Miracle-dz/UniFAR-FTUs huggingface dataset:
A method to apply bond‐angle constraints in molecular dynamics simulations

An algorithm to apply bond‐angle constraints in molecular dynamics simulations of macromolecules or molecular liquids is presented. It uses Cartesian coordinates and determines the Lagrange multipliers required for maintaining the constraints iteratively. It constitutes an alternative to the use of only distance constraints (DCs) between particles to maintain a particular geometry. DCs are unsuitable to maintain particular, for example, linear or flat, geometries of molecules. The proposed algorithm can easily handle bond‐length, bond‐angle, and dihedral‐angle constraints simultaneously, as when calculating a potential of mean force along a dihedral‐angle degree of freedom.
TALEN‐mediated generation of Nkx3.1 knockout rat model

Recent developments in gene editing, using transcriptional activator‐like effector nucleases (TALENs), have greatly helped the generation of genetically engineered animal models. The NK3 homeobox 1 (NKX3.1) protein plays important roles in prostate development and protein production, and functions as a tumor suppressor. Recently, NKX3.1 was shown to be associated with breast cancer in humans.
Academic Technologies for College Students With Intellectual Disability

Institutes of higher education have encountered an increase in enrollment of students with intellectual disability (ID). This increase is due, in part, to societal movements (e.g., inclusive participation in life activities) and federal legislation. There are potential benefits to both individuals with ID and society when students within this population complete college (e.g., earn certificates, a collection of completed courses and experiences, increased future employment opportunities). Nevertheless, there are barriers to college that students with ID need to overcome to have successful experiences, particularly in their academic or functional academic courses. This paper presents numerous instructional technologies grounded in behavior analytic strategies and Universal Design for Learning (UDL) that university faculty might implement in their courses and/or recommend to their students for studying to facilitate the learning of college students with ID and their classmates.
Transcatheter versus surgical aortic valve replacement in patients with chronic obstructive pulmonary disease

Abstract Objectives Although a number of studies compared mortality after transcatheter aortic valve implantation (TAVI) with that after surgical aortic replacement (SAVR) in patients with chronic obstructive pulmonary disease (COPD), no meta-analysis of them has been conducted to date. To determine whether TAVI or SAVR is associated with better postprocedural survival in patients with COPD, a meta-analysis of all studies currently available was performed. Design. To identify all comparative studies of TAVI with SAVR in patients with COPD, PubMed and Web of Science were searched through January 2020. Studies meeting the following criteria were included in the present meta-analysis: the design was an observational comparative study or a randomized controlled trial; the study population was patients with COPD; patients were assigned to TAVI versus SAVR; and outcomes included all-cause mortality. Adjusted (if unavailable, unadjusted) odds or hazard ratios with their confidence intervals (CIs) of mortality for TAVI versus SAVR were extracted from each study. Study-specific estimates were combined in the random-effects model. Results. Six eligible studies with a total of 4771 patients with COPD were identified and included in the present meta-analysis. The meta-analysis indicated significantly lower early (in-hospital or 30-day) mortality after TAVI than after SAVR (odds ratio, 0.69; 95% CI, 0.53–0.90; p = .006) but no significant difference in midterm (1-year to 5-year) mortality between TAVI and SAVR (hazard ratio, 1.07; 95% CI, 0.79–1.44; p = .68). Conclusions. In patients with COPD, TAVI was associated with reduced early mortality, while midterm mortality appeared similar, as compared with SAVR.
Precancerous Lesions and Liver Atrophy as Risk Factors for Hepatolithiasis-Related Death after Liver Resection for Hepatolithiasis

