseworkers’ Willingness to Help
Authors: Guul Thorbjørn Sejr , Pedersen Mogens Jin , Petersen Niels Bjørn Grund 
Published: August 2020

AbstractFrontline employees cope with high workloads and limited resources by directing their work attention and efforts toward particular clients. Yet, the role of client attributes in frontline employees’ efforts to help clients remains undertheorized and empirically understudied. Using a survey experimental vignette design (2 × 2 factorial) among 1,595 Danish caseworkers, the authors of this article provide new knowledge on how two generic nondemographic client attributes—competence and motivation—shape frontline employees’ willingness to help their clients. We found that both the competence and motivation of clients affect caseworkers’ willingness to exert extra time and effort helping clients. Specifically, caseworkers are most willing to help a client appearing both competent and motivated. Moreover, our data suggests that client motivation is more important than client competence for caseworkers’ willingness to help. We end the article with a discussion of policy implications and directions for future research.
Sensitivity Analysis for Publication Bias in Meta-Analyses
Authors: Mathur Maya B. , VanderWeele Tyler J. 
Published: August 2020

SummaryWe propose sensitivity analyses for publication bias in meta-analyses. We consider a publication process such that ‘statistically significant’ results are more likely to be published than negative or “non-significant” results by an unknown ratio, η. Our proposed methods also accommodate some plausible forms of selection based on a study's standard error. Using inverse probability weighting and robust estimation that accommodates non-normal population effects, small meta-analyses, and clustering, we develop sensitivity analyses that enable statements such as ‘For publication bias to shift the observed point estimate to the null, “significant” results would need to be at least 30 fold more likely to be published than negative or “non-significant” results’. Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval. To aid interpretation, we describe empirical benchmarks for plausible values of η across disciplines. We show that a worst-case meta-analytic point estimate for maximal publication bias under the selection model can be obtained simply by conducting a standard meta-analysis of only the negative and ‘non-significant’ studies; this method sometimes indicates that no amount of such publication bias could ‘explain away’ the results. We illustrate the proposed methods by using real meta-analyses and provide an R package: PublicationBias.
A Calibrated Sensitivity Analysis for Matched Observational Studies with Application to the Effect of Second-Hand Smoke Exposure on Blood Lead Levels in Children
Authors: Zhang Bo , Small Dylan S. 
Published: August 2020

SummaryWe conducted a matched observational study to investigate the causal relationship between second-hand smoke and blood lead levels in children. Our first analysis that assumes no unmeasured confounding suggests evidence of a detrimental effect of second-hand smoke. However, unmeasured confounding is a concern in our study as in other observational studies of second-hand smoke's effects. A sensitivity analysis asks how sensitive the conclusion is to a hypothesized unmeasured confounder U. For example, in our study, one potential unmeasured confounder is whether the child attends a public or private school. A commonly used sensitivity analysis for matched observational studies adopts a worst-case perspective, which assumes that, in each matched set, the unmeasured confounder is allocated to make the bias worst: in a matched pair, the child with higher blood lead level always attends public school and the other private school. This worst-case allocation of U does not correspond to any realistic distribution of U in the population and is difficult to compare with observed covariates. We proposed a new sensitivity analysis method that addresses these concerns. We apply the new method to our study and find that, to explain away the association between second-hand smoke exposure and blood lead levels as non-causal, the unmeasured confounder would have to be a bigger confounder than any measured confounder.
Recently acquired infection among HIV‐seropositive donors in the US from 2010‐2018
Authors: Quiner Claire , Bruhn Roberta , Grebe Eduard , Di Germanio Clara , Kessler Debra , Reik Rita , Williamson Phillip , Hampton Dylan , Fayed Rahima , Anderson Steve A. , Williams Alan E. , Glynn Simone A. , Busch Michael P. , Stramer Susan L. , Custer Brian ,   for the Transfusion‐Transmissible Infections Monitoring System (TTIMS)
Published: August 2020

AbstractBackgroundMonitoring of transfusion‐transmissible infections in the blood supply is essential for blood safety, as the donor population is not static, and changes in policy, donor behavior, or other factors could increase the risk of recipient infection. We assessed patterns of recently acquired HIV infection in US blood donors, including before and after the implementation of the 12‐month deferral for men who have sex with men (MSM).Study Design and MethodsA large convenience sample of donations from donors testing HIV‐1 nucleic acid testing (NAT) and serology‐reactive were further tested with the Sedia HIV‐1 Limiting Antigen enzyme immunoassay. Samples were analyzed across available demographic and donation data to provide an assessment of recently acquired HIV infection in US blood donors from 2010 to 2018.ResultsOverall, 317 of 1154 (27.5%; 95% confidence interval, 24.9%‐30.1%) donations from HIV NAT and serology‐reactive donors had recently acquired HIV infection. There was no evidence of change in the percentages of recent HIV infection by year over the study period, either in all donors or in male donors, including after the MSM policy change. In multivariable logistic regression analysis, donors aged 24 years or younger were over 2.7 times more likely and repeat donors 2.2 times more likely to have recently acquired HIV infection compared to donors aged 55 years or older and first‐time donors, respectively.ConclusionPatterns of recently acquired HIV infection varied by demographics but not over time. These findings suggest no impact of the MSM policy change on recently acquired HIV infection in US blood donors.
Efficacy of alginate‐and chitosan‐based scaffolds on the healing of diabetic skin wounds in animal experimental models and cell studies: A systematic review
Authors: Cai Hong , Li Guichen 
Published: August 2020

AbstractThis systematic literature review was aimed to investigate the use of cell culture and animal models to evaluate the efficacy of alginate‐and chitosan‐based scaffolds on diabetic wound healing. We electronically searched the articles published until July 2019. The databases included five English databases such as PubMed, Web of Science, Embase, the Cochrane Library, CINAHL, and three Chinese databases like CNKI, WanFang Data, and VIP. The related articles were manually searched to identify studies that were not searched by electronic database searches. Twenty‐nine studies met the inclusion criteria. We divided the results into three groups: chitosan, alginate, and a combination of chitosan and alginate. Chitosan‐, alginate‐, and a combination of chitosan and alginate‐based scaffolds showed good intervention effects on wound healing. Chitosan‐based scaffolds were effective in diabetic skin wound healing. The effects of alginate and the combination of chitosan‐and alginate‐based scaffolds on diabetic skin wounds still need more research. However, due to the heterogeneity of animal and cell preclinical trials and the validity of the statistical analysis used in these studies, it is necessary to conduct a thorough study using well‐designed experiments to confirm these results. In addition, properly designed chitosan‐and/or alginate‐based scaffolds with thorough preclinical evaluations are required prior to clinical applications.
Highly Efficient Mesoporous Mg/γ-Al2O3 Catalysts for Ozonation of Saline Petroleum Effluents
Authors: Xu Renshun , Nabet Hervé , Breton Audrey , Baldoni-Andrey Patrick , Lesage Nicolas , Cacciaguerra Thomas , Hulea Vasile , Fajula Francois , Galarneau Anne 
Published: August 2020

Abstract
γ-Al2O3 is promising for catalytic ozonation because it produces HO° radicals. To improve its basicity and/or its oxidative character, highly mesoporous γ-Al2O3 was doped with different metals M alone or in mixture (M = Mg, Ca, Zn, Fe, Ba, Zr, Cu, Co, Ni, Ce, Ti, with 0.05 < M/Al < 0.5 molar ratio) prepared either by incipient wetness deposition or by direct sol-gel. Tests to determine the basic and oxidative character of the catalysts have been set up. Results show that Mg-doped alumina materials exhibited the highest basicity and Cu,Mg-doped alumina materials the highest oxidative character. These materials (5 g/L) were tested in the catalytic ozonation of a synthetic saline (NaCl = 50 g/L) petroleum effluent such as produced water (TOC = 216 mg/L) containing phenols, acetic acid and polycyclic aromatic hydrocarbons. Among these catalysts, Mg-doped alumina with molar ratio Mg/Al = 0.1, 0.2 prepared by incipient wetness deposition were the more efficient catalysts. Under reuse the Mg-doped alumina catalyst (Mg/Al = 0.1) exhibited the highest ozonation rate with 98% TOC removal in 5 h. This remarkable behavior was attributed to the in-situ formation during ozonation of spinel (MgAl2O4) nanoparticles at the surface of Mg-doped alumina particles.
Impact of anxiety and depression on progression to glaucoma among glaucoma suspects
Authors: Berchuck Samuel , Jammal Alessandro , Mukherjee Sayan , Somers Tamara , Medeiros Felipe A 
Published: August 2020

AimsTo assess the impact of anxiety and depression in the risk of converting to glaucoma in a cohort of glaucoma suspects followed over time.MethodsThe study included a retrospective cohort of subjects with diagnosis of glaucoma suspect at baseline, extracted from the Duke Glaucoma Registry. The presence of anxiety and depression was defined based on electronic health records billing codes, medical history and problem list. Univariable and multivariable Cox proportional hazards models were used to obtain HRs for the risk of converting to glaucoma over time. Multivariable models were adjusted for age, gender, race, intraocular pressure measurements over time and disease severity at baseline.ResultsA total of 3259 glaucoma suspects followed for an average of 3.60 (2.05) years were included in our cohort, of which 911 (28%) were diagnosed with glaucoma during follow-up. Prevalence of anxiety and depression were 32% and 33%, respectively. Diagnoses of anxiety, or concomitant anxiety and depression were significantly associated with risk of converting to glaucoma over time, with adjusted HRs (95% CI) of 1.16 (1.01, 1.33) and 1.27 (1.07, 1.50), respectively.ConclusionA history of anxiety or both anxiety and depression in glaucoma suspects was associated with developing glaucoma during follow-up.