Miracle-dz/UniFAR-FTUs huggingface dataset:
Vascular Ehlers-Danlos syndrome in two Polish patients: identification of two novel COL3A1 gene mutations.

1070 gene, mostly heterozygous missense mutations, typically glycine substitutions in the Gly ‐X‐Y re‐ peat, or splice ‐site variants affecting the triple helical sequence leading to altered type III colla‐ gen synthesis and assembly.2,3 As a consequence of a molecular defect in the COL3A1 gene, resis‐ tance to mechanical stress of the arteries, bow‐ el, and uterus is decreased.4 Women with vEDS have an increased risk of obstetric complications including uterine rupture and dissection of ma‐ jor arteries and veins.5 To our knowledge, we report the first 2 Polish patients with vEDS in whom new causal muta‐ tions have been detected.
Using population-wide administrative and laboratory data to estimate type- and subtype-specific influenza vaccine effectiveness: a surveillance protocol

Introduction The appropriateness of using routinely collected laboratory data combined with administrative data for estimating influenza vaccine effectiveness (VE) is still being explored. This paper outlines a protocol to estimate influenza VE using linked laboratory and administrative data which could act as a companion to estimates derived from other methods. Methods and analysis We will use the test-negative design to estimate VE for each influenza type/subtype and season. Province-wide individual-level records of positive and negative influenza tests at the Provincial Laboratory for Public Health in Alberta will be linked, by unique personal health numbers, to administrative databases and vaccination records held at the Ministry of Health in Alberta to determine covariates and influenza vaccination status, respectively. Covariates of interests include age, sex, immunocompromising chronic conditions and healthcare setting. Cases will be defined based on an individual’s first positive influenza test during the season, and potential controls will be defined based on an individual’s first negative influenza test during the season. One control for each case will be randomly selected based on the week the specimen was collected. We will estimate VE using multivariable logistic regression. Ethics and dissemination Ethics approval was obtained from the University of Alberta’s Health Research Ethics Board—Health Panel under study ID Pro00075997. Results will be disseminated by public health officials in Alberta.
Geriatric Elements and Oral Anticoagulant Prescribing in Older Atrial Fibrillation Patients: SAGE‐AF

Oral anticoagulants are the cornerstone of stroke prevention in high‐risk patients with atrial fibrillation (AF). Geriatric elements, such as cognitive impairment and frailty, commonly occur in these patients and are often cited as reasons for not prescribing oral anticoagulants. We sought to systematically assess geriatric impairments in patients with AF and determine whether they were associated with oral anticoagulant prescribing.
Use of Patient-Reported Data to Match Depression Screening Intervals With Depression Risk Profiles in Primary Care Patients With Diabetes: Development and Validation of Prediction Models for Major Depression

Background Clinical guidelines recommend screening for depression in the general adult population but recognizes that the optimum interval for screening is unknown. Ideal screening intervals should match the patient risk profiles. Objective This study describes a predictive analytics approach for mining clinical and patient-reported data from a large clinical study for the identification of primary care patients at high risk for depression to match depression screening intervals with patient risk profiles. Methods This paper analyzed data from a large safety-net primary care study for diabetes and depression. A regression-based data mining technique was used to examine 53 demographics, clinical variables, and patient-reported variables to develop three prediction models for major depression at 6, 12, and 18 months from baseline. Predictors with the strongest predictive power that require low information collection efforts were selected to develop the prediction models. Predictive accuracy was measured by the area under the receiver operating curve (AUROC) and was evaluated by 10-fold cross-validation. The effectiveness of the prediction algorithms in supporting clinical decision making for six “typical” types of patients was demonstrated. Results The analysis included 923 patients who were nondepressed at the study baseline. Five patient-reported variables were selected in the prediction models to predict major depression at 6, 12, and 18 months: (1) Patient Health Questionnaire 2-item score; (2) the Sheehan Disability Scale; (3) previous problems with depression; (4) the diabetes symptoms scale; and (5) emotional burden of diabetes. All three depression prediction models had an AUROC>0.80, comparable with published depression prediction studies. Among the 6 “typical” types of patients, the algorithms suggest that patients who reported impaired daily functioning by health status are at an elevated risk for depression in all three periods. Conclusions This study demonstrated that leveraging patient-reported data and prediction models can help improve identification of high-risk patients and clinical decisions about the depression screening interval for diabetes patients. Implementation of this approach can be coupled with application of modern technologies such as telehealth and mobile health assessment for collecting patient-reported data to improve privacy, reducing stigma and costs, and promoting a personalized depression screening that matches screening intervals with patient risk profiles.
Chemoperception of Specific Amino Acids Controls Phytopathogenicity in Pseudomonas syringae pv. tomato

There is substantive evidence that chemotaxis is a key requisite for efficient pathogenesis in plant pathogens. However, information regarding particular bacterial chemoreceptors and the specific plant signal that they sense is scarce. Our work shows that the phytopathogenic bacterium Pseudomonas syringae pv. tomato mediates not only chemotaxis but also the control of pathogenicity through the perception of the plant abundant amino acids Asp and Glu. We describe the specificity of the perception of l- and d-Asp and l-Glu by the PsPto-PscA chemoreceptor and the involvement of this perception in the regulation of pathogenicity-related traits. Moreover, a saturating concentration of d-Asp reduces bacterial virulence, and we therefore propose that ligand-mediated interference of key chemoreceptors may be an alternative strategy to control virulence. ABSTRACT Chemotaxis has been associated with the pathogenicity of bacteria in plants and was found to facilitate bacterial entry through stomata and wounds. However, knowledge regarding the plant signals involved in this process is scarce. We have addressed this issue using Pseudomonas syringae pv. tomato, which is a foliar pathogen that causes bacterial speck in tomato. We show that the chemoreceptor P. syringae pv. tomato PscA (PsPto-PscA) recognizes specifically and with high affinity l-Asp, l-Glu, and d-Asp. The mutation of the chemoreceptor gene largely reduced chemotaxis to these ligands but also altered cyclic di-GMP (c-di-GMP) levels, biofilm formation, and motility, pointing to cross talk between different chemosensory pathways. Furthermore, the PsPto-PscA mutant strain showed reduced virulence in tomato. Asp and Glu are the most abundant amino acids in plants and in particular in tomato apoplasts, and we hypothesize that this receptor may have evolved to specifically recognize these compounds to facilitate bacterial entry into the plant. Infection assays with the wild-type strain showed that the presence of saturating concentrations of d-Asp also reduced bacterial virulence. IMPORTANCE There is substantive evidence that chemotaxis is a key requisite for efficient pathogenesis in plant pathogens. However, information regarding particular bacterial chemoreceptors and the specific plant signal that they sense is scarce. Our work shows that the phytopathogenic bacterium Pseudomonas syringae pv. tomato mediates not only chemotaxis but also the control of pathogenicity through the perception of the plant abundant amino acids Asp and Glu. We describe the specificity of the perception of l- and d-Asp and l-Glu by the PsPto-PscA chemoreceptor and the involvement of this perception in the regulation of pathogenicity-related traits. Moreover, a saturating concentration of d-Asp reduces bacterial virulence, and we therefore propose that ligand-mediated interference of key chemoreceptors may be an alternative strategy to control virulence.
Sex work among female workers in the traditional mining sector in Mali – results from the ANRS-12339 Sanu Gundo cross-sectional study in 2015

Female sex workers (FSW) in mining sites are considered to be at very high risk of HIV infection. We aimed to characterize FSW at the Kôkôyô artisanal gold mining site in Mali, and identify factors associated with sex work using data from ANRS-12339 Sanu Gundo, a cross-sectional survey conducted in 2015 at the mine by ARCAD-SIDA, a Malian non-governmental organisation. People attending HIV-prevention activities were invited to participate in the quantitative and qualitative parts of the survey. A probit logistic regression was used for data analysis. Of 101 women who participated in the survey, 26.7% reported sex work as their main activity. Multivariate analysis showed that the probability of sex work as a main activity decreased by 1% per 1-year age increase (p = 0.020). Sex work was significantly more likely to be reported by single, divorced and widowed women (25.4% probability; p = 0.007). FSW were significantly more likely to be non-Malian (36.3% probability; p = 0.003), more likely to have a secondary activity (77% probability; p = 0.002), to work fewer than 56h/week (40.2% probability; p = 0.001) and to be in good health (12.1% probability; p = 0.016). In addition, being aware of the existence of sexually transmitted infection, using psychoactive substances, and having unprotected receptive anal sex during the previous six months were significantly associated with sex work (50.2%; p = 0.006; 45.6%, p = 0.003; and 7.4%, p = 0.016 probability, respectively). Qualitative findings confirm that poverty and boyfriends’ refusal to use condoms remain key barriers to systematic condom use among FSW.
External Electromagnet FPCB Micromirror for Large Angle Laser Scanning

An external electromagnet plus moving PM (permanent magnet) FPCB (flexible printed circuit board) micromirror is proposed in this paper that can overcome two limitations associated with the previous FPCB micromirror with a configuration of an external PM plus moving coil, i.e., (1) it reduces the overall width beyond the mirror plate, and (2) increases the maximum rotation angle. The micromirror has two external electromagnets underneath an FPCB structure (two torsion beams and a middle seat) with two moving PM discs attached to the back and a metal-coated mirror plate bonded to the front of the FPCB middle seat. Modeling and simulation were introduced, and the prototype was fabricated and tested to verify the design. The achieved performance was better than that of the previous design: a maximum resonant rotation angle of 62° (optical) at a driving voltage of ±3 V with a frequency of 191 Hz, the required extra width beyond the mirror plate was 6 mm, and an aperture of 8 mm × 5.5 mm with a roughness of <10 nm and a flatness of >10 m (ROC, radius of curvature). The previous FPCB micromirror’s performance was: strain limited maximum rotation angle was 40° (optical), the extra width beyond the mirror plate was 14.7 mm, and had an aperture of 4 mm × 4 mm with a similar roughness and flatness.
Familial Aggregation and Heritability of Obstructive Sleep Apnea Using Children Probands.

STUDY OBJECTIVES Previous studies suggest the presence of familial aggregation of obstructive sleep apnea (OSA) in adults. However, similar data on childhood OSA are limited. This family study aimed to investigate the heritability and familial aggregation of childhood OSA and to examine whether significant differences existed between patients of normal weight and overweight. METHODS Children aged 6 to 18 years were recruited as probands either from attendants to sleep clinic (with habitual snoring) or the community (without habitual snoring). Parents and siblings of the probands were also invited to participate. All participants underwent nocturnal sleep study. RESULTS A total of 229 probands took part, of whom 33 had moderate to severe OSA, 70 had mild disease, and 126 had no OSA. A total of 412 relatives were also recruited. Although the overall heritability of obstructive apnea-hypopnea index (OAHI) was not significant (h² ± SE = 0.03 ± 0.09, P = .37), it was significant in overweight individuals on subgroup analysis (h² ± SE = 0.43 ± 0.24, P = .032). Significant interaction effect of overweight was demonstrated in both heritability and familial aggregation analyses. Bivariate genetic analysis found that the genetic correlation between OAHI and body mass index in overweight individuals (ρg ± SE = 0.63 ± 0.18) was significantly different from both 0 (P = .005) and 1 (P = .025). CONCLUSIONS The differential results of heritability and familial aggregation of OSA in normal weight and overweight subgroups substantiated the recommendation of separating childhood OSA into normal weight and overweight subtypes. In the overweight subgroup, there may be obesity-independent components involved in the genetic variance of OAHI, although a significant proportion of the genetic variance is shared with obesity.
Spatial Variability in the Effect of High Ambient Temperature on Mortality: An Analysis at Municipality Level within the Greater Athens Area

Spatial variability in temperature exists within metropolitan areas but very few studies have investigated intra-urban differentiation in the temperature-mortality effects. We investigated whether local characteristics of 42 Municipalities within the Greater Athens Area lead to modified temperature effects on mortality and if effect modifiers can be identified. Generalized Estimating Equations models were used to assess the effect of high ambient temperature on the total and cause-specific daily number of deaths and meta-regression to investigate effect modification. We found significant effects of daily temperature increases on all-cause, cardiovascular, and respiratory mortality (e.g., for all ages 4.16% (95% CI: 3.73,4.60%) per 1 °C increase in daily temperature (lags 0–3). Heterogeneity in the effect estimates between Municipalities was observed in several outcomes and environmental and socio-economic effect modifying variables were identified, such as % area coverage of buildings, length of roads/km2, population density, % unemployed, % born outside the EU countries and mean daily temperature. To further examine the role of temperature, we alternatively used modelled temperature per Municipality and calculated the effects. We found that heterogeneity was reduced but not eliminated. It appears that there are socioeconomic status and environmental determinants of the magnitude of heat-related effects on mortality, which are detected with some consistency and should be further investigated.
Pneumoproteins are associated with pulmonary function in HIV-infected persons

Background COPD is a common HIV comorbidity, and HIV-infected individuals have a higher incidence and earlier onset of COPD compared to HIV-uninfected individuals. While the pathogenesis of HIV-associated COPD is largely unknown, chronic inflammation may contribute. Four pneumoproteins known to be markers of lung injury and inflammation have been associated with COPD in HIV-uninfected individuals: PARC/CCL-18, SP-D, CC-16, and sRAGE. Objective To determine whether these pneumoproteins are also associated with pulmonary function and COPD Assessment Test (CAT) scores in HIV-infected individuals. Methods Associations between plasma pneumoprotein levels and pulmonary function were determined in a cross-sectional study of otherwise healthy HIV-infected individuals enrolled between September 2016 and June 2017. Covariates included HIV-associated (antiretroviral therapy, CD4 count, and viral load) and COPD-associated (smoking and BMI) covariates. Results Among 65 participants, 78.5% were male, 50.8% had undetectable viral load, and 76.9% were ever-smokers. Mean post-bronchodilator FEV1/FVC was 0.71, and mean DLco%predicted was 61%. Higher PARC/CCL-18 was associated with lower DLco%predicted and higher CAT score. Higher CC-16 was associated with lower DLco%predicted and lower FVC%predicted. Conclusions This exploratory analysis is the first to characterize associations between these four pneumoproteins and pulmonary function in an HIV-infected cohort. Our findings suggest the pathogenesis of HIV-associated COPD may differ from that of non-HIV-associated COPD due to HIV-specific inflammatory changes affecting DLco. PARC/CCL-18 is associated with structural and functional pulmonary abnormalities and may be an important COPD biomarker candidate in HIV infection. Our study is a preliminary step toward finding clinically relevant COPD biomarkers in high-risk populations.
The 3Rs and Humane Experimental Technique: Implementing Change

Simple Summary The 3Rs: Replacement, Reduction and Refinement, formulated by William Russell and Rex Burch, have become synonymous with the measures to improve the welfare of animals used in research and are now used as an ethical framework for improving laboratory animal welfare throughout the world. This introduction to a special issue on the 3Rs explains how a non-confrontational and scientific approach led to their development, and briefly summarizes their adoption around the world. Abstract In 1959, the Universities Federation for Animal Welfare (UFAW) Scholars Russell & Burch published the Principles of Humane Experimental Technique in which they laid out the principles of the Three Rs. However, the Three Rs owed much to others. It was UFAW and, in particular, UFAW’s Founder and Director, Major Charles Hume who identified the problem that needed to be tackled, and who developed the non-confrontational approach that was needed to both formulate the questions that needed answers and to obtain the answers from the research community. Russell & Burch’s work was also guided by an expert scientific and technical committee chaired by the Nobel Prize winner Sir Peter Medawar. This essay describes the history of the Three Rs using publications by the protagonists and others as well as material from UFAW’s archives. It describes the background to the employment of Russell & Burch, the methodology of Russell & Burch’s approach and the impact of their work up to the present day—where the Three Rs are incorporated in legislation throughout the world.
Quality of sleep, health and well-being in a population-based study

ABSTRACT OBJECTIVE To estimate the prevalence of poor self-rated sleep and to identify the population subgroups most susceptible to the problem. METHODS This is a cross-sectional, population-based study developed with data from the Health Survey conducted in the city of Campinas (ISACamp 2014/2015). Data from a sample of 1,998 individuals aged 20 years or older were analyzed. The self-rated quality of sleep was analyzed according to socio-demographic characteristics, morbidities, health behaviors and feeling of well-being. The association of sleep quality with different complaints and characteristics of sleep was also analyzed. Adjusted prevalence ratios were estimed using Poisson multiple regression model allowing for the sample weights. RESULTS Prevalence of poor self-rated sleep was 29.1% and showed to be significantly higher in women, in individuals aged from 40 to 50 years, migrants, without occupation, physically inactive in leisure context, with common mental disorder (PR = 1.59), with greater number of health problems (PR = 2.33), poor self-rated health (PR = 1.61), and life dissatisfaction. Poor sleep was strongly associated with reports of difficulty in initiating sleep (PR = 4.17), in maintaining sleep (PR = 4.40) and with never or almost never feeling well when waking up (PR = 4.52). CONCLUSIONS The results identify the population subgroups with poor quality of sleep that deserve greater attention. It also highlight the need to consider, in addition to the presence of comorbidities, mental health and the feeling of well-being in the care of patients with sleep problems and in the interventions planed for promoting healthy sleep.
Risk factors for surgical site infection after colorectal resection: a prospective single centre study. An analysis on 287 consecutive elective and urgent procedures within an institutional quality improvement project

Abstract Aim To determine the incidence and to investigate risk factors for surgical site infections (SSIs) in a cohort of patients undergoing colorectal surgery. Material & methods Data from all consecutive patients operated at our department in an elective or in an urgent setting over a 4-month period were prospectively collected and analysed. The updated Centres for Disease Control and Prevention guidelines were used to define and to score SSIs during weekly meetings. Multivariate analysis was performed considering a list of 20 potential perioperative risk factors. Results A total of 287 patients (mean age 56.9 ± 16.8 years, 51.2% male) were included. Thirty-five patients (12.2%) developed SSI. Independent risk factors for SSI were BMI <20 kg/m2 (OR 3.70; p = .022), cancer (OR 0.33; p = .046), respiratory comorbidity (OR 3.15; p = .035), presence of a preoperative stoma (OR 3.74; p = .003), and operative time ≥3 hours (OR 2.93; p = .014). Conclusion Identified incidence and risk factors for the development of SSI after colorectal surgery were consistent with those already reported in the literature. The possibility to develop a validated prediction model for SSIs warrants further investigation, in order to target specific preventive measures on high-risk population.
Mechanism of the action of bioactive proteins of vegetables in diabetes mellitus type 2

Abstract Background: Diabetes mellitus type 2 (DM2) is a chronic disease of significant prevalence causing hyperglycemia and several comorbidities. Evidences highlight the performance of non - protein bioactive compounds found in vegetables in the control of hyperglycemia. This study describes a protocol of a systematic review, which analyzes the action of proteins and bioactive peptides of plants in DM2. Methods: The Preferred Reporting Items guide this protocol for Systematic Reviews and Meta-Analyzes Protocols (PRISMA-P) was used. The databases that will be used for searching will be PubMed, ScienceDirect, Scopus, Web of Science, EMBASE, and Virtual Health Library, Brazil (VHL). Studies that use bioactive proteins and peptides of vegetal origin in DM2 will be included in the systematic review. The studies will be identified using clinical parameters and the effect on insulin resistance. The characteristics of the studies as control groups, test substance, dosage, intervention time, and the main results will be described. Selection of studies, data extraction, and methodological quality assessment will be performed independently by two experienced reviewers. Results: This protocol will be the basis for a systematic review identifying the mechanism of action of plant proteins and peptides in type 2 diabetes mellitus. Conclusion: Systematic reviews from this protocol will provide support for the construction of researches that analyze the effect of plant bioactive proteins and peptides on the control of hyperglycemia and how these molecules act in the control of DM2. Prospero Registration Number: CRD42019110956.