Background: Cholangiocarcinoma and secondary biliary cirrhosis can develop after liver resection for hepatolithiasis and are causes of hepatolithiasis-related death. We determined potential risk factors for hepatolithiasis-related death and subsequent cholangiocarcinoma, including precancerous lesions such as biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of the bile duct, in patients undergoing liver resection for hepatolithiasis. Methods: The study cohort included 62 patients who underwent liver resection for hepatolithiasis without concomitant cholangiocarcinoma and had surgical specimens available for pathological examination. Univariate and multivariate analyses were conducted to examine risk factors associated with subsequent cholangiocarcinoma after hepatolithiasis and hepatolithiasis-related death. In 28 patients with BilIN lesions, the specimens were immunohistochemically stained for γ-H2AX and S100P. Results: In the study cohort, the causes of death were subsequent cholangiocarcinoma, biliary cirrhosis, and other diseases in 5, 3, and 7 patients, respectively. Liver atrophy, precancerous lesions, postoperative repeated cholangitis, and jaundice for ≥1 week during the follow-up period were risk factors for hepatolithiasis-related death. Multivariate analysis showed that liver atrophy and precancerous lesions were independent risk factors for hepatolithiasis-related death. Liver atrophy or precancerous lesions were also risk factors for subsequent cholangiocarcinoma by univariate analysis. The positive expression of γ-H2AX and S100P was observed in 18 and 14 of the 28 BilIN lesions, respectively. Conclusions: Liver atrophy and precancerous lesions with malignant transformation were risk factors not only for subsequent cholangiocarcinoma but also hepatolithiasis-related death after liver resection for hepatolithiasis, indicating that long-term follow-up is necessary even after liver resection in patients harboring these risk factors.
Overconfidence in visual perception in Parkinson’s disease

Background Increased dependence on visual cues in Parkinson’s disease (PD) can unbalance the perception-action loop, impair multisensory integration, and affect everyday function of PD patients. It is currently unknown why PD patients seem to be more reliant on their visual cues. Objectives We hypothesized that PD patients may be overconfident in the reliability (precision) of their visual cues. In this study we tested coherent visual motion perception in PD, and probed subjective (self-reported) confidence in their visual motion perception. Methods 20 patients with idiopathic PD, 21 healthy aged-matched controls and 20 healthy young adult participants were presented with visual stimuli of moving dots (random dot kinematograms). They were asked to report: (1) whether the aggregate motion of dots was to the left or to the right, and (2) how confident they were that their perceptual discrimination was correct. Results Visual motion discrimination thresholds were similar (unimpaired) in PD compared to the other groups. By contrast, PD patients were significantly overconfident in their visual perceptual decisions (p=0.002 and p<0.001 vs. the age-matched and young adult groups, respectively). Conclusions These results suggest intact visual motion perception, but overestimation of visual cue reliability, in PD. Overconfidence in visual (vs. other, e.g., somatosensory) cues could underlie accounts of increased visual dependence and impaired multisensory integration in PD, and could contribute to gait and balance impairments. Future work should investigate PD confidence in somatosensory function. A better understanding of altered sensory reliance in PD might open up new avenues to treat debilitating symptoms.
Regulation Of Root Nutrient Transporters By CIPK23: "One Kinase To Rule Them All".

Protein kinases constitute essential regulatory components in the majority of cellular processes in eukaryotic cells. The CBL-INTERACTING PROTEIN KINASE (CIPK) family of plant protein kinases function in calcium (Ca2+)-related signaling pathways, and are therefore involved in the response to a wide variety of signals in plants. By covalently linking phosphate groups to their target proteins, CIPKs regulate the activity of downstream targets, their localization, their stability and their ability to interact with other proteins. In Arabidopsis, the CIPK23 kinase has emerged as a major hub driving root responses to diverse environmental stresses including drought, salinity and nutrient imbalances such as potassium, nitrate and iron deficiencies as well as ammonium, magnesium and non-iron metals toxicities. This review will chiefly report on the prominent roles of CIPK23 in the regulation of plant nutrient transporters and on the underlying molecular mechanisms. We will also discuss the different scenarios explaining how a single promiscuous kinase such as CIPK23 may convey specific responses to a myriad of signals.
The outcome of a preoperative one-minute sit-to-stand test is associated with ventilation time after cardiac surgery

Abstract Objectives. The One-minute Sit-To-Stand Test (STST) is a relatively novel physical performance test in the field of pulmonology. It measures the exercise tolerance of the patient. In this pilot study, we evaluated its predictive value for the postoperative course in cardiac surgery patients. Design. This was a prospective observational cohort study of patients undergoing elective aortic valve replacement. STST was applied in the patients, along with pulmonary function testing, a day prior to surgery, on postoperative day 7, and 3 months after surgery. A Short Form-36 health related quality of life survey (SF-36) was also included. The patients were divided into two groups according to the preoperative STST outcome: group A (≤20 repetitions, n = 12), and group B (>20 repetitions, n = 18). Results. We enrolled 30 patients in the study between May 2017 and May 2019. No complication were observed during the STST. The standard perioperative measures were identical for both groups. However, group A exhibited a significantly longer artificial ventilation time, as well as worse pulmonary function (VC, FVC, TLCO), on postoperative day 7. Concerning the SF-36, group A displayed a worse pre- and postoperative evaluation in both physical functioning and vitality. Conclusions. STST is a short and practical physical performance test that could enable a better prediction of the postoperative course after cardiac surgery. Patients with lower preoperative STST performance may require longer postoperative artificial ventilation, as they may present worse in some parameters of pulmonary functions and quality of life. However, these findings must be corroborated in larger studies.
A 3-min All-out Upper-body Ergometer Test For Competitive Swimmers

Abstract We examined the application of a land-based swimming ergometer 3-min all-out test to determine physiological predictors of swimming performance. Fourteen young elite swimmers participated (males: n=6; females: n=8). The swimmers completed two 3-min upper-body all-out tests on a swimming ergometer. Additionally, the swimmers completed freestyle swim races ranging from 50 m to 1500 m. High test-retest reproducibility (r=0.98 and coefficient of variation values <7.5%) was evident for ergometer derived peak, mean and critical power. Very strong correlations (r>0.87, p<0.001) were obtained between the 200-, 400-, 800- and 1500-m swimming performances and derived critical speed. Moreover, correlations were found between peak force and peak power and 50-m performance, in addition to critical power and performance for all distances. The critical speed was the dominant predictor of 200- to 1500-m performances (r=0.84−0.99). In conclusion, the land-based 3-min all-out swimming ergometer test is reliable and valid in predicting swimming performance in competitive swimmers and evaluates important physiological components in swimmers independent of technical abilities.
Poly(alizarin red S) modified glassy carbon electrode for square wave adsorptive stripping voltammetric determination of metronidazole in tablet formulation

Potentiodynamically fabricated poly(alizarin red s) modified GCE was characterized using CV and EIS techniques. In contrast to the cyclic voltammetric response of the unmodified GCE for metronidazole, an irreversible reduction peak with three-folds of current enhancement and reduced overpotential at the poly(alizarin red s) modified GCE showed the catalytic effect of the modifier towards reduction of metronidazole. While observed peak potential shift with increasing pH (4.0–10.0) indicated the involvement of protons during the reduction of metronidazole, peak potential shift with scan rate (20–300 mV s-1) confirmed the irreversibility of the reduction reaction of metronidazole at the modified GCE. A better correlation for the dependence of peak current on scan rate (r2 = 0.9883) than on square root of scan rate (r2 = 0.9740) supplemented by slope value of 0.38 for plot of log(current) versus log(scan rate) indicated the reduction reaction of metronidazole at the surface of the modified electrode was predominantly adsorption controlled. Under the optimized method and solution parameters, reductive current response of tablet sample showed linear dependence on spiked standard concentration in a wide range (0–125 μM) with excellent determination coefficient r2, LoD and LoQ of 0.9991, 0.38, and 1.25 μM, respectively. Spike recovery of 97.9% and interference recovery of 96.2–97.5% in the presence of 21.28 and 31.92 μM of uric acid and ascorbic acid validated the applicability of the present method for determination of metronidazole in tablet formulation. The metronidazole content of the tested tablet formulation using standard addition method was found to be 97.6% of what is claimed by the tablet manufacturer making the developed method an excellent potential candidate for its applicability to determine metronidazole in real samples with complex matrix.
Consumer Comprehension of the Nutrition Facts Label: A Comparison of the Original and Updated Labels

Purpose: Compare consumers’ overall label comprehension of the original Nutrition Facts (NF) label with the updated label. Design: Online survey conducted in 2019. Participants randomly assigned to original label, updated-single column, or updated-dual column labeling condition and asked to complete a series of label comprehension questions. Setting: Online survey; participants recruited through Prolific. Sample: N = 992 U.S. adults. Sample similar to U.S. population in terms of sex (49.2% female), race (73.3% White/Caucasian), and household size (mean = 2.7 members). However, sample was younger (median age: 29.0), more educated (98.8% high school graduate or higher), and exhibited a lower rate of obesity (22.6% obese) than the U.S. population. Measures: Dependent variables: objective (% correct) NF label comprehension. Independent variables: label condition, nutrition knowledge, and socio-demographic variables. Analysis: Regression analysis assessed relationships between label condition and label comprehension. Significance level of 5% used for analyses. Results: Average score for objective comprehension was 81.4%. The updates did not significantly improve label comprehension. Participants in the updated NF label conditions had trouble answering questions related to total and added sugars. Conclusions: Results suggest consumers may struggle to correctly utilize information on the updated NF label, specifically total and added sugars. Consumers may benefit from educational opportunities on using the new label.
Methicillin-resistant Staphylococcus aureus from infected skin lesions present several virulence genes and are associated with the CC30 in Brazilian children with atopic dermatitis

ABSTRACT Atopic dermatitis (AD) is a chronic inflammatory skin disease and colonization by Staphylococcus aureus may affect up to 100% of these patients. Virulent and resistant isolates can worsen AD patient clinical condition and jeopardize the treatment. We aimed to detect virulence genes and to evaluate the biofilm production of S. aureus isolates from infected skin lesions of children with AD. Methicillin resistance was detected by phenotypic and molecular tests and the virulence genes were detected by PCR. Biofilm formation was assessed by bacterial growing on microtiter plates and later stained with safranin. Genotyping was performed by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing. Among 106 AD patients, 55 (51.8%) had developed S. aureus cutaneous infections and 23 (41.6%) were methicillin-resistant (MRSA). All 55 isolates carried the fnbA, hla, icaA, sasG, and seu genes, and more than 70% presented cna, eap, ebpS, hlg, and pvl genes. Clonal complex (CC) 30 was the main lineage found (34.5%), especially among MRSA isolates (52.2%). The egc cluster and the bbp gene were significantly the most frequent in MRSA isolates and in USA1100/ST30/CC30 lineage. Most of the isolates (74.5%) were non-biofilm producers and many of them only started to produce it in the presence of fibrinogen. There was no significant association between S. aureus isolates features and the AD severity. This study demonstrated a high frequency of CC30 MRSA isolates presenting several virulence genes in infected skin lesions of AD children in Brazil, that may influence the severity of the disease and the treatments required.
Testosterone Replacement Therapy added to Intensive Lifestyle Intervention in Older Men with Obesity and Hypogonadism.

BACKGROUND Obesity and hypogonadism additively contribute to frailty in older men; however, appropriate treatment remains controversial. OBJECTIVE Determine whether testosterone replacement augments the effect of lifestyle therapy on physical function in older men with obesity and hypogonadism. DESIGN Randomized, double-blind, placebo-controlled trial. SETTING VA Medical Center. PARTICIPANTS Eight-three older (age≥65 years) men with obesity (BMI≥30 kg/m 2) and persistently low AM testosterone (<10.4 nmol/L) associated with frailty. INTERVENTIONS Participants were randomized to lifestyle therapy (weight management and exercise training) plus either testosterone (LT+Test) or placebo (LT+Pbo) for six months. OUTCOME MEASURES Primary outcome was change in Physical Performance Test (PPT) score. Secondary outcomes included other frailty measures, body composition, BMD, physical functions, hematocrit, PSA, and sex hormones. RESULTS PPT score increased similarly in LT+Test and LT+Pbo group (17% vs. 16%; P=.58). VO2peak increased more in LT+Test than LT+Pbo (23% vs. 16%; P=.03). Despite similar -9% weight loss, lean body mass and thigh muscle volume decreased less in LT+Test than LT+Pbo (-2% vs. -3 %; P=.01 and -2% vs -4%; P=04). Hip BMD was preserved in LT+Test compared with LT+Pbo (0.5% vs. -1.1%; P=.003). Strength increased similarly in LT+Test and LT+Pbo (23% vs. 22%; P=.94). Hematocrit but not PSA increased more in LT+Test than LT+Pbo (5% vs 1%; P<.001). Testosterone levels increased more in LT+Test than LT+Pbo (167% vs 27%; P<.001). CONCLUSION In older, obese hypogonadal men, adding testosterone for six months to lifestyle therapy does not further improve overall physical function. However, our findings suggest that testosterone may attenuate the weight loss-induced reduction in muscle mass and hip BMD and may further improve aerobic capacity.
The Role of the Axillary Artery as a Second Access Choice in TAVI Procedures

With transcatheter aortic valve implantation (TAVI) technology expanding its indications for low-risk patients, the number of TAVI-eligible patients will globally grow, requiring a better understanding about the second-best access choice. Regarding the potential access sites, the transfemoral retrograde route is recognized as the standard approach and first choice according to current guidelines. However, this approach is not suitable in up to 10-15% of patients, for whom an alternative non-femoral access is required. Among the alternative non-femoral routes, the transaxillary approach has received increasing recognition due to its proximity and relatively straight course from the axillary artery to the aortic annulus, which provides a more accurate device deployment. Here we discuss some particular aspects of the transaxillary access, either percutaneously performed or by cutdown dissection.
Analysis of the nonperfused volume ratio of adenomyosis from MRI images based on fewshot learning

The nonperfused volume (NPV) ratio is the key to the success of high intensity focused ultrasound (HIFU) ablation treatment of adenomyosis. However, there are no qualitative interpretation standards for predicting the NPV ratio of adenomyosis using magnetic resonance imaging (MRI) before HIFU ablation treatment, which leading to inter-reader variability. Convolutional neural networks (CNNs) have achieved state-of-the-art performance in the automatic disease diagnosis of MRI. Since the use of HIFU to treat adenomyosis is a novel treatment, there is not enough MRI data to support CNNs. We proposed a novel few-shot learning framework that extends CNNs to predict NPV ratio of HIFU ablation treatment for adenomyosis. We collected a dataset from 208 patients with adenomyosis who underwent MRI examination before and after HIFU treatment. Our proposed method was trained and evaluated by fourfold cross validation. This framework obtained sensitivity of 85.6%, 89.6% and 92.8% at 0.799, 0.980 and 1.180 FPs per patient. In the receiver operating characteristics analysis for NPV ratio of adenomyosis, our proposed method received the area under the curve of 0.8233, 0.8289, 0.8412, 0.8319, 0.7010, 0.7637, 0.8375, 0.8219, 0.8207, 0.9812 for the classifications of NPV ratio interval [0%–10%), [10%–20%), …, [90%–100%], respectively. The present study demonstrated that few-shot learning on NPV ratio prediction of HIFU ablation treatment for adenomyosis may contribute to the selection of eligible patients and the pre-judgment of clinical efficacy.
COMPARISON OF SHRINK‐SWELL POTENTIAL OF SEVEN ULTISOLS AND ONE ALFISOL USING TWO DEFFERENT COLE TECHNIQUES1

The coefficient of linear extensibility (COLE), used to estimate the shrink-swell hazard of natural soil fabric, requires that intact soil clods be collected when near saturation or be rewetted. Clods must be coated with saran, and significant laboratory equipment is needed to determine the clod shrinkage. A shrink-swell test is needed that can be used in a nonlaboratory setting to evaluate the shrink-swell potential of soils prior to the design of buildings, septic tank subsurface absorption systems (ST-SAS), and other structures. A technique for estimating COLE by extruding a soil paste in the shape of a rod (COLErod) and measuring shrinkage with drying is evaluated as an estimator for COLE determined with the standard technique COLEstd) for a group of Ultisols with a range of physical, chemical, and mineralogical properties. The COLE values of 39 discrete samples were determined by both techniques. The samples were collected from B and C horizons of eight soil types at multiple sites per soil type. COLErod is a highly significant estimator (r2 = 0.55, p < 0.001) of COLEstd. Variability is probably due to loss of soil fabric when determining COLErod, as well as limited precision with both techniques. COLErod agreed well with the similar linear shrinkage test (r2 = 0.96, p < 0.001), further suggesting that the COLErod methodology is acceptable.