Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.

RationaleThe monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment.ObjectiveWe utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy.MethodsSerum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points.ResultsA total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status.ConclusionA comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care

Motor Competence between Children with and without Additional Learning Needs: A Cross-Sectional Population-Level Study

The aim of this study was to examine associations in motor competence between children with additional learning needs (ALN) and typically developing children. This cross-sectional study involved a nationally representative cohort of 4555 children (48.98% boys; 11.35 ± 0.65 years) from sixty-five schools across Wales (UK). Demographic data were collected from schools, and children were assessed using the Dragon Challenge assessment of motor competence, which consists of nine tasks completed in a timed circuit. A multi-nominal multi-level model with random intercept was fitted to explore the proficiency between children with ALN and those without. In all nine motor competence tasks, typically developing children demonstrated higher levels of proficiency than their peers with ALN, with these associations evident after accounting for age, sex, ethnicity, and socioeconomic status. This study highlights motor competence inequalities at a population level and emphasises the need for policymakers, practitioners, and researchers to prioritise motor competence development, particularly for children with ALN

Clustered Cardiometabolic Risk, Cardiorespiratory Fitness and Physical Activity in 10-11 Year-Old Children. The CHANGE! Project Baseline

Objectives: The primary objective of this cross sectional pilot study was to report clustered risk scores combining traditional invasive with non invasive cardiometabolic risk markers in 10-11 year old children participating in the CHANGE! project at baseline. A secondary objective was to determine the relationship between clustered risk score and objectively measured physical activity (PA) and cardiorespiratory fitness (CRF). Methods: Habitual PA was measured using accelerometry and CRF (VO2peak) was assessed using an individually calibrated treadmill based protocol. Twenty-nine participants had valid data for all components of the clustered risk score, calculated using total cholesterol: high density lipoprotein-cholesterol (TC:HDL-C), glucose, systolic blood pressure (BP), LV Mass Index (g/m2.7), and trunk fat mass (g). Participants with a clustered risk score greater than 1SD above the mean, were categorised as ‘higher’ risk (n=6); all others were categorised as ‘normal’ risk. \ud \ud Results: Clustered risk score, controlling for somatic maturity and gender, was negatively correlated with VPA (r= -0.51, p=0.01), MVPA (r= -0.44, p=0.03) and VO2peak (r= -0.57, p<0.01). ANCOVA, with somatic maturity and gender as covariates, revealed that those in the ‘normal’ risk group were more fit than those in the ‘higher’ risk group [f (1,24)=4.518, p=0.044]). There were no statistically significant differences between risk groups and PA however mean data suggest that those in the ‘normal’ risk group accrued 4 minutes more daily VPA than the ‘higher’ risk group which may be clinically important. \ud \ud Conclusions: This provides further evidence of the importance of promoting CRF and VPA in children, to reduce cardiometabolic risk especially for those that are ‘higher’ risk

A cross-sectional study on the deprivation and sex differences in health-related fitness measures in school children

This study aimed to investigate deprivation and sex differences in selected health-relatedfitness measures in 9-12-year-old children. Data were captured on 3,407 children (49.3% boys; aged 10.5 ± 0.6 years). Cardiorespiratory fitness(20 m multistage shuttle run test; 20 m MSRT), muscular strength (handgrip strength) and body mass index (BMI) were measured. Welsh Index of Multiple Deprivation (WIMD) scores were used to make quintile groups. A two-way Analysis of Variance examined differences in BMI z-score by sex and WIMD quintiles. Two-wayAnalysis of Covariances investigated the effect of sex and WIMD quintiles on grip strength and shuttles achieved in 20 m MSRT, adjusting for BMI z-score and maturation, repectively. Independent of sex, children in the middle quintile had a significantly higher mean BMI z-score (p = 0.029) than their least deprived counterparts. There was a significant increase in grip strength (p = 0.005) and20 m MSRT (boys p < 0.001; girls p = 0.028) between most and least deprived quintiles. Significant differences in 20 m MSRT score were more apparent with decreases in deprivation in boys.Overall, inequalities exist in health-related fitness by sex and deprivation. These results can be used to inform focused services to improve current and future health

