Exploring miRNA-target gene pair detection in disease with coRmiT.

A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.

A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.

Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across participants at read level. Depending on the frequency of incorrect target reads, this either leads to correct or incorrect typing, whereby only minimal frequency deviations can randomly determine the final result. PCR preamplification, recent basecalling model updates and an optimized polishing strategy notably diminished the non-reproducible typing. Our study highlights the potential for new errors to appear with each newly sequenced strain and lays the foundation for computational approaches to reduce such typing errors. In conclusion, our multicenter study shows the necessity for a new validation concept for nanopore sequencing-based, standardized bacterial typing, where single nucleotide accuracy is critical.

Effects of high-intensity training on fatty infiltration in paraspinal muscles in elderly males with osteosarcopenia - the randomized controlled FrOST study.

BACKGROUND: Osteosarcopenia is a common geriatric syndrome with an increasing prevalence with age, leading to secondary diseases and complex consequences such as falls and fractures, as well as higher mortality and frailty rates. There is a great need for prevention and treatment strategies. METHODS: In this analysis, we used magnetic resonance imaging (MRI) data from the randomised controlled FrOST trial, which enrolled community-dwelling osteosarcopenic men aged > 72 years randomly allocated to 16 months of twice-weekly high-intensity resistance training (HIRT) or a non-training control group. MR Dixon imaging was used to quantify the effects of HIRT on muscle fat infiltration in the paraspinal muscles, determined as changes in muscle tissue, fat faction and intermuscular adipose tissue (IMAT) in the erector spinae and psoas major muscles. Intention-to-treat analysis with multiple imputation was used to analyse the data set. RESULTS: After 16 months of intervention, 15 men from the HIRT and 16 men from the CG were included in the MRI analysis. In summary, no positive effects on the fat infiltration of the erector spinae and psoas major muscles were observed. CONCLUSIONS: The previously reported positive effects on lumbar spine bone mineral density (BMD) suggest that mechanotransduction induces tropic effects on bone, but that fat infiltration of the erector spinae and psoas major muscles are either irreversible or, for some unknown reason, resistant to exercise. Because of the beneficial effects on spinal BMD, HIRT is still recommended in osteosarcopenic older men, but further research is needed to confirm appropriate age-specific training exercises for the paraspinal muscles. The potential of different MRI sequences to quantify degenerative and metabolic changes in various muscle groups must be better characterized. TRIAL REGISTRATIONS: FrOST was approved by the University Ethics Committee of the Friedrich-Alexander University of Erlangen-Nürnberg (number 67_15b and 4464b) and the Federal Office for Radiation Projection (BfS, number Z 5-2,246,212 - 2017-002). Furthermore, it fully complies with the Declaration of Helsinki and is registered at ClinicalTrials.gov: NCT03453463 (05/03/2018). JAMA 310:2191-2194, 2013.

Ready-to-use nanopore platform for label-free small molecule quantification: Ethanolamine as first example.

In recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance, as their detection is difficult or expensive using available methods such as HPLC or LC-MS. DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Herein, a method for quantifying small molecules using a ready-to-use sequencing platform is described. Taking ethanolamine as an example, a strand displacement assay is developed in which the target-binding aptamer is displaced from the surface of magnetic particles by ethanolamine. Non-displaced aptamer and thus the ethanolamine concentration are detected by the nanopore system and can be quantified in the micromolar range using our in-house developed analysis software. This method is thus the first to describe a label-free approach for the detection of small molecules in a protein nanopore system.

Factors predicting long-term outcomes following physiotherapy in patients with subacromial pain syndrome: a secondary analysis.

BACKGROUND: Although patients with shoulder complaints are frequently referred to physiotherapy, putative predictive factors for outcomes are still unclear. In this regard, only a limited amount of scientific data for patients with subacromial pain syndrome exist, with inconsistent results. An improved knowledge about the ability of baseline variables to predict outcomes could help patients make informed treatment decisions, prevent them from receiving ineffective treatments, and minimize the risk of developing chronic pain. AIM: The aims of this secondary longitudinal analysis are threefold: First, to investigate baseline differences between patients with and without successful long-term outcomes following physiotherapy. Second, to compare the predictive ability of two sets of putative predictive variables on outcomes, one based on the literature and one based on the data of the original trial. Third, to explore the contribution of short-term follow-up data to predictive models. METHODS: Differences between responders and nonresponders were calculated. The predictive ability of variables defined through literature and of variables based on the Akaike Information Criterion (AIC) from the original trial dataset on the Shoulder Pain and Disability Index and the Patients' Global Impression of Change at the one-year follow-up were analyzed. To test the robustness of the results, different statistical models were used. To investigate the contribution of follow-up data to prediction, short-term data were included in the analyses. RESULTS: A sample of 87 patients with subacromial pain syndrome was analyzed. 77% (n = 67) of these participants were classified as responders. Higher expectations and short-term change scores were positive, and higher fear avoidance beliefs, greater baseline disability and pain levels were negative predictors of long-term outcomes in patients with subacromial pain syndrome. CONCLUSIONS: Although our results are in line with previous research and support the use of clinical factors for prediction, our findings suggest that psychological factors, especially patient expectations and fear avoidance beliefs, also contribute to long-term outcomes and should therefore be considered in the clinical context and further research. However, the hypotheses and recommendations generated from our results need to be confirmed in further studies due to their explorative nature. TRIAL REGISTRATION: The original trial was registered at Current Controlled Trials under the trial registration number ISRCTN86900354 on March 17, 2010.

Non-Athletic Cohorts Enrolled in Longitudinal Whole-Body Electromyostimulation Trials-An Evidence Map.

Whole-body electromyostimulation (WB-EMS) can be considered as a time-efficient, joint-friendly, and highly customizable training technology that attracts a wide range of users. The present evidence map aims to provide an overview of different non-athletic cohorts addressed in WB-EMS research. Based on a comprehensive systematic search according to PRISMA, eighty-six eligible longitudinal trials were identified that correspond with our eligibility criteria. In summary, WB-EMS research sufficiently covers all adult age categories in males and females. Most cohorts addressed (58%) were predominately or exclusively overweight/obese, and in about 60% of them, diseases or conditions were inclusion criteria for the trials. Cohorts specifically enrolled in WB-EMS trials suffer from cancer/neoplasm (n = 7), obesity (n = 6), diabetes mellitus (n = 5), metabolic syndrome (n = 2), nervous system diseases (n = 2), chronic heart failure (n = 4), stroke (n = 1), peripheral arterial diseases (n = 2), knee arthrosis (n = 1), sarcopenia (n = 3), chronic unspecific low back pain (n = 4), and osteopenia (n = 3). Chronic kidney disease was an eligibility criterion in five WB-EMS trials. Finally, three studies included only critically ill patients, and two further studies considered frailty as an inclusion criterion. Of importance, no adverse effects of the WB-EMS intervention were reported. In summary, the evidence gaps in WB-EMS research were particular evident for cohorts with diseases of the nervous and cerebrovascular system.

Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.

Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.

Exercise training and bone mineral density in postmenopausal women: an updated systematic review and meta-analysis of intervention studies with emphasis on potential moderators.

The aim of this systematic review and meta-analysis was (1) to determine exercise effects on bone mineral density (BMD) in postmenopausal women and (2) to address the corresponding implication of bone and menopausal status or supervision in postmenopausal women. A comprehensive search of eight electronic databases according to the PRISMA statement up to August 9, 2022, included controlled exercise trials ≥ 6 months. BMD changes (standardized mean differences: SMD) at the lumbar spine (LS), femoral neck (FN), and total hip (TH) were considered as outcomes. Study group comparisons were conducted for osteopenia/osteoporosis versus normal BMD, early versus late postmenopausal women, and predominantly supervised versus predominantly non-supervised study arms. We applied an inverse heterogeneity (IVhet) model. In summary, 80 studies involving 94 training and 80 control groups with a pooled number of 5581 participants were eligible. The IVhet model determined SMDs of 0.29 (95% CI: 0.16-0.42), 0.27 (95% CI: 0.16-0.39), and 0.41 (95% CI: 0.30-0.52) for LS, FN, and THBMD, respectively. Heterogeneity between the trial results varied from low (I2 = 20%, TH BMD) to substantial (I2 = 68%, LS-BMD). Evidence for publication bias/small study effects was negligibly low (FN-, TH-BMD) to high (LSBMD). We observed no significant differences (p > .09) for exercise effects on LS-, FN-, or TH-BMD-LS between studies/study arms with or without osteopenia/osteoporosis, early versus late postmenopausal women, or predominantly supervised versus non-supervised exercise programs. Using robust statistical methods, the present work provides further evidence for a positive effect of exercise on BMD in postmenopausal women. Differences in bone status (osteopenia/osteoporosis versus normal bone), menopausal status (early versus late postmenopausal), and supervision (yes versus no) did not significantly affect the exercise effects on BMD at LS or proximal femur.

Exercise and the prevention of major osteoporotic fractures in adults: a systematic review and meta-analysis with special emphasis on intensity progression and study duration.

The role of exercise in preventing osteoporotic fractures is vague, and further recommendations for optimized exercise protocols are very rare. In the present work, we provided positive evidence for exercise effects on the number of osteoporotic fractures in adults, albeit without observing any significant relevance of intensity progression or study duration. INTRODUCTION: Osteoporotic fractures are a major challenge confronting our aging society. Exercise might be an efficient agent for reducing osteoporotic fractures in older adults, but the most promising exercise protocol for that purpose has yet to be identified. The present meta-analysis thus aimed to identify important predictors of the exercise effect on osteoporotic fractures in adults. METHODS: We conducted a systematic search of six literature databases according to the PRISMA guideline that included controlled exercise studies and reported the number of low-trauma major osteoporotic fractures separately for exercise (EG) and control (CG) groups. Primary study outcome was incidence ratio (IR) for major osteoporotic fractures. Sub-analyses were conducted for progression of intensity (yes vs. no) during the trial and the study duration (≤ 12 months vs. > 12 months). RESULTS: In summary, 11 studies with a pooled number of 9715 participant-years in the EG and 9592 in the CG were included. The mixed-effects conditional Poisson regression revealed positive exercise effects on major osteoporotic fractures (RR: 0.75, 95% CI: 0.54-0.94, p = .006). Although studies with intensity progression were more favorable, our subgroup analysis did not determine significant differences for diverging intensity progression (p = .133) or study duration (p = .883). Heterogeneity among the trials of the subgroups (I2 ≤ 0-7.1%) was negligible. CONCLUSION: The present systematic review and meta-analysis provided significant evidence for the favorable effect of exercise on major osteoporotic fractures. However, diverging study and exercise characteristics along with the close interaction of exercise parameters prevented the derivation of reliable recommendations for exercise protocols for fracture reductions. PROSPERO ID: CRD42021250467.

Long-term effects of smoking on serum concentrations of oxidative stress biomarkers: Results of a large, population-based cohort study.

INTRODUCTION: Cross-sectional studies have consistently shown an association between current smoking and oxidative stress biomarkers. However, no longitudinal studies have been performed so far. METHODS: The oxidative stress biomarkers "total thiol groups of serum proteins" (TTP), and "derivatives of reactive oxygen metabolites" (D-ROM) were measured in serum samples of 3835 participants of a population-based, German cohort study of older adults (age: 60-84 years) with repeated measurements for 2834 participants three years later. Multivariable linear regression models were applied and ß-coefficients with 95% confidence intervals were obtained. RESULTS: In both cross-sectional and longitudinal analysis, current smoking was statistically significantly associated with increased D-ROM levels, and a dose-response relationship between the amount of daily tobacco consumption and the D-ROM concentrations was observed that plateaued at ≥15 g of tobacco consumption per day. Former smoking was also associated with D-ROM levels. Only former smokers who quitted smoking more than 10 years ago had no increased D-ROM levels compared to never smokers. There was neither a cross-sectional nor longitudinal association between any of the smoking variables and TTP levels. CONCLUSION: This large population-based cohort of older German adults suggests that smoking has long-term effects on the oxidative stress burden. The further increasing D-ROM levels of current smokers at an older age and the observation that it may take more than 10 years until the redox balance is restored are solid arguments for quitting smoking as soon as possible at any age.