Bayesian clustering of multiple zero-inflated outcomes

Several applications involving counts present a large proportion of zeros (excess-of-zeros data). A popular model for such data is the hurdle model, which explicitly models the probability of a zero count, while assuming a sampling distribution on the positive integers. We consider data from multiple count processes. In this context, it is of interest to study the patterns of counts and cluster the subjects accordingly. We introduce a novel Bayesian approach to cluster multiple, possibly related, zero-inflated processes. We propose a joint model for zero-inflated counts, specifying a hurdle model for each process with a shifted Negative Binomial sampling distribution. Conditionally on the model parameters, the different processes are assumed independent, leading to a substantial reduction in the number of parameters as compared with traditional multivariate approaches. The subject-specific probabilities of zero-inflation and the parameters of the sampling distribution are flexibly modelled via an enriched finite mixture with random number of components. This induces a two-level clustering of the subjects based on the zero/non-zero patterns (outer clustering) and on the sampling distribution (inner clustering). Posterior inference is performed through tailored Markov chain Monte Carlo schemes. We demonstrate the proposed approach on an application involving the use of the messaging service WhatsApp. This article is part of the theme issue 'Bayesian inference: challenges, perspectives, and prospects'

Modeling of primary dendrite arm spacing variations in thin-slab casting of low carbon and low alloy steels

Solidification structure of a High Strength Low Alloy (HSLA) steel, in terms of dendrite arm spacing distribution across the shell thickness, is studied in a breakout shell from a thin-slab caster at Tata Steel in IJmuiden. Columnar dendrites were found to be the predominant morphology throughout the shell with size variations across the shell thickness. Primary Dendrite Arm Spacing (PDAS) increases by increasing the distance from meniscus or slab surface. Subsequently, a model is proposed to describe the variation of the PDAS with the shell thickness (the distance from slab surface) under solidifiction conditions experienced in the primary cooling zone of thin-slab casting. The proposed relationship related the PDAS to the shell thickness and, hence, can be used as a tool for predicting solidifcation structure and optimizing the thin-slab casting of low alloy steels

RESIDUAL RADIATION OF THE LRL 184-INCH CYCLOTRON

Residual radioactivity at the Lawrence Radiation Laboratory 184-Inch Cyclotron was measured during November 1960. The study was conducted along three principal lines: (1) general survey of radiation levels in the cyclotron vault, (2) activation of foils placed near the cyclotron, and (3) gamma-ray spectra of the cyclotron gap region, including dee structure. Initial radiation levels were less than 8 r/hr which dropped to abcut 10 mr/hr after 48 hr. The observed activities induced in copper foils were Cu/sup 64/ and Co/sup 58/; in iron foils, Mn/sup 52/, Mn/sup 54/, and Mn/sup 56/; in aluminum foils Na/sup / 2>s/sup 4/ The gamma-ray spectra from the gap region included two intense long-lived peaks, at 510 and 810 kev, caused principally by Co/sup 58/. (auth

Improving the aseptic transfer procedures in hospital pharmacies. Part B:evaluation of disinfection methods for materials with a non-sterile surface

Objectives To improve the disinfection methods for materials with a non-sterile surface to be used in aseptic handling. Methods The surface bioburden on ampoules (A) and injection vials (IV) is determined by contact plates and total immersion. The occurrence of spore-forming bacteria is determined by strain colouring and matrix-assisted laser desorption ionisation-time of flight mass spectrometry. The disinfection procedures of non-sterile materials in 10 hospital pharmacies are judged by observing. Results After wiping according to local disinfection methods, the mean surface bioburden determined by contact plates in 10 hospital pharmacies is 0.36 (plastic A), 0.50 (glass A) and 0.29 colony-forming unit (cfu) (IV). The observers found great differences in accuracy of wiping and degree of wetting the sterile gauzes. After improved wiping with commercially available alcohol impregnated sterile wipes and a two-towel technique (one-step TT disinfection), the mean surface bioburden determined by contact plates is 0.03 (plastic A), 0.2 (glass A) and 0.13 cfu (IV). Further improvement can be reached by submerging A and IV in ethanol 70% followed by improved wiping (two-step TT disinfection), but still micro-organisms will remain (mean surface bioburden determined by total immersion is 0 (plastic A) and 0.3 cfu (IV); glass A not determined). Two-step TT disinfection is more labour intensive. Spilling of alcohol is another disadvantage. However, we presume one-step TT disinfection is effective enough in daily practice. Routine surface bioburden determinations have to prove this. The effectiveness of the combination of spray and wipe is not examined because we observed a quick disappearance of alcohols from vertical as well as horizontal surfaces, which shortens the contact time to far below the advised 2 min. Spore-forming bacteria disappear as quickly as other micro-organisms during disinfection by alcohols. Conclusion Local disinfection procedures can be improved. Complete removal of micro-organisms from materials with a non-sterile surface, even after two-step TT disinfection, is impossible. Routine surface bioburden determinations have to prove if one-step TT disinfection is effective enough

