Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison between serum levels of interleukin-6 and CA125 in patients with endometriosis and normal women

Background: The purpose of the present study was to compare the serum levels of IL6 and CA125 in women with and without endometriosis. They were also compared in mild, moderate and severe cases. Methods: In this case-control study, CA125 and IL6 levels in 76 women with laparoscopic proven endometriosis were compared with 76 women without evidence of endometriosis. Sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were then calculated for each test. Results: Both groups did not show significant difference in their age, BMI, ESR and gravidity. Mean serum levels of IL-6 and CA125 were significantly higher in the case group (30.4±6.43 vs 13.9±3.17 Pg/ml and 62.6±10.69 vs 16.6±1.79 IU/ml respectively). Considering a cutoff point of 30 Pg/ml for IL-6, sensitivity, specifically, PPV and NPV value of 21.1%, 66.6%, 86.8% and 23.37% were obtained, respectively. Considering a cutoff point of 35 IU/ml for CA125, sensitivity, specifically, PPV and NPV were 44.76%, 94.73%, 89.47% and 63.15%, respectively. Area under the ROC curve was 0.69 for CA125 and 0.54 for IL6, which showed a low value for these tests. Conclusion: Although CA125 and IL-6 were higher than normal controls in endometriosis, area under the ROC curve, did not show significant any diagnostic value for these tests.
Anxiety and depression among dairy farmers: the impact of COPD

Background Chronic obstructive pulmonary disease (COPD) and farming are two conditions that have been associated with an increased risk of anxiety and depression. Dairy farming is an independent risk factor for COPD. Objective To test the hypotheses that the prevalence of anxiety and/or depression is higher in dairy farmers with COPD than in farmers without COPD, and higher in dairy farmers with COPD than in non-farmers with COPD. Methods Anxiety and depression were evaluated using the Hospital Anxiety and Depression Scale in 100 dairy farmers with COPD (DF-COPD), 98 dairy farmers without COPD (DF-controls), 85 non-farming patients with COPD (NF-COPD) and 89 non-farming subjects without COPD (NF-controls), all identified by screening in the Franche-Comté region of France. Anxiety and depression were considered present when the Hospital Anxiety and Depression Scale score was ≥8. COPD was defined by a post-bronchodilator forced expiratory volume in 1 second/forced vital capacity ratio <0.7. Results The crude prevalence of anxiety did not differ between the four groups, ranging from 36% in NF-controls to 47% in NF-COPD (p=0.15 between groups). Similarly, the prevalence of depression did not differ significantly between the four groups (p=0.16 between groups). In dairy farmers (n=198), the only factors associated with anxiety were quality of life and current smoking. Depression in dairy farmers was associated with airflow limitation (lower forced expiratory volume in 1 second and COPD grade 2 or more) as well as with some COPD-related features (dyspnea severity, current smoking, and poorer quality of life). In non-farmers, both anxiety and depression were associated with airflow limitation and COPD-related features. Conclusion In our population, the prevalence of anxiety and/or depression was similar in dairy farmers with and without COPD and in non-farmers with COPD. Nevertheless, the degree of airway obstruction and some COPD-related features were associated with depression among dairy farmers, whereas these factors were not associated with anxiety.
Management of lipid-lowering therapy in patients with cardiovascular events in the UK: a retrospective cohort study

Objectives To describe low-density lipoprotein (LDL) cholesterol management and lipid-lowering treatment patterns in patients with a cardiovascular (CV) event. Design Retrospective cohort study using Clinical Practice Research Datalink records linked with Hospital Episode Statistics data. Setting Routine clinical practice in the UK from 2006 to 2012. Participants Individuals ≥18 years were selected at their first CV-related hospitalisation (first event cohort) if they had received ≥2 lipid-lowering therapy prescriptions within 180 days beforehand. Patients were stratified into four mutually exclusive subgroups based on the presence or absence of vascular disease and of diabetes. Those with a second CV hospitalisation within 36 months were included in a separate cohort (second event cohort). Primary and secondary outcome measures LDL levels in the year prior to the CV event and 12 months later as well as measures of adherence to lipid-lowering therapy during the 12 months after the CV hospitalisation. Results There were 24 093 patients in the first event cohort, of whom 5274 were included in the second event cohort. Most received moderate intensity statins at baseline and 12 months. Among the four first event cohort subgroups at baseline, the proportions with an LDL of <1.8 mmol/L was similar between the two diabetic cohorts (36% to 38%) and were higher than those in the two non-diabetic cohorts (17% to 22%) and in the second event cohort (31%). An incremental 5% to 9% had an LDL below 1.8 mmol/L at 12 months, suggesting intensification of therapy. The proportion of adherent patients (medication possession ratio of≥0.8) was highest for statins, ranging from 68% to 72%. For ezetimibe, the range was 65% to 70%, and for fibrates, it was 48% to 62%. Conclusions Despite the existence of effective therapies for lowering cholesterol, patients do not reach achievable LDL targets.
Duck Interferon-Inducible Transmembrane Protein 3 Mediates Restriction of Influenza Viruses

ABSTRACT Interferon-inducible transmembrane proteins (IFITMs) can restrict the entry of a wide range of viruses. IFITM3 localizes to endosomes and can potently restrict the replication of influenza A viruses (IAV) and several other viruses that also enter host cells through the endocytic pathway. Here, we investigate whether IFITMs are involved in protection in ducks, the natural host of influenza virus. We identify and sequence duck IFITM1, IFITM2, IFITM3, and IFITM5. Using quantitative PCR (qPCR), we demonstrate the upregulation of these genes in lung tissue in response to highly pathogenic IAV infection by 400-fold, 30-fold, 30-fold, and 5-fold, respectively. We express each IFITM in chicken DF-1 cells and show duck IFITM1 localizes to the cell surface, while IFITM3 localizes to LAMP1-containing compartments. DF-1 cells stably expressing duck IFITM3 (but not IFITM1 or IFITM2) show increased restriction of replication of H1N1, H6N2, and H11N9 IAV strains but not vesicular stomatitis virus. Although duck and human IFITM3 share only 38% identity, critical residues for viral restriction are conserved. We generate chimeric and mutant IFITM3 proteins and show duck IFITM3 does not require its N-terminal domain for endosomal localization or antiviral function; however, this N-terminal end confers endosomal localization and antiviral function on IFITM1. In contrast to mammalian IFITM3, the conserved YXXθ endocytosis signal sequence in the N-terminal domain of duck IFITM3 is not essential for correct endosomal localization. Despite significant structural and amino acid divergence, presumably due to host-virus coevolution, duck IFITM3 is functional against IAV. IMPORTANCE Immune IFITM genes are poorly conserved across species, suggesting that selective pressure from host-specific viruses has driven this divergence. We wondered whether coevolution between viruses and their natural host would result in the evasion of IFITM restriction. Ducks are the natural host of avian influenza A viruses and display few or no disease symptoms upon infection with most strains, including highly pathogenic avian influenza. We have characterized the duck IFITM locus and identified IFITM3 as an important restrictor of several influenza A viruses, including avian strains. With only 38% amino acid identity to human IFITM3, duck IFITM3 possesses antiviral function against influenza virus. Thus, despite long coevolution of virus and host effectors in the natural host, influenza virus evasion of IFITM3 restriction in ducks is not apparent.
VERSE: Versatile Graph Embeddings from Similarity Measures

Embedding a web-scale information network into a low-dimensional vector space facilitates tasks such as link prediction, classification, and visualization. Past research has addressed the problem of extracting such embeddings by adopting methods from words to graphs, without defining a clearly comprehensible graph-related objective. Yet, as we show, the objectives used in past works implicitly utilize similarity measures among graph nodes. In this paper, we carry the similarity orientation of previous works to its logical conclusion; we propose VERtex Similarity Embeddings (VERSE), a simple, versatile, and memory-efficient method that derives graph embeddings explicitly calibrated to preserve the distributions of a selected vertex-to-vertex similarity measure. VERSE learns such embeddings by training a single-layer neural network. While its default, scalable version does so via sampling similarity information, we also develop a variant using the full information per vertex. Our experimental study on standard benchmarks and real-world datasets demonstrates that VERSE, instantiated with diverse similarity measures, outperforms state-of-the-art methods in terms of precision and recall in major data mining tasks and supersedes them in time and space efficiency, while the scalable sampling-based variant achieves equally good result as the non-scalable full variant.
Stem Cell-Derived Models of Viral Infections in the Gastrointestinal Tract

Studies on the intestinal epithelial response to viral infection have previously been limited by the absence of in vitro human intestinal models that recapitulate the multicellular complexity of the gastrointestinal tract. Recent technological advances have led to the development of “mini-intestine” models, which mimic the diverse cellular nature and physiological activity of the small intestine. Utilizing adult or embryonic intestinal tissue, enteroid and organoid systems, respectively, represent an opportunity to effectively model cellular differentiation, proliferation, and interactions that are specific to the specialized environment of the intestine. Enteroid and organoid systems represent a significant advantage over traditional in vitro methods because they model the structure and function of the small intestine while also maintaining the genetic identity of the host. These more physiologic models also allow for novel approaches to investigate the interaction of enteric viruses with the gastrointestinal tract, making them ideal to study the complexities of host-pathogen interactions in this unique cellular environment. This review aims to provide a summary on the use of human enteroid and organoid systems as models to study virus pathogenesis.
C/EBPβ-Thr217 Phosphorylation Signaling Contributes to the Development of Lung Injury and Fibrosis in Mice

Background Although C/EBPβko mice are refractory to Bleomycin-induced lung fibrosis the molecular mechanisms remain unknown. Here we show that blocking the ribosomal S-6 kinase (RSK) phosphorylation of the CCAAT/Enhancer Binding Protein (C/EBP)-β on Thr217 (a RSK phosphoacceptor) with either a single point mutation (Ala217), dominant negative transgene or a blocking peptide containing the mutated phosphoacceptor ameliorates the progression of lung injury and fibrosis induced by Bleomycin in mice. Methodology/Principal Findings Mice expressing the non-phosphorylatable C/EBPβ-Ala217 transgene had a marked reduction in lung injury on day-13 after Bleomycin exposure, compared to C/EBPβwt mice, judging by the decrease of CD68+ activated monocytes/macrophages, bone marrow-derived CD45+ cells and lung cytokines as well as by the normal surfactant protein-C expression by lung pneumocytes. On day-21 after Bleomycin treatment, C/EBPβwt mice but not mice expressing the dominant negative C/EBPβ-Ala217 transgene developed severe lung fibrosis as determined by quantitative collagen assays. All mice were of identical genetic background and back-crossed to the parental wild-type inbreed FVB mice for at least ten generations. Treatment of C/EBPβwt mice with a cell permeant, C/EBPβ peptide that inhibits phosphorylation of C/EBPβ on Thr217 (40 µg instilled intracheally on day-2 and day-6 after the single Bleomycin dose) also blocked the progression of lung injury and fibrosis induced by Bleomycin. Phosphorylation of human C/EBPβ on Thr266 (human homologue phosphoacceptor) was induced in collagen-activated human lung fibroblasts in culture as well as in activated lung fibroblasts in situ in lungs of patients with severe lung fibrosis but not in control lungs, suggesting that this signaling pathway may be also relevant in human lung injury and fibrosis. Conclusions/Significance These data suggest that the RSK-C/EBPβ phosphorylation pathway may contribute to the development of lung injury and fibrosis.
Model-Based Evaluation of Higher Doses of Rifampin Using a Semimechanistic Model Incorporating Autoinduction and Saturation of Hepatic Extraction

ABSTRACT Rifampin is a key sterilizing drug in the treatment of tuberculosis (TB). It induces its own metabolism, but neither the onset nor the extent of autoinduction has been adequately described. Currently, the World Health Organization recommends a rifampin dose of 8 to 12 mg/kg of body weight, which is believed to be suboptimal, and higher doses may potentially improve treatment outcomes. However, a nonlinear increase in exposure may be observed because of saturation of hepatic extraction and hence this should be taken into consideration when a dose increase is implemented. Intensive pharmacokinetic (PK) data from 61 HIV-TB-coinfected patients in South Africa were collected at four visits, on days 1, 8, 15, and 29, after initiation of treatment. Data were analyzed by population nonlinear mixed-effects modeling. Rifampin PKs were best described by using a transit compartment absorption and a well-stirred liver model with saturation of hepatic extraction, including a first-pass effect. Autoinduction was characterized by using an exponential-maturation model: hepatic clearance almost doubled from the baseline to steady state, with a half-life of around 4.5 days. The model predicts that increases in the dose of rifampin result in more-than-linear drug exposure increases as measured by the 24-h area under the concentration-time curve. Simulations with doses of up to 35 mg/kg produced results closely in line with those of clinical trials.
The World's Rediscovered Species: Back from the Brink?

