Exome chip analyses identify genes affecting mortality after HLA-matched unrelated-donor blood and marrow transplantation

© 2018 by The American Society of Hematology Although survival outcomes have significantly improved, up to 40% of patients die within 1 year of HLA-matched unrelated-donor blood and marrow transplantation (BMT). To identify non-HLA genetic contributors to mortality after BMT, we performed the first exome-wide association study in the DISCOVeRY-BMT cohorts using the Illumina HumanExome BeadChip. This study includes 2473 patients with acute myeloid leukemia, acute lymphoblastic leukemia, or myelodysplastic syndrome and 2221 10/10 HLA-matched donors treated from 2000 to 2011. Single-variant and gene-level analyses were performed on overall survival (OS), transplantation-related mortality (TRM), and disease-related mortality (DRM). Genotype mismatches between recipients and donors in a rare nonsynonymous variant of testis-expressed gene TEX38 significantly increased risk of TRM, which was more dramatic when either the recipient or donor was female. Using the SKAT-O test to evaluate gene-level effects, variant genotypes of OR51D1 in recipients were significantly associated with OS and TRM. In donors, 4 (ALPP, EMID1, SLC44A5, LRP1), 1 (HHAT), and 2 genes (LYZL4, NT5E) were significantly associated with OS, TRM, and DRM, respectively. Inspection of NT5E crystal structures showed 4 of the associated variants affected the enzyme structure and likely decreased the catalytic efficiency of the enzyme. Further confirmation of these findings and additional functional studies may provide individualized risk prediction and prognosis, as well as alternative donor selection strategies

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

Avianbase: a community resource for bird genomics

Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium

Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

To elucidate genome-level responses to drought and high-salinity stress in rice, a 70mer oligomer microarray covering 36,926 unique genes or gene models was used to profile genome expression changes in rice shoot, flag leaf and panicle under drought or high-salinity conditions. While patterns of gene expression in response to drought or high-salinity stress within a particular organ type showed significant overlap, comparison of expression profiles among different organs showed largely organ-specific patterns of regulation. Moreover, both stresses appear to alter the expression patterns of a significant number of genes involved in transcription and cell signaling in a largely organ-specific manner. The promoter regions of genes induced by both stresses or induced by one stress in more than one organ types possess relative enrichment of two cis-elements (ABRE core and DRE core) known to be associated with water stress. An initial computational analysis indicated that novel promoter motifs are present in the promoters of genes involved in rehydration after drought. This analysis suggested that rice might possess a mechanism that actively detects rehydration and facilitates rapid recovery. Overall, our data supports a notion that organ-specific gene regulation in response to the two abiotic stresses may primarily be mediated by organ-specific transcription responses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11103-006-9111-1) contains supplementary material, which is available to authorized users

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Chronic disease prevalence and care among the elderly in urban and rural Beijing, China - a 10/66 Dementia Research Group cross-sectional survey

<p>Abstract</p> <p>Background</p> <p>Demographic ageing is occurring at an unprecedented rate in China. Chronic diseases and their disabling consequences will become much more common. Public policy has a strong urban bias, and older people living in rural areas may be especially vulnerable due to limited access to good quality healthcare, and low pension coverage. We aim to compare the sociodemographic and health characteristics, health service utilization, needs for care and informal care arrangements of representative samples of older people in two Beijing communities, urban Xicheng and rural Daxing.</p> <p>Methods</p> <p>A one-phase cross-sectional survey of all those aged 65 years and over was conducted in urban and rural catchment areas in Beijing, China. Assessments included questionnaires, a clinical interview, physical examination, and an informant interview. Prevalence of chronic diseases, self-reported impairments and risk behaviours was calculated adjusting for household clustering. Poisson working models were used to estimate the independent effect of rural versus urban residence, and to explore the predictors of health services utilization.</p> <p>Results</p> <p>We interviewed 1002 participants in rural Daxing, and 1160 in urban Xicheng. Those in Daxing were more likely to be younger, widowed, less educated, not receiving a pension, and reliant on family transfers. Chronic diseases were more common in Xicheng, when based on self-report rather than clinical assessment. Risk exposures were more common in Daxing. Rural older people were much less likely to access health services, controlling for age and health. Community health services were ineffective, particularly in Daxing, where fewer than 3% of those with hypertension were adequately controlled. In Daxing, care was provided by family, who had often given up work to do so. In Xicheng, 45% of those needing care were supported by paid caregivers. Caregiver strain was higher in Xicheng. Dementia was strongly associated with care needs and caregiver strain, but not with medical helpseeking.</p> <p>Conclusion</p> <p>Apparent better health in Daxing might be explained by under-diagnosis, under-reporting or selective mortality. Far-reaching structural reforms may be needed to improve access and strengthen rural healthcare. The impact of social and economic change is already apparent in Xicheng, with important implications for future long-term care.</p

Higher harmonic anisotropic flow measurements of charged particles in Pb-Pb collisions at 2.76 TeV

We report on the first measurement of the triangular $v_3$, quadrangular $v_4$, and pentagonal $v_5$ charged particle flow in Pb-Pb collisions at 2.76 TeV measured with the ALICE detector at the CERN Large Hadron Collider. We show that the triangular flow can be described in terms of the initial spatial anisotropy and its fluctuations, which provides strong constraints on its origin. In the most central events, where the elliptic flow $v_2$ and $v_3$ have similar magnitude, a double peaked structure in the two-particle azimuthal correlations is observed, which is often interpreted as a Mach cone response to fast partons. We show that this structure can be naturally explained from the measured anisotropic flow Fourier coefficients.Comment: 10 pages, 4 figures, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/387

The Recognition of Excessive blood loss At ChildbirTh (REACT) Study: a two-phase exploratory, sequential mixed methods inquiry using focus groups, interviews and a pilot, randomised crossover study

Objectives: To explore how childbirth-related blood loss is evaluated and excessive bleeding recognised; and develop and test a theory of postpartum haemorrhage (PPH) diagnosis. Design: Two-phase, exploratory, sequential mixed methods design using focus groups, interviews and a pilot, randomised crossover study. Setting: Two hospitals in North West England. Sample: Women (following vaginal birth with and without PPH), birth partners, midwives and obstetricians. Methods: Phase one (qualitative): 8 focus groups and 20 one-to-one, semi-structured interviews were conducted with 15 women, 5 birth partners, 11 obstetricians, 1 obstetric anaesthetist and 19 midwives (n=51). Phase two (quantitative): 11 obstetricians and 10 midwives (n=21) completed two simulations of fast and slow blood loss using a high-fidelity childbirth simulator. Results: Responses to blood loss were described as automatic, intuitive reactions to the speed, nature and visibility of blood flow. Health professionals reported that quantifying volume was most useful after a PPH diagnosis, to validate intuitive decisions and guide on-going management. During simulations, PPH treatment was initiated at volumes at or below 200ml (fast mean blood loss 79.6ml, SD 41.1; slow mean blood loss 62.6ml, SD 27.7). All participants treated fast, visible blood loss, but only half treated slow blood loss, despite there being no difference in volumes (difference 18.2ml, 95% CI -5.6 to 42.2ml, p=0.124). Conclusions: Experience and intuition, rather than blood loss volume, inform recognition of excessive blood loss after birth. Women and birth partners want more information and open communication about blood loss. Further research exploring clinical decision-making and how to support it is required

Exclusive photoproduction of pi degrees up to large values of Mandelstam variables s, t, and u with CLAS

Exclusive photoproduction cross sections have been measured for the process $\gamma p \rightarrow p\pi^0(e^+e^-(\gamma))$ with the Dalitz decay final state using tagged photon energies in the range of $E_{\gamma} = 1.275-5.425$ GeV. The complete angular distribution of the final state $\pi^0$, for the entire photon energy range up to large values of $t$ and $u$, has been measured for the first time. The data obtained show that the cross section $d\sigma/dt$, at mid to large angles, decreases with energy as $s^{-6.89\pm 0.26}$. This is in agreement with the perturbative QCD quark counting rule prediction of $s^{-7}$. Paradoxically, the size of angular distribution of measured cross sections is greatly underestimated by the QCD based Generalized Parton Distribution mechanism at highest available invariant energy $s=11$ GeV$^2$. At the same time, the Regge exchange based models for $\pi^0$ photoproduction are more consistent with experimental data.Comment: 7 pages, 6 figure