Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of frequent and infrequent STI testing and STI diagnosis related to test frequency among men who have sex with men in the eastern part of the Netherlands: a 6-year retrospective study

Objective Men who have sex with men (MSM) remain vulnerable to sexually transmitted infections (STIs) and are advised to be tested at least twice a year. The aim of this study was to assess the determinants of test frequency and their associations with an STI diagnosis. Design A 6-year retrospective study. Setting 5 STI clinics in the eastern part of the Netherlands. Participants MSM whose mean test interval was 6 months or more were grouped as ‘infrequently tested’ (n=953), and those with a mean test interval less than 6 months were grouped as ‘frequently tested’ (n=658). Primary and secondary outcome measures Test frequency and STI diagnosis and determinants. Results MSM who were ever diagnosed with an STI (OR=1.4, 95% CI 1.1 to 1.7), MSM who had never had STI symptoms (OR=0.8, 95% CI 0.6 to 1.0), and MSM who had ever had sex with both men and women (OR=0.6, 95% CI 0.5 to 0.8) were more often frequently tested. Moreover, in both groups, MSM who had ever been notified by a partner (OR=2.2, 95% CI 1.7 to 2.9 infrequently tested; OR=2.0, 95% CI 1.4 to 2.9 frequently tested), MSM who had ever had STI symptoms (OR=1.6, 95% CI 1.2 to 2.1 infrequently tested; OR=1.8, 95% CI 1.3 to 2.6 frequently tested) and MSM who were ever diagnosed with HIV (OR=2.7, 95% CI 1.5 to 4.6 infrequently tested; OR=6.8, 95% CI 2.6 to 17.5 frequently tested) were more likely to be diagnosed with an STI. Conclusions Among MSM visiting STI clinics, those who were ever diagnosed with HIV were more often diagnosed with an STI, but did not visit STI clinics more frequently than HIV-negative MSM. This highlights the necessity of encouraging MSM who are diagnosed with HIV to have STI tests more frequently.
Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome

Roux-en-Y gastric bypass (RYGB) is an effective way to lose weight and reverse type 2 diabetes. We profiled the metabolome of 18 obese patients (nine euglycemic and nine diabetics) that underwent RYGB surgery and seven lean subjects. Plasma samples from the obese patients were collected before the surgery and one week and three months after the surgery. We analyzed the metabolome in association to five hormones (Adiponectin, Insulin, Ghrelin, Leptin, and Resistin), four peptide hormones (GIP, Glucagon, GLP1, and PYY), and two cytokines (IL-6 and TNF). PCA showed samples cluster by surgery time and many microbially driven metabolites (indoles in particular) correlated with the three months after the surgery. Network analysis of metabolites revealed a connection between carbohydrate (mannosamine and glucosamine) and glyoxylate and confirms glyoxylate association to diabetes. Only leptin and IL-6 had a significant association with the measured metabolites. Leptin decreased immediately after RYGB (before significant weight loss), whereas IL-6 showed no consistent response to RYGB. Moreover, leptin associated with tryptophan in support of the possible role of leptin in the regulation of serotonin synthesis pathways in the gut. These results suggest a potential link between gastric leptin and microbial-derived metabolites in the context of obesity and diabetes.
Time‐dependent contribution of BMP, FGF, IGF, and HH signaling to the proliferation of mesenchymal stroma cells during chondrogenesis

Early loss of up to 50% of cells is common for in vitro chondrogenesis of mesenchymal stromal cells (MSC) in pellet culture, reducing the efficacy and the tissue yield for cartilage engineering. Enhanced proliferation could compensate for this unwanted effect, but relevant signaling pathways remain largely unknown. The aim of this study was to identify the contribution of bone morphogenetic protein (BMP), fibroblast growth factor (FGF), insulin‐like growth factor (IGF), and hedgehog (HH) signaling toward cell proliferation during chondrogenesis and investigate whether a further mitogenic stimulation is possible and promising. Human MSC were subjected to chondrogenesis in the presence or absence of pathway inhibitors or activators up to Day 14 or from Days 14 to 28, before proliferation, DNA and proteoglycan content were quantified. [3H]‐thymidine incorporation revealed arrest of proliferation on Day 3, after which cell division was reinitiated. Although BMP signaling was essential for proliferation throughout chondrogenesis, IGF signaling was relevant only up to Day 14. In contrast, FGF and HH signaling drove proliferation only from Day 14 onward. Early BMP4, IGF‐1, or FGF18 treatment neither prevented early cell loss nor allowed further mitogenic stimulation. However, application of the HH‐agonist purmorphamine from Day 14 increased proliferation 1.44‐fold (p < 0.05) and late BMP4‐application enhanced the DNA and proteoglycan content, with significant effects on tissue yield. Conclusively, a differential and phase‐dependent contribution of the four pathways toward proliferation was uncovered and BMP4 treatment was promising to enhance tissue yield. Culture forms less prone to size limitations by nutrient/oxygen gradients and a focus on early apoptosis prevention may be considered as the next steps to further enhance chondrocyte formation from MSC.
Hunger, Food Cravings, and Diet Satisfaction are Related to Changes in Body Weight During a 6-Month Behavioral Weight Loss Intervention: The Beef WISE Study

Previously published findings from the Beef WISE Study (Beef’s Role in Weight Improvement, Satisfaction, and Energy) indicated equivalent weight loss between two energy-restricted higher protein (HP) diets: A HP diet with ≥4 weekly servings of lean beef (B; n = 60) and a HP diet restricted in all red meats (NB; n = 60). Long-term adherence to dietary prescriptions is critical for weight management but may be adversely affected by changes in appetite, food cravings, and diet satisfaction that often accompany weight loss. A secondary a priori aim of the Beef WISE Study was to compare subjective ratings of appetite (hunger and fullness), food cravings, and diet satisfaction (compliance, satisfaction, and deprivation) between the diets and determine whether these factors influenced weight loss. Subjective appetite, food cravings, and diet satisfaction ratings were collected throughout the intervention, and body weight was measured at the baseline, after the weight loss intervention (week 16), and after an eight-week follow-up period (week 24). Hunger and cravings were reduced during weight loss compared to the baseline, while fullness was not different from the baseline. The reduction in cravings was greater for B vs. NB at week 16 only. Higher deprivation ratings during weight loss were reported in NB vs. B at weeks 16 and 24, but participants in both groups reported high levels of compliance and diet satisfaction with no difference between groups. Independent of group assignment, higher baseline hunger and cravings were associated with less weight loss, and greater diet compliance, diet satisfaction, and lower feelings of deprivation were associated with greater weight loss. Strategies to promote reduced feelings of hunger, cravings, and deprivation may increase adherence to dietary prescriptions and improve behavioral weight loss outcomes.
New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe

Mating-type switching in Schizosaccharomyces pombe entails programmed gene conversion events regulated by DNA replication, heterochromatin, and the HP1-like chromodomain protein Swi6. The whole mechanism remains to be fully understood. Using a gene deletion library, we screened ~ 3400 mutants for defects in the donor selection step where a heterochromatic locus, mat2-P or mat3-M, is chosen to convert the expressed mat1 locus. By measuring the biases in mat1 content that result from faulty directionality, we identified in total 20 factors required for donor selection. Unexpectedly, these included the histone H3 lysine 4 (H3K4) methyltransferase complex subunits Set1, Swd1, Swd2, Swd3, Spf1 and Ash2, the BRE1-like ubiquitin ligase Brl2 and the Elongator complex subunit Elp6. The mutant defects were investigated in strains with reversed donor loci (mat2-M mat3-P) or when the SRE2 and SRE3 recombination enhancers, adjacent to the donors, were deleted or transposed. Mutants in Set1C, Brl2 or Elp6 altered balanced donor usage away from mat2 and the SRE2 enhancer, towards mat3 and the SRE3 enhancer. The defects in these mutants were qualitatively similar to heterochromatin mutants lacking Swi6, the NAD+-dependent histone deacetylase Sir2, or the Clr4, Raf1 or Rik1 subunits of the histone H3 lysine 9 (H3K9) methyltransferase complex, albeit not as extreme. Other mutants showed clonal biases in switching. This was the case for mutants in the NAD+-independent deacetylase complex subunits Clr1, Clr2 and Clr3, the casein kinase CK2 subunit Ckb1, the ubiquitin ligase component Pof3, and the CENP-B homologue Cbp1, as well as for double mutants lacking Swi6 and Brl2, Pof3, or Cbp1. Thus, we propose that Set1C cooperates with Swi6 and heterochromatin to direct donor choice to mat2-P in M cells, perhaps by inhibiting the SRE3 recombination enhancer, and that in the absence of Swi6 other factors are still capable of imposing biases to donor choice.
Roles of commitment and information in multi-period insurance contracting: A comprehensive review and new empirical evidence Abstract The central question in multi-period insurance contracting is the type of inter-temporal pricing

