Miracle-dz/UniFAR-FTUs huggingface dataset:
Origin, tempo, and mode of the spread of DENV-4 Genotype IIB across the state of São Paulo, Brazil during the 2012-2013 outbreak

BACKGROUND Dengue virus type 4 (DENV-4) was first reported in Brazil in 1982 and since then no more cases were detected again in Brazil until 2010, when the virus was reintroduced. Over the following years, the virus spread to several Brazilian states and resulted in about 1,400,000 dengue cases, in 2013. The largest number of cases were documented in the Southeast macro-region. OBJECTIVES To determine the phylogeography of DENV-4 Genotype IIB strains isolated during the epidemics in 2012-2013 in São Paulo, Brazil, we aimed to contextualise the contribution of viruses sampled in different localities across the overall movement of DENV-4 in Brazil. METHODS Based on the envelope gene sequences retrieved from GenBank, we employed a Bayesian phylogeographic approach to assess the spatiotemporal dynamics of DENV-4 Genotype IIB in São Paulo, Brazil. FINDINGS The dispersal dynamics of DENV-4 Genotype IIB in Brazil indicated Rio de Janeiro and Mato Grosso states as the most likely routes toward São Paulo before the 2012-2013 outbreak. Likewise, Guarujá and São José do Rio Preto facilitated viral spread and transmission to other localities in the South and Southeast macro-regions in Brazil. CONCLUSIONS The spread pattern of DENV-4 Genotype IIB strains across the country supports two independent introductions of the virus in São Paulo in a short period of time. Furthermore, São Paulo appears to have played a pivotal role in the dissemination of DENV-4 to other locations in Brazil.
Incidence of Interpersonal Violence among Individuals with Drug Addiction Receiving Compulsory Treatment: A Survey at Two Drug Detention Centers in Hunan, China.

doi: 10.3967/bes2018.119 This work is supported by the National Natural Science Foundation of China [No. 71774175]. 1. Zhou Enlai School of Government, Nankai University, Jinnan District, Tianjin 300050, China; 2. Department of Public Administration, Central South University, Changsha 410008, Hunan, China; 3. Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China; 4. Department of Social Medicine and Health Management, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China; 5. Department of Psychology, University of Alabama at Birmingham, Birmingham, 35294, Alabama, United States of America Letter to the Editor
TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses

Objective Mutations in TP53 are found in the majority of high grade serous ovarian cancers, leading to gain of function or loss of function of its protein product, p53, involved in oncogenesis. There have been conflicting reports as to the impact of the type of these on prognosis. We aim to further elucidate this relationship in our cohort of patients. Methods 229 patients with high grade serous ovarian cancer underwent tumor profiling through an institutional molecular screening program with targeted next generation sequencing. TP53 mutations were classified using methods previously described in the literature. Immunohistochemistry on formalin-fixed paraffin embedded tissue was used to assess for TP53 mutation. Using divisive hierarchal clustering, we generated patient clusters with similar clinicopathologic characteristics to investigate differences in outcomes. Results Six different classification schemes of TP53 mutations were studied. These did not show an association with first platinum-free interval or overall survival. Next generation sequencing reliably predicted mutation in 80% of cases, similar to the proportion detected by immunohistochemistry. Divisive hierarchical clustering generated four main clusters, with cluster 3 having a significantly worse prognosis (p<0.0001; log-rank test). This cluster had a higher concentration of gain of function mutations and these patients were less likely to have undergone optimal debulking surgery. Conclusions Different classifications of TP53 mutations did not show an impact on outcomes in this study. Immunohistochemistry was a good predictor for TP53 mutation. Cluster analysis showed that a subgroup of patients with gain of function mutations (cluster 3) had a worse prognosis.
Effectiveness of SIESTA on Objective and Subjective Metrics of Nighttime Hospital Sleep Disruptors

We created Sleep for Inpatients: Empowering Staff to Act (SIESTA), which combines electronic “nudges” to forgo nocturnal vitals and medications with interprofessional education on improving patient sleep. In one “SIESTA-enhanced unit,” nurses received coaching and integrated SIESTA into daily huddles; a standard unit did not. Six months pre- and post-SIESTA, sleep-friendly orders rose in both units (foregoing vital signs: SIESTA unit, 4% to 34%; standard, 3% to 22%, P < .001 both; sleep-promoting VTE prophylaxis: SIESTA, 15% to 42%; standard, 12% to 28%, P < .001 both). In the SIESTA- enhanced unit, nighttime room entries dropped by 44% (−6.3 disruptions/room, P < .001), and patients were more likely to report no disruptions for nighttime vital signs (70% vs 41%, P = .05) or medications (84% vs 57%, P = .031) than those in the standard unit. The standard unit was not changed. Although sleep-friendly orders were adopted in both units, a unit-based nursing empowerment approach was associated with fewer nighttime room entries and improved patient experience.
Amaranth Leaves and Skimmed Milk Powders Improve the Nutritional, Functional, Physico-Chemical and Sensory Properties of Orange Fleshed Sweet Potato Flour

Vitamin A deficiency (VAD) and under nutrition are major public health concerns in developing countries. Diets with high vitamin A and animal protein can help reduce the problem of VAD and under nutrition respectively. In this study, composite flours were developed from orange fleshed sweet potato (OFSP), amaranth leaves and skimmed milk powders; 78:2:20, 72.5:2.5:25, 65:5:30 and 55:10:35. The physico-chemical characteristics of the composite flours were determined using standard methods while sensory acceptability of porridges was rated on a nine-point hedonic scale using a trained panel. Results indicated a significant (p < 0.05) increase in protein (12.1 to 19.9%), iron (4.8 to 97.4 mg/100 g) and calcium (45.5 to 670.2 mg/100 g) contents of the OFSP-based composite flours. The vitamin A content of composite flours contributed from 32% to 442% of the recommended dietary allowance of children aged 6–59 months. The composite flours showed a significant (p < 0.05) decrease in solubility, swelling power and scores of porridge attributes with increase in substitution levels of skimmed milk and amaranth leaf powder. The study findings indicate that the OFSP-based composite flours have the potential to make a significant contribution to the improvement in the nutrition status of children aged 6–59 months in developing countries.
Robust Single-Sample Face Recognition by Sparsity-Driven Sub-Dictionary Learning Using Deep Features †

Face recognition using a single reference image per subject is challenging, above all when referring to a large gallery of subjects. Furthermore, the problem hardness seriously increases when the images are acquired in unconstrained conditions. In this paper we address the challenging Single Sample Per Person (SSPP) problem considering large datasets of images acquired in the wild, thus possibly featuring illumination, pose, face expression, partial occlusions, and low-resolution hurdles. The proposed technique alternates a sparse dictionary learning technique based on the method of optimal direction and the iterative ℓ0-norm minimization algorithm called k-LiMapS. It works on robust deep-learned features, provided that the image variability is extended by standard augmentation techniques. Experiments show the effectiveness of our method against the hardness introduced above: first, we report extensive experiments on the unconstrained LFW dataset when referring to large galleries up to 1680 subjects; second, we present experiments on very low-resolution test images up to 8×8 pixels; third, tests on the AR dataset are analyzed against specific disguises such as partial occlusions, facial expressions, and illumination problems. In all the three scenarios our method outperforms the state-of-the-art approaches adopting similar configurations.
Occurrence of Postpericardiotomy Syndrome: Association With Operation Type and Postoperative Mortality After Open‐Heart Operations

Background Postpericardiotomy syndrome (PPS) is a common complication after cardiac surgery. However, large‐scale epidemiological studies about the effect of procedure type on the occurrence of PPS and mortality of patients with PPS have not yet been performed. Methods and Results We studied the association of PPS occurrence with operation type and postoperative mortality in a nationwide follow‐up analysis of 28 761 consecutive patients entering coronary artery bypass grafting, aortic valve replacement, mitral valve replacement, or ascending aortic surgery. Only PPS episodes severe enough to result in hospital admission or to contribute as a cause of death were included. Data were collected from mandatory Finnish national registries between 2005 and 2014. Of all the patients included, 493 developed PPS during the study period. The occurrence of PPS was significantly higher after aortic valve replacement (hazard ratio, 1.97; 95% confidence interval, 1.58–2.46; P<0.001), mitral valve replacement (hazard ratio, 1.62; 95% confidence interval, 1.22–2.15; P<0.001), and aortic surgery (hazard ratio, 3.06; 95% confidence interval, 2.24–4.16; P<0.001), when compared with coronary artery bypass grafting in both univariable and multivariable analyses. The occurrence of PPS decreased significantly with aging (P<0.001). The occurrence of PPS was associated with an increased risk of mortality within the first year after the surgery (adjusted hazard ratio, 1.78; 95% confidence interval, 1.12–2.81; P=0.014). Conclusions The occurrence of PPS was higher after aortic valve replacement, mitral valve replacement, and aortic surgery when compared with the coronary artery bypass grafting procedure. Aging decreased the risk of PPS. The development of PPS was associated with higher mortality within the first year after cardiac or ascending aortic surgery.
ATM pathway activation limits R-loop-associated genomic instability in Werner syndrome cells

Abstract Werner syndrome (WS) is a cancer-prone disease caused by deficiency of Werner protein (WRN). WRN maintains genome integrity by promoting replication-fork stability after various forms of replication stress. Under mild replication stress, WS cells show impaired ATR-mediated CHK1 activation. However, it remains unclear if WS cells elicit other repair pathway. We demonstrate that loss of WRN leads to enhanced ATM phosphorylation upon prolonged exposure to aphidicolin, a specific inhibitor of DNA polymerases, resulting in CHK1 activation. Moreover, we find that loss of WRN sensitises cells to replication-transcription collisions and promotes accumulation of R-loops, which undergo XPG-dependent cleavage responsible for ATM signalling activation. Importantly, we observe that ATM pathway limits chromosomal instability in WS cells. Finally, we prove that, in WS cells, genomic instability enhanced upon chemical inhibition of ATM kinase activity is counteracted by direct or indirect suppression of R-loop formation or by XPG abrogation. Together, these findings suggest a potential role of WRN as regulator of R-loop-associated genomic instability, strengthening the notion that conflicts between replication and transcription can affect DNA replication, leading to human disease and cancer.
Liver R2* is affected by both iron and fat: A dual biopsy‐validated study of chronic liver disease

Liver iron content (LIC) in chronic liver disease (CLD) is currently determined by performing an invasive liver biopsy. MRI using R2* relaxometry is a noninvasive alternative for estimating LIC. Fat accumulation in the liver, or proton density fat fraction (PDFF), may be a possible confounder of R2* measurements. Previous studies of the effect of PDFF on R2* have not used quantitative LIC measurement.
Elucidating spray-dried dispersion dissolution mechanisms with focused beam reflectance measurement: contribution of polymer chemistry and particle properties to performance

Abstract Amorphous spray-dried dispersions (SDDs) are a key enabling technology for oral solid dosage formulations, used to improve dissolution behaviour and clinical exposure of poorly soluble active pharmaceutical ingredients (APIs). Appropriate assessment of amorphous dissolution mechanisms is an ongoing challenge. Here we outline the novel application using focused beam reflectance measurement (FBRM) to analyse particle populations orthogonal to USP 2 dissolution. The relative impact of polymer substitution and particle attributes on 25% BMS-708163/HPMC-AS SDD dissolution was assessed. Dissolution mechanisms for SDDs were categorized into erosion versus disintegration. Beyond an initial mixing period, FBRM particle counts diminish slowly and particles are detectable until the point where API dissolution is complete. There is correlation between FBRM particle count decay rate, representing loss of SDD particles in the dissolution media, and UV dissolution rate, measuring dissolved API. For the SDD formulation examined, the degree of succinoyl substitution for HPMC-AS, SDD particle size and surface area all had an impact on dissolution. These data indicate the SDD displayed an erosion mechanism and that FBRM is capturing a rate-limiting step. From this screening tool, the mechanistic understanding and measured impact of polymer chemistry and particle properties can inform a risk-assessment and control strategy for this compound.
UbiHub: a data hub for the explorers of ubiquitination pathways

Abstract Motivation Protein ubiquitination plays a central role in important cellular machineries such as protein degradation or chromatin-mediated signaling. With the recent discovery of the first potent ubiquitin-specific protease inhibitors, and the maturation of proteolysis targeting chimeras as promising chemical tools to exploit the ubiquitin-proteasome system, protein target classes associated with ubiquitination pathways are becoming the focus of intense drug-discovery efforts. Results We have developed UbiHub, an online resource that can be used to visualize a diverse array of biological, structural and chemical data on phylogenetic trees of human protein families involved in ubiquitination signaling, including E3 ligases and deubiquitinases. This interface can inform target prioritization and drug design, and serves as a navigation tool for medicinal chemists, structural and cell biologists exploring ubiquitination pathways. Availability and implementation https://ubihub.thesgc. org.
A Randomized clinical trial to evaluate the efficacy of Arimedadi oil pulling in plaque induced gingivitis, and its effect on metabolic marker in gingival crevicularfluid.

BACKGROUND : In the oral cavity, plaque forms biofilm/pellicle over the tooth surface, that harbours numerous microorganism. These microorganisms cause inflammation of the gingiva, which is termed as gingivitis. The changes noticed are red, swollen, spongy and bleeding gums. No studies till date have taken place to scientifically prove the efficacy of kabala (medicated oil pulling) in periodontal conditions. Arimedadi tailam, classical ayurvedic formulation is indicated in mukha rogas (diseases of face and oral cavity) in general and specific, oral conditions, danta vidradhi (alveolar abscess), seetada (spongy or bleeding gums), dantaharsha (odontitis), krimidanta (caries), dalana (tooth ache) and the like. AIM : To evaluate the efficacy of Arimedadi oil pulling (which is a medicated oil containing Ayurvedic medicaments) in plaque induced gingivitis and to assess the clinical and biochemical changes that take place. The patients are randomly selected. Clinical and biochemical parameters are assessed at baseline, II week and IV week. MATERIALS AND METHODS : Twenty nine patients who were diagnosed with gingivitis were advised to practice Oil pulling therapy or Chlorhexidine rinsing or Placebo mouthrinsing containing mint flavored distilled water for a period of 30 days. The baseline and post-intervention (II week and IV week) - Gingival Index, Plaque Index, Modified Sulcular Bleeding Index and GCF PGE2 levels were assessed to quantify the statistical difference between these two groups. RESULTS : Significant reduction was observed between the baseline and postintervention (II week and IV week) Gingival Index, Plaque Index, Bleeding scores and GCF PGE2 levels in the chlorhexidine group and Oil pulling group. However, this reduction was greater in Chlorhexidine group than oil pulling group. Overall from baseline to II week and IV week, when the reduction in PlI, GI, BOP and GCF PGE2 values were compared for the CHX and Oil pulling groups, the difference was statistically significant (P=0). CONCLUSION : The anti-plaque and anti-gingivitis activity of CHX was superior to Arimedadi Taila, though there was significant reduction observed in both groups. Overall, from baseline to II week and IV week, when the reduction in PlI, GI, BOP and GCF PGE2 values were compared for the CHX and Oil pulling groups, the difference was statistically significant (P=0). In the Placebo group there was no antiplaque and anti-gingivitis activity, which was in contrast to CHX and Oil pulling group. The present study results showed that PGE2 levels in GCF were found to be more sensitive to changes in gingival inflammation.
Long-term effects of pregnancy and childbirth on sleep satisfaction and duration of first-time and experienced mothers and fathers

STUDY OBJECTIVES To examine the changes in mothers' and fathers' sleep satisfaction and sleep duration across prepregnancy, pregnancy, and the postpartum period of up to 6 years after birth; it also sought to determine potential protective and risk factors for sleep during that time. METHODS Participants in a large population-representative panel study from Germany reported sleep satisfaction and sleep duration in yearly interviews. During the observation period (2008-2015), 2541 women and 2118 men reported the birth of their first, second, or third child and provided longitudinal data for analysis. Fixed-effects regression models were used to analyze changes in sleep associated with childbirth. RESULTS Sleep satisfaction and duration sharply declined with childbirth and reached a nadir during the first 3 months postpartum, with women more strongly affected (sleep satisfaction reduction compared with prepregnancy: women, 1.81 points on a 0 to 10 scale, d = 0.79 vs. men, 0.37 points, d = 0.16; sleep duration reduction compared with prepregnancy: women, 62 min, d = 0.90 vs. men, 13 min, d = 0.19). In both women and men, sleep satisfaction and duration did not fully recover for up to 6 years after the birth of their first child. Breastfeeding was associated with a slight decrease in maternal sleep satisfaction (0.72 points, d = 0.32) and duration (14 min, d = 0.21). Parental age, household income, and dual vs. single parenting were unrelated, or only very weakly related, to improved sleep. CONCLUSIONS Following the sharp decline in sleep satisfaction and duration in the first months postpartum, neither mothers' nor fathers' sleep fully recovers to prepregnancy levels up to 6 years after the birth of their first child.
Web-based learning tools: storing usage data makes a difference

Web-based learning tools are often introduced in addition to face-to-face teaching as an extra resource for students to train themselves outside the classroom. How can teachers know whether and how these tools represent an added value for students? In this paper we argue that usage data stored by such tools help teachers to get insight on the learning impact of those tools and that this must be taken into account at the design phase. This is illustrated with two web-based tools Logic-ITA and JFLAP.
Long-term results of intensity-modulated radiotherapy with three dose-fractionation regimens for localized prostate cancer

Abstract We evaluated long-term outcomes of three protocols of intensity-modulated radiation therapy (IMRT) for localized prostate cancer. Between 2005 and 2014, 348 patients were treated with 5-field IMRT. The first 74 patients were treated with a daily fraction of 2.0 Gy to 74 Gy (low-risk prostate cancer) or 78 Gy (intermediate- or high-risk prostate cancer); then 101 patients were treated with 2.1-Gy daily fractions to 73.5 or 77.7 Gy. More recently, 173 patients were treated with 2.2-Gy fractions to 72.6 or 74.8 Gy. The median age of all patients was 70 years and the median follow-up period was 82 months. The median follow-up periods were 124 months in the 2.0-Gy group, 98 months in the 2.1-Gy group, and 69 months in the 2.2-Gy group. The overall and prostate-specific antigen (PSA) failure-free survival (PSA-FFS) rates were, respectively, 89 and 68% at 10 years for the 2.0-Gy group, 91 and 84% at 8 years for the 2.1-Gy group, and 93 and 92% at 6 years for the 2.2-Gy group. The PSA-FFS rate for high-risk patients in all groups was 80% at 7 years. The cumulative incidences of Grade ≥2 late genitourinary (GU) and gastrointestinal (GI) toxicity were, respectively, 7.2 and 12.4% at 10 years for the 2.0-Gy group, 7.4 and 14.1% at 8 years for the 2.1-Gy group, and 7.1 and 7.9% at 6 years for the 2.2-Gy group. All three fractionation schedules yielded good tumor control with acceptable toxicities.
Phenolic compounds and bioactive properties of Verbascum glabratum subsp. bosnense (K. Malý) Murb., an endemic plant species

Abstract Detailed analysis of phenolic composition and antioxidant and antimicrobial activities of Verbascum glabratum subsp. bosnense (K. Malý) Murb. , an endemic species of southeastern Dinaric Alps was performed for the first time. The phenolic composition measured via UHPLC-MS/MS of four extract with different polarity suggested this plant species is very rich in both phenolic acids and flavonoids. Ethanol extract was chemically the most versatile containing 12 compounds with quercitrin and rosmarinic acid as the majors, while water extracts were rich in 4-hydroxybenzoic acid, salicylic acid, morin, and apigenin. All extracts showed high antioxidant potential measured spectrophotometrically with IC50 values ranging 0.139 - 0.021 mg/mL. Antimicrobial testing using agar diffusion test showed that ethanol extract was the most potent against all tested organisms. Also, these activities are correlated with the content of phenolic compounds, which suggest they are active ingredients of the extracts. Graphical Abstract