Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome

Gastric carcinoma (GC) is a leading cause of mortality. 10% of GC cases are related with EBV (Epstein-Barr virus) infection. The detailed mechanistic roles EBV genes play and especially the interaction between the viral genes and human genes in GC remain unclear. In this study, raw fastq data from 285 GC samples were downloaded from TCGA (The Cancer Genome Atlas), including 25 EBV positive (EBV+) GC samples and 260 EBV negative (EBV−) GC samples. RNA-seq based expression data were generated for both human genes (among all the samples) and for the EBV genes (among the 25 EBV+ samples). Bioinformatics analyses were performed to identify differentially expressed (DEx) human genes and DEx KEGG pathways in EBV+ vs. EBV− samples and co-expressed human gene modules and hub genes among the DEx genes. Within the EBV+ samples, analyses were conducted to find correlation between EBV gene expression and the human gene expression modules, between EBV gene expression and the human hub genes, and between EBV gene expression and the DEx human pathways. EBV genes LMP-1, BALF1 and BALF2 were found to have significant correlation with human hub genes, CNTD2 and VANGL2. EBV genes BALF4 and BALF5 were found to correlate with human pathways, including Jak-STAT signaling and Phosphatidylinositol Signaling System. Our study has revealed the coordinated expression patterns between EBV and human GC transcriptome and identified several key EBV genes that may play an important role in EBV+ GC pathogenesis through their interactions with human genes and pathways.
Lipid accumulation product is associated with metabolic syndrome in women with polycystic ovary syndrome.

OBJECTIVE There is a need for a simple and accurate method for the assessment of cardiovascular risk in polycystic ovary syndrome (PCOS). Lipid accumulation product (LAP) is based on the assessment of waist circumference and serum triglycerides that yield an estimation of lipid overaccumulation. We aimed to determine whether LAP is associated with metabolic syndrome (MetS) in Caucasian women with PCOS. DESIGN We studied 222 women with PCOS who were diagnosed using the Rotterdam criteria. In all the subjects and controls, LAP was determined and the MetS was assessed using three different international criteria, NCEP-ATP III, IDF, and JIS. ROC curve and logistic regression analyses were performed to determine and analyze associations with the MetS. RESULTS In the study population the prevalence of MetS was 16.2-19.4%. The cut-off value of 25.9 determined that LAP has the strongest association with MetS whichever international criteria are used, followed by HDL (NCEP-ATP III and JIS) and glucose (IDF). CONCLUSIONS LAP is used as an independent clinical indicator for MetS in our PCOS women of Caucasian origin. The high diagnostic accuracy of LAP is superseding the need for the use of multiple clinical indicators for the assessment of lipid accumulation as a prerequisite for diagnosis of metabolic and cardiovascular diseases in PCOS women.
Oxidation and degradation of polypropylene transvaginal mesh

Abstract Polypropylene (PP) transvaginal mesh (TVM) repair for stress urinary incontinence (SUI) has shown promising short-term objective cure rates. However, life-altering complications have been associated with the placement of PP mesh for SUI repair. PP degradation as a result of the foreign body reaction (FBR) has been proposed as a contributing factor to mesh complications. We hypothesized that PP oxidizes under in vitro conditions simulating the FBR, resulting in degradation of the PP. Three PP mid-urethral slings from two commercial manufacturers were evaluated. Test specimens (n = 6) were incubated in oxidative medium for up to 5 weeks. Oxidation was assessed by Fourier Transform Infrared Spectroscopy (FTIR), and degradation was evaluated by scanning electron microscopy (SEM). FTIR spectra of the slings revealed evidence of carbonyl and hydroxyl peaks after 5 weeks of incubation time, providing evidence of oxidation of PP. SEM images at 5 weeks showed evidence of surface degradation, including pitting and flaking. Thus, oxidation and degradation of PP pelvic mesh were evidenced by chemical and physical changes under simulated in vivo conditions. To assess changes in PP surface chemistry in vivo, fibers were recovered from PP mesh explanted from a single patient without formalin fixation, untreated (n = 5) or scraped (n = 5) to remove tissue, and analyzed by X-ray photoelectron spectroscopy. Mechanical scraping removed adherent tissue, revealing an underlying layer of oxidized PP. These findings underscore the need for further research into the relative contribution of oxidative degradation to complications associated with PP-based TVM devices in larger cohorts of patients.
Mathematical modelling of calcium influence on the activity of osteogenic cells

