Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into protein–DNA binding specificity from hydrogen bond based comparative study

Abstract Knowledge of protein–DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein–DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein–DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-binding proteins with different degrees of binding specificity, we found that highly specific DNA-binding proteins show balanced hydrogen bonding with each of the two DNA strands while multi-specific DNA binding proteins are generally biased towards one strand. Protein-base pair hydrogen bonds, in which both bases of a base pair are involved in forming hydrogen bonds with amino acid side chains, are more prevalent in the highly specific protein–DNA complexes than those in the multi-specific group. Amino acids involved in side chain-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding proteins while multi-specific DNA-binding proteins prefer helices.
Prepectoral Versus Subpectoral Direct to Implant Immediate Breast Reconstruction.

BACKGROUND Implant-based reconstruction is currently the most common postmastectomy breast reconstruction modality with over 86,000 procedures performed in 2017. Although various methods for reconstruction techniques have been described, partial subpectoral implant placement with or without acellular dermal matrix coverage remains the most popular approach. Recently, prepectoral implant placement has gained increased recognition as a method that avoids some of the potential morbidities of submuscular implant placement. Currently, few studies have examined the outcomes of performing this approach. The purpose of this study was to evaluate and compare the outcomes of prepectoral and subpectoral direct to implant (DTI) immediate breast reconstruction. METHODS Data from a prospective cohort of consecutive patients undergoing prepectoral DTI immediate breast reconstructions at our institution from February 2016 to November 2017 were collected. The incidence of complications such as mastectomy skin flap necrosis, seroma, hematoma, infection, implant loss, and unexpected reoperation were recorded and compared with a cohort of consecutive patients who underwent subpectoral DTI immediate breast reconstruction from May 2014 to July 2015. RESULTS One hundred twelve prepectoral DTI immediate breast reconstructions were performed on 62 patients. Four breasts (4.4%) were diagnosed with infection. There were 8 breasts (7.1%) that suffered from mastectomy skin flap necrosis (5 partial thickness necrosis, 3 full thickness necrosis). There was 1 implant loss related to full thickness necrosis that required salvage with autologous tissue reconstruction. Prepectoral breast reconstruction had less esthetic revisions and comparable complications when compared with the historical subpectoral cohort. CONCLUSIONS When compared with the subpectoral DTI approach, prepectoral DTI breast reconstruction grants favorable complication rates and improved esthetic outcomes. Prepectoral DTI breast reconstruction is a safe modality that should be considered in any patient who is a candidate for immediate breast reconstruction.
A Population-based Statistical Model for Investigating Heterogeneous Intraprostatic Sensitivity to Radiation Toxicity After 125I Seed Implantation

Aim: To develop a population-based statistical model in order to find a spatial pattern of dose distribution which is related to lower urinary tract symptoms (LUTS) after iodine-125 (125I) seed implantation for prostate cancer. Patients and Methods: A total of 75 patients underwent 125I seed implantation for prostate cancer. Principal component analysis was applied to the standardized dose array and for each patient dose distribution was uniquely characterized by a combination of weighted eigenvectors. The correlation between eigenvectors and the severity of LUTS was investigated with linear regression analysis. Results: Eight eigenvectors were identified as being significantly associated with the severity of LUTS (p<0.05). Multivariate regression model identified that intraprostatic parameters, which were positively associated with the severity of LUTS, were distributed around a portion of the urethral base and a peripheral region of the prostate. Conclusion: We established a population-based statistical model that may indicate a significant dose pattern associated with the severity of radiation toxicity.
Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis

ABSTRACT The yeast Brettanomyces bruxellensis (syn. Dekkera bruxellensis) is an emerging and undesirable contaminant in industrial low-sugar ethanol fermentations that employ the yeast Saccharomyces cerevisiae. High-affinity glucose import in B. bruxellensis has been proposed to be the mechanism by which this yeast can outcompete S. cerevisiae. The present study describes the characterization of two B. bruxellensis genes (BHT1 and BHT3) believed to encode putative high-affinity glucose transporters. In vitro-generated transcripts of both genes as well as the S. cerevisiae HXT7 high-affinity glucose transporter were injected into Xenopus laevis oocytes and subsequent glucose uptake rates were assayed using 14C-labelled glucose. At 0.1 mM glucose, Bht1p was shown to transport glucose five times faster than Hxt7p. pH affected the rate of glucose transport by Bht1p and Bht3p, indicating an active glucose transport mechanism that involves proton symport. These results suggest a possible role for BHT1 and BHT3 in the competitive ability of B. bruxellensis.
Investigating the role of communication between descriptive norms and exercise intentions and behaviors: findings among fitness tracker users

Abstract Objective This study investigates the relationship between fitness tracker users’ communication of exercise information and their exercise intentions and behaviors among college students. Participants: Data were collected from 186 undergraduate students. Methods: A quantitative online survey was conducted. Descriptive norm (perceptions of prevalence of others’ behaviors), communication (including exercise information giving and exercise information receiving), exercise behaviors, and exercise intentions were measured with reliable scales. Results: Both exercise information giving and information receiving were positively associated with exercise behaviors and intentions. Information giving moderated the association between descriptive norms and exercise intentions and behaviors, while information receiving moderated the association between descriptive norms and exercise intentions. Conclusion: The interaction effect between descriptive norm and communication suggests that health educators and campaign designers should focus on descriptive norm of exercise for college students who have limited communication activities. It is important to find innovative ways to promote positive health behaviors.
Two‐day‐treatment of Activin‐A leads to transient change in SV‐HFO osteoblast gene expression and reduction in matrix mineralization

Activins regulate bone formation by controlling osteoclasts and osteoblasts. We investigated Activin‐A mechanism of action on human osteoblast mineralization, RNA and microRNA (miRNA) expression profile. A single 2‐day treatment of Activin‐A at Day 5 of osteoblast differentiation significantly reduced matrix mineralization. Activin A‐treated osteoblasts responded with transient change in gene expression, in a 2‐wave‐fashion. The 38 genes differentially regulated during the first wave (within 8 hr after Activin A start) were involved in transcription regulation. In the second wave (1–2 days after Activin A start), 65 genes were differentially regulated and related to extracellular matrix. Differentially expressed genes in both waves were associated to transforming growth factor beta signaling. We identified which microRNAs modulating osteoblast differentiation were regulated by Activin‐A. In summary, 2‐day treatment with Activin‐A in premineralization period of osteoblast cultures influenced miRNAs, gene transcription, and reduced matrix mineralization. Modulation of Activin A signaling might be useful to control bone quality for therapeutic purposes.
OCR for Greek polytonic (multi accent) historical printed documents: development, optimization and quality control

This paper presents the development and implementation of a robust OCR tool and a related comprehensive workflow for the recognition of Greek printed polytonic scripts. This project is initiated and developed by an interdisciplinary team with expertise in the areas of document image processing, character segmentation and recognition, machine learning, corpus creation and digital humanities. Our paper aims to describe the design and development of the workflow around this project, including data gathering and structuring, OCR tool development, user interface development, experiments on the training procedure of the tool, evaluation, post-correction and quality control of the results.
Time-of-day effects in maximal anaerobic performance and blood lactate concentration during and after a supramaximal exercise

The purpose of the present study was to determine the time-of-day effects in maximal anaerobic power and capacity and in blood lactate responses during and after a supramaximal exercise. Fourteen undergraduate male students participated in the Wingate Test at three time points: 09:00, 13:00 and 17:00 hours on separate days. Before each test subjects' body weight, oral temperature and resting heart rate and subjects' peak power and mean power during the Wingate test were determined. Blood lactate concentrations were determined before, immediately after and at 3rd, 5th and 7th min of passive recovery period. A significant circadian rhythm was found for oral temperature ( p 0.05). It is concluded that a time-of-day effect was evident in maximal anaerobic power and capacity however this variation was not parallel with those of oral temperature. In addition a time-of-day effect did not exist for the blood lactate concentrations.
Does chronic high-intensity endurance training have an effect on cardiovascular markers of active populations and athletes? Systematic review and meta-analysis

Objective The objective of this study was to ascertain the effects of high-intensity chronic endurance training on cardiovascular markers of active populations and athletes. Methods This review was conducted in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. We used databases of PubMed, Science Direct, SPORTDiscus, Google Scholar and grey literatures with Mesh and free-text search as well as manual searches to identify relevant studies from June 2017 to September 2019. Weighted standardised mean differences and effect size of the intervention group versus the control group were calculated using a random effect model with 95% CI. Result There was significant improvement in high-density lipoprotein with weighted standardised mean difference and effect size=−1.06 (−1.83 to −0.30), p=0.006. We have also observed a significant reduction in low-density lipoprotein and total cholesterol with weighted standardised mean difference and effect size=−0.97 (−1.58 to −0.36), p=0.002, and = −0.78 (−1.34 to −0.22), p=0.007, respectively. There was a significant reduction in interleukin 6 (IL-6) using a fixed effect model with weighted standardised mean difference and effect size=−0.87 (−1.33 to −0.40), p=0.0003 and C reactive protein (CRP) with weighted standardised mean differences and effect size=−0.41 (−0.73 to −0.09), p=0.01. Conclusion Chronic high-intensity endurance training improves healthy lipid profiles (increase high-density lipoprotein, decreased low-density lipoprotein and total cholesterol). And decreased inflammatory markers (IL-6 and CRP) independent of age and sex and cannot be associated with an increased risk of developing cardiovascular disease. PROSPERO registration number CRD 42017081369.
The Effect of Surgical Approach on Outcomes Following Total Hip Arthroplasty Performed for Displaced Intracapsular Hip Fractures: An Analysis from the National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.

BACKGROUND Studies have suggested that the anterolateral approach is preferable to the posterior approach when performing total hip arthroplasty (THA) for a displaced intracapsular hip fracture, because of a perceived reduced risk of reoperations and dislocations. However, this suggestion comes from small studies with short follow-up. We determined whether surgical approach in THAs performed for hip fracture affects revision-free hip survival, patient survival, and intraoperative complications. METHODS We retrospectively analyzed all stemmed primary THAs for hip fracture that were recorded in the National Joint Registry for England, Wales, Northern Ireland and the Isle of Man that were performed between 2003 and 2015. The 2 surgical approach groups, posterior and anterolateral, were matched for patient and surgical confounding factors using propensity scores, with outcomes compared using regression modeling (with regression model ratios of <1 representing a reduced risk of the specified outcome in the posterior group). Outcomes were 5-year hip survival free from revision (all-cause revision, revision for dislocation and/or subluxation, and revision for periprosthetic fracture), patient survival (30 days, 1 year, and 5 years postoperatively), and intraoperative complications. RESULTS After matching, 14,536 THAs (7,268 per group) were studied. Five-year cumulative revision-free survival rates were similar (posterior group, 97.3%, and anterolateral group, 97.4%; subhazard ratio [SHR], 1.15 [95% confidence interval (CI), 0.93 to 1.42]). Five-year survival rates free from revision for dislocation (SHR, 1.28 [95% CI, 0.89 to 1.84]) and for periprosthetic fracture (SHR, 1.03 [95% CI, 0.68 to 1.56]) were also comparable between the 2 approach groups. Thirty-day patient survival was significantly higher following a posterior approach (99.5% compared with 98.8%; hazard ratio [HR], 0.44 [95% CI, 0.30 to 0.64]), which persisted at 1 year (HR, 0.73 [95% CI, 0.64 to 0.84]) and 5 years (HR, 0.87 [95% CI, 0.81 to 0.94]) postoperatively. The posterior approach was associated with a lower risk of intraoperative complications (odds ratio [OR], 0.59 [95% CI, 0.45 to 0.78]). CONCLUSIONS In THA for hip fracture, the posterior approach was associated with a similar risk of revision and a lower risk of both patient mortality and intraoperative complications compared with the anterolateral approach. We propose that the posterior approach is as safe as the anterolateral approach when performing THA for hip fracture and that either approach may be used according to surgeon preference. LEVEL OF EVIDENCE Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
An Analysis of User Survey Data for an Internet Program for Testing for Sexually Transmitted Infections, I Want the Kit (IWTK) in Maryland and Washington D.C.

We evaluated the results of an acceptability survey administered online to users of IWTK, which offers internet-requested kits for sexually transmitted infection (STI) screening. User satisfaction was high for IWTK, with many users in our survey being repeat patients of this program. Both male and female respondents preferred genital self-collected swabs over urine collected specimens. Strong interest was expressed in home testing options for other STIs.
Assessment of peripheral endothelial function predicts future risk of solid-tumor cancer

Aims Cardiovascular health metrics predict the risk not only of cardiovascular diseases but also of several types of cancers. Microvascular endothelial dysfunction can predict future cardiovascular adverse events, but the predictive value of microvascular endothelial dysfunction for future risk of solid-tumor cancer has not been characterized. Methods A total of 488 patients who underwent microvascular endothelial function assessment using reactive hyperemia peripheral arterial tonometry were included in this study. Microvascular endothelial dysfunction was defined as a reactive hyperemia peripheral arterial tonometry index ≤2.0. Results Of 221 patients with a baseline reactive hyperemia peripheral arterial tonometry index ≤2.0, 21 patients (9.5%) were diagnosed with incident solid-tumor cancer during follow-up, whereas of 267 patients with a baseline reactive hyperemia peripheral arterial tonometry index >2.0, 10 patients (3.7%) were diagnosed with incident solid-tumor cancer during follow-up (p = 0.009). Patients with a reactive hyperemia peripheral arterial tonometry index ≤2.0 had lower solid-tumor cancer-free survival compared to patients with a reactive hyperemia peripheral arterial tonometry index >2.0 (log-rank p = 0.017) (median follow-up 6.0 (3.0–9.1) years). Cox proportional hazard analyses showed that a reactive hyperemia peripheral arterial tonometry index ≤2.0 predicted the incidence of solid-tumor cancer, with a hazard ratio of 2.52 (95% confidence interval 1.17–5.45; p = 0.019) after adjusting for age, sex, and coronary artery disease, 2.83 (95% confidence interval 1.30–6.17; p = 0.009) after adjusting for diabetes mellitus, hypertension, smoking status, and body mass index >30 kg/m2, 2.79 (95% confidence interval 1.21–6.41; p = 0.016) after adjusting for fasting plasma glucose, systolic blood pressure, smoking status (current or former), and body mass index, and 2.43 (95% confidence interval 1.10–5.34; p = 0.028) after adjusting for Framingham risk score. Conclusion Microvascular endothelial dysfunction, as defined by a reactive hyperemia peripheral arterial tonometry index ≤2.0, was associated with a greater than two-fold increased risk of solid-tumor cancer. Microvascular endothelial dysfunction may be a useful marker to predict the future risk of solid-tumor cancer, in addition to its known ability to predict cardiovascular disease. Further research is necessary to develop adequate cancer screening strategies for patients with microvascular endothelial dysfunction.
Protein phase separation and determinants of in cell crystallization

Liquid‐liquid phase separation (LLPS) in cells is known as a complex physicochemical process causing the formation of membrane‐less organelles (MLOs). Cells have well‐defined different membrane‐surrounded organelles like mitochondria, endoplasmic reticulum, lysosomes, peroxisomes, etc., however, on demand they can create MLOs as stress granules, nucleoli and P bodies to cover vital functions and regulatory activities. However, the mechanism of intracellular molecule assembly into functional compartments within a living cell remains till now not fully understood. in vitro and in vivo investigations unveiled that MLOs emerge after preceding liquid‐liquid, liquid‐gel, liquid‐semi‐crystalline, or liquid‐crystalline phase separations. Liquid‐liquid and liquid‐gel MLOs form the majority of cellular phase separation events, while the occurrence of micro‐sized crystals in cells was only rarely observed, however can be considered as a result of a preceding protein phase separation event. In vivo, also known and termed as in cellulo crystals, are reported since 1853. In some cases, they have been linked to vital cellular functions, such as storage and detoxification. However, the occurrence of in cellulo crystals is also associated to diseases like cataract, hemoglobin C diseases, etc. Therefore, better knowledge about the involved molecular processes will support drug discovery investigations to cure diseases related to in cellulo crystallization. We summarize physical and chemical determinants known today required for phase separation initiation and formation and in cellulo crystal growth. In recent years it has been demonstrated that LLPS plays a crucial role in cell compartmentalization and formation of MLOs. Here we discuss potential mechanisms and potential crowding agents involved in protein phase separation and in cellulo crystallization.
Putting an end to the Pseudomonas aeruginosa IQS controversy

Despite published evidence that IQS (2‐(2‐hydroxylphenyl)‐thiazole‐4‐carbaldehyde) is in fact aeruginaldehyde, a by‐product of the siderophore pyochelin biosynthesis or degradation and that the ambABCDE genes are not responsible for IQS synthesis, several authors, including in top review journals, perpetuate the wrong information. I hope that this short comment will clarify the situation once and for all.
Leveraging Semantics in WordNet to Facilitate the Computer-Assisted Coding of ICD-11

The International Classification of Diseases (ICD) not only serves as the bedrock for health statistics but also provides a holistic overview of every health aspect of life. This study aims to facilitate the computer-assisted coding of the 11th revision of the ICD (ICD-11) by leveraging the data structures of ICD-11 and semantics in WordNet. First, a computer-assisted coding framework using WordNet and ICD-11 application programming interface (API) is proposed. Secondly, a network based on entity relations in ICD-11 and synonym sets in WordNet, called CodeNet, is developed. Thirdly, an algorithm for generating ICD-11 code candidates from CodeNet with two tuning parameters on the basis of the input of disease-related text is illustrated. Finally, the discharge summaries in the Medical Information Mart for Intensive Care III database and textual information from ICD-11 entities are used to evaluate the proposed method. Experimental results indicate that the proposed coding method achieves a precision of 84% and a recall of 89% relative to a precision of 65% and a recall of 81% achieved with the existing ICD-11 API. The proposed method also outperforms other methods in the literature by reducing a failure rate of up to 8% in ICD-11 coding. The proposed thresholds of similarity and percentage can be applied to tuning the performance of our method to meet different coding needs. In sum, improving the new structures of ICD-11 with the use of semantics in WordNet can help develop more reliable computer-aided coding systems for ICD-11 coders.