The Plant Ontology: A common reference ontology for plants

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms

The manifest association structure of the single-factor model: insights from partial correlations

The association structure between manifest variables arising from the single-factor model is investigated using partial correlations. The additional insights to the practitioner provided by partial correlations for detecting a single-factor model are discussed. The parameter space for the partial correlations is presented, as are the patterns of signs in a matrix containing the partial correlations that are not compatible with a single-factor model

Inferring the parallax of Westerlund 1 from Gaia DR2

Westerlund 1 (Wd1) is potentially the largest star cluster in the Galaxy. That designation critically depends upon the distance to the cluster, yet the cluster is highly obscured, making luminosity-based distance estimates difficult. Using {\it Gaia} Data Release 2 (DR2) parallaxes and Bayesian inference, we infer a parallax of $0.35^{+0.07}_{-0.06}$ mas corresponding to a distance of $2.6^{+0.6}_{-0.4}$ kpc. To leverage the combined statistics of all stars in the direction of Wd1, we derive the Bayesian model for a cluster of stars hidden among Galactic field stars; this model includes the parallax zero-point. Previous estimates for the distance to Wd1 ranged from 1.0 to 5.5 kpc, although values around 5 kpc have usually been adopted. The {\it Gaia} DR2 parallaxes reduce the uncertainty from a factor of 3 to 18\% and rules out the most often quoted value of 5 kpc with 99\% confidence. This new distance allows for more accurate mass and age determinations for the stars in Wd1. For example, the previously inferred initial mass at the main-sequence turn-off was around 40 M$_{\odot}$; the new {\it Gaia} DR2 distance shifts this down to about 22 M$_{\odot}$. This has important implications for our understanding of the late stages of stellar evolution, including the initial mass of the magnetar and the LBV in Wd1. Similarly, the new distance suggests that the total cluster mass is about four times lower than previously calculated.Comment: 14 pages, 10 figure

The correlation potential in density functional theory at the GW-level: spherical atoms

As part of a project to obtain better optical response functions for nano materials and other systems with strong excitonic effects we here calculate the exchange-correlation (XC) potential of density-functional theory (DFT) at a level of approximation which corresponds to the dynamically- screened-exchange or GW approximation. In this process we have designed a new numerical method based on cubic splines which appears to be superior to other techniques previously applied to the "inverse engineering problem" of DFT, i.e., the problem of finding an XC potential from a known particle density. The potentials we obtain do not suffer from unphysical ripple and have, to within a reasonable accuracy, the correct asymptotic tails outside localized systems. The XC potential is an important ingredient in finding the particle-conserving excitation energies in atoms and molecules and our potentials perform better in this regard as compared to the LDA potential, potentials from GGA:s, and a DFT potential based on MP2 theory.Comment: 13 pages, 9 figure

The Empirical Evidence for the Telemedicine Intervention in Diabetes Management

Objective: The research presented here assesses the scientific evidence for the telemedicine intervention in the management of diabetes (telediabetes), gestational diabetes, and diabetic retinopathy. The impetus derives from the confluence of high prevalence of these diseases, increasing incidence, and rising costs, while telemedicine promises to ameliorate, if not prevent, type 2 diabetes and its complications. Materials and Methods: A purposeful review of the literature identified relevant publications from January 2005 to December 2013. These were culled to retain only credible research articles for detailed review and analysis. The search yielded approximately 17,000 articles with no date constraints. Of these, 770 appeared to be research articles within our time frame. A review of the abstracts yielded 73 articles that met the criteria for inclusion in the final analysis. Evidence is organized by research findings regarding feasibility/acceptance, intermediate outcomes (e.g., use of service, and screening compliance), and health outcomes (control of glycemic level, lipids, body weight, and physical activity.) Results: Definitions of telediabetes varied from study to study vis-à-vis diabetes subtype, setting, technology, staffing, duration, frequency, and target population. Outcome measures also varied. Despite these vagaries, sufficient evidence was obtained from a wide variety of research studies, consistently pointing to positive effects of telemonitoring and telescreening in terms of glycemic control, reduced body weight, and increased physical exercise. The major contributions point to telemedicine's potential for changing behaviors important to diabetes control and prevention, especially type 2 and gestational diabetes. Similarly, screening and monitoring for retinopathy can detect symptoms early that may be controlled or treated. Conclusions: Overall, there is strong and consistent evidence of improved glycemic control among persons with type 2 and gestational diabetes as well as effective screening and monitoring of diabetic retinopathy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140288/1/tmj.2015.0029.pd

Monocot fossils suitable for molecular dating analyses

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111920/1/boj12233.pd

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MicrobiologyOpen 6 (2017): e467, doi:10.1002/mbo3.467.Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0.2-μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES-5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES-5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free-living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low-salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical “hotspot,” which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater–brackish water interface in the fast-flowing Columbia River estuary.National Science Foundation Grant Numbers: OCE 0424602, MCB 064446

The Evolution of Norovirus, the “Gastric Flu”

The authors discuss the implications of a new study that presents compelling data to show that norovirus evolution is driven by immune selection pressure

On the Gaia DR2 distances for Galactic Luminous Blue Variables

We examine parallaxes and distances for Galactic luminous blue variables (LBVs) in Gaia DR2. The sample includes 11 LBVs and 14 LBV candidates. For about half of the sample, DR2 distances are either similar to commonly adopted literature values, or the DR2 values have large uncertainties. For the rest, reliable DR2 distances differ significantly from values in the literature, and in most cases the Gaia DR2 distance is smaller. Two key results are that the S Doradus instability strip may not be as clearly defined as previously thought, and that there exists a population of LBVs at relatively low luminosities. LBVs seem to occupy a wide swath from the end of the main sequence at the blue edge to 8000 K at the red side, with a spread in luminosity reaching as low as log(L/Lsun)=4.5. The lower-luminosity group corresponds to effective single-star initial masses of 10-25 Msun, and includes objects that have been considered as confirmed LBVs. We discuss implications for LBVs including (1) their instability and origin in binary evolution, (2) connections to some supernova (SN) impostors such as the class of SN 2008S-like objects, and (3) LBVs that may be progenitors of SNe with dense circumstellar material across a wide initial mass range. Although some of the Gaia DR2 distances for LBVs have large uncertainty, this represents the most direct and consistent set of Galactic LBV distance estimates available in the literature.Comment: 20 pages, 5 figures, MNRAS accepted. Updated inclusion of excess astrometric noise and discussion of literature distance