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.

Effects of whole-body electromyostimulation with different impulse intensity on blood pressure changes in hyper- and normotensive overweight people. A pilot study.

Hypertension is a frequent condition in untrained middle-aged to older adults, who form the core group of whole-body electromyostimulation (WB-EMS) applicants. So far, the acute effects of varying impulse intensities on blood pressure responses have not been evaluated in normo- and hypertensive people. Thirteen hypertensive and twelve normotensive overweight WB-EMS novices, 40-70 years old, conducted the same WB-EMS protocol (20 min, bipolar, 85 Hz, 350 µs, 4 s impulse-4 s rest; combined with easy movements) with increasing impulse intensity (low, moderate, advanced) per session. Mean arterial blood pressure (MAP) as determined by automatic sphygmomanometry rose significantly (p < .001) from rest, 5 min pre-WB-EMS to immediately pre-WB-EMS assessment. Of importance, a 20-min WB-EMS application does not increase MAP further. In detail, maximum individual MAP does not exceed 128 mmHg (177 mmHg systolic or 110 mmHg diastolic) in any case. Two-min post-WB-EMS, MAP was significantly lower (p = .016) compared to immediately pre-WB-EMS. In contrast, heart rate increased significantly from immediately pre to immediately post-exercise (p < .001), though individual peak values did not exceed 140 beats/min-1 and heart rate decreased rapidly (p < .001) post-exercise. No significant differences in MAP and HR kinetics were observed for impulse intensity categories or hypertensive status. In summary, largely independently of impulse intensity and status, the acute effect of WB-EMS on MAP in novice applicants seem to be largely negligible. Although definite evidence might not have been provided by the present study, we conclude that hypertension, at least under treatment, should not be considered as a barrier for WB-EMS application in moderately old or older cohorts.

Meta-analysis towards FSHD reveals misregulation of neuromuscular junction, nuclear envelope, and spliceosome.

Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common autosomal dominant muscle disorders, yet no cure or amelioration exists. The clinical presentation is diverse, making it difficult to identify the actual driving pathomechanism among many downstream events. To unravel this complexity, we performed a meta-analysis of 13 original omics datasets (in total 171 FSHD and 129 control samples). Our approach confirmed previous findings about the disease pathology and specified them further. We confirmed increased expression of former proposed DUX4 biomarkers, and furthermore impairment of the respiratory chain. Notably, the meta-analysis provides insights about so far not reported pathways, including misregulation of neuromuscular junction protein encoding genes, downregulation of the spliceosome, and extensive alterations of nuclear envelope protein expression. Finally, we developed a publicly available shiny app to provide a platform for researchers who want to search our analysis for genes of interest in the future.

Effect of Buteyko breathing technique on clinical and functional parameters in adult patients with asthma: a randomized, controlled study.

BACKGROUND: The established therapy of asthma might be supported by additional non-pharmaceutical measures, such as the Buteyko breathing technique (BBT); however, the available data are mixed. To clarify the effects of BBT in patients with asthma, we investigated whether it led to clinical improvements with correlation to functional parameters. METHODS: Using a randomized, controlled design, we studied two groups (n = 30 each) of patients with asthma under either BBT or usual therapy (UT) w/o BBT over a period of 3 months. The primary outcome comprised the voluntary control pause (CP) after 3 months, secondary outcomes an additional breathhold parameter, forced expiratory volume in 1 s (FEV1), capnovolumetry, exhaled nitric oxide (FeNO), Asthma Control Questionnaire (ACQ) and Nijmegen Questionnaire (NQ), and the use of medication (ß2-agonists; inhaled corticosteroids, ICS). RESULTS: CP showed significant time-by-group interaction [F(1,58.09) = 28.70, p < 0.001] as well as main effects for study group [F(1,58.27) = 5.91, p = 0.018] and time [F(1,58.36) = 17.67, p < 0.001]. ACQ and NQ scores were significantly (p < 0.05 each) improved with BBT. This was associated with reductions in the use of ß2-agonists and ICS (p < 0.05 each) by about 20% each. None of these effects occurred in the UT group. While FEV1 and the slopes of the capnovolumetric expiratory phases 2 and 3 did not significantly change, the capnovolumetric threshold volume at tidal breathing increased (p < 0.05) with BBT by about 10 mL or 10%, compared to baseline, suggesting a larger volume of the central airways. No significant changes were seen for FeNO. CONCLUSIONS: BBT was clinically effective, as indicated by the fact that the improvement in symptom scores and the small increase in bronchial volume occurred despite the significant reduction of respiratory pharmacotherapy. As the self-controlled Buteyko breathing therapy was well-accepted by the participants, it could be considered as supporting tool in asthma therapy being worth of wider attention in clinical practice. Trial registration Retrospectively registered on 10 March 2017 at ClinicalTrials.gov (NCT03098849).

Evaluation of university and training standards in clinical perfusion, an European-wide survey.

OBJECTIVES: Adequate theoretical and practical training of prospective clinical perfusionists is essential for maintaining clinical standards and ensuring patient safety during cardiac surgery procedures. Perfusion schools play a crucial role in establishing and maintaining higher education and training standards in clinical perfusion. The aim of this study is to obtain a comprehensive overview of European training standards in clinical perfusion in 2023. METHODS: For this study, 53 perfusion schools in Europe were found and contacted, of which 30 (56.6%) responded, giving a sample size of n = 30, which were then included in the data analysis. The quantitative data of the survey are analysed using descriptive methods. RESULTS: The university and training standards in clinical perfusion in Europe vary in many respects. Starting with the entry criterion for studies (most frequently a required bachelor's degree 36.7% or 2nd most common an university entrance qualification 30%), the duration [from <12 months (13.3%) up to 36 months (13.3%)] and regarding the content of the teaching in clinical perfusion [<30 European Credit Transfer System (ECTS) (33.3%) and more than 180 ECTS (6.7%)]. The mean value for teaching in clinical perfusion content is 62.63 ECTS credits. CONCLUSIONS: The obtained results show important differences between countries and schools. As such, they form a valuable database for future discussions establishing a common European curriculum and training standards for perfusionists. For the generalizability of the results, further evaluations and larger samples are needed.