Quantification of finger grasps during activities of daily life using convolutional neural networks : a pilot study

Quantifying finger kinematics can improve the authors’ understanding of finger function and facilitate the design of efficient prosthetic devices while also identifying movement disorders and assessing the impact of rehabilitation interventions. Here, the authors present a study that quantifies grasps depicted in taxonomies during selected Activities of Daily Living (ADL). A single participant held a series of standard objects using specific grasps which were used to train Convolutional Neural Networks (CNN) for each of the four fingers individually. The experiment also recorded hand manipulation of objects during ADL. Each set of ADL finger kinematic data was tested using the trained CNN, which identified and quantified the grasps required to accomplish each task. Certain grasps appeared more often depending on the finger studied, meaning that even though there are physiological interdependencies, fingers have a certain degree of autonomy in performing dexterity tasks. The identified and most frequent grasps agreed with the previously reported findings, but also highlighted that an individual might have specific dexterity needs which may vary with profession and age. The proposed method can be used to identify and quantify key grasps for finger/hand prostheses, to provide a more efficient solution that is practical in their day-to-day tasks

Towards development of a statistical framework to evaluate myotonic dystrophy type 1 mRNA biomarkers in the context of a clinical trial

Myotonic dystrophy type 1 (DM1) is a rare genetic disorder, characterised by muscular dystrophy, myotonia, and other symptoms. DM1 is caused by the expansion of a CTG repeat in the 3'-untranslated region of DMPK. Longer CTG expansions are associated with greater symptom severity and earlier age at onset. The primary mechanism of pathogenesis is thought to be mediated by a gain of function of the CUG-containing RNA, that leads to transdysregulation of RNA metabolism of many other genes. Specifically, the alternative splicing (AS) and alternative polyadenylation (APA) of many genes is known to be disrupted. In the context of clinical trials of emerging DM1 treatments, it is important to be able to objectively quantify treatment efficacy at the level of molecular biomarkers. We show how previously described candidate mRNA biomarkers can be used to model an effective reduction in CTG length, using modern high-dimensional statistics (machine learning), and a blood and muscle mRNA microarray dataset. We show how this model could be used to detect treatment effects in the context of a clinical trial

Support from the UK Department of Health through its Health Technology Assessment Programme and Arthritis Research

ABSTRACT. Objective. Our aim was to determine areal bone mineral density (BMD a ) and disease-related factors linked with BMD a in adults with a history of juvenile idiopathic arthritis (JIA). Methods. Men and women with a history of JIA attending a young adult rheumatology clinic in Newcastle, UK, underwent dual energy x-ray absorptiometry (DEXA) of the lumbar spine and total hip. Information was obtained about disease duration and subtype, previous treatment including corticosteroid and methotrexate therapy, and large-joint replacement. Subjects completed the modified Health Assessment Questionnaire (HAQ). Blood was taken for assessment of C-reactive protein, erythrocyte sedimentation rate, and rheumatoid factor (RF). Results. Seventy-one women and 16 men, mean age 28.7 and 31.4 years, and mean disease duration 20.6 and 24.0 years, respectively, were studied. Mean BMD a was 0.982 (Z-score = -0.328; 95% CI -0.657, 0.001) and 1.028 g/cm 2 (Z-score = -0.251; 95% CI -1.266, 0.764) in women and men, respectively, at the spine and 0.817 (Z-score = -0.542; 95% CI -0.975, -0.109) and 0.857 g/cm 2 (Z-score = -0.176; 95% CI -2.323, 1.971) at the hip. After adjusting for age and sex, increasing HAQ score was associated with both lower spine BMD a and hip BMD a . Compared with patients with oligoarticular disease, those with enthesitis-related arthritis had higher BMD a at the spine, while those with extended oligoarticular and polyarticular RF-negative disease had lower hip BMD a . Oral corticosteroids and the presence of a large-joint replacement were associated with lower BMD a at both the spine and hip. Conclusion. There was a trend toward low BMD a in women with a history of JIA. These patients may be at risk of the complications of osteoporosis including fragility fractures and should be considered for targeted preventive measures. (First Release June 15 2011

Molecular and neurological characterizations of three Saudi families with lipoid proteinosis

