Hemostatic efficacy of pathogen-inactivated vs untreated platelets: a randomized controlled trial

Pathogen inactivation of platelet concentrates reduces the risk for blood-borne infections. However, its effect on platelet function and hemostatic efficacy of transfusion is unclear. We conducted a randomized noninferiority trial comparing the efficacy of pathogen-inactivated platelets using riboflavin and UV B illumination technology (intervention) compared with standard plasma-stored platelets (control) for the prevention of bleeding in patients with hematologic malignancies and thrombocytopenia. The primary outcome parameter was the proportion of transfusion-treatment periods in which the patient had grade 2 or higher bleeding, as defined by World Health Organization criteria. Between November 2010 and April 2016, 469 unique patients were randomized to 567 transfusion-treatment periods (283 in the control arm, 284 in the intervention arm). There was a 3% absolute difference in grade 2 or higher bleeding in the intention-to-treat analysis: 51% of the transfusion-treatment periods in the control arm and 54% in the intervention arm (95% confidence interval [CI], -6 to 11; P=.012 for noninferiority). However, in the per-protocol analysis, the difference in grade 2 or higher bleeding was 8%: 44% in the control arm and 52% in the intervention arm (95% CI22 to 18; P=.19 for noninferiority). Transfusion increment parameters were similar to 50% lower in the intervention arm. There was no difference in the proportion of patients developing HLA class I alloantibodies. In conclusion, the noninferiority criterion for pathogen-inactivated platelets was met in the intention-to-treat analysis. This finding was not demonstrated in the per-protocol analysis. This trial was registered at The Netherlands National Trial Registry as # NTR2106 and at www. clinicaltrials. gov as # NCT02783313

Global diversity, population stratification, and selection of human copy-number variation

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load

Global diversity, population stratification, and selection of human copy-number variation

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.This project has been funded in part with federal funds from the National Cancer Institute, NIH, under contract HHSN26120080001E. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. This work was also partly supported by NIH grant 2R01HG002385 and a grant (11631) from the Paul G. Allen Family Foundation to E.E.E. The sequencing for this study was supported by a grant from the Simons Foundation to D.R. (SFARI 280376) and by a HOMINID grant from the NSF to D.R. (BCS-1032255). T.K. is supported by a European Research Council Starting Investigator grant (FP7 - 26213). R.S. and S.D. received support from the Ministry of Education and Science, Russian Federation (14.Z50.31.0010). H.S., E.M., R.V., and M.M. are supported by Institutional Research Funding from the Estonian Research Council IUT24-1 and by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu. S.A.T. is supported by NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01. C.T.-S. is supported by Wellcome Trust grant 098051. C.M.B. is supported by the NSF (award numbers 0924726 and 1153911). Data are deposited into ENA (PRJEB9586 or ERP010710), and variant calls are deposited in dbVar (PRJNA285786

Global diversity, population stratification, and selection of human copy-number variation.

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans

Using remote sensing to estimate snow depth and snow water equivalence

Snow is an important source of water. However, data is often lacking on the water content (snow water equivalence - SWE), extent and depth of the seasonal snow cover. This paper presents results from a research project that determined the amount of water in a snow pack from snow depth and SWE in an areal manner using remote sensing and photogrammetry. Five field campaigns were undertaken within the Falls Creek Ski Resort, over 18 months, to establish a framework of positional points, collect snow data and acquire aerial imagery. A GPS survey was completed concurrent with the image capture of snow-covered terrain to obtain appropriate validation points of the snow surface and to coordinate photo control. Spectral reflectance measurements, supported by manual sampling of the snow surface, were collected in conjunction with snow surface GPS measurements. Digital photogrammetric methods were used to create digital elevation models (DEMs) of the snow surface and the terrain. The digital aerial photography was acquired with a ground sample distance of 8 cm. Derived DEM values have been consistently higher than GPS elevations (mean differences of 15 cm; standard deviation of 8 cm). Spectral reflectance signatures were used to infer the properties of snow, such as snow grain size. A prominent absorption feature (~1030 nm) of the snow reflectance was found to be highly correlated with grain size (R = 0.71, p <0.05) allowing for the estimation of SWE, at least for the snow surface. The potential of this methodology is to allow for the automated estimation of both snow depth and water content at a landscape scale

Ancient human genomes suggest three ancestral populations for present-day Europeans

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes ¹⁻⁴ with 2,345 contemporary humans to show thatmost present-day Europeans derive from atleast three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians³, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages