Mixture models for distance sampling detection functions

Funding: EPSRC DTGWe present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.Publisher PDFPeer reviewe

DNA content analysis of colorectal cancer defines a distinct ‘microsatellite and chromosome stable’ group but does not predict response to radiotherapy

Colorectal cancers (CRC) are thought to have genetic instability in the form of either microsatellite instability (MSI) or chromosomal instability (CIN). Recently, tumours have been described without either MSI or CIN, that is, microsatellite and chromosome stable (MACS) CRCs. We investigated the (i) frequency of the MACS-CRCs and (ii) whether this genotype predicted responsiveness to neoadjuvant chemoradiotherapy. To examine the frequency of MACS-CRCs, DNA content (ploidy) was examined in 89 sporadic microsatellite-stable CRCs using flow cytometry. The tumours were also screened for mutations in KRAS/BRAF/TP53/PIK3CA by QMCPCR. To examine the value of tumour ploidy in predicting response to chemoradiotherapy, DNA content was tested in a separate group of 62 rectal cancers treated with neoadjuvant chemoradiotherapy. Fifty-one of 89 CRCs (57%) were aneuploid and 38 (43%) were diploid. There was no significant association between mutations in TP53/KRAS/BRAF/PIK3CA and ploidy. Testing of association between mutations revealed only mutual exclusivity of KRAS/BRAF mutation (P < 0.001). Of the 62 rectal cancers treated with neoadjuvant chemoradiotherapy, 22 had responded (Mandard tumour regression grade 1/2) and 40 failed to respond (Grade 3–5). Twenty-five of 62 (40%) tumours were diploid, but there was no association between ploidy and response to therapy. We conclude that MACS-CRCs form a significant proportion of microsatellite-stable CRCs with a mutation profile overlapping that of CRCs with CIN. A diploid genotype does not, however, predict the responsiveness to radiotherapy

Synthesis of polyanionic C5-modified 2'-deoxyuridine and 2'-deoxycytidine-5'-triphosphates and their properties as substrates for DNA polymerases

Modified 2'-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG6 to PEG24 could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor

Identifying Urine Patches on Intensively Managed Grassland Using Aerial Imagery Captured From Remotely Piloted Aircraft Systems

The deposition of livestock urine and feces in grazed fields results in a sizable input of available nitrogen (N) in these soils; therefore significantly increasing potential nitrogen pollution from agricultural areas in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3−). Livestock deposition events contributes to high spatial variability within the field and generate uncertainties when assessing the contribution that animal waste has on nitrogen pollution pathways. This study investigated an innovative technique for identifying the spatial coverage of urine deposition in grasslands without the need for manual soil measurements. A Remotely Piloted Aircraft System (RPAS) using a twin camera system was used to identify urine patches in a 5 ha field, which had been grazed by sheep 3 weeks previous to measurements. The imagery was processed using Agisoft Photoscan (Agisoft LLC) to produce true and false color orthomosaic imagery of the entire field. Imagery of five areas (225 m2) within the field were analyzed using a custom R script. For a total of 1,125 m2 of grassland, 12.2% of the area consisted of what was classified as urine patch. A simple up-scaling method was applied to these data to calculate N2O emissions for the entire field providing an estimate of 1.3–2.0 kg N2O-N ha−1 emissions from urine and fertilizer inputs

Distance software: design and analysis of distance sampling surveys for estimating population size

1.Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance

Robotic Pollination - Targeting kiwifruit flowers for commercial application

This paper contains the initial evaluation of a novel platform mounted robotic pollination system. Advancement in artificial pollination is an important step forward in agricultural sectors due to the global decline of natural pollinators. Robotic pollination allows for potentially autonomous, precision operation; however, background research suggested that prior development in the area has been sparse. The featured wet-application robotic pollination system was capable of detecting >70% of flowers whilst driving at a slow-pace through kiwifruit orchard rows. Over 80% of flowers were robotically pollinated

Probing short-term face memory in developmental prosopagnosia

It has recently been proposed that the face recognition deficits seen in neurodevelopmental disorders may reflect impaired short-term face memory. For example, introducing a brief delay between the presentation of target and test faces seems to disproportionately impair matching or recognition performance on individuals with Autism Spectrum Disorders. The present study sought to determine whether deficits of short-term face memory contribute to impaired face recognition seen in Developmental Prosopagnosia. To determine whether developmental prosopagnosics exhibit impaired short-term face memory, the present study used a six-alternative-forced-choice match-to-sample procedure. Memory demand was manipulated by employing a short or long delay between the presentation of the target face, and the six test faces. Crucially, the perceptual demands were identical in both conditions, thereby allowing the independent contribution of short-term face memory to be assessed. Prosopagnostics showed clear evidence of a category-specific impairment for face-matching in both conditions; they were both slower and less accurate than matched controls. Crucially however, the prosopagnosics showed no evidence of disproportionate face recognition impairment in the long-interval condition. While individuals with developmental prosopagnosia may have problems with the perceptual encoding of faces, it appears that their representations are stable over short durations. These results suggest that the face recognition difficulties seen in developmental prosopagnosia and autism may be qualitatively different, attributable to deficits of perceptual encoding and perceptual maintenance, respectively