The central question in multi-period insurance contracting is the type of inter-temporal pricing pattern. Some products have a highballing (front-loaded) pattern, others are lowballing (back-loaded), and still others are flat. These patterns are sensitive to commitment and informational conditions of insurance products. This paper presents the first comprehensive review of theoretical and empirical research to uncover the roles of commitment and information in determining the type of inter-temporal pricing pattern. Moreover, a new two-sample empirical design is constructed, which excludes heterogeneity in firms, markets, and time periods, thus to isolate the impact of insurer’s commitment on its inter-temporal pricing strategy. Insurer learning is also a necessary informational condition for a lowballing pricing strategy; however whether the learning is asymmetric or symmetric turns out to be irrelevant. The paper emphasizes the control of insurance demand and supply factors in addition to the risk type when empirically examining the risk-based dynamic selection.
Shaping ability of BioRace, ProTaper NEXT and Genius nickel‐titanium instruments in curved canals of mandibular molars: a MicroCT study

AIM To evaluate and compare the canal shaping ability of BioRace, ProTaper NEXT and Genius engine-driven nickel-titanium (NiTi) file systems in extracted mandibular first molars using micro-computed tomography (MCT). METHODOLOGY Sixty mesial root canals of mandibular first molars were randomly divided into three equal groups, according to the instrument system used for root canal preparation (n = 20): BioRace (BR), ProTaper NEXT (PTN) or Genius (GN). Root canals were prepared to the full WL using a crown-down technique up to size 35, . 04 taper instruments for BR and GN groups and size 30, . 07 taper instruments for the PTN group. MCT was used to scan the specimens before and after canal instrumentation. Changes in dentine volume, the percentage of uninstrumented canal surface and degree of canal transportation were evaluated in the coronal, middle and apical thirds of canals. Data were analysed statistically using one-way analysis of variance and Tuckey's post hoc tests with the significance level set at 5%. RESULTS There were no significant differences between the three groups in the terms of dentine removed after preparation and determination of the root canal volume, or percentage of uninstrumented canal surface (P > 0.05). No significant differences were found between the systems for canal transportation in any canal third (P > 0.05). CONCLUSIONS The shaping ability of the BR, PTN and GN NiTi file systems was equally effective. All instrumentation systems prepared curved root canal systems with no evidence of undesirable changes in 3D parameters or significant shaping errors.
CNN Technology-Tools and Applications

Cellular neural/nonlinear networks were invented almost 30 years ago. The CNN research led to high performance computational architectures, neuromorphic modells of the visual and auditory pathways, stability results for arrays of coupled dynamic processors, and for practical image processing results. The main stages of the research and the results are summarized in this paper.
Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites

Membrane contact sites are cellular structures that mediate interorganelle exchange and communication. The two major tether proteins of the endoplasmic reticulum (ER), VAP‐A and VAP‐B, interact with proteins from other organelles that possess a small VAP‐interacting motif, named FFAT [two phenylalanines (FF) in an acidic track (AT)]. In this study, using an unbiased proteomic approach, we identify a novel ER tether named motile sperm domain‐containing protein 2 (MOSPD2). We show that MOSPD2 possesses a Major Sperm Protein (MSP) domain which binds FFAT motifs and consequently allows membrane tethering in vitro. MOSPD2 is an ER‐anchored protein, and it interacts with several FFAT‐containing tether proteins from endosomes, mitochondria, or Golgi. Consequently, MOSPD2 and these organelle‐bound proteins mediate the formation of contact sites between the ER and endosomes, mitochondria, or Golgi. Thus, we characterized here MOSPD2, a novel tethering component related to VAP proteins, bridging the ER with a variety of distinct organelles.
Applicability of McDonald 2010 and Magnetic Resonance Imaging in Multiple Sclerosis (MAGNIMS) 2016 Magnetic Resonance Imaging Criteria for the Diagnosis of Multiple Sclerosis in Sri Lanka

Background and Purpose The magnetic resonance imaging in multiple sclerosis (MAGNIMS) group recently proposed guidelines to replace the existing dissemination-in-space criteria in McDonald 2010 magnetic resonance imaging (MRI) criteria for diagnosing multiple sclerosis. There has been insufficient research regarding their applicability in Asians. Objective of this study was to determine the sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) of McDonald 2010 and MAGNIMS 2016 MRI criteria with the aim of verifying their applicability in Sri Lankan patients. Methods Patients with clinically isolated syndrome diagnosed by consultant neurologists were recruited from five major neurology centers. Baseline and follow-up MRI scans were performed within 3 months from the initial presentation and at one year after baseline MRI, respectively. McDonald 2010 and MAGNIMS 2016 MRI criteria were applied to all MRI scans. Patients were followed-up for 2 years to assess the conversion to clinically definite multiple sclerosis (CDMS). The sensitivity, specificity, accuracy, PPV, and NPV for predicting the conversion to CDMS were calculated. Results Forty-two of 66 patients converted to CDMS. Thirty-seven fulfilled the McDonald 2010 MRI criteria, and 33 converted to CDMS. MAGNIMS 2016 MRI criteria were fulfilled by 29, with 28 converting to CDMS. The sensitivity, specificity, accuracy, PPV, and NPV were 78%, 83%, 64%, 89%, and 69%, respectively, for the McDonald 2010 criteria, and 67%, 96%, 77%, 96%, and 62% for the MAGNIMS 2016 MRI criteria. Conclusions MAGNIMS 2016 MRI criteria were superior to McDonald 2010 MRI criteria in specificity, accuracy, and PPV, but inferior in sensitivity and NPV.
Sperm storage and degradation in the ovary of a marine copulating sculpin, Alcichthys alcicornis (Teleostei: Scorpaeniformes): Role of intercellular junctions between inner ovarian epithelial cells

The morphology of female sperm storage during the spawning period and the morphology of sperm degradation after the spawning period were investigated by electron microscopy in a copulating teleost, Alcichthys alcicornis. The spermatozoa were maintained in the ovarian cavity, floating in the ovarian fluid during the spawning period. The spermatozoa then degenerated and were phagocytized by macrophages invading the ovarian cavity after the spawning period. In the ovary during the spawning period, horseradish peroxidase used as a tracer revealed tight junctional complexes connecting adjacent cells of the inner ovarian epithelia (ovarian wall epithelium and ovigerous lamella epithelium). This indicates that a compartmentalization of the ovarian cavity occurs during the spawning period. The junctional complexes were breached after the spawning period, as shown by the fact that horseradish peroxidase penetrated the ovarian cavity via the intercellular space between the adjoining ovigerous lamella epithelia. These results suggest that the spermatozoa in the ovarian cavity are isolated from the maternal immune system by the tight junctional complexes between the adjoining inner ovarian epithelia during the spawning period, and then are eliminated by immune cells following the breakdown of the junctional complexes after the spawning period. J. Morphol. 233:153–163, 1997. © 1997 Wiley‐Liss, Inc.
Comparative morphology of Western Australian varanid lizards (Squamata: Varanidae)

Varanid lizards, which vary considerably in body mass both interspecifically and intraspecifically, are generally considered to be morphologically similar. However, significant and non‐isometric variation in the relative appendage dimensions for 17 species of Western Australian goannas suggest that these lizards are not morphologically conservative. The first and second canonical variates clearly distinguish the two subgeneral Odatria and Varanus, and species are generally sexually dimorphic. The morphological variation observed among these 17 species of goanna is associated with foraging mode and ecology. However, no single or small group of morphological dimensions discriminates phylogenetic groups, sexes, or ecological groups, and body size is an important component in these analyses. J. Morphol. 233:127–152, 1997. © 1997 Wiley‐Liss, Inc.
Enhancement of alfalfa yield and quality by plant growth-promoting rhizobacteria under saline-alkali conditions.

BACKGROUND Bacteria with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity could decrease the ethylene level, confer resistance of plant, and stimulate plant growth under biotic and abiotic stress conditions. RESULTS Plant growth-promoting rhizobacteria (PGPR) strains Enterobacter aerogenes (LJL-5) and Pseudomonas aeruginosa (LJL-13) were obtained from the rhizosphere of alfalfa grown under saline-alkali conditions. The ACC deaminase activity of E. aerogenes (LJL-5) and Ps. aeruginosa (LJL-13) was approximately 2-5 µmol mg-1 h-1 . indole acetic acid synthesis was increased with the increasing concentration of l-tryptophan. Siderophore production and phosphate solubilization in Ps. aeruginosa (LJL-13) were higher than those in E. aerogenes (LJL-5). Compared to the non-inoculated seedlings (1.31 ng mL-1 h-1 ), inoculated alfalfa seedlings with E. aerogenes (LJL-5) (0.90 ng mL-1 h-1 ) and Ps. aeruginosa (LJL-13) (0.78 ng mL-1 h-1 ) emitted lower levels of ethylene. Under saline-alkali conditions in the greenhouse, inoculation with E. aerogenes (LJL-5) and Ps. aeruginosa (LJL-13) increased the biomass, soil and plant analyzer development (SPAD), and P content of alfalfa plants, and also induced the activity of antioxidant enzymes (superoxide dismutase, peroxidase and catalase), promoted the accumulation of antioxidant substances and removed various harmful substances. Under saline-alkali conditions in the field (2012, 2013, and 2014), inoculation of alfalfa with E. aerogenes (LJL-5) and Ps. aeruginosa (LJL-13) significantly increased the shoot height, fresh and dry weights, yield and crude protein content of alfalfa plants, but decreased the fiber content. CONCLUSION Two PGPR strains were isolated from the rhizosphere of alfalfa in saline-alkali conditions. Both strains could promote alfalfa growth in saline-alkali soil, and could be used as biofertilizer to promote plant growth under stress and reduce environmental pollution caused by fertilizers simultaneously. © 2018 Society of Chemical Industry.
Extracellular matrix components indicate remodelling activity in different fibrosis stages of human non‐alcoholic fatty liver disease

The composition of several important extracellular matrix components (ECM) has not yet been elucidated in human non‐alcoholic fatty liver disease (NAFLD). We aim to investigate the proportion of hepatic stellate cells (HSCs) and activity of matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) in human NAFLD liver tissue with respect to severity of inflammation and fibrosis.
PROMIS, global analysis of PROtein–metabolite interactions using size separation in Arabidopsis thaliana

Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named PROtein–Metabolite Interactions using Size separation (PROMIS), that allows simultaneous, global analysis of endogenous protein–small molecule and of protein–protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein–protein (PPIs) and protein–metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr–Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors.
Chemical exchange rotation transfer (CERT) on human brain at 3 Tesla

To test the ability of a novel pulse sequence applied in vivo at 3 Tesla to separate the contributions to the water signal from amide proton transfer (APT) and relayed nuclear Overhauser enhancement (rNOE) from background direct water saturation and semisolid magnetization transfer (MT). The lack of such signal source isolation has confounded conventional chemical exchange saturation transfer (CEST) imaging.