Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting RNA SHAPE scores with deep learning

ABSTRACT Secondary structure prediction approaches rely typically on models of equilibrium free energies that are themselves based on in vitro physical chemistry. Recent transcriptome-wide experiments of in vivo RNA structure based on SHAPE-MaP experiments provide important information that may make it possible to extend current in vitro-based RNA folding models in order to improve the accuracy of computational RNA folding simulations with respect to the experimentally measured in vivo RNA secondary structure. Here we present a machine learning approach that utilizes RNA secondary structure prediction results and nucleotide sequence in order to predict in vivo SHAPE scores. We show that this approach has a higher Pearson correlation coefficient with experimental SHAPE scores than thermodynamic folding. This could be an important step towards augmenting experimental results with computational predictions and help with RNA secondary structure predictions that inherently take in-vivo folding properties into account.
Feasibility and Effects of a Supervised Exercise Program Suitable for Independent Training at Home on Physical Function and Quality of Life in Head and Neck Cancer Patients: A Pilot Study

Introduction: Head and neck cancer patients often suffer from physical and cognitive impairments after cancer treatment. During rehabilitation, exercise therapy can improve physical function and quality of life (QoL). Surveys demonstrated patients’ preference for home training with low- to moderate-intensity. This study was conducted in order to develope a suitable home-based training program. Therefore, the feasibility and effects of a low- to moderate-intensity exercise intervention on physical functions and QoL were evaluated. Methods: Training was conducted as supervised group training and consisted of mobilization, coordination, resistance, stretching, and relaxation exercises. The intervention lasted 12 weeks with 2 training sessions per week. Feasibility, attendance rate, physical function (eg, range of motion, 6-minute walk test [6MWT]), and QoL (eg, EORTC QLQ-30) were analyzed. Results: Ten out of 12 participants completed the intervention (83%) with an average attendance rate of 83%. Participants showed significant improvements in selected physical functions. For example, head rotation increased by 11.2° (P = .042), walking distance in the 6MWT increased by an average of 43.3 m (P = .010), and the global QoL scale improved by 8.2 points (P = .059). Additionally, there were positive changes in the physical function scale (P = .008), cognitive function scale (P = .015), and social function scale (P = .031) of the EORTC QLQ-30. Conclusion: Data indicate that the exercise program was feasible and had positive effects on physical function and QoL. Future research will analyze the effects of a home-based exercise program on physical function and QoL in a large-scale study.
The copy-number and varied strengths of MELT motifs in Spc105 balance the strength and responsiveness of the spindle assembly checkpoint

The Spindle Assembly Checkpoint (SAC) maintains genome stability while enabling timely anaphase onset. To maintain genome stability, the SAC must be strong so that it delays cell division even if one chromosome is unattached, but for timely anaphase onset, it must be responsive to silencing mechanisms. How it meets these potentially antagonistic requirements is unclear. Here we show that the balance between SAC strength and responsiveness is determined by the number of ‘MELT’ motifs in the kinetochore protein Spc105/KNL1 and their Bub3-Bub1 binding affinities. Spc105/KNL1 must contain many strong MELT motifs to prevent chromosome missegregation, but not too many, because this delays SAC silencing and anaphase onset. We demonstrate this by constructing a Spc105 variant that trades SAC responsiveness for significantly improved chromosome segregation accuracy. We propose that the necessity of balancing SAC strength with responsiveness drives the evolutionary trend of MELT motif number amplification and degeneration of their functionally optimal amino acid sequence.
Effect of Sodium Bicarbonate and of Roughage on Milk Yield and Milk Composition of Goats and on Rumen Fermentation of Sheep

