Report on the 2018 trials of the multistatic NeXtRAD dual band polarimetric radar

NeXtRAD is a polarimetric, L and X Band, multistatic (three nodes), pulse Doppler radar, developed by UCT and UCL, as a follow on to the NetRAD sensor. This paper reports on the trials carried out in 2018, mostly in Simon's Bay, South Africa. The sensors (one active, two passive) are connected by WiFi communications link, with a maximum separation of 40 km. Practically, results are reported with 8 km maximum baselines. The focus is on targets in sea clutter and micro-Doppler. We report on the final integration and test of the system command and control system that allows for scheduling of measurement and recording of bursts of pulses, as well as video of the radar field of view. Some innovations have been made in terms of digital hardware, firmware, and high performance computing technology. The system is synchronised with the UCT GPS Disciplined Oscillators (one per node), but we also report on bistatic measurements with White Rabbit, fibre timing system, as well as the consequences of GPS failure (GPS Denied Environment)

Predictors of mortality for delirium in palliative care

© Mary Ann Liebert, Inc. 2016. Introduction: Delirium has a high mortality rate. Understanding predictors of prognosis in patients with delirium will aid treatment decisions and communication. This study aimed to explore variables associated with death during an established episode of delirium in palliative care when haloperidol treatment had been commenced. Methods: A consecutive cohort of palliative care patients, from 14 centers across four countries, is reported. The outcome of interest was death within 14 days from commencement of haloperidol treatment for delirium. Clinicodemographic variables explored were delirium severity, age, gender, primary life limiting illness, body mass index (BMI), total daily haloperidol dose at baseline (mg), functional status, and comorbidities. Results: One hundred and sixteen palliative care patients where vital status was known were included in the analysis; 45% (n = 52) died within 10 days, and 56% (n = 65) died within 14 days. In multivariate analyses no clinical or demographic variables predicted death, apart from lower BMI in noncancer patients. Conclusion: This study has shown a very high mortality rate within two weeks of commencing haloperidol for delirium in palliative care, with no clear clinical predictors for those with a higher chance of dying. Having a higher BMI offered some benefit in survival, but only in noncancer patients. When delirium occurs in advanced illness, discussion should be initiated about the gravity of the clinical situation

Energy-dependent tunneling from few-electron dynamic quantum dots

We measure the electron escape rate from surface-acoustic-wave dynamic quantum dots (QDs) through a tunnel barrier. Rate equations are used to extract the tunneling rates, which change by an order of magnitude with tunnel-barrier-gate voltage. We find that the tunneling rates depend on the number of electrons in each dynamic QD because of Coulomb energy. By comparing this dependence to a saddle-point-potential model, the addition energies of the second and third electron in each dynamic QD are estimated. The scale (similar to a few meV) is comparable to those in static QDs as expected

Response to ‘High Risk of Neutropenia for Hormone-naive Prostate Cancer Patients Receiving STAMPEDE-style Upfront Docetaxel Chemotherapy in Usual Clinical Practice’, by Tanguay et al

Madam — Tanguay and colleagues presented data on patients treated with docetaxel [1]. We agree that the reported rates of neutropenia-based toxicities vary across the trials, as do the categories against which toxicities are reported

Non-invasive charge detection in surface-acoustic-wave-defined dynamic quantum dots

Using a non-invasive charge detection method, we detect a flow of electrons trapped in dynamic quantum dots. The dynamic quantum dots are defined by surface acoustic waves (SAWs) and move through a long depleted one-dimensional channel. A one-dimensional constriction is placed next to the SAW channel but in a separate circuit; the current induced by the SAWs through this detector constriction is sensitive to the number of electrons trapped in the SAW minima. We observe steps in the detector acoustoelectric current as the number of electrons carried by SAWs are varied as 1, 2, 3....This work was funded by the UK EPSRC. M.R.A. and I.F. thank Toshiba for funding

On the Use of Variance per Genotype as a Tool to Identify Quantitative Trait Interaction Effects: A Report from the Women's Genome Health Study

Testing for genetic effects on mean values of a quantitative trait has been a very successful strategy. However, most studies to date have not explored genetic effects on the variance of quantitative traits as a relevant consequence of genetic variation. In this report, we demonstrate that, under plausible scenarios of genetic interaction, the variance of a quantitative trait is expected to differ among the three possible genotypes of a biallelic SNP. Leveraging this observation with Levene's test of equality of variance, we propose a novel method to prioritize SNPs for subsequent gene–gene and gene–environment testing. This method has the advantageous characteristic that the interacting covariate need not be known or measured for a SNP to be prioritized. Using simulations, we show that this method has increased power over exhaustive search under certain conditions. We further investigate the utility of variance per genotype by examining data from the Women's Genome Health Study. Using this dataset, we identify new interactions between the LEPR SNP rs12753193 and body mass index in the prediction of C-reactive protein levels, between the ICAM1 SNP rs1799969 and smoking in the prediction of soluble ICAM-1 levels, and between the PNPLA3 SNP rs738409 and body mass index in the prediction of soluble ICAM-1 levels. These results demonstrate the utility of our approach and provide novel genetic insight into the relationship among obesity, smoking, and inflammation

Tools for efficient epistasis detection in genome-wide association study

<p>Abstract</p> <p>Background</p> <p>Genome-wide association study (GWAS) aims to find genetic factors underlying complex phenotypic traits, for which epistasis or gene-gene interaction detection is often preferred over single-locus approach. However, the computational burden has been a major hurdle to apply epistasis test in the genome-wide scale due to a large number of single nucleotide polymorphism (SNP) pairs to be tested.</p> <p>Results</p> <p>We have developed a set of three efficient programs, FastANOVA, COE and TEAM, that support epistasis test in a variety of problem settings in GWAS. These programs utilize permutation test to properly control error rate such as family-wise error rate (FWER) and false discovery rate (FDR). They guarantee to find the optimal solutions, and significantly speed up the process of epistasis detection in GWAS.</p> <p>Conclusions</p> <p>A web server with user interface and source codes are available at the website <url>http://www.csbio.unc.edu/epistasis/</url>. The source codes are also available at SourceForge <url>http://sourceforge.net/projects/epistasis/</url>.</p

A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass- and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI-associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646-kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10-6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations

Stemming the tide: progress towards resolving the causes of decline and implementing management responses for the disappearing mammal fauna of northern Australia

Introduction: Recent studies at sites in northern Australia have reported severe and rapid decline of several native mammal species, notwithstanding an environmental context (small human population size, limited habitat loss, substantial reservation extent) that should provide relative conservation security. All of the more speciose taxonomic groups of mammals in northern Australia have some species for which their conservation status has been assessed as threatened, with 53 % of dasyurid, 47 % of macropod and potoroid, 33 % of bandicoot and bilby, 33 % of possum, 30 % of rodent, and 24 % of bat species being assessed as extinct, threatened or near threatened. However, the geographical extent and timing of declines, and their causes, remain poorly resolved, limiting the application of remedial management actions.\ud \ud Material and methods: Focusing on the tropical savannas of northern Australia, this paper reviews disparate recent and ongoing studies that provide information on population trends across a broader geographic scope than the previously reported sites, and examines the conservation status and trends for mammal groups (bats, macropods) not well sampled in previous monitoring studies. It describes some diverse approaches of studies seeking to document conservation status and trends, and of the factors that may be contributing to observed patterns of decline.\ud \ud Results and Discussion: Current trends and potential causal factors for declines. The studies reported demonstrate that the extent and timing of impacts and threats have been variable across the region, although there is a general gradational pattern of earlier and more severe decline from inland lower rainfall areas to higher rainfall coastal regions. Some small isolated areas appear to have retained their mammal species, as have many islands which remain critical refuges. There is now some compelling evidence that predation by feral cats is implicated in the observed decline, with those impacts likely to be exacerbated by prevailing fire regimes (frequent, extensive and intense fire), by reduction in ground vegetation cover due to livestock and, in some areas, by 'control' of dingoes. However the impacts of dingoes may be complex, and are not yet well resolved in this area. The relative impacts of these individual factors vary spatially (with most severe impacts in higher rainfall and more rugged areas) and between different mammal species, with some species responding idiosyncratically: the most notable example is the rapid decline of the northern quoll (Dasyurus hallucatus) due to poisoning by the introduced cane toad (Rhinella marina), which continues to spread extensively across northern Australia. The impact of disease, if any, remains unresolved.\ud \ud Conservation Management Responses. Recovery of the native mammal fauna may be impossible in some areas. However, there are now examples of rapid recovery following threat management. Priority conservation actions include: enhanced biosecurity for important islands, establishment of a network of feral predator exclosures, intensive fire management (aimed at increasing the extent of longer-unburnt habitat and in delivering fine scale patch burning), reduction in feral stock in conservation reserves, and acquisition for conservation purposes of some pastoral lands in areas that are significant for mammal conservation