bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Load Status Before Switching to Dolutegravir-Containing Antiretroviral Therapy and Associations With Human Immunodeficiency Virus Treatment Outcomes in Sub-Saharan Africa
Authors: Romo Matthew L , Edwards Jessie K , Semeere Aggrey S , Musick Beverly S , Urassa Mark , Odhiambo Francesca , Diero Lameck , Kasozi Charles , Murenzi Gad , Lelo Patricia , Wyka Katarzyna , Kelvin Elizabeth A , Sohn Annette H , Wools-Kaloustian Kara K , Nash Denis ,   International epidemiology Databases to Evaluate AIDS (IeDEA)
Published: December 2021

Abstract

Background
Dolutegravir is being rolled out globally as part of preferred antiretroviral therapy (ART) regimens, including among treatment-experienced patients. The role of viral load (VL) testing before switching patients already on ART to a dolutegravir-containing regimen is less clear in real-world settings.

Methods
We included patients from the International epidemiology Databases to Evaluate AIDS consortium who switched from a nevirapine- or efavirenz-containing regimen to one with dolutegravir. We used multivariable cause-specific hazards regression to estimate the association of the most recent VL test in the 12 months before switching with subsequent outcomes.

Results
We included 36 393 patients at 37 sites in 5 countries (Democratic Republic of the Congo, Kenya, Rwanda, Tanzania, Uganda) who switched to dolutegravir from July 2017 through February 2020, with a median follow-up of approximately 11 months. Compared with those who switched with a VL &lt;200 copies/mL, patients without a recent VL test or with a preswitch VL ≥1000 copies/mL had significantly increased hazards of an incident VL ≥1000 copies/mL (adjusted hazard ratio [aHR], 2.89; 95% confidence interval [CI], 1.99–4.19 and aHR, 6.60; 95% CI, 4.36–9.99, respectively) and pulmonary tuberculosis or a World Health Organization clinical stage 4 event (aHR, 4.78; 95% CI, 2.77–8.24 and aHR, 13.97; 95% CI, 6.62–29.50, respectively).

Conclusions
A VL test before switching to dolutegravir may help identify patients who need additional clinical monitoring and/or adherence support. Further surveillance of patients who switched to dolutegravir with an unknown or unsuppressed VL is needed.
Does Your Class Give More than a Hint of Your Lifetime Earnings?: Assessing Indicators for Lifetime Earnings Over the Life Course for Sweden
Authors: Shahbazian Roujman , Bihagen Erik 
Published: December 2021

AbstractFrom a sociological stratification perspective, we would expect occupationally based measures to be valid proxies for lifetime earnings, but recent research suggests that annual earnings outperform occupational measures. In this article, we examine how class, occupation, education, and annual earnings are associated with lifetime earnings across almost complete working lives, at ages of around 20–65 years for Swedish cohorts born in the 1940s. Our results indicate that while annual earnings are considerably more accurate proxies for the lion’s share of working life, occupational measures are as expected more stable and somewhat better at the start and end of working lives. Our results also support the idea that micro-classes are better proxies of lifetime earnings than big classes. Contrary to some previous research, occupational measures perform better for women than for men in this respect, and occupational measures are better than education. Our main conclusions are that proxies for lifetime earnings have life-cycle biases that should be considered in, for instance, analyses of intergenerational mobility, and that occupationally based measures are more stable than annual earnings but, overall, are not very valid as indicators of lifetime earnings compared to annual earnings.
Presence of bacteria capable of PCB biotransformation in stormwater bioretention cells
Authors: Cao Siqi , Davis Allen , Kjellerup Birthe V 
Published: December 2021

ABSTRACTCore samples from bioretention cell media as well as surface stormwater sediment samples from seven urban areas were collected to assess the potential for biotransformation activity of polychlorinated biphenyls (PCBs). The presence of putative organohalide-respiring bacteria in these samples was studied. Based on extracted DNA, Dehalobacter, Dehalogenimonas and Dehalococcoides were detected. Other organohalide-respiring bacteria like Desulfitobacterium and Sulfurospirillum were not studied. Bacteria containing the genes encoding for biphenyl 2,3-dioxygenase (bphA) or 2,3-dihydroxybiphenyl 1,2-dioxygenase (bphC) were detected in 29 of the 32 samples. These genes are key factors in PCB aerobic degradation. Transcribed bacterial genes from putative organohalide-respiring bacteria as well as genes encoding for bphA and bphC were obtained from the microbial community, thus showing the potential of organohalide respiration of PCBs and aerobic PCB degradation under both aerobic and anaerobic conditions in the surface samples collected at the bioretention site. Presence and concentrations of 209 PCB congeners in the bioretention media were also assessed. The total PCB concentration ranged from 38.4 ± 2.3 ng/g at the top layer of the inlet to 11.6 ± 1.2 ng/g at 20–30 cm at 3 m from the inlet. These results provide documentation that bacteria capable of PCB transformation, including both anaerobic dechlorination and aerobic degradation, were present and active in the bioretention.
The Paid and Unpaid Working Life Expectancy at 50 in Europe
Authors: Ophir Ariane 
Published: December 2021

Abstract

Objectives
Amid growing concerns about the economic implications of population aging and the sustainability of older adults’ working life, unpaid family care work receives less attention despite its direct relevance to population aging. This article systematically compares the paid and unpaid working life expectancy at age 50 to understand the overlap and trade-off between paid and unpaid work among older European adults.

