32 research outputs found
Validation of the DECAF score to predict hospital mortality in acute exacerbations of COPD
Background
Hospitalisation due to acute
exacerbations of COPD (AECOPD) is common, and
subsequent mortality high. The DECAF score was derived
for accurate prediction of mortality and risk strati
fi
cation
to inform patient care. We aimed to validate the DECAF
score, internally and externally, and to compare its
performance to other predictive tools.
Methods
The study took place in the two hospitals
within the derivation study (internal validation) and in
four additional hospitals (external validation) between
January 2012 and May 2014. Consecutive admissions
were identi
fi
ed by screening admissions and searching
coding records. Admission clinical data, including DECAF
indices, and mortality were recorded. The prognostic
value of DECAF and other scores were assessed by the
area under the receiver operator characteristic (AUROC)
curve.
Results
In the internal and external validation cohorts,
880 and 845 patients were recruited. Mean age was
73.1 (SD 10.3) years, 54.3% were female, and mean
(SD) FEV
1
45.5 (18.3) per cent predicted. Overall
mortality was 7.7%. The DECAF AUROC curve for
inhospital mortality was 0.83 (95% CI 0.78 to 0.87) in
the internal cohort and 0.82 (95% CI 0.77 to 0.87) in
the external cohort, and was superior to other
prognostic scores for inhospital or 30-day mortality.
Conclusions
DECAF is a robust predictor of mortality,
using indices routinely available on admission. Its
generalisability is supported by consistent strong
performance; it can identify low-risk patients (DECAF
0
–
1) potentially suitable for Hospital at Home or early
supported discharge services, and high-risk patients
(DECAF 3
–
6) for escalation planning or appropriate early
palliation.
Trial registration number
UKCRN ID 14214
Linear stability analysis of transverse dunes
Sand-moving winds blowing from a constant direction in an area of high sand
availability form transverse dunes, which have a fixed profile in the direction
orthogonal to the wind. Here we show, by means of a linear stability analysis,
that transverse dunes are intrinsically unstable. Any along-axis perturbation
on a transverse dune amplify in the course of dune migration due to the
combined effect of two main factors, namely: the lateral transport through
avalanches along the dune's slip-face, and the scaling of dune migration
velocity with the inverse of the dune height. Our calculations provide a
quantitative explanation for recent observations from experiments and numerical
simulations, which showed that transverse dunes moving on the bedrock cannot
exist in a stable form and decay into a chain of crescent-shaped barchans.Comment: 8 pages, 4 figure
In the name of the rose: a roadmap for rose research in the genome era
The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions
A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits
Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe
Multi-allelic QTL analysis of protein content in a biparental population of cultivated tetraploid potato
Protein content is a key quality trait for thepotato starch industry. The objective of this study wasto identify allele-specific quantitative trait loci (QTLs)for tuber protein content in cultivated potato (Solanumtuberosum L.) at the tetraploid level
Tools for Genetic Studies in Experimental Populations of Polyploids
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticatedplant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can alsohelp elucidate the mode of inheritance (disomic, polysomic or a mixture of bothas in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive
Cytogenetics of structural rearrangements in Musa hybrids and cultivars
Edible bananas are diploid or triploid Musa acuminata, or hybrids of M. acuminata x M. balbisi-ana, producing nutritious seedless fruit of different taste and structure. Breeding for high yield and host plant resistance to pathogens and pests as well as adaptation to abiotic stress of im-portant cultivars is challenging because of seedless and parthenocarpic fruit. In addition, cross-ings and selections of diploid cultivars and wild relatives are severely hampered by transloca-tions and inversions that are widespread in the M. acuminata populations. In this study we pre-sent an overview of cytogenetics, genetics and genomics research carried out to elucidate the meiotic chromosome behaviour in the hybrids and the mapping of genes, and to analyse the dif-ferent classes of DNA sequences in the banana genomes. Finally, we illustrate cytogenetic and linkage mapping of a diploid M. acuminata ssp. malaccensis using the diploid M. acuminata ‘Pa-hang’ as a genome reference and focus on the occurrence of structural rearrangements
Using molecular markers in breeding: ornamentals catch up
Thanks to advances in next generation sequencing it is now straightforward to develop tens or even hundreds of thousands of SNP markers. Advances in genotyping technology have made it feasible to genotype progenies of crosses, panels of genotypes, or even a complete breeding program, by using arrays with tens of thousands of SNPs, or by random or targeted sequencing technologies. Recently software has been developed for dosage scoring and linkage mapping in polyploid crops. This means that advanced genetic analyses can now also be performed in many polyploid ornamentals. A DNA marker, such as a single nucleotide polymorphism (SNP), linked to a trait enables following a gene or allele during crosses and in a breeding program. Association of a SNP marker to a trait or a component of a trait may be done through QTL analysis in segregating populations, by genome-wide association analysis (GWAS) in a set of accessions, or through an analysis across a pedigree. In these analyses, a dense linkage map is a very important tool, to delineate and possibly narrow down the QTL interval and to filter away false positive SNPs. New developments in linkage mapping include paying attention to even marker coverage, and new ways to use markers to infer haplotypes. The latter is especially important in polyploids, in populations with multiple parents, or in wide panels used for association studies. In such cases multiple functional alleles may segregate simultaneously, that cannot all be tagged uniquely by single biallelic SNP markers.</p