1,800 research outputs found
Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm
We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/
Characterization of extrasolar terrestrial planets from diurnal photometric variability
The detection of massive planets orbiting nearby stars has become almost
routine, but current techniques are as yet unable to detect terrestrial planets
with masses comparable to the Earth's. Future space-based observatories to
detect Earth-like planets are being planned. Terrestrial planets orbiting in
the habitable zones of stars-where planetary surface conditions are compatible
with the presence of liquid water-are of enormous interest because they might
have global environments similar to Earth's and even harbor life. The light
scattered by such a planet will vary in intensity and colour as the planet
rotates; the resulting light curve will contain information about the planet's
properties. Here we report a model that predicts features that should be
discernible in light curves obtained by low-precision photometry. For
extrasolar planets similar to Earth we expect daily flux variations up to
hundreds of percent, depending sensitively on ice and cloud cover. Qualitative
changes in surface or climate generate significant changes in the predicted
light curves. This work suggests that the meteorological variability and the
rotation period of an Earth-like planet could be derived from photometric
observations. Other properties such as the composition of the surface (e.g.,
ocean versus land fraction), climate indicators (for example ice and cloud
cover), and perhaps even signatures of Earth-like plant life could be
constrained or possibly, with further study, even uniquely determined.Comment: Published in Nature. 9 pages including 3 figure
Species by Environment Interactions Affect Pyrrolizidine Alkaloid Expression in Senecio jacobaea, Senecio aquaticus, and Their Hybrids
We examined the effects of water and nutrient availability on the expression of the defense pyrrolizidine alkaloids (PAs) in Senecio jacobaea and S. aquaticus. Senecio jacobaea, and S. aquaticus are adapted to different natural habitats, characterized by differing abiotic conditions and different selection pressures from natural enemies. We tested if PA concentration and diversity are plastic over a range of water and nutrient treatments, and also whether such plasticity is dependent on plant species. We also tested the hypothesis that hybridization may contribute to PA diversity within plants, by comparing PA expression in parental species to that in artificially generated F1 hybrids, and also in later generation natural hybrids between S. jacobaea and S. aquaticus. We showed that total PA concentration in roots and shoots is not dependent on species, but that species determines the pattern of PA diversification. Pyrrolizidine alkaloid diversity and concentration are both dependent on environmental factors. Hybrids produce a putatively novel PA, and this PA is conserved in natural hybrids, that are backcrossed to S. jacobaea. Natural hybrids that are backcrossed several times to S. jacobaea are with regard to PA diversity significantly different from S. jacobaea but not from S. aquaticus, while F1 hybrids are in all cases more similar to S. jacobaea. These results collectively suggest that PA diversity is under the influence of natural selection
The need for biochemical testing in beta‐enolase deficiency in the genomic era
Glycogen storage disease type XIII (GSDXIII) is a very rare inherited metabolic myopathy characterized by autosomal‐recessive mutations in the ENO3 gene resulting in muscle β‐enolase deficiency, an enzymatic defect of the distal part of glycolysis. Enzyme kinetic studies of two patients presenting with exertion intolerance and recurrent rhabdomyolysis are reported. Next generation sequencing confirmed patient 1 was homozygous for p.E187K in ENO3, while patient 2 was homozygous for p.C357Y. ENO3 variants pathogenicity was confirmed by functional studies in skeletal muscle. p.E187K caused extremely low total enolase activity. p.C357Y was associated with a higher level of residual activity but kinetic studies showed a lower maximum work rate (Vmax). This study illustrates that GSDXIII may be caused by either null mutations leading to β‐enolase deficiency or by mutations that alter the enzyme's kinetic profile. This study highlights the importance of carrying out functional studies as part of the diagnostic process following the identification of variants with next generation sequencing
CMT subtypes and disease burden in patients enrolled in the Inherited Neuropathies Consortium natural history study: a cross-sectional analysis
BACKGROUND: The international Inherited Neuropathy
Consortium (INC) was created with the goal of obtaining
much needed natural history data for patients with
Charcot-Marie-Tooth (CMT) disease. We analysed clinical
and genetic data from patients in the INC to determine
the distribution of CMT subtypes and the clinical
impairment associated with them.
