Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer

Abstract Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, and efficient approaches to quantify RiboSis activity are still limited. Here, we have established an in silico approach to conveniently score RiboSis activity based on individual transcriptome data. By employing this novel approach and RNA-seq data of 14 645 samples from TCGA/GTEx dataset and 917 294 single-cell expression profiles across 13 cancer types, we observed the elevated activity of RiboSis in malignant cells of various human cancers, and high risk of severe outcomes in patients with high RiboSis activity. Our mining of pan-cancer multi-omics data characterized numerous molecular alterations of RiboSis, and unveiled the predominant somatic alteration in RiboSis genes was copy number variation. A total of 128 RiboSis genes, including EXOSC4, BOP1, RPLP0P6 and UTP23, were identified as potential therapeutic targets. Interestingly, we observed that the activity of RiboSis was associated with TP53 mutations, and hyperactive RiboSis was associated with poor outcomes in lung cancer patients without TP53 mutations, highlighting the importance of considering TP53 mutations during therapy by impairing RiboSis. Moreover, we predicted 23 compounds, including methotrexate and CX-5461, associated with the expression signature of RiboSis genes. The current study generates a comprehensive blueprint of molecular alterations in RiboSis genes across cancers, which provides a valuable resource for RiboSis-based anti-tumor therapy.
Tragoportax Pilgrim, 1937 and Miotragocerus Stromer, 1928 (Mammalia, Bovidae) from the Turolian of Hadjidimovo, Bulgaria, and a revision of the late Miocene Mediterranean Boselaphini

A taxonomic revision of the late Miocene Boselaphini is proposed on the basis of the description of abundant Turolian material from the locality of Hadjidimovo, Bulgaria. The genus Tragoportax Pilgrim, 1937 as usually understood is divided into two genera -Tragoportax and Miotragocerus Stromer, 1928- the latter itself divided into two subgenera -M. (Miotragocerus) Stomer, 1928 and M. (Pikermicerus) Kretzoi, 1941. The sexual dimorphism and the paleoecology of the taxa are discussed as well as the taphonomy of Tragoportax from Hadjidimovo.
Should we really use graph neural networks for transcriptomic prediction?

Abstract The recent development of deep learning methods have undoubtedly led to great improvement in various machine learning tasks, especially in prediction tasks. This type of methods have also been adapted to answer various problems in bioinformatics, including automatic genome annotation, artificial genome generation or phenotype prediction. In particular, a specific type of deep learning method, called graph neural network (GNN) has repeatedly been reported as a good candidate to predict phenotypes from gene expression because its ability to embed information on gene regulation or co-expression through the use of a gene network. However, up to date, no complete and reproducible benchmark has ever been performed to analyze the trade-off between cost and benefit of this approach compared to more standard (and simpler) machine learning methods. In this article, we provide such a benchmark, based on clear and comparable policies to evaluate the different methods on several datasets. Our conclusion is that GNN rarely provides a real improvement in prediction performance, especially when compared to the computation effort required by the methods. Our findings on a limited but controlled simulated dataset shows that this could be explained by the limited quality or predictive power of the input biological gene network itself.
Variation in symptoms of common mental disorders in the general population during the COVID-19 pandemic: longitudinal cohort study

Background A significant rise in mental health disorders was expected during the COVID-19 pandemic. However, referrals to mental health services dropped for several months before rising to pre-pandemic levels. Aims To identify trajectories of incidence and risk factors for common mental disorders among the general population during 14 months of the COVID-19 pandemic, to inform potential mental health service needs. Method A cohort of 33 703 adults in England in the University College London COVID-19 Social Study provided data from March 2020 to May 2021. Growth mixture modelling was used to identify trajectories based on the probability of participants reporting symptoms of depression (Patient Health Questionnaire-9) or anxiety (Generalised Anxiety Disorder-7) in the clinical range, for each month. Sociodemographic and personality-related characteristics associated with each trajectory class were explored. Results Five trajectory classes were identified for depression and anxiety. Participants in the largest class (62%) were very unlikely to report clinically significant symptom levels. Other trajectories represented participants with a high likelihood of clinically significant symptoms throughout, early clinically significant symptoms that reduced over time, clinically significant symptoms that emerged as the pandemic unfolded and a moderate likelihood of clinically significant symptoms throughout. Females, younger adults, carers, those with existing mental health diagnoses, those that socialised frequently pre-pandemic and those with higher neuroticism scores were more likely to experience depression or anxiety. Conclusions Nearly 40% of participants followed trajectories indicating risk of clinically significant symptoms of depression or anxiety. The identified risk factors could inform public health interventions to target individuals at risk in future health emergencies.
Estimating the Incidence and Economic Cost of Lyme Disease Cases in Canada in the 21st Century with Projected Climate Change

Background: Lyme disease (LD) is emerging in Canada owing to the range expansion of the tick vector Ixodes scapularis (I. scapularis). Objectives: Our objective was to estimate future LD incidence in Canada, and economic costs, for the 21st century with projected climate change. Methods: Future regions of climatic suitability for I. scapularis were projected from temperature output of the North American Coordinated Regional Climate Downscaling Experiment regional climate model ensemble using greenhouse gas Representative Concentration Pathways (RCPs) 4.5 and 8.5. Once regions became climatically suitable for ticks, an algorithm derived from tick and LD case surveillance data projected subsequent increasing LD incidence. Three scenarios (optimistic, intermediate, and pessimistic) for maximum incidence at endemicity were selected based on LD surveillance, and underreporting estimates, from the United States. Health care and productivity cost estimates of LD cases were obtained from the literature. Results: Projected annual LD cases for Canada ranged from 120,000 to >500,000 by 2050. Variation in incidence was mostly due to the maximum incidence at endemicity selected, with minor contributions from variations among climate models and RCPs. Projected annual costs were substantial, ranging from CA$0.5 billion to $2.0 billion a year by 2050. There was little difference in projected incidence and economic cost between RCPs, and from 2050 to 2100, because projected climate up to 2050 is similar for RCP4.5 and RCP8.5 (mitigation of greenhouse gas emissions captured in RCP4.5 does not impact climate before the 2050s) and by 2050 the most densely populated areas of the study region are projected to be climatically suitable for ticks. Conclusions: Future incidence and economic costs of LD in Canada are likely to be substantial, but uncertainties remain. Because densely populated areas of Canada are projected to become endemic under conservative climate change scenarios, mitigation of greenhouse gas emissions is unlikely to provide substantial health co-benefits for LD. https://doi.org/10.1289/EHP13759
Mindful self-compassion for veteran women with a history of military sexual trauma: feasibility, acceptability, potential benefits, and considerations

ABSTRACT Background: Military sexual trauma (MST) is reported by up to 74% of women veterans in the United States and is a driver of poor behavioural and physical health. Self-compassion is a transdiagnostic, protective factor linked with improved posttraumatic stress disorder (PTSD), depression, and health behaviours. Thus, Mindful Self-Compassion training (MSC) may help ameliorate MST-related impacts. However, MSC can also temporarily increase distress (i.e. backdraft). Delivering it with elective trauma-informed yoga (TIY), which regulates acute distress, may help address this issue. Objective: This VA quality improvement project examined feasibility, acceptability, and reported benefits and challenges of a manualized 8-week MSC including within non-randomized subgroups: MSC (n = 4) and MSC+ elective TIY classes (MSC+; n = 4). Methods: Nine women veterans with a history of MST at a Vet Center in the Northeastern U.S.A. enrolled; eight completed, excluding one MSC+ participant. Measures included attrition (n = 9), attendance (n = 8), weekly (n = 8) and posttreatment acceptability (n = 6), validated symptom severity assessments (n = 7), and an exit interview (n = 8). Results: Among completers, MSC attendance was excellent (89%) and higher among in MSC+ vs. MSC (94% vs. 84% sessions completed). On average across the two groups, depressive and PTSD symptom severity decreased by 21% and 30%, respectively. In exit interviews, participants across groups described improved coping with distress and psychiatric symptoms, reduced stress, and improved self-care and health behaviours. Although women in both groups reported backdraft during the programme, MSC+ also reported healthier coping and improved emotional processing. Conclusion: The results of this programme evaluation infer MSC may be feasible, acceptable, and beneficial for women survivors of MST in one Vet Center in the Northeastern USA. Further, temporary elevations in MSC-related distress may be ameliorated with adjunctive TIY. Given requests of women veterans in the USA. for additional complementary and integrative health treatment options, formal research on these approaches is warranted.
Visual Field Dependence Persists in Age-Related Central Visual Field Loss

Purpose To examine whether the age-related increase in visual field dependence persists in older adults with central field loss (CFL). Methods Twenty individuals with CFL were grouped into participants with age-related binocular CFL (CFL, n = 9), age-related monocular CFL/relative scotomata (mCFL, n = 8), and CFL occurring at a young age (yCFL, n = 3). Seventeen controls were age-matched to the older CFL groups (OA) and three to the yCFL group (yOA). Participants judged the tilt direction of a rod presented at various orientations under conditions with and without a visual reference. Visual field dependence was determined as the difference in judgment bias between trials with and without the visual reference. Visual field dependence was examined between groups and relative to visual acuity and contrast sensitivity. Results All older groups performed similarly without the visual reference. The CFL group showed greater visual field dependence than the OA group (Mann–Whitney U test; U = 39, P = 0.045). However, there was no group difference when considering all three older groups (Kruskal–Wallis ANOVA; H(2, N = 34) = 4.31, P = 0.116). Poorer contrast sensitivity correlated with greater visual field dependence (P = 0.017; ρ = −0.43). Conclusions Visual field dependence persists in older adults with CFL and seems exacerbated in those with dense binocular scotomata. This could be attributed to the sensitivity of the spared peripheral retina to orientation and motion cues. The relationship with contrast sensitivity further suggests that a decline in visual function is associated with an increase in visual field dependence beyond the effects of normal aging. These observations can guide tailored care and rehabilitation in older adults with CFL.
Impact of semen microbiota on the composition of seminal plasma

ABSTRACT Several studies have found associations between specific bacterial genera and semen parameters. Bacteria are known to influence the composition of their niche and, consequently, could affect the composition of the seminal plasma. This study integrated microbiota profiling and metabolomics to explore the influence of seminal bacteria on semen metabolite composition in infertile couples, revealing associations between specific bacterial genera and metabolite profiles. Amino acids and acylcarnitines were the predominant metabolite groups identified in seminal plasma. Different microbiota profiles did not result in globally diverse metabolite compositions in seminal plasma. Nevertheless, levels of specific metabolites increased in the presence of a dysbiotic microbiota. Urocanate was significantly increased in abnormal semen samples (adjusted P-value < 0.001) and enriched in samples dominated by Prevotella spp. (P-value < 0.05), which was previously linked to a negative impact on semen. Therefore, varying microbiota profiles can influence the abundance of certain metabolites, potentially having an immunomodulatory effect, as seen with urocanate. IMPORTANCE Male infertility is often considered idiopathic since the specific cause of infertility often remains unidentified. Recently, variations in the seminal microbiota composition have been associated with normal and abnormal semen parameters and may, therefore, influence male infertility. Bacteria are known to alter the metabolite composition of their ecological niches, and thus, seminal bacteria might affect the composition of the seminal fluid, crucial in the fertilization process. Our research indicates that distinct seminal microbiota profiles are not associated with widespread changes in the metabolite composition of the seminal fluid. Instead, the presence of particular metabolites with immunomodulatory functions, such as urocanate, could shed light on the interplay between seminal microbiota and variations in semen parameters.
Nutrient Cycling and the Role of Arbuscular Mycorrhizae in Created and Natural Wetlands of Central Ohio

This dissertation details a comprehensive study of the ecology and development of the soil and carbon, nitrogen and phosphorus cycles in freshwater marshes. Beyond broadening our understanding of wetland development and ecology, this work intents to enlighten evaluation of wetland mitigation policy, as well as facilitate the success of wetland creation projects. Ten created and five natural freshwater marshes of central Ohio are the focus throughout the study. One of the central chapters (Ch. 3) compares structure and function between created and natural wetlands. The most important finding is that there are significant differences between created and natural wetland soils; this leads to smaller nutrient stocks and slower nutrient cycles in the created wetlands. Time-to-equilibrium estimates for the development of soil and nutrient-related functions are explored in Ch. 4. It is determined that overcoming these differences will require more time than is acceptable for most mitigation policies. The final two chapters explore the habit and ecology of arbuscular mycorrhizae (AM) in created and natural marshes. The presence of AM was high in both created and natural wetlands and across created wetland age. Given their prevalence and known role in other ecosystems, including AM in wetland creation and restoration projects deserves more focus.
Exploring public health nurses’ acceptability of clinical assessment tools in a Norwegian child health centre

Background: Infants’ symptoms of mental struggle are often diffuse and undifferentiated, and health services do not identify many infants at risk of poor development. However, primary health care is advantageous for early identification, given there are frequent consultations during the infant’s first two years. Health policy encourages using evidence-based screening but use varies in primary health care. The Alarm Distress Baby Scale (ADBB) is an assessment tool targeting social withdrawal in infants 2-24 months of age. Aim: To explore contextual factors related to public health nurses’ (PHNs) acceptability of clinical assessment tools in a Norwegian child health centre. Methods: Prior to an upcoming ADBB training, we used focus group discussions with PHNs to explore their views on their professional role and practice and how this concurs with using assessment tools. Findings: Thematic analysis resulted in the following themes: (1) A Role requiring Supporting the Parents and Safeguarding the Infant; (2) The Challenge of Interpreting Infant Expressions; and (3) Organisational Preconditions for Accepting New Methods. Conclusion: Our findings show that PHNs regard assessment tools as an aid to detect infants at risk, but that systematic use of such tools can hinder their ability to be flexible, egalitarian, and resource-focused. We also find that acceptability of assessment tools requires a system for continuous training and a well-established referral routine.
Cardiovascular and renal safety outcomes of hypoxia-inducible factor prolyl-hydroxylase inhibitor roxadustat for anemia patients with chronic kidney disease: a systematic review and meta-analysis

Abstract This systematic review and meta-analysis were conducted to evaluate the cardiac and kidney-related adverse effects of roxadustat for the treatment of anemia in CKD patients. 18 trials with a total of 8806 participants were identified for analysis. We employed a fixed-effects model for analysis. The pooled result revealed no significant difference in the risk of occurrence of cardiac disorders when comparing CKD patients receiving roxadustat with the placebo (RR = 1.049; CI [0.918 to 1.200]) or ESA (RR = 1.066; CI [0.919 to 1.235]), in both dialysis-dependent (DD) (RR = 1.094; CI [0.925 to 1.293]) or non-dialysis-dependent (NDD) (RR = 1.036; CI [0.916 to 1.171]) CKD patients. No significant difference was observed in the risk of kidney-related adverse events when comparing roxadustat with the placebo (RR = 1.088; CI [0.980 to 1.209]) or ESA (RR = 0.968; CI [0.831 to 1.152]), in DD (RR = 2.649; CI [0.201 to 34.981]) or NDD (RR = 1.053; CI [0.965 to 1.149]) CKD patients. A high risk of hyperkalemia was observed in the roxadustat group in DD (RR = 0.939; CI [0.898 to 0.981]). Incidence of hypertension was higher in the roxadustat for NDD patients (RR = 1.198; CI [1.042 to 1.377]), or compared to the placebo (RR = 1.374; CI [1.153 to 1.638]). In summary, the risk of cardiac or kidney-related events observed in the roxadustat was not significantly increase whether in DD or NDD patients. However, attention must be paid to the occurrence of hyperkalemia for DD patients and hypertension in NDD patients using roxadustat.
Characterization of Acinetobacter baumannii core oligosaccharide synthesis reveals novel aspects of lipooligosaccharide assembly

ABSTRACT A fundamental feature of Gram-negative bacteria is their outer membrane that protects the cell against environmental stressors. This defense is predominantly due to its asymmetry, with glycerophospholipids located in the inner leaflet and lipopolysaccharide (LPS) or lipooligosaccharide (LOS) confined to the outer leaflet. LPS consists of a lipid A anchor, a core oligosaccharide, and a distal O-antigen while LOS lacks O-antigen. While LPS/LOS is typically essential for growth, this is not the case for Acinetobacter baumannii. Despite this unique property, the synthesis of the core oligosaccharide of A. baumannii LOS is not well-described. Here, we characterized the LOS chemotypes of A. baumannii strains with mutations in a predicted core oligosaccharide locus via tandem mass spectrometry. This allowed for an extensive identification of genes required for core assembly that can be exploited to generate precise structural LOS modifications in many A. baumannii strains. We further investigated two chemotypically identical yet phenotypically distinct mutants, ∆2903 and ∆lpsB, that exposed a possible link between LOS and the peptidoglycan cell wall—two cell envelope components whose coordination has not yet been described in A. baumannii. Selective reconstruction of the core oligosaccharide via expression of 2903 and LpsB revealed that these proteins rely on each other for the unusual tandem transfer of two residues, KdoIII and N-acetylglucosaminuronic acid. The data presented not only allow for better usage of A. baumannii as a tool to study outer membrane integrity but also provide further evidence for a novel mechanism of core oligosaccharide assembly. IMPORTANCE Acinetobacter baumannii is a multidrug-resistant pathogen that produces lipooligosaccharide (LOS), a glycolipid that confers protective asymmetry to the bacterial outer membrane. The core oligosaccharide is a ubiquitous component of LOS that typically follows a well-established model of synthesis. In addition to providing an extensive analysis of the genes involved in the synthesis of the core region, we demonstrate that this organism has evidently diverged from the long-held archetype of core synthesis. Moreover, our data suggest that A. baumannii LOS assembly is important for cell division and likely intersects with the synthesis of the peptidoglycan cell wall, another essential component of the Gram-negative cell envelope. This connection between LOS and cell wall synthesis provides an intriguing foundation for a unique method of outer membrane biogenesis and cell envelope coordination.
Étude d'une population de Pouillot siffleur Phylloscopus sibilatrix dans une foret du Perche (Normandie)

As part of a trans-Saharan migrants study program initiated by the Centre de Recherches sur la Biologie des Populations d'Oiseaux (French ringing organisation) we have undertaken a 5 years (1992-1996) study of Wood Warbler in a 40 ha forest in Normandy. 95 adults and 374 pulli were ringed. Small numbers of locally ringed bird controls were never more 3 years apart. Morphometrical data were collected (folded wing length) and breeding was monitored from spring arrival until juveniles leaving the nest. Brood success rate at 6-7 day was 77.8% with a yearly production of 3.8-4.1 juvenile per breeding pair. Polygamy and second broods were occasionally noted.
OMIP-101: 27-color flow cytometry panel for immunophenotyping of major leukocyte populations in fixed whole blood

Purpose and appropriate sample types This 27-color flow cytometry antibody panel allows broad immune-profiling of major leukocyte subsets in human whole blood (WB). It includes lineage markers to identify myeloid and lymphoid cell populations including granulocytes, monocytes, myeloid dendritic cells (mDCs), natural killer (NK) cells, NKT-like cells, B cells, conventional CD4 and CD8 T cells, γδ T cells, mucosa-associated invariant T (MAIT) cells and innate lymphoid cells (ILC). To further characterize each of these populations, markers defining stages of cell differentiation (CCR7, CD27, CD45RA, CD127, CD57), cytotoxic potential (perforin, granzyme B) and cell activation/proliferation (HLA-DR, CD38, Ki-67) were included. This panel was developed for quantifying absolute counts and phenotyping major leukocyte populations in cryopreserved, fixed WB collected from participants enrolled in large multi-site tuberculosis (TB) vaccine clinical trials (Table 1). This antibody panel can be applied to profile major leukocyte subsets in other sample types such as fresh WB or peripheral blood mononuclear cells (PBMCs) with only minor additional optimization.