Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic characterization of P[8] rotavirus strains circulated in Iran between 2009 and 2017

Group A rotavirus (RVA) is the most common cause of acute gastroenteritis worldwide, which is responsible for causing an estimated 120 000 deaths in children under 5 years of age, which mostly occur in the lower‐income countries of Asia and Africa. The G1P[8] is a common genotype of RVA that has spread throughout the world, including Iran and this genotype is present in two commonly used RVA vaccines, RotarixTM and RotaTeqTM. In this study, we investigated the genetic diversity, viral evolution, and differences between antigenic epitopes of Iran's P[8] strains and two licensed vaccines. The phylogenetic and evolutionary analysis was carried out, using MEGA version 6.0 and BEAST, respectively. Antigenic epitopes of VP8* were compared to determine the differences between strains from Iran and RotarixTM and RotaTeqTM. The P[8]‐lineages III and IV were found as the predominant P genotype that circulated in Iran. The TMRCA of P[8]‐lineages III and IV was estimated in 1987 and 2009, respectively. The P[8]‐lineage III strains showed 12 amino acid changes compared to RotarixTM and 10 amino acid changes compared to RotaTeqTM. The P[8]‐lineage IV strains showed 10 amino acid variations for both RotarixTM and RotaTeqTM strains. The results revealed that the P[8] strains circulating in Iran differ from RotarixTM and RotaTeqTM strains. To monitor the long‐term effects of vaccines on the emergence of P[8] strains with different lineages, routine and successful monitoring of these strains will be crucial.
The technological, organizational and environmental determinants of adoption of mobile health applications (m-health) by hospitals in Kenya

Introduction Sub-Saharan Africa lags in adoption of mobile health (m-health) applications and in leveraging m-health for sustainable development goals. There is a need for a comprehensive investigation of determinants of hospitals’ adoption of m-health in Sub-Saharan Africa to inform policies, practices and investments. Methods This investigation used a logit regression model to analyze the determinants of m-health adoption in Kenyan hospitals applying the Technological, Organizational and Environmental (TOE) framework and the Diffusion of Innovation (DOI) theory. A representative sample of 211 executives of Level 4–6 hospitals in 24 counties provided primary data on Patient-Centered (PC) and Facility-Centered (FC) m-health applications. Results Both PC and FC m-health adoption were predicted by competition for patients (PC p = 0.041, FC p = 0.021), IT human resource capacity (PC p = 0.048, FC p = 0.037), and hospital pursuit of market growth through technological leadership (PC p = 0.010, FC p = 0.020). Further determinants of PC m-health adoption included hospital access to slack financial resources (p = 0.006), acquisition strategy (p = 0.011), compatibility with the hospital systems (p = 0.015), trialability (p = 0.019), medical insurance company support (p = 0.025),patient pressure (p = 0.036), and perceived effect of global medical tourism (p = 0.039). FC m-health adoption was predicted by hospital size (p = 0.008), ICT infrastructure capacity (p = 0.041), and government support (p = 0.013). Conclusion A differentiated approach is required to scale up m-health adoption. PC m-health requires emphasis on establishing national and regional compatibility and interoperability, developing trialability processes and validation mechanisms, incentivizing patient competition and mobility, establishing innovative and cost-effective acquisition strategies, and ensuring integration of digital services within national insurance schemes and policies. These policies require support from patients and communities to drive demand and spur investment in adequate IT human resources to maintain reliability. Pilot PC m-health projects should prioritize hospitals with slack financial resources, while FC m-health should target large facility size. FC m-health applications are more complex and costly than PC, requiring government incentives to trigger hospital investments and national investment in ICT infrastructure. Investors and hospital managers should integrate m-health into market growth strategies for sustainable m-health scale-up in Kenya and beyond.
Monkeypox in a Traveler Returning from Nigeria — Dallas, Texas, July 2021

Monkeypox is a rare, sometimes life-threatening zoonotic infection that occurs in west and central Africa. It is caused by Monkeypox virus, an orthopoxvirus similar to Variola virus (the causative agent of smallpox) and Vaccinia virus (the live virus component of orthopoxvirus vaccines) and can spread to humans. After 39 years without detection of human disease in Nigeria, an outbreak involving 118 confirmed cases was identified during 2017-2018 (1); sporadic cases continue to occur. During September 2018-May 2021, six unrelated persons traveling from Nigeria received diagnoses of monkeypox in non-African countries: four in the United Kingdom and one each in Israel and Singapore. In July 2021, a man who traveled from Lagos, Nigeria, to Dallas, Texas, became the seventh traveler to a non-African country with diagnosed monkeypox. Among 194 monitored contacts, 144 (74%) were flight contacts. The patient received tecovirimat, an antiviral for treatment of orthopoxvirus infections, and his home required large-scale decontamination. Whole genome sequencing showed that the virus was consistent with a strain of Monkeypox virus known to circulate in Nigeria, but the specific source of the patient's infection was not identified. No epidemiologically linked cases were reported in Nigeria; no contact received postexposure prophylaxis (PEP) with the orthopoxvirus vaccine ACAM2000.
Complex association of apolipoprotein E–containing HDL with coronary artery disease burden in cardiovascular disease

Background Although traditional lipid parameters and coronary imaging techniques are valuable for cardiovascular disease (CVD) risk prediction, better diagnostic tests are still needed. Methods In a prospective, observational study, 795 individuals had extensive cardiometabolic profiling, including emerging biomarkers, such as apolipoprotein E–containing HDL-cholesterol (ApoE-HDL-C). Coronary artery calcium (CAC) score was assessed in the entire cohort, and quantitative coronary computed tomography angiography (CCTA) characterization of total burden, noncalcified burden (NCB), and fibrous plaque burden (FB) was performed in a subcohort (n = 300) of patients stratified by concentration of ApoE-HDL-C. Total and HDL-containing apolipoprotein C-III (ApoC-III) were also measured. Results Most patients had a clinical diagnosis of coronary artery disease (CAD) (n = 80.4% of 795), with mean age of 59 years, a majority being male (57%), and about half on statin treatment. The low ApoE-HDL-C group had more severe stenosis (11% vs. 2%, overall P < 0.001), with higher CAC as compared with high ApoE-HDL-C. On quantitative CCTA, the high ApoE-HDL-C group had lower NCB (β = –0.24, P = 0.0001), which tended to be significant in a fully adjusted model (β = –0.32, P = 0.001) and altered by ApoC-III in HDL levels. Low ApoE-HDL-C was significantly associated with LDL particle number (β = 0.31; P = 0.0001). Finally, when stratified by FB, ApoC-III in HDL showed a more robust predictive value of CAD over ApoE-HDL-C (AUC: 0.705, P = 0.0001) in a fully adjusted model. Conclusion ApoE-containing HDL-C showed a significant association with early coronary plaque characteristics and is affected by the presence of ApoC-III, indicating that low ApoE-HDL-C and high ApoC-III may be important markers of CVD severity. Trial Registration ClinicalTrials.gov: NCT01621594. Funding This work was supported by the NHLBI at the NIH Intramural Research Program.
Predictors of glycemic control in children and adolescents with type 1 diabetes at 12 months after diagnosis

Identifying risk factors for suboptimal glycemic control during the first year after diagnosis with type 1 diabetes (T1D) may provide early appropriate and individualized management. Our aim was to study possible predictors of early glycemic control during the first year after diagnosis with T1D in children and adolescents in Jordan. This is a retrospective study conducted through a review of medical records at Jordan University Hospital and the National Centre for Diabetes, Endocrinology and Genetics. Children and adolescents diagnosed with T1D at age younger than 16 years and with diabetes duration of at least 2 years were included. Demographic, clinical and socioeconomic factors were collected, in addition to glycosylated hemoglobin (HbA1c) values during the first year after diagnosis. Average age at diagnosis of the 337 patients who were enrolled in the study was 7.7 ± 3.8 years. HbA1c at diagnosis was 10.9 ± 1.9% (95.64 ± 20.76 mmol/mol). Factors such as the involvement of children's mothers in deciding insulin doses, higher mother's educational level and higher family monthly income were associated with better early glycemic control. HbA1c at 6 months after diagnosis, parental marital status and compliance to counting carbohydrates were significant predictors of glycemic control at 12 months after diagnosis. Many clinical and socioeconomic factors were associated with early glycemic control at 12 months after diagnosis. Modifiable risk factors must be addressed as early as possible to decrease future complications. Children with nonmodifiable risk factors should be identified early for closer observation and providing individualized diabetes care plan.
Declining trends in HIV and other sexually transmitted infections among female sex workers in Iran could be attributable to reduced drug injection: a cross-sectional study

Objective The HIV trend among female sex workers (FSWs) is understudied. We assessed the prevalence and trend of HIV and five other STIs among FSWs in Iran. Methods We recruited FSWs (1337 in 2015, 1005 in 2010) from 21 sites in 13 cities in two cross-sectional biobehavioural surveys. Eligible FSWs were women aged ≥18 years who reported selling sex to more than one male client in the past 12 months. Consenting FSWs were interviewed using a behavioural questionnaire and tested for HIV and five other STIs. We considered study sites as clusters in the analysis and two-sided Fisher’s exact test to compare the HIV prevalence between the two survey rounds. Results HIV prevalence was 2.1% in 2015 (vs 4.0% in 2010, p=0.007). Lifetime drug injection was reported by 6.1% of participants in 2015 (vs 14.6% in 2010, p=0.003). In 2015, among FSWs with history of lifetime drug injection, HIV prevalence was 8.6% (vs 9.8% in 2010, p=0.425). The prevalence of other STIs in 2015 was 0.4% (95% CI 0.2 to 1.0) for syphilis, 1.3% (95% CI 0.8 to 2.1) for gonorrhoea, 6.0% (95% CI 4.8 to 7.4) for chlamydia, 11.9% (95% CI 8.5 to 16.5) for trichomoniasis and 41.8% (95% CI 39.2 to 44.5) for human papillomavirus. Conclusions HIV prevalence among FSWs in Iran decreased, but remains considerably high. The decrease in HIV prevalence compared with 2010 might be explained by a decrease in drug injection. Other STIs are also high in this population. Harm reduction programmes need to be continued and scaled up among this underserved population in Iran.
Change in the inflammatory potential of diet over 10 years and subsequent mortality: the Multiethnic Cohort Study

Abstract Dietary inflammatory potential assessed by the Dietary Inflammatory Index (DII®) has been associated with health outcomes. However, longitudinal changes in the DII in relation to health outcomes rarely have been studied. This study aimed to examine change in the DII score over 10 years and its association with subsequent mortality in the Multiethnic Cohort. The analysis included 56 263 African American, Japanese American, Latino, Native Hawaiian and White participants who completed baseline (45–75 years) and 10-year follow-up surveys, including a FFQ. Mean energy-adjusted DII (E-DII) decreased over 10 years in men (from −0·85 to −1·61) and women (from −1·80 to −2·47), reflecting changes towards a more anti-inflammatory diet. During an average follow-up of 13·0 years, 16 363 deaths were identified. In multivariable Cox models, compared with anti-inflammatory stable individuals, risk of all-cause mortality was increased with pro-inflammatory change in men (hazard ratio (HR) = 1·13, 95 % CI 1·03, 1·23) and women (HR = 1·22, 95 % CI 1·13, 1·32). Per one-point increase in E-DII score over time, HR was 1·02 (95 % CI 1·00, 1·03) for men and 1·06 (95 % CI 1·04, 1·07) for women (P for heterogeneity < 0·001). While no heterogeneity by race and ethnicity was observed for men, the increased risk per one-point increase among women was stronger in non-Whites than in Whites (P for heterogeneity = 0·004). Our findings suggest that a change towards a more pro-inflammatory diet is associated with an increased risk of mortality both in men and women, and that the association is stronger in women, especially non-White women, than in men.
Predicting the Sequence Specificities of DNA-Binding Proteins by DNA Fine-Tuned Language Model With Decaying Learning Rates

DNA-binding proteins (DBPs) play vital roles in the regulation of biological systems. Although there are already many deep learning methods for predicting the sequence specificities of DBPs, they face two challenges as follows. Classic deep learning methods for DBPs prediction usually fail to capture the dependencies between genomic sequences since their commonly used one-hot codes are mutually orthogonal. Besides, these methods usually perform poorly when samples are inadequate. To address these two challenges, we developed a novel language model for mining DBPs using human genomic data and ChIP-seq datasets with decaying learning rates, named DNA Fine-tuned Language Model (DFLM). It can capture the dependencies between genome sequences based on the context of human genomic data and then fine-tune the features of DBPs tasks using different ChIP-seq datasets. First, we compared DFLM with the existing widely used methods on 69 datasets and we achieved excellent performance. Moreover, we conducted comparative experiments on complex DBPs and small datasets. The results show that DFLM still achieved a significant improvement. Finally, through visualization analysis of one-hot encoding and DFLM, we found that one-hot encoding completely cut off the dependencies of DNA sequences themselves, while DFLM using language models can well represent the dependency of DNA sequences. Source code are available at: https://github.com/Deep-Bioinfo/DFLM.
A snapshot of progenitor–derivative speciation in Iberodes (Boraginaceae)

Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographical barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction‐site‐associated DNA sequencing (RAD‐seq), (ii) genetic structure analyses, (iii) demographic modelling, (iv) morphometrics, and (v) climatic niche modelling and niche overlap analysis. The results revealed a history of recurrent progenitor–derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread Iberodes linifolia during the Late Pliocene. Meanwhile, geographical isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographical barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.
The effects of challenge and threat states on coping flexibility: evidence from framing and exemplar priming

ABSTRACT Background and Objectives Challenge and threat states have divergent effects on cognitive, affective, and behavioral responses. The present research used two experiments to investigate whether challenge and threat states influence coping flexibility differently. Design Study 1 (N = 93) used loss-framed and gain-framed task instructions to elicit situation-specific threat and challenge evaluations, respectively, with a Null condition as a control. Study 2 (N = 86) used an online single-session Cognitive Bias Modification for Interpretation (CBM-I) paradigm to present participants with exemplars related to either positive or negative resolutions of stressful situations to engender a stress-is-a-challenge or stress-is-a-threat mindset, with a mixed condition as a control. Results Loss-framed task instruction generated situation-specific threat evaluation, debilitated effective attention, and reduced positive affect, without altering coping flexibility measured in other scenarios. CBM-I engendered a stress-is-a-challenge mindset and maintained positive affect and coping flexibility, whereas the negative and mixed groups decreased coping flexibility. A stress-is-a-challenge mindset was positively associated with coping flexibility prior to and after exemplar priming. Conclusions Findings enrich the literature on stress coping and shed light on future practice by illustrating the different effects of framing and CBM-I on challenge/threat situation-specific evaluation and stress mindset, and the positive relation of stress-is-a-challenge mindset to coping flexibility.
Evaluating the presence of domestic cat hepadnavirus viraemia in cats with biochemical alterations suggestive of liver disease.

BACKGROUND The association between domestic cat hepadnavirus (DCH) infection and feline chronic hepatitis and hepatocellular carcinoma has been suggested. However, studies focused on the association between DCH infection and clinicopathological changes consistent with liver disease in cats are not available. METHODS This retrospective investigation included sera obtained from 96 cats that had the serum activity of at least alanine aminotransferase or alkaline phosphatase measured during initial diagnostic work-up. Based on these haematobiochemical results, cats were categorised according to their likelihood of having liver disease (absent, low, intermediate or high). DCH DNA was detected using real-time PCR, nested PCR and sequencing. RESULTS Overall, potential liver damage was observed in 44 cats, including cats with low (n = 14), intermediate (n = 10) and high (n = 20) likelihood of liver disease. Four cats (4.2%) were DCH-positive, with three positive cats belonging to the liver disease group (two with low and one with intermediate likelihood of liver disease). CONCLUSIONS Although the pathogenic potential of DCH in cats still has to be clarified, these results suggest that DCH testing should not be based only on the presence of biochemical changes potentially consistent with liver disease.
Cardiac-disease-induced posttraumatic stress symptoms (CDI-PTSS) among cardiac patients' partners: A longitudinal study.

OBJECTIVE Cardiac-disease-induced posttraumatic stress symptoms (CDI-PTSS) have been detected among a substantial number of cardiac patients. Even though patients' caregiving partners are also susceptible to CDI-PTSS, the research on cardiac partners' CDI-PTSS is scarce. Based on the ecological model of trauma and recovery, we investigated levels of partners' CDI-PTSS over time, and factors that potentially contribute to it. METHOD During patients' hospitalizations, partners (N = 143) provided data regarding demographic variables and peritraumatic emotional distress (depression and anxiety). Four months later, partners' CDI-PTSS, their emotional distress, fear of patients' illness progression, and perceived social support were assessed. Eight months posthospitalization, partners filled out questionnaires tapping CDI-PTSS. Hypotheses were tested using structural equation modeling (SEM). RESULTS A mild level of CDI-PTSS was detected among partners, 4 and 8 months after patients' cardiac event. Partners' distress as measured during patients' hospitalization, and their fear of patients' illness progression, contributed to the manifestation of CDI-PTSS over time. CONCLUSIONS The findings shed light on potential risk factors for partners' CDI-PTSS. Interventions to ameliorate partners' distress and fear of illness progression should be designed toward reducing the development of CDI-PTSS among partners. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
Sodium, added sugar and saturated fat intake in relation to mortality and CVD events in adults: Canadian National Nutrition Survey linked with vital statistics and health administrative databases

Abstract This study aimed to determine whether higher intakes of Na, added sugars and saturated fat are prospectively associated with all-cause mortality and CVD incidence and mortality in a diverse population. The nationally representative Canadian Community Health Survey-Nutrition 2004 was linked with the Canadian Vital Statistics – Death Database and the Discharge Abstract Database (2004–2011). Outcomes were all-cause mortality and CVD incidence and mortality. There were 1722 mortality cases within 115 566 person-years of follow-up (median (interquartile range) of 7·48 (7·22–7·70) years). There was no statistically significant association between Na density or energy from saturated fat and all-cause mortality or CVD events for all models investigated. The association of usual percentage of energy from added sugars and all-cause mortality was significant in the base model with participants consuming 11·47 % of energy from added sugars having 1·34 (95 % CI 1·01, 1·77) times higher risk of all-cause mortality compared with those consuming 4·17 % of energy from added sugars. Overall, our results did not find statistically significant associations between the three nutrients and risk of all-cause mortality or CVD events at the population level in Canada. Large-scale linked national nutrition datasets may not have the discrimination to identify prospective impacts of nutrients on health measures.