AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

SUMMARY: Genome assembly projects have grown exponentially due to breakthroughs in sequencing technologies and assembly algorithms. Evaluating the quality of genome assemblies is critical to ensure the reliability of downstream analysis and interpretation. To fulfil this task, we have developed the AssemblyQC pipeline that performs file-format validation, contaminant checking, contiguity measurement, gene- and repeat-space completeness quantification, telomere inspection, taxonomic assignment, synteny alignment, scaffold examination through Hi-C contact-map visualization, and assessments of completeness, consensus quality and phasing through k-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualizations. AVAILABILITY AND IMPLEMENTATION: The pipeline uses Nextflow for workflow orchestration and adheres to the best-practice established by the nf-core community. This pipeline offers a reproducible, scalable, and portable method to assess the quality of genome assemblies-the code is available online at GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc.

The effect of chronotropic incompetence on physiologic responses during progressive exercise in people with Parkinson's disease.

PURPOSE: Heart rate (HR) response is likely to vary in people with Parkinson's disease (PD), particularly for those with chronotropic incompetence (CI). This study explores the impact of CI on HR and metabolic responses during cardiopulmonary exercise test (CPET) in people with PD, and its implications for exercise intensity prescription. METHODS: Twenty-eight participants with mild PD and seventeen healthy controls underwent CPET to identify the presence or absence of CI. HR and metabolic responses were measured at submaximal (first (VT1) and second (VT2) ventilatory thresholds), and at peak exercise. Main outcome measures were HR, oxygen consumption (VO2), and changes in HR responses (HR/WR slope) to an increase in exercise demand. RESULTS: CI was present in 13 (46%) PD participants (PDCI), who during CPET, exhibited blunted HR responses compared to controls and PD non-CI beyond 60% of maximal workload (p ≤ 0.05). PDCI presented a significantly lower HR at VT2, and peak exercise compared to PD non-CI and controls (p ≤ 0.001). VO2 was significantly lower in PDCI than PD non-CI and controls at VT2 (p = 0.003 and p = 0.036, respectively) and at peak exercise (p = 0.001 and p = 0.023, respectively). CONCLUSION: Although poorly understood, the presence of CI in PD and its effect on HR and metabolic responses during incremental exercise is significant and important to consider when programming aerobic exercises.

Assessing Gait & Balance in Adults with Mild Balance Impairment: G&B App Reliability and Validity.

Smartphone applications (apps) that utilize embedded inertial sensors have the potential to provide valid and reliable estimations of different balance and gait parameters in older adults with mild balance impairment. This study aimed to assess the reliability, validity, and sensitivity of the Gait&Balance smartphone application (G&B App) for measuring gait and balance in a sample of middle- to older-aged adults with mild balance impairment in Pakistan. Community-dwelling adults over 50 years of age (N = 83, 50 female, range 50-75 years) with a Berg Balance Scale (BBS) score between 46/56 and 54/56 were included in the study. Data collection involved securing a smartphone to the participant's lumbosacral spine. Participants performed six standardized balance tasks, including four quiet stance tasks and two gait tasks (walking looking straight ahead and walking with head turns). The G&B App collected accelerometry data during these tasks, and the tasks were repeated twice to assess test-retest reliability. The tasks in quiet stance were also recorded with a force plate, a gold-standard technology for measuring postural sway. Additionally, participants completed three clinical measures, the BBS, the Functional Reach Test (FRT), and the Timed Up and Go Test (TUG). Test-retest reliability within the same session was determined using intraclass correlation coefficients (ICCs) and the standard error of measurement (SEM). Validity was evaluated by correlating the G&B App outcomes against both the force plate data and the clinical measures using Pearson's product-moment correlation coefficients. To assess the G&B App's sensitivity to differences in balance across tasks and repetitions, one-way repeated measures analyses of variance (ANOVAs) were conducted. During quiet stance, the app demonstrated moderate reliability for steadiness on firm (ICC = 0.72) and compliant surfaces (ICC = 0.75) with eyes closed. For gait tasks, the G&B App indicated moderate to excellent reliability when walking looking straight ahead for gait symmetry (ICC = 0.65), walking speed (ICC = 0.93), step length (ICC = 0.94), and step time (ICC = 0.84). The TUG correlated with app measures under both gait conditions for walking speed (r -0.70 and 0.67), step length (r -0.56 and -0.58), and step time (r 0.58 and 0.50). The BBS correlated with app measures of walking speed under both gait conditions (r 0.55 and 0.51) and step length when walking with head turns (r = 0.53). Force plate measures of total distance wandered showed adequate to excellent correlations with G&B App measures of steadiness. Notably, G&B App measures of walking speed, gait symmetry, step length, and step time, were sensitive to detecting differences in performance between standard walking and the more difficult task of walking with head turns. This study demonstrates the G&B App's potential as a reliable and valid tool for assessing some gait and balance parameters in middle-to-older age adults, with promise for application in low-income countries like Pakistan. The app's accessibility and accuracy could enhance healthcare services and support preventive measures related to fall risk.

The validity of smartphone-based spatiotemporal gait measurements during walking with and without head turns: Comparison with the GAITRite® system.

Smartphone accelerometry has potential to provide clinicians with specialized gait analysis not available in most clinical settings. The Gait&Balance Application (G&B App) uses smartphone accelerometry to assess spatiotemporal gait parameters under two conditions: walking looking straight ahead and walking with horizontal head turns. This study investigated the validity of G&B App gait parameters compared with the GAITRite® pressure-sensitive walkway. Healthy young and older adults (age range 21-85 years) attended a single session where a smartphone was secured over the lumbosacral junction. Data were collected concurrently with the app and GAITRite® systems as participants completed the two walking conditions. Spatiotemporal gait parameters for 54 participants were determined from both systems and agreement evaluated with partial Pearson's correlation coefficients and limits of agreement. The results demonstrated moderate to excellent validity for G&B App measures of step time (rp 0.97, 95 % CI [0.96, 0.98]), walking speed (rp 0.83 [0.78, 0.87]), and step length (rp 0.74, [0.66, 0.80]) when walking looking straight ahead, and results were comparable with head turns. The validity of walking speed and step length measures was influenced by sex and height. G&B App measures of step length variability, step time variability, step length asymmetry, and step time asymmetry had poor validity. The G&B App has potential to provide valid measures of unilateral and bilateral step time, unilateral and bilateral step length, and walking speed, under two walking conditions in healthy young and older adults. Further research should validate this tool in clinical conditions and optimise the algorithm for demographic characteristics.

Impact of multiple isolation procedures on the differentiation potential of adipose derived canine mesenchymal stem cells.

OBJECTIVE: In regenerative biology, the most commonly used cells are adipose tissue-derived mesenchymal stem cells (AD-MSCs). This is due to the abundance and easy accessibility of AD-MSCs. METHODS: In this study, canine AD-MSCs were harvested from different anatomical locations, i.e., subcutaneous (SC), omental (OM), and perirenal (PR). Various isolation techniques namely explants (TRT-I), collagenase-digestion (TRT-II), collagenase-digested explants (TRT-III), and trypsin-digested explants (TRT-IV) were used to segregate the MSCs to evaluate cell doubling time, viability, and adipogenic/osteogenic lineage differentiation potential. RESULTS: The study showed that the SC stem cells had superior growth kinetics compared to other tissues, while the cells isolated through TRT-II performed better than the other cell isolation procedures. The metabolic status of cells isolated from dog adipose tissue indicated that all cells had adequate metabolic rates. However, SC-MSCs derived from TRT-III and TRT-IV outperformed those derived from TRT-I and TRT-II. The differentiation analysis revealed that cells differentiate into adipogenic and osteogenic lineage regardless of treatment, as demonstrated by positive oil red O (ORO) and Alizarin Red S (ALZ) stain. It is worth mentioning that cells derived from TRT-III had larger and more intracellular droplets compared to the other treatments. The TRT-I, -II, and -III showed greater osteogenic differentiation in cells isolated from PR and OM regions compared to SC-derived cells. However, the TRT-IV resulted in better osteogenic differentiation in cells from SC, followed by the OM and PR-derived cells. CONCLUSION: It is concluded that all methods of MSCs isolation from adipose tissues are successful; however, the TRT-II had the highest rate of cell re-assortment from the SC, while, TRT-II and -IV are most suitable for isolating cells from PR and OM adipose tissue.

The effects of chiropractic adjustment on inattention, hyperactivity, and impulsivity in children with attention deficit hyperactivity disorder: a pilot RCT.

Background: Attention deficit hyperactivity disorder (ADHD) is a neurobiological disorder characterized by inattention, hyperactivity, and impulsivity. We hypothesized that chiropractic adjustments could improve these symptoms by enhancing prefrontal cortex function. This pilot study aimed to explore the feasibility and efficacy of 4 weeks of chiropractic adjustment on inattention, hyperactivity, and impulsivity in children with ADHD. Methods: 67 children with ADHD were randomly allocated to receive either chiropractic adjustments plus usual care (Chiro+UC) or sham chiropractic plus usual care (Sham+UC). The Vanderbilt ADHD Diagnostic Teacher Rating Scale (VADTRS), Swanson, Nolan and Pelham Teacher and Parents Rating Scale (SNAP-IV), and ADHD Rating Scale-IV were used to assess outcomes at baseline, 4 weeks, and 8 weeks. Feasibility measures such as recruitment, retention, blinding, safety, and adherence were recorded. Linear mixed regression models were used for data analysis. Results: 56 participants (mean age ± SD: 10.70 ± 3.93 years) were included in the analysis. Both the Chiro+UC and Sham+UC groups showed significant improvements in total and subscale ADHD scores at 4 weeks and 8 weeks. However, there were no significant differences between the two groups. Conclusion: This pilot study demonstrated that it was feasible to examine the effects of chiropractic adjustment when added to usual care on ADHD outcomes in children. While both groups showed improvements, the lack of significant between-group differences requires caution in interpretation due to the small sample size. Further research with larger samples and longer follow-up periods is needed to conclusively evaluate the effects of chiropractic adjustments on ADHD in children.

Haptic Nudging Using a Wearable Device to Promote Upper Limb Activity during Stroke Rehabilitation: Exploring Diurnal Variation, Repetition, and Duration of Effect.

Haptic nudging via wearable devices promotes physical activity and may increase upper limb movement in stroke rehabilitation. This study investigated the optimal approach to haptic nudging by examining diurnal variation, duration of effect, and repeated nudging. The study analysed data from a multiple-period randomised crossover study. A 12 h inpatient rehabilitation day was divided into 72 intervals in which participants with stroke (n = 20) randomly received either a 'nudge' or 'no nudge'. Upper limb movement was observed, classified, and analysed using longitudinal mixed models. The odds of affected upper limb movement following a nudge compared with no nudge were significantly higher during active periods such as breakfast, lunch, and morning and afternoon activities (odds ratios (ORs) 2.01-4.63, 95% CIs [1.27-2.67, 3.17-8.01]), but not dinner (OR 1.36, 95% CI [0.86, 2.16]). The effect of nudging was no longer statistically significant at 50-60 s post-nudge. Consecutive delays in nudging significantly decreased the odds of moving when a nudge was eventually delivered. Contrary to expectations, people with stroke appear more responsive to haptic nudging during active periods rather than periods of inactivity. By understanding the optimal timing and frequency of haptic nudging, the design of wearable devices can be optimised to maximise their therapeutic benefits.

Challenge Level Contributes to the Efficacy of Treadmill Interventions after Stroke: A Systematic Review and Meta-Analysis.

Intervention parameters such as the challenge, amount, and dosage (challenge × amount) have the potential to alter the efficacy of rehabilitation interventions after stroke. This systematic review investigated the effect of intervention parameters of challenge, amount, and dosage on improvements in walking outcomes following treadmill training (TT) and comparison interventions in people with stroke. Randomized controlled trials were included if they: (i) investigated interventions of TT or bodyweight-supported TT (BWSTT); (ii) made comparisons with other physiotherapy interventions, other types of TT, or no intervention; (iii) studied people with stroke; (iv) reported sufficient data on challenge and amount parameters; and (v) measured walking speed or endurance. Completeness of reporting was evaluated using the TIDieR-Rehab checklist and risk of bias was assessed using the revised Cochrane risk-of-bias tool. The review included 26 studies; 15 studies compared TT or BWSTT with other physiotherapy interventions and 11 studies compared different types of TT. Meta-analyses provided evidence with low to moderate certainty that greater differences in challenge and dosage between treadmill and comparison physiotherapy interventions produced greater effects on walking endurance (p < 0.01). However, challenge and dosage did not influence walking speed outcomes. The analysis of intervention amount was limited by the lack of studies that manipulated the amount of intervention. Overall, the findings indicate that, after stroke, some of the efficacy of TT on walking endurance can be explained by the challenge level during training. This supports the implementation of TT at higher challenge levels in stroke rehabilitation practice.