Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of abnormal microRNA expression in Helicobacter pylori associated gastric cancer

Abstract Epidemiological studies have shown that Helicobacter pylori (HP) infection is a risk factor for gastric cancer (GC). HP infection may induce the release of pro-inflammatory mediators, and abnormally increase the level of reactive oxygen species (ROS), nitric oxide (NO), and cytokines in mucosal epithelial cells of the stomach. However, the specific mechanism underlying the pathogenesis of HP-associated GC is still poorly understood. Recent studies have revealed that abnormal microRNA expression may affect the proliferation, differentiation, and apoptosis of mucosal epithelial cells of the stomach to further influence GC occurrence, development, and metastasis. Herein, we summarize the role of abnormal microRNAs in the regulation of HP-associated GC progression. Abnormal microRNA expression in HP-positive GC may be a biomarker for GC diagnosis, occurrence, and development as well as its targeted treatment and prognosis.
Comparisons of Clinical Features in Japanese Patients with Behçet’s Uveitis Treated in the 1990s and the 2000s

ABSTRACT Purpose: We investigated clinical characteristics of ocular Behçet’s disease (BD) patients treated in the 1990s and the 2000s. Methods: We retrospectively examined records of 68 newly arrived patients with ocular BD followed for more than 4 months during the 2000s and compared to those of 107 patients during the 1990s. Patient profiles, ocular and systemic symptoms, frequency of ocular attacks, BD ocular attack score 24–6 months (BOS24-6M), best-corrected visual acuity (BCVA), and immunomodulatory treatment were noted. Results: Clinical characteristics in the 2000s showed increases in iridocyclitis type, intestinal-, vasculo-, and neuro-BD cases, oral corticosteroid, methotrexate, and infliximab therapy usage, cataract and glaucoma surgery, and pseudophakia, and decreases in BOS24-6M and cyclophosphamide usage. BCVA of 20/30 or better at the final visit was slightly increased in the 2000s. Conclusions: Milder ocular BD tendency was seen in cases in the 2000s, whereas the incidence of special type of BD might be increasing.
Adjustment to vision loss in a mixed sample of adults with established visual impairment.

PURPOSE To determine factors associated with the level of adjustment to vision loss in a cross-sectional sample of adults with mixed visual impairment. METHODS One hundred participants were administered the Acceptance and Self-Worth Adjustment Scale (AS-WAS) to assess adjustment to vision loss. The severity of vision loss was determined using binocular clinical visual function assessments including visual acuity, contrast sensitivity, reading performance, and visual fields. Key demographics including age, duration of visual impairment, general health, education, and living arrangements were evaluated, as were self-reported vision-related activity limitation (VRAL), depression, social support, and personality. RESULTS Multivariate analysis showed that higher levels of depressive symptoms (β = -0.26, P < 0.01) and of the personality trait neuroticism (β = -0.33, P < 0.001), and lower levels of the personality trait of conscientiousness (β = 0.29, P < 0.01), were associated with poorer adjustment to vision loss, explaining 56% variance. CONCLUSIONS Adjustment to vision loss is significantly associated with depression and certain traits of personality (specifically neuroticism and conscientiousness), independent of the severity of vision loss, VRAL, and duration of vision loss. The results suggest certain individuals may be predisposed to exhibiting less adjustment to vision loss due to personality characteristics, and exhibit poorer adjustment owing to or as a consequence of depression, rather than due to other factors such as the onset and severity of visual impairment.
Effects of Short-Term In-Season Weightlifting Training on the Muscle Strength, Peak Power, Sprint Performance, and Ball-Throwing Velocity of Male Handball Players.