Abstract Forty Damascus dairy goats and 12 Chios wether were used to assess effects of sodium bicarbonate and roughage on milk yield and milk composition of Damascus goats and rumen fermentation and apparent digestion coefficients of Chios wether sheep. Addition of sodium bicarbonate increased apparent digestibility coefficients of dry matter, organic matter, gross energy, and of crude fiber on low roughage diet only. Wethers on diets supplemented with sodium bicarbonate gave higher urinary sodium output. Water intake was correlated . 62 with volume of urine, . 58 with urinary sodium output, and . 61 with dry matter intake. Roughage was more efficient than bicarbonate in elevating rumen pH, isovalerate, and acetate molar proportions. Sodium bicarbonate increased acetate and reduced propionate molar proportion. There were no significant differences among diets in rumen ammonia nitrogen concentration. High roughage decreased live-weight gain. Neither bicarbonate nor roughage had significant effect on conversion efficiencies of dry matter to milk and fat-corrected milk. The sodium bicarbonate diet proved acceptable to the animals. Absolute and fat-corrected milk yields were not affected, but the bicarbonate diet caused an increase in fat content and total solids content of milk.
Forest Fragmentation Alters the Population Dynamics of a Late‐successional Tropical Tree

Tropical late‐successional tree species are at high risk of local extinction due to habitat loss and fragmentation. Population‐growth rates in fragmented populations are predicted to decline as a result of reduced fecundity, survival and growth. We examined the demographic effects of habitat fragmentation by comparing the population dynamics of the late‐successional tree Poulsenia armata (Moraceae) in southern Mexico between a continuous forest and several forest fragments using integral projection models (IPMs) during 2010–2012. Forest fragmentation did not lead to differences in population density and even resulted in a higher population‐growth rate (λ) in fragments compared to continuous forests. Habitat fragmentation had drastic effects on the dynamics of P. armata, causing the population structure to shift toward smaller sizes. Fragmented populations experienced a significant decrease in juvenile survival and growth compared to unaltered populations. Adult survival and growth made the greatest relative contributions to λ in both habitat types during 2011–2012. However, the relative importance of juvenile survival and growth to λ was highest in the fragmented forest in 2010–2011. Our Life Table Response Experiment analysis revealed that positive contributions of adult fecundity explained most of the variation of λ between both habitats and annual periods. Finally, P. armata has a relatively slow speed of recovery after disturbances, compromising persistence of fragmented populations. Developing a mechanistic understanding of how forest fragmentation affects plant population dynamics, as done here, will prove essential for the preservation of natural areas.
Safety, tolerability and efficacy of LEGA-Kid® mechanical percussion device versus conventional chest physiotherapy in children: a randomised, single-blind controlled study.

INTRODUCTION Chest physiotherapy (CPT) may benefit children aged < 5 years who suffer from lower respiratory tract infection (LRTI). However, its effects are technique-dependent. This study aimed to determine whether mechanical CPT using the LEGA-Kid® mechanical percussion device is superior to manual CPT in children with LRTI. METHODS Children aged 5 months to 5 years who were admitted and referred for CPT from January to April 2017 were randomised to either manual CPT or mechanical CPT with LEGA-Kid®. Outcomes measured at pre-intervention and 2 hours post-intervention were respiratory rate (RR), oxygen saturation and modified Respiratory Distress Assessment Instrument (mRDAI) score. RESULTS All 30 enrolled patients had significant reduction in post-intervention RR and mRDAI scores. There was an 8% reduction in RR for the manual CPT group (p = 0.002) and a 16.5% reduction in the mechanical CPT group (p = 0.0001), with a significantly greater reduction in the latter (p = 0.024). mRDAI scores decreased by 2.96 in the manual group (p = 0.0001) and 3.62 in the mechanical group (p = 0.002), with no significant difference between the groups. There was no significant improvement in oxygen saturation, and no adverse events were observed after CPT. CONCLUSION Children receiving either manual or mechanical CPT showed improvements in respiratory distress symptoms with no adverse effects. A combined strategy of nebulised hypertonic saline followed by CPT for LRTI removes airway secretions and results in improvements of moderately severe respiratory distress. The LEGA-Kid mechanical CPT method was superior in reducing RR.
Endometrial α-2 Macroglobulin; Localization by in Situ Hybridization and Effect on Mouse Embryo Development in Vitro

α-2 macroglobulin (A2M) is a 718,000-kDa broad spectrum plasma protease inhibitor whose production by the human endometrium was recently reported. The multifunctional A2M receptor, also known as low-density lipoprotein receptor-related protein, was also recently immunolocalized to the endometrial stroma. The objective of this study was to further characterize the endometrial site of expression of A2M, and to study its effects on mouse embryo development in vitro, to gain some insight into the functional significance of its endometrial production. Formalin-fixed, paraffin-embedded human endometrium from hysterectomy and endometrial biopsy specimen was used for in situ hybridization analysis, with 35S-labeled riboprobes representing subcloned A2M complementary DNA (cDNA) fragments. Duplicate sections of human endometrium were hybridized with sense and antisense probe and coated with photographic emulsion. Resultant autoradiograms were analyzed qualitatively by light- and darkfield microscopy and quantitativ.
Obesity and hypoalbuminaemia are independent risk factors for readmission and reoperation following primary total knee arthroplasty.

AIMS Rates of readmission and reoperation following primary total knee arthroplasty (TKA) are under scrutiny due to new payment models, which penalize these negative outcomes. Some risk factors are more modifiable than others, and some conditions considered modifiable such as obesity may not be as modifiable in the setting of advanced arthritis as many propose. We sought to determine whether controlling for hypoalbuminaemia would mitigate the effect that prior authors had identified in patients with obesity. METHODS We reviewed the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database for the period of January 2008 to December 2016 to evaluate the rates of reoperation and readmission within 30 days following primary TKA. Multivariate logistic regression modelling controlled for preoperative albumin, age, sex, and comorbidity status. RESULTS Readmission rates only differed significantly between patients with Normal Weight and Obesity Class II, with a decreased rate of readmission in this group (odds ratio (OR) 0.82; 95% confidence interval (CI) 0.71 to 0.96; p = 0.010). The only group demonstrating association with increased risk of reoperation within 30 days was the Obesity Class III group (OR 1.38; 95% CI 1.05 to 1.82; p = 0.022). Hypoalbuminaemia (preoperative albumin < 35 g/L) was significantly associated with readmission (OR 1.62; 95% CI 1.41 to 1.86; p < 0.001) and reoperation (OR 1.52; 95% CI 1.18 to 1.96; p = 0.001) within 30 days. CONCLUSION In this study, hypoalbuminaemia appears to be a more significant risk factor for readmission and reoperation than even the highest obesity categories. Future studies may assess whether preoperative albumin restoration or weight loss may improve outcomes for patients with hypoalbuminaemia. The implications of this study may allow surgeons to discuss risk of surgery with obese patients planning to undergo primary TKA procedures if other comorbidities are adequately controlled. Cite this article: Bone Joint J 2020;102-B(6 Supple A):31-35.
The role of right temporoparietal junction in processing social prediction error across relationship contexts

Abstract How do people update their impressions of close others? Although people may be motivated to maintain their positive impressions, they may also update their impressions when their expectations are violated (i.e. prediction error). Combining neuroimaging and computational modeling, we test the hypothesis that brain regions associated with theory of mind, especially right temporoparietal junction (rTPJ), underpin both motivated impression maintenance and impression updating evoked by prediction error. Participants had money either given to or taken away from them by a friend or a stranger and were then asked to rate each partner on trustworthiness and closeness across trials. Overall, participants engaged in less impression updating for friends vs strangers. Decreased rTPJ activity in response to a friend’s negative behavior (taking money) was associated with reduced negative updating and increased positive ratings of the friend. However, to the extent that participants did update their impressions (more negative ratings) of friends, this behavioral pattern was explained by greater prediction error and greater rTPJ activity. These findings suggest that rTPJ recruitment represents the integration of prediction error signals and the capacity to overcome people’s motivation to maintain positive impressions of friends in the face of conflicting evidence.
Development and validation of a quality of life scale in Familial Mediterranean Fever (FMFQoL)

Abstract Objective To develop a valid and reliable quality-of-life (QoL) scale in familial Mediterranean fever (FMF). Methods After producing question pool by using psychometric methods, high-performance questions were obtained according to expert panel. The principal component analysis (PCA) was done with varimax rotation for factor analysis. The final version of the scale (FMF-QoL) was examined for reliability and validity. Internal consistency with Cronbach alpha was calculated. The face, content, convergent and discriminant validity were analyzed. PRAS score used to assess the disease activity. Spearman correlation coefficient (rho) was used to assess the convergent and discriminant validity. Results In our study, 123 FMF patients were recruited. According to the factor analysis the FMF-QoL were represented by 4 factor groups (eigenvalues >1) which were physical impact, social and recreational impact, psychological impact, and impact of sleep. All questions’ factor loadings after Varimax rotation were bigger than 0.5 and the cumulative variance of the scale was 68.11%. The strongest correlation of the FMF-QoL was found with other QoL scales like EUROHIS (rho: −0.64, p < .0005) and Short Form 36 physical functioning subscale (rho: −0.63, p < .0005). The correlations between the FMF-QoL and functional parameters were found to be moderate [Beck Depression Inventory-Primary Care (rho: 0.46, p < .0005), Jenkins Sleep Scale (rho: 0.44, p < .0005), Health Assessment Questionnaire (rho: 0.44, p < .0005)]. FMF-QoL was also correlated with the disease specific measures [PRAS (rho: 0.42, p < .0005), number of attacks in the previous year (rho: 0.44, p < .0005)]. Conclusion A valid, reliable, practical, not time-consuming FMF-specific QoL scale that can be used in the clinical follow-up and treatment of these patients was developed and validated.
Toxicologic Evaluation of Cellulon™ Fiber; Genotoxicity, Pyrogenicity, Acute and Subchronic Toxicity

CellulonTM fiber, a cellulose produced by a bacterial fermentation process employing a strain of Acetobacter aceti subsp. xylinum, was tested for genotoxicity in four assays: (1) microbial reverse mutation assay in Salmonella typhimurium (Ames assay), (2) an assay for chromosomal aberrations in Chinese hamster ovary (CHO) cells, (3) an assay for induction of unscheduled DNA synthesis (UDS) in rat primary hepatocytes, and (4) the CHO/HGPRT forward mutation assay. Each assay was conducted at a wide range of dose levels, both with and without metabolic activation (assay 1, 2, and 4). Test results gave no indication that Cellulon fiber possessed any genotoxic potential. The pyrogenicity of five batches of Cellulon fiber was tested in the Limulus Amebocyte Lysate assay, gel-clot method. Test results were negative for the presence of gram-negative bacterial endotoxin. The primary eye and dermal irritation potential of Cellulon fiber were examined in New Zealand White rabbits. The Draize method was employed to evaluate and grade ocular and dermal irritation as a result of test material administration. Test results indicated that Cellulon fiber is a minor ocular irritant up to 1 hour postadministration. However, the resultant irritation was considered to be mechanical and related to the dry, granular form of the test material. In addition, test results indicated that Cellulon fiber is not a dermal irritant in the rabbit. The acute oral toxicity of Cellulon fiber was determined in Sprague-Dawley rats, and the LD50 was found to be greater than 2000 mg/kg of body weight. The subchronic toxicity of Cellulon fiber was examined in Sprague-Dawley rats fed diets containing 0, 5, and 10% Cellulon fiber or microcrystalline cellulose for 13 weeks. No dose-related effects on survival, growth, hematology, blood chemistry, organ weights, or pathologic lesions were observed. The results of these studies indicate that Cellulon fiber and microcrystalline cellulose are toxicologically equivalent and that Cellulon fiber does not possess genotoxic potential, is nonpyrogenic, and that animals are not adversely affected by acute or subchronic exposure to Cellulon fiber.
Prevalence of Cutaneous Leishmaniasis in Iran (2000-2016): A Systematic Review and Meta-analysis Study.

Cutaneous leishmaniasis (CL) is the most common form of leishmaniasis affecting humans. The purpose of this study was to determine the prevalence and epidemiological features of CL in Iran by a systematic review and meta-analysis. The literature search was performed in the SID, Magiran, IranDoc, PubMed, Scopus, Medlib, as well as the Google Scholar search engine databases to find studies on the prevalence of CL. The reference lists of the found articles were also reviewed to obtain additional relevant articles. Studies that were related to treatment and reservoirs of CL were excluded. Forty-four studies were selected for final analysis. Metaanalysis with random effects model showed that the prevalence of leishmaniasis in Iran was 77 per 100,000 population. Overall, 60% of the patients were men. Most cases of CL occurred in autumn, and majority of the patients had one lesion mostly on hands. The most common age group was 20-30 years. In conclusion, CL is an endemic disease in Iran, and its prevalence is largely affected by geographical locations and regional customs. Appropriate preventing measures should be considered to decrease the incidence of CL in Iran.
Balloon-expandable versus self-expanding transcatheter aortic valve replacement for bioprosthetic dysfunction: A systematic review and meta-analysis

Background Transcatheter aortic valve-in-valve (VIV) procedure is a safe alternative to conventional reoperation for bioprosthetic dysfunction. Balloon-expandable valve (BEV) and self-expanding valve (SEV) are the 2 major types of devices used. Evidence regarding the comparison of the 2 valves remains scarce. Methods A systematic review and meta-analysis was conducted to compare the outcomes of BEV and SEV in transcatheter VIV for aortic bioprostheses dysfunction. A computerized search of Medline, PubMed, Embase, and Cochrane databases was performed. English-language journal articles reporting SEV or BEV outcomes of at least 10 patients were included. Results In total, 27 studies were included, with 2,269 and 1,671 patients in the BEV and SEV groups, respectively. Rates of 30-day mortality and stroke did not differ significantly between the 2 groups. However, BEV was associated with significantly lower rates of postprocedural permanent pacemaker implantation (3.8% vs. 12%; P < 0.001). Regarding echocardiographic parameters, SEV was associated with larger postprocedural effective orifice area at 30 days (1.53 cm2 vs. 1.23 cm2; P < 0.001) and 1 year (1.55 cm2 vs. 1.22 cm2; P < 0.001). Conclusions For patients who underwent transcatheter aortic VIV, SEV was associated with larger postprocedural effective orifice area but higher rates of permanent pacemaker implantation. These findings provide valuable information for optimizing device selection for transcatheter aortic VIV.
The effect of Shexiang Tongxin Dropping Pills on coronary microvascular dysfunction (CMVD) among those with a mental disorder and non-obstructive coronary artery disease based on stress cardiac magnetic resonance images

Abstract Introduction: Coronary microvascular dysfunction (CMVD), highly prevalent among patients with a mental disorder (anxiety or depression), is closely related to adverse cardiac events, including hospitalization, sudden cardiac death, and myocardial infarction. Shexiang Tongxin Dropping Pills (STDP), a traditional Chinese medicine, exerts endothelial protective function by anti-inflammation, anti-oxidative stress, and promoting blood circulation. STDP protects against CMVD in previous fundamental studies. The present trial is aiming at evaluating the effect of STDP on CMVD among depressed or anxious patients with non-obstructive coronary artery disease (NOCAD). Methods and analysis: Seventy-two depressed or anxious patients diagnosed with NOCAD combined with CMVD utilizing coronary artery angiography and stress cardiac magnetic resonance (CMR) will be recruited in the present study. These patients will be randomized into two groups, namely, Nicorandil group (Nicorandil combined with routine medicine), and STDP groups (STDP combined with routine medicine). The change of CMVD status by assessing absolute myocardial blood flow and myocardial reperfusion using stress CMR 3-month after discharge is defined as the primary endpoint. Major adverse cardiac events (MACEs), quality of life (QOL), and metal disorder improvement are defined as the secondary endpoints. Seattle angina questionnaire (SAQ) which is used to assess angina pectoris and QOL will be recorded at 1-, 3-, 6-, 9-, 12-month of follow-up. Seven-item Generalized Anxiety Disorder Scale (GAD-7) and 9-item depression module from the Patient Health Questionnaire (PHQ9) which utilized to evaluate anxiety and depression, respectively, will be recorded at 1-, 3-, 6-, 9-, 12-month of follow-up. This study will first evaluate the efficacy of STDP on CMVD among patients with a mental disorder and NOCAD, and discuss the potential mechanisms, providing therapeutic evidence for the STDP for these patients.