Training Big Random Forests with Little Resources

Without access to large compute clusters, building random forests on large datasets is still a challenging problem. This is, in particular, the case if fully-grown trees are desired. We propose a simple yet effective framework that allows to efficiently construct ensembles of huge trees for hundreds of millions or even billions of training instances using a cheap desktop computer with commodity hardware. The basic idea is to consider a multi-level construction scheme, which builds top trees for small random subsets of the available data and which subsequently distributes all training instances to the top trees' leaves for further processing. While being conceptually simple, the overall efficiency crucially depends on the particular implementation of the different phases. The practical merits of our approach are demonstrated using dense datasets with hundreds of millions of training instances.Comment: 9 pages, 9 Figure

Scott Polar Research Institute Arctic Airborne Radio-Echo Sounding Datasets: Canadian Arctic 2000

This data set contains radar sounder profiles from the SPRI 100 MHz ice-penetrating radar instrument over Devon and Ellesmere islands in the Canadian Arctic (CA). Along with the radar profile data, the archive includes derived and ancillary data, plus software code produced for acquisition and working up of data. The data were collected under funding from a UK Natural Environment Research Council (NERC) grant (GR3/12469) to Prof. J. A. Dowdeswell. Please consult the 'MetadataCA2000.pdf' file for a detailed description of the dataset and its contents.Funding: The collection of these data was funded by NERC grant GR3/12469 to J.A. Dowdeswell, as well as by grants from the Meteorological Service of Canada (CRYSYS program) to M.J. Sharp. Further funding (to J.A. Dowdeswell) for development of the dataset was provided by the NERC Centre for Polar Observation and Modelling, UK, and the EU SPICE Project

Glacier velocities and dynamic ice discharge from the Queen Elizabeth Islands, Nunavut, Canada

Recent studies indicate an increase in glacier mass loss from the Canadian Arctic Archipelago as a result of warmer summer air temperatures. However, no complete assessment of dynamic ice discharge from this region exists. We present the first complete surface velocity mapping of all ice masses in the Queen Elizabeth Islands and show that these ice masses discharged ~2.6 ± 0.8 Gt a−1 of ice to the oceans in winter 2012. Approximately 50% of the dynamic discharge was channeled through non surge-type Trinity and Wykeham Glaciers alone. Dynamic discharge of the surge-type Mittie Glacier varied from 0.90 ± 0.09 Gt a−1 during its 2003 surge to 0.02 ± 0.02 Gt a−1 during quiescence in 2012, highlighting the importance of surge-type glaciers for interannual variability in regional mass loss. Queen Elizabeth Islands glaciers currently account for ~7.5% of reported dynamic discharge from Arctic ice masses outside Greenland.We thank NSERC, Canada Foundation for Innovation, Ontario Research Fund, ArcticNet, Ontario Graduate Scholarship, University of Ottawa and the NSERC Canada Graduate Scholarship for funding. RADARSAT-2 data were provided by MacDonald, Dettwiler and Associates under the RADARSAT-2 Government Data Allocation administrated by the Canadian Space Agency. Support to DB is provided through the Climate Change Geosciences Program, Earth Sciences Sector, Natural Resources Canada (ESS Contribution #20130293). We also acknowledge support from U.K NERC for grants R3/12469 and NE/K004999 to JAD.This is the accepted version of an article published in Geophysical Research Letters. An edited version of this paper was published by AGU. Copyright (2014) American Geophysical Union. The final version is available at http://onlinelibrary.wiley.com/doi/10.1002/2013GL058558/abstract;jsessionid=6A3AD907C4383DA5D4E20C4924D6EC18.f02t02

Long-term nitrofurantoin:an analysis of complication awareness, monitoring, and pulmonary injury cases

BACKGROUND: Long-term nitrofurantoin (NF) treatment can result in pulmonary and hepatic injury. Current guidelines do not outline the type or frequency of monitoring required for detection of these injuries. AIM: To assess 1) awareness of NF complications among prescribers; 2) monitoring practice; and 3) to describe the pulmonary sequelae of NF-related complications. DESIGN & SETTING: Evaluation of prescribing habits by questionnaires and review of GP databases, and case-note review in secondary care. METHOD: The following study procedures were undertaken: 1) an electronic questionnaire was distributed to prescribers, interrogating prescribing and monitoring practices, and awareness of complications; 2) an analysis was undertaken (June–July 2020) of NF monitoring among GPs in the local clinical commissioning group (CCG); and 3) a case review was carried out of patients diagnosed with NF-induced interstitial lung disease (NFILD) at the interstitial lung disease (ILD) centre (2014–2020). RESULTS: A total of 125 prescribers of long-term NF responded to the questionnaire (82.4% GPs; 12.0% urologists). Many were unaware of the potential for liver (42.4%) and lung (28.0%) complications; 40.8% and 52.8% never monitored for these, respectively. Only 53.3% of urologists believed themselves responsible for arranging monitoring, while nearly all GPs believed this to be the prescriber’s responsibility (94.2%). One-third of all responders considered current British National Formulary (BNF) guidelines 'not at all sufficient/clear', with mean clarity scoring of 2.2/5. Among patients with NFILD (n = 46), NF had been prescribed most often (69.6%) for treatment of recurrent UTI and 58.6% (n = 27) were prescribed for >6 months. On withdrawal of the medication 61.4% displayed resolution (completely or minimal fibrosis), while 15.9% of patients had progressive lung fibrosis. CONCLUSION: NF can cause marked or irreversible lung complications and there is currently a shortfall in awareness and monitoring. Existing monitoring guidelines should be augmented

Screening for type 2 diabetes and population mortality over 10 years (ADDITION-Cambridge): a cluster-randomised controlled trial.