Method
Using data from the Survey of Health and Retirement in Europe with the Sullivan method, the article presents gender differences across 17 countries in life expectancy at age 50 at various paid (employment) and unpaid (caregiving) role configurations.

Results
When work is defined to include unpaid family caregiving, women and men have similar working life expectancies at age 50, in contrast to prior research. However, its paid and unpaid components are gendered. The results also show that at age 50, women are expected to spend a similar number of years providing grandchild care and activities of daily living/instrumental activities of daily living care and that most of these years take place after retirement.

Discussion
The results highlight that the gendered tension between paid and unpaid work persists into older adulthood and needs to be accounted for in working life expectancy measures. The results also underscore the gendered implications of population aging and unpaid work in older adulthood for retirement age policies and strategies for promoting gender equality in later life.
Measuring Sex and Gender in Aging and Alzheimer’s Research: Results of a National Survey
Authors: Stites Shana D , Cao Hannah , Harkins Kristin , Flatt Jason D 
Published: December 2021

AbstractObjectivesDifferences between men and women are common in published research on aging and Alzheimer’s disease and Alzheimer’s disease-related dementias (AD/ADRD). What do these differences mean? To answer this, rigorous measurement is needed. We investigated current methods for measuring sex/gender in aging and AD/ADRD cohort studies.MethodsAn online survey was sent to National Institute on Aging-funded Alzheimer’s Disease Research Centers (n = 38) and investigator-initiated cohort studies (n = 38) to assess practices around enrollment of men and women and measurement of sex and gender.ResultsThe response rate was 65.8% (n = 50). All enrolled men and all but two investigator-initiated studies enrolled women. Most cohorts (43/50) had no documented definitions for categories of “men” or “women.” Over 85% of cohorts relied solely on self-report questions to capture sex/gender data (n = 43/50). Issues with administration were also identified (n = 7).DiscussionOur findings identify gaps in current approaches used to measure sex and gender in aging and AD/ADRD research. We discuss opportunities to bridge these gaps and advance measurement of sex and gender in aging and AD/ADRD research. Changes are needed to ensure inclusion and representation of sociocultural diversity in research samples, and consistency in data collection in aging and AD/ADRD research.
Prenatal Poly I:C Challenge Affects Behaviors and Neurotransmission via Elevated Neuroinflammation Responses in Female Juvenile Rats
Authors: Su Yueqing , Lian Jiamei , Hodgson James , Zhang Wenchang , Deng Chao 
Published: December 2021

Abstract

Background
Exposure to polyriboinosinic-polyribocytidylic acid (Poly I:C) in pregnant rats has been reported to cause schizophrenia-like behaviors and abnormal neurotransmissions in adult, particularly male, offspring. However, what is less well understood are the effects of maternal Poly I:C exposure on adolescent behaviors and neurotransmission in female juvenile rats.

Methods
Female adolescent Poly I:C offspring were constructed by treating with 5 mg/kg Poly I:C on timed pregnant rats (gestation day 15). A battery of behavioral tests was conducted during postnatal day 35–60. Neurotransmitter receptors and inflammation markers in brain regions were evaluated by RT-qPCR on postnatal day 60.

Results
Open field, elevated plus maze, and forced swimming tests revealed that prenatal Poly I:C exposure led to elevated anxiety-like and depression-like behaviors in female adolescent offspring. Deficits in pre-pulse inhibition and social interaction were also observed. However, the Poly I:C rats had better performance than the controls in the novel object recognition memory test, which demonstrated a behavioral phenotype with improved cognitive function. Prenatal Poly I:C exposure caused brain region–specific elevation of the P2X7 receptor- and NF-κB-NLRP3-IL-1β inflammatory signaling in female juvenile rats. Prenatal Poly I:C exposure decreased expression of GABAA receptor subunits Gabrb3 in the prefrontal cortex and Gabrb1 and dopamine D2 receptor in the hippocampus, but increased NMDA receptor subunit Grin2a in the prefrontal cortex, 5-HT2A in the hippocampus, and Gabrb3 and D2 receptor in the nucleus accumben.

Conclusions
Prenatal Poly I:C challenge causes behavioral deficits and brain-specific neurotransmission changes via elevated neuroinflammation responses in female adolescent offspring rats.
An EjbHLH14-EjHB1-EjPRX12 module is involved in methyl jasmonate alleviation of chilling-induced lignin deposition in loquat fruit
Authors: Zhang Mengxue , Shi Yanna , Liu Zimeng , Zhang Yijin , Yin Xueren , Liang Zihao , Huang Yiqing , Grierson Donald , Chen Kunsong 
Published: December 2021

Abstract
Loquat fruit are susceptible to chilling injuries induced by postharvest storage at low temperature. The major symptoms are increased lignin content and flesh firmness, which cause a leathery texture. Pretreatment with methyl jasmonate (MeJA) can alleviate this low-temperature-induced lignification, but the mechanism is not understood. In this study, we characterized a novel class III peroxidase, EjPRX12, and studied its relationship to lignification. Transcript levels of EjPRX12 were attenuated following MeJA pretreatment, consistent with the reduced lignin content in fruit. In vitro enzyme activity assay indicated that EjPRX12 polymerized sinapyl alcohol, and overexpression of EjPRX12 in Arabidopsis promoted lignin accumulation, indicating that it plays a functional role in lignin polymerization. We also identified an HD-ZIP transcription factor, EjHB1, repressed by MeJA pretreatment, which directly bound to and significantly activated the EjPRX12 promoter. Overexpression of EjHB1 in Arabidopsis promoted lignin accumulation with induced expression of lignin-related genes, especially AtPRX64. Furthermore, a JAZ-interacting repressor, EjbHLH14, was characterized, and it is proposed that MeJA pretreatment caused EjbHLH14 to be released to repress the expression of EjHB1. These results identified a novel regulatory pathway involving EjbHLH14-EjHB1-EjPRX12 and revealed the molecular mechanism whereby MeJA alleviated lignification of loquat fruit at low temperature.
Halo concentration strengthens dark matter constraints in galaxy–galaxy strong lensing analyses
Authors: Amorisco Nicola C , Nightingale James , He Qiuhan , Amvrosiadis Aristeidis , Cao Xiaoyue , Cole Shaun , Etherington Amy , Frenk Carlos S , Li Ran , Massey Richard , Robertson Andrew 
Published: December 2021

ABSTRACT
A defining prediction of the cold dark matter cosmological model is the existence of a very large population of low-mass haloes. This population is absent in models in which the dark matter particle is warm (WDM). These alternatives can, in principle, be distinguished observationally because haloes along the line of sight can perturb galaxy–galaxy strong gravitational lenses. Furthermore, the WDM particle mass could be deduced because the cut-off in their halo mass function depends on the mass of the particle. We systematically explore the detectability of low-mass haloes in WDM models by simulating and fitting mock lensed images. Contrary to previous studies, we find that haloes are harder to detect when they are either behind or in front of the lens. Furthermore, we find that the perturbing effect of haloes increases with their concentration: Detectable haloes are systematically high-concentration haloes, and accounting for the scatter in the mass–concentration relation boosts the expected number of detections by as much as an order of magnitude. Haloes have lower concentration for lower particle masses and this further suppresses the number of detectable haloes beyond the reduction arising from the lower halo abundances alone. Taking these effects into account can make lensing constraints on the value of the mass function cut-off at least an order of magnitude more stringent than previously appreciated.
Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels
Authors: Peng Junhui , Svetec Nicolas , Zhao Li 
Published: December 2021

AbstractProteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.
Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases
Authors: Jiang Lin , Jiang Hui , Dai Sheng , Chen Ying , Song Youqiang , Tang Clara Sze-Man , Pang Shirley Yin-Yu , Ho Shu-Leong , Wang Binbin , Garcia-Barcelo Maria-Mercedes , Tam Paul Kwong-Hang , Cherny Stacey S , Li Mulin Jun , Sham Pak Chung , Li Miaoxin 
Published: December 2021

Abstract
Identifying rare variants that contribute to complex diseases is challenging because of the low statistical power in current tests comparing cases with controls. Here, we propose a novel and powerful rare variants association test based on the deviation of the observed mutation burden of a gene in cases from a baseline predicted by a weighted recursive truncated negative-binomial regression (RUNNER) on genomic features available from public data. Simulation studies show that RUNNER is substantially more powerful than state-of-the-art rare variant association tests and has reasonable type 1 error rates even for stratified populations or in small samples. Applied to real case-control data, RUNNER recapitulates known genes of Hirschsprung disease and Alzheimer's disease missed by current methods and detects promising new candidate genes for both disorders. In a case-only study, RUNNER successfully detected a known causal gene of amyotrophic lateral sclerosis. The present study provides a powerful and robust method to identify susceptibility genes with rare risk variants for complex diseases.
HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries
Authors: Marchal Claire , Singh Nivedita , Corso-Díaz Ximena , Swaroop Anand 
Published: December 2021

Abstract
Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any Hi-C experimental design. Here, we present the mathematical concepts to estimate the resolution of a dataset and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to several Hi-C libraries.
Regulation of AR mRNA translation in response to acute AR pathway inhibition
Authors: Somasekharan Syam Prakash , Saxena Neetu , Zhang Fan , Beraldi Eliana , Huang Jia Ni , Gentle Christina , Fazli Ladan , Thi Marisa , Sorensen Poul H , Gleave Martin 
Published: December 2021

AbstractWe report a new mechanism of androgen receptor (AR) mRNA regulation and cytoprotection in response to AR pathway inhibition (ARPI) stress in prostate cancer (PCA). AR mRNA translation is coordinately regulated by RNA binding proteins, YTHDF3 and G3BP1. Under ambient conditions m6A-modified AR mRNA is bound by YTHDF3 and translationally stimulated, while m6A-unmodified AR mRNA is bound by G3BP1 and translationally repressed. When AR-regulated PCA cell lines are subjected to ARPI stress, m6A-modified AR mRNA is recruited from actively translating polysomes (PSs) to RNA-protein stress granules (SGs), leading to reduced AR mRNA translation. After ARPI stress, m6A-modified AR mRNA liquid–liquid phase separated with YTHDF3, while m6A-unmodified AR mRNA phase separated with G3BP1. Accordingly, these AR mRNA messages form two distinct YTHDF3-enriched or G3BP1-enriched clusters in SGs. ARPI-induced SG formation is cell-protective, which when blocked by YTHDF3 or G3BP1 silencing increases PCA cell death in response to ARPI stress. Interestingly, AR mRNA silencing also delays ARPI stress-induced SG formation, highlighting its supportive role in triggering this stress response. Our results define a new mechanism for stress adaptive cell survival after ARPI stress involving SG-regulated translation of AR mRNA, mediated by m6A RNA modification and their respective regulatory proteins.
Interim analysis of the COSA (COVID-19 patients treated with the Seraph® 100 Microbind® Affinity filter) registry
Authors: Schmidt Julius J , Borchina Dan Nicolae , van't Klooster Mariet , Bulhan-Soki Khalida , Okioma Reuben , Herbst Larissa , Rodríguez Diego Sandoval , Premužić Vedran , Büttner Stefan , Bader Birgit , Serednicki Wojciech , Zasada Ewa , Schmitz Michael , Quabach Ralf A , Hrincheva Maria , Fühner Thomas , Kielstein Jan T 
Published: December 2021

ABSTRACT

Background
The Seraph® 100 Microbind® Affinity Blood Filter is a haemoperfusion device that is licensed for the reduction of pathogens, including several viruses, in the blood. It received Emergency Use Authorization for the treatment of severe coronavirus disease 2019 (COVID-19) by the Food and Drug Administration (FDA). Several studies have shown that the blood viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) correlates with adverse outcomes and removal of the nucleocapsid of the SARS-CoV-2 virus by the Seraph® 100 has been recently demonstrated. The aim of this registry was to evaluate the safety and efficacy of Seraph® 100 treatment for COVID-19 patients.

Methods
Twelve hospitals from six countries representing two continents documented patient and treatment characteristics as well as outcome parameters without reimbursement. Additionally, mortality and safety results of the device were reported. A total of 102 treatment sessions in 82 patients were documented in the registry. Four patients were excluded from mortality analysis due to incomplete outcome data, which were available in the other 78 patients.

Results
Overall, a 30-day mortality rate of 46.2% in the 78 patients with complete follow-up was reported. The median treatment time was 5.00 h (4.00–13.42) and 43.1% of the treatments were performed as haemoperfusion only. Adverse events of the Seraph® 100 treatment were reported in 8.8% of the 102 treatments and represented the premature end of treatment due to circuit failure. Patients who died were treated later in their intensive care unit (ICU) stay and onset of COVID symptoms. They also had higher ferritin levels. Multivariate Cox regression revealed that delayed Seraph® 100 treatment after ICU admission (&gt;60 h), as well as bacterial superinfection, were associated with mortality. While average predicted mortality rate according to Sequential Organ Failure Assessment (SOFA) score in ICU patients was 56.7%, the observed mortality was 50.7%. In non-ICU patients, Coronavirus Clinical Characterisation Consortium (4C) score average predicted a mortality rate of 38.0%, while the observed mortality rate was 11.1%.

Conclusions
The treatment of COVID-19 patients with Seraph® 100 is well tolerated and the circuit failure rate was lower than previously reported for kidney replacement therapy (KRT) in COVID-19 patients. Mortality correlated with late initiation of Seraph treatment after ICU admission and bacterial superinfection. Compared with predicted mortality according to 4C and SOFA scores, mortality of Seraph® 100-treated patients reported in the registry was lower.