Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Within-Otolith Variability in Chemical Fingerprints: Implications for Sampling Designs and Possible Environmental Interpretation

Largely used as a natural biological tag in studies of dispersal/connectivity of fish, otolith elemental fingerprinting is usually analyzed by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). LA-ICP-MS produces an elemental fingerprint at a discrete time-point in the life of a fish and can generate data on within-otolith variability of that fingerprint. The presence of within-otolith variability has been previously acknowledged but not incorporated into experimental designs on the presumed, but untested, grounds of both its negligibility compared to among-otolith variability and of spatial autocorrelation among multiple ablations within an otolith. Here, using a hierarchical sampling design of spatial variation at multiple scales in otolith chemical fingerprints for two Mediterranean coastal fishes, we explore: 1) whether multiple ablations within an otolith can be used as independent replicates for significance tests among otoliths, and 2) the implications of incorporating within-otolith variability when assessing spatial variability in otolith chemistry at a hierarchy of spatial scales (different fish, from different sites, at different locations on the Apulian Adriatic coast). We find that multiple ablations along the same daily rings do not necessarily exhibit spatial dependency within the otolith and can be used to estimate residual variability in a hierarchical sampling design. Inclusion of within-otolith measurements reveals that individuals at the same site can show significant variability in elemental uptake. Within-otolith variability examined across the spatial hierarchy identifies differences between the two fish species investigated, and this finding leads to discussion of the potential for within-otolith variability to be used as a marker for fish exposure to stressful conditions. We also demonstrate that a 'cost'-optimal allocation of sampling effort should typically include some level of within-otolith replication in the experimental design. Our findings provide novel evidence to aid the design of future sampling programs and improve our general understanding of the mechanisms regulating elemental fingerprints.

Deep sampling and testing in soft stratified clay

A 37-m thick layer of stratified clay encountered during a site investigation at Swann's Bridge, near the sea-coast at Limavady, Northern Ireland, is one of the deepest and thickest layers of this type of material recorded in Ireland. A study of the relevant literature and stratigraphic evidence obtained from the site investigation showed that despite being close to the current shoreline, the clay was deposited in a fresh-water glacial lake formed approximately 13 000 BP. The 37-m layer of clay can be divided into two separate zones. The lower zone was deposited as a series of laminated layers of sand, silt, and clay, whereas the upper zone was deposited as a largely homogeneous mixture. A comprehensive series of tests was carried out on carefully selected samples from the full thickness of the deposit. The results obtained from these tests were complex and confusing, particularly the results of tests done on samples from the lower zone. The results of one-dimensional compression tests, unconsolidated undrained triaxial tests, and consolidated undrained triaxial compression tests showed that despite careful sampling, all of the specimens from the lower zone exhibited behaviour similar to that of reconstituted clays. It was immediately clear that the results needed explanation. This paper studies possible causes of the results from tests carried out on the lower Limavady clay. It suggests a possible mechanism based on anisotropic elasticity, yielding, and destructuring that provides an understanding of the observed behaviour.Key words: clay, laminations, disturbance, yielding, destructuring, reconstituted.

Can we characterise ‘openness’ in the Holocene palaeoenvironmental record? Modern analogue studies of insect faunas and pollen spectra from Dunham Massey deer park and Epping Forest, England

This paper examines the degree to which tree-associated Coleoptera (beetles) and pollen could be used to predict the degree of ‘openness’ in woodland. The results from two modern insect and pollen analogue studies from ponds at Dunham Massey, Cheshire and Epping Forest, Greater London are presented. We explore the reliability of modern pollen rain and sub-fossil beetle assemblages to represent varying degrees of canopy cover for up to 1000m from a sampling site. Modern woodland canopy structure around the study sites has been assessed using GIS-based mapping at increasing radial distances as an independent check on the modern insect and pollen data sets. These preliminary results suggest that it is possible to use tree-associated Coleoptera to assess the degree of local vegetation openness. Additionally, it appears that insect remains may indicate the relative intensity of land use by grazing animals. Our results also suggest most insects are collected from within a 100m to 200m radius of the sampling site. The pollen results suggest that local vegetation and density of woodland in the immediate area of the sampling site can have a strong role in determining the pollen signal.

Studies on the persistence of estradiol benzoate and nortestosterone decanoate in hair of cattle following treatment with growth promoters, determined by ultra-high-performance liquid chromatography-tandem mass spectrometry

Measurement of steroid esters in bovine hair samples, using sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS), provides a powerful tool for identifying animals treated illicitly with growth promoters. The successful application of such testing requires appropriate sampling of hair from treated animals. This paper describes the results of hair analysis by LC-MS/MS for two animal studies in which animals were treated with estradiol-3-benzoate and nortestosterone decanoate. The results from the first animal study indicate that animals treated with these anabolic steroids may not always be identified from analysis of hair samples; positive test results occur sporadically and only for some of the treated animals. The results from the second animal study identify conditions attaching to positive hair samples, such as, that concentrations of steroid esters in hair are related to distance of sampling from point of injection and to time post-treatment, that concentrations of steroid esters in hair are related to dose given to the animal but that this relationship may vary over time post-treatment, and that steroid esters may be measured in regrowth hair taken some weeks after treatment. Steroid esters are determined along the length of the hair, confirming that accumulation of steroid esters into hair occurs from various sources, including blood, sweat and sebum. The reported research provides some useful insights into the mechanisms governing the persistence of steroid esters in bovine hair following illicit treatment with growth promoters. (C) 2009 Elsevier B.V. All rights reserved.

The quality of reporting of diagnostic accuracy studies in glaucoma using scanning laser polarimetry

PURPOSE: Scanning laser polarimetry (SLP) has been proposed as a useful diagnostic test for glaucoma. This study was conducted to evaluate the quality of reporting of published studies using the SLP for diagnosing glaucoma. METHODS: A validated Medline and hand search of English-language articles reporting on measures of diagnostic accuracy of the SLP for glaucoma was performed. Two reviewers independently selected and appraised the manuscripts. The Standards for Reporting of Diagnostic Accuracy (STARD) checklist was used to evaluate the quality of each publication. RESULTS: A total of 47 papers were identified of which the first 10 (from 1997 to 2000) and the last 10 articles (from 2004 to 2005) were appraised. Interobserver rating agreement of STARD items was high (85.5% agreement, ?=0.796). The number of STARD items properly reported ranged from 3/25 to 19/25. Only a quarter of studies (5/20) explicitly reported more than half of the STARD items. Important aspects of the methodology were often missing such as participant sampling (reported in 40% of manuscripts), masking of the readers of the index test and reference standard (reported in 20% of manuscripts), and estimation of uncertainty (eg, 95% confidence intervals, reported in 25% of manuscripts). There was a slight increase in the number of STARD items reported with time. CONCLUSIONS: The quality of reporting of diagnostic accuracy tests for glaucoma with SLP is suboptimal. The STARD initiative may be a useful tool for appraising the strengths and weaknesses of diagnostic accuracy studies. © 2007 Lippincott Williams & Wilkins, Inc.

The quality of reporting of diagnostic accuracy studies in glaucoma using the Heidelberg retina tomograph

PURPOSE. Scanning laser tomography with the Heidelberg retina tomograph (HRT; Heidelberg Engineering, Heidelberg, Germany) has been proposed as a useful diagnostic test for glaucoma. This study was conducted to evaluate the quality of reporting of published studies using the HRT for diagnosing glaucoma. METHODS. A validated Medline and hand search of English-language articles reporting on measures of diagnostic accuracy of the HRT for glaucoma was performed. Two reviewers selected and appraised the papers independently. The Standards for Reporting of Diagnostic Accuracy (STARD) checklist was used to evaluate the quality of each publication. RESULTS. A total of 29 articles were included. Interobserver rating agreement was observed in 83% of items (? = 0.76). The number of STARD items properly reported ranged from 5 to 18. Less than a third of studies (7/29) explicitly reported more than half of the STARD items. Descriptions of key aspects of the methodology were frequently missing. For example, the design of the study (prospective or retrospective) was reported in 6 of 29 studies, and details of participant sampling (e.g., consecutive or random selection) were described in 5 of 29 publications. The commonest description of diagnostic accuracy was sensitivity and specificity (25/29) followed by area under the ROC curve (13/29), with 9 of 29 publications reporting both. CONCLUSIONS. The quality of reporting of diagnostic accuracy tests for glaucoma with HRT is suboptimal. The STARD initiative may be a useful tool for appraising the strengths and weaknesses of diagnostic accuracy studies. Copyright © Association for Research in Vision and Ophthalmology.

The Quality of Reporting of Diagnostic Accuracy Studies of Optical Coherence Tomography in Glaucoma

Objective: To evaluate the quality of reporting of diagnostic accuracy studies using optical coherence tomography (OCT) in glaucoma. Design: Descriptive series of published studies. Participants: Published studies reporting a measure of the diagnostic accuracy of OCT for glaucoma. Methods: Review of English language papers reporting measures of diagnostic accuracy of OCT for glaucoma. Papers were identified from a Medline literature search performed in June 2006. Articles were appraised using the 25 items provided by the Standards for Reporting of Diagnostic Accuracy (STARD) initiative. Each item was recorded as full, partially, or not reported. Main Outcome Measures: Degree of compliance with the STARD guidelines. Results: Thirty papers were appraised. Eight papers (26.7%) fully reported more than half of the STARD items. The lowest number of fully reported items in a study was 5 and the highest was 17. Descriptions of key aspects of methodology frequently were missing. For example, details of participant sampling (e.g., consecutive or random selection) were described in only 8 (26.7%) of 30 publications. Measures of statistical uncertainty were reported in 18 (60%) of 30 publications. No single STARD item was fully reported by all the papers. Conclusions: The standard of reporting of diagnostic accuracy studies in glaucoma using OCT was suboptimal. It is hoped that adoption of the STARD guidelines will lead to an improvement in reporting of diagnostic accuracy studies, enabling clearer evidence to be produced for the usefulness of OCT for the diagnosis of glaucoma. © 2007 American Academy of Ophthalmology.

