Miracle-dz/UniFAR-FTUs huggingface dataset:
Consensus molecular subtype classification of colorectal adenomas

Consensus molecular subtyping is an RNA expression‐based classification system for colorectal cancer (CRC). Genomic alterations accumulate during CRC pathogenesis, including the premalignant adenoma stage, leading to changes in RNA expression. Only a minority of adenomas progress to malignancies, a transition that is associated with specific DNA copy number aberrations or microsatellite instability (MSI). We aimed to investigate whether colorectal adenomas can already be stratified into consensus molecular subtype (CMS) classes, and whether specific CMS classes are related to the presence of specific DNA copy number aberrations associated with progression to malignancy. RNA sequencing was performed on 62 adenomas and 59 CRCs. MSI status was determined with polymerase chain reaction‐based methodology. DNA copy number was assessed by low‐coverage DNA sequencing (n = 30) or array‐comparative genomic hybridisation (n = 32). Adenomas were classified into CMS classes together with CRCs from the study cohort and from The Cancer Genome Atlas (n = 556), by use of the established CMS classifier. As a result, 54 of 62 (87%) adenomas were classified according to the CMS. The CMS3 ‘metabolic subtype’, which was least common among CRCs, was most prevalent among adenomas (n = 45; 73%). One of the two adenomas showing MSI was classified as CMS1 (2%), the ‘MSI immune’ subtype. Eight adenomas (13%) were classified as the ‘canonical’ CMS2. No adenomas were classified as the ‘mesenchymal’ CMS4, consistent with the fact that adenomas lack invasion‐associated stroma. The distribution of the CMS classes among adenomas was confirmed in an independent series. CMS3 was enriched with adenomas at low risk of progressing to CRC, whereas relatively more high‐risk adenomas were observed in CMS2. We conclude that adenomas can be stratified into the CMS classes. Considering that CMS1 and CMS2 expression signatures may mark adenomas at increased risk of progression, the distribution of the CMS classes among adenomas is consistent with the proportion of adenomas expected to progress to CRC. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
The 2015/2016 El Niño Event in Context of the MERRA-2 Reanalysis: A Comparison of the Tropical Pacific with 1982/1983 and 1997/1998.

The 2015/2016 El Niño is analyzed using atmospheric/oceanic analysis produced using the Goddard Earth Observing System (GEOS) data assimilation systems. As well as describing the structure of the event, a theme of the work is to compare and contrast it with two other strong El Niños, in 1982/1983 and 1997/1998. These three El Niño events are included in the Modern-Era Retrospective analysis for Research and Applications (MERRA) and in the more recent MERRA-2 reanalyses. MERRA-2 allows a comparison of fields derived from the underlying GEOS model, facilitating a more detailed comparison of physical forcing mechanisms in the El Niño events. Various atmospheric/oceanic structures indicate that the 2015/2016 El Niño maximized in the Niño3. 4 region, with the large region of warming over most of the Pacific and Indian Ocean. The eastern tropical Indian Ocean, Maritime Continent, and western tropical Pacific are found to be less dry in boreal winter, compared to the earlier two strong events. While the 2015/2016 El Niño had an earlier occurrence of the equatorial Pacific warming and was the strongest event on record in the central Pacific, the 1997/1998 event exhibited a more rapid growth due to stronger westerly wind bursts and Madden-Julian Oscillation during spring, making it the strongest El Niño in the eastern Pacific. Compared to 1982/1983 and 1997/1998, the 2015/2016 event has a shallower thermocline over the eastern Pacific with a weaker zonal contrast of sub-surface water temperatures along the equatorial Pacific. While the three major ENSO events have similarities, each are unique when looking at the atmosphere and ocean surface and sub-surface.
IL (Interleukin)-10–STAT3–Galectin-3 Axis Is Essential for Osteopontin-Producing Reparative Macrophage Polarization After Myocardial Infarction

Background: Both osteopontin (OPN) and galectin-3 have been implicated in phagocytic clearance of dead cells and reparative fibrosis during wound healing. CD206+ macrophages are involved in tissue repair through phagocytosis and fibrosis after myocardial infarction (MI). However, the relationship among OPN, galectin-3, and macrophage polarization in the context of MI remains unclear. Methods: The time course of Spp1 (encoding OPN) expression in the heart after MI showed a strong activation of Spp1 on day 3 after MI. To identify where in the body and in which cells the transcriptional activity of Spp1 increased after MI, we analyzed EGFP (enhanced green fluorescent protein)-Spp1 knockin reporter mice on day 3 after MI. Results: The transcriptional activity of Spp1 increased only in CD206+ macrophages in the infarct myocardium, and most of CD206+ macrophages have strong transcriptional activation of Spp1 after MI. The temporal expression pattern of Lgal3 (encoding galectin-3) in cardiac macrophages after MI was similar to that of Spp1, and OPN is almost exclusively produced by galectin-3hiCD206+ macrophages. Although both interleukin (IL)–4 and IL-10 were reported to promote CD206+ macrophage-mediated cardiac repair after MI, IL-10– but not IL-4–stimulated CD11b+Ly6G− cells could differentiate into OPN-producing galectin-3hiCD206+ macrophages and showed enhanced phagocytic ability. Inhibition of STAT3 tyrosine phosphorylation suppressed IL-10–induced expression of intracellular galectin-3 and transcriptional activation of Spp1. Knockdown of galectin-3 suppressed their ability to differentiate into OPN-producing cells, but not STAT3 activation. The tyrosine phosphorylation of STAT3 and the appearance rate of galectin-3hiCD206+ cells on cardiac CD11b+Ly6G− cells in Spp1 knockout mice were the same as those in wild-type mice. Spp1 knockout mice showed vulnerability to developing post-MI left ventricular chamber dilatation and the terminal deoxynucleo-tidyltransferase 2‘-Deoxyuridine-5‘-triphosphate nick-end labeling (TUNEL)–positive cells in the infarcted myocardium after MI remained higher in number in Spp1 knockout mice than in wild-type mice. Conclusions: OPN is almost exclusively produced by galectin-3hiCD206+ macrophages, which specifically appear in the infarct myocardium after MI. The IL-10–STAT3–galectin-3 axis is essential for OPN-producing reparative macrophage polarization after myocardial infarction, and these macrophages contribute to tissue repair by promoting fibrosis and clearance of apoptotic cells. These results suggest that galectin-3 may contribute to reparative fibrosis in the infarct myocardium by controlling OPN levels.
Stimulation of the Prefrontal Cortex Reduces Intentions to Commit Aggression: A Randomized, Double-Blind, Placebo-Controlled, Stratified, Parallel-Group Trial

Although prefrontal brain impairments are one of the best-replicated brain imaging findings in relation to aggression, little is known about the causal role of this brain region. This study tests whether stimulating the dorsolateral prefrontal cortex using transcranial direct current stimulation (tDCS) reduces the likelihood of engaging in aggressive acts, and the mechanism underlying this relationship. In a double-blind, stratified, placebo-controlled, parallel-group, randomized trial, 81 human adults (36 males, 45 females) were randomly assigned to an active (N = 39) or placebo (N = 42) condition, and then followed up 1 d after the experiment session. Intentions to commit aggressive acts and behavioral aggression were assessed using hypothetical vignettes and a behavioral task, respectively. The secondary outcome was the perception of the moral wrongfulness of the aggressive acts. Compared with the sham controls, participants who received anodal stimulation reported being less likely to commit physical and sexual assault (p < 0.01). They also judged aggressive acts as more morally wrong (p < 0.05). Perceptions of greater moral wrongfulness regarding the aggressive acts accounted for 31% of the total effect of tDCS on intentions to commit aggression. Results provide experimental evidence that increasing activity in the prefrontal cortex can reduce intentions to commit aggression and enhance perceptions of the moral wrongfulness of the aggressive acts. Findings shed light on the biological underpinnings of aggression and theoretically have the potential to inform future interventions for aggression and violence. SIGNIFICANCE STATEMENT Aggressive behaviors pose significant public health risks. Understanding the etiology of aggression is paramount to violence reduction. Investigations of the neural basis of aggression have largely supported correlational, rather than causal, interpretations, and the mediating processes underlying the prefrontal–aggression relationship remain to be well elucidated. Through a double-blind, stratified, placebo-controlled, parallel-group, randomized trial, this study tested whether upregulation of the prefrontal cortex reduces the likelihood of engaging in aggression. Results provide experimental evidence that increasing prefrontal cortical activity can reduce intent to commit aggressive acts. They also shed light on moral judgment as one mechanism that may link prefrontal deficits to aggression and, in theory, have the potential to inform future approaches toward reducing aggression.
Comparison of Patient Food Intake, Satisfaction and Meal Quality Between Two Meal Service Styles in a Geriatric Inpatient Unit

Abstract This pilot study evaluated the introduction of a bistro evening meal service in a geriatric inpatient unit by comparing patient intake, satisfaction and meal quality of this new service to the usual central preplated service. Ten meals were observed under each condition (n = 30; mean age 79 years, 47% male). Data were collected on intake of each meal component (none, ¼, ½, ¾, all; converted to energy and protein using known food composition data), patient satisfaction with meals (meal flavor/taste, appearance, quality, staff demeanor; seven-point scale) and meal quality (sensory properties, temperature; five-point scale). Independent t-tests were used to compare energy and protein intakes between bistro and preplated services. There was no difference in mean energy or protein intake (energy: 2524 ± 927 kJ vs. 2692 ± 857 kJ, p = 0.612; protein: 29 ± 12 g vs. 27 ± 11 g, p = 0.699) patient satisfaction or meal quality between the bistro and preplated meal services. Patients were provided with fewer meal items during the bistro service, but ate a higher proportion of what was provided to them. Implementing a bistro service did not increase intake, satisfaction or meal quality in this study, suggesting that meal plating may be only one of many factors influencing intake and satisfaction of older inpatients.
Sword bean variants and different pretreatments influence protein extraction and protein properties

ABSTRACT Two variants of the sword bean (Canavalia gladiata), namely the white sword bean (WSB) and the red sword bean (RSB), are known. The MgCl2 concentration-dependent canavalin solubility showed different behavior among the extracts from distinct beans prepared by distinct pretreatments. Pretreatment and bean selection are important factors for use in food chemical and biochemical experiments.
Open Science Is Liberating and Can Foster Creativity

Some scholars think that Open Science practices constrain researchers in ways that reduce their creativity, arguing, for instance, that preregistration discourages data exploration and so stifles discovery. In this article, we argue the opposite: Open Science practices are liberating and can foster creativity. Open Science practices are liberating because they (a) enable us to explore data transparently and comfortably; (b) reward quality, which is under our control, rather than outcomes, which are not; and (c) reduce the choke hold of needing to find “positive” results for career advancement. Open Science practices can foster creativity because they cultivate an open and flexible mind-set, create a more collaborative and constructive climate, and generate more accurate information and make it more accessible. In sum, Open Science liberates researchers more than it constrains them.
Comparing disability between traumatic brain injury and spinal cord injury using the 12-item WHODAS 2.0 and the WHO minimal generic data set covering functioning and health

Objective: To compare disability between two patient groups using short validated tools based on International Classification of Functioning, Disability and Health (ICF). Design: Cross-sectional study. Setting: University hospital specialist outpatient clinic. Subjects: A total of 94 patients with traumatic brain injury and 59 with spinal cord injury. Main measures: Disability evaluated using self-reported and proxy 12-item WHODAS 2.0 (World Health Organization Disability Assessment Schedule), and physician-rated WHO minimal generic data set covering functioning and health. Results: The two measures used showed severe but very different disabilities in these patient groups. Disability was assessed worse by physicians in the spinal cord injury population (sum 15.8 vs. 12.7, P = 0.0001), whereas disability assessed by the patients did not differ significantly between the two groups (sum 18.4 vs. 21.2). Further analysis revealed that in patients with “high disability” (the minimal generic data set score ⩾15), self-reported functioning was more severely impaired in the traumatic brain injury group compared to the spinal cord injury group (29.7 vs. 21.4, P < 0.0001), with no difference between these two diagnostic groups in patients with “low disability” (the minimal generic data set below 15). Patients with traumatic brain injury perceived more difficulties in cognition, getting along and participation, patients with spinal cord injury in mobility and self-care. Conclusion: Both generic measures were able to detect severe disability but also to detect differences between two patient populations with different underlying diagnoses.
Extracellular Fluid Excess Is Significantly Associated With Coronary Artery Calcification in Patients With Chronic Kidney Disease

Background Extracellular fluid (ECF) excess is an independent predictor of cardiovascular morbidity in patients undergoing dialysis. This study aimed to investigate the relationship between ECF status, which is affected by renal function, and coronary artery calcification (CAC), which is a marker of cardiovascular disease, in patients with chronic kidney disease (CKD). Methods and Results A total of 1741 patients at all stages of pre‐dialysis CKD from the prospective observational cohort of CMERC‐HI (Cardiovascular and Metabolic Disease Etiology Research Center‐High Risk) were analyzed for the association between ECF status and CAC. ECF status was defined as extracellular water‐to‐total body water ratio (ECW/TBW) measured using bioelectrical impedance analysis. ECF excess was defined as ECW/TBW ≥0.390 or ≥0.400 depending on its severity. To define CAC, Agatston coronary artery calcium scores were measured. A total coronary artery calcium score of ≥400 was defined as CAC. The CKD stages were defined according to estimated glomerular filtration rate calculated using the CKD Epidemiology Collaboration equation. ECW/TBW and the proportion of ECF excess increased with progressing CKD stages. Multivariable logistic regression analyses showed that ECW/TBW was independently associated with CAC (per 0.01 increase of ECW/TBW, odds ratio 1.168, 95% confidence interval, 1.079–1.264, P<0.001). The adjusted R 2 for predicting higher coronary artery calcium scores and CAC significantly improved after ECW/TBW was added to conventional factors. This association was further confirmed by net reclassification and integrated discriminant improvements, sensitivity analysis, and subgroup analysis. Conclusions ECF status is independently associated with a high risk of CAC in patients with CKD. Study Registration URL: https://www.clinicaltrials. gov/. Unique identifier: NCT02003781.
Supplemental methionine sources have a neutral impact on oxidative status in broiler chickens

To determine the effect of different dietary Met sources on oxidative status, male Cobb 500 broiler chickens were fed from day of hatch to 26 days of age (d26) a diet deficient in sulfur amino acids (control) or a diet containing 0.22% DL-Met, 0.22% L-Met or 0.31% Met precursor, DL-2-hydroxy-4-(methylthio) butanoic acid (DL-HMTBA) to meet the Met + Cys requirements. Liver, breast muscle, duodenum, jejunum, and ileum were collected at day 10 (d10) and d26 to assay markers of oxidative stress, including total glutathione (TGSH), oxidized glutathione (GSSG), reduced glutathione (rGSH), protein carbonyls, thiobarbituric acid reactive substances (TBARS) and ferric reducing/antioxidant power (FRAP). In breast muscle, TGSH and rGSH were greater in L-Met and DL-HMTBA groups than in the control group (p < 0.05). An interaction of treatment and age was observed for TGSH in ileum (p = 0.01) and jejunum (p = 0.01), for GSSG in jejunum (p < 0.001), and for rGSH in ileum (p = 0.02). The ratios of rGSH to GSSG and GSSG to TGSH, which define oxidative status, were not affected by Met source. Protein carbonyls varied among groups in jejunum (p = 0.05) and breast muscle (p < 0.001), but were in the normal physiological range. No difference among treatment groups was observed for TBARS and FRAP in different tissues. Age effects were observed in all tissues for multiple oxidative stress markers. In conclusion, consuming different sources of supplementary Met did not alter the oxidative status in several tissues of broilers. Met + Cys deficiency did not compromise antioxidant capacity of chickens although growth was retarded.
Psychosocial Stress Over the Lifespan, Psychological Factors, and Cardiometabolic Risk in the Community

Objective The complex relationship between psychosocial stress over the lifetime, psychological factors, and cardiometabolic risk is still poorly understood. Accordingly, our aims were (1) to independently assess the associations between childhood adversity, life-event stress in remote (earlier than the last 5 years), and recent adulthood and cardiometabolic risk, and (2) to determine the role of psychological factors including personality, coping, and depression in these associations. Methods The sample included 2674 adults, aged 35 to 66 years, randomly selected from urban area. Participants underwent a physical examination including the assessment of obesity markers, blood pressure, and blood lipid and glucose levels. Stress during adulthood was determined using the severity scores of 52 stressful life events. Information on adverse childhood experiences and major depressive disorders was collected using semistructured interviews, whereas personality traits and coping mechanisms were evaluated through questionnaires. Results Both childhood adversity and stress in remote adulthood were associated with elevated body mass index (&bgr; [95% confidence interval {CI}] = 0.249 [0.029 to 0.468]; 0.020 [0.006 to 0.034]), waist circumference (&bgr; [95% CI] = 0.061 [0.024 to 0.099]; 0.08 [0.04 to 0.11]), and the global cardiometabolic risk score (&bgr; [95% CI] = 0.278 [0.017 to 0.540]; 0.017 [0.001 to 0.033]) after adjustment for sociodemographic, lifestyle, and psychological factors. In addition, childhood adversity was associated with low high density lipoprotein levels (&bgr; [95% CI] = −0.021 [−0.042 to 0.000]), as well as increased fat mass and systolic blood pressure levels (&bgr; [95% CI] = 0.506 [0.165 to 0.846]; 0.952 [0.165 to 1.740]) and stress in remote adulthood with apolipoprotein B levels (&bgr; [95% CI] = 0.607 [0.312 to 0.901]). Psychological factors did not account for these associations and were not effect modifiers. Conclusions Our data demonstrate that psychosocial stress during childhood and remote adulthood favor adiposity and abnormal lipid metabolism.
Accuracy (trueness and precision) of dental models fabricated using additive manufacturing methods.

OBJECTIVE This study evaluated the accuracy (trueness and precision) of dental models fabricated using additive manufacturing (AM) methods such as PolyJet and fused deposition modeling (FDM). MATERIALS AND METHODS 10 stone models were acquired for the control group by scanning a complete arch model. For the experimental groups, 10 PolyJet models and 10 FDM models were fabricated from digital impressions using an intraoral scanner. All 30 models were then scanned, and root mean square values were measured using three-dimensional (3D) analysis software. RESULTS Trueness did not significantly differ between the stone and PolyJet models. The precision of the AM models was significantly higher than that of the stone models. The layer thicknesses of the FDM models were greater than those of the PolyJet models. CONCLUSION The results of this study show that it might be possible for the dental models fabricated using additive manufacturing methods to be used in clinical settings.
Perinatal asphyxia in a rural Nigerian hospital: Incidence and determinants of early outcome.

BACKGROUND Perinatal asphyxia is an important cause of morbidity and mortality in the neonatal period, accounting for 20-30% of neonatal mortality. A substantial proportion (estimated at 26%) of the 1 million annual intrapartum stillbirths result from asphyxia. Probably higher than the mortality is the plethora of morbidity associated with asphyxia, especially long term neuro-developmental problems including cerebral palsy.The real burden of perinatal asphyxia is difficult to establish because of paucity of information from the rural communities where the majority of neonatal morbidity and deaths occur. Extended Apgar scores and HIE grade have been identified as predictive tools in prognosticating asphyxia, however HIE staging require a certain level of medical expertise which is not widely available. AIM To determine the incidence of asphyxia, the mortality rate and factors associated with mortality in Irrua Specialist Hospital. METHOD It was a descriptive, retrospective study of neonates admitted into the special care baby unit (SCBU) between October 2013 and September 2014 with diagnosis of perinatal asphyxia. Data was obtained from babies' and mother's case notes. The outcome was classified as survived or died. RESULTS Perinatal asphyxia accounted for 45 out of 347 (13%) of admissions within the review period. The mean gestational age and birth weight of the subjects were 39.2±2.2 weeks and 3020±520 grams respectively. The mortality rate was 31.1% and the factors significantly associated with mortality include lack of antenatal care and HIE stage III. CONCLUSION The burden of perinatal asphyxia in Irrua Specialist Hospital is comparable to figures from similar settings in the developing world. Lack of antenatal care and HIE stage III are associated with mortality. Continuous efforts should be made to improve the uptake of antenatal care and high risk pregnancies should be delivered in centres with facilities for neonatal care.