Each year, numerous species thought to have disappeared are rediscovered. Yet, do these rediscoveries represent the return of viable populations or the delayed extinction of doomed species? We document the number, distribution and conservation status of rediscovered amphibian, bird, and mammal species globally. Over the past 122 years, at least 351 species have been rediscovered, most occurring in the tropics. These species, on average, were missing for 61 years before being rediscovered (range of 3–331 years). The number of rediscoveries per year increased over time and the majority of these rediscoveries represent first documentations since their original description. Most rediscovered species have restricted ranges and small populations, and 92% of amphibians, 86% of birds, and 86% of mammals are highly threatened, independent of how long they were missing or when they were rediscovered. Under the current trends of widespread habitat loss, particularly in the tropics, most rediscovered species remain on the brink of extinction.
Feeding Behaviour, Swimming Activity and Boldness Explain Variation in Feed Intake and Growth of Sole (Solea solea) Reared in Captivity

The major economic constraint for culturing sole (Solea solea) is its slow and variable growth. The objective was to study the relationship between feed intake/efficiency, growth, and (non-) feeding behaviour of sole. Sixteen juveniles with an average (SD) growth of 2.7 (1.9) g/kg0.8/d were selected on their growth during a 4-week period in which they were housed communally with 84 other fish. Selected fish were housed individually during a second 4-week period to measure individual feed intake, growth, and behaviour. Fish were hand-fed three times a day during the dark phase of the day until apparent satiation. During six different days, behaviour was recorded twice daily during 3 minutes by direct observations. Total swimming activity, frequency of burying and of escapes were recorded. At the beginning and end of the growth period, two sequential behavioural tests were performed: “Novel Environment” and “Light Avoidance”. Fish housed individually still exhibited pronounced variation in feed intake (CV = 23%), growth (CV = 25%) and behavior (CV = 100%). Differences in feed intake account for 79% of the observed individual differences in growth of sole. Fish with higher variation in feed intake between days and between meals within days had significantly a lower total feed intake (r = −0.65 and r = −0.77) and growth. Active fish showed significantly higher feed intake (r = 0.66) and growth (r = 0.58). Boldness during both challenge tests was related to fast growth: (1) fish which reacted with a lower latency time to swim in a novel environment had significantly higher feed intake (r = −0.55) and growth (r = −0.66); (2) fish escaping during the light avoidance test tended to show higher feed intake (P<0.1) and had higher growth (P<0.05). In conclusion, feeding consistency, swimming activity in the tank, and boldness during behavioral tests are related to feed intake and growth of sole in captivity.
Latent structure of cognitive performance in the adult children study

ABSTRACT Objective: The Adult Children Study (ACS) at the Knight Alzheimer’s Disease Research Center is a longitudinal investigation designed to identify and validate potential biomarkers of preclinical Alzheimer’s disease (AD) in cognitively normal individuals with and without a family history of AD. The purpose of the current study was to validate the proposed latent structure of the ACS psychometric battery. Method: Confirmatory factor analyses of baseline data in a sample of 229 (75 men) cognitively normal middle-aged to older adult individuals assessed a hypothesized 4-factor model of cognitive performance. Measurement invariance was investigated as a function of family history of AD and apolipoprotein E (APOE) status. Results: This study confirmed a priori hypotheses of 4 latent cognitive domains in a unique longitudinal sample of cognitively normal adults. In addition, there was evidence of a similar factor structure for family history and APOE status groups. Conclusion: These robust indicators of a broad range of cognitive domains will be used in future investigations to track the influence of family history of AD on cognitive performance over time. In addition, associations with fluid, structural, and molecular biomarkers of preclinical AD will be further examined, both cross-sectionally and longitudinally in this sample.
Comment on ‘Adult skin-derived precursor Schwann cell grafts form growths in the injured spinal cord of Fischer rats’

In this study, GFP+ skin-derived precursor Schwann cells (SKP-SCs) from adult rats were grafted into the injured spinal cord of immunosuppressed rats. Our goal was to improve grafted cell survival in the injured spinal cord, which is typically low. Cells were grafted in hyaluronan-methylcellulose hydrogel (HAMC) or hyaluronan-methylcellulose modified with laminin- and fibronectin-derived peptide sequences (eHAMC). The criteria for selection of hyaluronan was for its shear-thinning properties, making the hydrogel easy to inject, methylcellulose for its inverse thermal gelation, helping to keep grafted cells in situ, and fibronectin and laminin to improve cell attachment and, thus, prevent cell death due to dissociation from substrate molecules (i.e., anoikis). Post-mortem examination revealed large masses of GFP+ SKP-SCs in the spinal cords of rats that received cells in HAMC (5 out of n = 8) and eHAMC (6 out of n = 8). Cell transplantation in eHAMC caused significantly greater spinal lesions compared to lesion and eHAMC only control groups. A parallel study showed similar masses in the contused spinal cord of rats after transplantation of adult GFP+ SKP-SCs without a hydrogel or immunosuppression. These findings suggest that adult GFP+ SKP-SCs, cultured/transplanted under the conditions described here, have a capacity for uncontrolled proliferation. Growth-formation in pre-clinical research has also been documented after transplantation of: human induced pluripotent stem cell-derived neural stem cells (Itakura et al., 2015), embryonic stem cells and embryonic stem cell-derived neurons (Brederlau et al., 2006; Dressel et al., 2008), bone marrow derived mesenchymal stem cells (Jeong et al., 2011) and rat nerve-derived SCs following in vitro expansion for ˃11 passages (Funk et al., 2007; Langford et al., 1988; Morrissey et al., 1991). It is of upmost importance to define the precise culture/transplantation parameters for maintenance of normal cell function and safe and effective use of cell therapy.
It’s not just ‘What’ you do, it’s also the ‘Way’ that you do it: Patient and Public Involvement in the Development of Health Research

Purpose This article presents a reflective account of Patient and Public Involvement (PPI) in the development of obesity and binge eating research. Method We established Patient Advisory Groups (PAGs) at two English regional National Health Service (NHS) weight management services. PPI was evaluated as follows: (i) PAG members completed a Post Participation Evaluation Questionnaire, (ii) PAG meetings captured group discussion on PPI involvement, (iii) practitioner and researchers produced written reflections on PPI and (iv) sources one to three were consolidated during reflections that took place via e-mail and telephone correspondence between researchers and practitioners, culminating in a summary SKYPE meeting between one practitioner and one researcher involved in the PAGs. Results Results in the form of reflections suggest guidelines on undertaking PPI were helpful with regard 'what to do', but less helpful on 'how'. For example, suggestions for the management of interpersonal factors such as eliciting self-disclosure and managing power differentials are insufficiently addressed in existing guidelines. Conclusions The present case study illustrated how interpersonal considerations can help or hinder the optimal use of PPI. Recommendations for practitioners and researchers planning PPI are offered.
A 320 mW 342 GOPS Real-Time Dynamic Object Recognition Processor for HD 720p Video Streams

A heterogeneous multi-core processor is proposed to achieve real-time dynamic object recognition on HD 720p video streams. The context-aware visual attention model is proposed to reduce the required computing power for HD object recognition based on enhanced attention accuracy. In order to realize real-time execution of the proposed algorithm, the processor adopts a 5-stage task-level pipeline that maximizes the utilization of its 31 heterogeneous cores, comprising four simultaneous multithreading feature extraction clusters, a cache-based feature matching processor and a machine learning engine. Dynamic resource management is applied to adaptively tune thread allocation and power management during execution based on the detected amount of tasks and hardware utilization to increase energy efficiency. As a result, the 32 mm2 chip, fabricated in 0.13 μm CMOS technology, achieves 30 frame/sec with 342 8-bit GOPS peak performance and 320 mW average power dissipation, which are a 2.72 times performance improvement and 2.54 times per-pixel energy reduction compared to the previous state-of-the-art.