bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunological dysfunction persists for 8 months following initial mild-moderate SARS-CoV-2 infection
Authors: Phetsouphanh Chansavath , Darley David , Wilson Daniel B , Howe Annett , Ling Munier C. Mee , Patel Sheila K , Juno Jennifer A , Burrell Louise M , Kent Stephen J , Dore Gregory J , Kelleher Anthony D , Matthews Gail V 
Published: June 2021

AbstractA proportion of patients surviving acute COVID-19 infection develop post-COVID syndrome (long COVID) encompassing physical and neuropsychiatric symptoms lasting longer than 12 weeks. Here we studied a prospective cohort of individuals with long COVID compared to age/gender matched subjects without long COVID (from the ADAPT study), healthy donors and individuals infected with other non-SARS CoV2 human coronaviruses (the ADAPT-C study). We found highly activated innate immune cells and an absence of subsets of un-activated naïve T and B cells in peripheral blood of long COVID subjects, that did not reconstitute over time. These activated myeloid cells may contribute to the elevated levels of type I (IFN-β) and III interferon (IFN-λ1) that remained persistently high in long COVID subjects at 8 months post-infection. We found positive inter-analyte correlations that consisted of 18 inflammatory cytokines in symptomatic long COVID subjects that was not observed in asymptomatic COVID-19 survivors. A linear classification model was used to exhaustively search through all 20475 combinations of the 29 analytes measured, that had the strongest association with long COVID and found that the best 4 analytes were: IL-6, IFN-γ, MCP-1 (CCL2) and VCAM-1. These four inflammatory biomarkers gave an accuracy of 75.9%, and an F1 score of 0.759, and have also previously been associated with acute severe disease. In contrast, plasma ACE2 levels, while elevated in the serum of people previously infected with SARS-CoV-2 were not further elevated in subjects with long COVID symptoms. This work defines immunological parameters associated with long COVID and suggests future opportunities to prevention and treatment.
Factors associated with home birth in Peru: An analysis of the Demographic and Health Survey, 2019
Authors: Huapaya-Torres Jackeline , Santos-Rosales Yuly , Moquillaza-Alcántara Victor 
Published: June 2021

ABSTRACTObjectiveTo determine the proportion and factors associated with home birth in Peru, 2019.Material and methodsCross-sectional analytical design study where the 2019 Peruvian Demographic and Family Health Survey was analyzed. The association was evaluated using Poisson Regression, supplemented with the crude prevalence ratio (cPR) and adjusted (aPR).ResultsThe records of 18,401 women were evaluated, where 5.39% (95%CI:4.83-6.03%) presented home birth. The probability of a home birth occurs increases when the pregnant woman is from the andean (aPR:1.24; 95%CI:1.02-1.48) and amazon region (aPR:1.38; 95%CI:1.16-1.64), resides in rural areas (aPR:3.34; 95%CI:2.61-4.29), presents less than 6 prenatal care (aPR:1.66; 95%CI:1.39 -1.96), it is very poor (aPR:9.62; 95%CI:5.13-18.1) or poor (aPR:2.39; 95%CI:1.26-4.52), it has not studied (aPR:2.66; 95%CI:2.02-3.50) or reached primary education (aPR:2.18: 95%CI:1.85-2.58) and has 2 children (aPR:1.64; 95%CI:1.46-1.85) or 3 or more children (aPR:2.18; 95%CI:1.67-2.87). On the other hand, having higher educational instruction (aPR:0.49; 95%CI:0.31-0.78) is associated with a lower probability of a home birth.ConclusionsThere is a low proportion of home births; however, this indicator increases significantly according to various geographical, sociodemographic, and obstetric factors that have been identified.HIGHLIGHTSThe proportion of home births in Peru is low, although it reaches high values in the amazon and rural areas.Sociodemographic determinants such as poverty and low educational level are risk factors for home birth.Obstetric determinants such as having few prenatal controls or had having previously multiple deliveries are risk factors for home birth.
Occupational inequalities in the prevalence of COVID-19: A longitudinal observational study of England, August 2020 to January 2021
Authors: Green Mark A. , Semple Malcolm G. 
Published: June 2021

AbstractBackgroundThe COVID-19 pandemic has reinforced, amplified and created new health inequalities. There is less evidence on how COVID-19 prevalence varies by measures of work and occupation which represent a key social determinant of health. The aim of the study is to evaluate how occupational inequalities in the prevalence of COVID-19 varies across England and their possible explanatory factors.MethodsWe used data for 363,651 individuals (2,178,835 observations) aged 18 years and over between 1st May 2020 and 31st January 2021 from the ONS Covid Infection Survey, a representative longitudinal survey of individuals in England. We focus on two measures of work; employment status for all adults, and work sector of individuals currently working. Multi-level binomial regression models were used to estimate the likelihood of testing positive of COVID-19, adjusting for known explanatory covariates.Results0.9% of participants tested positive for COVID-19 over the study period. COVID-19 prevalence was higher among adults who were students or furloughed (i.e., temporarily not working). Among adults currently working, COVID-19 prevalence was highest in adults employed in the hospitality sector, with higher prevalence for individuals employed in transport, social care, retail, health care and educational sectors. Inequalities by work were not consistent over time.ConclusionsWe find an unequal distribution of infections relating to COVID-19 by work and employment status. Our findings demonstrate the need for greater workplace interventions to protect employees, but also that a large proportion of SARS-CoV-2 transmission occurs outside of work. In particular, populations who experienced social and economic harms through being furloughed were also more likely to experience a double burden of increased likelihood of COVID-19.
Choosing questions before methods in dementia research with competing events and causal goals
Authors: Rojas-Saunero L. Paloma , Young Jessica G. , Didelez Vanessa , Ikram M. Arfan , Swanson Sonja A. 
Published: June 2021

ABSTRACTSeveral of the hypothesized or studied exposures that may affect dementia risk are known to increase the risk of death. This may explain counterintuitive results, where exposures that are known to be harmful for mortality risk sometimes seem protective for the risk of dementia. Authors have attempted to explain these counterintuitive results as biased, but the bias associated with a particular analytic method cannot be defined or assessed if the causal question is not explicitly specified. Indeed, we can consider several causal questions when competing events like death, which cannot be prevented by design, are present. Current dementia research guidelines have not explicitly considered what constitutes a meaningful causal question in this setting or, more generally, how this choice justifies and should drive particular analytic decisions. To contextualize current practices, we first perform a systematic review of the conduct and interpretation of longitudinal studies focused on dementia outcomes where death is a competing event. We then describe and demonstrate how to address different causal questions (referred here as “the total effect” and “the controlled direct effect”) with traditional analytic approaches under explicit assumptions. Our application focuses on smoking cessation in late-midlife. To illustrate core concepts, we discuss this example both in terms of a hypothetical randomized trial and with an emulation of such a trial using observational data from the Rotterdam Study.
Effects of Acute Normovolemic Hemodilution on Post-Cardiopulmonary Bypass Coagulation Tests and Allogeneic Blood Transfusion in Thoracic Aortic Repair Surgery: An Observational Cohort Study
Authors: Mladinov Domagoj , Eudailey Kyle W. , Padilla Luz A. , Norman Joseph B. , Leahy Benjamin , Enslin Jacob , Parker Keli , Cornelius Katherine F. , Davies James E. 
Published: June 2021

AbstractBackground and AimPerioperative blood transfusion is associated with increased morbidity and mortality. Acute normovolemic hemodilution (ANH) is a blood conservation strategy associated with variable success, and rarely studied in more complex cardiac procedures. The study aim was to evaluate whether acute ANH improves coagulopathy and reduces blood transfusions in thoracic aortic surgeries.MethodsSingle-center observational cohort study comparing ANH and standard institutional practice in patients who underwent thoracic aortic repair from 2019 to 2021.Results89 patients underwent ANH and 116 standard practice. There were no significant differences between the groups in terms of demographic or major perioperative characteristics. In the ANH group coagulation tests before and after transfusion of autologous blood showed decreased INR and increased platelets, fibrinogen, all with p<0.0005. Coagulation results in the ANH and control groups were not statistically different. The average number of transfused allogeneic products per patient was lower in the ANH vs control group: FFP 1.1 ±1.6 vs 1.9 ±2.3 (p=0.003), platelets 0.6 ±0.8 vs 1.2 ±1.3 (p=0.0008), and cryoprecipitate 0.3 ±0.7 vs 0.7 ±1.1 (p=0.008). Reduction in RBC transfusion was not statistically significant. The percentage of patients who received any transfusion was 53.9% in ANH and 59.5% in the control group (p=0.42). There was no significant difference in major adverse outcomes.ConclusionsANH is a safe blood conservation strategy for surgical repairs of the thoracic aorta. Laboratory data suggests that ANH can improve coagulopathy after separation from CPB, and significantly reduce the number of transfused FFP, platelets and cryoprecipitate.
Interaction of a photochromic UV sensor protein Rc-PYP with PYP-binding protein
Authors: Kim Suhyang , Nakasone Yusuke , Takakado Akira , Yamazaki Yoichi , Kamikubo Hironari , Terazima Masahide 
Published: June 2021

AbstractPhotoactive yellow protein (PYP) from Halorhodospira halophila is one of typical light sensor proteins. Although its photoreaction has been extensively studied, no downstream partner protein has been identified to date. In this study, the intermolecular interaction dynamics observed between PYP from Rhodobacter capsulatus (Rc-PYP) and a possible downstream protein, PYP-binding protein (PBP), were studied. It was found that UV light-induced a long-lived product (pUV*), which interacts with PBP to form a stable hetero-hexamer (Complex-II). The reaction scheme for this interaction was revealed using transient absorption and transient grating methods. Time-resolved diffusion detection showed that a hetero-trimer (Complex-I) is formed transiently, which produced Complex-II via a second-order reaction. Any other intermediates, including those from pBL do not interact with PBP. The reaction scheme and kinetics are determined. Interestingly, long-lived Complex-II dissociates upon excitation with blue light. These results demonstrate that Rc-PYP is a photochromic and new type of UV sensor, of which signaling process is similar to that of other light sensor proteins in the visible light region. The photochromic heterogeneous intermolecular interactions formed between PYP and PBP can be used as a novel and useful tool in optogenetics.Graphical Abstract
DNase treatment improves viral enrichment in agricultural soil viromes
Authors: Sorensen Jackson W. , Zinke Laura A. , ter Horst Anneliek M. , Santos-Medellin Christian , Schroeder Alena , Emerson Joanne B. 
Published: June 2021

AbstractThe small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size-fraction metagenomics (viromics) protocols facilitate enrichment of viral DNA from environmental samples, and these protocols typically include a DNase treatment of the post-0.2 μm viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here we compared 15 soil viromes (7 DNase-treated, 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less non-viral microbial DNA, and recovered more viral populations (vOTUs) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable, in terms of ecological patterns across viral communities. Although results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a ~225 times greater proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible.ImportanceViromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure sequences are of viral origin. However, some samples may not be amendable to DNase treatment due to viral particles being compromised either in storage (i.e. frozen) or during other sample processing. To date, the effect of DNase treatment on the recovery of viruses and downstream ecological interpretations of soil viral communities is not thoroughly understood. This work sheds light on these questions and indicates that while DNase treatment of soil viromes improves recovery of viral populations, this improvement is modest in comparison to the gains made by viromics over total soil metagenomics. Further, DNase treatment may not be necessary to observe the ecological patterns structuring soil viral communities.
Association between Maternal Depression during Pregnancy and Newborn DNA Methylation
Authors: Drzymalla Emily , Gladish Nicole , Koen Nastassja , Epstein Michael P. , Kobor Michael S. , Zar Heather J. , Stein Dan J. , Huels Anke 
Published: June 2021

AbstractAround 15% to 65% of women globally experience depression during pregnancy, prevalence being particularly high in low- and middle-income countries. Prenatal depression has been associated with adverse birth and child development outcomes. DNA methylation (DNAm) may aid in understanding this association. In this project, we analyzed associations between prenatal depression and DNAm from cord blood from participants of the South African Drakenstein Child Health Study. We examined DNAm in an epigenome wide association study (EWAS) of 248 mother child pairs. DNAm was measured using the Infinium MethylationEPIC (N=145) and the Infinium HumanMethylation450 (N=103) arrays. Prenatal depression scores, obtained with the Edinburgh Postnatal Depression Scale (EPDS) and the Beck Depression Inventory II (BDI-II), were analyzed as continuous and dichotomized variables. We used linear robust models to estimate associations between depression and newborn DNAm, adjusted for measured (smoking status, household income, sex, preterm birth, cell type proportions, and genetic principal components) and unmeasured confounding using Cate and Bacon algorithms. Bonferroni correction was used to adjust for multiple testing. DMRcate was used to test for differentially methylated regions (DMRs). Differential DNAm in GNAS (cg22798925, Δ beta per IQR(EPDS)=0.0066, p= 1.06 × 10−7) was significantly associated with EPDS. For dichotomized BDI-II thresholds, Differential DNAm in CTNNA2 (cg04859497, Δ beta=-0.064, p= 8.09 × 10−10) and OSBPL10 (cg27278221, Δ beta=-0.020, p= 5.40 × 10−8) was significantly associated with the dichotomized BDI-II variables. Eight DMRs were associated with at least two depression scales. Further studies are needed to replicate these findings and investigate their biological impact.
Antiviral Effect of Hyunggaeyungyo-tang on A549 Cells Infected with Human Coronavirus
Authors: Won Seo-Young , Seol In-Chan , Yoo Ho-Ryong , Kim Yoon-Sik 
Published: June 2021

