ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data

Single-cell RNA-seq allows researchers to identify cell populations based on unsupervised clustering of the transcriptome. However, subpopulations can have only subtle transcriptomic differences and the high dimensionality of the data makes their identification challenging.\nWe introduce ILoReg, an R package implementing a new cell population identification method that improves identification of cell populations with subtle differences through a probabilistic feature extraction step that is applied before clustering and visualization. The feature extraction is performed using a novel machine learning algorithm, called iterative clustering projection (ICP), that uses logistic regression and clustering similarity comparison to iteratively cluster data. Remarkably, ICP also manages to integrate feature selection with the clustering through L1-regularization, enabling the identification of genes that are differentially expressed between cell populations. By combining solutions of multiple ICP runs into a single consensus solution, ILoReg creates a representation that enables investigating cell populations with a high resolution. In particular, we show that the visualization of ILoReg allows segregation of immune and pancreatic cell populations in a more pronounced manner compared with current state-of-the-art methods.\nILoReg is available as an R package at https://bioconductor.org/packages/ILoReg.\nSupplementary data are available at Supplementary Information and Supplementary Files 1 and 2.\nMOTIVATION\nRESULTS\nAVAILABILITY\nSUPPLEMENTARY INFORMATIO

scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data

MotivationComputational models are needed to infer a representation of the cells, i.e. a trajectory, from single-cell RNA-sequencing data that model cell differentiation during a dynamic process. Although many trajectory inference methods exist, their performance varies greatly depending on the dataset and hence there is a need to establish more accurate, better generalizable methods.ResultsWe introduce scShaper, a new trajectory inference method that enables accurate linear trajectory inference. The ensemble approach of scShaper generates a continuous smooth pseudotime based on a set of discrete pseudotimes. We demonstrate that scShaper is able to infer accurate trajectories for a variety of trigonometric trajectories, including many for which the commonly used principal curves method fails. A comprehensive benchmarking with state-of-the-art methods revealed that scShaper achieved superior accuracy of the cell ordering and, in particular, the differentially expressed genes. Moreover, scShaper is a fast method with few hyperparameters, making it a promising alternative to the principal curves method for linear pseudotemporal ordering.Availability and implementationscShaper is available as an R package at https://github.com/elolab/scshaper. The test data are available at https://doi.org/10.5281/zenodo.5734488.</p

Stable Iterative Variable Selection

Motivation: The emergence of datasets with tens of thousands of features, such as high-throughput omics biomedical data, highlights the importance of reducing the feature space into a distilled subset that can truly capture the signal for research and industry by aiding in finding more effective biomarkers for the question in hand. A good feature set also facilitates building robust predictive models with improved interpretability and convergence of the applied method due to the smaller feature space. Results: Here, we present a robust feature selection method named Stable Iterative Variable Selection (SIVS) and assess its performance over both omics and clinical data types. As a performance assessment metric, we compared the number and goodness of the selected feature using SIVS to those selected by Least Absolute Shrinkage and Selection Operator regression. The results suggested that the feature space selected by SIVS was, on average, 41% smaller, without having a negative effect on the model performance. A similar result was observed for comparison with Boruta and caret RFE. Availability and implementation: The method is implemented as an R package under GNU General Public License v3.0 and is accessible via Comprehensive R Archive Network (CRAN) via https://cran.r-project.org/package¼sivs. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.</p

Easy-to-use tool for evaluating the elevated acute kidney injury risk against reduced cardiovascular disease risk during intensive blood pressure control

Objective: The Systolic Blood Pressure Intervention Trial (SPRINT) reported that lowering SBP to below 120 mmHg (intensive treatment) reduced cardiovascular morbidity and mortality among adults with hypertension but increased the incidence of adverse events, particularly acute kidney injury (AKI). The goal of this study was to develop an accurate risk estimation tool for comparing the risk of cardiovascular events and adverse kidney-related outcomes between standard and intensive antihypertensive treatment strategies.Methods: By applying Lasso regression on the baseline characteristics and health outcomes of 8760 participants with complete baseline information in the SPRINT trial, we developed predictive models for primary cardiovascular disease (CVD) outcome and incidence of AKI. Both models were validated against an independent test set of the SPRINT trial (one third of data not used for model building) and externally against the cardiovascular and renal outcomes available in Action to Control Cardiovascular Risk in Diabetes Blood Pressure trial, consisting of 4733 participants with type 2 diabetes mellitus.Results: Lasso regression identified a subset of variables that accurately predicted the primary CVD outcome and the incidence of AKI (areas under receiver-operating characteristic curves 0.70 and 0.77, respectively). Based on the validated risk models, an easy-to-use risk assessment tool was developed and made available as an easy-to-use online tool.Conclusion: By predicting the risks of CVD and AKI at baseline, the developed tool can be used to weigh the benefits of intensive versus standard blood pressure control and to identify those who are likely to benefit most from intensive treatment.</p

Maximum shear strain-based algorithm can predict proteoglycan loss in damaged articular cartilage

Post-traumatic osteoarthritis (PTOA) is a common disease, where the mechanical integrity of articular cartilage is compromised. PTOA can be a result of chondral defects formed due to injurious loading. One of the first changes around defects is proteoglycan depletion. Since there are no methods to restore injured cartilage fully back to its healthy state, preventing the onset and progression of the disease is advisable. However, this is problematic if the disease progression cannot be predicted. Thus, we developed an algorithm to predict proteoglycan loss of injured cartilage by decreasing the fixed charge density (FCD) concentration. We tested several mechanisms based on the local strains or stresses in the tissue for the FCD loss. By choosing the degeneration threshold suggested for inducing chondrocyte apoptosis and cartilage matrix damage, the algorithm driven by the maximum shear strain showed the most substantial FCD losses around the lesion. This is consistent with experimental findings in the literature. We also observed that by using coordinate system-independent strain measures and selecting the degeneration threshold in an ad hoc manner, all the resulting FCD distributions would appear qualitatively similar, i.e., the greatest FCD losses are found at the tissue adjacent to the lesion. The proposed strain-based FCD degeneration algorithm shows a great potential for predicting the progression of PTOA via biomechanical stimuli. This could allow identification of high-risk defects with an increased risk of PTOA progression.</p

Long-term blood metal ion levels and clinical outcome after Birmingham hip arthroplasty

Background and objective: Our aim was to assess long-term metal ion level changes and clinical outcome in patients with a Birmingham hip arthroplasty. Methods: For the purpose of this study, we identified all BHR hip resurfacing arthroplasty (HRA) and total hip arthroplasty (THA) operations performed in Turku University Hospital. A random coefficient model was used to compare the change between the first and last metal ion measurement. A Kaplan-Meier estimator was used to assess the survivorship of the BHR HRA and BHR THA with metal related adverse events (pseudotumor, elevated metal ions above the safe upper limit, revision due to metallosis), or revision due to any reason as endpoints with 95% confidence intervals (CIs). Results: BHR HRA was used in 274 hips (233 patients). In addition, we identified 38 BHR-Synergy THAs (38 patients). Operations were performed between 2003 and 2010. Median follow-up time was 14 years for BHR HRA (range: 0.6-17) and 11 years for BHR THA (range: 4.7-13). In the BHR HRA group, geometric means of Cr and Co levels decreased from 2.1 to 1.6 ppb and 2.4 to 1.5 ppb, respectively, during a 3.0-year measurement interval. Metal ion levels in the BHR THA group did not show notable increase. The survivorship of BHR HRA was 66% in 16 years and 34% for BHR THA at 12 years for any metal-related adverse event. Conclusions: Patients with a Birmingham hip device do not seem to benefit from frequent repeated metal ion measurements. The amount of patients with metal-related adverse events was relatively high, but many of them did not require surgery

Repeated metal ion measurements and long-term outcome of Durom/MMC total hip arthroplasty

Background and purpose — Data regarding long-term behavior of metal ion levels in metal-on-metal total hip arthroplasty (MoM THA) patients is scarce. Therefore, we assessed whether there is any change in whole blood (WB) chromium (Cr), and cobalt (Co) ion measurements in Durom and MMC MoM THA patients over time. The secondary aim was to report the clinical outcomes using these devices in a single district.Patients and methods — Durom and MMC cups were used in 249 MoM THAs from 2005 to 2011 in our district. Median follow-up time was 12 years for Durom THA (interquartile range [IQR] = 3) and 9 years for MMC THA (IQR = 1). A random coefficient model was used to compare individual differences in repeated WB Cr and Co ion measurements. The Kaplan–Meier estimator was used to analyze implant survival with any reason for revision as the endpoint.Results — Geometric means of Cr in Durom THA and MMC THA patients decreased from 2.2 ppb (geometric standard deviation [SD] = 1.9) to 1.5 ppb (geometric SD = 2.5, pInterpretation — WB Cr levels decreased over time, and Co levels remained unchanged at long-term follow-up. Despite this we recommend continuing the follow-up of these devices due to relatively low implant survival. </p

Weight Loss Trajectories in Healthy Weight Coaching : Cohort Study

Background: As global obesity prevalence continues to increase, there is a need for accessible and affordable weight management interventions, such as web-based programs. Objective: This paper aims to assess the outcomes of healthy weight coaching (HWC), a web-based obesity management program integrated into standard Finnish clinical care. Methods: HWC is an ongoing, structured digital 12-month program based on acceptance and commitment therapy. It includes weekly training sessions focused on lifestyle, general health, and psychological factors. Participants received remote one-on-one support from a personal coach. In this real-life, single-arm, prospective cohort study, we examined the total weight loss, weight loss profiles, and variables associated with weight loss success and program retention in 1189 adults (963 women) with a BMI >25 kg/m(2) among participants of the program between October 2016 and March 2019. Absolute (kg) and relative (%) weight loss from the baseline were the primary outcomes. We also examined the weight loss profiles, clustered based on the dynamic time-warping distance, and the possible variables associated with greater weight loss success and program retention. We compared different groups using the Mann-Whitney test or Kruskal-Wallis test for continuous variables and the chi-squared test for categorical variables. We analyzed changes in medication using the McNemar test. Results: Among those having reached the 12-month time point (n=173), the mean weight loss was 4.6% (SE 0.5%), with 43% (n=75) achieving clinically relevant weight loss (>= 5%). Baseline BMI >= 40 kg/m(2) was associated with a greater weight loss than a lower BMI (mean 6.6%, SE 0.9%, vs mean 3.2%, SE 0.6%; P=.02). In addition, more frequent weight reporting was associated with greater weight loss. No significant differences in weight loss were observed according to sex, age, baseline disease, or medication use. The total dropout rate was 29.1%. Dropouts were slightly younger than continuers (47.2, SE 0.6 years vs 49.2, SE 0.4 years; P=.01) and reported their weight less frequently (3.0, SE 0.1 entries per month vs 3.3, SE 0.1 entries per month; P Conclusions: A comprehensive web-based program such as HWC is a potential addition to the repertoire of obesity management in a clinical setting. Heavier patients lost more weight, but weight loss success was otherwise independent of baseline characteristics.Peer reviewe

Risk factors for prosthetic joint infections following total hip arthroplasty based on 33,337 hips in the Finnish Arthroplasty Register from 2014 to 2018

Background and purpose - Periprosthetic joint infection (PJI) is a devastating complication and more information on risk factors for PJI is required to find measures to prevent infections. Therefore, we assessed risk factors for PJI after primary total hip arthroplasty (THA) in a large patient cohort. Patients and methods - We analyzed 33,337 primary THAs performed between May 2014 and January 2018 based on the Finnish Arthroplasty Register (FAR). Cox proportional hazards regression was used to estimate hazard ratios with 95% confidence intervals (CI) for first PJI revision operation using 25 potential patient- and surgical-related risk factors as covariates. Results - 350 primary THAs were revised for the first time due to PJI during the study period. The hazard ratios for PJI revision in multivariable analysis were 2.0 (CI 1.3-3.2) for ASA class II and 3.2 (2.0-5.1) for ASA class III-IV compared with ASA class I, 1.4 (1.1-1.7) for bleeding > 500 mL compared with 120 minutes compared with 45-59 minutes, and 2.6 (1.4-4.9) for simultaneous bilateral operation. In the univariable analysis, hazard ratios for PJI revision were 2.3 (1.7-3.3) for BMI of 31-35 and 5.0 (3.5-7.1) for BMI of > 35 compared with patients with BMI of 21-25. Interpretation - We found several modifiable risk factors associated with increased PJI revision risk after THA to which special attention should be paid preoperatively. In particular, high BMI may be an even more prominent risk factor for PJI than previously assessed.Peer reviewe

Median 10-year whole blood metal ion levels and clinical outcome of ReCap-M2a-Magnum metal-on-metal total hip arthroplasty

Background and purposeWe have previously reported that the whole blood (WB) chromium (Cr) and cobalt (Co) ion levels decrease in the short term after ReCap-M2a-Magnum large-diameter head (LDH) metal-on-metal (MoM) total hip arthroplasty (THA). This study reports long-term metal ion levels and clinical outcomes after ReCap-Magnum THA.Patients and methodsReCap-M2a-Magnum LDH THA was used in 1,450 patients in our hospital district from 2005 to 2012. Median follow-up time was 10 years. 991 patients had 2 or more metal ion measurements. The median measurement interval was 4 years. Individual metal ion change was assessed using logarithmic metal ion values in a random coefficient model. Kaplan–Meier survival estimates were calculated for revision surgery for any reason for revision, and separately for metal-related adverse events (metalions above safe upper limit [SUL], revision due to ARMD, or pseudotumor).ResultsGeometric mean of Cr decreased from 1.8 ppb (geometric standard deviation [GSD] 1.8) to 1.0 ppb (GSD 2.8, p InterpretationWB Cr and Co levels continued to decrease in the long-term follow-up of ReCap-M2a-Magnum THA patients. The amount of metal-related adverse events was rather high, but revision surgery was seldom required. We suggest that after 10 years from the implantation a 5-year measurement interval may be sufficient for asymptomatic ReCap-M2a-Magnum patients.</p