Miracle-dz/UniFAR-FTUs huggingface dataset:
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis

MOTIVATION Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e., their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited. RESULTS By concentrating on a representative set of word-frequency based AF functions, we perform the first coherent and uniform evaluation of the power, involving also Type I error for completeness. Two Alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), a wide range of sequence lengths from a few thousand to millions, and different values of k have been used. As a result, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. Remarkably, of the fifteen functions that we have considered, only four stand out, with small differences between small and short sequence length scenarios. Finally, in order to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public. AVAILABILITY The software is available at: https://github.com/pipp8/power_statistics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The mediating role of students’ academic resilience in the relationship between self-efficacy and test anxiety

BACKGROUND: There is growing acknowledgment that medical education can be a stressful experience for students and may have a devastating effect on their psychological well-being. The present article, therefore, aimed at investigating students' academic resilience as a mediating variable in self-efficacy-test anxiety relation. MATERIALS AND METHODS: In this cross-sectional correlational study, a convenience sample of 243 medical students was selected and participated, three prevalidated questionnaires were applied, that is, general self-efficacy questionnaire, academic resilience questionnaire, and test anxiety questionnaire. To analyze the data, Pearson's correlation coefficient as well as structural equation modeling (SEM) were used. RESULTS: According to Pearson's coefficients, self-efficacy was found to be positively correlated with academic resilience (r = 0.437, P ≤ 0.01) and negatively with test anxiety (r = −0.475, P ≤ 0.01). SEM results also indicated that self-efficacy positively impacts on academic resilience (β = 0.43, P < 0.001) and negatively on test anxiety (β = −0.37, P < 0.001). In addition, results demonstrated the mediating role of academic resilience in self-efficacy-test anxiety relationship (β = −0.108, P < 0.001). CONCLUSION: This study showed that academic resilience could play a mediating role in students' self-efficacy-test anxiety relationship.
Therapeutic Effects of 25-Hydroxyvitamin D on the Pathological Process of Benign Prostatic Hyperplasia: An In Vitro Evidence

The pathogenesis of benign prostatic hyperplasia (BPH) is extremely complicated which involving the multiple signaling pathways. The deficiency of vitamin D is an important risk factor for BPH, and exogenous vitamin D is effective for the treatment of BPH. In this study, we provided in vitro mechanical evidence of vitamin D as a treatment for BPH using BPH-1, WPMY-1, and PBMC cells. We found that 25-hydroxyvitamin D (25-OH D) level is decreased in BPH and closely correlated with age, prostate volume, maximum flow, international prostate symptom score, and prostate-specific antigen of the BPH patients. We further revealed that 25-OH D ameliorated TGF-β1 induces epithelial-mesenchymal transition (EMT) of BPH-1 cells and proliferation of WPMY-1 cells via blocking TGF-β signaling. Moreover, 25-OH D was able to block NF-κB signaling in PBMCs of BPH patients and STAT3 signaling in BPH cells to relieve inflammation. 25-OH D also protects BPH cells from inflammatory cytokines selected by PBMCs. Finally, we uncovered that 25-OH D alleviated prostate cell oxidative stress by triggering Nrf2 signaling. In conclusion, our data verified that 25-OH D regulated multiple singling pathways to restrain prostate cell EMT, proliferation, inflammation, and oxidative stress. Our study provides in vitro mechanical evidence to support clinical use of vitamin D as a treatment for BPH.
3D Laparoscopic common bile duct exploration with primary repair by absorbable barbed suture is safe and feasible

Background and aim: Endoscopic retrograde cholangiopancreatography (ERCP), with interval laparoscopic cholecystectomy (LC), is the most common treatment approach for common bile duct (CBD) stones. However, recent studies show that single-stage laparoscopic CBD exploration (LCBDE) is safe and feasible. Three-dimensional (3D) laparoscopy enhances depth perception and facilitates intracorporeal suturing. The application of 3D technology for LCBDE is emerging, and we report our case series of 3D LCBDE. Methods: We audited the 27 consecutive 3D LCBDE performed from July 2017 to January 2020. We have a liberal policy for magnetic resonance cholangiopancreatography (MRCP) in patients with deranged liver function tests (LFT). All CBD explorations were done through choledochotomy with a 5 mm flexible choledochoscope and primarily repaired with an absorbable barbed suture without a stent or T-tube. Results: The mean age of patients was 68 (range 44-91) years, and 12 (44%) were male. The indications for surgery were choledocholithiasis 67% (n=18), cholangitis 22% (n=6), and gallstone pancreatitis 11% (n=3). About 67% (n=18) had pre-operative ERCP. About 37% (n=10) had pre-operative biliary stent. Pre-operative MRCP was done in 74% (n=20), and the mean diameter of CBD was 14.5 mm (range 7–30). The median operative time was 160 (range 80–265) min. The operative drain was inserted in 18 patients. One patient each (4%) had a bile leak and a retained stone. There was no open conversion, readmission, or mortality. Conclusion: 3D LCBDE with primary repair by an absorbable barbed suture is safe and feasible. Relevance for patients: This paper emphasized that one stage LCBDE should be a treatment option which is comparable with two stage ERCP followed by LC to treat CBD stones. In addition, 3D technology and barbed sutures use in LCBDE are safe and useful.
KPNA1 regulates nuclear import of NCOR2 splice variant BQ323636.1 to confer tamoxifen resistance in breast cancer

Dear Editor, Tamoxifen is a first-line treatment option for estrogenreceptor-α positive (ER+) breast cancer. Drug resistance significantly compromises its clinical efficacy. Nuclear receptor corepressor-2 (NCOR2) is a transcriptional coregulatory protein. We previously identified a novel splice variant of NCOR2, that is, BQ323636.1 (BQ), which retains only the N-terminus repression domain-1 of the NCOR2 wild-type protein (Figure S1). 1 BQ nuclear overexpression is found significantly associated with tamoxifen resistance in ER+ primary breast cancer, nuclear localization being essential in modulating tamoxifen response.2 This study reports a possible molecular mechanism behind BQ nuclear localization mediated by KPNA1 (importin-α5). We generated two expression constructs in which the BQ expression vector was fused with either a nuclearlocalization signal (BQ-NLS) or with a nuclear-export signal (BQ-NES), and confirmed that BQ-NLS was predominantly localized in the nucleus, further promoted cell proliferation and enhanced tamoxifen resistance (Figure S2A–D). Using cNLS Mapper,3 we identified a putative NLS (PQRRRPSLLS) in BQ (NLSBQ; Figure S3A). Through RaptorX,4 we found that the NLS in BQ had greater relative surface accessibility than for that in NCOR2 (Figure S3B), suggesting it might be more functional. By coimmunoprecipitation, only KPNA1 interacted with BQ and importin-β1 (Figure 1A). An expression construct that expressed GFP fused with NLSBQ was cloned and coimmunoprecipitation confirmed that GFP-NLSBQ could interact with KPNA1 (Figure S3C). Knockdown of KPNA1 resulted in reduced nuclear-BQ (Figures 1B, C and S4A–C) in BQ-overexpressed cells. LCC2, a tamoxifen resistant cell-line derived from MCF-7, has a high endogenous BQexpression (Figure S5A). Knockdown of KPNA1 in LCC2 reduced BQ levels in the nucleus (Figures 1D and S5B–D). These results suggested that NLSBQ was functional and KPNA1 may mediate the nuclear import of BQ in breast cancer cells.
Slit ventricle syndrome: Historical considerations, diagnosis, pathophysiology, and treatment review

After the introduction of shunt treatment for the management of childhood hydrocephalus, a wide variety of complications related to this treatment modality have been recognized. The entity of slit ventricle syndrome (alternatively, symptomatic ventricular coaptation) is one of them, is frequently encountered in the pediatric population and its symptom complex resembles that of shunt failure. We conducted research on PubMed®, MEDLINE®, and Web of Science®, using the keywords: “slit ventricles,” “slit ventricle syndrome,” “SVS” and “ventricular coaptation. ” The aim of our review was to trace the advances made through the past decades, concerning our knowledge about the clinical characteristics, pathophysiology, and treatment options of this entity. The discrepancy among researchers about the offending etiology and the optimum treatment algorithm of this entity, as well as the necessity of an updated concept regarding shunt over drainage is analyzed. The multiple treatment modalities proposed and pathophysiologic mechanisms implicated for the treatment of slit ventricle syndrome illustrate the complexity of this entity. Consequently, the issue requires more detailed evaluation. In this review, we comment on all the main facets related to shunt over drainage and the resultant slit ventricle syndrome.
Acute Versus Delayed Surgical Intervention in Multiligament Knee Injuries: A Systematic Review

Background: The optimal timing of surgical intervention for multiligament knee injuries remains controversial. Purpose: To review the clinical and functional outcomes after acute and delayed surgical intervention for multiligament knee injuries. Study Design: Systematic review; Level of evidence, 4. Methods: We performed a search of the PubMed, Embase, Cochrane Library, and Web of Science databases from inception to September 2020. Eligible studies reported on knee dislocations, multiligament knee injuries, or bicruciate ligament injuries in adult patients (age, ≥18 years). In addition to comparing outcomes between acute and delayed surgical intervention groups, we conducted 3 subgroup analyses for outcomes within isolated knee injuries, knee injuries with concomitant polytrauma/fractures, and high-level (level 2) studies. Results: Included in the analysis were 31 studies, designated as evidence level 2 (n = 3), level 3 (n = 8), and level 4 (n = 20). These studies reported on 2594 multiligament knee injuries sustained by 2585 patients (mean age, 25.1-65.3 years; mean follow-up, 12-157.2 months). At the latest follow-up timepoint, the mean Lysholm (n = 375), International Knee Documentation Committee (IKDC) (n = 286), and Tegner (n = 129) scores for the acute surgical intervention group were 73.60, 67.61, and 5.06, respectively. For the delayed surgical intervention group, the mean Lysholm (n = 196), IKDC (n = 172), and Tegner (n = 74) scores were 85.23, 72.32, and 4.85, respectively. The mean Lysholm (n = 323), IKDC (n = 236), and Tegner (n = 143) scores for our isolated subgroup were 83.7, 74.8, and 5.0, respectively. By comparison, the mean Lysholm (n = 270), IKDC (n = 236), and Tegner (n = 206) scores for the polytrauma/fractures subgroup were 83.3, 64.5, and 5.0, respectively. Conclusion: The results of our systematic review did not elucidate whether acute or delayed surgical intervention produced superior clinical and functional outcomes. Although previous evidence has supported acute surgical intervention, future prospective randomized controlled trials and matched cohort studies must be completed to confirm these findings.
Application of MAT Methodology in the Evaluation of Prescribing Adherence to Clinical Practice Guidelines for Secondary Prevention of Coronary Heart Disease in Post-Acute Coronary Syndrome Patients in Kuwait

Quantification of prescribers’ adherence to evidence-based guidelines can be used as an outcome measure to assess the impact of services on the quality of medication use. Additionally, it can help in reducing inappropriate interventions and ensure that high-quality care is provided to patients. This study aimed to evaluate prescribing practices for secondary prevention of coronary heart disease (CHD) in post-acute coronary syndromes (ST-elevation myocardial infarction [STEMI] or non-ST elevation acute coronary syndrome [NSTEACS]) patients using two medication assessment tools (MATs) at secondary and tertiary health-care settings in Kuwait. Both MATs were developed and validated based on the relevant guidelines issued by the European Society of Cardiology and the American College of Cardiology/American Heart Association. A quantitative cross-sectional multicenter study was conducted on 460 patients’ medical records collected randomly from six health-care facilities in Kuwait. Application of MATSTEMI on 232 patients’ medication records (with 85.9% applicability) resulted in intermediate overall adherence (69.8%; 95% CI: 67.6–72.0). Application of MATNSTEACS on 228 patients’ medication records (with applicability 83.2%) resulted in intermediate overall adherence (73.3%; 95% CI: 70.5–76.0). There was no significant difference between the percentages of overall adherence among patients managed post-NSTEACS compared to those managed post-STEMI (p = 0.05). Multivariable logistic regression analysis revealed that the overall adherence to the MATSTEMI criteria was significantly higher among the specialized cardiac centers than among the general hospitals (OR: 1.6; 95% CI: 1.1–2.3; p = 0.02). The overall adherence to the MATNSTEACS criteria was found to be significantly lower among non-Kuwaitis than among Kuwaitis (OR: 0.6; 95% CI: 0.5–0.9; p = 0.01) and patients with a serum LDL ≥1.8 mmol/L than those with a serum LDL-C < 1.8 mmol/L (OR: 0.5; 95% CI: 0.4–0.7; p < 0.001). The present findings revealed that both MATs were useful tools in identifying the standard of clinical performances and highlighting areas for improvement regarding secondary prevention of CHD in post-acute coronary syndrome patients.
The Multifaceted Therapeutic Mechanisms of Curcumin in Osteosarcoma: State-of-the-Art

Osteosarcoma is a major form of malignant bone tumor that typically occurs in young adults and children. The combination of aggressive surgical strategies and chemotherapy has led to improvements in survival time, although individuals with recurrent or metastatic conditions still have an extremely poor prognosis. This disappointing situation strongly indicates that testing novel, targeted therapeutic agents is imperative to prevent the progression of osteosarcoma and enhance patient survival time. Curcumin, a naturally occurring phenolic compound found in Curcuma longa, has been shown to have a wide variety of anti-tumor, anti-oxidant, and anti-inflammatory activities in many types of cancers including osteosarcoma. Curcumin is a highly pleiotropic molecule that can modulate intracellular signaling pathways to regulate cell proliferation, inflammation, and apoptosis. These signaling pathways include RANK/RANKL, Notch, Wnt/β-catenin, apoptosis, autophagy, JAK/STAT, and HIF-1 pathways. Additionally, curcumin can regulate the expression of various types of microRNAs that are involved in osteosarcoma. Therefore, curcumin may be a potential candidate for the prevention and treatment of osteosarcoma. This comprehensive review not only covers the use of curcumin in the treatment of osteosarcoma and its anti-cancer molecular mechanisms but also reveals the novel delivery strategies and combination therapies with the aim to improve the therapeutic effect of curcumin.
Perception about myths and facts regarding COVID-19 pandemic infection among science and technology faculties

BACKGROUND: COVID-19 was declared as pandemic by the WHO in March 2020. Social distancing and hand hygiene is advised during the pandemic to contain the spread of the virus. Rapid sharing of scientific information in an extraordinary way is the characteristic of the COVID-19 pandemic. There may be gap between information provided and received. Perception and practices in the community regarding handling materials need to be pointed out. the aim of this study was to assess the perception about myths and facts and change in the practices before and during the COVID-19 pandemic among the faculties. MATERIALS AND METHODS: A cross-sectional survey was conducted during May–June 2020 among the faculties of Science and Technology. By multistage sampling technique, five districts from Maharashtra state and then one institution from each district was selected. A questionnaire was shared by Internet to institutional faculties. Descriptive and inferential statistics (Chi-square test) is applied. RESULTS: Out of 276 faculties, 248 had responded. Most of the faculties were aware about basic preventive measures for COVID-19 infection. However, 25% of the faculties were unaware about the safe physical distance. Eating garlic and pepper protect against COVID-19 as per 63 (25.3%) and 59 (23.9%) faculties, respectively, was effective, whereas 56.8% of participants did not believe so. 93 (37.5%) respondents believed that respiratory function ultimately indicates the presence or absence of disease. About 95% of participants adopted new hygienic practices during the pandemic (P < 0.0001). CONCLUSION: COVID-19 can spread rapidly if the basic preventive measures are ignored by the small proportion of unaware people Hence, awareness needs to be improved. People have adapted to new hygienic practices for handling the material during the pandemic.
Association between obesity and chronic periodontitis

Abstract Previous studies have suggested that obesity might be associated with chronic periodontitis (CP); however, no clear conclusions have been reached so far. In this retrospective cohort study, we aimed to investigate the association between obesity and CP by using a large population-based dataset in Taiwan. A population-based retrospective cohort study was conducted using the Longitudinal Health Insurance Database 2010 (LHID2010) derived from the National Health Insurance Research database in Taiwan, from 2000 to 2013. Obesity and non-obesity groups were matched with sex, age, urbanization level, socioeconomic status, and the related comorbidities by using the propensity score method at a 1:2 ratio. An obese cohort (n = 4140) and a non-obese cohort (n = 8280) were included in this study, with an average age of 41.7 ± 13.8 years and 42.0 ± 14.0 years, respectively. The risk of CP for the patients with obesity was 1.12-fold compared with those without obesity (hazard ratio, 1.12; 95% confidence interval, 1.01–1.25). In the subgroup analysis according to age and sex, the hazard ratio of CP were 1.98 (95% confidence interval, 1.22–3.22) in the subgroup of age equal to or older than 65 years. The risk of CP showed no difference between obesity and non-obesity groups in both sex. This population-based cohort study demonstrated that obesity was associated with the development of CP in Taiwan.
Assessment of Quality of Life in Patients With Cardiovascular Disease Using the SF-36, MacNew, and EQ-5D-5L Questionnaires

Background Cardiovascular disease (CVD) is responsible for 18 million annual deaths worldwide. CVD affects patients’ Quality of Life (QoL) mainly in physical, emotional and social dimension. Aim To assess the QoL of patients with CVD in Northern Greece, using three different instruments. Methods The study was conducted in one large hospital located in a major Greek city. A convenience sample of 80 patients participated. A questionnaire including Short Form-36 Health Survey (SF-36), EuroQoL 5-dimensions 5-levels (EQ-5D-5L), MacNew, demographic, and clinical characteristics was used to collect data. Results The mean age of the patients was 63.31±14.07. Analysis revealed statistically significant main effects of age on the physical limitations, emotional limitations, social functioning, and pain. Also, the analysis showed significant main effects of education on the MacNew Physical, MacNew Social, and the EQ-5D-5L index (p< 0.05). Participants who had graduated primary school had significantly lower quality of life scores than higher education graduates in the MacNew physical (p< 0.02). Furthermore, in the SF-36 pain subscale, the heart failure group had a significantly lower quality of life than the other heart diseases (p= 0.03). Conclusion Quality of life is affected by factors such as age, type of heart disease, therapy, and comorbidities. Health care providers should be knowledgeable of the factors that affect the quality of life sectors (physical, emotional, and social life) of patients with CVD in order to meet their needs and have the most suitable treatment.
Socio-behavioral factors, oral hygiene level and periodontitis prevalence in a 35-44-year-old Greek adult population: A cross-sectional survey

Background Sub-optimal oral hygiene is considered as a primary risk factor for periodontitis occurrence. Various socio-behavioral determinants may contribute either independently or by influencing adversely the oral hygiene (OH) level. The aim of the present study was to examine the periodontal status of 35-44-year-old Greek adults and determine the contribution of risk indicators, including the socio-behavioral aspects and the population’s oral hygiene level, on disease prevalence. Material and Methods In 1218 participants, Community Periodontal Index (CPI), Loss of Attachment (LoA) and simplified Oral Hygiene Index (OHI-S) were calculated. Multivariable regression models examined the effect of socio-behavioral factors with/without the inclusion of OHI-S level on pocket depth (PD)≥4mm and LoA≥4mm presence. Results 11.8% of the participants had healthy periodontium, whereas 37.3% and 5.6% presented with shallow and deep pocketing, respectively. 60.4%, 28.8%, and 10.8. % of the adults demonstrated LoA≤3mm, 4-5mm, and ≥6mm, accordingly. Fair and poor oral hygiene significantly increased the likelihood for PD≥4mm (OR=4.8-20.3) and LoA≥4mm (OR=3.3-6.0) presence. ‘Emergency-oriented dental visiting pattern’ significantly elevated the chance for PD≥4mm presence (OR=1.7). ‘Lower education level’ ‘urban location’, and ‘using an interdental brush’ were significantly independently linked to LoA≥4mm occurrence (OR=1.7-2.1, 1.5, and 2.0, respectively). Lower educated individuals demonstrated inferior oral hygiene status, which in turn elevated significantly the chances of PD≥4mm presence. Smoking more than 10 cigarettes/day, emergency-oriented dental attendance pattern and not flossing were linked to worse oral hygiene levels, which consequently increased significantly the likelihood of LoA≥4mm occurrence. Conclusions Fair and poor oral hygiene contribute strongly to periodontitis occurrence. Various socio-behavioral factors may influence adversely oral hygiene maintenance, leading to periodontitis manifestations. Key words:Community periodontal index, periodontal attachment loss, oral hygiene, adults 35-44, cross-sectional survey, socio-behavioral indicators.