Classification of accelerometer wear and non-wear events in seconds for monitoring free-living physical activity

_____________________________________________________________ This article is brought to you by Swansea University. Any person downloading material is agreeing to abide by the terms of the repository licence. Authors are personally responsible for adhering to publisher restrictions or conditions. When uploading content they are required to comply with their publisher agreement and the SHERPA RoMEO database to judge whether or not it is copyright safe to add this version of the paper to this repository. Design: A bi-moving-window-based approach was used to combine acceleration and skin temperature data to identify wear and non-wear time events in triaxial accelerometer data that monitor physical activity. Setting: Local residents in Swansea, Wales, UK. Participants: 50 participants aged under 16 years (n=23) and over 17 years (n=27) were recruited in two phases: phase 1: design of the wear/non-wear algorithm (n=20) and phase 2: validation of the algorithm (n=30). Methods: Participants wore a triaxial accelerometer (GeneActiv) against the skin surface on the wrist (adults) or ankle (children). Participants kept a diary to record the timings of wear and non-wear and were asked to ensure that events of wear/non-wear last for a minimum of 15 min. Results: The overall sensitivity of the proposed method was 0.94 (95% CI 0.90 to 0.98) and specificity 0.91 (95% CI 0.88 to 0.94). It performed equally well for children compared with adults, and females compared with males. Using surface skin temperature data in combination with acceleration data significantly improved the classification of wear/non-wear time when compared with methods that used acceleration data only ( p&lt;0.01). Conclusions: Using either accelerometer seismic information or temperature information alone is prone to considerable error. Combining both sources of data can give accurate estimates of non-wear periods thus giving better classification of sedentary behaviour. This method can be used in population studies of physical activity in free-living environments

Associations between cardiorespiratory fitness, physical activity and clustered cardiometabolic risk in children and adolescents: the HAPPY study

Clustering of cardiometabolic risk factors can occur during childhood and predisposes individuals to cardiometabolic disease. This study calculated clustered cardiometabolic risk in 100 children and adolescents aged 10-14 years (59 girls) and explored differences according to cardiorespiratory fitness (CRF) levels and time spent at different physical activity (PA) intensities. CRF was determined using a maximal cycle ergometer test, and PA was assessed using accelerometry. A cardiometabolic risk score was computed as the sum of the standardised scores for waist circumference, blood pressure, total cholesterol/high-density lipoprotein ratio, triglycerides and glucose. Differences in clustered cardiometabolic risk between fit and unfit participants, according to previously proposed health-related threshold values, and between tertiles for PA subcomponents were assessed using ANCOVA. Clustered risk was significantly lower (p < 0.001) in the fit group (mean 1.21 ± 3.42) compared to the unfit group (mean -0.74 ± 2.22), while no differences existed between tertiles for any subcomponent of PA. Conclusion These findings suggest that CRF may have an important cardioprotective role in children and adolescents and highlights the importance of promoting CRF in youth

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. IMPORTANCE The initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants

The role of EGFR in influenza pathogenicity: Multiple network-based approaches to identify a key regulator of non-lethal infections

Despite high sequence similarity between pandemic and seasonal influenza viruses, there is extreme variation in host pathogenicity from one viral strain to the next. Identifying the underlying mechanisms of variability in pathogenicity is a critical task for understanding influenza virus infection and effective management of highly pathogenic influenza virus disease. We applied a network-based modeling approach to identify critical functions related to influenza virus pathogenicity using large transcriptomic and proteomic datasets from mice infected with six influenza virus strains or mutants. Our analysis revealed two pathogenicity-related gene expression clusters; these results were corroborated by matching proteomics data. We also identified parallel downstream processes that were altered during influenza pathogenesis. We found that network bottlenecks (nodes that bridge different network regions) were highly enriched in pathogenicity-related genes, while network hubs (highly connected network nodes) were significantly depleted in these genes. We confirmed that this trend persisted in a distinct virus: Severe Acute Respiratory Syndrome Coronavirus (SARS). The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. We demonstrate that EGFR is important during influenza infection, but the role it plays changes for lethal versus non-lethal infections. Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene’s involvement in influenza virus pathogenicity. We also demonstrate the utility of employing multiple network approaches for analyzing host response data from viral infections