Miracle-dz/UniFAR-FTUs huggingface dataset:
The Zambian Preterm Birth Prevention Study (ZAPPS): Cohort characteristics at enrollment

Background: Sub-Saharan Africa bears a disproportionate burden of preterm birth and other adverse outcomes. A better understanding of the demographic, clinical, and biologic underpinnings of these adverse outcomes is urgently needed to plan interventions and inform new discovery. Methods: The Zambian Preterm Birth Prevention Study (ZAPPS) is a prospective observational cohort established at the Women and Newborn Hospital (WNH) in Lusaka, Zambia. We recruit pregnant women from district health centers and the WNH and offer ultrasound examination to determine eligibility. Participants receive routine obstetrical care, lab testing, midtrimester cervical length measurement, and serial fetal growth monitoring. At delivery, we assess gestational age, birthweight, vital status, and sex and assign a delivery phenotype. We collect blood, urine, and vaginal swab specimens at scheduled visits and store them in an on-site biorepository. In September 2017, enrollment of the ZAPPS Phase 1—the subject of this report—was completed. Phase 2, which is limited to HIV-uninfected women, reopened in January 2018. Results: Between August 2015 and September 2017, we screened 1784 women, of whom 1450 (81.2%) met inclusion criteria and were enrolled. The median age at enrollment was 27 years (IQR 23–32) and median gestational age was 16 weeks (IQR 13–18). Among women with a previous pregnancy (n=1042), 19% (n=194) reported a prior miscarriage. Among parous women (n=992), 41% (n=411) reported a prior preterm birth and 14% (n=126) reported a prior stillbirth. The HIV seroprevalence was 24%. Discussion: We have established a large cohort of pregnant women and newborns at the WNH to characterize the determinants of adverse birth outcomes in Lusaka, Zambia. Our overarching goal is to elucidate biological mechanisms in an effort to identify new strategies for early detection and prevention of adverse outcomes. We hope that findings from this cohort will help guide future studies, clinical care, and policy.
Contribution à la connaissance des orthoptéroïdes de corse (orthoptera, phasmoptera, mantodea)

Lors d'un sejour en Corse entre la fin juillet et debut aout 2005, les auteurs ont effectue des prospections diurnes et nocturnes permettant de rencontrer 66 taxons d'Orthopteroides (36 Ensiferes, 25 Caeliferes, deux Phasmes et trois Mantides), sur les 89 especes connues a ce jour pour l'ile. Les recherches nocturnes ont ete realisees avec l'aide d'un detecteur ultrasonore. Les commentaires des differentes especes inventoriees mettent l'accent sur les genres Rhacocleis, Uromenus et Eupholidoptera parmi les Ensiferes, et Locusta migratoria parmi les Caeliferes. La presence du grillon Modicogryllus palmetorum (Krauss, I902) est discutee sur la seule base des enregistrements acoustiques. Un autre grillon, inconnu de la faune de France, est egalement signale par ses stridulations.
Interventions to increase research publications in graduate medical education trainees: a systematic review

Introduction Competency-based educational models recommend trainee exposure to research, but the best methods for Graduate Medical Education (GME) programs to accomplish this have not been clarified. The objective of this study was to quantify published interventions to generate resident research and compare effectiveness among those interventions. Material and methods A systematic review of English-language articles of studies of GME programs was performed, describing resident research interventions and quantifying the number of publications as an outcome. Results The search produced 13,688 potentially relevant articles, and included 47 articles in the final synthesis. Publication effectiveness was calculated as publications per year. The top ten programs for publication effectiveness were compared to others for interventions chosen. Interventions were characterized as research director, protected time, research requirement, research mentor, curricula, research assistant, biostatistician, information technology support, research fund, pay-for-performance plans, and celebration of accomplishments. Total number of different interventions was not significantly associated with primary outcome (r = 0.20, p = 0.18). When comparing the top ten programs to the others, appointment of a research director was statistically more prevalent in those programs (70% vs. 30%, p = 0.02), while presence of a defined curriculum was more common (90% vs. 57%, p = 0.052) but not statistically significantly. Conclusions Leadership interventions (directors, curricula) are associated with successful GME research efforts.
[Zhenwu Decoction delays ventricular hypertrophy in rats with uremic cardiomyopathy].

OBJECTIVE To investigate the inhibitory effect of Zhenwu Decoction on ventricular hypertrophy in rats with uremic cardiomyopathy and explore the mechanism. METHODS Cardiocytes isolated from suckling rats were divided into control group and indoxyl sulfate (IS) group, and the protein synthesis was assayed with [3H]- leucine incorporation and cellular protein expressions were detected using Western blotting. Fifty SD rats were randomly divided into sham operation group, model group, and low- and high-dose Zhenwu Decoction treatment groups, and except for those in the sham operation group, all the rats underwent 5/6 nephrectomy. Four weeks after the operation, the rats in low- and high-dose treatment groups were given Zhenwu Decoction via gavage at the dose of 4.5 g/kg and 13.5 g/kg, respectively; the rats in the sham-operated and model groups were given an equal volume of distilled water. After 4 weeks of treatment, serum levels of IS were determined, and cardiac and ventricular mass indexes were measured in the rats; cardiac ultrasound was performed and Western blotting was used to measure the expressions of BNP, p-ERK1/2, p-p38 and p-JNK in the myocardium. RESULTS Rat cardiomyocytes treated with IS showed significantly enhanced protein synthesis and increased expression levels of BNP, p-erk1/2, and p-p38 as compared with the control cells (P < 0.01), but the expression of p-jnk was comparable between the two groups. In the animal experiment, the rats in the model group showed significantly increased serum creatinine (SCr) and urea nitrogen (BUN) levels, 24-h urine protein (24 hUpro), plasma IS level, left ventricular mass index (LVMI) and whole heart mass index (HMI) compared with those in the sham group (P < 0.01); Both LVESD and LVEDD were significantly reduced and LVAWS, LVAWD, LVPWS and LVPWD were significantly increased in the model rat, which also presented with obvious cardiomyocyte hypertrophy and increased myocardial expressions of BNP, p-ERK1/2, p-p38 and p-jnk (P < 0.01). Compared with the rats in the model group, the rats treated with low-dose and high-dose Zhenwu Decoction had significantly lowered levels of SCr, BUN, 24 hUpro and IS (P < 0.05) and decreased LVMI and HMI; LVESD, LVEDD, LVPWS, LVAWS, and LVAWD were improved more obviously in the high-dose group, and the myocardial expressions of BNP, p-ERK1/2, p-p38 and p-JNK was significantly downregulated after the treatment. CONCLUSIONS Zhenwu Decoctin can reduce plasma IS levels and inhibit ventricular hypertrophy to delay ventricular remodeling in rats with uremic cardiomyopathy.
Phyllodes tumour of the breast and margins: How much is enough

Summary Phyllodes breast tumours are fairly uncommon, and they can be benign, borderline or malignant. General surgeons usually encounter them following the surgical excision of a breast lump that had the appearance of a fibroepithelial lesion. The surgeon is then faced with the question of what to do to establish an acceptable treatment margin. In this discussion, we recommend a plan for the management of Phyllodes tumours based on a review of the recent literature, confirmed by a retrospective review of the results from our centre. A negative margin is acceptable treatment following a lumpectomy for Phyllodes tumours. Only patients with a positive margin should undergo a revision.
Predicting the optimal growth temperatures of prokaryotes using only genome derived features

Motivation Optimal growth temperature is a fundamental characteristic of all living organisms. Knowledge of this temperature is central to the study of a prokaryote, the thermal stability and temperature dependent activity of its genes, and the bioprospecting of its genome for thermally adapted proteins. While high throughput sequencing methods have dramatically increased the availability of genomic information, the growth temperatures of the source organisms are often unknown. This limits the study and technological application of these species and their genomes. Here, we present a novel method for the prediction of growth temperatures of prokaryotes using only genomic sequences. Results By applying the reverse ecology principle that an organism's genome includes identifiable adaptations to its native environment, we can predict a species' optimal growth temperature with an accuracy of 5.17 °C root-mean-square error and a coefficient of determination of 0.835. The accuracy can be further improved for specific taxonomic clades or by excluding psychrophiles. This method provides a valuable tool for the rapid calculation of organism growth temperature when only the genome sequence is known. Availability and implementation Source code, genomes analyzed, and features calculated are available at: https://github.com/DavidBSauer/OGT_prediction. Supplementary information Supplementary data are available at Bioinformatics online.
Naturally-Derived Biphasic Calcium Phosphates through Increased Phosphorus-Based Reagent Amounts for Biomedical Applications

Calcium carbonate from marble and seashells is an eco-friendly, sustainable, and largely available bioresource for producing natural bone-like calcium phosphates (CaPs). Based on three main objectives, this research targeted the: (i) adaptation of an indirect synthesis route by modulating the amount of phosphorus used in the chemical reaction, (ii) comprehensive structural, morphological, and surface characterization, and (iii) biocompatibility assessment of the synthesized powdered samples. The morphological characterization was performed on digitally processed scanning electron microscopy (SEM) images. The complementary 3D image augmentation of SEM results also allowed the quantification of roughness parameters. The results revealed that both morphology and roughness were modulated through the induced variation of the synthesis parameters. Structural investigation of the samples was performed by Fourier transform infrared spectroscopy and X-ray diffraction. Depending on the phosphorus amount from the chemical reaction, the structural studies revealed the formation of biphasic CaPs based on hydroxyapatite/brushite or brushite/monetite. The in vitro assessment of the powdered samples demonstrated their capacity to support MC3T3-E1 pre-osteoblast viability and proliferation at comparable levels to the negative cytotoxicity control and the reference material (commercial hydroxyapatite). Therefore, these samples hold great promise for biomedical applications.
The effects of an alternative diet regimen with natural methionine ingredients on white striping breast myopathy in broiler chickens

&NA; Conventional broiler diets include synthetic methionine to optimize fast muscle growth. Recently, a conventional synthetic methionine‐rich diet was compared to alternative diet regimens providing natural sources of methionine. Broilers fed diets with natural methionine sources grew at a slightly slower rate. From this study, we hypothesized that the difference in a growth rate would be reflected in features of the breast muscle from broilers fed the alternative diet. We hypothesized that white striping of pectoralis major muscle would be reduced in slower growing broilers fed the alternative diet regimen with natural methionine. We also hypothesized that there would be associated differences in gene expression for cell differentiation and pathology markers. Broilers fed a conventional corn/soy diet regimen with synthetic methionine were compared to those fed roasted cowpea and sunflower seed meal (60% corn/soy, 20% sunflower seed meal, and 20% roasted cowpea) and no synthetic methionine. Overall broiler growth, muscle gene expression, and muscle collagen content data were compared. Expression analyses of combinations of MYOD1, PPARG, COL1A2, TRIM63, SOD1, PTGS2, and CD36 genes were used to examine differentiation and inflammation in the pectoralis muscles. The group fed an alternative diet gained less weight than those fed the control diet in the starter and grower phases but not in the finisher phase. Ultimately, the conventional diet resulted in a greater final weight for the broilers. However, mean white striping scores for the pectoralis major muscles were greater in the conventional control diet regimen. Gene expression results indicated greater expression of PPARG, PTGS2, and CD36 in the muscle of broilers fed the control diet. These data associate white striping with fat deposition and inflammation. Thus, whether due to differences in feed intake, growth rate, or actual compositional differences, the alternative diet with natural methionine sources seemed to curtail amounts of white striping in broiler muscle. More studies are necessary to further discern the effect of growth rate and natural methionine sources on white striping.
Renoprotective Effect of the Histone Deacetylase Inhibitor CG200745 in DOCA-Salt Hypertensive Rats

The novel histone deacetylase inhibitor CG200745 was initially developed to treat various hematological and solid cancers. We investigated the molecular mechanisms associated with the renoprotective effects of CG200745 using deoxycorticosterone acetate (DOCA)-salt hypertensive (DSH) rats. DOCA strips (200 mg/kg) were implanted into rats one week after unilateral nephrectomy. Two weeks after DOCA implantation, DSH rats were randomly divided into two groups that received either physiological saline or CG200745 (5 mg/kg/day) for another two weeks. The extent of glomerulosclerosis and tubulointerstitial fibrosis was determined by Masson’s trichrome staining. The renal expression of fibrosis and inflammatory markers was detected by semiquantitative immunoblotting, a polymerase chain reaction, and immunohistochemistry. Pathological signs such as glomerulosclerosis, tubulointerstitial fibrosis, increased systolic blood pressure, decreased creatinine clearance, and increased albumin-to-creatinine ratios in DSH rats were alleviated by CG200745 treatment compared to those manifestations in positive control animals. Furthermore, this treatment counteracted the increased expression of αSMA, TGF-β1, and Bax, and the decreased expression of Bcl-2 in the kidneys of DSH rats. It also attenuated the increase in the number of apoptotic cells in DSH rats. Thus, CG200745 can effectively prevent the progression of renal injury in DSH rats by exerting anti-inflammatory, anti-fibrotic, and anti-apoptotic effects.
Community-level chlamydial serology for assessing trachoma elimination in trachoma-endemic Niger

Background Program decision-making for trachoma elimination currently relies on conjunctival clinical signs. Antibody tests may provide additional information on the epidemiology of trachoma, particularly in regions where it is disappearing or elimination targets have been met. Methods A cluster-randomized trial of mass azithromycin distribution strategies for trachoma elimination was conducted over three years in a mesoendemic region of Niger. Dried blood spots were collected from a random sample of children aged 1–5 years in each of 24 study communities at 36 months after initiation of the intervention. A multiplex bead assay was used to test for antibodies to two Chlamydia trachomatis antigens, Pgp3 and CT694. We compared seropositivity to either antigen to clinical signs of active trachoma (trachomatous inflammation—follicular [TF] and trachomatous inflammation—intense [TI]) at the individual and cluster level, and to ocular chlamydia prevalence at the community level. Results Of 988 children with antibody data, TF prevalence was 7.8% (95% CI 6.1 to 9.5) and TI prevalence was 1.6% (95% CI 0.9 to 2.6). The overall prevalence of antibody positivity to Pgp3 was 27.2% (95% CI 24.5 to 30), and to CT694 was 23.7% (95% CI 21 to 26.2). Ocular chlamydia infection prevalence was 5.2% (95% CI 2.8 to 7.6). Seropositivity to Pgp3 and/or CT694 was significantly associated with TF at the individual and community level and with ocular chlamydia infection and TI at the community level. Older children were more likely to be seropositive than younger children. Conclusion Seropositivity to Pgp3 and CT694 correlates with clinical signs and ocular chlamydia infection in a mesoendemic region of Niger. Trial registration ClinicalTrials.gov NCT00792922.
GABAergic regulation of pancreatic islet cells: Physiology and antidiabetic effects

Diabetes occurs when pancreatic β‐cell death exceeds β‐cell growth, which leads to loss of β‐cell mass. An effective therapy must have two actions: promotion of β‐cell replication and suppression of β‐cell death. Previous studies have established an important role for γ‐aminobutyric acid (GABA) in islet‐cell hormone homeostasis, as well as the maintenance of the β‐cell mass. GABA exerts paracrine actions on α cells in suppressing glucagon secretion, and it has autocrine actions on β cells that increase insulin secretion. Multiple studies have shown that GABA increases the mitotic rate of β cells. In mice, following β‐cell depletion with streptozotocin, GABA therapy can restore the β‐cell mass. Enhanced β‐cell replication appears to depend on growth and survival pathways involving Akt activation. Some studies have also suggested that it induces transdifferentiation of α cells into β cells, but this has been disputed and requires further investigation. In addition to proliferative effects, GABA protects β cells against injury and markedly reduces their apoptosis under a variety of conditions. The antiapoptotic effects depend at least in part on the enhancement of sirtuin‐1 and Klotho activity, which both inhibit activation of the NF‐κB inflammatory pathway. Importantly, in xenotransplanted human islets, GABA therapy stimulates β‐cell replication and insulin secretion. Thus, the intraislet GABAergic system is a target for the amelioration of diabetes therapy, including β‐cell survival and regeneration. GABA (or GABAergic drugs) can be combined with other antidiabetic drugs for greater effect.
‘Full price, full body’: norms, brideprice and intimate partner violence in highlands Papua New Guinea

Abstract This paper draws on qualitative research in Jiwaka Province, in the highlands of Papua New Guinea (PNG), to examine the changing nature of marriage in that context. In particular, it examines how changes in the practice of brideprice have been associated with an increase in intimate partner violence. Violence, a relational process, is to be understood in the context of the customary unequal power relations between men and women. It is argued that men in the highlands of PNG see any gain in power for women as a loss for themselves, and so actively resist it. Men who see their power over women challenged resort to the discourse of brideprice, arguing that the payment of brideprice gives them absolute authority over wives. A good understanding of the norms that sanction violence is a vital step in developing interventions to prevent violence.
Effects of HIIT and MICT on cardiovascular risk factors in adults with overweight and/or obesity: A meta-analysis

Objective The purpose of this study was to evaluate the effects of high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) on cardiovascular disease (CVD) risk factors in adults with overweight and obesity. Methods Twenty-two articles were included by searching six databases, the total number of subjects was 620 in these articles. Outcomes were synthesised using a random-effects meta-analysis of the Standardized mean difference (SMD) in CVD risk factors. Results HIIT and MICT resulted in statistically significant reductions in Weight, BMI, fat%, total cholesterol(TC), and improvement in VO2max. Compared with MICT, subgroup of durations of HIIT training interval ≥2 min can significantly increase VO2max (SMD = 0.444, 95% CI:0.037~0.851,P = 0.032), subgroup of energy expenditure of HIIT equal to MICT can significantly increase VO2max (SMD = 0.399, 95% CI:0.106~0.692,P = 0.008). Conclusions HIIT appears to provide similar benefits to MICT for improving body composition, VO2maxand TC, but HIIT spent less time than MICT by 9.7 min on one session. HIIT is superior to MICT in improving cardiopulmonary fitness when durations of HIIT training interval ≥2 min or energy expenditure of HIIT same as MICT. PROSPERO ID: CRD42016045835.
[LC-MS/MS-based screening of new protein biomarkers for cervical precancerous lesions and cervical cancer].

OBJECTIVE To screen potential plasma protein biomarkers for the progression of cervical precancerous lesions into cervical carcinoma and analyze their functions. METHODS Plasma samples obtained from healthy control subjects, patients with low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL), cervical cancer (CC), and patients with CC after treatment were enriched for low-abundance proteins for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The MS data of the samples were analyzed using Discoverer 2.2 software, and the differential proteins (peptide coverage ≥20%, unique peptides≥2) were screened by comparison of LSIL, HSIL and CC groups against the control group followed by verification using target proteomics technology. Protein function enrichment and coexpression analyses were carried out to explore the role of the differentially expressed proteins as potential biomarkers and their pathological mechanisms. RESULTS Compared with the control group, both LSIL group and HSIL group showed 9 differential proteins; 5 differentially expressed proteins were identified in CC group. The proteins ORM2 and HPR showed obvious differential expressions in LSIL and HSIL groups compared with the control group, and could serve as potential biomarkers for the progression of cervical carcinoma. The expression of F9 increased consistently with the lesion progression from LSIL to HSIL and CC, suggesting its value as a potential biomarker for the progression of cervical cancer. CFI and AFM protein levels were obviously decreased in treated patients with CC compared with the patients before treatment, indicating their predictive value for the therapeutic efficacy. Protein function enrichment analysis showed that all these differentially expressed proteins were associated with the complement system and the coagulation cascades pathway. CONCLUSIONS We identified 5 new protein biomarkers (F9, CFI, AFM, HPR, and ORM2) for cervical precancerous lesions and for prognostic evaluation of CC, and combined detection of these biomarkers may help in the evaluation of the development and progression of CC and also in improving the diagnostic sensitivity and specificity of cervical lesions.