2,015 research outputs found
Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)
Background: Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results: Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion: Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics
Accounting for the growth of observation stays in the assessment of Medicare\u27s Hospital Readmissions Reduction Program
IMPORTANCE: Decreases in 30-day readmissions following the implementation of the Medicare Hospital Readmissions Reduction Program (HRRP) have occurred against the backdrop of increasing hospital observation stay use, yet observation stays are not captured in readmission measures.
OBJECTIVE: To examine whether the HRRP was associated with decreases in 30-day readmissions after accounting for observation stays.
DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study included a 20% sample of inpatient admissions and observation stays among Medicare fee-for-service beneficiaries from January 1, 2009, to December 31, 2015. Data analysis was performed from November 2021 to June 2022. A differences-in-differences analysis assessed changes in 30-day readmissions after the announcement of the HRRP and implementation of penalties for target conditions (heart failure, acute myocardial infarction, and pneumonia) vs nontarget conditions under scenarios that excluded and included observation stays.
MAIN OUTCOMES AND MEASURES: Thirty-day inpatient admissions and observation stays.
RESULTS: The study included 8 944 295 hospitalizations (mean [SD] age, 78.7 [8.2] years; 58.6% were female; 1.3% Asian; 10.0% Black; 2.0% Hispanic; 0.5% North American Native; 85.0% White; and 1.2% other or unknown). Observation stays increased from 2.3% to 4.4% (91.3% relative increase) of index hospitalizations among target conditions and 14.1% to 21.3% (51.1% relative increase) of index hospitalizations for nontarget conditions. Readmission rates decreased significantly after the announcement of the HRRP and returned to baseline by the time penalties were implemented for both target and nontarget conditions regardless of whether observation stays were included. When only inpatient hospitalizations were counted, decreasing readmissions accrued into a -1.48 percentage point (95% CI, -1.65 to -1.31 percentage points) absolute reduction in readmission rates by the postpenalty period for target conditions and -1.13 percentage point (95% CI, -1.30 to -0.96 percentage points) absolute reduction in readmission rates by the postpenalty period for nontarget conditions. This reduction corresponded to a statistically significant differential change of -0.35 percentage points (95% CI, -0.59 to -0.11 percentage points). Accounting for observation stays more than halved the absolute decrease in readmission rates for target conditions (-0.66 percentage points; 95% CI, -0.83 to -0.49 percentage points). Nontarget conditions showed an overall greater decrease during the same period (-0.76 percentage points; 95% CI, -0.92 to -0.59 percentage points), corresponding to a differential change in readmission rates of 0.10 percentage points (95% CI, -0.14 to 0.33 percentage points) that was not statistically significant.
CONCLUSIONS AND RELEVANCE: The findings of this study suggest that the reduction of readmissions associated with the implementation of the HRRP was smaller than originally reported. More than half of the decrease in readmissions for target conditions appears to be attributable to the reclassification of inpatient admission to observation stays
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Physical activity and risk of inflammatory bowel disease: prospective study from the Nurses’ Health Study cohorts
Objective: To examine the association between physical activity and risk of ulcerative colitis and Crohn’s disease. Design: Prospective cohort study. Setting: Nurses’ Health Study and Nurses’ Health Study II. Participants: 194 711 women enrolled in the Nurses’ Health Study and Nurses’ Health Study II who provided data on physical activity and other risk factors every two to four years since 1984 in the Nurses’ Health Study and 1989 in the Nurses’ Health Study II and followed up through 2010. Main outcome measure Incident ulcerative colitis and Crohn’s disease. Results: During 3 421 972 person years of follow-up, we documented 284 cases of Crohn’s disease and 363 cases of ulcerative colitis. The risk of Crohn’s disease was inversely associated with physical activity (P for trend 0.02). Compared with women in the lowest fifth of physical activity, the multivariate adjusted hazard ratio of Crohn’s disease among women in the highest fifth of physical activity was 0.64 (95% confidence interval 0.44 to 0.94). Active women with at least 27 metabolic equivalent task (MET) hours per week of physical activity had a 44% reduction (hazard ratio 0.56, 95% confidence interval 0.37 to 0.84) in risk of developing Crohn’s disease compared with sedentary women with 0.35). Conclusion: In two large prospective cohorts of US women, physical activity was inversely associated with risk of Crohn’s disease but not of ulcerative colitis
The parasitic lifestyle of an archaeal symbiont
DPANN archaea are a diverse group of microorganisms characterised by small cells and reduced genomes. To date, all cultivated DPANN archaea are ectosymbionts that require direct cell contact with an archaeal host species for growth and survival. However, these interactions and their impact on the host species are poorly understood. Here, we show that a DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. During these interactions, the nanohaloarchaeon appears to enter, or be engulfed by, the host cell. Our results provide experimental evidence for a predatory-like lifestyle of an archaeon, suggesting that at least some DPANN archaea may have roles in controlling host populations and their ecology
Control of magnetic anisotropy by orbital hybridization in (La0.67Sr0.33MnO3)n/(SrTiO3)n superlattice
The asymmetry of chemical nature at the hetero-structural interface offers an
unique opportunity to design desirable electronic structure by controlling
charge transfer and orbital hybridization across the interface. However, the
control of hetero-interface remains a daunting task. Here, we report the
modulation of interfacial coupling of (La0.67Sr0.33MnO3)n/(SrTiO3)n
superlattices by manipulating the periodic thickness with n unit cells of
SrTiO3 and n unit cells La0.67Sr0.33MnO3. The easy axis of magnetic anisotropy
rotates from in-plane (n = 10) to out-of-plane (n = 2) orientation at 150 K.
Transmission electron microscopy reveals enlarged tetragonal ratio > 1 with
breaking of volume conservation around the (La0.67Sr0.33MnO3)n/(SrTiO3)n
interface, and electronic charge transfer from Mn to Ti 3d orbitals across the
interface. Orbital hybridization accompanying the charge transfer results in
preferred occupancy of 3d3z2-r2 orbital at the interface, which induces a
stronger electronic hopping integral along the out-of-plane direction and
corresponding out-of-plane magnetic easy axis for n = 2. We demonstrate that
interfacial orbital hybridization in superlattices of strongly correlated
oxides may be a promising approach to tailor electronic and magnetic properties
in device applications
A Bayesian Nonparametric Approach to Modeling Motion Patterns
The most difficult—and often most essential—
aspect of many interception and tracking tasks is constructing
motion models of the targets to be found. Experts can
often provide only partial information, and fitting parameters
for complex motion patterns can require large amounts
of training data. Specifying how to parameterize complex
motion patterns is in itself a difficult task.
In contrast, nonparametric models are very flexible and
generalize well with relatively little training data. We propose
modeling target motion patterns as a mixture of Gaussian
processes (GP) with a Dirichlet process (DP) prior over
mixture weights. The GP provides a flexible representation
for each individual motion pattern, while the DP assigns observed
trajectories to particular motion patterns. Both automatically
adjust the complexity of the motion model based
on the available data. Our approach outperforms several parametric
models on a helicopter-based car-tracking task on
data collected from the greater Boston area
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