Miracle-dz/UniFAR-FTUs huggingface dataset:
Early onset colorectal cancer in Canterbury, New Zealand

The overall incidence of colorectal cancer is decreasing in much of the world, yet the incidence in those under 50 years of age is increasing (early onset colorectal cancer (EOCRC)). The reasons for this are unclear. This study was undertaken to describe the clinical, pathological and familial characteristics of patients with EOCRC and their oncological outcomes and compare this with previously published data on late onset colorectal cancer (LOCRC).
Obstructive sleep apnea screening in children with asthma

Obstructive sleep apnea is highly prevalent in children with asthma, particularly in obese children. The sleep‐related breathing disorder screening questionnaire has low screening accuracy for obstructive sleep apnea in children with asthma. Our goal was to identify the questions on the sleep‐related breathing disorder survey associated with obstructive sleep apnea in children with asthma.
German Medical Named Entity Recognition Model and Data Set Creation Using Machine Translation and Word Alignment: Algorithm Development and Validation

Background Data mining in the field of medical data analysis often needs to rely solely on the processing of unstructured data to retrieve relevant data. For German natural language processing, few open medical neural named entity recognition (NER) models have been published before this work. A major issue can be attributed to the lack of German training data. Objective We developed a synthetic data set and a novel German medical NER model for public access to demonstrate the feasibility of our approach. In order to bypass legal restrictions due to potential data leaks through model analysis, we did not make use of internal, proprietary data sets, which is a frequent veto factor for data set publication. Methods The underlying German data set was retrieved by translation and word alignment of a public English data set. The data set served as a foundation for model training and evaluation. For demonstration purposes, our NER model follows a simple network architecture that is designed for low computational requirements. Results The obtained data set consisted of 8599 sentences including 30,233 annotations. The model achieved a class frequency–averaged F1 score of 0.82 on the test set after training across 7 different NER types. Artifacts in the synthesized data set with regard to translation and alignment induced by the proposed method were exposed. The annotation performance was evaluated on an external data set and measured in comparison with an existing baseline model that has been trained on a dedicated German data set in a traditional fashion. We discussed the drop in annotation performance on an external data set for our simple NER model. Our model is publicly available. Conclusions We demonstrated the feasibility of obtaining a data set and training a German medical NER model by the exclusive use of public training data through our suggested method. The discussion on the limitations of our approach includes ways to further mitigate remaining problems in future work.
Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning

With the advances in single-cell sequencing techniques, numerous analytical methods have been developed for delineating cell development. However, most are based on Euclidean space, which would distort the complex hierarchical structure of cell differentiation. Recently, methods acting on hyperbolic space have been proposed to visualize hierarchical structures in single-cell RNA-seq (scRNA-seq) data and have been proven to be superior to methods acting on Euclidean space. However, these methods have fundamental limitations and are not optimized for the highly sparse single-cell count data. To address these limitations, we propose scDHMap, a model-based deep learning approach to visualize the complex hierarchical structures of scRNA-seq data in low-dimensional hyperbolic space. The evaluations on extensive simulation and real experiments show that scDHMap outperforms existing dimensionality-reduction methods in various common analytical tasks as needed for scRNA-seq data, including revealing trajectory branches, batch correction, and denoising the count matrix with high dropout rates. In addition, we extend scDHMap to visualize single-cell ATAC-seq data.
Draft Genome Sequences of Three “Candidatus Symbiopectobacterium” Isolates Collected from Potato Tubers Grown in New Zealand

The draft genome sequences of three “Candidatus Symbiopectobacterium” isolates that were collected from New Zealand-grown potato tubers represent the first report of this proposed taxon in the Southern Hemisphere. Their symbiosis with insects and nematodes and their presence on plants may lead to new strategies for pest control and crop management. ABSTRACT The draft genome sequences of three “Candidatus Symbiopectobacterium” isolates that were collected from New Zealand-grown potato tubers represent the first report of this proposed taxon in the Southern Hemisphere. Their symbiosis with insects and nematodes and their presence on plants may lead to new strategies for pest control and crop management.
An observational study of safety and clinical outcome measures across patient groups in the United Kingdom Medical Cannabis Registry

ABSTRACT Background There is a paucity of high-quality data on patient outcomes and safety after initiating treatment with cannabis-based medicinal products (CBMPs). The aim of this study was to assess the clinical outcomes and safety of CBMPs by analyzing patient-reported outcome measures and adverse events across a broad spectrum of chronic conditions. Research design and methods This study analyzed patients enrolled in the UK Medical Cannabis Registry. Participants completed the EQ-5D-5L to assess health-related quality of life, Generalized Anxiety Disorder-7 (GAD-7) questionnaire to measure anxiety severity, and the Single-item Sleep Quality Scale (SQS) to rate sleep quality at baseline and follow-up after 1, 3, 6, and 12 months. Results A total of 2833 participants met inclusion criteria. The EQ-5D-5L index value, GAD-7, and SQS all improved at each follow-up (p < 0.001). There was no difference in EQ-5D-5L index values between former or current illicit cannabis consumers and naïve patients (p > 0.050). Adverse events were reported by 474 (16.73%) participants. Conclusions This study suggests that CBMPs are associated with an improvement in health-related quality of life in UK patients with chronic diseases. Treatment was tolerated well by most participants, but adverse events were more common in female and cannabis-naïve patients.
Response to: Influence of Tensioner’s Mobilization on the Centralization of Symptoms in Cervicobrachial Pain Syndrome: A Randomized Controlled Trial

Copyright C 2023 by Korean Society of Spine Surgery This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Asian Spine Journal • pISSN 1976-1902 eISSN 1976-7846 • www.asianspinejournal. org Received Jan 9, 2023; Accepted Jan 19, 2023 Corresponding author: Meena Makhija Department of Physiotherapy, Indian Spinal Injuries Centre-Institute of Rehabilitation Sciences, Vasant Kunj, New Delhi, India Tel: +91-9910011816, Fax: +91-26898810, E-mail: makhijameena81@gmail.com
Fluctuation effects on microphase separation in a random copolymer Hamiltonian

We investigate the effect of fluctuations in the effective Hamiltonian that describes the microphase separation in random copolymers. This Hamiltonian is previously studied on the level of mean-field theory where a phase transition to a phase with periodic microdomain structure was predicted. It is shown that the one-loop treatment of fluctuations is exact in the thermodynamic limit and that the phase predicted by the mean field is unstable within the framework of the studied Hamiltonian.
Turkish validity and reliability study for the perceived control of asthma questionnaire

Abstract Rationale The prevalence of asthma is high in Turkish people. however, there is no measurement tool that evaluates the patient’s perception that affects asthma management. Aim In this study, the aim was to test the validity and reliability of the Perceived Control of Asthma Questionnaire (PCAQ) among adults with asthma and to investigate the psychometric features. Method A total of 152 people aged 18 and over, who were diagnosed with asthma at least 1 year ago by a pulmonologist and volunteered to participate in the study were included in the study. The validity of the scale was investigated with exploratory factor analysis, confirmatory factor analysis and criterion validity, while the reliability of the scale was investigated with the Cronbach alpha coefficient and test-repeat test method. Item analysis, corrected item-total point correlations and mean item points for lower-upper 27% groups were investigated. Results According to exploratory factor analysis results, the Turkish form of the PCAQ appeared to explain 53.093% of total variance related to the feature measured. The results of confirmatory factor analysis calculated the goodness-of-fit values for the scale as χ2/sd = 1.507, RMSEA = 0.058, GFI = 0.928, IFI = 0.958, and NFI = 0.886. Additionally, factor loads were ranked from 0.46 to 0.79. The Cronbach alpha internal consistency coefficient was 0.85. The corrected item-total coefficient correlations varied from 0.48 to 0.69. Conclusion All these results show the Perceived Control of Asthma Questionnaire (PCAQ) is a valid and reliable scale tool that can be used for Turkish adults with asthma.
Proportion of falls reported in persons with Parkinson's disease: A meta-analysis

Objective Falls can be highly debilitating and have an important negative impact on the quality of life of patients with Parkinson's disease (PD). The aim of this systematic review and meta-analysis is to provide an up-to-date overview of the prevalence of ≥1 fall and ≥2 falls in idiopathic PD. Data Sources MEDLINE, Web of Science, Embase and Cinahl databases were systematically searched until 04 July 2022 for prospective studies reporting fall prevalence in persons with idiopathic PD. Methods Pooled prevalence rates with 95% confidence intervals (CIs) were computed using random-effects models. Heterogeneity among studies was assessed using the I2 statistic. Results A total of 54 studies (7546 participants) were included, and random-effects meta-analysis yielded a pooled proportional fall rate of 0.48 (95% CI [0.43–0.52], I2 = 93%, 46 studies, 6874 participants) for classification 1 (≥1 fall) and a pooled proportional fall rate of 0.32 (95% CI [0.27–0.37], I2 = 78%, 31 studies, 5672 participants) for classification 2 (≥2 falls). Subgroup analysis on the classification of falls, and length and method of monitoring falls did not reveal significant differences and did not reduce between-study variability. Conclusion Pooled estimates suggest that one in two persons with PD fall at least once, and one in three fall at least twice within the registered time period. Substantial variability remains after pooling fall prevalence rates according to the length and method of monitoring. Therefore, no recommendations can be made concerning these methodological aspects. Future research on falls in PD is encouraged to implement best practice recommendations to monitor and report fall data.
Retailer’s Density and Single Stick Cigarette’s Accessibility among School-Age Children in Indonesia

Objective: The density of single-stick cigarette sales is related to the increase in tobacco epidemic-related diseases. This study aims to provide evidence of retailers’ density and radius around the school location, accessibility of single-stick cigarette selling among school-age children, and retailers’ response regarding the restriction policy options in urban areas in Indonesia. Methods: It is a cross-sectional study. The retailers’ spatial density and the radius around schools in Daerah Khusus Ibukota (DKI) Jakarta Province were investigated using Google Maps and Google Street View (GSV). The coordinates of retailers and schools were geo-coded to Kernel Density Map. The accessibility of single-stick cigarettes among children and restriction policy options for cigarette selling were derived from random sampling using surveys of 64 retailers based on Google Data results. Result: Virtually walking using google maps and GSV found 8,371 retailers in DKI Jakarta. There were ± 15 cigarette retailers every 1 km2, and an average of ± one cigarette retailer in every 1,000 residents. There were 456 (21.67%) retailers with a radius ≤ 100 meters around elementary schools, even an increase around junior high school locations of 167 (26.05%) retailers. The accessibility of cigarettes among children is easy because the price is relatively low, at Rp1,500/ $0.11 per stick. In addition, 58.1% of retailers allowed customers to buy on debt. Eleven percent of cigarette retailers intended to reduce the sale of cigarettes if the prohibition of single-stick cigarette sales were applied. Conclusion: Cigarette retailers were very dense and single-stick cigarettes were still accessible to children in Indonesia. The implementation of the prohibition on single-stick cigarette sales should be added for future tobacco control in developing countries such as Indonesia.
Improving neuropathic pain treatment - by rigorous stratification from bench to bedside.