Bone formation is a very complex physiological process, involving the participation of many different cell types and regulated by countless biochemical and mechanical factors. In this Master’s thesis a bioregulatory model of the effect of calcium phosphate biomaterials and Ca2+ on the activity of osteogenic cells was developed and implemented. The mathematical framework consists of six differential equations that describe the temporal evolution of the osteogenic cells, the collagen and mineral matrix and several biochemical factors. The predicted amount of bone formation corresponds to the amount measured experimentally under similar conditions. Moreover, the model is able to qualitatively predict some impaired bone formation conditions. Various strategies to compensate for insufficient cell seeding densities were designed. The most influential parameters of the model were determined using a sensitivity analysis by design of experiments. This work compared three different methods and the results clearly indicated the strengths and shortcomings of every method. In the last part of this Master’s thesis, the calcium model was extended to spatial coordinates. In summary, this work illustrates the potential of mathematical models in further unraveling the complex biological process of bone formation and designing more efficient calcium phosphate scaffolds and therapies.
Methodological Quality and Outcome of Systematic Reviews Reporting on Orthopaedic Treatment for Class III Malocclusion: Overview of Systematic Reviews

Objectives The aim of this overview of systematic reviews was to investigate methodological quality and outcome of current systematic reviews (SRs) reporting on orthopaedic treatment for class III malocclusion. Materials and methods Computerized and manual searches were performed in Medline, Google Scholar, Cochrane Library, Embase, LILACS, SciELO, American Journal of Orthodontics and Dentofacial Orthopaedics, Angle Orthodontist, European Journal of Orthodontics, Journal of Orthodontics, Conference abstracts and Grey literature. No restrictions were set on language or date of publication. The search covered the starting date of the relevant databases until 30 April 2015. MeSH terms and free-text terms included ‘malocclusion’, ‘Angle class III’, ‘orthodontic appliances’, ‘functional’, facemask, review and meta-analysis. Screening of eligible studies, assessment of the methodological quality of the SRs and data extraction were conducted in duplicate and independently by two reviewers. Methodological quality was assessed using AMSTAR (assessment of multiple systematic reviews). Results A total of 222 studies were retrieved and after removal of duplicates, irrelevant studies, literature reviews and surgical approach treatments, 14 SRs and/or meta-analyses were included for qualitative synthesis. Mean AMSTAR score was 7.7/11 with a range of 3–10. There was evidence to demonstrate that face mask therapy can move the maxilla forward whilst causing a backward rotation of the mandible and increased facial height. There was also some evidence of mandibular growth retardation with chin cup therapy. Conclusions Orthopaedic appliances can improve a class III malocclusion in growing patients over the short-term; however, each appliance has a characteristic effect on the underlying skeletal pattern.
Thyroid function during critical illness

The metabolic support of the critically ill patient is a relatively new target of active research and little is as yet known about the effects of critical illness on metabolism. The nonthyroidal illness syndrome, also known as the low T3 syndrome or euthyroid sick syndrome, describes a condition characterized by abnormal thyroid function tests encountered in patients with acute or chronic systemic illnesses. The laboratory parameters of this syndrome include low serum levels of triiodothyronine (T3) and high levels of reverse T3, with normal or low levels of thyroxine (T4) and normal or low levels of thyroid-stimulating hormone (TSH). This condition may affect 60 to 70% of critically ill patients. The changes in serum thyroid hormone levels in the critically ill patient seem to result from alterations in the peripheral metabolism of the thyroid hormones, in TSH regulation, in the binding of thyroid hormone to transport-protein and in receptor binding and intracellular uptake. Medications also have a very important role in these alterations. Hormonal changes can be seen within the first hours of critical illness and, interestingly, these changes correlate with final outcome. Data on the beneficial effect of thyroid hormone treatment on outcome in critically ill patients are so far controversial. Thyroid function generally returns to normal as the acute illness resolves.
Endocrine determinants of haemostasis and thrombosis risk: Focus on thyroid hormone

This thesis explores endocrine determinants of the haemostatic system and thrombosis risk with main focus on thyroid hormone. It describes, in three parts, the effects of thyroid hormone on the haemostatic system, the effects of thyroid hormone (mimetics) on lipids and the effects of other hormones such as parathyroid hormone and prolactin on the haemostatic system and thrombosis risk. This thesis entails both studies on markers of coagulation and fibrinolysis as well as epidemiological studies on clinical endpoints (mainly venous thrombosis and bleeding). Besides, the evidence of the effect of thyroid hormone on the haemostatic system and on the risk of bleeding and venous thrombosis is reviewed. We aimed to elucidate the mechanism by which hyperthyroidism leads to a hypercoagulable state. We observed that the procoagulant effects observed in hyperthyroidism are mediated via the thyroid hormone receptor β (TRβ) which provides further insight into the pathophysiology of the increased risk of venous thrombosis in patients with hyperthyroidism. Based on these results, the question arises whether the use of TRβ-specific thyromimetics (e.g., eprotirome) could be associated with hypercoagulability. Some other findings described in this thesis regard the glucocorticoid receptor (GR) and the use of mineralocorticoid receptor antagonists. The polymorphism 23EK in the GR gene is associated with an increased risk of VTE which suggests that genetically determined cortisol sensitivity might be involved in the pathogenesis of venous thrombosis. Our systematic review and meta-analysis pointed out that mineralocorticoid receptor antagonists can be considered as safe regarding their effects on haemostasis.
Studying folktale diffusion needs unbiased dataset

Bortolini et al. (1) claim to infer patterns of folktale diffusion using genomic data. What is not said in their paper is that such a proposal is not new. For example, Korotayev and Khaltourina (2) showed statistical correlation between spatial distributions of mythological motifs and genetic markers, considerably above the 4,000 km proposed by Bortolini et al. (1). Such correlations allow us to reconstruct in detail the … [↵][1]1To whom correspondence should be addressed. Email: Julien.dHuy{at}malix.univ-paris1.fr. [1]: #xref-corresp-1-1
Feeding time can alleviate negative effects of heat stress on performance, meat quality and health status of turkey

ABSTRACT 1. A total of 180 one-day-old turkeys were randomly assigned to 6 equal groups to investigate the effect of feeding time on growth performance, carcass characteristics, meat quality, leg problems and physiological responses of growing turkeys under the high temperature conditions of summer. 2. Birds of the first group were ad libitum fed and were considered as the controls (C). The second group (T1) was given 80% of diet in the morning and 20% of diet in the afternoon, the third group (T2) was given 60% of diet in the morning and 40% of diet in the afternoon, the fourth group (T3) was given 40% of diet in the morning and 60% of diet in the afternoon, the fifth group (T4) was given 20% of diet in the morning and 80% of diet in the afternoon and the sixth group (T5) was given 100% of diet in the afternoon. 3. Body weight, body weight gain and feed conversion ratio were improved with T2, T3, T4 and T5 in comparison to control or T1 under heat stress conditions. No significant impacts on carcass traits and meat quality due to changing the time of feeding were seen, except for tenderness and juiciness. 4. Feeding in the afternoon (100%) decreased body temperature and tonic immobility test score, which were positively related with the health condition of the birds. 5. The incidence of leg problems, plumage condition and breast blisters were not significantly different among the experimental groups. 6. It is concluded that feeding turkeys mainly or totally in the afternoon (T4 and T5, birds were fed with 80% or 100% of the diet in the afternoon) can be used as a strategy and a managerial tool for improving growth rate, feed utilisation, carcass and meat quality, as well as health status of growing turkeys reared under hot climate conditions.
Investigating Factors Affecting Elderly's Intention to Use m-Health Services: An Empirical Study.

BACKGROUND m-Health as an important part of e-health has recently become one of the most influential initiative in healthcare sector all over the world. In developing countries healthcare service providers started to provide m-health services from the last few years. Despite the widespread acceptance of mobile phones, the adoption of m-health among elderly is significantly low in developing countries. However, little research has been conducted to explore factors influencing elderly's intention to use m-health services particularly in developing countries. The objective of this study is to identify the factors that influence the elderly's intention to use m-health services. MATERIALS AND METHODS To assess elderly's intention to use m-health services, this study applied the Unified Theory of Acceptance and Use of Technology (UTAUT). Data were collected from participants of age 60 years and above. The partial least square method based on structural equation modeling was used to analyze data. RESULTS The study found that performance expectancy, effort expectancy, social influence, and perceived credibility (p < 0.05) had significant influence on elderly's intention to use m-health services. However, facilitating condition (p > 0.05) had no significant influence on elderly's intention to use m-health services. CONCLUSIONS The findings of this study may become beneficial for the governments, policy makers, and healthcare service providers in developing countries.
Does Who I Am or How I Regulate Matter? Consequences of Manipulation of Emotion Regulation Strategies

This study experimentally examined the affective and social consequences of emotion regulation in men and women from young adulthood to old age. Participants were instructed to reappraise, suppress, or given no instructions while recalling a negative memory about their romantic relationship. Participants were 191 adults in a Trinidadian lifespan sample. Engaging in suppression resulted in higher relationship satisfaction, particularly for women, whereas engaging in reappraisal reduced negative affect for middle-aged versus younger adults. Reappraisal was, however, particularly consequential for young women who experienced higher levels of negative affect compared with men of the same age and older aged women. Regardless of instructions, older adults experienced higher relationship satisfaction, higher positive and lower negative affect than younger aged adults. Results are discussed considering the positivity effect for older adults, and how the current and historical climate of Trinidad influences the way women regulate their emotions.
Usefulness of phalangeal quantitative ultrasound in identifying reduced bone mineral status and increased fracture risk in adolescents with Turner syndrome

OBJECTIVE. Bone health is a major concern in patients with Turner syndrome (TS). There are few studies assessing bone mineral status in TS adolescents and none have reported a clear relationship with the risk of fracture. We assessed bone mineral status at three different skeletal sites by two different densitometric techniques in a group of TS adolescents. DESIGN. In 24 TS adolescents (17.1 ± 3.1 years) we evaluated lumbar and femoral volumetric bone mineral density (vBMD) with dual energy X-ray absorptiometry (DXA), amplitude-dependent speed of sound (AD-SoS) and bone transmission time (BTT) with phalangeal quantitative ultrasound (QUS). RESULTS. Mean lumbar vBMD Z-score was normal, while mean femoral vBMD, ADSoS and BTT Z-score were reduced. 8/24 (33.3%) and 13/24 (54.2%) girls had AD-SoS and BTT ≤-2 Z-score, respectively, while lumbar vBMD and femoral vBMD were ≤-2 Z-score only in 2/24 (8.4%) and 1/24 (4.2%) patients. Overall, we documented 15 fractures (three pathological) in 8 girls. Patients who reported at least one fracture had lower AD-SoS and BTT Z-score values than fracture-free girls. The presence of a value of BTT ≤-2.0 Z-score was associated with a significant OR of positive history of fracture of 11.67 (χ2 = 5.906, p =0.015, C.I. 95% 1.14–119.54). Lumbar and femoral vBMD were not related to fracture risk. CONCLUSIONS. TS adolescents may have impaired bone mineral status in skeletal sites with predominant cortical bone. Phalangeal QUS represents a useful method to identify subjects with increased fracture risk.
Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity

Unlike cytosolic processing and presentation of viral Ags by virus-infected cells, Ags first expressed in infected nonprofessional APCs, such as CD4+ T cells in the case of HIV, are taken up by dendritic cells and cross-presented. This generally requires entry through the endocytic pathway, where endosomal proteases have first access for processing. Thus, understanding virus escape during cross-presentation requires an understanding of resistance to endosomal proteases, such as cathepsin S (CatS). We have modified HIV-1MN gp120 by mutating a key CatS cleavage site (Thr322Thr323) in the V3 loop of the immunodominant epitope IGPGRAFYTT to IGPGRAFYVV to prevent digestion. We found this mutation to facilitate cross-presentation and provide evidence from MHC binding and X-ray crystallographic structural studies that this results from preservation of the epitope rather than an increased epitope affinity for the MHC class I molecule. In contrast, when the protein is expressed by a vaccinia virus in the cytosol, the wild-type protein is immunogenic without this mutation. These proof-of-concept results show that a virus like HIV, infecting predominantly nonprofessional presenting cells, can escape T cell recognition by incorporating a CatS cleavage site that leads to destruction of an immunodominant epitope when the Ag undergoes endosomal cross-presentation.
Combining Primed Photoconversion and UV-Photoactivation for Aberration-Free, Live-Cell Compliant Multi-Color Single-Molecule Localization Microscopy Imaging

Super-resolution fluorescence microscopy plays a major role in revealing the organization and dynamics of living cells. Nevertheless, single-molecule localization microscopy imaging of multiple targets is still limited by the availability of suitable fluorophore combinations. Here, we introduce a novel imaging strategy which combines primed photoconversion (PC) and UV-photoactivation for imaging different molecular species tagged by suitable fluorescent protein combinations. In this approach, the fluorescent proteins can be specifically photoactivated/-converted by different light wavelengths using PC and UV-activation modes but emit fluorescence in the same spectral emission channel. We demonstrate that this aberration-free, live-cell compatible imaging method can be applied to various targets in bacteria, yeast and mammalian cells and can be advantageously combined with correlative imaging schemes.
Increased primary autoimmune thyroid diseases and thyroid antibodies in sarcoidosis: evidence for an under-recognised extrathoracic involvement in sarcoidosis?

OBJECTIVE AND DESIGNSarcoidosis has been associated with thyroid diseases. However, until today no definite conclusions have been drawn. We aimed to assess the frequency of thyroid disorders and the levels of thyroid hormones and thyroid antibodies in 68 sarcoidosis patients and 75 controls. Additionally, we performed ultrasonography and fine-needle aspiration.RESULTSIn this prospective case control study conducted in the University Hospital of Larissa, Greece, overt thyroid disease was present in 29.4% of patients and 16.1% of patients presented clinical autoimmune thyroid disease. sarcoidosis patients had a significantly higher frequency of serological autoimmunity. Female patients had significantly increased frequency of positive TSH receptor antibodies (TRAbs) and antithyroid peroxidase antibodies (TPOAbs) when compared to gender-matched controls (40% vs 0%, p<0.001, and 28.8% vs 11.86%, p = 0.029, respectively). The hypoechoic pattern of the thyroid was more frequent in female patients vs controls (p<0.001). Male patients had a higher frequency of TRAbs and hypoechoic pattern of the thyroid gland (43.4% vs 0%, p = 0.002, and 39.1% vs 6.25%, p = 0.021, respectively). Indices of thyroid autoimmune disease were significantly more frequent in sarcoidosis patients vs gender-matched controls. Increased TPOAbs were significantly associated with clinical autoimmune disease in sarcoidosis.CONCLUSIONSOverall, the findings derived from this study suggest that thyroid disorders are frequent in sarcoidosis. This association may potentially be the result of increased thyroid antibodies.