<p>Abstract</p> <p>Background</p> <p>Lipoid proteinosis is a rare autosomal recessive disease characterized by cutaneous and mucosal lesions and hoarseness appearing in early childhood. It is caused by homozygous or compound heterozygous mutations in the <it>ECM1 </it>gene. The disease is largely uncharacterized in Arab population and the mutation(s) spectrum in the Arab population is largely unknown. We report the neurologic and neuroradiologic characteristics and <it>ECM1 </it>gene mutations of seven individuals with lipoid proteinosis (LP) from three unrelated consanguineous families.</p> <p>Methods</p> <p>Clinical, neurologic, and neuro-ophthalmologic examinations; skin histopathology; brain CT and MRI; and sequencing of the full<it>ECM1 </it>gene.</p> <p>Results</p> <p>All seven affected individuals had skin scarring and hoarseness from early childhood. The two children in Family 1 had worse skin involvement and worse hoarseness than affected children of Families 2 and 3. Both children in Family 1 were modestly mentally retarded, and one had typical calcifications of the amygdalae on CT scan. Affected individuals in Families 2 and 3 had no grossneurologic, neurodevelopmental, or neuroimaging abnormalities. Skin histopathology was compatible with LP in all three families. Sequencing the full coding region of <it>ECM1 </it>gene revealed two novel mutationsin Family 1 (c.1300-1301delAA) and Family 2 (p.Cys269Tyr) and in Family 3 a previously described 1163 bp deletion starting 34 bp into intron 8.</p> <p>Conclusions</p> <p>These individuals illustrate the neurologic spectrum of LP, including variable mental retardation, personality changes, and mesial temporal calcificationand imply that significant neurologic involvement may be somewhat less common than previously thought. The cause of neurologic abnormalities was not clear from either neuroimaging or from what is known about <it>ECM1 </it>function. The severity of dermatologic abnormalities and hoarseness generally correlated with neurologic abnormalities, with Family 1 being somewhat more affected in all spheres than the other two families. Nevertheless, phenotype-genotype correlation was not obvious, possibly because of difficulty quantifying the neurologic phenotype and because of genetic complexity.</p

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

The Effect of Consumers and Mutualists of Vaccinium membranaceum at Mount St. Helens: Dependence on Successional Context

In contrast to secondary succession, studies of terrestrial primary succession largely ignore the role of biotic interactions, other than plant facilitation and competition, despite the expectation that simplified interaction webs and propagule-dependent demographics may amplify the effects of consumers and mutualists. We investigated whether successional context determined the impact of consumers and mutualists by quantifying their effects on reproduction by the shrub Vaccinium membranaceum in primary and secondary successional sites at Mount St. Helens (Washington, USA), and used simulations to explore the effects of these interactions on colonization. Species interactions differed substantially between sites, and the combined effect of consumers and mutualists was much more strongly negative for primary successional plants. Because greater local control of propagule pressure is expected to increase successional rates, we evaluated the role of dispersal in the context of these interactions. Our simulations showed that even a small local seed source greatly increases population growth rates, thereby balancing strong consumer pressure. The prevalence of strong negative interactions in the primary successional site is a reminder that successional communities will not exhibit the distribution of interaction strengths characteristic of stable communities, and suggests the potential utility of modeling succession as the consequence of interaction strengths

This work was supported by The Department of the Interior Alaska Climate Adaptation Science Center, which is managed by the USGS National Climate Adaptation Science Center.

53 pages : color illustrations, color maps ; 28 cmThis report is designed as a living document to inform the community, decision makers, and academics and to serve as a learning and teaching tool. The nine key messages summarized on pages 6 and 7 are intended for use as a quick reference. Unique for this type of report, these key messages highlight actions by Juneau's civil society, including local nonprofit organizations.We thank the City and Borough of Juneau (CBJ) for its support in bringing this vital information on climate change to the Juneau community and to others. Thanks especially to all the co-authors and other contributors. The inclusion of such a diverse array of material, including local knowledge, was made possible by the many elders, scientists, and local experts who contributed their time and expertise. The report is online at acrc.alaska.edu/ juneau-climate-report. It is an honor to be the lead editor and project manager for this critical effort. We have a chance to save our world from the most extreme effects of climate change. Let us take it. Gunalchéesh, sincerely, James E. Powell (Jim), PhD, Alaska Coastal Rainforest Center, UASWelcome / Thomas F. Thornton -- Juneau's climate report: History and background / Bruce Botelho -- Using this report -- Acknowledgements / James E. Powell -- A regional Indigenous perspective on adaptation: The Central Council of Tlingit & Haida Indian Tribes of Alaska's Climate Change Adaptation Plan / Raymond Paddock -- Nine key messages -- What we're experiencing: Atmospheric, marine, terrestrial, and ecological effects. Climate. Setting and seasons / Tom Ainsworth -- More precipitation / Rick Thoman -- Higher temperatures / Rich Thoman -- Less snowfall / Eran Hood -- Ocean. Surface uplift and sea level rise / Eran Hood -- Extensive effects of a warming ocean / Heidi Pearson -- Increasing ocean acidification / Robert Foy -- Land. More landslides / Sonia Nagorski & Aaron Jacobs -- Mendenhall Glacier continues to retreat / Jason Amundson -- Tongass Forest impacts and carbon / Dave D'Amore -- Animals. Terrestrial vertebrates in A¿¿ak'w & T'aak¿łu Aani¿¿ / Richard Carstensen -- Three animals as indicators of change / Richard Carstensen -- Insects / Bob Armstrong -- What we're doing: Community response. Upgrading ifrastructure and mitigation / Katie Koester -- Upgrading utilities and other energy consumers / Alec Mesdag -- Growing demand for hydropower / Duff Mitchell -- Leading a shift in transportation / Duff Mitchell -- Maintaining mental health through community and recreation / Linda Kruger & Kevin Maier -- Food security / Darren Snyder & Jim Powell -- Large cruise ship air emissions / Jim Powell -- Tourists' views on climate change mitigation / Jim Powell -- Lowering greenhouse gas emissions / Jim Powell & Peggy Wilcox -- Residents taking action / Andy Romanoff & Jim Powell -- Summary and Recommendations -- References -- Graphics and data sources -- Appendix: Juneau nonprofit climate change organization

