Miracle-dz/UniFAR-FTUs huggingface dataset:
A risk assessment model for transfusion transmission of dengue

Dengue virus (DENV) is a disease‐causing agent normally transmitted from person to person through the bite of an infected mosquito. In addition to mosquito‐borne cases of dengue, there are instances of transmission of dengue after receipt of blood products or donor organs or tissue. To improve blood safety, we developed a quantitative risk assessment model to estimate the dengue risk of transmission to blood transfusion recipients from preclinical and subclinical blood donors. We derived predictive coefficients from model simulations for predicting the risk outcomes such as monthly infectious blood units and transfusion‐transmitted DENV cases based on the rate of reported clinical cases. The model was validated with a previous study where donor blood samples from the 2012 dengue transmission season in Rio de Janeiro, Brazil were tested for DENV RNA by a transcription‐mediated amplification (TMA) assay. In that study, about 69·4% of donations were tested by the TMA assay and 78 samples were found positive, indicating that 112 DENV RNA‐positive donations would have been detected if testing screening had been performed on all donations. Our model estimated a mean of 93 (2.5–97.5th%ile: 47–186) infected units among the donations, which was consistent with the reported numbers.
Public trust and mistrust of climate science: A meta-narrative review

This systematic meta-narrative literature review aims to explore the narratives of trust evident in literature on public (mis)trust relating to climate science published up until May 2021, and to present the main findings from these papers. We identified six narratives of trust: attitudinal trust, cognitive trust, affective trust, contingencies of trust, contextual trust and communicated trust. The papers’ main findings spanned theoretical conclusions on the importance of positionality to trust and morality to trustworthiness, to qualitative findings that the scientific community was mainly trusted, to quantitative findings that explored how trust functioned as an independent, dependent or mediating variable. This literature review sheds important light on the interrelationship between climate science and publics, highlights areas for further research, and in its characterisation of trust narratives provides a language for conceptualising trust that can further interdisciplinary engagement.
Developing a conceptual framework to identify and classify sources of parental stress following pediatric concussion

ABSTRACT Objectives To create a conceptual framework that classifies the various stresses parents experience following their child’s concussion. Methods Twelve parents of children with concussion completed a semi-structured interview with the lead author. Questions broadly focused on post-concussion stress, with specific probes for caregiving responsibilities, concussion knowledge, and athletic participation. Data were analyzed using thematic analysis. Results Ten mothers and 2 fathers participated. Five themes stemmed from our analysis: 1) Concussion Knowledge (central theme): stressors related to sources of concussion information; 2) Child Health Factors: stressors related to injury and illness, including concussion; 3) Activity Factors: stressors related to academic and athletic performance; 4) Parent-Injured Child Relationship Factors: stressors related to providing care to the child; and 5) Personal Factors: stressors unrelated to the concussion (e.g. family, social, career, etc.). Child Health Factors was most frequently identified as the primary stressor (n = 9). Conclusions Sources of parental stress were varied following pediatric concussion. Issues relating to the child’s post-injury dysfunction and the uncertain recovery from concussion were key stressors identified by parents. Moving forward, this framework can be used to ground the development of specific parental stress screening tools and interventions, which may benefit the parent’s mental health and the child’s clinical recovery.
Can tandem alternative splicing and evasion of premature termination codon surveillance contribute to attenuated Peutz–Jeghers syndrome?

Alternative use of short distance tandem sites such as NAGNnAG are a common mechanism of alternative splicing; however, single nucleotide variants are rarely reported as likely to generate or to disrupt tandem splice sites. We identify a pathogenic intron 5 STK11 variant (NM_000455.4:c.[735‐6A>G];[=]) segregating with the mucocutaneous features but not the hamartomatous polyps of Peutz–Jeghers syndrome in two individuals. By RNAseq analysis of peripheral blood mRNA, this variant was shown to generate a novel and preferentially used tandem proximal splice acceptor (AAGTGAAG). The variant transcript (NM_000455.4:c.734_734 + 1insTGAAG), which encodes a frameshift (p.[Tyr246Glufs*43]) constituted 36%–43% of STK11 transcripts suggesting partial escape from nonsense mediated mRNA decay and translation of a truncated protein. A review of the ClinVar database identified other similar variants. We suggest that nucleotide changes creating or disrupting tandem alternative splice sites are a pertinent disease mechanism and require contextualization for clinical reporting. Additionally, we hypothesize that some pathogenic STK11 variants cause an attenuated phenotype.
Insight into the kinetic analysis of acid mine drainage treated by carbonate rock

ABSTRACT Acid mine drainage (AMD) has caused a great impact on soil, surface water, groundwater, plants or other organisms in the mining environment because of its high acidity, high sulphate content, and contains a variety of heavy metals. AMD treated by carbonate rocks have been regarded as a feasible technology for pollution control and applied widely in mine area. However, to date, the kinetics of the reaction between carbonate rock and AMD have not been investigated, resulting in the lack of systematic theoretical guidance for the implementation of this technology. In this study, effects of carbonate particle sizes and reaction temperature on AMD treatment were investigated. The dissolution efficiency of Ca2+ was used to quantitatively reflect extent of reaction, and the leaching kinetics was analysed based on the shrinking core model. The results showed that carbonate rocks with a particle size of 0.5–1.0 mm had the best pH-enhancing performance for AMD and highest removal efficiency for Fe3+ (>98.00%), while the Mn2+ and SO42− were temperature sensitive. The diffusion of solid product layer was the controlling step of the leaching reaction, and the apparent activation energy of the reaction was 12.63 kJ·mol−1. GRAPHICAL ABSTRACT
Sex differences in rates of permanent pacemaker implantation and in-hospital complications: A statewide cohort study of over 7 million persons from 2009–2018

Background Whether a bias exists in the implantation of permanent pacemakers (PPI) and complications according to sex and age in the Australian population is unclear. Hypothesis Population rate of PPI and its complications differed between men and women. Methods We examined the prevalence of PPI from January-2009 to December-2018 from datasets held by the New South Wales (NSW) Centre-for-Health-Record-Linkage, including patient’s characteristics and in-hospital complications. All analysis was stratified by sex and age by decade. Results A total of 28,714 admissions involved PPI (40% women). The mean PPI rate (±standard-deviation) and median age (interquartile range) was 2,871±242 per-annum and 80yrs (73-86yrs), respectively. At the same time-period, the mean NSW population size was 7,487,393±315,505 persons (50% women; n = 3,773,756±334,912). The mean annual age-adjusted rate of PPI was 125.5±11.6 per-100,000-men, compared to 63.4±14.3 per-100,000-women (P<0.01). The mean annual rate of PPI increased from 2009–2017 by 0.9±3.3% in men, compared to 0.4±4.4% in women (P<0.01) suggesting a widening disparity. Total non-fatal in-hospital complications was higher in women compared to men (8.2% vs 6.6%, P<0.01), and this persisted throughout study period even after adjusting for multiple covariates. Overall, in-hospital mortality was low (0.73%) and similar between sexes. Conclusion In a statewide Australian population exceeding 7 million, PPI rates were consistently nearly two-fold higher for men compared to women over 10-years, with an apparently widening disparity, that was not explained by age. Overall complication rates were higher in women. Future studies should examine the aetiology behind this disparity in PPI rates, as well as its complications.
Temporal trends in COVID-19 outcomes among patients with systemic autoimmune rheumatic diseases: from the first wave through the initial Omicron wave

Objectives To investigate temporal trends in incidence and severity of COVID-19 among patients with systemic autoimmune rheumatic diseases (SARDs) from the first wave through the initial Omicron wave. Methods We conducted a retrospective cohort study investigating COVID-19 outcomes among patientswith SARD systematically identified to have confirmed COVID-19 from 1 March 2020 to 31 January 2022 at Mass General Brigham. We tabulated COVID-19 counts of total and severe cases (hospitalisations or deaths) and compared the proportion with severe COVID-19 by calendar period and by vaccination status. We used logistic regression to estimate the ORs for severe COVID-19 for each period compared with the early COVID-19 period (reference group). Results We identified 1449 patients with SARD with COVID-19 (mean age 58.4 years, 75.2% female, 33.9% rheumatoid arthritis). There were 399 (28%) cases of severe COVID-19. The proportion of severe COVID-19 outcomes declined over calendar time (p for trend <0.001); 46% of cases were severe in the early COVID-19 period (1 March 2020–30 June 2020) vs 15% in the initial Omicron wave (17 December 2021–31 January 2022; adjusted OR 0.29, 95% CI 0.19 to 0.43). A higher proportion of those unvaccinated were severe compared with not severe cases (78% vs 60%). Conclusions The proportion of patients with SARD with severe COVID-19 has diminished since early in the pandemic, particularly during the most recent time periods, including the initial Omicron wave. Advances in prevention, diagnosis and treatment of COVID-19 may have improved outcomes among patients with SARD.
The mental health burden of racial and ethnic minorities during the COVID-19 pandemic

Racial/ethnic minorities have been disproportionately impacted by COVID-19. The effects of COVID-19 on the long-term mental health of minorities remains unclear. To evaluate differences in odds of screening positive for depression and anxiety among various racial and ethnic groups during the latter phase of the COVID-19 pandemic, we performed a cross-sectional analysis of 691,473 participants nested within the prospective smartphone-based COVID Symptom Study in the United States (U.S.) and United Kingdom (U.K). from February 23, 2021 to June 9, 2021. In the U.S. (n=57,187), compared to White participants, the multivariable odds ratios (ORs) for screening positive for depression were 1·16 (95% CI: 1·02 to 1·31) for Black, 1·23 (1·11 to 1·36) for Hispanic, and 1·15 (1·02 to 1·30) for Asian participants, and 1·34 (1·13 to 1·59) for participants reporting more than one race/other even after accounting for personal factors such as prior history of a mental health disorder, COVID-19 infection status, and surrounding lockdown stringency. Rates of screening positive for anxiety were comparable. In the U.K. (n=643,286), racial/ethnic minorities had similarly elevated rates of positive screening for depression and anxiety. These disparities were not fully explained by changes in leisure time activities. Racial/ethnic minorities bore a disproportionate mental health burden during the COVID-19 pandemic. These differences will need to be considered as health care systems transition from prioritizing infection control to mitigating long-term consequences.
Loneliness, internalizing symptoms, and inflammatory markers in adolescent COVID‐19 survivors

Abstract Background Concerns about the psychiatric sequelae after COVID‐19 infection have increased as the pandemic spreads worldwide. The increase in self‐isolation during this pandemic period has also revealed the importance of feelings of loneliness. This study aimed to examine the relationship between baseline inflammation levels, internalizing symptoms, and feelings of loneliness in adolescent COVID‐19 survivors in the long term. Methods A total of 74 adolescents (41 girls, 55.4%, mean age 14.88) and their parents were included in the study. This cross‐sectional study assessed internalizing symptoms via Revised Children's Anxiety and Depression Scale (RCADS) and feelings of loneliness using the UCLA‐loneliness scale. Baseline inflammatory markers at COVID‐19 diagnosis were collected. Logistic regression analysis was used to determine predictors for depression in adolescents. Results The most common disorder was Major Depressive Disorder (MDD) (25.7%), and 33.8% of the adolescents were in the clinical range in at least one internalizing domain. Baseline C‐Reactive Protein (CRP) levels correlated weakly with MDD scores. Loneliness scores correlated with all internalizing symptoms, strong association with MDD scores. Loneliness, anxiety, and parental anxiety were associated with an increased likelihood of MDD. Baseline CRP positivity did not predict MDD in adolescent COVID‐19 survivors. Conclusions This study indicates that anxiety, loneliness, and parental anxiety play an important role in adolescents' experience of depressive symptoms after COVID‐19 infection. Thus, screening parental psychopathology and loneliness in COVID‐19 survivors seems to be preventive for adolescent mental health problems.
Synthetic OH Band Spectra in G and K Stars

Carbon, nitrogen and oxygen are of interest for stellar and galactic evolution for four main reasons. Firstly, they comprise most of the mass of elements heavier than helium, so their abundance reflects the bulk of chemical enrichment. Secondly, all of the oxygen, much of the carbon and perhaps some of the nitrogen is believed to be produced in shorter-lived stars more massive than those responsible for the Fe production (Tinsley 1979), so their abundance relative to Fe in very metal deficient objects should provide key information for modelling the chemical history of galaxies. Thirdly, because C and O comprise the bulk of the metals in stellar material (Fe:C:N:0 = 1:12:2.5:21 in the Sun) it is their abundance as well as that of iron, which is needed to compute evolutionary tracks for different metallicities. Finally, the O abundance will indicate whether CNO material has been mixed to the surface.
Outcomes of Interferon-free Treatment of Hepatitis C Virus Infection Seven Years after Approval and Problems with Drop out during and after Treatment: A Retrospective, Single-center Study

Objective This retrospective, single-center study assessed the effects of interferon (IFN)-free treatment of hepatitis C virus (HCV) infection, which has been approved for seven years; calculated the incidence of hepatocellular carcinoma (HCC) after achieving a sustained virologic response (SVR); and elucidated problems with follow-up for surveillance of post-SVR HCC, particularly the impact of the coronavirus disease 2019 (COVID-19) pandemic. Methods We summarized the SVR achievement rate of 286 HCV-infected patients who received 301 IFN-free treatments and analyzed the cumulative incidence of initial HCC and the cumulative continuation rate of follow-up after SVR in the 253 patients who achieved SVR and did not have a history of HCC. Results Among 286 patients who received IFN-free treatments, 14 dropped out, and the 272 remaining patients achieved an SVR after receiving up to third-line treatment. Post-SVR HCC occurred in 18 (7.1%) of the 253 patients without a history of HCC, with a cumulative incidence at 3 and 5 years after SVR of 6.6% and 10.0%, respectively; the incidence of cirrhosis at those time points was 18.2% and 24.6%, respectively. Of the 253 patients analyzed, 58 (22.9%) discontinued follow-up after SVR. Patients who had no experience with IFN-based therapy tended to drop out after SVR. Notably, the number of dropouts per month has increased since the start of the pandemic. Conclusion Currently, IFN-free treatment is showing great efficacy. However, the incidence of HCC after SVR should continue to be monitored. In this study, the COVID-19 pandemic did not affect treatment outcomes, but it may affect surveillance for post-SVR HCC.
Hypoxia‐induced miR‐182‐5p regulates vascular smooth muscle cell phenotypic switch by targeting RGS5

In response to vascular injury or alterations in the local environment, such as hypoxia and hypertension, contractile vascular smooth muscle cells (VSMCs) are able to switch to a synthetic phenotype characterized by increased extracellular matrix synthesis with decreased expression of contractile markers. miR‐182‐5p has recently been reported to play a regulatory role in VSMCs proliferation. However, little is known about its target genes and related pathways in VSMCs phenotypic switch. Here, we investigated the function of miR‐182‐5p in VSMCs phenotypic switch. The results showed that upregulation of miR‐182‐5p promoted the switching of VSMCs from a contractile to a synthetic phenotype under hypoxic conditions. Mechanistically, hypoxia elevated miR‐182‐5p, leading to a reduction in expression of contractile markers and weakened RhoA signaling. Using bioinformatics analysis, dual‐luciferase reporter assays and rescue assays, we demonstrated that miR‐182‐5p suppressed RhoA signaling by targeting RGS5. Collectively, the results from the present study indicated that miR‐182‐5p/RGS5/RhoA axis regulated hypoxia‐induced VSMCs phenotypic switch.
First-Episode Psychosis Patients Who Deteriorated in the Premorbid Period Do Not Have Higher Polygenic Risk Scores Than Others: A Cluster Analysis of EU-GEI Data

Abstract Cluster studies identified a subgroup of patients with psychosis whose premorbid adjustment deteriorates before the onset, which may reflect variation in genetic influence. However, other studies reported a complex relationship between distinctive patterns of cannabis use and cognitive and premorbid impairment that is worthy of consideration. We examined whether: (1) premorbid social functioning (PSF) and premorbid academic functioning (PAF) in childhood and adolescence and current intellectual quotient (IQ) define different clusters in 802 first-episode of psychosis (FEP) patients; resulting clusters vary in (2) polygenic risk scores (PRSs) for schizophrenia (SCZ_PRS), bipolar disorder (BD_PRS), major depression (MD_PRS), and IQ (IQ_PRS), and (3) patterns of cannabis use, compared to 1,263 population-based controls. Four transdiagnostic clusters emerged (BIC = 2268.5): (1) high-cognitive-functioning (n = 205), with the highest IQ (Mean = 106.1, 95% CI: 104.3, 107.9) and PAF, but low PSF. (2) Low-cognitive-functioning (n = 223), with the lowest IQ (Mean = 73.9, 95% CI: 72.2, 75.7) and PAF, but normal PSF. (3) Intermediate (n = 224) (Mean_IQ = 80.8, 95% CI: 79.1, 82.5) with low-improving PAF and PSF. 4) Deteriorating (n = 150) (Mean_IQ = 80.6, 95% CI: 78.5, 82.7), with normal-deteriorating PAF and PSF. The PRSs explained 7.9% of between-group membership. FEP had higher SCZ_PRS than controls [F(4,1319) = 20.4, P < . 001]. Among the clusters, the deteriorating group had lower SCZ_PRS and was likelier to have used high-potency cannabis daily. Patients with FEP clustered according to their premorbid and cognitive abilities. Pronounced premorbid deterioration was not typical of most FEP, including those more strongly predisposed to schizophrenia, but appeared in a cluster with a history of high-potency cannabis use.
Natal origin of Pacific bluefin tuna Thunnus orientalis determined by SIMS oxygen isotope analysis of otoliths

Accurate understanding of changing population dynamics associated with climate change is critical for managing highly migratory fish species. However, long-term data on population dynamics and the resulting recruitment variability is still lacking for many species, making it difficult to predict and integrate the effects of ocean warming into management schemes. In this study, high-resolution stable oxygen isotope (δ18O) analysis was performed on the otoliths of adult Pacific bluefin tuna Thunnus orientalis using secondary ion mass spectrometry (SIMS) to determine the natal origin of an individual fish. The core δ18Ootolith corresponding to the larval stage greatly varied among the individuals, indicating that the larvae experienced a wide range of thermal environments. The non-hierarchical cluster analysis performed on the core δ18Ootolith grouped fish into those with higher δ18Ootolith (lower temperature) and those with lower δ18Ootolith (higher temperature), most likely representing relative temperature difference experienced between fish born in the Sea of Japan and in the Nansei Islands area. The Nansei Islands area cluster showed more variability in the early otolith growth indicating a longer spawning season, which is consistent with the observed longer spawning duration in this area. The absolute temperature estimates based on the SIMS-measured core δ18Ootolith were significantly higher than those expected from sea surface temperature data, suggesting the effects of matrix-related bias on the temperature offsets. The relative temperature difference, however, matched well with the known spawning temperature range of the two spawning grounds. The recruitment contribution from each spawning ground (all year-classes pooled, n = 51) was 45% in the Sea of Japan and 55% in the Nansei Islands area. Overall, this study demonstrated the effectiveness of SIMS δ18Ootolith analysis for investigating the natal origin of fish and its potential application in fish population dynamics studies.