Tuberculosis in Dr Granville's mummy: a molecular re-examination of the earliest known Egyptian mummy to be scientifically examined and given a medical diagnosis

‘Dr Granville's mummy’ was described to the Royal Society of London in 1825 and was the first ancient Egyptian mummy to be subjected to a scientific autopsy. The remains are those of a woman, Irtyersenu, aged about 50, from the necropolis of Thebes and dated to about 600 BC. Augustus Bozzi Granville (1783–1872), an eminent physician and obstetrician, described many organs still in situ and attributed the cause of death to a tumour of the ovary. However, subsequent histological investigations indicate that the tumour is a benign cystadenoma. Histology of the lungs demonstrated a potentially fatal pulmonary exudate and earlier studies attempted to associate this with particular disease conditions. Palaeopathology and ancient DNA analyses show that tuberculosis was widespread in ancient Egypt, so a systematic search for tuberculosis was made, using specific DNA and lipid biomarker analyses. Clear evidence for Mycobacterium tuberculosis complex DNA was obtained in lung tissue and gall bladder samples, based on nested PCR of the IS6110 locus. Lung and femurs were positive for specific M. tuberculosis complex cell-wall mycolic acids, demonstrated by high-performance liquid chromatography of pyrenebutyric acid–pentafluorobenzyl mycolates. Therefore, tuberculosis is likely to have been the major cause of death of Irtyersenu

Solitary magnetic perturbations at the ELM onset

Edge localised modes (ELMs) allow maintaining sufficient purity of tokamak H-mode plasmas and thus enable stationary H-mode. On the other hand in a future device ELMs may cause divertor power flux densities far in excess of tolerable material limits. The size of the energy loss per ELM is determined by saturation effects in the non-linear phase of the ELM, which at present is hardly understood. Solitary magnetic perturbations (SMPs) are identified as dominant features in the radial magnetic fluctuations below 100kHz. They are typically observed close (+-0.1ms) to the onset of pedestal erosion. SMPs are field aligned structures rotating in the electron diamagnetic drift direction with perpendicular velocities of about 10km/s. A comparison of perpendicular velocities suggests that the perturbation evoking SMPs is located at or inside the separatrix. Analysis of very pronounced examples showed that the number of peaks per toroidal turn is 1 or 2, which is clearly lower than corresponding numbers in linear stability calculations. In combination with strong peaking of the magnetic signals this results in a solitary appearance resembling modes like palm tree modes, edge snakes or outer modes. This behavior has been quantified as solitariness and correlated to main plasma parameters. SMPs may be considered as a signature of the non-linear ELM-phase originating at the separatrix or further inside. Thus they provide a handle to investigate the transition from linear to non-linear ELM phase. By comparison with data from gas puff imaging processes in the non-linear phase at or inside the separatrix and in the scrape-off-layer (SOL) can be correlated. A connection between the passing of an SMP and the onset of radial filament propagation has been found. Eventually the findings related to SMPs may contribute to a future quantitative understanding of the non-linear ELM evolution.Comment: submitted to Nuclear Fusio

Questioning the Influence of Sunspots on Amazon Hydrology: Even a Broken Clock Tells the Right Time Twice a Day

It was suggested in a recent article that sunspots drive decadal variation in Amazon River flow. This conclusion was based on a novel time series decomposition method used to extract a decadal signal from the Amazon River record. We have extended this analysis back in time, using a new hydrological proxy record of tree ring oxygen isotopes (δ¹⁸OTR). Consistent with the findings of Antico and Torres, we find a positive correlation between sunspots and the decadal δ¹⁸OTR cycle from 1903 to 2012 (r = 0.60, p < 0.001). However, the relationship does not persist into the preceding century and even becomes weakly negative (r = −0.30, p = 0.11, 1799–1902). This result casts considerable doubt over the mechanism by which sunspots are purported to influence Amazon hydrology

Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysis

<p>Abstract</p> <p>Background</p> <p>Rhomboids are ubiquitous proteins with diverse functions in all life kingdoms, and are emerging as important factors in the biology of some pathogenic apicomplexa and <it>Providencia stuartii</it>. Although prokaryotic genomes contain one rhomboid, actinobacteria can have two or more copies whose sequences have not been analyzed for the presence putative rhomboid catalytic signatures. We report detailed phylogenetic and genomic analyses devoted to prokaryotic rhomboids of an important genus, <it>Mycobacterium</it>.</p> <p>Results</p> <p>Many mycobacterial genomes contained two phylogenetically distinct active rhomboids orthologous to Rv0110 (rhomboid protease 1) and Rv1337 (rhomboid protease 2) of <it>Mycobacterium tuberculosis </it>H37Rv, which were acquired independently. There was a genome-wide conservation and organization of the orthologs of Rv1337 arranged in proximity with glutamate racemase (<it>mur1</it>), while the orthologs of Rv0110 appeared evolutionary unstable and were lost in <it>Mycobacterium leprae </it>and the <it>Mycobacterium avium </it>complex. The orthologs of Rv0110 clustered with eukaryotic rhomboids and contained eukaryotic motifs, suggesting a possible common lineage. A novel nonsense mutation at the Trp73 codon split the rhomboid of <it>Mycobacterium avium </it>subsp. <it>Paratuberculosis </it>into two hypothetical proteins (MAP2425c and MAP2426c) that are identical to MAV_1554 of <it>Mycobacterium avium</it>. Mycobacterial rhomboids contain putative rhomboid catalytic signatures, with the protease active site stabilized by Phenylalanine. The topology and transmembrane helices of the Rv0110 orthologs were similar to those of eukaryotic secretase rhomboids, while those of Rv1337 orthologs were unique. Transcription assays indicated that both mycobacterial rhomboids are possibly expressed.</p> <p>Conclusions</p> <p>Mycobacterial rhomboids are active rhomboid proteases with different evolutionary history. The Rv0110 (rhomboid protease 1) orthologs represent prokaryotic rhomboids whose progenitor may be the ancestors of eukaryotic rhomboids. The Rv1337 (rhomboid protease 2) orthologs appear more stable and are conserved nearly in all mycobacteria, possibly alluding to their importance in mycobacteria. MAP2425c and MAP2426c provide the first evidence for a split homologous rhomboid, contrasting whole orthologs of genetically related species. Although valuable insights to the roles of rhomboids are provided, the data herein only lays a foundation for future investigations for the roles of rhomboids in mycobacteria.</p

Catalytic Dehydrogenation of Amine-Boranes using Geminal Phosphino-Boranes

The reaction of the intramolecular frustrated Lewis pair (FLP) tBu2PCH2BPh2 with the amine-boranes NH3·BH3 and Me2NH·BH3 leads to the formation of the corresponding FLP-H2 adducts as well as novel five-membered heterocycles that result from capturing the in situ formed amino-borane by a second equivalent of FLP. The sterically more demanding tBu2PCH2BMes2 does not form such a five-membered heterocycle when reacted with Me2NH·BH3 and its H2 adduct liberates dihydrogen at elevated temperatures, promoting the metal-free catalytic dehydrogenation of amine-boranes.Peer reviewe