Correlation of Inter-Locus Polyglutamine Toxicity with CAG•CTG Triplet Repeat Expandability and Flanking Genomic DNA GC Content

Dynamic expansions of toxic polyglutamine (polyQ)-encoding CAG repeats in ubiquitously expressed, but otherwise unrelated, genes cause a number of late-onset progressive neurodegenerative disorders, including Huntington disease and the spinocerebellar ataxias. As polyQ toxicity in these disorders increases with repeat length, the intergenerational expansion of unstable CAG repeats leads to anticipation, an earlier age-at-onset in successive generations. Crucially, disease associated alleles are also somatically unstable and continue to expand throughout the lifetime of the individual. Interestingly, the inherited polyQ length mediating a specific age-at-onset of symptoms varies markedly between disorders. It is widely assumed that these inter-locus differences in polyQ toxicity are mediated by protein context effects. Previously, we demonstrated that the tendency of expanded CAG•CTG repeats to undergo further intergenerational expansion (their ‘expandability’) also differs between disorders and these effects are strongly correlated with the GC content of the genomic flanking DNA. Here we show that the inter-locus toxicity of the expanded polyQ tracts of these disorders also correlates with both the expandability of the underlying CAG repeat and the GC content of the genomic DNA flanking sequences. Inter-locus polyQ toxicity does not correlate with properties of the mRNA or protein sequences, with polyQ location within the gene or protein, or steady state transcript levels in the brain. These data suggest that the observed inter-locus differences in polyQ toxicity are not mediated solely by protein context effects, but that genomic context is also important, an effect that may be mediated by modifying the rate at which somatic expansion of the DNA delivers proteins to their cytotoxic state

A genome-wide association study of anorexia nervosa

Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome wide association study (GWAS) have yielded significant and replicated results. We performed a GWAS in 2,907 cases with AN from 14 countries (15 sites) and 14,860 ancestrally matched controls as part of the Genetic Consortium for AN (GCAN) and the Wellcome Trust Case Control Consortium 3 (WTCCC3). Individual association analyses were conducted in each stratum and meta-analyzed across all 15 discovery datasets. Seventy-six (72 independent) SNPs were taken forward for in silico (two datasets) or de novo (13 datasets) replication genotyping in 2,677 independent AN cases and 8,629 European ancestry controls along with 458 AN cases and 421 controls from Japan. The final global meta-analysis across discovery and replication datasets comprised 5,551 AN cases and 21,080 controls. AN subtype analyses (1,606 AN restricting; 1,445 AN binge-purge) were performed. No findings reached genome-wide significance. Two intronic variants were suggestively associated: rs9839776 (P=3.01×10−7) in SOX2OT and rs17030795 (P=5.84×10−6) in PPP3CA. Two additional signals were specific to Europeans: rs1523921 (P=5.76×10−6) between CUL3 and FAM124B and rs1886797 (P=8.05×10−6) near SPATA13. Comparing discovery to replication results, 76% of the effects were in the same direction, an observation highly unlikely to be due to chance (P= 4×10−6), strongly suggesting that true findings exist but that our sample, the largest yet reported, was underpowered for their detection. The accrual of large genotyped AN case-control samples should be an immediate priority for the field

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant