A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Arenas Gomez, C. M., Woodcock, M. R., Smith, J. J., Voss, S. R., & Delgado, J. P. A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia. Data in Brief, 29, (2020): 105256, doi:10.1016/j.dib.2020.105256.The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.This work was funded by a research grant from COLCIENCIAS 569 (GRANT 027-2103) and CODI (Programa Sostenibilidad) 2013–2014 of the University of Antioquia. A PhD fellowship to the first author, Claudia Arenas was funded by the COLCIENCIAS 567 Grant. We thank the lab of Juan Fernando Alzate from the University of Antioquia for their help in developing our bioinformatic methodological approach. We thank Andrea Gómez and Melisa Hincapie for their help in animal collection and husbandry

Separating baryons and dark matter in cluster cores: a full 2-D lensing and dynamic analysis of Abell 383 and MS2137-23

(abridged) We utilize existing imaging and spectroscopic data for the galaxy clusters MS2137-23 and Abell 383 to present improved measures of the distribution of dark and baryonic material in the clusters' central regions. Our method, based on the combination of gravitational lensing and dynamical data, is uniquely capable of separating the distribution of dark and baryonic components at scales below 100 kpc. We find a variety of strong lensing models fit the available data, including some with dark matter profiles as steep as expected from recent simulations. However, when combined with stellar velocity dispersion data for the brightest member, shallower inner slopes than predicted by numerical simulations are preferred. For Abell 383, the preferred shallow inner slopes are statistically a good fit only when the multiple image position uncertainties associated with our lens model are assumed to be 0\farcs5, to account for unknown substructure. No statistically satisfactory fit was obtained matching both the multiple image lensing data and the velocity dispersion profile of the brightest cluster galaxy in MS2137-23. This suggests that the mass model we are using, which comprises a pseudo-elliptical generalized NFW profile and a brightest cluster galaxy component may inadequately represent the inner cluster regions. This may plausibly arise due to halo triaxiality or by the gravitational interaction of baryons and dark matter in cluster cores. However, the progress made via this detailed study highlights the key role that complementary observations of lensed features and stellar dynamics offer in understanding the interaction between dark and baryonic matter on non-linear scales in the central regions of clusters.Comment: 18 pages, 9 figures; accepted for publication in the Astrophysical Journa

Rabies in Sri Lanka: Splendid Isolation

Rabies virus exists in dogs on Sri Lanka as a single, minimally divergent lineage only distantly related to other rabies virus lineages in Asia. Stable, geographically isolated virus populations are susceptible to local extinction. A fully implemented rabies-control campaign could make Sri Lanka the first Asian country in >30 years to become free of rabies virus

Probabilistic earthquake locations of induced seismicity in the Groningen region, the Netherlands

The Groningen gas reservoir, situated in the northeast of the Netherlands, is western Europe’s largest producing gas field and has been in production since 1963. The gas production has induced both subsidence and seismicity. Seismicity is detected and located using the Koninklijk Nederlands Meteorologisch Instituut shallow-borehole array for the period 2015–2017, incorporating the back projection techniques of QuakeMigrate and the nonlinear location procedure to constrain earthquake locations and depths. The uncertainties on the estimated depths are estimated taking into account velocity model, changes in station array geometry and uncertainties in the measurement of arrival times of the P and S waves. We show that the depth distribution of seismicity is consistent with nucleation within the reservoir (28 per cent) or in the overburden (60 per cent) within ∼500 m from the top of the reservoir. Earthquakes with hypocentres in the overburden likely originate from overlying Zechstein anhydrite caprock. Based on their depth distribution, it seems like the earthquakes are primarily driven by the elastic strain in the reservoir and overburden, induced by the reservoir compaction. We estimate the probability of earthquakes nucleating beneath the reservoir in the underlying Carboniferous limestone and basement, to be no more than 12 per cent

Fact Sheet #1: How Family-Centered is MaineCare?

Parent reports on family experiences of care can provide health plans, systems and providers with crucial information on their performance in the domain of family-centeredness. The Maine Department of Health and Human Services (DHHS) conducts an annual survey to gather this kind of information for MaineCare, the state of Maine’s Medicaid and Child Health Insurance (CHIP) program

Fact Sheet #2: How Do MaineCare Providers Perform on Childhood Screening and Prevention?

The annual Survey of Children Served by MaineCare, which collects a wealth of data on the experiences of MaineCare families, examines the extent to which MaineCare providers follow Bright Futures guidelines during well-child visits. This fact sheet presents findings on Bright Futures adherence from the 2013 survey

Strategies for a Successful PhD Program: Words of Wisdom From the \u3cem\u3eWJNR\u3c/em\u3e Editorial Board

Nursing doctoral programs prepare students for research-focused careers within academic settings. The purpose of this Editorial Board Special Article is to provide PhD students and advisors with suggestions for making the most of their doctoral experience. Editorial Board members provide their individual insights on the skills and attributes students must acquire during the course of their doctoral education in order to succeed. The authors provide practical tips and advice on how to excel in a PhD program, including how to select an advisor and a dissertation committee, the importance of attending conferences to increase visibility and develop a network of colleagues, presenting and publishing research while still a student, and balancing work and personal life. Students who take full advantage of the opportunities available to them during the course of their doctoral programs will graduate well prepared to take on the multiple responsibilities of research, teaching, and leadership

On the signature of tensile blobs in the scattering function of a stretched polymer

We present Monte Carlo data for a linear chain with excluded volume subjected to a uniform stretching. Simulation of long chains (up to 6000 beads) at high stretching allows us to observe the signature of tensile blobs as a crossover in the scaling behavior of the chain scattering function for wave vectors perpendicular to stretching. These results and corresponding ones in the stretching direction allow us to verify for the first time Pincus prediction on scaling inside blobs. Outside blobs, the scattering function is well described by the Debye function for a stretched ideal chain.Comment: 4 pages, 4 figures, to appear in Physical Review Letter

Emerging Pattern of Rabies Deaths and Increased Viral Infectivity

Most human rabies deaths in the United States can be attributed to unrecognized exposures to rabies viruses associated with bats, particularly those associated with two infrequently encountered bat species (Lasionycteris noctivagans and Pipistrellus subflavus). These human rabies cases tend to cluster in the southeastern and northwestern United States. In these regions, most rabies deaths associated with bats in nonhuman terrestrial mammals are also associated with virus variants specific to these two bat species rather than more common bat species; outside of these regions, more common bat rabies viruses contribute to most transmissions. The preponderance of rabies deaths connected with the two uncommon L. noctivagans and P. subflavus bat rabies viruses is best explained by their evolution of increased viral infectivity

LoCuSS: First Results from Strong-lensing Analysis of 20 Massive Galaxy Clusters at z~0.2

We present a statistical analysis of a sample of 20 strong lensing clusters drawn from the Local Cluster Substructure Survey (LoCuSS), based on high resolution Hubble Space Telescope imaging of the cluster cores and follow-up spectroscopic observations using the Keck-I telescope. We use detailed parameterized models of the mass distribution in the cluster cores, to measure the total cluster mass and fraction of that mass associated with substructures within R<250kpc.These measurements are compared with the distribution of baryons in the cores, as traced by the old stellar populations and the X-ray emitting intracluster medium. Our main results include: (i) the distribution of Einstein radii is log-normal, with a peak and 1sigma width of =1.16+/-0.28; (ii) we detect an X-ray/lensing mass discrepancy of =1.3 at 3 sigma significance -- clusters with larger substructure fractions displaying greater mass discrepancies, and thus greater departures from hydrostatic equilibrium; (iii) cluster substructure fraction is also correlated with the slope of the gas density profile on small scales, implying a connection between cluster-cluster mergers and gas cooling. Overall our results are consistent with the view that cluster-cluster mergers play a prominent role in shaping the properties of cluster cores, in particular causing departures from hydrostatic equilibrium, and possibly disturbing cool cores. Our results do not support recent claims that large Einstein radius clusters present a challenge to the CDM paradigm.Comment: 28 pages, 14 figures, accepted for publication in MNRAS, replaced with accepted versio