Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

Ecological interpretations of nitrogen isotope ratios of terrestrial plants and soils

Background Knowledge of biological and climatic controls in terrestrial nitrogen (N) cycling within and across ecosystems is central to understanding global patterns of key ecosystem processes. The ratios of 15N:14N in plants and soils have been used as indirect indices of N cycling parameters, yet our understanding of controls over N isotope ratios in plants and soils is still developing. Scope In this review, we provide background on the main processes that affect plant and soil N isotope ratios. In a similar manner to partitioning the roles of state factors and interactive controls in determining ecosystem traits, we review N isotopes patterns in plants and soils across a number of proximal factors that influence ecosystem properties as well as mechanisms that affect these patterns. Lastly, some remaining questions that would improve our understanding of N isotopes in terrestrial ecosystems are highlighted. Conclusion Compared to a decade ago, the global patterns of plant and soil N isotope ratios are more resolved. Additionally, we better understand how plant and soil N isotope ratios are affected by such factors as mycorrhizal fungi, climate, and microbial processing. A comprehensive understanding of the N cycle that ascribes different degrees of isotopic fractionation for each step under different conditions is closer to being realized, but a number of process-level questions still remain

Correlated variability in the blazar 3C 454.3

The blazar 3C 454.3 was revealed by the Fermi Gamma-ray Space Telescope to be in an exceptionally high flux state in July 2008. Accordingly, we performed a multi-wavelength monitoring campaign on this blazar using IR and optical observations from the SMARTS telescopes, optical, UV and X-ray data from the Swift satellite, and public-release gamma-ray data from Fermi. We find an excellent correlation between the IR, optical, UV and gamma-ray light curves, with a time lag of less than one day. The amplitude of the infrared variability is comparable to that in gamma-rays, and larger than at optical or UV wavelengths. The X-ray flux is not strongly correlated with either the gamma-rays or longer wavelength data. These variability characteristics find a natural explanation in the external Compton model, in which electrons with Lorentz factor gamma~10^(3-4) radiate synchrotron emission in the infrared-optical and also scatter accretion disk or emission line photons to gamma-ray energies, while much cooler electrons (gamma~10^(1-2)) produce X-rays by scattering synchrotron or other ambient photons.Comment: 7 pages, 3 figures, submitted to ApJ Letter

Measuring the spin of the primary black hole in OJ287

The compact binary system in OJ287 is modelled to contain a spinning primary black hole with an accretion disk and a non-spinning secondary black hole. Using Post Newtonian (PN) accurate equations that include 2.5PN accurate non-spinning contributions, the leading order general relativistic and classical spin-orbit terms, the orbit of the binary black hole in OJ287 is calculated and as expected it depends on the spin of the primary black hole. Using the orbital solution, the specific times when the orbit of the secondary crosses the accretion disk of the primary are evaluated such that the record of observed outbursts from 1913 up to 2007 is reproduced. The timings of the outbursts are quite sensitive to the spin value. In order to reproduce all the known outbursts, including a newly discovered one in 1957, the Kerr parameter of the primary has to be $0.28 \pm 0.08$. The quadrupole-moment contributions to the equations of motion allow us to constrain the `no-hair' parameter to be $1.0\:\pm\:0.3$ where 0.3 is the one sigma error. This supports the `black hole no-hair theorem' within the achievable precision. It should be possible to test the present estimate in 2015 when the next outburst is due. The timing of the 2015 outburst is a strong function of the spin: if the spin is 0.36 of the maximal value allowed in general relativity, the outburst begins in early November 2015, while the same event starts in the end of January 2016 if the spin is 0.2Comment: 12 pages, 6 figure

Intervention Now to Eliminate Repeat Unintended Pregnancy in Teenagers (INTERUPT): a systematic review of intervention effectiveness and cost-effectiveness, and qualitative and realist synthesis of implementation factors and user engagement.

BACKGROUND: Unintended repeat conceptions can result in emotional, psychological and educational harm to young women, often with enduring implications for their life chances. This study aimed to identify which young women are at the greatest risk of repeat unintended pregnancies; which interventions are effective and cost-effective; and what are the barriers to and facilitators for the uptake of these interventions. METHODS: We conducted a mixed-methods systematic review which included meta-analysis, framework synthesis and application of realist principles, with stakeholder input and service user feedback to address this. We searched 20 electronic databases, including MEDLINE, Excerpta Medica database, Applied Social Sciences Index and Abstracts and Research Papers in Economics, to cover a broad range of health, social science, health economics and grey literature sources. Searches were conducted between May 2013 and June 2014 and updated in August 2015. RESULTS: Twelve randomised controlled trials (RCTs), two quasi-RCTs, 10 qualitative studies and 53 other quantitative studies were identified. The RCTs evaluated psychosocial interventions and an emergency contraception programme. The primary outcome was repeat conception rate: the event rate was 132 of 308 (43%) in the intervention group versus 140 of 289 (48%) for the control group, with a non-significant risk ratio (RR) of 0.92 [95% confidence interval (CI) 0.78-1.08]. Four studies reported subsequent birth rates: 29 of 237 (12%) events for the intervention arm versus 46 out of 224 (21%) for the control arm, with an RR of 0.60 (95% CI 0.39-0.93). Many repeat conceptions occurred in the context of poverty, low expectations and aspirations and negligible opportunities. Qualitative and realist evidence highlighted the importance of context, motivation, future planning and giving young women a central and active role in the development of new interventions. CONCLUSIONS: Little or no evidence for the effectiveness or cost-effectiveness of any of the interventions to reduce repeat pregnancy in young women was found. Qualitative and realist evidence helped to explain gaps in intervention design that should be addressed. More theory-based, rigorously evaluated programmes need to be developed to reduce unintended repeat pregnancy in young women. TRIAL REGISTRATION: PROSPERO, CRD42012003168 . Cochrane registration number: i = fertility/0068

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity

The Prevalence of Children with a History of Sexual Abuse Hospitalized in the Psychiatric Setting

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72548/1/j.1744-6171.1991.tb00489.x.pd

Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.EEA FamailláFil: Stanschewski, Clara S. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Rey, Elodie. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Fiene, Gabriele. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Craine, Evan B. Washington State University. Department of Crop and Soil Sciences; Estados UnidosFil: Wellman, Gordon. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Melino, Vanessa J. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Patiranage, Dilan S.R. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia SauditaFil: Patiranage, Dilan S.R. Christian-Albrechts-University of Kiel. Plant Breeding Institute; AlemaniaFil: Johansen, Kasper. King Abdullah University of Science and Technology. Water Desalination and Reuse Center; Arabia SauditaFil: Schmöckel, Sandra M. University of Hohenheim. Institute of Crop Science. Department Physiology of Yield Stability; AlemaniaFil: Erazzu, Luis Ernesto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.Fil: Tester, Mark. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudit

HCV treatment rates and sustained viral response among people who inject drugs in seven UK sites: real world results and modelling of treatment impact.

Hepatitis C virus (HCV) antiviral treatment for people who inject drugs (PWID) could prevent onwards transmission and reduce chronic prevalence. We assessed current PWID treatment rates in seven UK settings and projected the potential impact of current and scaled-up treatment on HCV chronic prevalence. Data on number of PWID treated and sustained viral response rates (SVR) were collected from seven UK settings: Bristol (37-48% HCV chronic prevalence among PWID), East London (37-48%), Manchester (48-56%), Nottingham (37-44%), Plymouth (30-37%), Dundee (20-27%) and North Wales (27-33%). A model of HCV transmission among PWID projected the 10-year impact of (i) current treatment rates and SVR (ii) scale-up with interferon-free direct acting antivirals (IFN-free DAAs) with 90% SVR. Treatment rates varied from <5 to over 25 per 1000 PWID. Pooled intention-to-treat SVR for PWID were 45% genotypes 1/4 [95%CI 33-57%] and 61% genotypes 2/3 [95%CI 47-76%]. Projections of chronic HCV prevalence among PWID after 10 years of current levels of treatment overlapped substantially with current HCV prevalence estimates. Scaling-up treatment to 26/1000 PWID annually (achieved already in two sites) with IFN-free DAAs could achieve an observable absolute reduction in HCV chronic prevalence of at least 15% among PWID in all sites and greater than a halving in chronic HCV in Plymouth, Dundee and North Wales within a decade. Current treatment rates among PWID are unlikely to achieve observable reductions in HCV chronic prevalence over the next 10 years. Achievable scale-up, however, could lead to substantial reductions in HCV chronic prevalence