Miracle-dz/UniFAR-FTUs huggingface dataset:
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at a species-level. Here, we generated and analyzed the pan-transcriptome of ∼1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of the transcriptome divergence. Global gene expression patterns combined with population structure show that the heritable expression variation mainly lies within subpopulation-specific signatures, for which the accessory genes are overrepresented. Genome-wide association analyses consistently highlight that the accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.
DNA methylation-environment interactions in the human genome

Previously we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures—one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.
Ordinary differential equations to construct invertible generative models of cell type and tissue-specific regulatory networks

Single-cell RNA-Seq (scRNA-seq) transcriptomics can elucidate gene regulatory networks (GRNs) of complex phenotypes, but raw sequencing observations only provide ”snap-shots” of data and are inherently noisy. scRNA-seq trajectory inference has been utilized to solve for the missing observations, but disentangling complex dynamics of gene-gene interactions at different time points from aggregated data is a non-trivial task and computationally expensive. Here we describe our Non-Stiff Dynamic Invertible Model of CO-Regulatory Networks (NS-DIMCORN) to define the genetic nexus underpinning specific cellular functions using invertible warping of flexible multivariate Gaussian distributions by neural Ordinary differential equations. Our results yield a generative model with unbiased density estimation from RNA-seq read-count data only. This resulted in scalable time-flexible sampling of each gene’s expression level thence allowing ab initio assembly of gene regulatory networks in specific cells. We demonstrate our proposed methodology is superior to the state-of-the-art algorithms in accurately recovering genome-wide functional interactions, whether from synthetic or empirical data. We optimized our algorithm for GPU-based implementation thereby further enhancing the utility of our proposed methodology in comparison to the ten benchmarked methods.
Team Faultline Measures

Team faultlines—hypothetical dividing lines based on member attributes that split a team into relatively homogeneous subgroups—influence team processes across contexts, as recent meta-analytic findings show. We review the available faultline measures with regard to their properties and identify several limitations, including dealing with more than two subgroups. We thus propose a new cluster-based approach, average silhouette width (ASW), that identifies the number of subgroups and subgroup membership. We then compare the measures with 1,400 simulated teams with varying properties and investigate their factor structure and their behavior under missing values. We also investigate the predictive validity of the measures with data from real work teams. Results show that different measures respond to different team features in different ways but that most of them load on two correlated factors. Taken together, the ASW measure had the most favorable attributes and was the only measure that accurately determined subgroup membership in the presence of more than two subgroups. We discuss limitations and further research opportunities pertaining to faultline measures and provide software for calculating all investigated measures at http://www.group-faultlines.org.
Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells

To cope with novel virus infections to which no prior adaptive immunity exists, the body strongly relies on the innate immune system. In such cases, including infections with SARS-CoV-2, children tend to fair better than adults. In the context of COVID-19, it became evident that a rapid interferon response at the site of primary infection is key for successful control of the virus and prevention of severe disease. The airway epithelium of children was shown to exhibit a primed state already at homeostasis and to respond particularly well to SARS-CoV-2 infection. However, the underlying mechanism for this priming remained elusive. Here we show that interactions between airway mucosal immune cells and epithelial cells are stronger in children, and via cytokine-mediated signaling lead to IRF-1-dependent upregulation of the viral sensors RIG-I and MDA5. Based on a cellular in vitro model we show that stimulated human peripheral blood mononuclear cells (PBMC) can induce a robust interferon-beta response towards SARS-CoV-2 in a lung epithelial cell line otherwise unresponsive to this virus. This is mediated by type I interferon, interferon-gamma and TNF, and requires induction of both, RIG-I and MDA5. In single cell-analysis of nasal swab samples the same cytokines are found to be elevated in mucosal immune cells of children, correlating with elevated epithelial expression of viral sensors. In vitro analysis of PBMC derived from healthy adolescents and adults confirm that immune cells of younger individuals show increased cytokine production and potential to prime epithelial cells. In co-culture with SARS-CoV-2-infected A549 cells, PBMC from adolescents significantly enhance the antiviral response. Taken together, our study suggests that higher numbers and a more vigorous activity of innate immune cells in the airway mucosa of children tune the set-point of the epithelial antiviral system. This likely is a major contributor to the robust immune response to SARS-CoV-2 in children. Our findings shed light on the molecular underpinnings of the stunning resilience of children towards severe COVID-19, and may propose a novel concept for immunoprophylactic treatments.
Schizandrin C regulates lipid metabolism and inflammation in liver fibrosis by NF-κB and p38/ERK MAPK signaling pathways

Liver fibrosis is considered a sustained wound healing response and metabolic syndrome, and its therapy is of great significance for chronic liver disease. Schizandrin C, as one lignan from hepatic protectant Schisandra chinensis, can depress the oxidative effect and lipid peroxidation, and protect against liver injury. In this study, C57BL/6J mice were used to estimate a liver fibrosis model by CCl4, and Schizandrin C exerted an anti-hepatic fibrosis effect, as evidenced by decreased alanine aminotransferase, aspartate aminotransferase and total bilirubin activities in serum, lower hydroxyproline content, recuperative structure and less collagen accumulation in the liver. In addition, Schizandrin C reduced the expressions of alpha-smooth muscle actin and type Ι collagen in the liver. In vitro experiments also revealed that Schizandrin C attenuated hepatic stellate cell activation in both LX-2 and HSC-T6 cells. Furthermore, lipidomics and quantitative real-time PCR analysis revealed that Schizandrin C regulated the lipid profile and related metabolic enzymes in the liver. In addition, the mRNA levels of inflammation factors were downregulated by Schizandrin C treatment, accompanied by lower protein levels of IκB-Kinase-β, nuclear factor kappa-B p65, and phospho-nuclear factor kappa-B p65. Finally, Schizandrin C inhibited the phosphorylation of p38 MAP kinase and extracellular signal-regulated protein kinase, which were activated in the CCl4 fibrotic liver. Taken together, Schizandrin C can regulate lipid metabolism and inflammation to ameliorate liver fibrosis by nuclear factor kappa-B and p38/ERK MAPK signaling pathways. These findings supported Schizandrin C as a potential drug for liver fibrosis.
High risk of osteoporosis and fracture following solid organ transplantation: a population-based study

Background Osteoporosis and fractures increase morbidity and mortality rates after solid organ transplantation (SOT), but few studies have analyzed the risk of osteoporosis and related fractures after SOT. In this retrospective cohort study, we investigated the risk of osteoporosis and fractures in different SOT recipients. Methods This study was a retrospective cohort study using a nationally representative database in Taiwan. We collected the data of SOT recipients and used the propensity score matching method to obtain a comparison cohort. To reduce bias, we excluded patients who had been diagnosed with osteoporosis or fracture before inclusion. All participants were followed up until the date of diagnosis as having a pathological fracture, death, or the end of 2018, whichever occurred first. The Cox proportional hazards model was used to investigate the risk of osteoporosis and pathological fracture in SOT recipients. Results After adjustment for the aforementioned variables, SOT recipients were observed to have a higher risk of osteoporosis (hazard ratio (HR) = 1.46, 95% confidence interval (CI): 1.29–1.65) and fracture (HR: 1.19, 95% CI: 1.01–1.39) than the general individuals. Among the different SOT recipients, the highest risk of fractures was noted in heart or lung transplant recipients, with a HR of 4.62 (95% CI: 2.05–10.44). Among the age groups, patients aged >61 years had the highest HRs for osteoporosis (HR: 11.51; 95% CI, 9.10–14.56) and fracture (HR: 11.75, 95% CI: 8.97–15.40). Conclusion SOT recipients had a higher risk of osteoporosis and related fractures than the general population, with the highest risks observed in patients receiving heart or lung transplants, older patients, and patients with CCI scores of >3.
Insights into anti-tumor immunity via the polyomavirus shared across human Merkel cell carcinomas

Understanding and augmenting cancer-specific immunity is impeded by the fact that most tumors are driven by patient-specific mutations that encode unique antigenic epitopes. The shared antigens in virus-driven tumors can help overcome this limitation. Merkel cell carcinoma (MCC) is a particularly interesting tumor immunity model because (1) 80% of cases are driven by Merkel cell polyomavirus (MCPyV) oncoproteins that must be continually expressed for tumor survival; (2) MCPyV oncoproteins are only ~400 amino acids in length and are essentially invariant between tumors; (3) MCPyV-specific T cell responses are robust and strongly linked to patient outcomes; (4) anti-MCPyV antibodies reliably increase with MCC recurrence, forming the basis of a standard clinical surveillance test; and (5) MCC has one of the highest response rates to PD-1 pathway blockade among all solid cancers. Leveraging these well-defined viral oncoproteins, a set of tools that includes over 20 peptide-MHC class I tetramers has been developed to facilitate the study of anti-tumor immunity across MCC patients. Additionally, the highly immunogenic nature of MCPyV oncoproteins forces MCC tumors to develop robust immune evasion mechanisms to survive. Indeed, several immune evasion mechanisms are active in MCC, including transcriptional downregulation of MHC expression by tumor cells and upregulation of inhibitory molecules including PD-L1 and immunosuppressive cytokines. About half of patients with advanced MCC do not persistently benefit from PD-1 pathway blockade. Herein, we (1) summarize the lessons learned from studying the anti-tumor T cell response to virus-positive MCC; (2) review immune evasion mechanisms in MCC; (3) review mechanisms of resistance to immune-based therapies in MCC and other cancers; and (4) discuss how recently developed tools can be used to address open questions in cancer immunotherapy. We believe detailed investigation of this model cancer will provide insight into tumor immunity that will likely also be applicable to more common cancers without shared tumor antigens.
Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery

Introduction Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. Methods In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Results Our results suggested soil microbial a-diversity decreased under high C10–C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10–C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. Discussion The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.
Should I post? The relationships among social media use, emotion recognition, and mental health

Introduction While increased time spent on social media can be negatively related to one’s overall mental health, social media research often fails to account for what behaviors users are actually engaging in while they are online. The present research helps to address this gap by measuring participants’ active and passive social media behavioral styles and investigates whether and how these two social media behavioral styles are related to depression, anxiety, and stress, and the mediating role of emotion recognition ability in this relationship. Methods A pre-study (N = 128) tested whether various social media behaviors reliably grouped into active and passive behavioral styles, and a main study (N = 139) tested the relationships between social media use style, emotion recognition, and mental health. Results While we did not find evidence of a mediating relationship between these variables, results supported that more active social media use was related to more severe anxiety and stress as well as poorer emotion recognition skill, while passive social media use was unrelated to these outcomes. Discussion These findings highlight that, beyond objective time spent on social media, future research must consider how users are spending their time online.
Comparative dosimetric study of radiotherapy in high-grade gliomas based on the guidelines of EORTC and NRG-2019 target delineation

Purpose Radiotherapy is one of the most important treatments for high-grade glioma (HGG), but the best way to delineate the target areas for radiotherapy remains controversial, so our aim was to compare the dosimetric differences in radiation treatment plans generated based on the European Organization for Research and Treatment of Cancer (EORTC) and National Research Group (NRG) consensus to provide evidence for optimal target delineation for HGG. Methods We prospectively enrolled 13 patients with a confirmed HGG from our hospital and assessed dosimetric differences in radiotherapy treatment plans generated according to the EORTC and NRG-2019 guidelines. For each patient, two treatment plans were generated. Dosimetric parameters were compared by dose–volume histograms for each plan. Results The median volume for planning target volume (PTV) of EORTC plans, PTV1 of NRG-2019 plans, and PTV2 of NRG-2019 plans were 336.6 cm3 (range, 161.1–511.5 cm3), 365.3 cm3 (range, 123.4–535.0 cm3), and 263.2 cm3 (range, 116.8–497.7 cm3), respectively. Both treatment plans were found to have similar efficiency and evaluated as acceptable for patient treatment. Both treatment plans showed well conformal index and homogeneity index and were not statistically significantly different (P = 0.397 and P = 0.427, respectively). There was no significant difference in the volume percent of brain irradiated to 30, 46, and 60 Gy according to different target delineations (P = 0.397, P = 0.590, and P = 0.739, respectively). These two plans also showed no significant differences in the doses to the brain stem, optic chiasm, left and right optic nerves, left and right lens, left and right eyes, pituitary, and left and right temporal lobes (P = 0.858, P = 0.858, P = 0.701 and P = 0.794, P = 0.701 and P = 0.427, P = 0.489 and P = 0.898, P = 0.626, and P = 0.942 and P = 0.161, respectively). Conclusion The NRG-2019 project did not increase the dose of organs at risk (OARs) radiation. This is a significant finding that further lays the groundwork for the application of the NRG-2019 consensus in the treatment of patients with HGGs. Clinical trial registration The effect of radiotherapy target area and glial fibrillary acidic protein (GFAP) on the prognosis of high-grade glioma and its mechanism, number ChiCTR2100046667. Registered 26 May 2021.
Editorial: Stress-induced weight changes

