bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous preterm birth
Authors: Gomez-Lopez Nardhy , Romero Roberto , Galaz Jose , Bhatti Gaurav , Done Bogdan , Miller Derek , Ghita Corina , Motomura Kenichiro , Farias-Jofre Marcelo , Jung Eunjung , Pique-Regi Roger , Hassan Sonia S , Chaiworapongsa Tinnakorn , Tarca Adi L 
Published: December 2021

AbstractThe complex physiologic process of parturition includes the onset of labor, which requires the orchestrated stimulation of a common pathway involving uterine contractility, cervical ripening, and chorioamniotic membrane activation. However, the labor-specific processes taking place in these tissues have limited use as predictive biomarkers unless they can be probed in non-invasive samples, such as the peripheral blood. Herein, we utilized a transcriptomic dataset to assess labor-specific changes in the peripheral blood of women who delivered at term. We identified a set of genes that were differentially expressed with labor and enriched for immunological processes, and these gene expression changes were strongly correlated with results from prior studies, providing in silico validation of our findings. We then identified significant correlations between labor-specific transcriptomic changes in the maternal circulation and those detected in the chorioamniotic membranes, myometrium, and cervix of women at term, demonstrating that tissue-specific labor signatures are partly mirrored in the peripheral blood. Finally, we demonstrated a significant overlap between the peripheral blood transcriptomic changes in term parturition and those observed in asymptomatic women, prior to the diagnosis of preterm prelabor rupture of the membranes, who ultimately delivered preterm. Collectively, we provide evidence that the normal process of labor at term is characterized by a unique immunological expression signature, which may serve as a useful tool for assessing labor status and for potentially identifying women at risk for preterm birth.
Developmental exposure to methylmercury and ADHD, a literature review of epigenetic studies
Authors: Ke Tao , Tinkov Alexey A , Skalny Antoly V , Bowman Aaron B , Rocha Joao B T , Santamaria Abel , Aschner Michael 
Published: December 2021

AbstractAttention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder that affects the competence of academic performance and social wellness in children and adults. The causes of ADHD are unclear. Both genetic and environmental factors contribute to the development of ADHD. The behavioral impairments in ADHD are associated with epigenetic changes in genes that are important for neurodevelopment. Among environmental causes of ADHD, the neurotoxin methylmercury (MeHg) is associated with an increased risk for ADHD. Developing children are susceptible to neurotoxic effects of prenatal MeHg exposure. Human epidemiology studies have shown that prenatal MeHg exposure could invoke epigenetic changes in genes that are involved in ADHD. In addition, the pathogenesis of ADHD involves dopaminergic system, which is a target of developmental MeHg exposure. MeHg-induced alterations in the dopaminergic system have a profound impact on behavioral functions in adults. As a trace level of MeHg (around nM) can induce long-lasting behavioral alterations, potential mechanisms of MeHg-induced functional changes in the dopaminergic system may involve epigenetic mechanisms. Here, we review the relevant evidence on developmental MeHg exposures and the risk for ADHD. We also point out research gaps in understanding environmental causes of ADHD.
Global, regional, and national burden and quality of care index of endocarditis: the global burden of disease study 1990–2019
Authors: Momtazmanesh Sara , Saeedi Moghaddam Sahar , Malakan Rad Elaheh , Azadnajafabad Sina , Ebrahimi Narges , Mohammadi Esmaeil , Rouhifard Mahtab , Rezaei Negar , Masinaei Masoud , Rezaei Nazila , Keykhaei Mohammad , Aminorroaya Arya , Ghamari Azin , Larijani Bagher , Farzadfar Farshad 
Published: December 2021

Abstract

Aims
Endocarditis accounts for significant morbidity and mortality. Timely diagnosis and prompt treatment are of paramount importance for optimal patient outcome. However, only few studies have assessed quality of care (QoC) in endocarditis. We aimed to describe QoC and changes in epidemiological features of endocarditis from 1990 to 2019.

Methods and results
Using primary indices of mortality, incidence, years of life lost, years lived with disability, and disability-adjusted life year, obtained from the Global Burden of Disease Study 2019, we calculated four secondary measures. Principal component analysis was performed to calculate QoC index (QCI), scored on a scale of 0–100 with higher values indicating better QoC, for different locations, age groups, and genders from 1990 to 2019. The all-ages incidence rate of endocarditis was estimated to increase significantly from 1990 to 2019, while mortality rate did not change. The age-standardized QCI was 73.6% globally, with higher values in high-income countries than in low-income countries. High-income North America (82.0%) and Asia Pacific (81.1%) had the highest QCI, whereas Eastern Europe (43.3%) had the lowest. Globally, the 30–49 and 95+ age groups had the highest (91.3%) and the lowest (71.7%) QCI, respectively. In most countries, particularly those with lower socio-demographic index, women had better QCI.

Conclusion
This is the first global assessment of QCI, shedding light on the current trends and highlighting the necessity of improving the endocarditis QoC, mainly by timely case detection, adherence to antibiotic prophylaxis guidelines, utilizing targeted antibiotics and advanced treatments, in the African region and resolving gender inequality in selected countries.
Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations
Authors: Bear Sydney E , Seward James D , Lamit Louis Jamie , Basiliko Nathan , Moore Tim , Lilleskov Erik , Yavitt Joseph B , Schadt Christopher W , Smith Dave Solance , Mclaughlin Jim , Siljanen Henri , Mykytczuk Nadia , Williams Shanay , Roulet Nigel , Harris Lorna , Carson Michael A , Watmough Shaun , Bräuer Suzanna L 
Published: December 2021

Abstract
Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.
Iterative mutagenesis induced by atmospheric and room temperature plasma treatment under multiple selection pressures for the improvement of coenzyme Q10 production by Rhodobacter sphaeroides
Authors: Wang Yong , Chen Shaofei , Huo Kai , Wang Bin , Liu Junguo , Zhao Guoqun , Liu Jinlong 
Published: December 2021

Abstract
CoQ10, which has been widely applied in medicine by dietary supplement, possesses important functions in antioxidant process and bioenergy generation. Iterative mutagenesis introduced by atmospheric and room temperature plasma (ARTP) treatment was studied to improve the coenzyme Q10 (CoQ10) production of Rhodobacter sphaeroides (R. sphaeroides), and multiple selection pressures including vitamin K3 (VK3), Na2S and benzoic acid (BA) were adopted for the first time. After two rounds of mutation and screening, a mutant strain R.S 17 was obtained, and the product titer was increased by 80.37%. The CoQ10 titer and cell density reached 236.7 mg L−1 and 57.09 g L−1, respectively, in the fed-batch fermentation, and the CoQ10 content was 22.1% higher than that of the parent strain. In addition, the spectral scanning results indicated the metabolic flux improvement contributing to the CoQ10 production in R.S 17, and the genetic stability was validated. Based on the iterative mutagenesis introduced by ARTP under multiple selection pressures, the promotion of CoQ10 production by R. sphaeroides was achieved. The significant improvement in fermentation performances and the good genetic stability of R.S 17 indicate a potential way for the efficient biosynthesis of CoQ10.
Analysis of changes in the microbial community structure and physicochemical properties during the fermentation of sand crab juice
Authors: Luo Meiyan , Chen Leilei , Liu Huanming , Jiang Jiahui , Lai Chongxi , Zhou Chunxia , Hong Pengzhi , Gao Ping 
Published: December 2021

Abstract
The structure of the microbial community during sand crab juice fermentation was analyzed using culture-based methods and high-throughput 16S rRNA gene sequencing. Additionally, the changes in amino acid nitrogen (AAN) and total volatile basic nitrogen (TVB-N) were evaluated. Staphylococcus equorum, Staphylococcus arlettae, Staphylococcus saprophyticus, Salinicoccus amylolyticus, and Bacillus cereus were isolated by traditional culture isolation technique. The Good's coverage obtained by high-throughput sequencing was over 99.5%, and the Chao1 and Simpson indices showed small fluctuations, indicating that the species abundance and diversity did not change significantly during the fermentation process, although the abundance decreased. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla observed during fermentation, whereas Aquabacterium, Roseovarius, Muribaculaceae, and Silicimonas were the dominant bacterial genera. The AAN content increased from 0.15 to 0.43 g/100 mL during the 15-day fermentation, indicating the production of small peptides and amino acids during fermentation. The TVB-N content (25.2 mg/100 mL) on day 15 indicated slight spoilage of sand crab juice, although the freshness conformed to the production standard. These results provide a theoretical basis for improving the quality and optimizing the production process of sand crab juice.
Supercomplex Organization of the Electron Transfer System in Marine Bivalves, a Model of Extreme Longevity
Authors: Rodríguez Enrique , Radke Amanda , Hagen Tory M , Blier Pierre U 
Published: December 2021

Abstract
The mitochondrial oxidative stress theory of aging suggests that the organelle’s decay contributes to the aging phenotype via exacerbated oxidative stress, loss of organ coordination and energetics, cellular integrity, and activity of the mitochondrial electron transfer system (ETS). Recent advances in understanding the structure of the ETS show that the enzymatic complexes responsible for oxidative phosphorylation are arranged in supramolecular structures called supercomplexes that lose organization during aging. Their exact role and universality among organisms are still under debate. Here, we take advantage of marine bivalves as an aging model to compare the structure of the ETS among species ranging from 28 to 507 years in maximal life span. Our results show that regardless of life span, the bivalve ETS is arrayed as a set of supercomplexes. However, bivalve species display varying degrees of ETS supramolecular organization with the highest supercomplex structures found in Arctica islandica, the longest-lived of the bivalve species under study. We discuss this comparative model in light of differences in the nature and stoichiometry of these complexes and highlight the potential link between the complexity of these superstructures and longer life spans.
Navigating Black Aging: The Biological Consequences of Stress and Depression
Authors: Forrester Sarah N , Whitfield Keith E , Kiefe Catarina I , Thorpe Roland J 
Published: December 2021

Abstract

Objectives
Black persons in the United States are more likely to suffer from social inequality. Chronic stress caused by social inequality and racial discrimination results in weathering of the body that causes physiological dysregulation and biological age being higher than chronological age (accelerated aging). Depression has been linked to both racial discrimination and accelerated aging and accelerated aging has been demonstrated to be higher in Black than White persons, on average. However, we know little about accelerated aging across the life course in Black Americans.

Methods
We used mixed-effects growth models to measure biological age acceleration, measured with cardiometabolic markers, over a 20-year period in Black participants of the Coronary Artery Risk Development in Young Adults Study who were aged 27–42 years at analytic baseline. We included an interaction between depressive symptoms and time to determine whether risk of depression was associated with a faster rate of biological aging.

Results
We found that the rate of biological aging increased over a 20-year span and that those at risk for depression had a faster rate of biological aging than those not at risk. We also found that various social factors were associated with biological age acceleration over time.

Discussion
Given the known association between perceived racial discrimination and depressive symptoms, we provide a novel instance of the long-term effects of social inequality. Specifically, biological age acceleration, a marker of physiological dysregulation, is associated with time among Black persons and more strongly associated among those with depressive symptoms.
Excess Mortality by Individual and Spousal Education for Recent and Long-Term Widowed
Authors: Östergren Olof , Fors Stefan , Rehnberg Johan 
Published: December 2021

Abstract

Objectives
The loss of a spouse is followed by a dramatic but short-lived increase in the mortality risk of the survivor. Contrary to expectations, several studies have found this increase to be larger among those with high education. Having a spouse with high education is associated with lower mortality, which suggests that losing a spouse with high education means the loss of a stronger protective factor than losing a spouse with low education. This may disproportionately affect the high educated because of educational homogamy.

Methods
We use Swedish total population registers to construct an open cohort of 1,842,487 married individuals aged 60–89 during 2007–2016, observing 239,276 transitions into widowhood and 277,946 deaths. We use Poisson regression to estimate relative and absolute mortality risks by own and spousal education among the married and recent and long-term widows.

Results
We find an absolute increase in mortality risk, concentrated to the first 6 months of widowhood across all educational strata. The relative increase in mortality risk is larger in higher educational strata. Losing a spouse with high education is associated with higher excess mortality, which attenuates this difference.

Discussion
When considering the timing and the absolute level of excess mortality, we find that the overall patterns of excess mortality are similar across educational strata. We argue that widowhood has a dramatic impact on health, regardless of education.
Ethical and Methodological Challenges in Research With Hard-to-Reach Groups: Examples From Research on Family Caregivers for Migrant Older Adults Living With Dementia
Authors: Tezcan-Güntekin Hürrem , Özer-Erdogdu Ilknur , Yilmaz-Aslan Yüce , Aksakal Tugba , Bird Rona 
Published: December 2021

Abstract
Family caregivers of migrants with dementia constitute a population group that is hard to reach for research participation due to factors such as shame about the disease and past experiences of discrimination. In this article, research-ethical challenges associated with participant recruitment and qualitative data collection among relatives of migrants with dementia are discussed. Over a period of 8 years, 3 studies were conducted to investigate the experiences of family caregivers for persons with dementia of Turkish descent in Germany. Across these studies, a total of 32 family caregivers were interviewed. In this article, based on the “Principles of Biomedical Ethics” according to Beauchamp and Childress (2009), research-ethical conflicts associated with sampling methods and the presence of third parties during qualitative interviews are discussed. The potential risks emanating from sampling strategies and the presence of third parties during interviews regarding the voluntary nature of study participation are examined. Additionally, this article formulates recommendations for ensuring truly voluntary participation and protecting both the participants (family caregivers) and relatives with dementia from harm. These practical recommendations aim to help future researchers to avoid ethical pitfalls and represent a roadmap for making necessary methodological decisions.
Fat metabolism is associated with telomere length in six population-based studies
Authors: van der Spek Ashley , Karamujić-Čomić Hata , Pool René , Bot Mariska , Beekman Marian , Garmaeva Sanzhima , Arp Pascal P , Henkelman Sandra , Liu Jun , Alves Alexessander Couto , Willemsen Gonneke , van Grootheest Gerard , Aubert Geraldine ,   BBMRI Metabolomics Consortium, Ikram M Arfan , Jarvelin Marjo-Riitta , Lansdorp Peter , Uitterlinden André G , Zhernakova Alexandra , Slagboom P Eline , Penninx Brenda W J H , Boomsma Dorret I , Amin Najaf , van Duijn Cornelia M 
Published: December 2021

Abstract
Telomeres are repetitive DNA sequences located at the end of chromosomes, which are associated to biological aging, cardiovascular disease, cancer and mortality. Lipid and fatty acid metabolism have been associated with telomere shortening. We have conducted an in-depth study investigating the association of metabolic biomarkers with telomere length (LTL). We performed an association analysis of 226 metabolic biomarkers with LTL using data from 11 775 individuals from six independent population-based cohorts (BBMRI-NL consortium). Metabolic biomarkers include lipoprotein lipids and subclasses, fatty acids, amino acids, glycolysis measures and ketone bodies. LTL was measured by quantitative polymerase chain reaction or FlowFISH. Linear regression analysis was performed adjusting for age, sex, lipid-lowering medication and cohort-specific covariates (model 1) and additionally for body mass index (BMI) and smoking (model 2), followed by inverse variance-weighted meta-analyses (significance threshold Pmeta = 6.5 × 10−4). We identified four metabolic biomarkers positively associated with LTL, including two cholesterol to lipid ratios in small VLDL (S-VLDL-C % and S-VLDL-CE %) and two omega-6 fatty acid ratios (FAw6/FA and LA/FA). After additionally adjusting for BMI and smoking, these metabolic biomarkers remained associated with LTL with similar effect estimates. In addition, cholesterol esters in very small VLDL (XS-VLDL-CE) became significantly associated with LTL (P = 3.6 × 10−4). We replicated the association of FAw6/FA with LTL in an independent dataset of 7845 individuals (P = 1.9 × 10−4). To conclude, we identified multiple metabolic biomarkers involved in lipid and fatty acid metabolism that may be involved in LTL biology. Longitudinal studies are needed to exclude reversed causation.
Reducing Pain in Experimental Models of Intestinal Inflammation Affects the Immune Response
Authors: Golusda Laura , Kühl Anja A , Siegmund Britta , Paclik Daniela 
Published: December 2021

Abstract
The incidence of inflammatory bowel disease with its two main manifestations, colitis ulcerosa and Crohn’s disease, is rising globally year after year. There is still a tremendous need to study the underlying pathomechanisms and a well-established tool in order to better understand the disease are colitis models in rodents. Since the concept of the 3Rs was proposed by Russell and Burch, this would include pain medication in animal models of intestinal inflammation as a reduction of suffering. This review argues against pain medication because the administration of pain medication in its current form has an impact on the inflammatory process and the immune response, thus falsifying the results and the reproducibility and therefore leading to misconceptions.
Patient-derived gene and protein expression signatures of NGLY1 deficiency
Authors: Rauscher Benedikt , Mueller William F , Clauder-Münster Sandra , Jakob Petra , Islam M Saiful , Sun Han , Ghidelli-Disse Sonja , Boesche Markus , Bantscheff Marcus , Pflaumer Hannah , Collier Paul , Haase Bettina , Chen Songjie , Hoffman Rene , Wang Guangwen , Benes Vladimir , Drewes Gerard , Snyder Michael , Steinmetz Lars M 
Published: December 2021

Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing four different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared with parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.