Chronic pain is a constantly recurring and persistent illness, presenting a formidable healthcare challenge for patients and physicians alike. Current first line analgesics offer only low-modest efficacy when averaged across populations, further contributing to this debilitating disease burden. Moreover, many recent trials for novel analgesics have not met primary efficacy endpoints, which is particularly striking considering the pharmacological advances have provided a range of highly relevant new drug targets. Heterogeneity within chronic pain cohorts is increasingly understood to play a critical role in these failures of treatment and drug discovery, with some patients deriving substantial benefit from a given intervention whilst it has little-to-no effect in others. As such, current treatment failures may not result from a true lack of efficacy, but rather a failure to target them to individuals whose pain is driven by mechanisms which it therapeutically modulates. This necessitates a move towards phenotypical stratification of patients in order to delineate responders and non-responders in a mechanistically driven manner. In this article, we outline a bench-to-bedside roadmap for this transition to mechanistically informed personalised pain medicine. We emphasise how successful identification of novel analgesics is dependent on rigorous experimental design as well as validity of models and translatability of outcome measures between animal model and patients. Subsequently, we discuss general and specific aspects of human trial design to address heterogeneity in patient populations to increase the chance of identifying effective analgesics. Finally, we show how stratification approaches can be brought into clinical routine to the benefit of patients.
Local Regulator AcrR Regulates Persister Formation by Repression of AcrAB Efflux Pump during Exponential Growth in Aeromonas veronii

Bacterial persisters refer to a small fraction of dormant variants that survive treatment with high concentrations of antibiotics. Increasing research indicates that multidrug efflux pumps play a major role in persister formation in many Gram-negative organisms. ABSTRACT Bacterial persisters refer to a small fraction of dormant variants that survive treatment with high concentrations of antibiotics. Increasing research indicates that multidrug efflux pumps play a major role in persister formation in many Gram-negative organisms. In the present study, the roles of the repressor of the AcrAB efflux pump, AcrR, in the regulation of the activity and function of the efflux, as well as in the production of persisters, were investigated in the pathogen Aeromonas veronii, which causes huge economic losses in the aquatic industry and threatens human health. We observed that exclusively in exponential-phase cells, not in stationary-phase cells, the deletion of the acrR gene significantly (P < 0.05) promoted the expression of the acrA and acrB genes and reduced the intracellular accumulation of the efflux substrate Hoechst 33342. Moreover, overexpression of acrR triggered decreased transcription of the promoter of the acrAB operon. The persister assay indicated that the loss of the AcrAB pump decreased the formation of persisters under challenge with all tested antibiotic types of chloramphenicol, fluoroquinolone, tetracycline, and β-lactam, while deletion of acrR caused an exponential-phase-specific increase in persister formation against chloramphenicol, tetracycline, and β-lactam. Our results provide molecular insights into the mechanism of bacterial persistence by demonstrating for the first time that the local regulator AcrR is involved in the modulation of persister formation in A. veronii through its repressive activity on the function of the AcrAB efflux pump during the exponential growth period.
Frequency, risk factors, and impacts on quality of life of the restless legs syndrome and side effects among antidepressant users in a tertiary hospital: an observational cross-sectional study

Restless leg syndrome (RLS) is a common but underestimated sensorimotor disorder that significantly affects the quality of life (QoL) which can be induced by antidepressants. This study aims to investigate the frequency and potential risk factors of RLS and side effects in selective serotonin reuptake inhibitors/serotonin and noradrenaline reuptake inhibitors (SSRI/SNRI) users. This cross-sectional study included 198 outpatients who received SSRI/SNRI for 4–8 weeks. Clinical evaluation was performed using the International Restless Leg Syndrome Study Group rating scale for RLS, Udvalg for Kliniske Undersøgelser side effects rating scale, and a short form 36 (SF-36) questionnaire for QoL. The frequency of RLS was 25%. RLS significantly increased with smoking and habituality. Also, habituality increased neurologic side effects reporting. The use of antipsychotics and calcium channel blockers decreased reporting of autonomic side effects. QoL decreased with RLS, psychiatric, neurologic, autonomic, and other side effects in different domains of SF-36. These findings suggested that SSRI/SNRI use could be associated with a higher risk of RLS, especially in smokers. QoL could be influenced negatively by RLS and all side effects. However, further prospective studies are needed to confirm these associations in large samples.
Agreement Between Dual-Energy X-ray Absorptiometry and Bioelectric Impedance Analysis for Assessing Body Composition in Athletes: A Systematic Review and Meta-Analysis

Objective: To compare dual-energy x-ray absorptiometry (DXA) and bioelectric impedance analysis (BIA) in the assessment of body composition in athletes. Data Sources: A systematic review and meta-analysis was conducted collating peer-reviewed studies that compared BIA with DXA for the assessment of body composition in athletes that indexed in MEDLINE, CINAHL, EMBASE, and PsycINFO databases. Main Results: After duplicate removal, 267 articles remained for full-text screening. Sixty-three studies remained for the final inclusion, with 8 focused on athletes (n = 461). Five studies were included in the meta-analysis and were rated as positive after risk of bias assessment, whereas the remaining were neutral. BIA overestimated fat-free mass (FFM) over DXA 2.78 (1.38-4.18) (mean difference ± 95% CI) with an effect size of 3.9(P < 0.001). Conclusions: BIA was found to overestimate total FFM when compared with DXA. Correlations are high between BIA and DXA; however, the limits of agreement are wide. Hence, BIA may not be a suitable substitute for DXA body composition scanning of athletes. Because of the low level of ionizing radiation exposure, the use of DXA should always be medically justified, and therefore, it is not recommended for repeat, longitudinal measurements in healthy subjects. We recommend that clinicians do not use BIA interchangeably with DXA in the assessment of body composition in athletes. Considerations should be made over the safety and appropriateness of DXA in young healthy adults. For long-term use, BIA can be warranted for athletes. PROSPERO Registration Number: CRD42020183777
Effects of forward collision warning and automatic emergency braking on rear-end crashes involving pickup trucks

Abstract Objective Forward collision warning (FCW) and automatic emergency braking (AEB) have found to be effective on cars, SUVs, and large trucks. The objective of this study was to extend prior work and estimate the effects of FCW and AEB on pickups. Methods Rear-end crashes where a pickup with optional FCW or AEB was the striking vehicle were identified in 25 U.S. states during 2017–2020. Quasi-induced exposure was performed with logistic regression to compare rear-end-striking crashes between vehicles with and without the systems relative to being struck in the rear. Rear-end-striking crash rates per registered vehicle year were also compared between equipped and non-equipped pickups with Poisson regression. The association of the systems with severity in the rear-end-striking crashes that occurred was examined with logistic regression. Results In the quasi-induced exposure analysis, AEB was associated with statistically significant 34% reductions in the risk of a rear-end-striking crash of any severity and with any injuries, and a 76% reduction in the risk of a rear-end-striking crash with serious or fatal injuries (p = 0.09). FCW was associated with statistically significant declines of 22% in the risk of a rear-end-striking crash with any injuries and 71% in the risk of a rear-end-striking crash with serious or fatal injuries, but FCW was not associated with a change in all rear-end-striking crashes. Results were similar in Poisson regression models for all but FCW’s effect on all rear-end-striking crashes. The odds that rear-end-striking crashes involving pickups with FCW resulted in any injuries were 26% lower, and serious/fatal injuries were 75% lower, than those involving pickups without the system. AEB was associated with a nonsignificant reduction in the odds of serious/fatal injuries when a rear-end strike occurred and no change in the odds of any injuries. Discussion Consistent benefits for front crash prevention systems have been demonstrated for a wide range of vehicle types, now including a sample of pickups. Gaps in proposed U.S. regulations should be filled so that AEB is required equipment on all new vehicles.
Rab3 mediates a pathway for endocytic sorting and plasma membrane recycling of ordered microdomains

Significance Membrane microdomains known as lipid rafts have been posited as an important mechanism for sorting and trafficking of membrane components between various organelles. Using genetic probes designed to quantitatively tune protein preference for raft microdomains, we have evaluated the pathways and protein players involved in sorting proteins that associate with these ordered membrane microdomains. We identified the GTPase Rab3 as a central mediator of this pathway, revealing a route for sorting of certain membrane proteins by their preference for ordered membrane environments.