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

Semantics and Proof Theory of the Epsilon Calculus

The epsilon operator is a term-forming operator which replaces quantifiers in ordinary predicate logic. The application of this undervalued formalism has been hampered by the absence of well-behaved proof systems on the one hand, and accessible presentations of its theory on the other. One significant early result for the original axiomatic proof system for the epsilon-calculus is the first epsilon theorem, for which a proof is sketched. The system itself is discussed, also relative to possible semantic interpretations. The problems facing the development of proof-theoretically well-behaved systems are outlined.Comment: arXiv admin note: substantial text overlap with arXiv:1411.362

On the Energy Dependence of the Dipole-Proton Cross Section in Deep Inelastic Scattering

We study the dipole picture of high-energy virtual-photon-proton scattering. It is shown that different choices for the energy variable in the dipole cross section used in the literature are not related to each other by simple arguments equating the typical dipole size and the inverse photon virtuality, contrary to what is often stated. We argue that the good quality of fits to structure functions that use Bjorken-x as the energy variable - which is strictly speaking not justified in the dipole picture - can instead be understood as a consequence of the sign of scaling violations that occur for increasing Q^2 at fixed small x. We show that the dipole formula for massless quarks has the structure of a convolution. From this we obtain derivative relations between the structure function F_2 at large and small Q^2 and the dipole-proton cross section at small and large dipole size r, respectively.Comment: 27 page

Dual mobility cup reduces dislocation rate after arthroplasty for femoral neck fracture

<p>Abstract</p> <p>Background</p> <p>Hip dislocation after arthroplasty for femoral neck fractures remains a serious complication. The aim of our study was to investigate the dislocation rate in acute femoral neck fracture patients operated with a posterior approach with cemented conventional or dual articulation acetabular components.</p> <p>Methods</p> <p>We compared the dislocation rate in 56 consecutive patients operated with conventional (single mobility) cemented acetabular components to that in 42 consecutive patients operated with dual articulation acetabular components. All the patients were operated via posterior approach and were followed up to one year postoperatively.</p> <p>Results</p> <p>There were 8 dislocations in the 56 patients having conventional components as compared to no dislocations in those 42 having dual articulation components (p = 0.01). The groups were similar with respect to age and gender distribution.</p> <p>Conclusions</p> <p>We conclude that the use of a cemented dual articulation acetabular component significantly reduces the dislocation rates in femoral neck fracture patients operated via posterior approach.</p

Farnesol induces cell detachment from established S. epidermidis biofilms

Antibiotic resistance is a serious problem in Staphylococcus epidermidis infections as many clinical isolates of this organism are resistant to up to eight different antibiotics. The increased resistance to conventional antibiotic therapy has lead to the search for new antimicrobial therapeutic agents. Farnesol, an essential oil found in many plants, has been shown to be active against S. epidermidis. Using a type control strain we recently described that although farnesol was not efficient at killing biofilm bacteria, a strong reduction on biofilm biomass was detected, and we hypothesize that farnesol could, somehow, induce biofilm detachment. In this report, to test our hypothesis we used 36 representative clinical strains of S. epidermidis from different geographic locations and characterized them in terms of genetic variability by multilocus sequence typing and staphylococcal chromosome cassette mec. Strains were tested for biofilm formation, and the presence of ica, bhp and aap genes was determined. Stronger biofilms had always the presence of ica operon but often co-harbored bhp and aap genes. Farnesol was then used in biofilm-forming strains, and biofilm detachment was detected in half of the strains tested. Furthermore, we also showed that farnesol inability to kill biofilm bacteria was not the result of the biofilm structure but was related to high cell density. Our results demonstrate, for the first time, that the biomass reduction previously found by us, and many other groups, is the result not of cell killing but instead is the result of biofilm detachment.We thank Herminia de Lencastre for reviewing the manuscript. Support for this work was provided by project P-99911 from Fundacao Calouste Gulbenkian and CONCORD-HEALTH-F3-2008/Project Number 222718/European Commission. This work was also supported by Fundacao para a Ciencia e a Tecnologia through grant #PEst-OE/EQB/LA0004/2011 awarded to ITQB

Effects of Deliberate Ingestion of Organophosphate or Paraquat on Brain Stem Auditory-Evoked Potentials

Organophosphate (OP) and paraquat (PQ) ingestion is a serious health problem. A common pathology behind OP or PQ poisoning is the generation of reactive oxygen species (ROS) which is known to cause ototoxicity. The aim of the study was to identify the effects of deliberate ingestion of OP or PQ on brain stem auditory-evoked potentials (BAEPs). Consecutive patients with deliberate self-poisoning with OP or PQ who were admitted to a secondary and a tertiary care hospital in the Southern province of Sri Lanka and matched controls were recruited. BAEPs were performed at 1 week (first assessment) and 6 weeks (second assessment) after the exposure. Interpeak latencies of I–III, III–V, and I–V were measured. There were 70 and 28 patients in the OP and PQ arms with the mean age of 32 ± 12 and 29 ± 12 years, respectively. There were 70 controls and their mean age was 33 ± 12 years. In OP and PQ poisoning, 53/70 and 18/28 came for the second assessment, respectively. The interpeak latency was not statistically different in the controls vs the first assessment, controls vs the second assessment, and the first vs the second assessment. There were no significant lesions in the auditory pathway in OP or PQ poisoned patients. The generation of ROS within the perilymphatic space following the ingestion of OP or PQ may not be sufficient to cause lesions in the auditory pathway. Further studies with the assessment of auditory threshold are needed

Genetic differentiation and geographical Relationship of Asian barley landraces using SSRs

Genetic diversity in 403 morphologically distinct landraces of barley (Hordeum vulgare L. subsp. vulgare) originating from seven geographical zones of Asia was studied using simple sequence repeat (SSR) markers from regions of medium to high recombination in the barley genome. The seven polymorphic SSR markers representing each of the chromosomes chosen for the study revealed a high level of allelic diversity among the landraces. Genetic richness was highest in those from India, followed by Pakistan while it was lowest for Uzbekistan and Turkmenistan. Out of the 50 alleles detected, 15 were unique to a geographic region. Genetic diversity was highest for landraces from Pakistan (0.70 ± 0.06) and lowest for those from Uzbekistan (0.18 ± 0.17). Likewise, polymorphic information content (PIC) was highest for Pakistan (0.67 ± 0.06) and lowest for Uzbekistan (0.15 ± 0.17). Diversity among groups was 40% compared to 60% within groups. Principal component analysis clustered the barley landraces into three groups to predict their domestication patterns. In total 51.58% of the variation was explained by the first two principal components of the barley germplasm. Pakistan landraces were clustered separately from those of India, Iran, Nepal and Iraq, whereas those from Turkmenistan and Uzbekistan were clustered together into a separate group

Fitness Ranking of Individual Mutants Drives Patterns of Epistatic Interactions in HIV-1

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Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited