bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral Nirmatrelvir and Ritonavir for Coronavirus Disease 2019 in Vaccinated, Nonhospitalized Adults Aged 18–50 Years
Authors: Faust Jeremy Samuel , Kumar Ashish , Shah Jui , Khadke Sumanth , Dani Sourbha S , Ganatra Sarju , Sax Paul E 
Published: June 2023

Abstract

Background
The effects of nirmatrelvir/ritonavir (NMV/r [Paxlovid]) on coronavirus disease 2019 (COVID-19) outcomes in younger vaccinated adults are unclear. The objective of this study was to assess if NMV/r use in vaccinated adults aged ≤50 years is associated with improved outcomes and to identify beneficial and nonbeneficial subgroups.

Methods
In this cohort study, we generated 2 propensity-matched cohorts of 2547 patients from an 86 119-person cohort assembled from the TriNetX database. Patients in 1 cohort received NMV/r, and patients in the matched control cohort did not. The main outcome was composite of all-cause emergency department visits, hospitalization, and mortality.

Results
The composite outcome was detected in 4.9% of the NMV/r cohort and 7.0% of the non-NMV/r cohort (odds ratio, 0.683 [95% confidence interval, .540–.864]; P = .001), indicating a 30% relative risk reduction. The number needed to treat (NNT) for the primary outcome was 47. Subgroup analyses found significant associations for patients with cancer (NNT = 45), cardiovascular disease (NNT = 30), and both conditions (NNT = 16). No benefit was found for patients with only chronic lower respiratory disorders (asthma/chronic obstructive pulmonary disease [COPD]) or without serious comorbidities. Thirty-two percent of NMV/r prescriptions in the overall database were for 18- to 50-year-olds.

Conclusions
NMV/r use in vaccinated adults aged 18–50 years, especially with serious comorbidities, was associated with reduced all-cause hospital visits, hospitalization, and mortality in the first 30 days of COVID-19 illness. However, NMV/r in patients without significant comorbidities or with only asthma/COPD had no association of benefit. Therefore, identifying high-risk patients should be a priority and overprescription should be avoided.
Long-term follow-up of IgA nephropathy: clinicopathological features and predictors of outcomes
Authors: Haaskjold Yngvar Lunde , Lura Njål Gjærde , Bjørneklett Rune , Bostad Lars Sigurd , Knoop Thomas , Bostad Leif 
Published: June 2023

ABSTRACT

Background
The establishment of the Oxford classification and newly developed prediction models have improved the prognostic information for immunoglobulin A nephropathy (IgAN). Considering new treatment options, optimizing prognostic information and improving existing prediction models are favorable.

Methods
We used random forest survival analysis to select possible predictors of end-stage kidney disease among 37 candidate variables in a cohort of 232 patients with biopsy-proven IgAN retrieved from the Norwegian Kidney Biopsy Registry. The predictive value of variables with relative importance &gt;5% was assessed using concordance statistics and the Akaike information criterion. Pearson's correlation coefficient was used to identify correlations between the selected variables.

Results
The median follow-up period was 13.7 years. An isolated analysis of histological variables identified six variables with relative importance &gt;5%: T %, segmental glomerular sclerosis without characteristics associated with other subtypes (not otherwise specified, NOS), normal glomeruli, global sclerotic glomeruli, segmental adherence and perihilar glomerular sclerosis. When histopathological and clinical variables were combined, estimated glomerular filtration rate (eGFR), proteinuria and serum albumin were added to the list. T % showed a better prognostic value than tubular atrophy/interstitial fibrosis (T) lesions with C-indices at 0.74 and 0.67 and was highly correlated with eGFR. Analysis of the subtypes of segmental glomerulosclerosis (S) lesions revealed that NOS and perihilar glomerular sclerosis were associated with adverse outcomes.

Conclusions
Reporting T lesions as a continuous variable, normal glomeruli and subtypes of S lesions could provide clinicians with additional prognostic information and contribute to the improved performance of the Oxford classification and prognostic tools.
Systematic review of how racialized health inequities are addressed in Epidemiologic Reviews articles (1979–2021): a critical conceptual and empirical content analysis and recommendations for best practices
Authors: Javadi Dena , Murchland Audrey R , Rushovich Tamara , Wright Emily , Shchetinina Anna , Siefkas Anna C , Todd Kieran P , Gitelman Julian , Hall Enjoli , Wynne Jhordan O , Zewge-Abubaker Nishan , Krieger Nancy 
Published: June 2023

Abstract
Critical analysis of the determinants of current and changing racialized health inequities, including the central role of racism, is an urgent priority for epidemiology, for both original research studies and epidemiologic review articles. Motivating our systematic overview review of Epidemiologic Reviews articles is the critical role of epidemiologic reviews in shaping discourse, research priorities, and policy relevant to the social patterning of population health. Our approach was first to document the number of articles published in Epidemiologic Reviews (1979–2021; n = 685) that either: (1) focused the review on racism and health, racial discrimination and health, or racialized health inequities (n = 27; 4%); (2) mentioned racialized groups but did not focus on racism or racialized health inequities (n = 399; 59%); or (3) included no mention of racialized groups or racialized health inequities (n = 250; 37%). We then conducted a critical content analysis of the 27 review articles that focused on racialized health inequities and assessed key characteristics, including (1) concepts, terms, and metrics used regarding racism and racialized groups (notably only 26% addressed the use or nonuse of measures explicitly linked to racism; 15% provided explicit definitions of racialized groups); (2) theories of disease distribution guiding (explicitly or implicitly) the review’s approach; (3) interpretation of findings; and (4) recommendations offered. Guided by our results, we offer recommendations for best practices for epidemiologic review articles for addressing how epidemiologic research does or does not address ubiquitous racialized health inequities.
Physical activity during early life and the risk of all-cause mortality in midlife: findings from a birth cohort study
Authors: Feter Natan , Leite Jayne S , Weymar Marina K , Dumith Samuel C , Umpierre Daniel , Caputo Eduardo L 
Published: June 2023

Abstract

Background
The objective of this study was to examine the association between physical activity during childhood and adolescence and the risk of all-cause mortality in midlife. We analyzed data from a birth cohort (The 1958 National Child Development Survey), including births in England, Wales and Scotland.

Methods
Physical activity was assessed using questionnaires at ages 7, 11 and 16. Death certificates defined all-cause mortality. Cumulative exposure, sensitive and critical periods, and physical activity trajectory from childhood to adolescence were tested using multivariate Cox proportional hazard models. The sweep the death was confirmed was defined as the time event.

Results
From age 23 to 55, 8.9% of participants (n = 9398) died. Physical activity in childhood and adolescence affected the risk of all-cause mortality in midlife. In men, physical activity at ages 11 [hazard ratio (HR): 0.77; 95% confidence interval (CI): 0.60–0.98] and 16 (HR: 0.60; 95% CI: 0.46–0.78) was associated with reduced risk of all-cause mortality. In women, physical activity at age 16 (HR: 0.68; 95% CI: 0.48–0.95) was associated with reduced risk of all-cause mortality. Physical activity in adolescence eliminated the risk of all-cause mortality associated with physical inactivity in adulthood in women.

Conclusions
Physical activity during childhood and adolescence was associated with reduced risk of all-cause mortality with different effects by sex.
Divorce Law, the Revolution of 1830 and the Novel: Aloïse de Carlowitz’s Le Pair de France ou Le Divorce (1835)
Authors: Amann Elizabeth 
Published: June 2023

Abstract
Divorce was legalized in France during the French Revolution and remained legal (though more restricted) during the Napoleonic period. With the return of the Bourbons in 1815, however, it was almost immediately outlawed. The Revolution of 1830 and the ascension of the more progressive Louis-Philippe d’Orléans led to hopes that divorce would soon be reinstated, but they were quickly disappointed as the conservative Chamber of Peers squashed all attempts at restoring it. This article examines an 1835 novel, Aloïse Christine de Carlowitz’s Le Pair de France ou Le Divorce, which traces the debates about divorce in the years before and after 1830. The first section focuses on Carlowitz’s representation of these discussions and of various perspectives on the law and social reform. The second section considers how Carlowitz relates the divorce plot to the political changes in France between 1830 and 1834 through a series of parallels between historical events and the private drama of the protagonists.
Mediator subunit MDT-15 promotes expression of propionic acid breakdown genes to prevent embryonic lethality in Caenorhabditis elegans
Authors: Goh Grace Ying Shyen , Beigi Arshia , Yan Junran , Doering Kelsie R S , Taubert Stefan 
Published: June 2023

