Modeling large scale species abundance with latent spatial processes

Modeling species abundance patterns using local environmental features is an important, current problem in ecology. The Cape Floristic Region (CFR) in South Africa is a global hot spot of diversity and endemism, and provides a rich class of species abundance data for such modeling. Here, we propose a multi-stage Bayesian hierarchical model for explaining species abundance over this region. Our model is specified at areal level, where the CFR is divided into roughly $37{,}000$ one minute grid cells; species abundance is observed at some locations within some cells. The abundance values are ordinally categorized. Environmental and soil-type factors, likely to influence the abundance pattern, are included in the model. We formulate the empirical abundance pattern as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. An important point in this analysis is that only $28$ of the grid cells have been sampled and that, for sampled grid cells, the number of sampled locations ranges from one to more than one hundred. Still, we are able to develop potential and transformed abundance surfaces over the entire region. In the hierarchical framework, categorical abundance classifications are induced by continuous latent surfaces. The degradation model above is built on the latent scale. On this scale, an areal level spatial regression model was used for modeling the dependence of species abundance on the environmental factors.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS335 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Attenuated Virulence and Biofilm Formation in Staphylococcus aureus following Sublethal Exposure to Triclosan

Sub-effective exposure of Staphylococcus aureus to the biocide triclosan can reportedly induce a small colony variant (SCV) phenotype in Staphylococcus aureus. S. aureus SCVs are characterised by slow growth rates, reduced pigmentation and lowered antimicrobial susceptibility. Whilst they may exhibit enhanced intracellular survival, there are conflicting reports regarding their pathogenicity. The current study reports the characteristics of a SCV-like strain of S. aureus, created by repeated passage on sub-lethal triclosan concentrations. S. aureus ATCC 6538 (P0) was serially exposed ten times to concentration gradients of triclosan to generate strain P10. This strain was then further passaged ten times on triclosan-free medium (designated x10). The minimum inhibitory and bactericidal concentrations of triclosan for P0, P10 and x10 were determined and growth rates measured in biofilm and planktonic culture. Haemolysin, DNAse and coagulase activities were measured and virulence determined using a Galleria mellonella pathogenicity model. Strain P10 exhibited decreased susceptibility to triclosan and characteristics of a SCV phenotype, including considerably reduced growth rate and the formation of pinpoint colonies. However, this strain also had delayed coagulase production, impaired haemolysis (p<0.01), was defective in biofilm formation and DNAase activity, and displayed significantly attenuated virulence. Colony size, haemolysis, coagulase activity and virulence were only partially restored in strain x10, whereas planktonic growth rate was fully restored. However, x10 was at least as defective in biofilm formation and DNAse production as P10. These data suggest that although repeated exposure to triclosan may result in a SCV-like phenotype, this is not necessarily associated with increased virulence, and adapted bacteria may exhibit other functional deficiencies

Challenges and methodologies in using progression free survival as a surrogate for overall survival In oncology

Objectives: A primary outcome in oncology trials is overall survival (OS). However, to estimate OS accurately requires a sufficient number of patients to have died, which may take a long time. If an alternative end point is sufficiently highly correlated with OS, it can be used as a surrogate. Progression-free survival (PFS) is the surrogate most often used in oncology, but does not always satisfy the correlation conditions for surrogacy. We analyze the methodologies used when extrapolating from PFS to OS. Methods: Davis et al. previously reviewed the use of surrogate end points in oncology, using papers published between 2001 and 2011. We extend this, reviewing papers published between 2012 and 2016. We also examine the reporting of statistical methods to assess the strength of surrogacy. Results: The findings from 2012 to 2016 do not differ substantially from those of 2001 to 2011: the same factors are shown to affect the relationship between PFS and OS. The proportion of papers reporting individual patient data (IPD), strongly recommended for full assessment of surrogacy, remains low: 33 percent. A wide range of methods has been used to determine the appropriateness of surrogates. While usually adhering to reporting standards, the standard of scholarship appears sometimes to be questionable and the reporting of results often haphazard. Conclusions: Standards of analysis and reporting PFS to OS surrogate studies should be improved by increasing the rigor of statistical reporting and by agreeing to a minimum set of reporting guidelines. Moreover, the use of IPD to assess surrogacy should increase

Predicting the sound insulation of lightweight sandwich panels

The sound insulation of three sandwich panels was modelled using simple sound insulation prediction methods, but the agreement between theory and experiment was not very good. The effective Young&#039;s modulus was determined over a wide frequency from the resonant frequencies of three beams of different lengths. The effective Young&#039;s modulus was found to reduce with increasing frequency as has been predicted in the literature. This decrease is due to the core starting to shear rather than bend because its Young&#039;s modulus is much less than the Young&#039;s moduli of the skins. Unfortunately the agreement between theory and experiment was still not very good. This is because many of the prediction frequencies occur in the critical frequency dip because of the variation of the Young&#039;s modulus with frequency

Dissociative Autoionization in (1+2)-photon Above Threshold Excitation of H2 Molecules

We have theoretically studied the effect of dissociative autoionization on the photoelectron energy spectrum in (1+2)-photon above threshold ionization(ATI) of H2 molecules. We have considered excitation from the ground state X-singlet-Sigma-g+(v=0,j) to the doubly excited autoionizing states of singlet-Sigma-u+ and singlet-Pi-u+ symmetry, via the intermediate resonant B-singlet-Sigma-u+(v=5,j) states. We have shown that the photoelectron energy spectrum is oscillatory in nature and shows three distinct peaks above the photoelectron energy 0.7 eV. This feature has been observed in a recent experiment by Rottke et al, J. Phys. B, Vol. 30, p-4049 (1997).Comment: 11 pages and 4 figure

Developing a health state classification system from NEWQOL for epilepsy using classical psychometric techniques and Rasch analysis: a technical report

Aims: Resource allocation amongst competing health care interventions is informed by evidence of both clinical- and cost-effectiveness. Cost-utility analysis is increasingly used to assess cost effectiveness through the use of Quality Adjusted Life Years (QALYs). This requires health state values. Generic measures of health related quality of life (HRQL) are usually used to produce these values, but there are concerns about their relevance and sensitivity in epilepsy. This study develops a health state classification system for epilepsy from the NEWQOL battery, a validated questionnaire measuring QoL in epilepsy. The classification system will be amenable to valuation for calculating QALYs. Methods: Factor and other psychometric analyses were undertaken to investigate the factor structure of the battery, and assess the validity and responsiveness of the items. These analyses were used alongside Rasch analysis to select the dimensions included in the classification system, and the items used to represent each domain. Analysis was carried out on a trial dataset of patients with epilepsy (n=1611). Rasch and factor analysis were performed on one half of the sample and validated on the remaining half. Dimensions and items were selected that performed well across all analyses. Results: The battery was found to demonstrate reliability and validity but responsiveness across time periods for many of the items was low. A six dimension classification system was developed: worry about seizures, depression, memory, cognition, stigmatism and control, each with four response levels. Conclusions: It is feasible to develop a health state classification system from a battery of instruments using a combination of classical psychometric, factor and Rasch analysis. This is the first condition-specific health state classification developed for epilepsy and the next stage will produce preference weights to enable the measure to be used in cost-utility analysis.quality adjusted life years; health related quality of life; Rasch analysis; preference-based measures of health; health states; epilepsy

Cm-Wavelength Total Flux and Linear Polarization Properties of Radio-Loud BL Lacertae Objects

Results from a long-term program to quantify the range of behavior of the cm-wavelength total flux and linear polarization variability properties of a sample of 41 radio-loud BL Lac objects using weekly to tri-monthly observations with the University of Michigan 26-m telescope operating at 14.5, 8.0, and 4.8 GHz are presented; these observations are used to identify class-dependent differences between these BL Lacs and QSOs in the Pearson-Readhead sample. The BL Lacs are found to be more highly variable in total flux density than the QSOs, exhibiting changes that are often nearly-simultaneous and of comparable amplitude at 14.5 and 4.8 GHz in contrast to the behavior in the QSOs and supporting the existence of class-dependent differences in opacity within the parsec-scale jet flows. Structure function analyses of the flux observations quantify that a characteristic timescale is identifiable in only 1/3 of the BL Lacs. The time-averaged fractional linear polarizations are only on the order of a few percent and are consistent with the presence of tangled magnetic fields within the emitting regions. In many sources a preferred long-term orientation of the EVPA is present; when compared with the VLBI structural axis, no preferred position angle difference is identified. The polarized flux typically exhibits variability with timescales of months to a few years and shows the signature of a propagating shock during several resolved outbursts. The observations indicate that the source emission is predominately due to evolving source components and support the occurrence of more frequent shock formation in BL Lac parsec-scale flows than in QSO jets. The differences in variability behavior and polarization between BL Lacs and QSOs can be explained by differences in jet stability.Comment: 1 LaTex (aastex) file, 21 postscript figure files, 2 external LaTex table files. To appear in the Astrophysical Journa

Development of text mining tools for information retrieval from patents

Biomedical literature is composed of an ever increasing number of publications in natural language. Patents are a relevant fraction of those, being important sources of information due to all the curated data from the granting process. However, their unstructured data turns the search of information a challenging task. To surpass that, Biomedical text mining (BioTM) creates methodologies to search and structure that data. Several BioTM techniques can be applied to patents. From those, Information Retrieval is the process where relevant data is obtained from collections of documents. In this work, a patent pipeline was developed and integrated intoFEDER -Federación Española de Enfermedades Raras(NORTE-01-0145-FEDER-000004)info:eu-repo/semantics/publishedVersio

Vacuum-UV negative photoion spectroscopy of CF3Cl, CF3Br and CF3I

Using synchrotron radiation negative ions have been detected by mass spectrometry following vacuum-UV photoexcitation of trifluorochloromethane (CF$_3$Cl), trifluorobromomethane (CF$_3$Br) and trifluoroiodomethane (CF$_3$I). The anions F$^-$, X$^-$, F$_2^-$, FX$^-$, CF$^-$, CF$_2^-$ and CF$_3^-$ were observed from all three molecules, where X = Cl, Br or I, and their ion yields recorded in the range 8-35 eV. With the exception of Br$^-$ and I$^-$, the anions observed show a linear dependence of signal with pressure, showing that they arise from unimolecular ion-pair dissociation. Dissociative electron attachment, following photoionization of CF$_3$Br and CF$_3$I as the source of low-energy electrons, is shown to dominate the observed Br$^-$ and I$^-$ signals, respectively. Cross sections for ion-pair formation are put on to an absolute scale by calibrating the signal strengths with those of F$^-$ from both SF$_6$ and CF$_4$. These anion cross sections are normalized to vacuum-UV absorption cross sections, where available, and the resulting quantum yields are reported. Anion appearance energies are used to calculate upper limits to 298 K bond dissociation energies for $D^0$(CF$_3$-X) which are consistent with literature values. We report new data for $D^0$(CF$_2$I$^-$-F) ≤ 2.7 ± 0.2 eV and $\Delta_fH^0_{298}$ (CF$_2$I$^+$) ≤ (598 ± 22) kJ mol$^{-1}$. No ion-pair formation is observed below the ionization energy of the parent molecule for CF$_3$Cl and CF$_3$Br, and only weak signals (in both I$^-$ and F$^-$) are detected for CF$_3$I. These observations suggest neutral photodissociation is the dominant exit channel to Rydberg state photoexcitation at these lower energies

Developing a health state classification system from NEWQOL for epilepsy using classical psychometric techniques and Rasch analysis: A technical report

Aims: Resource allocation amongst competing health care interventions is informed by evidence of both clinical- and cost-effectiveness. Cost-utility analysis is increasingly used to assess cost effectiveness through the use of Quality Adjusted Life Years (QALYs). This requires health state values. Generic measures of health related quality of life (HRQL) are usually used to produce these values, but there are concerns about their relevance and sensitivity in epilepsy. This study develops a health state classification system for epilepsy from the NEWQOL battery, a validated questionnaire measuring QoL in epilepsy. The classification system will be amenable to valuation for calculating QALYs. Methods: Factor and other psychometric analyses were undertaken to investigate the factor structure of the battery, and assess the validity and responsiveness of the items. These analyses were used alongside Rasch analysis to select the dimensions included in the classification system, and the items used to represent each domain. Analysis was carried out on a trial dataset of patients with epilepsy (n=1611). Rasch and factor analysis were performed on one half of the sample and validated on the remaining half. Dimensions and items were selected that performed well across all analyses. Results: The battery was found to demonstrate reliability and validity but responsiveness across time periods for many of the items was low. A six dimension classification system was developed: worry about seizures, depression, memory, cognition, stigmatism and control, each with four response levels. Conclusions: It is feasible to develop a health state classification system from a battery of instruments using a combination of classical psychometric, factor and Rasch analysis. This is the first condition-specific health state classification developed for epilepsy and the next stage will produce preference weights to enable the measure to be used in cost-utility analysis