Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust deep learning pipeline for PVC beats localization

BACKGROUND: Premature ventricular contraction (PVC) is among the most frequently occurring types of arrhythmias. Existing approaches for automated PVC identification suffer from a range of disadvantages related to hand-crafted features and benchmarking on datasets with a tiny sample of PVC beats. OBJECTIVE: The main objective is to address the drawbacks described above in the proposed framework, which takes a raw ECG signal as an input and localizes R peaks of the PVC beats. METHODS: Our method consists of two neural networks. First, an encoder-decoder architecture trained on PVC-rich dataset localizes the R peak of both Normal and anomalous heartbeats. Provided R peaks positions, our CardioIncNet model does the delineation of healthy versus PVC beats. RESULTS: We have performed an extensive evaluation of our pipeline with both single- and cross-dataset paradigms on three public datasets. Our approach results in over 0.99 and 0.979 F1-measure on both single- and cross-dataset paradigms for R peaks localization task and above 0.96 and 0.85 F1 score for the PVC beats classification task. CONCLUSIONS: We have shown a method that provides robust performance beyond the beats of Normal nature and clearly outperforms classical algorithms both in the case of a single and cross-dataset evaluation. We provide a Github1 repository for the reproduction of the results.
Identification and validation of potential mRNA- microRNA- long-noncoding RNA (mRNA-miRNA-lncRNA) prognostic signature for cervical cancer

ABSTRACT Cervical cancer is one of the most common causes of cancer deaths in women due to poor prognosis and high mortality rates. A novel mRNA-miRNA-lncRNA signature linked to prognosis of cervical cancer is needed to help clinicians judge the prognosis of individual patients more accurately. On the basis of GEO datasets, a total of 161 upregulated and 242 downregulated DE-mRNAs were identified firstly. Among them, eight potential biomarkers were found to have prognostic values with cervical cancer and miRNAs-lncRNAs related to these biomarkers were then analyzed to create mRNA-miRNA-lncRNA networks in cervical cancer. Moreover, in vitro experiments such as qRT-PCR, western blot and Edu assays were also performed to validate these promising targets. On the basis of these findings, a total of eight mRNA-miRNA-lncRNA subnetworks were finally established as a novel mRNA-miRNA-lncRNA signature and independent prognostic indicator of clinically relevant parameters by ROC analysis, univariate and multivariate Cox regression. Since some work of validation was done, it is believed that this mRNA-miRNA-lncRNA prognostic signature may be applied as a potential clinical judgment to estimate the prognosis of cervical cancer. GraphicalAbstract
Tandem repeat interval pattern identifies animal taxa

MOTIVATION We discover that maximality of information content among intervals of Tandem Repeats (TRs) in animal genome segregates over taxa such that taxa identification becomes swift and accurate. Successive TRs of a motif occur at intervals over the sequence, forming a trail of TRs of the motif across the genome. We present a method, Tandem Repeat Information Mining (TRIM), that mines 4k number of TR trails of all k length motifs from a whole genome sequence and extracts the information content within intervals of the trails. TRIM vector formed from the ordered set of interval entropies becomes instrumental for genome segregation. RESULTS Reconstruction of correct phylogeny for animals from whole genome sequences proves precision of TRIM. Identification of animal taxa by TRIM vector upon feature selection is the most significant achievement. These suggest Tandem Repeat Interval Pattern (TRIP) is a taxa-specific constitutional characteristic in animal genome. AVAILABILITY Source and executable code of TRIM along with usage manual are made available at https://github.com/BB-BiG/TRIM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Disaster Management in Rural and Remote Primary Health Care: A Scoping Review

Abstract Objective: This scoping review aims to map the roles of rural and remote primary health care professionals (PHCPs) during disasters. Introduction: Disasters can have catastrophic impacts on society and are broadly classified into natural events, man-made incidents, or a mixture of both. The PHCPs working in rural and remote communities face additional challenges when dealing with disasters and have significant roles during the Prevention, Preparedness, Response, and Recovery (PPRR) stages of disaster management. Methods: A Johanna Briggs Institute (JBI) scoping review methodology was utilized, and the search was conducted over seven electronic databases according to a priori protocol. Results: Forty-one papers were included and sixty-one roles were identified across the four stages of disaster management. The majority of disasters described within the literature were natural events and pandemics. Before a disaster occurs, PHCPs can build individual resilience through education. As recognized and respected leaders within their community, PHCPs are invaluable in assisting with disaster preparedness through being involved in organizations’ planning policies and contributing to natural disaster and pandemic surveillance. Key roles during the response stage include accommodating patient surge, triage, maintaining the health of the remaining population, instituting infection control, and ensuring a team-based approach to mental health care during the disaster. In the aftermath and recovery stage, rural and remote PHCPs provide long-term follow up, assisting patients in accessing post-disaster support including delivery of mental health care. Conclusion: Rural and remote PHCPs play significant roles within their community throughout the continuum of disaster management. As a consequence of their flexible scope of practice, PHCPs are well-placed to be involved during all stages of disaster, from building of community resilience and contributing to early alert of pandemics, to participating in the direct response when a disaster occurs and leading the way to recovery.
The Cost-Effectiveness of Lenvatinib in the Treatment of Advanced or Unresectable Hepatocellular Carcinoma from a Canadian Perspective

Lenvatinib is an oral multikinase inhibitor indicated for the first-line treatment of unresectable hepatocellular carcinoma (uHCC). In the Phase III REFLECT trial, lenvatinib was noninferior in the primary endpoint of overall survival versus sorafenib, the only systemic therapy funded in Canada prior to the introduction of lenvatinib. Lenvatinib also demonstrated statistically significant improvement compared to sorafenib in secondary endpoint progression-free survival, time to progression, and objective response rate. The aim of this analysis was to estimate the cost-effectiveness of lenvatinib versus sorafenib for the first-line treatment of patients with uHCC from a Canadian perspective. A cost-utility analysis was conducted using partitioned survival modelling, with health states representing progression-free disease, progressed disease, and death. Health effects were measured using quality-adjusted life years (QALYs), and costs were represented in Canadian dollars. Clinical inputs were derived from the REFLECT trial, with outcomes extrapolated using parametric survival models. EQ-5D data collected in REFLECT were used to determine health state utility values, and estimates of resource use came from a survey of clinicians. The model predicted incremental costs of-$5,021 and incremental QALYs of 0.17, making lenvatinib dominant over sorafenib. The model demonstrates lenvatinib to be a cost-effective use of resources versus sorafenib in Canada for the treatment of uHCC. Overall costs are lower compared with sorafenib, while health benefits are greater, with modelled progression-free and overall survival extended by 4.1 and 2.6 months in the lenvatinib arm, respectively.
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts

SUMMARY Post-sequencing quality control is a crucial component of RNA sequencing (RNA-seq) data generation and analysis, as sample quality can be affected by sample storage, extraction, and sequencing protocols. RNA-seq is increasingly applied to cohorts ranging from hundreds to tens of thousands of samples in size, but existing tools do not readily scale to these sizes, and were not designed for a wide range of sample types and qualities. Here, we describe RNA-SeQC 2, an efficient reimplementation of RNA-SeQC (DeLuca et al., 2012) that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols. AVAILABILITY AND IMPLEMENTATION The command-line tool, documentation, and C ++ source code are available at the GitHub repository https://github.com/getzlab/rnaseqc. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Protease-Activated Receptor 1 Contributes to Microcirculation Failure and Tubular Damage in Renal Ischemia-Reperfusion Injury in Mice

Ischemia-reperfusion- (IR-) induced kidney injury is difficult to avoid during renal transplantation and robot-assisted partial nephrectomy. Renal IR injury is characterized by tubular damage, microcirculation failure, and inflammation, which coordinately augment renal injury; however, no specific treatment is available for these conditions. Protease-activated receptor-1 (PAR-1) and its ligand, thrombin, are involved in coagulation and were shown to be associated with epithelial cell injury. Here, we hypothesized that PAR-1 exaggerated renal IR-induced tubular cell damage and microcirculation failure and that pharmacological inhibition of PAR-1 by Q94 could prevent these injuries. Renal warm IR increased the expression of PAR-1 in the renal tubules. Q94 attenuated renal IR-induced changes and histopathological damage. Microcirculation failure analyzed by congestion in the histopathology and blood cell flow examined by intravital multiphoton microscopy were suppressed by Q94 treatment. Q94 also dramatically increased tubular cell proliferation despite the lower renal damage. Thrombin suppressed cell proliferation and induced apoptosis in the tubules; these effects were prevented by Q94 treatment. Taken together, PAR-1 was associated with renal IR injury. Inhibition of PAR-1 ameliorated injury possibly by improving renal microcirculation and tubular cell survival/proliferation.
Metal ion adsorption behavior of lignocellulosic fiber–ethylene vinyl acetate composites

This study describes the applicability of lignocellulosic fiber dispersed in ethylene vinyl acetate (EVA) to adsorb Pb(II), Cr(III), and Cr(VI) ions in aqueous solutions. Water absorption studies revealed that metal-ion uptake does not only take place on the surface of the adsorbent but ions can also diffuse into the composite. The adsorption of the metal ions under different experimental conditions was studied. Solute concentration, pH, and contact time were used to assess the adsorption capacity and efficiency. The amount of metal adsorbed increased to 7 mg/g with an increase in solute concentration but compromising the efficiency. Adsorption equilibrium was reached after 3 h, when the maximum lead adsorption was above 80%. The optimum pH for the adsorption of Pb(II) and Cr(III) was 6.5, and pH 2.5 was used for the adsorption of Cr(VI). Competitive adsorption revealed the order of adsorption to be: Pb(II) > Cr(VI) > Cr(III). POLYM. ENG. SCI., 52:760–767, 2012. a 2011 Society of Plastics Engineers
The Efficacy of Ramucirumab in the Treatment of Gastric or Gastroesophageal Junction Cancer: A Meta-Analysis of RCTs

Five electronic databases were searched for eligible records. Outcomes were presented and analyzed according to the objective response rate (ORR), progression-free survival (PFS) rate, and overall survival (OS) rate. Five records involving 2,024 participants were included in the study. The pooled analysis of OS and PFS were longer with ramucirumab (RAM) therapy than without RAM for OS (odds ratio (OR) = 0.90, 95% confidence interval (CI) = 0.82–1.00, p = 0.05) and PFS (OR = 0.74, 95%CI = 0.57–0.96, p = 0.02). Moreover, compared with the current first-line chemotherapy, the OS (OR = 0.93, 95%CI = 0.83–1.04, p = 0.19) and PFS (OR = 0.82, 95%CI = 0.64–1.06, p = 0.13) results were not significantly higher with RAM. The ORRs of the patients in the RAM therapy groups were significantly higher than those in the groups without RAM (OR = 1.40, 95%CI = 1.14–1.73, p = 0.001).
The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses

ABSTRACT The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as Arabidopsis, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in Solanum lycopersicum. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive cis-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.
Autonomous nervous system regulation of pain in children with cerebral palsy

ABSTRACT Aim: Children with cerebral palsy (CP) have increased pain sensitivity and recurrent pain episodes; however, pain is underreported in children with intellectual impairment. Cardiac autonomic regulation is imbalanced in chronic pain conditions and neurological disorders. This study aims at exploring the autonomous nervous system regulation of pain in children with CP compared with typically developing peers (TDP). Method: Heart rate variability (HRV) was recorded during 24 hours in 26 children with CP and 26 TDP, and examined offline at baseline (sleeping, seated rest) and during spontaneous pain events. Pain and fatigue, HRV indices (linear indices on time – IBI, SDNN, RMSSD – and frequency domains – high, low, and very low frequency – and non-linear indices – Hurst coefficient and multiscale entropy) were computed.Results: Children with CP showed comparable HRV during daily conditions and similar reductions after pain events than their TDP, regardless of their level of intellectual impairment. Interpretation: Children with CP have an intact autonomic regulation in acute pain events. HRV could be an accurate pain biomarker in children with CP and intellectual disability. What this paper adds: Autonomic regulation in acute pain is efficient in children with cerebral palsy. Heart rate variability indices can be reliable pain biomarkers in intellectual impairment.
The complete chloroplast genomes of two species from Capparaceae

Abstract Capparis spinosa L. and Capparis decidua Forsk. belong to the Capparaceae family. The two species are important medicinal plants uses in treatment of various ailments. In this study, we present the complete chloroplast genomes of the two species. The complete plastome genomes of the two species have a circular structure and a length of 157,728 bp in Capparis spinosa and 157,573 bp in Capparis decidua and GC content of 35.91, 35.96% respectively. The chloroplast genome of C. spinosa and C. decidua is divided into four regions: LSC of 86,732 and 85,950 bp respectively, SSC from 18,322 to 18,621 bp and a pair of inverted repeats 26,337 and 26,501 bp each. Both of the chloroplast genomes contained 115 different genes, including 80 protein coding genes, 31 tRNA genes and four rRNA genes. A phylogenetic analysis demonstrated that C. spinosa is sister to Capparis urophylla. The two species are sister to C. decidua.
Clinical development of valbenazine for tics associated with Tourette syndrome

ABSTRACT Introduction: Significant need exists for effective, well-tolerated pharmacologic treatments for Tourette syndrome (TS). Medications that inhibit vesicular monoamine transporters (i.e. VMAT2 inhibitors) downregulate presynaptic packaging and release of dopamine into the neuronal synapse and are effective in treating hyperkinetic movement disorders such as Huntington’s chorea and tardive dyskinesia (TD); thus, they may be useful in treating TS. Areas covered: This review describes the clinical program evaluating the safety and efficacy of valbenazine in the treatment of involuntary tics associated with TS in adult and pediatric subjects. While there was a trend in the 6 completed trials toward greater improvement in valbenazine-treated versus placebo subjects on the primary efficacy endpoint (Yale Global Tic Severity Scale Total Tic Score), this difference did not reach statistical significance. Valbenazine was generally well-tolerated in the studies, and treatment-emergent adverse events were consistent with valbenazine studies in TD. Expert opinion: Due to the failure to meet the primary endpoint in these trials, further investigation of valbenazine for TS is unlikely. Given the need for safe and effective TS therapies and the key role of VMAT2 in modulating dopaminergic activity, it is reasonable for future studies to investigate other VMAT2 inhibitors as potential treatments for TS.
Chromium Determination in Leather and Other Matrices: A Review

Abstract Leather industry plays an essential role in the world’s economy; however, it also has a negative environmental impact due to the generation of significant quantities of wastes, some of which are classified as hazardous chemicals. Chrome tanning, the most popular tanning process, employs chromium salts, acids, and some other chemicals. Some dyes can be also a source of chromium. As a result, hexavalent chromium, a known carcinogenic and mutagenic, can be found in leather products and cause allergic dermatitis or trigger other diseases. For this reason, it is important to quantify the total amount of chromium in final leather goods, as well as the oxidation state in which this element is found. This paper aims to summarize chromium contamination due to the leather production processes, and to review the analytical methods that have been used to determine chromium’s most abundant species: Cr(III) and Cr(VI) in leather and other matrices (foodstuffs, cosmetic products, environmental, and pharmaceutical samples). The international and European regulations are presented as well as the last academic developments to extract and quantify chromium species. The future outlook of pretreatment and quantification techniques are also discussed in this work, with a special focus on chromium interconversions.
Higher protein intake during resistance training does not potentiate strength, but modulates gut microbiota, in middle-aged adults: a randomized control trial.

Protein intake above the Recommended Dietary Allowance (RDA) and resistance training are known anabolic stimuli to support healthy aging. Specifically, protein supplementation after resistance exercise and nightly are strategies to maximize utilization of protein intake above the RDA in healthy adults. As such, the primary objective was to examine the efficacy of protein supplementation and nutritional counseling resulting in either moderate (MOD: ~1.0 g·kg-1·d-1) or higher (HIGH: ~1.6 g·kg-1·d-1) protein intake during resistance training on strength (one-repetition maximum, 1-RM; isokinetic and isometric peak torque) in healthy middle-aged adults. Exploratory analyses include diet-exercise effects on lean body mass (LBM), clinical biomarkers, gut microbiota, and diet composition. 50 middle-aged adults (age: 50 ± 8 y, BMI: 27.2 ± 4.1 kg·m-2) were randomized to either MOD or HIGH protein intake during a 10-week resistance training program (3 × week). Participants received dietary counseling and consumed either 15 g (MOD) or 30 g (HIGH) of protein from lean beef in the immediate post-exercise period and each evening. Maximal strength (1-RM) for all upper and lower body exercises significantly increased with no effect of protein intake (P<0.050). There was a main effect of time for LBM (P<0.005). Cardiovascular, renal, or glycemic biomarkers were not affected by the intervention. Gut microbiota were associated with several health outcomes (P<0.050). In conclusion, higher protein intake above moderate amounts does not potentiate resistance training adaptations in previously untrained middle-aged adults. This trial was registered at clinicaltrials.gov as NCT03029975.
Alkaloids constituents from the roots of Phragmites australis (Cav.) Trin. ex Steud. with their cytotoxic activities

Abstract Two new alkaloids, phranisines A–B (1–2), along with two known compounds, N-p-Coumaroyl serotonin (3) and N-p-coumaroyl-tryptamine (4), were isolated from the roots of Phragmites australis. The structures of 1–4 were established on the basis of extensive spectroscopic. The absolute configuration of compounds 1–2 were identified through quantum-chemical electronic circular dichroism (ECD) calculation compared with their experimental CD. All the isolated compounds were tested for their cytotoxic activities against HeLa and MCF-7 human cancer cell lines, and compounds 2–4 showed moderate cytotoxic activities against HeLa cell lines with IC50 values ranging from 13.2 to 18.6 μM. GRAPHICAL ABSTRACT
The Military Service Sleep Assessment: an instrument to assess factors precipitating sleep disturbances in U.S. military personnel.

STUDY OBJECTIVES Military personnel frequently experience sleep difficulties, but little is known regarding which military or life events most impact their sleep. The Military Service Sleep Assessment (MSSA) was developed to assess the impact of initial military training, first duty assignment, permanent change of station, deployments, redeployments, and stressful life events on sleep. This study presents an initial psychometric evaluation of the MSSA and descriptive data in a cohort of service members. METHODS The MSSA was administered to 194 service members in a military sleep disorders clinic as part of a larger study. RESULTS Average sleep quality on the MSSA was 2.14 (on a Likert scale, with "1" indicating "low" and "5" indicating "high" sleep quality), and 72.7% (n = 140) rated their sleep quality as "low" to "low average. " The events most reported to negatively impact sleep were stressful life events (41.8%) followed by deployments (40.6%). Military leadership position (24.7%) and birth/adoption of a child (9.7%) were the most frequently reported stressful life events to negatively impact sleep. There were no significant differences in current sleep quality among service members with a history of deployment compared to service members who had not deployed. CONCLUSIONS The MSSA is the first military-specific sleep questionnaire. This instrument provides insights into the events during a service member's career, beyond deployments, which precipitate and perpetuate sleep disturbances and likely chronic sleep disorders. Further evaluation of the MSSA in non-treatment-seeking military populations and veterans is required.