Abstract
The micronutrient vitamin B12 is an essential cofactor for two enzymes: methionine synthase, which plays a key role in the one-carbon cycle; and methylmalonyl-CoA mutase, an enzyme in a pathway that breaks down branched-chain amino acids and odd-chain fatty acids. A second, vitamin B12-independent pathway that degrades propionic acid was recently described in Caenorhabditis elegans, the propionate shunt pathway. Activation of five shunt pathway genes in response to low vitamin B12 availability or high propionic acid levels is accomplished by a transcriptional regulatory mechanism involving two nuclear hormone receptors, NHR-10 and NHR-68. Here, we report that the C. elegans Mediator subunit mdt-15 is also essential for the activation of the propionate shunt pathway genes, likely by acting as a transcriptional coregulator for NHR-10. C. elegans mdt-15 mutants fed with a low vitamin B12 diet have transcriptomes resembling those of wild-type worms fed with a high vitamin B12 diet, with low expression of the shunt genes. Phenotypically, the embryonic lethality of mdt-15 mutants is specifically rescued by diets high in vitamin B12, but not by dietary polyunsaturated fatty acids, which rescue many other phenotypes of the mdt-15 mutants. Finally, NHR-10 binds to MDT-15 in yeast two-hybrid assays, and the transcriptomes of nhr-10 mutants share overlap with those of mdt-15 mutants. Our data show that MDT-15 is a key coregulator for an NHR regulating propionic acid detoxification, adding to roles played by NHR:MDT-15 partnerships in metabolic regulation and pinpointing vitamin B12 availability as a requirement for mdt-15 dependent embryonic development.
A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence
Authors: Kang Taekyu , Moore Emily C , Kopania Emily E K , King Christina D , Schilling Birgit , Campisi Judith , Good Jeffrey M , Brem Rachel B 
Published: June 2023

Abstract
Cellular senescence is a program of cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in metazoan cells. Landmark studies in laboratory mice have characterized a number of master senescence regulators, including p16INK4a, p21, NF-κB, p53, and C/EBPβ. To discover other molecular players in senescence, we developed a screening approach to harness the evolutionary divergence between mouse species. We found that primary cells from the Mediterranean mouse Mus spretus, when treated with DNA damage to induce senescence, produced less cytokine and had less-active lysosomes than cells from laboratory Mus musculus. We used allele-specific expression profiling to catalog senescence-dependent cis-regulatory variation between the species at thousands of genes. We then tested for correlation between these expression changes and interspecies sequence variants in the binding sites of transcription factors. Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, upstream stimulatory factor 2 (USF2), for molecular validation. In acute irradiation experiments, cells lacking USF2 had compromised DNA damage repair and response. Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program—shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type. We interpret these findings under a model of pro-repair, anti-senescence regulatory function by USF2. Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.
A chromosome-level genome assembly of longnose gar, Lepisosteus osseus
Authors: Mallik Rittika , Carlson Kara B , Wcisel Dustin J , Fisk Michael , Yoder Jeffrey A , Dornburg Alex 
Published: June 2023

Abstract
Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As the teleost genome duplication occurred after teleosts diverged from holosteans, holosteans have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome-sequenced to date, and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50 of 116.61 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.12% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar and bowfin to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements, and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)
Authors: Squires Theodore E , Rödin-Mörch Patrik , Formenti Giulio , Tracey Alan , Abueg Linelle , Brajuka Nadolina , Jarvis Erich , Halapi Eva C , Melsted Páll , Höglund Jacob , Magnússon Kristinn Pétur 
Published: June 2023

Abstract
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).
Quantification of spatial and seasonal trends in the atmosphere and construction of statistical models for infrasonic propagation
Authors: Blom Philip , Waxler Roger , Frazier Garth 
Published: June 2023

SUMMARY
Infrasonic waves are influenced by variations in the density, pressure and temperature as well as the ambient winds. Modelling infrasonic propagation can be challenging due to the dynamic nature of the atmosphere as well as the sparseness of measurements which result in variability and notable uncertainty. A framework is presented to quantify spatial and seasonal trends in atmospheric structure via analysis of the effective sound speed profile and identification of temporal trends in the middle atmospheric waveguide produced by the circumpolar vortex winds. Seasonal definitions identifying typical atmospheric structures during the summer, winter and spring/fall transition periods are identified using atmospheric data from 2010 through 2020. Seasonal trend analysis is conducted for a number of locations across the contiguous United States to quantify spatial variations in atmospheric structure that impact infrasonic propagation. For each season and location, empirical orthogonal function analysis is used to reduce the historical archive of atmospheric data into a smaller representative set that can be analysed using numerical tools more efficiently. Infrasonic ray tracing and finite-frequency modal propagation analyses are applied to construct propagation path geometry and transmission loss statistics which are useful in localization and yield estimation for infrasonic sources, respectively. An example application is detailed in which transmission loss statistics are combined with an explosive source model and noise statistics to quantify the capability of a network to detect nearby sources.
The PERK pathway: beneficial or detrimental for neurodegenerative diseases and tumor growth and cancer
Authors: Talukdar Gourango , Orr Harry T , Lei Zhixin 
Published: June 2023

Abstract
Protein kinase R (PKR)-like endoplasmic reticulum (ER) kinase (PERK) is one of the three major sensors in the unfolded protein response (UPR). The UPR is involved in the modulation of protein synthesis as an adaptive response. Prolonged PERK activity correlates with the development of diseases and the attenuation of disease severity. Thus, the current debate focuses on the role of the PERK signaling pathway either in accelerating or preventing diseases such as neurodegenerative diseases, myelin disorders, and tumor growth and cancer. In this review, we examine the current findings on the PERK signaling pathway and whether it is beneficial or detrimental for the above-mentioned disorders.
Systematic exclusion at study commencement masks earlier menopause for Black women in the Study of Women’s Health Across the Nation (SWAN)
Authors: Reeves Alexis , Elliott Michael R , Karvonen-Gutierrez Carrie A , Harlow Siobán D 
Published: June 2023

AbstractBackgroundShorter average lifespans for minoritized populations are hypothesized to stem from ‘weathering’ or accelerated health declines among minoritized individuals due to systemic marginalization. However, evidence is mixed on whether racial/ethnic differences exist in reproductive ageing, potentially due to selection biases in cohort studies that may systematically exclude ‘weathered’ participants. This study examines racial/ethnic disparities in the age of menopause after accounting for differential selection ‘into’ (left truncation) and ‘out of’ (right censoring) a cohort of midlife women.MethodsUsing data from the Study of Women’s Health Across the Nation (SWAN) cross-sectional screener (N = 15 695) and accompanying ∼20-year longitudinal cohort (N = 3302) (1995–2016), we adjusted for potential selection bias using inverse probability weighting (left truncation) to account for socio-demographic/health differences between the screening and cohort study, and multiple imputation (right censoring) to estimate racial/ethnic differences in age at menopause (natural and surgical).ResultsUnadjusted for selection, no Black/White differences in menopausal timing [hazard ratio (HR)=0.98 (0.86, 1.11)] were observed. After adjustment, Black women had an earlier natural [HR = 1.13 (1.00, 1.26)] and surgical [HR= 3.21 (2.80, 3.62)] menopause than White women with natural menopause—corresponding to a 1.2-year Black/White difference in menopause timing overall.ConclusionsFailure to account for multiple forms of selection bias masked racial/ethnic disparities in the timing of menopause in SWAN. Results suggest that there may be racial differences in age at menopause and that selection particularly affected the estimated menopausal age for women who experienced earlier menopause. Cohorts should consider incorporating methods to account for all selection biases, including left truncation, as they impact our understanding of health in ‘weathered’ populations.
Analysis of Taurine in Infant Formulas and Adult Nutritionals by Hydrophilic Interaction Liquid Chromatography–Mass Spectrometry: First Action 2022.03
Authors: Gill Brendon D , Wood Jackie E 
Published: June 2023

Abstract

Background
Taurine is recognized as an essential growth factor and as being critical in the maintenance of functional tissue regulation.

Objective
To evaluate the analytical performance of a hydrophilic interaction liquid chromatography–tandem mass spectrometry (HILIC-MS/MS) method for compliance with AOAC Standard Method Performance Requirements (SMPR®) for taurine analysis described in SMPR 2014.013.

Method
Following protein precipitation with Carrez solutions, taurine is extracted and separated by HILIC with detection by triple quadrupole MS using multiple reaction monitoring (MRM). Stable isotope labeled (SIL) taurine internal standard is used for quantification to correct for losses in extraction and variations in ionization in the ion source.

Results
The method was shown to meet the requirements specified in the SMPR with a linear range of 0.27–2700 mg/hg RTF (ready-to-feed), a limit of detection of 0.14 mg/hg RTF, acceptable recovery of 97.2–100.1%, and acceptable repeatability of 1.6–6.4% relative standard deviation. Additionally, the method was found to have no statistically significant bias compared with reference values for National Institute of Standards and Technology (NIST) 1849a certified reference material (CRM) (P-value = 0.95) and 1869 CRM (P-value = 0.31), and with results from AOAC 997.05 (P-value = 0.10).

Conclusions
A recent review of the method and validation data by the Stakeholder Program on Infant Formula and Adult Nutritionals (SPIFAN) Expert Review Panel (ERP) found that this method met all the criteria for analysis of taurine specified in SMPR 2014.013 and voted to adopt this method as First Action AOAC Official MethodSM2022.03.

Highlights
A method for the analysis of taurine in infant formulas and adult nutritionals by HILIC–MS/MS is described. A single-laboratory validation (SLV) study demonstrated the applicability of the method to meet requirements of SMPR 2014.013. In December 2022, the SPIFAN ERP voted to adopt this method as First Action AOAC Official Method 2022.03.