The infrared imaging spectrograph (IRIS) for TMT: the science case

The InfraRed Imaging Spectrograph (IRIS) is a first-light instrument being designed for the Thirty Meter Telescope (TMT). IRIS is a combination of an imager that will cover a 16.4" field of view at the diffraction limit of TMT (4 mas sampling), and an integral field unit spectrograph that will sample objects at 4-50 mas scales. IRIS will open up new areas of observational parameter space, allowing major progress in diverse fields of astronomy. We present the science case and resulting requirements for the performance of IRIS. Ultimately, the spectrograph will enable very well-resolved and sensitive studies of the kinematics and internal chemical abundances of high-redshift galaxies, shedding light on many scenarios for the evolution of galaxies at early times. With unprecedented imaging and spectroscopy of exoplanets, IRIS will allow detailed exploration of a range of planetary systems that are inaccessible with current technology. By revealing details about resolved stellar populations in nearby galaxies, it will directly probe the formation of systems like our own Milky Way. Because it will be possible to directly characterize the stellar initial mass function in many environments and in galaxies outside of the the Milky Way, IRIS will enable a greater understanding of whether stars form differently in diverse conditions. IRIS will reveal detailed kinematics in the centers of low-mass galaxies, allowing a test of black hole formation scenarios. Finally, it will revolutionize the characterization of reionization and the first galaxies to form in the universe.Comment: to appear in Proc. SPIE 773

Mixed policies give more options in multifunctional tropical forest landscapes

This archive stores data utilised in: Mixed policies give more options in multifunctional tropical forest landscapesLaw E.A., Bryan B.A., Meijaard E., Mallawaarachchi T., Struebig M.J., Watts M., Wilson K.A.Journal of Applied Ecology 2016Corresponding author:Elizabeth A. Law*The University of Queensland, School of Biological [email protected]: Jan 18, 2016----------------------DETAILS:Along with this txt file, this archive contains five csv files included, and one folder containing a shape file. These are in the typical format required for input into Marxan with Zones, available from http://www.uq.edu.au/marxan/ (also see new cloud development on Marxan.net). The data time frames relate to a start year of 2008 (see associated publication for further details.Readme.txt - this documentZones.csv - contains zone identification numbers (zoneid) and names (zonenames)FeatureTargets.csv - contains feature id (id), the targets (target; units are specified in supplementary material), species penalty factor (spf; weighting number to determine if the feature is considered as an optimisation threshold constraint, 1, or not, 0), and feature names (name; features 1-9 and 19-20 represent primate species, 10-14 forest types, and 15-17 production values smallholder agriculture, timber, and oil palm, and 18 carbon emissions reduction.Extant.csv - contains planning unit id (pu), the extant class (class; using descriptive codes), and the area (area.ha, in hectares).PuVsFeatures.csv - for every planning unit and feature combination, the 'amount' gives the maximum possible achievement for that feature in that planning unit. Units of measurement are indicated in the main text/supplementary methods and associated papers detailing data development.BaselineZoneContributions.csv - for every zone, planning unit, and feature combination (identified using zoneid, puid, featid codes found in their respective files), this gives the fraction of the full amount possible to achieve within that pu for that feature. Pulayer folder - contains a shape file created in arcgis for the planning units. Coordinate reference system is WGS 84 / UTM zone 49S. One column in the attribute table, indicating the planning unit number (pu)

Identifying areas of improvement for cultural competence in pharmacy curricula: A multi-school study using the self-assessment of perceived level of cultural competence (SAPLCC) questionnaire

Introduction: The implementation of culturally competent healthcare services has been considered a key strategy for the provision of patient-centered care; however, a need remains to address the requirements of teaching cultural competence, including identifying gaps, designing and evaluating curricula, and assessing students' progress toward program objectives. The objective of this study was to explore the applicability of the Self-Assessment of Perceived Level of Cultural Competence (SAPLCC) questionnaire in the identification of improvement areas in cultural competence content in pharmacy curricula. Methods: This study used previously-collected SAPLCC data from student pharmacists at eight United States pharmacy schools. Total and factor-specific SAPLCC scores were calculated based on the 14 factors published previously and grouped into six domains (knowledge, skills, attitudes, encounters, abilities, and awareness). Differences in overall scores by domain and factors across various student characteristics were examined using analysis of variance. Results: The overall mean total SAPLCC score was classified as moderate. Third-year students had significantly higher SAPLCC mean scores than first-year students, and African American students scored significantly higher than their counterparts. At the factor-level, students scored higher in the Attitudes and Awareness domains and scored lower in the Knowledge, Skills, and Encounters domains. Conclusions: The application of the SAPLCC in schools participating in this preliminary study allowed for the identification of content areas that may benefit from revision. The SAPLCC may be a useful tool for mapping cultural competence curricular content by each specific domain and identifying areas of potential improvement regarding cultural competence training within pharmacy curricula.Dr. Margarita Echeverri's contribution was supported in part by funds from the Health Resources and Services Administration of the US Department of Health and Human Services under grant number (No.) D34HP00006; the Research Centers in Minority Institutions Program of the National Institute on Minority Health and Health Disparities (NIMHD) grant No. 2U54MD007595; the Xavier's NIMHD funded Center for Minority Health and Health Disparities Research and Education grant No. 5S21MD0000100, and the National Institute of General Medical Sciences' funded Louisiana Clinical and Translational Science Center grant No. U54GM104940. The contents and views in this manuscript are those of the authors and should not be construed to represent the views of the National Institutes of Health and other funders

Wood traits explain microbial but not termite‐driven decay in Australian tropical rainforest and savanna

1. Variation in decay rates across woody species is a key uncertainty in predicting the fate of carbon stored in deadwood, especially in the tropics. Quantifying the relative contributions of biotic decay agents, particularly microbes and termites, under different climates and across species with diverse wood traits could help explain this variation. 2. To fill this knowledge gap, we deployed woody stems from 16 plant species native to either rainforest (n = 10) or savanna (n = 6) in northeast Australia, with and without termite access. For comparison, we also deployed standardized, non-native pine blocks at both sites. We hypothesized that termites would increase rates of deadwood decay under conditions that limit microbial activity. Specifically, termite contributions to wood decay should be greater under dry conditions and in wood species with traits that constrain microbial decomposers. 3. Termite discovery of stems was surprisingly low with only 17.6% and 22.6% of accessible native stems discovered in the rainforest and savanna respectively. Contrary to our hypothesis, stems discovered by termites decomposed faster only in the rainforest. Termites discovered and decayed pine blocks at higher rates than native stems in both the rainforest and savanna. 4. We found significant variation in termite discovery and microbial decay rates across native wood species within the same site. Although wood traits explained 85% of the variation in microbial decay, they did not explain termite-driven decay. For stems undiscovered by termites, decay rates were greater in species with higher wood nutrient concentrations and syringyl:guiacyl lignin ratios but lower carbon concentrations and wood densities. 5. Synthesis. Ecosystem-scale predictions of deadwood turnover and carbon storage should account for the impact of wood traits on decomposer communities. In tropical Australia, termite-driven decay was lower than expected for native wood on the ground. Even if termites are present, they may not always increase decomposition rates of fallen native wood in tropical forests. Our study shows how the drivers of wood decay differ between Australian tropical rainforest and savanna; further research should test whether such differences apply world-wide

Design of synthetic bacterial communities for predictable plant phenotypes

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communitie

Changing landscapes, livelihoods and village welfare in the context of oil palm development

The United Nations’ Sustainable Development Goals underscore the need for improved understanding of relationships between changes in landscapes, livelihoods, and social welfare, and how these relate to tackling poverty, inequality, and environmental degradation. Such assessments are especially relevant in the context of oil palm agricultural expansion, which has rapidly replaced traditional livelihoods and generates ongoing political debates around the world. Proponents of the oil palm industry have used economic objectives to justify expansion, while opponents have raised the negative socioecological impacts on communities. To assist the debate, we assessed the association between the change in land-uses and climate, the change in village primary livelihoods towards monocultural oil palm cultivation, and the change in village welfare after adopting oil palm across Kalimantan, Indonesian Borneo, between 2000 and 2014. We show that the change in village primary livelihoods towards monocultural oil palm cultivation during this period was associated with complex interrelations between the expansion of agricultural industries, and conducive climate and market conditions for supporting agricultural production. The shift to oil palm monoculture brought significant economic benefit to villages, but this was limited to those with past exposure to plantation management and the market economy, such as in polyculture plantation villages. For villages where the majority of communities practiced traditional subsistence-based livelihoods (farming, foraging and fishing), the economic benefit from a shift to oil palm lasted only a few years after transition, while the socioecological welfare deteriorated. Furthermore, the shift to oil palm monoculture jeopardized food security among these subsistence livelihood villages. Baseline economic and socioecological conditions of villages, therefore, critically determine the success of the oil palm sector in providing economic benefits over the long term. Our study urgently calls for considering oil palm development objectives not only in terms of regional economic gain, but also the future maintenance of socioecological welfare of village communities

Homozygous microdeletion of exon 5 in ZNF277 in a girl with specific language impairment

Peer reviewedPublisher PD

All-cause mortality in HIV-positive adults starting combination antiretroviral therapy: correcting for loss to follow-up

Objective: To estimate mortality in HIV-positive patients starting combination antiretroviral therapy (ART) and to discuss different approaches to calculating correction factors to account for loss to follow-up. Methods: A total of 222 096 adult HIV-positive patients who started ART 2009–2014 in clinics participating in the International epidemiology Databases to Evaluate AIDS collaboration in 43 countries in sub-Saharan Africa, Asia Pacific, Latin America, and North America were included. To allow for underascertainment of deaths due to loss to follow-up, two correction factors (one for the period 0–6 months on ART and one for later periods) or 168 correction factors (combinations of two sexes, three time periods after ART initiation, four age groups, and seven CD4þ groups) based on tracing patients lost in Kenya and data linkages in South Africa were applied. Corrected mortality rates were compared with a worst case scenario assuming all patients lost to follow-up had died. Results: Loss to follow-up differed between regions; rates were lowest in central Africa and highest in east Africa. Compared with using two correction factors (1.64 for the initial ART period and 2.19 for later), applying 168 correction factors (range 1.03–4.75) more often resulted in implausible mortality rates that exceeded the worst case scenario. Corrected mortality rates varied widely, ranging from 0.2 per 100 person-years to 54 per 100 person-years depending on region and covariates. Conclusion: Implausible rates were less common with the simpler approach based on two correction factors. The corrected mortality rates will be useful to international agencies, national programmes, and modellers

Model comparisons for estimating carbon emissions from North American wildland fire

Research activities focused on estimating the direct emissions of carbon from wildland fires across North America are reviewed as part of the North American Carbon Program disturbance synthesis. A comparison of methods to estimate the loss of carbon from the terrestrial biosphere to the atmosphere from wildland fires is presented. Published studies on emissions from recent and historic time periods and five specific cases are summarized, and new emissions estimates are made using contemporary methods for a set of specific fire events. Results from as many as six terrestrial models are compared. We find that methods generally produce similar results within each case, but estimates vary based on site location, vegetation (fuel) type, and fire weather. Area normalized emissions range from 0.23 kg C m−2 for shrubland sites in southern California/NW Mexico to as high as 6.0 kg C m−2 in northern conifer forests. Total emissions range from 0.23 to 1.6 Tg C for a set of 2003 fires in chaparral-dominated landscapes of California to 3.9 to 6.2 Tg C in the dense conifer forests of western Oregon. While the results from models do not always agree, variations can be attributed to differences in model assumptions and methods, including the treatment of canopy consumption and methods to account for changes in fuel moisture, one of the main drivers of variability in fire emissions. From our review and synthesis, we identify key uncertainties and areas of improvement for understanding the magnitude and spatial-temporal patterns of pyrogenic carbon emissions across North America

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis

Objective The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the ‘shared susceptibility epitope (SE)’. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection. Indigenous North American (INA) populations have high risk of early-onset ACPA-positive RA, whereby HLA-DRB1*04:04 and HLA-DRB1*14:02 are implicated as risk factors for RA in INA. However, HLA-DRB1*14:02 has a His13βSer polymorphism. Therefore, we aimed to verify this association and determine its molecular mechanism. Methods HLA genotype was compared in 344 INA patients with RA and 352 controls. Structures of HLA-DRB1*1402-class II loaded with vimentin-64Arg59-71, vimentin-64Cit59-71 and fibrinogen β−74Cit69-81 were solved using X-ray crystallography. Vimentin-64Cit59-71-specific and vimentin59-71-specific CD4+ T cells were characterised by flow cytometry using peptide-histocompatibility leukocyte antigen (pHLA) tetramers. After sorting of antigen-specific T cells, TCRα and β-chains were analysed using multiplex, nested PCR and sequencing. Results ACPA+ RA in INA was independently associated with HLA-DRB1*14:02. Consequent to the His13βSer polymorphism and altered P4 pocket of HLA-DRB1*14:02, both citrulline and arginine were accommodated in opposite orientations. Oligoclonal autoreactive CD4+ effector T cells reactive with both citrulline and arginine forms of vimentin59-71 were observed in patients with HLA-DRB1*14:02+ RA and at-risk ACPA- first-degree relatives. HLA-DRB1*14:02-vimentin59-71-specific and HLA-DRB1*14:02-vimentin-64Cit59-71-specific CD4+ memory T cells were phenotypically distinct populations. Conclusion HLA-DRB1*14:02 broadens the capacity for citrullinated and native self-peptide presentation and T cell expansion, increasing risk of ACPA+ RA