Assessing suspended sediment dynamics in relation to ecological thresholds and sampling strategies in two Irish headwater catchments

Prediction of the impact of suspended sediment on aquatic ecosystems requires adequate knowledge of sediment dynamics in surface waters. Often, studies reporting the response of aquatic biota to suspended sediment are concerned with concentrations, while catchment erosion studies often report sediment delivery as annual loads and yields, making the comparison to documented ecological impacts difficult. Similarly, the European Union Freshwater Fish Directive (FFD) (78/659/EC) stipulates a guideline value of 25mgl which should not be exceeded, with the exception of floods and droughts. In this respect, the significance of suspended sediment in two Irish rivers was assessed using turbidity sensors calibrated for suspended sediment. Sediment yields of 0.07 tonnes (t) hayear and 0.44thayear and annual FFD exceedance frequency of 8.3% and 17.8% were estimated for the two catchments. Contrasts in the frequency of exceedance events between both catchments was observed, yet duration was typically short (

Monte Carlo studies of quantum and classical annealing on a double well

We present results for a variety of Monte Carlo annealing approaches, both classical and quantum, benchmarked against one another for the textbook optimization exercise of a simple one-dimensional double well. In classical (thermal) annealing, the dependence upon the move chosen in a Metropolis scheme is studied and correlated with the spectrum of the associated Markov transition matrix. In quantum annealing, the path integral Monte Carlo approach is found to yield nontrivial sampling difficulties associated with the tunneling between the two wells. The choice of fictitious quantum kinetic energy is also addressed. We find that a "relativistic" kinetic energy form, leading to a higher probability of long real-space jumps, can be considerably more effective than the standard nonrelativistic one.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

ALEA: Fine-Grain Energy Profiling with Basic Block Sampling

Energy efficiency is an essential requirement for all contemporary computing systems. We thus need tools to measure the energy consumption of computing systems and to understand how workloads affect it. Significant recent research effort has targeted direct power measurements on production computing systems using on-board sensors or external instruments. These direct methods have in turn guided studies of software techniques to reduce energy consumption via workload allocation and scaling. Unfortunately, direct energy measurements are hampered by the low power sampling frequency of power sensors. The coarse granularity of power sensing limits our understanding of how power is allocated in systems and our ability to optimize energy efficiency via workload allocation.
We present ALEA, a tool to measure power and energy consumption at the granularity of basic blocks, using a probabilistic approach. ALEA provides fine-grained energy profiling via sta- tistical sampling, which overcomes the limitations of power sens- ing instruments. Compared to state-of-the-art energy measurement tools, ALEA provides finer granularity without sacrificing accuracy. ALEA achieves low overhead energy measurements with mean error rates between 1.4% and 3.5% in 14 sequential and paral- lel benchmarks tested on both Intel and ARM platforms. The sampling method caps execution time overhead at approximately 1%. ALEA is thus suitable for online energy monitoring and optimization. Finally, ALEA is a user-space tool with a portable, machine-independent sampling method. We demonstrate two use cases of ALEA, where we reduce the energy consumption of a k-means computational kernel by 37% and an ocean modelling code by 33%, compared to high-performance execution baselines, by varying the power optimization strategy between basic blocks.

Magnetic studies of the Late Cretaceous magmatism in Portugal : from Iberian plate kinematics to magnetic fabrics

Tese de doutoramento (co-tutela), Ciências Geofísicas e da Geoinformação (Geofísica), Université de Toulouse, Universidade de Lisboa, 2013

Radioactivity studies in Porto urban area: gamma radiation of Paranhos sector

A set of radiation measurements were carried out in several public and private institutions. These were selected with basis on the people affluence and passage to these sites. These measurements were registration formed either indoor, outdoor or underground and were compiled in three Case Studies. Radiation doses measurements were also made, surface and underground locations, and compiled in other two Case Studies. There were sampled, at the same time, humidity, temperature, atmospheric pressure and relevant construction materials at sampling locations. They were collected and registration formed to analyse if there is any relation or contribution for the measured value in each specific place. Geostatistical models were used to elaborate maps of the results both for radiation values and for doses. Preliminary relations were established among the measured parameters.