Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeographic patterns of the yellow fever virus around the metropolitan region of São Paulo, Brazil, 2016–2019

From 2016 to 2019, the largest outbreak caused by the Yellow Fever virus (YFV) in the 21st century in the Americas occurred in southeastern Brazil. A sylvatic cycle of transmission was reported near densely populated areas, such as the large metropolitan area of the city of São Paulo. Here, we describe the origin, spread, and movement of the YFV throughout the state of São Paulo. Whole-genome sequences were obtained from tissues of two patients who died due to severe yellow fever, during 2018–2019. Molecular analysis indicated that all analyzed tissues were positive for YFV RNA, with the liver being the organ with the highest amount of viral RNA. Sequence analysis indicates that genomes belonged to the South American genotype I and were grouped in the epidemic clade II, which includes sequences from the states of Goiás, Minas Gerais, and São Paulo of previous years. The analysis of viral dispersion indicates that the outbreak originated in Goiás at the end of 2014 and reached the state of São Paulo through the state of Minas Gerais after 2016. When the virus reached near the urban area, it spread towards both the east and south regions of the state, not establishing an urban transmission cycle in the metropolitan region of São Paulo. The virus that moved towards the east met with YFV coming from the south of the state of Rio de Janeiro, and the YFV that was carried to the south reached the Brazilian states located in the south region of the country.
The cell biology of primary cell walls during salt stress

Abstract Salt stress simultaneously causes ionic toxicity, osmotic stress, and oxidative stress, which directly impact plant growth and development. Plants have developed numerous strategies to adapt to saline environments. Whereas some of these strategies have been investigated and exploited for crop improvement, much remains to be understood, including how salt stress is perceived by plants and how plants coordinate effective responses to the stress. It is, however, clear that the plant cell wall is the first contact point between external salt and the plant. In this context, significant advances in our understanding of halotropism, cell wall synthesis, and integrity surveillance, as well as salt-related cytoskeletal rearrangements, have been achieved. Indeed, molecular mechanisms underpinning some of these processes have recently been elucidated. In this review, we aim to provide insights into how plants respond and adapt to salt stress, with a special focus on primary cell wall biology in the model plant Arabidopsis thaliana.
Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome

Hypoplastic left heart syndrome (HLHS) is a rare but fatal birth defect in which the left side of the heart is underdeveloped. HLHS accounts for 2% to 4% of congenital heart anomalies. Whole genome sequencing (WGS) was conducted for a family trio consisting of a proband and his parents. A homozygous rare variant was detected in the PTPRB (Protein Tyrosine Phosphatase Receptor Type B) gene of the proband by functional annotation and co‐segregation analysis. Sanger sequencing was used to confirm genotypes of the variant. The in silico prediction tools, including Mutation Taster, SpliceAI, and CADD, were used to predict the impact of the mutation. The allele frequencies across populations were compared based on multiple databases, including “1000 genomes” and “gnomAD”. We used two vectors (pcMINI and pcDNA3.1) to generate a minigene construct to validate the mutational effect at the transcriptional level. Family‐based WGS analyses showed that only a homozygous splice acceptor variant (NC_000012.12: g.70636068T>G, NM_001109754.4: c.56‐2A>C, NG_029940.2: g.6373A>C) at the exon‐intron border of PTPRB gene associates with HLHS. This variant is also within the region with the enhancer activity based on UCSC genome annotation. Genotyping and Sanger sequencing revealed that the proband's parents are heterozygous for this variant. Evolutionary conservation analysis revealed that the site (NC_000012.12: g.70636068) is extremely conserved across species, supporting the evolutionary functional constraints of the ancestral wild type (T). In silico tools universally predicted a deleterious or disease‐causing impact of the mutation from T to G. The mutation was not found in the 1000 genomes and gnomAD databases, which indicates that this mutation is very rare in most human populations. A splicing assay indicated that the mutated minigene caused aberrant splicing of mRNA, in which a 3 bp missing in the second exon resulted in the deletion of one amino acid (NP_001103224.1:p.Glu19del) compared to the normal protein of PRPTB (also the VE‐PTP). Structure prediction revealed that the deletion occurred within the C‐region of the signal peptide of VE‐PTP, suggesting signal peptide‐related defects as a potential mechanism for the HLHS cellular pathogeny. We report a rare homozygous variant with splicing error in PTPRB associated with HLHS. Previous model species studies revealed conserved functions of PTPRB in cardiovascular and heart development in mice and zebrafish. Our study is the first report to show the association between PTPRB and HLHS in humans.
‘Foreign body’: a social history of Implanon in South Africa’s Eastern Cape

Abstract This article explores the reception of the contraceptive implant, Implanon, by healthcare workers and patients in family planning units in South Africa’s public health sector. Based on observations conducted at public health facilities in the Eastern Cape Province, and on interviews with nurses and patients in the same province, the study explored real-world experiences of the implant. This article examines the strategies used by nurses to promote use of the device, and explores how patients themselves responded to a widescale, national rollout of the implant within government family planning services. The study examines the reception of Implanon in the context of the post-Apartheid era in South Africa, in which the vestiges of Apartheid-era healthcare provision, and lack thereof, continue to animate personal experiences of contraception.
Abrupt onset and slow seasonal evolution of summer monsoon in an idealized GCM simulation

The world's greatest monsoons and deserts co-exist at the same latitudes on the subtropical Afro-Eurasian Continent. To investigate the mechanisms for these diverse subtropical climates, we conduct atmospheric general circulation model experiments under an idealized land-sea distribution featuring an Asian continent with a straight south coast at 17°N. Sea surface temperature and land surface parameters are all set zonally uniform to avoid a priori longitudinal preference for rainfall. The model with flat land surface produces a realistic zonal distribution of precipitation, with arid (wet) conditions over the western (eastern) part of subtropical Afro-Eurasia in association with a gigantic high pressure system over the ocean surface. The key to maintaining the western deserts is the slow precipitation-soil moisture interaction, which keeps the northward migration of the monsoon rainbelt to lag behind the sun. This is demonstrated by conducting a perpetual summer integration, where the Sahara and Arabia are soaked in heavy rain. The model monsoon starts abruptly in late June, three months after the spring equinox when a northward temperature gradient is established near the ground on the south coast. The onset is associated with explosive growth of a westward-traveling moist baroclinic wave. Further analysis suggests a Geostrophic Monsoon model: The geostrophy resists and delays the formation of a thermally direct circulation, until baroclinic instability triggers the rapid onset.
Real-world satisfaction and menstrual bleeding pattern with available LNG-IUD among Spanish young women

Abstract Objective The aim of this study was to evaluate the satisfaction and menstrual bleeding pattern with levonorgestrel-releasing intrauterine systems (LNG-IUD) in young women. Methods A prospective, multicentre, non-interventional study with 1-year follow-up was conducted in Spain. Participants were women between 18 and 30 years old who freely choose any available LNG-IUD for contraception. Satisfaction with LNG-IUD was measured with a 5-point Likert scale. Type of LNG-IUD, menstrual bleeding pattern and satisfaction with it, easiness of insertion and pain during procedure were collected. Results A total of 555 women (37.3% parous, 62.7% nulliparous) (mean age 25.8 ± 3.5) completed the study. After 12 months, 92.4% of women were satisfied or very satisfied with the LNG-IUD, with no differences by parity status, type of IUD or baseline menstrual bleeding pattern. Satisfaction with the LNG-IUD correlated with satisfaction with menstrual bleeding pattern at 12 months. Up to 88.7% of women were satisfied or very satisfied with their menstrual bleeding pattern at 12 months in comparison to 41.5% at baseline (p < 0.001). Adverse events (AE)-related discontinuation rate was low (2.2%). Conclusions Satisfaction with LNG-IUD is very high among young Spanish women, regardless of parity and menstrual bleeding pattern at baseline.
The impact of renal denervation procedure on use of antihypertensive drugs in the real-life setting

Abstract Purpose. Randomised controlled trials have shown that renal denervation lowers office and ambulatory blood pressure. The aim of the present study was to evaluate whether patients undergoing renal denervation procedure in a real-life setting have a reduction in antihypertensive drug prescription over the subsequent years. Material and methods. Using the healthcare utilisation database of the Lombardy Region (Italy), the 136 patients who, during the period 2011–2016, were prescribed four or more antihypertensive drugs and underwent renal denervation were included in the study cohort. The number and type of antihypertensive drugs were assessed over the year before and during the three-year period after renal denervation. Results. The median age of the patients was 67 years and 68% of them were men. Based on a multisource comorbidity score, about 40% of patients showed a poor or very poor clinical status. Before renal denervation, the majority of the patients were prescribed four or five antihypertensive drugs. The number of drugs decreased after the denervation and reached 55% after three years. Over the same period, patients prescribed six drugs decreased from 18% to 2%. All antihypertensive drugs were less prescribed throughout the post denervation period. Compared to the year before the denervation, after three years prescription of diuretics was reduced by 15%, calcium channel blockers by 21%, ACE-inhibitors by 32%, angiotensin receptor blockers by 22%, beta-blockers by 20%, and alfa-blockers by 30%. Use of antihypertensive drugs exhibited a reduction also in an age, sex, and clinically matched control group with no renal denervation to an extent, however, much lower than in denervated patients (p-value = 0.013). Conclusion. In the real-life setting, patients who underwent renal denervation had a clearcut reduction in antihypertensive drug prescription over the following years. Plain Language Summary Patients exhibited a reduction in the prescription of antihypertensive drugs during the three years that followed the denervation procedure The decrease in the number of antihypertensive drugs was marked, started after a relatively short time (six months), and involved all drugs prescribed before the denervation The number of hospitalisations for a cardiovascular event was similar before and after renal denervation Albeit blood pressure values were not recorded in our database, all these findings taken together suggest the renal denervation procedure has a favourable influence on blood pressure control and is not associated with an increase in the risk of major cardiovascular complications
French Norms for the Online Sussex-Waterloo Scale of Hypnotizability

ABSTRACT This article presents French norms for the online version of the Sussex-Waterloo Scale of Hypnotizability. This scale is an online adaptation of the well-established Waterloo-Stanford Group C Scale of Hypnotic Susceptibility: with both behavioral and subjective scores. Insofar as hypnotizability (the ability to respond to suggestions in a hypnotic context) varies substantially in the general population and remains generally stable throughout life, it is important to measure it in experiments using hypnotic suggestion. However, these scales are time consuming, as they often require multiple sessions to achieve a suitable sample size for subsequent participant screening. One promising route for overcoming this inconvenience is to perform hypnotizability assessment online. The Sussex-Waterloo Scale of Hypnotizability is the first to have demonstrated the viability of online measurement. The authors demonstrate that their translation of this scale yields similar statistics.
Adverse Outcome Pathways for Chronic Copper Toxicity to Fish and Amphibians

In the present review, we synthesize information on the mechanisms of chronic copper (Cu) toxicity using an adverse outcome pathway framework and identify three primary pathways for chronic Cu toxicity: disruption of sodium homeostasis, effects on bioenergetics, and oxidative stress. Unlike acute Cu toxicity, disruption of sodium homeostasis is not a driving mechanism of chronic toxicity, but compensatory responses in this pathway contribute to effects on organism bioenergetics. Effects on bioenergetics clearly contribute to chronic Cu toxicity with impacts at multiple lower levels of biological organization. However, quantitatively translating these impacts into effects on apical endpoints such as growth, amphibian metamorphosis, and reproduction remains elusive and requires further study. Copper‐induced oxidative stress occurs in most tissues of aquatic vertebrates and is clearly a significant driver of chronic Cu toxicity. Although antioxidant responses and capacities differ among tissues, there is no clear indication that specific tissues are more sensitive than others to oxidative stress. Oxidative stress leads to increased apoptosis and cellular damage in multiple tissues, including some that contribute to bioenergetic effects. This also includes oxidative damage to tissues involved in neuroendocrine axes and this damage likely alters the normal function of these tissues. Importantly, Cu‐induced changes in hormone concentrations and gene expression in endocrine‐mediated pathways such as reproductive steroidogenesis and amphibian metamorphosis are likely the result of oxidative stress‐induced tissue damage and not endocrine disruption. Overall, we conclude that oxidative stress is likely the primary driver of chronic Cu toxicity in aquatic vertebrates, with bioenergetic effects and compensatory response to disruption of sodium homeostasis contributing to some degree to observed effects on apical endpoints. Environ Toxicol Chem 2022;41:2911–2927. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Use of gonadotropin-releasing hormone agonists for ovarian preservation in patients receiving cyclophosphamide for systemic lupus erythematosus: A meta-analysis

Background Cyclophosphamide (CYC) has known cytotoxic effects on ovarian reserve and has been linked to premature ovarian failure (POF) in systemic lupus erythematosus (SLE). The concurrent use of gonadotropin-releasing hormone agonists (GnRHas) is postulated to preserve ovarian function by reducing the number of follicles exposed to CYC, but there is paucity of data to establish its efficacy. We conducted a meta-analysis to summarize the effect of concurrent GnRHa use in persevering ovarian function and pregnancy. Methods English language databases of PubMed, Embase, and Cochrane were searched to include studies published between 2000 and 2021. Studies in females with rheumatic diseases receiving concurrent GnRHa and CYC therapy to evaluate ovarian preservation as defined by amenorrhea, follicle stimulating hormone (FSH), anti-mullerian hormone (AMH), or estradiol levels or successful pregnancy were included. We used a fixed effect, exact, Mantel-Haenszel approach to estimate the overall odds ratio (OR) and associated 95% confidence intervals (95% CIs). Results Seven studies with 218 female patients were included. The ovarian function was preserved in 125/132 (94.6%) of women who received GnRHa concurrently with CYC compared to 50/86 (58%) of women who did not receive GnRHa (OR = 10.3, CI = 4.83–36.29). The OR for pregnancy with GnRHa use = 2.94 (CI = 1.04–9.89). Conclusion Our results based on limited published studies suggest that concurrent GnRHa use preserves ovarian function and increase odds of pregnancy. It can be considered for premenopausal SLE females receiving CYC. Long-term follow-up studies are needed to establish the efficacy and safety of GnRHa use for ovarian preservation.
Dieudonné operators on C(K,E)

A Banach space operator is called a Dieudonne operator if it maps weakly Cauchy sequences to weakly convergent sequences. A space E is said to have property (D) if, whenever K is a compact Hausdorff space and T is an operator from C(K,E) into a space F , T is a Dieudonne operator if and only if its representing measure is both strongly additive and has for its values Dieudonne operators from E into F . The purpose of this paper is to show that if E ∗ has the Radon-Nikodým property then E has (D) if and only if E ∗∗ has the Radon-Nikodým property.
Burden of multidrug and extensively drug-resistant ESKAPEE pathogens in a secondary hospital care setting in Greece

Abstract Bacterial antibiotic resistance (AMR) is a significant threat to public health, with the sentinel ‘ESKAPEE’ pathogens, being of particular concern. A cohort study spanning 5.5 years (2016–2021) was conducted at a provincial general hospital in Crete, Greece, to describe the epidemiology of ESKAPEE-associated bacteraemia regarding levels of AMR and their impact on patient outcomes. In total, 239 bloodstream isolates were examined from 226 patients (0.7% of 32 996 admissions) with a median age of 75 years, 28% of whom had severe comorbidity and 46% with prior stay in ICU. Multidrug resistance (MDR) was lowest for Pseudomonas aeruginosa (30%) and Escherichia coli (33%), and highest among Acinetobacter baumannii (97%); the latter included 8 (22%) with extensive drug-resistance (XDR), half of which were resistant to all antibiotics tested. MDR bacteraemia was more likely to be healthcare-associated than community-onset (RR 1.67, 95% CI 1.04–2.65). Inpatient mortality was 22%, 35% and 63% for non-MDR, MDR and XDR episodes, respectively (P = 0.004). Competing risks survival analysis revealed increasing mortality linked to longer hospitalisation with increasing AMR levels, as well as differential pathogen-specific effects. A. baumannii bacteraemia was the most fatal (14-day death hazard ratio 3.39, 95% CI 1.74–6.63). Differences in microbiology, AMR profile and associated mortality compared to national and international data emphasise the importance of similar investigations of local epidemiology.
Recurrent tumors of ameloblastoma: Clinicopathologic features and diagnostic outcome

Context: Ameloblastoma is a benign epithelial odontogenic tumor with a tendency for recurrence. Some recurrent tumors could behave unpredictably with atypical microscopic changes. Aim: To study the clinicopathologic features and diagnoses of recurrent tumors of ameloblastoma. Settings and Design: This is a 5-year (2012–2017) retrospective study of 17 consecutive patients with recurrent tumors of ameloblastoma in a Teaching Hospital in Enugu. Methods and Material: The relevant clinicopathologic information, histology slides, and blocks were retrieved and reviewed. Descriptive analysis was used to determine the frequency, tables for categorical variables, and a Chi-square test was used to determine the statistical significance. Result: Recurrent tumors constituted 33.3% (17/51) of all confirmed diagnoses of ameloblastoma. The histopathologic diagnosis of the recurrent tumors includes conventional ameloblastoma 58.8% (10/17), unicystic ameloblastoma 5.9% (1/17), and ameloblastic carcinoma 35.3% (6/17). There was bilateral mandibular involvement in 60.0%, pain 58.8%, ulceration 29.4%, and matted lymph nodes 5.9%. Tumors with positive fluid aspirates 82.4% (14/17) yielded dark-brown fluids in 90.0% (9/10) of recurrent ameloblastomas and in 66.7% (2/3) of ameloblastic carcinomas. Conclusion: There was a high recurrence rate of recurrent tumors of ameloblastoma demonstrated in the present study, with a malignant presentation in some cases.
Knowledge of chronic kidney disease among undergraduate and postgraduate students in a public university in Klang Valley, Malaysia: A cross sectional study

The prevalence of chronic kidney disease (CKD) risk factors such as diabetes mellitus, hypertension, and obesity among the young Malaysians are increasing. Understanding the factors associated with CKD knowledge could assists healthcare providers to design health education programmes. There are scarce local studies on CKD knowledge and its associated factors among university students. This subpopulation comprises of young people with diverse background and characteristics. This study was aimed to assess the CKD knowledge and its associated factors among university students. A cross-sectional study was conducted among Universiti Kebangsaan Malaysia students from July 2020 to August 2020. A convenience sampling method was applied. All students were invited to complete an online survey using Google Forms that were sent to their email. The survey consisted of questions related to their sociodemographic, socioeconomics, university programme enrolled, medical history, lifestyle characteristics and CKD knowledge. The data were analysed using SPSS Statistics 26.0. Multiple logistic regression analysis was performed to identify the final associated factors after controlling for confounders. A total of 3074 students participated and 32.6% of them had below average CKD knowledge. Students of male gender, enrolment in undergraduate programmes and non-health-related faculties/institutes were more likely to have below average CKD knowledge. Students who are Chinese, from high monthly household income family and with family history of CKD were less likely to have below average CKD knowledge. Almost one-third of the students had below average CKD knowledge. The six associated factors with CKD knowledge were non-modifiable. Of the six factors, three were associated with students being more likely to have below average CKD knowledge; another three were associated with students being less likely to have below average CKD knowledge. Future health education programmes to enhance CKD knowledge should be designed focusing on students who are more likely to have below average CKD knowledge.