NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.

Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. VIDEO ABSTRACT.This work was supported by the Medical Research Council [MRC file reference U105188491] and European Research Council Starting and Consolidator Grants to G.S.X.E.J., who is an EMBO Young Investigator.This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.neuron.2016.06.01

Non-Emergency Medical Transportation Needs of Middle-Aged and Older Adults: A Rural-Urban Comparison in Delaware, USA.

Background: Older adults in rural areas have unique transportation barriers to accessing medical care, which include a lack of mass transit options and considerable distances to health-related services. This study contrasts non-emergency medical transportation (NEMT) service utilization patterns and associated costs for Medicaid middle-aged and older adults in rural versus urban areas. Methods: Data were analyzed from 39,194 NEMT users of LogistiCare-brokered services in Delaware residing in rural (68.3%) and urban (30.9%) areas. Multivariable logistic analyses compared trip characteristics by rurality designation. Results: Rural (37.2%) and urban (41.2%) participants used services more frequently for dialysis than for any other medical concern. Older age and personal accompaniment were more common and wheel chair use was less common for rural trips. The mean cost per trip was greater for rural users (difference of $2910 per trip), which was attributed to the greater distance per trip in rural areas. Conclusions: Among a sample who were eligible for subsidized NEMT and who utilized this service, rural trips tended to be longer and, therefore, higher in cost. Over 50% of trips were made for dialysis highlighting the need to address prevention and, potentially, health service improvements for rural dialysis patients

Early weight gain predicts treatment response in adolescents with anorexia nervosa enrolled in a family‐based partial hospitalization program

ObjectiveImproved treatment outcome in family‐based treatment (FBT) for anorexia nervosa (AN) is predicted by weight gain occurring early in the course of treatment (i.e., about 4 lbs by week 4). Although prior work suggests that early weight gain in higher levels of care (e.g., partial hospitalization programs [PHP]) predicts weight restoration at discharge, no study has examined the specific rate of gain within FBT‐informed PHP programs that best predicts treatment response.MethodThis study examined rate of weight gain in pounds and percent expected body weight (EBW) that predicts positive outcome in 70 patients (M age = 15.49 years, SD = 2.56) with AN who were enrolled in a family‐based PHP.ResultsReceiver operator characteristic analyses demonstrated that changes in %EBW during weeks 2–5 were more useful than changes in weight in predicting positive outcome. Gaining at least 8.9 pounds or over 8% of EBW in the first 4 weeks of treatment significantly predicted positive outcome.DiscussionFindings suggest that positive outcome in an FBT‐informed PHP is predicted by rapid weight gain in the initial weeks of treatment. Research is needed to identify specific family and patient characteristics that facilitate weight gain and to develop corresponding interventions to improve outcome.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154930/1/eat23248_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154930/2/eat23248.pd

Automatic alignment of stacks of filament data

We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually

Defining genes: a computational framework

The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous work, we proposed an approach for constructing gene concepts that combines genomic heritability with elements of function. Here, we introduce a definition of the gene within a computational framework of cellular interactions. The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology

SynBlast: Assisting the analysis of conserved synteny information

<p>Abstract</p> <p>Motivation</p> <p>In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.</p> <p>Results</p> <p>Here we present the <monospace>SynBlast</monospace> pipeline that is designed to construct and evaluate local synteny information. <monospace>SynBlast</monospace> uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how <monospace>SynBlast</monospace> is applied to retrieving orthologous and paralogous clusters using the vertebrate <it>Hox </it>and <it>ParaHox </it>clusters as examples.</p> <p>Software</p> <p>The <monospace>SynBlast</monospace> package written in <monospace>Perl</monospace> is available under the GNU General Public License at <url>http://www.bioinf.uni-leipzig.de/Software/SynBlast/</url>.</p

Age-dependent leaf function and consequences for carbon uptake of leaves, branches, and the canopy during the dry season in an Amazon evergreen forest.

Abstract COS 124-3

Characterisation of Conventional 87Sr/86Sr Isotope Ratios in Cement, Limestone and Slate Reference Materials Based on an Interlaboratory Comparison Study

An interlaboratory comparison (ILC) was organised to characterise 87Sr/86Sr isotope ratios in geological and industrial reference materials by applying the so-called conventional method for determining 87Sr/86Sr isotope ratios. Four cements (VDZ 100a, VDZ 200a, VDZ 300a, IAG OPC-1), one limestone (IAG CGL ML-3) and one slate (IAG OU-6) reference materials were selected, covering a wide range of naturally occurring Sr isotopic signatures. Thirteen laboratories received aliquots of these six reference materials together with a detailed technical protocol. The consensus values for the six reference materials and their associated measurement uncertainties were obtained by applying a Gaussian, linear mixed effects model fitted to all the measurement results. By combining the consensus values and their uncertainties with an uncertainty contribution for potential heterogeneity, reference values ranging from 0.708134 mol mol-1 to 0.729778 mol mol-1 were obtained with relative expanded uncertainties of ≤ 0.007 %. This study represents an ILC on conventional 87Sr/86Sr isotope ratios, within which metrological principles were considered and the compatibility of measurement results obtained by MC-ICP-MS and by MC-TIMS is demonstrated. The materials characterised in this study can be used as reference materials for validation and quality control purposes and to estimate measurement uncertainties in conventional 87Sr/86Sr isotope ratio measurement