METHODS: We analysed data from 1652 patients
evaluated at 13 INC centres. The distribution of CMT
subtypes and pathogenic genetic mutations were
determined. The disease burden of all the mutations was
assessed by the CMT Neuropathy Score (CMTNS) and
CMT Examination Score (CMTES).
RESULTS: 997 of the 1652 patients (60.4%) received
a genetic diagnosis. The most common CMT subtypes
were CMT1A/PMP22 duplication, CMT1X/GJB1
mutation, CMT2A/MFN2 mutation, CMT1B/MPZ
mutation, and hereditary neuropathy with liability to
pressure palsy/PMP22 deletion. These five subtypes of
CMT accounted for 89.2% of all genetically confirmed
mutations. Mean CMTNS for some but not all subtypes
were similar to those previously reported.
CONCLUSIONS: Our findings confirm that large numbers
of patients with a representative variety of CMT subtypes
have been enrolled and that the frequency of achieving
a molecular diagnosis and distribution of the CMT
subtypes reflects those previously reported. Measures of
severity are similar, though not identical, to results from
smaller series. This study confirms that it is possible to
assess patients in a uniform way between international
centres, which is critical for the planned natural history
study and future clinical trials. These data will provide a
representative baseline for longitudinal studies of CMT.
CLINICAL TRIAL REGISTRATION ID NUMBER: NCT0119307
Treatment adherence with the easypod™ growth hormone electronic auto-injector and patient acceptance: survey results from 824 children and their parents
<p>Abstract</p> <p>Background</p> <p>Accurately monitoring adherence to treatment with recombinant human growth hormone (r-hGH) enables appropriate intervention in cases of poor adherence. The electronic r-hGH auto-injector, easypod™, automatically records the patient's adherence to treatment. This study evaluated adherence to treatment of children who started using the auto-injector and assessed opinions about the device.</p> <p>Methods</p> <p>A multicentre, multinational, observational 3-month survey in which children received r-hGH as part of their normal care. Physicians reviewed the recorded dose history and children (with or without parental assistance) completed a questionnaire-based survey. Children missing ≤2 injections per month (92% of injections given) were considered adherent to treatment. Adherence was compared between GH treatment-naïve and treatment-experienced children.</p> <p>Results</p> <p>Of 834 recruited participants, 824 were evaluated. The median (range) age was 11 (1-18) years. From the recorded dose history, 87.5% of children were adherent to treatment over the 3-month period. Recorded adherence was higher in treatment-naïve (89.7%, n = 445/496) than in treatment-experienced children (81.7%, n = 152/186) [Fisher's exact test FI(X) = 7.577; <it>p </it>= 0.0062]. According to self-reported data, 90.2% (607/673) of children were adherent over 3 months; 51.5% (421/817) missed ≥1 injection over this period (mainly due to forgetfulness). Concordance between reported and recorded adherence was 84.3%, with a trend towards self-reported adherence being higher than recorded adherence. Most children liked the auto-injector: over 80% gave the top two responses from five options for ease of use (720/779), speed (684/805) and comfort (716/804). Although 38.5% (300/780) of children reported pain on injection, over half of children (210/363) considered the pain to be less or much less than expected. Given the choice, 91.8% (732/797) of children/parents would continue using the device.</p> <p>Conclusions</p> <p>easypod™ provides an accurate method of monitoring adherence to treatment with r-hGH. In children who received treatment with r-hGH using easypod™, short-term adherence is good, and significantly higher in treatment-naïve children compared with experienced children. Children/parents rate the device highly. The high level of acceptability of the device is reflected by a desire to continue using it by over 90% of the children in the survey.</p
The stellar and sub-stellar IMF of simple and composite populations
The current knowledge on the stellar IMF is documented. It appears to become
top-heavy when the star-formation rate density surpasses about 0.1Msun/(yr
pc^3) on a pc scale and it may become increasingly bottom-heavy with increasing
metallicity and in increasingly massive early-type galaxies. It declines quite
steeply below about 0.07Msun with brown dwarfs (BDs) and very low mass stars
having their own IMF. The most massive star of mass mmax formed in an embedded
cluster with stellar mass Mecl correlates strongly with Mecl being a result of
gravitation-driven but resource-limited growth and fragmentation induced
starvation. There is no convincing evidence whatsoever that massive stars do
form in isolation. Various methods of discretising a stellar population are
introduced: optimal sampling leads to a mass distribution that perfectly
represents the exact form of the desired IMF and the mmax-to-Mecl relation,
while random sampling results in statistical variations of the shape of the
IMF. The observed mmax-to-Mecl correlation and the small spread of IMF
power-law indices together suggest that optimally sampling the IMF may be the
more realistic description of star formation than random sampling from a
universal IMF with a constant upper mass limit. Composite populations on galaxy
scales, which are formed from many pc scale star formation events, need to be
described by the integrated galactic IMF. This IGIMF varies systematically from
top-light to top-heavy in dependence of galaxy type and star formation rate,
with dramatic implications for theories of galaxy formation and evolution.Comment: 167 pages, 37 figures, 3 tables, published in Stellar Systems and
Galactic Structure, Vol.5, Springer. This revised version is consistent with
the published version and includes additional references and minor additions
to the text as well as a recomputed Table 1. ISBN 978-90-481-8817-
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Combined use of the Consolidated Framework for Implementation Research (CFIR) and the Theoretical Domains Framework (TDF): A systematic review
Background: Over 60 implementation frameworks exist. Using multiple frameworks may help researchers to address multiple study purposes, levels, and degrees of theoretical heritage and operationalizability; however, using multiple frameworks may result in unnecessary complexity and redundancy if doing so does not address study needs. The Consolidated Framework for Implementation Research (CFIR) and the Theoretical Domains Framework (TDF) are both well-operationalized, multi-level implementation determinant frameworks derived from theory. As such, the rationale for using the frameworks in combination (i.e., CFIR + TDF) is unclear. The objective of this systematic review was to elucidate the rationale for using CFIR + TDF by (1) describing studies that have used CFIR + TDF, (2) how they used CFIR + TDF, and (2) their stated rationale for using CFIR + TDF.
Methods: We undertook a systematic review to identify studies that mentioned both the CFIR and the TDF, were written in English, were peer-reviewed, and reported either a protocol or results of an empirical study in MEDLINE/PubMed, PsycInfo, Web of Science, or Google Scholar. We then abstracted data into a matrix and analyzed it qualitatively, identifying salient themes.
Findings: We identified five protocols and seven completed studies that used CFIR + TDF. CFIR + TDF was applied to studies in several countries, to a range of healthcare interventions, and at multiple intervention phases; used many designs, methods, and units of analysis; and assessed a variety of outcomes. Three studies indicated that using CFIR + TDF addressed multiple study purposes. Six studies indicated that using CFIR + TDF addressed multiple conceptual levels. Four studies did not explicitly state their rationale for using CFIR + TDF.
Conclusions: Differences in the purposes that authors of the CFIR (e.g., comprehensive set of implementation determinants) and the TDF (e.g., intervention development) propose help to justify the use of CFIR + TDF. Given that the CFIR and the TDF are both multi-level frameworks, the rationale that using CFIR + TDF is needed to address multiple conceptual levels may reflect potentially misleading conventional wisdom. On the other hand, using CFIR + TDF may more fully define the multi-level nature of implementation. To avoid concerns about unnecessary complexity and redundancy, scholars who use CFIR + TDF and combinations of other frameworks should specify how the frameworks contribute to their study.
Trial registration: PROSPERO CRD4201502761
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