Hermassi, S, Schwesig, R, Aloui, G, Shephard, RJ, and Chelly, MS. Effects of short-term in-season weightlifting training on the muscle strength, peak power, sprint performance, and ball-throwing velocity of male handball players. J Strength Cond Res XX(X): 000-000, 2019-This study analyzed the effects of in-season weightlifting training, conducted biweekly for 12 weeks. Twenty-two male handball players were divided into experimental (age: 20.3 ± 0.5 years, height: 1.85 ± 0.04 m, and body mass: 86.3 ± 9.4 kg) and control (age: 20.1 ± 0.5 years, height: 1.81 ± 0.05 m, and body mass: 83.9 ± 10.3 kg) groups, and performance was assessed before and after the intervention. Peak power was determined by a cycle ergometer force-velocity test, a vertical squat jump, and a countermovement jump. Measures of 1 repetition maximal strength included bench press, back half-squats, snatch, and clean and jerk. Handball-throwing velocity was assessed by standing, running, and jump throws. The change of direction T-half test and sprint times over 5, 15, and 30 m were recorded by paired photocells. The intraclass correlation coefficient of all parameters exceeded 0.75. Significant training effects were seen for all sprint (3/3) and throwing (3/3) measures, but only 7/14 strength parameters and 3/10 jump parameters. The largest increases of performance were for snatch (η = 0.627; d = 2.85) and 15-m sprinting (η = 0.852; d = 2.73). Countermovement jump force showed a negative response (d = -0.62). Three other parameters (V0 power for the upper and lower limbs, countermovement jump power) showed only small effect sizes (d = 0.45, d = 0.31, and d = 0.23, respectively). We conclude that 12 weeks of biweekly in-season weight training improved the peak power, maximal strength, sprinting, and throwing in handball players, but that their jump performance did not increase with this kind of intervention.
Endometriosis and nuclear receptors.

BACKGROUND Endometriosis is recognized as a steroid-dependent disorder; however, the precise roles of nuclear receptors (NRs) in steroid responsiveness and other signaling pathways are not well understood. OBJECTIVE AND RATIONALE Over the past several years, a number of paradigm-shifting breakthroughs have occurred in the area of NRs in endometriosis. We review and clarify new information regarding the mechanisms responsible for: (i) excessive estrogen biosynthesis, (ii) estrogen-dependent inflammation, (iii) defective differentiation due to progesterone resistance and (iv) enhanced survival due to deficient retinoid production and action in endometriosis. We emphasize the roles of the relevant NRs critical for these pathological processes in endometriosis. SEARCH METHODS We conducted a comprehensive search using PubMed for human, animal and cellular studies published until 2018 in the following areas: endometriosis; the steroid and orphan NRs, estrogen receptors alpha (ESR1) and beta (ESR2), progesterone receptor (PGR), steroidogenic factor-1 (NR5A1) and chicken ovalbumin upstream promoter-transcription factor II (NR2F2); and retinoids. OUTCOMES Four distinct abnormalities in the intracavitary endometrium and extra-uterine endometriotic tissue underlie endometriosis progression: dysregulated differentiation of endometrial mesenchymal cells, abnormal epigenetic marks, inflammation activated by excess estrogen and the development of progesterone resistance. Endometriotic stromal cells compose the bulk of the lesions and demonstrate widespread epigenetic abnormalities. Endometriotic stromal cells also display a wide range of abnormal NR expression. The orphan NRs NR5A1 and NR2F2 compete to regulate steroid-synthesizing genes in endometriotic stromal cells; NR5A1 dominance gives rise to excessive estrogen formation. Endometriotic stromal cells show an abnormally low ESR1:ESR2 ratio due to excessive levels of ESR2, which mediates an estrogen-driven inflammatory process and prostaglandin formation. These cells are also deficient in PGR, leading to progesterone resistance and defective retinoid synthesis. The pattern of NR expression, involving low ESR1 and PGR and high ESR2, is reminiscent of uterine leiomyoma stem cells. This led us to speculate that endometriotic stromal cells may display stem cell characteristics found in other uterine tissues. The biologic consequences of these abnormalities in endometriotic tissue include intense inflammation, defective differentiation and enhanced survival. WIDER IMPLICATIONS Steroid- and other NR-related abnormalities exert genome-wide biologic effects via interaction with defective epigenetic programming and enhance inflammation in endometriotic stromal cells. New synthetic ligands, targeting PGR, retinoic acid receptors and ESR2, may offer novel treatment options.
Spermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies

Abstract The aim of this study was to investigate the spermine effect on the thermal denaturation, conformation and activity of elastase at three temperatures of 303, 313 and 323 K in the Tris buffer, at pH 8.5, using UV–vis spectrophotometry, spectrofluorometry and circular dichroism as well as molecular docking and molecular simulation. The increased absorption of elastase in the presence of spermine suggested a change in the environment of tryptophan. It was found that under the influence of spermine, the emission intensity of elastase extremely was reduced, and the use of the Stern-Volmer equation showed that some static quenching had occurred. The thermodynamic parameters values (enthalpy and entropy) and the molecular docking technique also revealed that van der Waals forces or hydrogen bonding interactions played an important role in the binding process. The spermine–elastase complex formation led to increasing the value of the catalytic constant (kcat). So it could be considered as an activator. Slight changes were observed in the second structure of elastase (1.06% increase for the α-helix and 0.048% decrease the β-sheet) and the thermal stability effect. Molecular docking results also demonstrated that spermine could bind to porcine pancreatic elastase, and van der Waals forces or hydrogen bonding interactions played the major role in the binding process. Overall, our results showed that spermine could induce structural alterations in elastase, acting as a partial stabilizer and an activator for the enzyme. Communicated by Ramaswamy H. Sarma
Thoracolumbar Fusion in Extreme Obesity: Complications and Patient-Reported Outcomes

ABSTRACT Background: Extreme obesity (class III) is defined by the Centers for Disease Control as a body mass index (BMI) value ≥40. Recent studies suggest that obese patients have poor outcomes after thoracolumbar spinal fusions. The objective of this study was to analyze 30-day adverse events and patient-reported outcomes (PROs) for this population. Patients and Methods: A retrospective chart review of spinal fusion surgeries performed at a single institution from 2006 to 2016 was executed. All patients had a preoperative BMI ≥40. Patient characteristics, including age, sex, BMI, American Society of Anesthesiologists (ASA) score, Charlson Comorbidity Index (CCI), and others, were collected. Thirty-day adverse events (complications, readmissions, reoperations, and mortality) and PROs (Oswestry Disability Index [ODI] and visual analog scale [VAS]) were recorded. Results: Fifty-six patients were identified, including 30 men (54%). Mean age was 55.7 years (range, 31–74 years). Mean BMI was 44.2 (range, 40.0–54.7). Mean ASA was 2.7 (range, 2–3), and mean CCI was 1.1 (range, 0–6). Mean number of fused levels was 2.3 (range, 1–14). Mean length of stay was 4.4 ± 2.1 days. Mean number of complications was 0.7 ± 1.1, with 30.4% of patients having had at least 1 complication. The 30-day all-cause readmission rate was 5.4%, and 30-day reoperation rate was 3.6%. For 30 patients (54%) with 1-year PROs, mean preoperative ODI was 65.2 ± 11.1, and mean preoperative VAS was 6.6 ± 1.6. Mean ODI change was −19.9 ± 20.1 (P < .001), and mean VAS change was −2.6 ± 2.3 (P < .001). A total of 15 patients (50%) achieved the minimum clinically important difference in ODI (12.8), with a mean follow-up of 18.9 months. Conclusions: Patients with extreme obesity who undergo thoracolumbar fusion have acceptable 30-day adverse events and potentially can achieve significant improvement in pain and disability.
Most gene fusions in cancer are stochastic events

Cancer‐associated gene fusions resulting in chimeric proteins or aberrant expression of one or both partner genes are pathogenetically and clinically important in several hematologic malignancies and solid tumors. Since the advent of different types of massively parallel sequencing (MPS), the number of identified gene fusions has increased dramatically, prompting the question whether they all have a biologic impact. By ascertaining the chromosomal locations of 8934 genes involved in 10 861 gene fusions reported in the literature, we here show that there is a highly significant association between gene content of chromosomes and chromosome bands and number of genes involved in fusions. This strongly suggests that a clear majority of gene fusions detected by MPS are stochastic events associated with the number of genes available to participate in fusions and that most reported gene fusions are passengers without any pathogenetic importance.
A Large-Scale Query Spelling Correction Corpus

We present a new large-scale collection of 54,772 queries with manually annotated spelling corrections. For 9,170 of the queries (16.74%), spelling variants that are different to the original query are proposed. With its size, our new corpus is an order of magnitude larger than other publicly available query spelling corpora. In addition to releasing the new large-scale corpus, we also provide an implementation of the winner of the Microsoft Speller Challenge from~2011 and compare it on the different publicly available corpora to spelling corrections mined from Google and Bing. This way, we also shed some light on the spelling correction performance of state-of-the-art commercial search systems.
Feasibility of single-cell analysis of model cancer and foetal cells in blood after isolation by cell picking

The objective of the present feasibility study was to transfer single cell line cells to either microscopy slides for downstream immune characterization or to polymerase chain reaction tubes for downstream DNA quantitation. Tumour cell lines, SKBR3 and MCF7 and trophoblast cell line JEG-3 were spiked in healthy donor blood. The CytoTrack system was used to scan the spiked blood samples to identify target cells. Individual target cells were identified, picked by use of a CytoPicker and deposited to either a microscopic slide or a polymerase chain reaction tube (PCR). Single tumour cells on microscopic slides were further immunostained with human epidermal growth factor receptor 2 (Her2) and epithelial cell adhesion molecule (EpCAM). From the picked cells in polymerase chain reaction tubes, DNA was amplified, quantified and used for Short Tandem Repeat genotyping. Depositing rare cells to microscopy slides was laborious with only five cells per hour. In this study with a trained operator, the picked cells had an 80.5% recovery rate. Depositing single trophoblast cells in PCR tubes was a faster process with 10 cells in 5 min. Immunostaining of isolated cells by both Her2 and EpCAM was possible but showed varying staining intensity. Presence of trophoblasts and contaminating white blood cells in PCR tubes after cell picking was confirmed based on DNA yield and mixed Short Tandem Repeat profiles in five out of eight samples. Using the CytoPicker tool, single tumour and trophoblast cells were successfully isolated and moved from blood samples, allowing subsequent immunostaining or Short Tandem Repeat genotyping.
Reduction of bacterial resistance with inhaled antibiotics in the intensive care unit.

RATIONALE Multidrug-resistant organisms (MDRO) are the dominant airway pathogens in the intensive care unit (ICU) and present a major treatment challenge to intensivists. Aerosolized antibiotics (AA) result in airway concentrations of drug 100-fold greater than the minimal inhibitory concentration of most bacteria including MDRO. These levels, without systemic toxicity, may eradicate MDRO and reduce the pressure for selection of new resistant organisms. OBJECTIVES To determine if AA effectively eradicate MDRO in the intubated patient without promoting new resistance. METHODS In a double-blind placebo-controlled study, critically ill intubated patients were randomized if they exhibited signs of respiratory infection (purulent secretions and Clinical Pulmonary Infection Score ≥6). Using a well-characterized aerosol delivery system, AA or saline placebo was given for 14 days or until extubation. The responsible clinician determined administration of systemic antibiotics for ventilator-associated pneumonia and any other infection. MEASUREMENTS AND MAIN RESULTS AA eradicated 26 of 27 organisms present at randomization compared with 2 of 23 organisms with placebo (P < 0.0001). AA eradicated the original resistant organism on culture and Gram stain at end of treatment in 14 out of 16 patients compared with 1 of 11 for placebo (P < 0.001). New drug resistance to AA was not seen. Compared with AA, resistance to systemic antibiotics significantly increased in placebo patients (P = 0.03). Compared with placebo, AA significantly reduced Clinical Pulmonary Infection Score (mean ± SEM, 9.3 ± 2.7 to 5.3 ± 2.6 vs. 8.0 ± 23 to 8.6 ± 2.10; P = 0.0008). CONCLUSIONS In chronically intubated critically ill patients, AA successfully eradicated existing MDRO organisms and reduced the pressure from systemic agents for new respiratory resistance. Clinical trial registered with www.clinicaltrials. gov (NCT 01878643).
Peritoneal dialysis as therapeutic option in heart failure patients

Each episode of acute decompensated heart failure (HF) incrementally adds to mortality. Peritoneal dialysis (PD) offers an alternative therapeutic option in refractory HF and reduces the incidence of decompensation episodes. The objective of this study was to determine the efficacy of PD, in terms of functional status, surrogate endpoints, rate of hospitalizations, and mortality.
Young and Older Adults May Utilize Different Cognitive Abilities When Performing a Spatial Recognition Memory Test With Varying Levels of Similarity

We used signal detection theory to evaluate spatial recognition memory utilizing a behavioral test hypothesized to tax pattern separation. Correlations with standardized neuropsychological tests also were examined. Healthy young (n = 40) and older (n = 30) adults completed a spatial recognition memory test involving high- and low-similarity conditions. Using d’ as the dependent variable, we found that older adults were significantly impaired relative to young adults on the high- and low-similarity conditions (ps < .05). Both groups performed significantly better in the low-similarity condition compared to the high-similarity condition (p < .05), with young adults exhibiting greater improvement relative to older adults. We also found that young adults may rely on spatial attention abilities when performing our test, while older adults might rely on memory and executive function abilities. These findings indicate that young and older adults may utilize different cognitive abilities when performing certain spatial memory tests.
Setting Policy Priorities for Front-of-Pack Health Claims and Symbols in the European Union: Expert Consensus Built by Using a Delphi Method

Despite the fact that front-of-pack nutrition labels such as health claims and symbols have received growing attention in consumer behavior research, comprehensive conclusions could not yet be drawn to develop concrete policy actions, owing to the complexity of the subject and a constantly changing market environment. In this study, evidence-based policy recommendations and communication guidelines have been derived from the findings of the EU FP7 project CLYMBOL (“Role of health-related CLaims and sYMBOLs in consumer behavior”, Grant Agreement 311963), and have been evaluated and prioritized by European stakeholders using a three-round Delphi method. A moderate level of consensus was achieved and results suggest that policy priority should focus on ways to improve consumer motivation and interest in healthy eating. Consumers’ interest in healthy eating could be increased by adopting appropriate communication strategies such as using innovative ways to communicate the importance of healthy eating, which may aim to change the possible negative association between healthiness and tastiness. The highest-rated finding was related to consumers’ favorable attitude towards health claims with shorter and less complex messages and health symbols with a visible endorsement. Meanwhile, there was a clear consensus that health claims need to be scientifically substantiated and credible but phrased without using overly complex scientific wordings, in order to be meaningful for consumers. Furthermore, stakeholders from academia and industry believe that consumer awareness about existing health claims should be increased. The identified policy recommendations and communication guidelines stem from recent empirical evidence and provide useful insights that guide future policy development aligning consumer protection issues as well as public health and food marketing communication interests.
Differential DNA Methylation of MicroRNA Genes in Temporal Cortex from Alzheimer's Disease Individuals

This study investigated for the first time the genomewide DNA methylation changes of noncoding RNA genes in the temporal cortex samples from individuals with Alzheimer's disease (AD). The methylome of 10 AD individuals and 10 age-matched controls were obtained using Illumina 450 K methylation array. A total of 2,095 among the 15,258 interrogated noncoding RNA CpG sites presented differential methylation, 161 of which were associated with miRNA genes. In particular, 10 miRNA CpG sites that were found to be hypermethylated in AD compared to control brains represent transcripts that have been previously associated with the disease. This miRNA set is predicted to target 33 coding genes from the neuregulin receptor complex (ErbB) signaling pathway, which is required for the neurons myelination process. For 6 of these miRNA genes (MIR9-1, MIR9-3, MIR181C, MIR124-1, MIR146B, and MIR451), the hypermethylation pattern is in agreement with previous results from literature that shows downregulation of miR-9, miR-181c, miR-124, miR-146b, and miR-451 in the AD brain. Our data implicate dysregulation of miRNA methylation as contributor to the pathogenesis of AD.
The pluripotency factor NANOG controls primitive hematopoiesis and directly regulates Tal1

Progenitors of the first hematopoietic cells in the mouse arise in the early embryo from Brachyury‐positive multipotent cells in the posterior‐proximal region of the epiblast, but the mechanisms that specify primitive blood cells are still largely unknown. Pluripotency factors maintain uncommitted cells of the blastocyst and embryonic stem cells in the pluripotent state. However, little is known about the role played by these factors during later development, despite being expressed in the postimplantation epiblast. Using a dual transgene system for controlled expression at postimplantation stages, we found that Nanog blocks primitive hematopoiesis in the gastrulating embryo, resulting in a loss of red blood cells and downregulation of erythropoietic genes. Accordingly, Nanog‐deficient embryonic stem cells are prone to erythropoietic differentiation. Moreover, Nanog expression in adults prevents the maturation of erythroid cells. By analysis of previous data for NANOG binding during stem cell differentiation and CRISPR/Cas9 genome editing, we found that Tal1 is a direct NANOG target. Our results show that Nanog regulates primitive hematopoiesis by directly repressing critical erythroid lineage specifiers.