Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler

<p>Abstract</p> <p>Background</p> <p>The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage.</p> <p>Results</p> <p>We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats <it>Pteropus vampyrus </it>and <it>Myotis lucifugus</it>. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in <it>P. vampyrus</it>, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli.</p> <p>Conclusion</p> <p>The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.</p

Impacts of Red Imported Fire Ants on Northern Bobwhite Nest Survival

Invasive species are a large management issue because of extensive environmental and economic damage. The red imported fire ant (RIFA, Solenopsis invicta) is an invasive species of growing concern in wildlife management in the United States because of its increasing distribution, difficulty to suppress, and aggressive predation on native invertebrates, herpetofauna, birds, and small mammals. Managers of the northern bobwhite (Colinus virginianus) have questioned the direct impact of RIFA on bobwhite nest success, particularly the factors that might influence the level of nest predation. We hypothesized that RIFA predation on northern bobwhite would vary by location and correlate with drier weather conditions. To test our hypothesis we analyzed bobwhite nest data gathered from 3 properties in the southeastern United States. The nest data are part of a larger research effort on bobwhites, collected by Tall Timbers Research Station and the Albany Quail Project using radiotelemetry from 1992 to 2015. Over these 23 years we tracked bobwhites and located nests (n = 3,207) daily to determine nest fate (success or failure) based on field sign and evidence attributed to specific causes of mortality. We used the nest-survival model in Program MARK to estimate nest survival. Average nest survival varied annually for the Albany and Tall Timbers study areas, respectively. The overall effect of RIFAs on nest survival was generally small, with an average annual loss in Albany of 5.13% (range = 0–15.59%) and 2.17% in Tall Timbers (range = 0–5.83%), but in some years was as high as 15.6%. Greater losses occurred late in the breeding season when it was typically drier and the loss rate in general was higher on the drier of the 2 study sites. Despite the relatively small direct impact on nesting success demonstrated, indirect effects of RIFAs on bobwhite populations are poorly understood at present. Quantifying the influence of indirect factors, such as soil type and habitat disturbance, on RIFA abundance and the subsequent impact on bobwhites, will provide additional insight to the ecological interaction with a highly pervasive and expanding invasive species and help inform management options

Evaluation of the effect of patient education on rates of falls in older hospital patients: Description of a randomised controlled trial

Background. Accidental falls by older patients in hospital are one of the most commonly reported adverse events. Falls after discharge are also common. These falls have enormous physical, psychological and social consequences for older patients, including serious physical injury and reduced quality of life, and are also a source of substantial cost to health systems worldwide. There have been a limited number of randomised controlled trials, mainly using multifactorial interventions, aiming to prevent older people falling whilst inpatients. Trials to date have produced conflicting results and recent meta-analyses highlight that there is still insufficient evidence to clearly identify which interventions may reduce the rate of falls, and falls related injuries, in this population. Methods and design. A prospective randomised controlled trial (n = 1206) is being conducted at two hospitals in Australia. Patients are eligible to be included in the trial if they are over 60 years of age and they, or their family or guardian, give written consent. Participants are randomised into three groups. The control group continues to receive usual care. Both intervention groups receive a specifically designed patient education intervention on minimising falls in addition to usual care. The education is delivered by Digital Video Disc (DVD) and written workbook and aims to promote falls prevention activities by participants. One of the intervention groups also receives follow up education training visits by a health professional. Blinded assessors conduct baseline and discharge assessments and follow up participants for 6 months after discharge. The primary outcome measure is falls by participants in hospital. Secondary outcome measures include falls at home after discharge, knowledge of falls prevention strategies and motivation to engage in falls prevention activities after discharge. All analyses will be based on intention to treat principle. Discussion. This trial will examine the effect of a single intervention (specifically designed patient education) on rates of falls in older patients in hospital and after discharge. The results will provide robust recommendations for clinicians and researchers about the role of patient education in this population. The study has the potential to identify a new intervention that may reduce rates of falls in older hospital patients and could be readily duplicated and applied in a wide range of clinical settings. Trial Registration. ACTRN12608000015347

Impact of tailored falls prevention education for older adults at hospital discharge on engagement in falls prevention strategies postdischarge: Protocol for a process evaluation

Introduction: Older adults recently discharged from hospital have greater incidence of adverse events, functional decline, falls and subsequent readmission. Providing education to hospitalised patients on how to prevent falls at home could reduce postdischarge falls. There has been limited research investigating how older adults respond to tailored falls prevention education provided at hospital discharge. The aim of this study is to evaluate how providing tailored falls prevention education to older patients at the point of, and immediately after hospital discharge in addition to usual care, affects engagement in falls prevention strategies in the 6-months postdischarge period, including their capability and motivation to engage in falls prevention strategies. Methods and analyses: This prospective observational cohort study is a process evaluation of a randomized controlled trial, using an embedded mixed-method design. Participants (n=390) who have been enrolled in the trial are over the age of 60 years, scoring greater than 7/10 on the Abbreviated Mental Test Score. Participants are being discharged from hospital rehabilitation wards in Perth, Western Australia, and followed up for 6 months postdischarge. Primary outcome measures for the process evaluation are engagement in falls prevention strategies, including exercise, home modifications and receiving assistance with activities of daily living. Secondary outcomes will measure capability, motivation and opportunity to engage in falls prevention strategies, based on the constructs of the Capability Opportunity Motivation Behaviour system. Quantitative data are collected at baseline, then at 6 months postdischarge using structured phone interviews. Qualitative data are collected from a purposive sample of the cohort, using semistructured in-depth phone interviews. Quantitative data will be analysed using regression modelling and qualitative data will be analysed using interpretive phenomenological analysis. Ethics and dissemination: Results will be presented in peer-reviewed journals and at conferences worldwide. This study is approved by hospital and university Human Research Ethics Committees

Tailored Education Increased Capability and Motivation for Fall Prevention in Older People After Hospitalization

Recently hospitalized older people are at risk of falls and face barriers to undertaking fall prevention strategies after they return home from hospital. The authors examined the effects of tailored education delivered by physiotherapists on the knowledge (capability) and the motivation of older people to engage in fall prevention after hospital discharge. Utilizing data gathered from a recent trial, data was analyzed from 390 people who were 60 years and over without impaired cognition (>7/10 abbreviated mental test score) and discharged from three Australian hospitals. Motivation and capability were measured at baseline in the hospital and at 6-months after hospital discharge by blinded assistants using structured surveys. Bivariate analysis using generalized linear modeling explored the impact of education on the capability and motivation. Engagement in fall prevention strategies was entered as an independent variable during analysis to determine associations with capability and motivation. The education significantly improved capability [−0.4, 95% CI (−0.7, −0.2), p < 0.01] and motivation [−0.8, 95% CI (−1.1, −0.5), p < 0.01] compared with social-control at the time of hospital discharge. In contrast, social-control participants gained capability and motivation over the 6-months, and no significant differences were found between groups in capability [0.001, 95% CI (−0.2, 0.2), p = 0.9] and motivation [−0.01, 95% CI (−0.3, 0.3), p = 0.9] at follow-up. Tailored fall prevention education is recommended around hospital discharge. Participants still needed to overcome barriers to falls prevention engagement post hospitalization. Thus, tailored education along with direct clinical services such as physiotherapy and social supports is warranted for older people to avoid falls and regain function following hospitalization

Observation and Spectral Measurements of the Crab Nebula with Milagro

The Crab Nebula was detected with the Milagro experiment at a statistical significance of 17 standard deviations over the lifetime of the experiment. The experiment was sensitive to approximately 100 GeV - 100 TeV gamma ray air showers by observing the particle footprint reaching the ground. The fraction of detectors recording signals from photons at the ground is a suitable proxy for the energy of the primary particle and has been used to measure the photon energy spectrum of the Crab Nebula between ~1 and ~100 TeV. The TeV emission is believed to be caused by inverse-Compton up-scattering scattering of ambient photons by an energetic electron population. The location of a TeV steepening or cutoff in the energy spectrum reveals important details about the underlying electron population. We describe the experiment and the technique for distinguishing gamma-ray events from the much more-abundant hadronic events. We describe the calculation of the significance of the excess from the Crab and how the energy spectrum is fit. The fit is consistent with values measured by IACTs between 1 and 20 TeV. Fixing the spectral index to values that have been measured below 1 TeV by IACT experiments (2.4 to 2.6), the fit to the Milagro data suggests that Crab exhibits a spectral steepening or cutoff between about 20 to 40 TeV.Comment: Submitted to Astrophysical Journa

B844: Checklist of the Vascular Plants of Maine Third Revision

This is the third revision of the Checklist of Vascular Plants of Maine. Like its predecessors, it lists all ferns and related plants, conifers, and flowering plants native and naturalized in Maine and records their county-level distribution in the state. The first Check- list (Ogden et al. 1948) was based on specimens in herbaria at the University of Maine (hereafter referred to as MAINE), Portland Society of Natural History, New England Botanical Club, Gray Herbarium of Harvard University, and the private collection of Glen D. Chamberlain of Presque Isle, Maine (now part of MAINE). Bean et al. (1966) revised the checklist to include additions to the flora and update the nomenclature to follow Fernald (1950). Richards et al. (1983) added many new state and county records in the second revision. The purpose of this revision is twofold. First, we have included many new county and state records. Since Richards et al. (1983) there has been considerable collecting in Maine, much of it directed at searching for new state and county records in relatively neglected regions of the state. Second, there have been numerous changes in the scientific names of Maine plants since Fernald (1950), the nomenclatural basis of Richards et al. (1983). We have largely followed Kartesz\u27s (1994) nomenclature (see Taxonomy and Nomenclature section). Recent work on rare plants and establishment of an official list of endangered and threatened plants in Maine (Dibble et al. 1989; Maine State Planning Office 1990) also motivate updating the known distribution and taxonomy of Maine\u27s flora.https://digitalcommons.library.umaine.edu/aes_bulletin/1121/thumbnail.jp

Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR

Plasmids are potent vehicles for spread of antibiotic resistance genes in bacterial populations and often persist in the absence of selection due to efficient maintenance mechanisms. We previously constructed non-conjugative high copy number plasmid vectors that efficiently displace stable plasmids from enteric bacteria in a laboratory context by blocking their replication and neutralising their addiction systems. Here we assess a low copy number broad-host-range self-transmissible IncP-1 plasmid as a vector for such curing cassettes to displace IncF and IncK plasmids. The wild type plasmid carrying the curing cassette displaces target plasmids poorly but derivatives with deletions near the IncP-1 replication origin that elevate copy number about two-fold are efficient. Verification of this in mini IncP-1 plasmids showed that elevated copy number was not sufficient and that the parB gene, korB, that is central to its partitioning and gene control system, also needs to be included. The resulting vector can displace target plasmids from a laboratory population without selection and demonstrated activity in a mouse model although spread is less efficient and requires additional selection pressure

The XMM Cluster Survey: Active Galactic Nuclei and Starburst Galaxies in XMMXCS J2215.9-1738 at z=1.46

We use Chandra X-ray and Spitzer infrared observations to explore the AGN and starburst populations of XMMXCS J2215.9-1738 at z=1.46, one of the most distant spectroscopically confirmed galaxy clusters known. The high resolution X-ray imaging reveals that the cluster emission is contaminated by point sources that were not resolved in XMM observations of the system, and have the effect of hardening the spectrum, leading to the previously reported temperature for this system being overestimated. From a joint spectroscopic analysis of the Chandra and XMM data, the cluster is found to have temperature T=4.1_-0.9^+0.6 keV and luminosity L_X=(2.92_-0.35^+0.24)x10^44 erg/s extrapolated to a radius of 2 Mpc. As a result of this revised analysis, the cluster is found to lie on the sigma_v-T relation, but the cluster remains less luminous than would be expected from self-similar evolution of the local L_X-T relation. Two of the newly discovered X-ray AGN are cluster members, while a third object, which is also a prominent 24 micron source, is found to have properties consistent with it being a high redshift, highly obscured object in the background. We find a total of eight >5 sigma 24 micron sources associated with cluster members (four spectroscopically confirmed, and four selected using photometric redshifts), and one additional 24 micron source with two possible optical/near-IR counterparts that may be associated with the cluster. Examining the IRAC colors of these sources, we find one object is likely to be an AGN. Assuming that the other 24 micron sources are powered by star formation, their infrared luminosities imply star formation rates ~100 M_sun/yr. We find that three of these sources are located at projected distances of <250 kpc from the cluster center, suggesting that a large amount of star formation may be taking place in the cluster core, in contrast to clusters at low redshift.Comment: Accepted for publication in ApJ, 16 pages, 10 figure

Reducing falls in older adults recently discharged from hospital: A systematic review and meta-analysis

Background: Older adults are known to have increased falls rates and functional decline following hospital discharge, with substantial economic healthcare costs. This systematic review aimed to synthesise the evidence for effective falls prevention interventions in older adults recently discharged from hospital. Methods: Literature searches of six databases of quantitative studies conducted from 1990 to June 2017, reporting falls outcomes of falls prevention interventions for community-dwelling older adults discharged from hospital were included. Study quality was assessed using a standardised JBI critical appraisal tool (MAStARI) and data pooled using Rev-Man Review Manager® Results: Sixteen studies (total sample size N= 3,290, from eight countries, mean age 77) comprising 12 interventions met inclusion criteria. We found home hazard modification interventions delivered to those with a previous falls history (1 study), was effective in reducing the number of falls (RR 0.63, 95%CI 0.43, 0.93, Low GRADE evidence). Home exercise interventions (3 studies) significantly increased the proportion of fallers (OR 1.74, 95%CI 1.17, 2.60, Moderate GRADE evidence), and did not significantly reduce falls rate (RR 1.27, 95%CI 0.99, 1.62, Very Low GRADE evidence) or falls injury rate (RR1.16, 95%CI, 0.83,1.63, Low GRADE evidence). Nutritional supplementation for malnourished older adults (1 study) significantly reduced the proportion of fallers (HR 0.41, 95% CI 0.19, 0.86, Low GRADE evidence). Conclusion: The recommended falls prevention interventions for older adults recently discharged from hospital are to provide home hazard minimisation particularly if they have a recent previous falls history and consider nutritional supplementation if they are malnourished