BACKGROUND: The increasing prevalence of type 2 diabetes poses a major public health challenge. Population-based screening and early treatment for type 2 diabetes could reduce this growing burden. However, uncertainty persists around the benefits of screening for type 2 diabetes. We assessed the effect of a population-based stepwise screening programme on mortality. METHODS: In a pragmatic parallel group, cluster-randomised trial, 33 general practices in eastern England were randomly assigned by the method of minimisation in an unbalanced design to: screening followed by intensive multifactorial treatment for people diagnosed with diabetes (n=15); screening plus routine care of diabetes according to national guidelines (n=13); and a no-screening control group (n=5). The study population consisted of 20,184 individuals aged 40-69 years (mean 58 years), at high risk of prevalent undiagnosed diabetes, on the basis of a previously validated risk score. In screening practices, individuals were invited to a stepwise programme including random capillary blood glucose and glycated haemoglobin (HbA(1c)) tests, a fasting capillary blood glucose test, and a confirmatory oral glucose tolerance test. The primary outcome was all-cause mortality. All participants were flagged for mortality surveillance by the England and Wales Office of National Statistics. Analysis was by intention-to-screen and compared all-cause mortality rates between screening and control groups. This study is registered, number ISRCTN86769081. FINDINGS: Of 16,047 high-risk individuals in screening practices, 15,089 (94%) were invited for screening during 2001-06, 11,737 (73%) attended, and 466 (3%) were diagnosed with diabetes. 4137 control individuals were followed up. During 184,057 person-years of follow up (median duration 9·6 years [IQR 8·9-9·9]), there were 1532 deaths in the screening practices and 377 in control practices (mortality hazard ratio [HR] 1·06, 95% CI 0·90-1·25). We noted no significant reduction in cardiovascular (HR 1·02, 95% CI 0·75-1·38), cancer (1·08, 0·90-1·30), or diabetes-related mortality (1·26, 0·75-2·10) associated with invitation to screening. INTERPRETATION: In this large UK sample, screening for type 2 diabetes in patients at increased risk was not associated with a reduction in all-cause, cardiovascular, or diabetes-related mortality within 10 years. The benefits of screening might be smaller than expected and restricted to individuals with detectable disease. FUNDING: Wellcome Trust; UK Medical Research Council; National Health Service research and development support; UK National Institute for Health Research; University of Aarhus, Denmark; Bio-Rad

An electrochemical sensor concept for the detection of virulence factors from <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>

This work presents an electrochemical sensor concept for bacterial toxin detection using biomimetic lipid vesicles containing potassium ferricyanide. The toxin mediated release of redox couples from the vesicles was quantified by measuring the redox current on screen printed electrodes, and the detection limits to rhamnolipid, delta toxin and bacterial supernatants from clinical wound pathogens were examined. Overall detection limits of both redox and carboxyfluorescein containing vesicles were one order of magnitude lower than the cytotoxic dose of studied toxins to T lymphocytes. Keywords: Staphylococcus aureus, Pseudomonas aeruginosa, Lipid vesicles, Potassium ferricyanide, Rhamnolipid, Delta toxi

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Field trial of three different Plasmodium vivax-detecting rapid diagnostic tests with and without evaporative cool box storage in Afghanistan

<p>Abstract</p> <p>Background</p> <p>Accurate parasitological diagnosis of malaria is essential for targeting treatment where more than one species coexist. In this study, three rapid diagnostic tests (RDTs) (AccessBio CareStart (CSPfPan), CareStart PfPv (CSPfPv) and Standard Diagnostics Bioline (SDBPfPv)) were evaluated for their ability to detect natural <it>Plasmodium vivax </it>infections in a basic clinic setting. The potential for locally made evaporative cooling boxes (ECB) to protect the tests from heat damage in high summer temperatures was also investigated.</p> <p>Methods</p> <p>Venous blood was drawn from <it>P. vivax </it>positive patients in Jalalabad, Afghanistan and tested against a panel of six RDTs. The panel comprised two of each test type; one group was stored at room temperature and the other in an ECB. RDT results were evaluated against a consensus gold standard based on two double-read reference slides and PCR. The sensitivity, specificity and a measure of global performance for each test were determined and stratified by parasitaemia level and storage condition.</p> <p>Results</p> <p>In total, 306 patients were recruited, of which 284 were positive for <it>P. vivax</it>, one for <it>Plasmodium malariae </it>and none for <it>Plasmodium falciparum</it>; 21 were negative. All three RDTs were specific for malaria. The sensitivity and global performance index for each test were as follows: CSPfPan [98.6%, 95.1%], CSPfPv [91.9%, 90.5%] and SDBPfPv [96.5%, 82.9%], respectively. CSPfPv was 16% less sensitive to a parasitaemia below 5,000/μL. Room temperature storage of SDBPfPv led to a high proportion of invalid results (17%), which reduced to 10% in the ECB. Throughout the testing period, the ECB maintained ~8°C reduction over ambient temperatures and never exceeded 30°C.</p> <p>Conclusions</p> <p>Of the three RDTs, the CSPfPan test was the most consistent and reliable, rendering it appropriate for this <it>P. vivax </it>predominant region. The CSPfPv test proved unsuitable owing to its reduced sensitivity at a parasitaemia below 5,000/μL (affecting 43% of study samples). Although the SDBPfPv device was more sensitive than the CSPfPv test, its invalid rate was unacceptably high. ECB storage reduced the proportion of invalid results for the SDBPfPv test, but surprisingly had no impact on RDT sensitivity at low parasitaemia.</p

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies