The validity and reliability of the Microsoft Kinect for measuring trunk compensation during reaching

Compensatory movements at the trunk are commonly utilized during reaching by persons with motor impairments due to neurological injury such as stroke. Recent low-cost motion sensors may be able to measure trunk compensation, but their validity and reliability for this application are unknown. The purpose of this study was to compare the first (K1) and second (K2) generations of the Microsoft Kinect to a video motion capture system (VMC) for measuring trunk compensation during reaching. Healthy participants (n = 5) performed reaching movements designed to simulate trunk compensation in three different directions and on two different days while being measured by all three sensors simultaneously. Kinematic variables related to reaching range of motion (ROM), planar reach distance, trunk flexion and lateral flexion, shoulder flexion and lateral flexion, and elbow flexion were calculated. Validity and reliability were analyzed using repeated-measures ANOVA, paire

Personalized Virtual Reality for Upper Extremity Rehabilitation: Moving from the Clinic to a Home Exercise Program

Introduction: Traditional rehabilitation does not provide adequate repetitions for maximal motor recovery in the clinic and home exercise programs (HEPs) have low compliance rates. Personalized virtual reality (PVR) is a promising low-cost therapeutic tool for improving compliance by incorporating the client's interests, abilities, and goals into a motivating and engaging intervention using internet games. Objectives: The current study aimed to develop and refine a clinic-to-home PVR intervention, determine its feasibility and usability in an outpatient rehabilitation clinic and as a HEP, and examine its effects on motivation/engagement, compliance, motor repetitions, and functional motor performance. Methods: The PVR system utilizes a Microsoft Kinect sensor to track the participants' movements, free software to translate movements to keystrokes, and free internet games. The therapist matched participants' interests to internet games, customized therapeutic movements for game play, and increased the movement thresholds for game activation as participants improved. Two participants who had strokes resulting in upper extremity (UE) hemiplegia were recruited. The participants attended outpatient occupational therapy (OT) services twice weekly. Following training, the participants used the PVR system at home in place of their UE HEP. They continued to receive traditional OT once a week and clinic-PVR once a week for 5-8 weeks. Results: The PVR intervention was successfully implemented in the clinic and the clients' homes. PVR increased motivation and treatment compliance. The clients exhibited improvements in UE active range of motion, function, symptoms, and occupational performance. Conclusion: Preliminary evidence suggests PVR can improve motivation, compliance, function, and occupational performance. However, larger scale studies and protocol refinement are necessary

The Effects of Virtual Reality on the Upper Extremity Skills of Girls with Rett Syndrome: A Single Case Study

Introduction: Rett Syndrome (RTT) is a genetic disorder primarily seen in females that inhibits the use of a girl's hands in everyday activities. A girl with RTT spends the majority of her day engaged in stereotypical hand wringing/mouthing movements at midline of the body. The probable cause behind the neurological effects of RTT is a mutation in the gene that encodes for methyl-CpG protein 2 (MeCP2). The hand wringing/mouthing behaviors preclude a girl with RTT from using the upper extremities in purposeful tasks such as school work, play skills, and other activities of daily living.Objectives: To develop a virtual reality (VR)-based therapeutic intervention that 1) decreases upper extremity stereotypies (repetitive movements that serve no function) that interfere with purposeful arm and hand use and 2) promotes purposeful, goal-directed arm function; improve upper extremity motor skills in girls with RTT.Materials and Methods: Using FAAST Software and Microsoft Kinect sensor, one girl with RTT participated in a 12-week IVR intervention (1 hour/session, 3 sessions/week, 36 total hours). Pre- and post-assessments were administered to examine any changes in upper extremity function.Results: The VR intervention led to improvements in use of the upper extremities to complete self-care activities, an increased number of reaches completed in a 15-minute period, and decreased time engaged in stereotypical hand movements.Conclusion: Future work will add additional support to determine the effectiveness of virtual reality as an intervention for girls with RTT

Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1329–1343, doi:10.4319/lo.2013.58.4.1329.Based on noninvasive eddy correlation measurements at a marine and a freshwater site, this study documents the control that current flow and light have on sediment–water oxygen fluxes in permeable sediments. The marine sediment was exposed to tidal-driven current and light, and the oxygen flux varied from night to day between −29 and 78 mmol m−2 d−1. A fitting model, assuming a linear increase in oxygen respiration with current flow, and a photosynthesis–irradiance curve for light-controlled production reproduced measured fluxes well (R2 = 0.992) and revealed a 4-fold increase in oxygen uptake when current velocity increased from ∼ 0 to 20 cm s−1. Application of the model to a week-long measured record of current velocity and light showed that net ecosystem metabolism varied substantially among days, between −27 and 31 mmol m−2 d−1, due to variations in light and current flow. This variation is likely typical of many shallow-water systems and highlights the need for long-term flux integrations to determine system metabolism accurately. At the freshwater river site, the sediment–water oxygen flux ranged from −360 to 137 mmol m−2 d−1. A direct comparison during nighttime with concurrent benthic chamber incubations revealed a 4.1 times larger eddy flux than that obtained with chambers. The current velocity during this comparison was 31 cm s−1, and the large discrepancy was likely caused by poor imitation by the chambers of the natural pore-water flushing at this high current velocity. These results emphasize the need for more noninvasive oxygen flux measurements in permeable sediments to accurately assess their role in local and global carbon budgets.Support for this study was provided by the following National Science Foundation grants: OCE-0420575, OCE- 0536431, and OCE-1061364

Systematic pathological component scores for skin-containing vascularized composite allografts

Clinical management of skin-containing vascularized composite allografts (VCA) requires accurate assessment of the graft status, typically based on skin biopsies. The Banff 2007 Working Classification proposed 4 grades of acute rejection, but did not score individual features or include vascular rejection. Here we report a systematic scoring system developed from MHC-mismatched porcine skin-containing VCA. Biopsies from 20 VCA, 9 autologous skin flaps and 9 normal skin were analyzed to optimize the methodology and set thresholds. The components quantified were: perivascular cells/dermal vessel (pc), perivascular dermal infiltrate area (pa), luminal leukocytes/capillary or venule (c), epidermal infiltrate (ei), epidermal apoptosis or necrosis (e), endarteritis (v), and chronic allograft vasculopathy (cav). To evaluate prognostic value, we scored a separate group of 28 serial biopsies from 8 recipients (4 that were ultimately accepted and 4 that rejected. Parameters on the initial biopsies predicting later graft rejection included pc (p < 0.02), pa (p < 0.03), ei (p < 0.0005), e (p < 0.003) and c (p < 0.005). Reproducibility between 2 pathologists blinded to clinical data was acceptable, with weighted kappa scores for pc (0.673), pa (0.399), ei (0.464), e (0.663), v (0.766), and c (0.642). This component scoring system can be adapted clinically, since human and porcine skin are highly similar. Vascular lesions in VCA are also highlighted in this system and could impact graft outcome. The component score approach complements Banff 2007 grades and will enable the establishment of clinically significant thresholds

Information and resolution in electromagnetic optical systems

Published versio

Two Plant Viral Suppressors of Silencing Require the Ethylene-Inducible Host Transcription Factor RAV2 to Block RNA Silencing

RNA silencing is a highly conserved pathway in the network of interconnected defense responses that are activated during viral infection. As a counter-defense, many plant viruses encode proteins that block silencing, often also interfering with endogenous small RNA pathways. However, the mechanism of action of viral suppressors is not well understood and the role of host factors in the process is just beginning to emerge. Here we report that the ethylene-inducible transcription factor RAV2 is required for suppression of RNA silencing by two unrelated plant viral proteins, potyvirus HC-Pro and carmovirus P38. Using a hairpin transgene silencing system, we find that both viral suppressors require RAV2 to block the activity of primary siRNAs, whereas suppression of transitive silencing is RAV2-independent. RAV2 is also required for many HC-Pro-mediated morphological anomalies in transgenic plants, but not for the associated defects in the microRNA pathway. Whole genome tiling microarray experiments demonstrate that expression of genes known to be required for silencing is unchanged in HC-Pro plants, whereas a striking number of genes involved in other biotic and abiotic stress responses are induced, many in a RAV2-dependent manner. Among the genes that require RAV2 for induction by HC-Pro are FRY1 and CML38, genes implicated as endogenous suppressors of silencing. These findings raise the intriguing possibility that HC-Pro-suppression of silencing is not caused by decreased expression of genes that are required for silencing, but instead, by induction of stress and defense responses, some components of which interfere with antiviral silencing. Furthermore, the observation that two unrelated viral suppressors require the activity of the same factor to block silencing suggests that RAV2 represents a control point that can be readily subverted by viruses to block antiviral silencing

Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression

Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study

Therapeutic and Prognostic Implications of BRAF V600E in Pediatric Low-Grade Gliomas.

Purpose BRAF V600E is a potentially highly targetable mutation detected in a subset of pediatric low-grade gliomas (PLGGs). Its biologic and clinical effect within this diverse group of tumors remains unknown. Patients and Methods A combined clinical and genetic institutional study of patients with PLGGs with long-term follow-up was performed (N = 510). Clinical and treatment data of patients with BRAF V600E mutated PLGG (n = 99) were compared with a large international independent cohort of patients with BRAF V600E mutated-PLGG (n = 180). Results BRAF V600E mutation was detected in 69 of 405 patients (17%) with PLGG across a broad spectrum of histologies and sites, including midline locations, which are not often routinely biopsied in clinical practice. Patients with BRAF V600E PLGG exhibited poor outcomes after chemotherapy and radiation therapies that resulted in a 10-year progression-free survival of 27% (95% CI, 12.1% to 41.9%) and 60.2% (95% CI, 53.3% to 67.1%) for BRAF V600E and wild-type PLGG, respectively ( P \u3c .001). Additional multivariable clinical and molecular stratification revealed that the extent of resection and CDKN2A deletion contributed independently to poor outcome in BRAF V600E PLGG. A similar independent role for CDKN2A and resection on outcome were observed in the independent cohort. Quantitative imaging analysis revealed progressive disease and a lack of response to conventional chemotherapy in most patients with BRAF V600E PLGG. Conclusion BRAF V600E PLGG constitutes a distinct entity with poor prognosis when treated with current adjuvant therapy