COPYRIGHT © 2023 Heshmati, Luzi, Greenway and Rebello. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 22 May 2023 DOI 10.3389/fendo.2023. 1209975
“Attitudes to voices”: a survey exploring the factors influencing clinicians’ intention to assess distressing voices and attitudes towards working with young people who hear voices

Introduction Due to the general psychopathological vulnerability of young people who hear distressing voices, research has stressed the importance for clinicians to assess this experience in youth. Nonetheless, the limited literature on the topic comes from studies with clinicians in adult health services and it primarily reports that clinicians do not feel confident in systematically assessing voice-hearing and doubt the appropriateness of doing so. We applied the Theory of Planned Behavior and identified clinicians’ job attitudes, perceived behavioral control, and perceived subjective norms as putative predictors of their intent to assess voice-hearing in youth. Method Nine hundred and ninety-six clinicians from adult mental health services, 467 from Child and Adolescent Mental Health (CAMHS) and Early Intervention in Psychosis (EIP) services and 318 primary care clinicians across the UK completed an online survey. The survey gathered data on attitudes toward working with people who hear voices, stigmatizing beliefs, and self-perceived confidence in voice-related practices (screening for, discussing and providing psychoeducation material about voice-hearing). Responses from youth mental health clinicians were compared with professionals working in adult mental health and primary care settings. This study also aimed to identify what youth mental health clinicians believe about assessing distressing voices in adolescents and how beliefs predict assessment intention. Results Compared to other clinicians, EIP clinicians reported the most positive job attitudes toward working with young voice-hearers, the highest self-efficacy in voice-hearing practices, and similar levels of stigma. Job attitudes, perceived behavioral control and subjective norms explained a large part of the influences on clinician’s intention to assess voice-hearing across all service groups. In both CAMHS and EIP services, specific beliefs relating to the usefulness of assessing voice-hearing, and perceived social pressure from specialist mental health professionals regarding assessment practices predicted clinician intention. Discussion Clinicians’ intention to assess distressing voices in young people was moderately high, with attitudes, subjective norms and perceived behavioral control explaining a large part of its variance. Specifically in youth mental health services, promoting a working culture that encourages opening and engaging in discussions about voice-hearing between clinicians, and with young people, and introducing supportive assessment and psychoeducation material about voice-hearing could encourage conversations about voices.
Number of prior live births is associated with higher arterial stiffness but not its change in older women: the atherosclerosis risk in communities study

Introduction Although studies have demonstrated a J-shaped association between parity and cardiovascular disease (CVD), the association with arterial stiffness is not fully understood. Methods We examined the association between parity and carotid-femoral pulse wave velocity (cfPWV), a measure of central arterial stiffness. We conducted a longitudinal analysis of 1220 women (mean age 73.7 years) who attended the Atherosclerosis Risk in Communities Study visit 5 (2011-2013). At visit 2 (1990-1992), women self-reported parity (number of prior live births), which we categorized as: 0 (never pregnant or pregnant with no live births); 1-2 (referent); 3-4; and 5+ live births. Technicians measured cfPWV at visit 5 (2011-2013) and visit 6 or 7 (2016-2019). Multivariable linear regression modeled the associations of parity with visit 5 cfPWV and cfPWV change between visit 5 and 6/7 adjusted for demographics and potential confounding factors. Results Participants reported 0 (7.7%), 1-2 (38.7%), 3-4 (40.0%), or 5+ (13.6%) prior live births. In adjusted analyses, women with 5+ live births had a higher visit 5 cfPWV (β=50.6 cm/s, 95% confidence interval: 3.6, 97.7 cm/s) than those with 1-2 live births. No statistically significant associations were observed for other parity groups with visit 5 cfPWV or with cfPWV change. Discussion In later life, women with 5+ live births had higher arterial stiffness than those with 1-2 live births, but cfPWV change did not differ by parity, suggesting women with 5+ live births should be targeted for early primary prevention of CVD given their higher arterial stiffness at later-life.