A Mixed Methods Small Pilot Study to Describe the Effects of Upper Limb Training Using a Virtual Reality Gaming System in People with Chronic Stroke

Introduction. This small pilot study aimed to examine the feasibility of an upper limb rehabilitation system (the YouGrabber) in a community rehabilitation centre, qualitatively explore participant experiences, and describe changes after using it. Methods and Material. Chronic stroke participants attending a community rehabilitation centre in the UK were randomised to either a YouGrabber or a gym group and completed 18 training sessions over 12 weeks. The motor activity log, box and block, and fatigue severity score were administered by a blinded assessor before and after the intervention. Semistructured interviews were used to ascertain participants’ views about using the YouGrabber. Results. Twelve participants (6 females) with chronic stroke were recruited. All adhered to the intervention. There were no adverse events, dropouts, or withdrawal. There were no significant differences between the YouGrabber and gym groups although there were significant within group improvements on the motor activity log (median change: 0.59, range: 0.2–1.25; ) within the YouGrabber group. Participants reported that the YouGrabber was motivational but they expressed frustration with technical challenges. Conclusions. The YouGrabber appeared practical and may improve upper limb activities in people several months after stroke. Future work could examine cognition, cost effectiveness, and different training intensities

Kodoja : a workflow for virus detection in plants using k-mer analysis of RNA-sequencing data

This work was supported by the Biotechnology and Biological Sciences Research Council [BB/N023293/1]. The work of L.T., S.J., S.M. and P.C.was additionally supported by the Scottish Government’s Rural and Environment Science and Analytical Services division (RESAS)RNA-sequencing of plant material allows for hypothesis-free detection of multiple viruses simultaneously. This methodology relies on bioinformatics workflows for virus identification. Most workflows are designed for human clinical data, and few go beyond sequence mapping for virus identification. We present a new workflow (Kodoja) for the detection of plant virus sequences in RNA-sequence data. Kodoja uses k-mer profiling at the nucleotide level and sequence mapping at the protein level by integrating two existing tools Kraken and Kaiju. Kodoja was tested on three existing RNA-seq datasets from grapevine, and two new RNA-seq datasets from raspberry. For grapevine, Kodoja was shown to be more sensitive than a method based on contig building and blast alignments (27 viruses detected compared to 19). The application of Kodoja to raspberry, showed that field-grown raspberries were infected by multiple viruses, and that RNA-seq can identify lower amounts of virus material than reverse transcriptase PCR. This work enabled the design of new PCR-primers for detection of Raspberry yellow net virus and Beet ringspot virus. Kodoja is a sensitive method for plant virus discovery in field samples and enables the design of more accurate primers for detection. Kodoja is available to install through Bioconda and as a tool within Galaxy.PostprintPeer reviewe

Maternal Depression: Relationship to Food Insecurity and Preschooler Fruit/Vegetable Consumption

Background: Maternal Depression (MD) has been implicated in the etiology of obesity. The present study investigated MD and both child fruit/vegetable consumption (FVC) and household food insecurity (FI) in an early childhood population. Methods: This cross-sectional study was conducted in Arkansas, United States, in 26 Head Start centers. Teachers obtained the Family Map (FM), an interview assessment tool used by Head Start staff to identify potential risk factors that affect child learning and development. The FM contains a two-item screener of parent depression—the Patient Health Questionaire-2, two questions about family FI, and two questions about FVC. The FM was completed in 693 households. Chi square analyses and logistic regressions utilizing adjusted and unadjusted odds ratios were utilized to compare differences in risk for children of mothers with no symptoms compared to mothers with low- or high-level depressive symptoms. Results: Children whose mothers had high MD were 2.90 (CI: 1.21–7.00) and 7.81 (CI: 3.71–16.45) times more likely to be at risk for low FVC and FI, respectively, compared to children of mothers with no MD. Similar findings but at lower magnitude were found for mothers with low symptoms of MD in comparison with mothers with no MD—both for Low FVC (1.57 times more likely; CI: 1.01–2.45) and FI (2.14 times more likely; CI: 1.28–3.58). The results presented are Odds Ratios from the multivariable adjusted models. Conclusions: Implications for the etiology of obesity, prevention/intervention efforts, and future research are offered, including recommended addition of maternal depression and household FI screening in early childhood programs

Fibroblast growth factor receptor 1 (FGFR1) copy number is an independent prognostic factor in non-small cell lung cancer

Fibroblast growth factor receptor 1 ( FGFR1) is an oncogene that can potentially be targeted by tyrosine kinase inhibitors. We aimed to investigate the prevalence and prognostic significance of alterations in FGFR1 copy number in non-small cell lung cancer (NSCLC). FGFR1 status was evaluated by chromogenic silver in situ hybridisation (ISH) in tissue microarray sections from a retrospective cohort of 304 surgically resected NSCLCs and results were correlated with the clinicopathological features and overall survival. High FGFR1 gene copy number (amplification or high-level polysomy) was significantly more frequent in squamous cell carcinomas (SCC) (24.8%) and large cell carcinomas (LCC) (25%) compared to adenocarcinomas (11.3%) ( p= 0.01 and p= 0.03 respectively). Among NSCLC there was no significant correlation between FGFR1-positive status and other clinicopathological features including age, gender, smoking history, tumour size, lymph node status, stage, grade, vascular, lymphatic or perineural invasion. FGFR1-positive patients showed a tendency to longer overall survival in univariate analysis ( p= 0.14). Multivariate survival analysis using Cox regression model confirmed FGFR1-positive patients had a significant reduction in the risk of death compared to FGFR1-negative patients (HR 0.6; p= 0.02). High. FGFR1 gene copy number is a common finding in SCC and LCC and is an independent favourable prognostic factor

Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance)

PURPOSE: Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581.PATIENTS AND METHODS: C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables.RESULTS: Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P &lt; .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk.CONCLUSION: ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis.</p