AbstractBackgroundHerbal medicine is widely recommended to treat viral infectious diseases. Over 123,000,000 individuals have been infected with the coronavirus since a worldwide pandemic was declared in March 2020. We conducted this research to confirm the potential of herbal medicine as a treatment for coronavirus.MethodsWe infected the A549 cell line with beta coronavirus OC43 then treated with 100 μg/mL Hyunggaeyungyo-tang (HGYGT) or distilled water with a control of HGYGT. We measured the mRNA expression levels of pro-inflammatory cytokines and interferon stimulated genes (ISGs) to confirm the effectiveness of HGYGT upon coronavirus infection.ResultsWe found the effects of HYGYT decrease the expression level of pPKR, peIF2α, IFI6, IFI44, IFI44L, IFI27, IRF7, OASL and ISG15 when administered to cells with coronavirus infection. The expressions of IL-1, TNF-α, COX-2, NF-κB, iNOS and IKK mRNA were also significantly decreased in the HGYGT group than in the control group.ConclusionThrough the reduction of the amount of coronavirus RNA, our research indicates that HGYGT has antiviral effects. The reduction of IKK and iNOS mRNA levels indicate that HGYGT reduces coronavirus RNA expression and may inhibits the replication of coronavirus by acting on NF-kB/Rel pathways to protect oxidative injury. In addition, decreases in mRNA expression levels of pro-inflammatory cytokines indicate that the HGYGT may relieve the symptoms of coronavirus infections.
Tatajuba ― Exploring the distribution of homopolymer tracts
Authors: de Oliveira Martins Leonardo , Bloomfield Samuel , Stoakes Emily , Grant Andrew , Page Andrew J. , Mather Alison E. 
Published: June 2021

AbstractLength variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialised bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source license GNU GPL version 3 from https://github.com/quadram-institute-bioscience/tatajuba.
Inactivation of EMILIN-1 by proteolysis and secretion in small extracellular vesicles favors melanoma progression and metastasis
Authors: Lopez Ana Amor , Mazariegos Marina S. , Capuano Alessandra , Ximénez-Embún Pilar , Hergueta-Redondo Marta , Ángel Recio Juan , Muñoz Eva , Al-Shahrour Fátima , Muñoz Javier , Megías Diego , Doliana Roberto , Spessotto Paola , Peinado Héctor 
Published: June 2021

AbstractSeveral studies have demonstrated that melanoma-derived extracellular vesicles (EVs) are involved in lymph node metastasis; however, the molecular mechanisms involved are not defined completely. Here, we found that EMILIN-1 is proteolyzed and secreted in small EVs (sEVs) as a novel mechanism to reduce its intracellular levels favoring metastasis in lymph node metastatic cells. Interestingly, we observed that EMILIN-1 has intrinsic tumor and metastasis suppressive-like properties reducing effective migration, cell viability, primary tumor growth and metastasis in mouse melanoma models. Finally, analysis in human melanoma samples showed that tumor cells with high levels of EMILIN-1 are reduced in metastatic lesions compared to primary tumors or nevi. Overall, our analysis suggests that the inactivation of EMILIN-1 by proteolysis and secretion in sEVs reduce its intrinsic tumor suppressive activities in melanoma favoring tumor progression and metastasis.
Real-time individual benefit from social interactions before and during the lockdown: The crucial role of personality, neurobiology and genes
Authors: Monninger Maximilian , Aggensteiner Pascal-M. , Pollok Tania M. , Reinhard Iris , Hall Alisha S.M. , Zillich Lea , Streit Fabian , Witt Stephanie-H. , Reichert Markus , Ebner-Priemer Ulrich , Meyer-Lindenberg Andreas , Tost Heike , Brandeis Daniel , Banaschewski Tobias , Holz Nathalie E. 
Published: June 2021

AbstractBackground:Social integration is a major resilience factor for staying healthy. However, the COVID-19-pandemic led to unprecedented restrictions in social life. The consequences of these social lockdowns on momentary well-being are yet not fully understood.Method:We investigated the individual affective benefit from social interactions in a longitudinal birth cohort study. We used two real-time, real-life ecological momentary assessments once before and once during the initial lockdown of the pandemic (N~6800 total observations) to determine the protective role of social interactions on well-being. Moreover, we used a multimethod approach combining the ecological assessment data with individual risk and resilience factors to analyze the moderating mechanisms of personality, neurobiology and genes.Results:Social contacts were linked to higher positive affect both during normal times and during the COVID-19 pandemic, highlighting the beneficial role of social embedding. Moreover, this relationship was moderated by amygdala volume, neuroticism and polygenic risk for schizophrenia. In detail, participants with a larger left amygdala volume and higher trait neuroticism exhibited an affective benefit from more social interactions prior to the pandemic. This pattern changed during the pandemic with participants with smaller amygdala volumes and lower neurotic traits showing a social affective gain during the pandemic. Moreover, participants with low genetic risk for schizophrenia showed an affective benefit from social interactions irrespective of the time point.Conclusion:Our results highlight the protective role of social integration on momentary well-being. Thereby, we offer new insights into how this relationship is differently affected by a person’s, neurobiology, personality, and genes under adverse circumstances.