Integrating Automatic Transcription into the Language Documentation Workflow: Experiments with Na Data and the Persephone Toolkit

Automatic speech recognition tools have potential for facilitating language documentation, but in practice these tools remain little-used by linguists for a variety of reasons, such as that the technology is still new (and evolving rapidly), user-friendly interfaces are still under development, and case studies demonstrating the practical usefulness of automatic recognition in a low-resource setting remain few. This article reports on a success story in integrating automatic transcription into the language documentation workflow, specifically for Yongning Na, a language of Southwest China. Using Persephone, an open-source toolkit, a single-speaker speech transcription tool was trained over five hours of manually transcribed speech. The experiments found that this method can achieve a remarkably low error rate (on the order of 17%), and that automatic transcriptions were useful as a canvas for the linguist. The present report is intended for linguists with little or no knowledge of speech processing. It aims to provide insights into (i) the way the tool operates and (ii) the process of collaborating with natural language processing specialists. Practical recommendations are offered on how to anticipate the requirements of this type of technology from the early stages of data collection in the field.National Foreign Language Resource Cente

AmFm and lithium gap stars: Stellar evolution models with mass loss

A thorough study of the effects of mass loss on internal and surface abundances of A and F stars is carried out in order to constrain mass loss rates for these stars, as well as further elucidate some of the processes which compete with atomic diffusion. Self-consistent stellar evolution models of 1.3 to 2.5 M_sun stars including atomic diffusion and radiative accelerations for all species within the OPAL opacity database were computed with mass loss and compared to observations as well as previous calculations with turbulent mixing. Models with unseparated mass loss rates between 5 x 10^-14 and 10^-13 M_sun/yr reproduce observations for many cluster AmFm stars as well as Sirius A and o Leonis. These models also explain cool Fm stars, but not the Hyades lithium gap. Like turbulent mixing, these mass loss rates reduce surface abundance anomalies; however, their effects are very different with respect to internal abundances. For most of the main sequence lifetime of an A or F star, surface abundances in the presence of such mass loss depend on separation which takes place between log(Delta M/M_star)= -6 and -5. The current observational constraints do not allow us to conclude that mass loss is to be preferred over turbulent mixing (induced by rotation or otherwise) in order to explain the AmFm phenomenon. Internal concentration variations which could be detectable through asteroseismic tests should provide further information. If atomic diffusion coupled with mass loss are to explain the Hyades Li gap, the wind would need to be separated.Comment: 27 pages, 25 figures, accepted for publication in A&

WIYN Open Cluster Study. XXXIX. Abundances in NGC 6253 from HYDRA Spectroscopy of the Li 6708 A Region

High-dispersion spectra of 89 potential members of the old, super-metal-rich open cluster, NGC 6253, have been obtained with the HYDRA multi-object spectrograph. Based upon radial-velocity measurements alone, 47 stars at the turnoff of the cluster color-magnitude diagram (CMD) and 18 giants are identified as potential members. Five turnoff stars exhibit evidence of binarity while proper-motion data eliminates two of the dwarfs as members. The mean cluster radial velocity from probable single-star members is -29.4 +/- 1.3 km/sec (sd). A discussion of the current estimates for the cluster reddening, derived independently of potential issues with the BV cluster photometry, lead to an adopted reddening of E(B-V) = 0.22 +/- 0.04. From equivalent width analyses of 38 probable single-star members near the CMD turnoff, the weighted average abundances are found to be [Fe/H] = +0.43 +/- 0.01, [Ni/H] = +0.53 +/- 0.02 and [Si/H] = +0.43 (+0.03,-0.04), where the errors refer to the standard errors of the weighted mean. Weak evidence is found for a possible decline in metallicity with increasing luminosity among stars at the turnoff. We discuss the possibility that our turnoff stars have been affected by microscopic diffusion. For 15 probable single-star members among the giants, spectrum synthesis leads to abundances of +0.46 (+0.02,-0.03) for [Fe/H]. While less than half the age of NGC 6791, NGC 6253 is at least as metal-rich and, within the uncertainties, exhibits the same general abundance pattern as that typified by super-metal-rich dwarfs of the galactic bulge.Comment: 5 Tables, 9 figures, 45 page

Fiducial Stellar Population Sequences for the VJKs Photometric System

We have obtained broad-band near-infrared photometry for seven Galactic star clusters (M92, M15, M13, M5, NGC1851, M71 and NGC6791) using the WIRCam wide-field imager on the Canada-France-Hawaii Telescope, supplemented by images of NGC1851 taken with HAWK-I on the VLT. In addition, 2MASS observations of the [Fe/H] ~ 0.0 open cluster M67 were added to the cluster database. From the resultant (V-J)-V and (V-Ks)-V colour-magnitude diagrams (CMDs), fiducial sequences spanning the range in metallicity, -2.4 < [Fe/H] < +0.3, have been defined which extend (for most clusters) from the tip of the red-giant branch (RGB) to ~ 2.5 magnitudes below the main-sequence turnoff. These fiducials provide a valuable set of empirical isochrones for the interpretation of stellar population data in the 2MASS system. We also compare our newly derived CMDs to Victoria isochrones that have been transformed to the observed plane using recent empirical and theoretical colour-Teff relations. The models are able to reproduce the entire CMDs of clusters more metal rich than [Fe/H] ~ -1.4 quite well, on the assumption of the same reddenings and distance moduli that yield good fits of the same isochrones to Johnson-Cousins BV(RI)C photometry. However, the predicted giant branches become systematically redder than the observed RGBs as the cluster metallicity decreases. Possible explanations for these discrepancies are discussed.Comment: 18 pages, 20 figures, Accepted for publication in A

PlantRNA, a database for tRNAs of photosynthetic eukaryotes.

International audiencePlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community

Rho and F-actin self-organize within an artificial cell cortex

The cell cortex, comprised of the plasma membrane and underlying cytoskeleton, undergoes dynamic reorganizations during a variety of essential biological processes including cell adhesion, cell migration, and cell division(1,2). During cell division and cell locomotion, for example, waves of filamentous-actin (F-actin) assembly and disassembly develop in the cell cortex in a process termed “cortical excitability”(3–7). In developing frog and starfish embryos, cortical excitability is generated through coupled positive and negative feedback, with rapid activation of Rho-mediated F-actin assembly followed in space and time by F-actin-dependent inhibition of Rho(7,8). These feedback loops are proposed to serve as a mechanism for amplification of active Rho signaling at the cell equator to support furrowing during cytokinesis, while also maintaining flexibility for rapid error correction in response to movement of the mitotic spindle during chromosome segregation(9). In this paper, we develop an artificial cortex based on Xenopus egg extract and supported lipid bilayers (SLBs), to investigate cortical Rho and F-actin dynamics(10). This reconstituted system spontaneously develops two distinct types of self-organized cortical dynamics: singular excitable Rho and F-actin waves, and non-traveling oscillatory Rho and F-actin patches. Both types of dynamic patterns have properties and dependencies similar to the excitable dynamics previously characterized in vivo(7). These findings directly support the long-standing speculation that the cell cortex is a self-organizing structure and present a novel approach for investigating mechanisms of Rho-GTPase-mediated cortical dynamics

Abundances in Turn-off Stars in the Old, Metal-Rich Open Cluster, NGC 6791

Open clusters have long been used to illuminate both stellar evolution and Galactic evolution. The oldest clusters, though rather rare, can reveal the chemical and nucleosynthetic processes early in the history of the Galaxy. We have studied two turn-off stars in the old, metal-rich open cluster, NGC 6791. The Keck + HIRES spectra have a resolution of 45,000 and signal-to-noise ratios of 40 per pixel. We confirm the high value for [Fe/H] finding +0.30 $\pm$0.08, in agreement with earlier results from evolved stars in other parts of the HR diagram. We have also determined abundances for Na, Si, Ca, Ti, Cr, Ni, Y and Ba. These are compared to a sample of old, metal-rich field stars. With the probable exception of enhanced Ni in the cluster stars, the field and cluster stars show similar abundances of the elements. Model predictions show that the Ni enhancement could result from enrichment of the pre-cluster gas by SN Ia. Orbital evidence indicates that NGC 6791 could have originated near the inner regions of the Galaxy where the metallicity is generally higher than it is in the disk or halo. Subsequent perturbations and migrations may have resulted in its current heliocentric distance of 4 kpc and 1 kpc above the Galactic plane.Comment: 10 pages, 4 figures, 7 tables accepted by The Astronomical Journal for June, 200

Linkage analysis and exome sequencing identify a novel mutation in KCTD7 in patients with progressive myoclonus epilepsy with ataxia

Epilepsy affects approximately 1% of the world\u27s population. Genetic factors and acquired etiologies, as well as a range of environmental triggers, together contribute to epileptogenesis.Wehave identified a family with three daughters affected with progressive myoclonus epilepsy with ataxia. Clinical details of the onset and progression of the neurologic presentation, epileptic seizures, and the natural history of progression over a 10-year period are described. Using autozygosity genetic mapping, we identified a high likelihood homozygous region on chromosome 7p12.1-7q11.22. We subsequently applied whole-exome sequencing and employed a rare variant prioritization analysis within the homozygous region. We identified p.Tyr276Cys in the potassium channel tetramerization domain-containing seven gene, KCTD7, which is expressed predominantly in the brain. Mutations in this gene have been implicated previously in epileptic phenotypes due to disturbances in potassium channel conductance. Pathogenicity of the mutation was supported by bioinformatic predictive analyses and variant cosegregation within the family. Further biologic validation is necessary to fully characterize the pathogenic mechanisms that explain the phenotypic causes of epilepsy with ataxia in these patients

Phenotype Presentation and Molecular Diagnostic Yield in Non-5q Spinal Muscular Atrophy

BACKGROUND AND OBJECTIVES: Spinal muscular atrophy (SMA) is mainly caused by homozygous SMN1 gene deletions on 5q13. Non-5q SMA patients' series are lacking, and the diagnostic yield of next-generation sequencing (NGS) is largely unknown. The aim of this study was to describe the clinical and genetic landscape of non-5q SMA and evaluate the performance of neuropathy gene panels in these disorders. METHODS: Description of patients with non-5q SMA followed in the different neuromuscular reference centers in France as well as in London, United Kingdom. Patients without a genetic diagnosis had undergone at least a neuropathy or large neuromuscular gene panel. RESULTS: Seventy-one patients from 65 different families were included, mostly sporadic cases (60.6%). At presentation, 21 patients (29.6%) showed exclusive proximal weakness (P-SMA), 35 (49.3%) showed associated distal weakness (PD-SMA), and 15 (21.1%) a scapuloperoneal phenotype (SP-SMA). Thirty-two patients (45.1%) had a genetic diagnosis: BICD2 (n = 9), DYNC1H1 (n = 7), TRPV4 (n = 4), VCP, HSBP1, AR (n = 2), VRK1, DNAJB2, MORC2, ASAH1, HEXB, and unexpectedly, COL6A3 (n = 1). The genetic diagnostic yield was lowest in P-SMA (6/21, 28.6%) compared with PD-SMA (16/35, 45.7%) and SP-SMA (10/15, 66.7%). An earlier disease onset and a family history of the disease or consanguinity were independent predictors of a positive genetic diagnosis. Neuropathy gene panels were performed in 59 patients with a 32.2% diagnostic yield (19/59). In 13 additional patients, a genetic diagnosis was achieved through individual gene sequencing or an alternative neuromuscular NGS. DISCUSSION: Non-5q SMA is genetically heterogeneous, and neuropathy gene panels achieve a molecular diagnosis in one-third of the patients. The diagnostic yield can be increased by sequencing of other neuromuscular and neurometabolic genes. Nevertheless, there is an unmet need to cluster these patients to aid in the identification of new genes