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Species distribution models (SDMs) are statistical tools used to develop continuous predictions of species occurrence. ‘Integrated SDMs’ (ISDMs) are an elaboration of this approach with potential advantages that allow for the dual use of opportunistically collected presence-only data and site-occupancy data from planned surveys. These models also account for survey bias and imperfect detection through the use of a hierarchical modelling framework that separately estimates the species–environment response and detection process. This is particularly helpful for conservation applications and predictions for rare species, where data are often limited and prediction errors may have significant management consequences. Despite this potential importance, ISDMs remain largely untested under a variety of scenarios. We performed an exploration of key modelling decisions and assumptions on an ISDM using the endangered Baird’s tapir (Tapirus bairdii) as a test species. We found that site area had the strongest effect on the magnitude of population estimates and underlying intensity surface and was driven by estimates of model intercepts. Selecting a site area that accounted for the individual movements of the species within an average home range led to population estimates that coincided with expert estimates. ISDMs that do not account for the individual movements of species will likely lead to less accurate estimates of species intensity (number of individuals per unit area) and thus overall population estimates. This bias could be severe and highly detrimental to conservation actions if uninformed ISDMs are used to estimate global populations of threatened and data-deficient species, particularly those that lack natural history and movement information. However, the ISDM was consistently the most accurate model compared to other approaches, which demonstrates the importance of this new modelling framework and the ability to combine opportunistic data with systematic survey data. Thus, we recommend researchers use ISDMs with conservative movement information when estimating population sizes of rare and data-deficient species. ISDMs could be improved by using a similar parameterization to spatial capture–recapture models that explicitly incorporate animal movement as a model parameter, which would further remove the need for spatial subsampling prior to implementation.
Errors pertinent in dual beam absorptiometry have been studied. Five areas are given in detail: 1. Scattering, in which a computer analysis of multiple scattering shows little error. 2. Geometrical configuration effects, in which the shape of the sample influences accuracy. 3. Poisson variations, in which dosage and statistical error are minimized. 4. Absorption coefficients, in which variations in compilations are examined. 5. Filtering, wherein is shown the need for Kβ filtering. A zero filter system is outlined.
Major depressive disorder (MDD) is a leading cause of disease burden worldwide, with lifetime prevalence in the United States of 17%. Here we present the results of the first prospective, large-scale, patient- and rater-blind, randomized controlled trial evaluating the clinical importance of achieving congruence between combinatorial pharmacogenomic (PGx) testing and medication selection for MDD.
1,167 outpatients diagnosed with MDD and an inadequate response to ≥1 psychotropic medications were enrolled and randomized 1:1 to a Treatment as Usual (TAU) arm or PGx-guided care arm. Combinatorial PGx testing categorized medications in three groups based on the level of gene-drug interactions: use as directed, use with caution, or use with increased caution and more frequent monitoring. Patient assessments were performed at weeks 0 (baseline), 4, 8, 12 and 24. Patients, site raters, and central raters were blinded in both arms until after week 8. In the guided-care arm, physicians had access to the combinatorial PGx test result to guide medication selection. Primary outcomes utilized the Hamilton Depression Rating Scale (HAM-D17) and included symptom improvement (percent change in HAM-D17 from baseline), response (50% decrease in HAM-D17 from baseline), and remission (HAM-D17<7) at the fully blinded week 8 time point. The durability of patient outcomes was assessed at week 24. Medications were considered congruent with PGx test results if they were in the ‘use as directed’ or ‘use with caution’ report categories while medications in the ‘use with increased caution and more frequent monitoring’ were considered incongruent. Patients who started on incongruent medications were analyzed separately according to whether they changed to congruent medications by week8.
At week 8, symptom improvement for individuals in the guided-care arm was not significantly different than TAU (27.2% versus 24.4%, p=0.11). However, individuals in the guided-care arm were more likely than those in TAU to achieve remission (15% versus 10%; p<0.01) and response (26% versus 20%; p=0.01). Remission rates, response rates, and symptom reductions continued to improve in the guided-treatment arm until the 24week time point. Congruent prescribing increased to 91% in the guided-care arm by week 8. Among patients who were taking one or more incongruent medication at baseline, those who changed to congruent medications by week 8 demonstrated significantly greater symptom improvement (p<0.01), response (p=0.04), and remission rates (p<0.01) compared to those who persisted on incongruent medications.
Combinatorial PGx testing improves short- and long-term response and remission rates for MDD compared to standard of care. In addition, prescribing congruency with PGx-guided medication recommendations is important for achieving symptom improvement, response, and remission for MDD patients.
Funding Acknowledgements: This study was supported by Assurex Health, Inc.
Pigs selected for high performance may be more at risk of developing diseases. This study aimed to assess the health and performance of two pig lines divergently selected for residual feed intake (RFI) (low RFI (LRFI) v. high RFI (HRFI)) and housed in two contrasted hygiene conditions (poor v. good) using a 2×2 factorial design (n=40/group). The challenge period (Period 1), started on week zero (W0) when 12-week-old pigs were transferred to good or poor housing conditions. At week 6 (W6), half of the pigs in each group were slaughtered. During a recovery period (Period 2) from W6 to W13 to W14, the remaining pigs (n=20/group) were transferred in good hygiene conditions before being slaughtered. Blood was collected every three (Period 1) or 2 weeks (Period 2) to assess blood indicators of immune and inflammatory responses. Pulmonary lesions at slaughter and performance traits were evaluated. At W6, pneumonia prevalence was greater for pigs housed in poor than in good conditions (51% v. 8%, respectively, P<0.001). Irrespective of hygiene conditions, lung lesion scores were lower for LRFI pigs than for HRFI pigs (P=0.03). At W3, LRFI in poor conditions had the highest number of blood granulocytes (hygiene×line, P=0.03) and at W6, HRFI pigs in poor conditions had the greatest plasma haptoglobin concentrations (hygiene×line, P=0.02). During Period 1, growth rate and growth-to-feed ratio were less affected by poor hygiene in LRFI pigs than in HRFI pigs (hygiene×line, P=0.001 and P=0.02, respectively). Low residual feed intake pigs in poor conditions ate more than the other groups (hygiene×line, P=0.002). Irrespective of the line, fasting plasma glucose concentrations were higher in poor conditions, whereas fasting free fatty acids concentrations were lower than in good conditions. At the end of Period 2, pneumonia prevalence was similar for both housing conditions (39% v. 38%, respectively). During Period 2, plasma protein concentrations were greater for pigs previously housed in poor than in good conditions during Period 1. Immune traits, gain-to-feed ratio, BW gain and feed consumption did not differ during Period 2. Nevertheless, at W12, BW of HRFI previously housed in poor conditions was 13.4 kg lower than BW of HRFI pigs (P<0.001) previously housed in good conditions. In conclusion, health of the most feed efficient LRFI pigs was less impaired by poor hygiene conditions. This line was able to preserve its health, growth performance and its feed ingestion to a greater extent than the less efficient HRFI line.
This review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant (P<0.001) line differences for RFI (−165 g/day in the low RFI (LRFI) line compared with high RFI line) and daily feed intake (−270 g/day). Low responses were observed on growth rate (−12.8 g/day, P<0.05) and body composition (+0.9 mm backfat thickness, P=0.57; −2.64% lean meat content, P<0.001) with a marked response on feed conversion ratio (−0.32 kg feed/kg gain, P<0.001). Reduced ultimate pH and increased lightness of the meat (P<0.001) were observed in LRFI pigs with minor impact on the sensory quality of the meat. These changes in meat quality were associated with changes of the muscular energy metabolism. Reduced maintenance energy requirements (−10% after five generations of selection) and activity (−21% of time standing after six generations of selection) of LRFI pigs greatly contributed to the gain in energy efficiency. However, the impact of selection for RFI on the protein metabolism of the pig remains unclear. Digestibility of energy and nutrients was not affected by selection, neither for pigs fed conventional diets nor for pigs fed high-fibre diets. A significant improvement of digestive efficiency could likely be achieved by selecting pigs on fibre diets. No convincing genetic or blood biomarker has been identified for explaining the differences in RFI, suggesting that pigs have various ways to achieve an efficient use of feed. No deleterious impact of the selection on the sow reproduction performance was observed. The resource allocation theory states that low RFI may reduce the ability to cope with stressors, via the reduction of a buffer compartment dedicated to responses to stress. None of the experiments focussed on the response of pigs to stress or challenges could confirm this theory. Understanding the relationships between RFI and responses to stress and energy demanding processes, as such immunity and lactation, remains a major challenge for a better understanding of the underlying biological mechanisms of the trait and to reconcile the experimental results with the resource allocation theory.
We analyze photoluminescence (PL) and electroluminescence (EL) using a hyperspectral imager that records spectrally resolved luminescence images of solar cell absorbers. The system is calibrated to yield the luminescence flux in absolute values. This system enables to quantitatively image physical parameters such as the photovoltage with an uncertainty of less than 30mV. The wide field illumination, low power excitation and fast acquisition brings new insights compare to classical setups such as confocal microscope. Several types of absorbers have been analyzed. For instance, we can investigate spatial fluctuations of the Quasi Fermi Levels splitting in CIGS polycristalline absorbers and link those fluctuations to transport properties. The method is general to the point that third generation PV cells absorbers can also be evaluated. We illustrate the great potential of our setup by imaging quasi Fermi levels splitting in Intermediate Band Solar cells. Such techniques, directly evaluating the performance of photovoltaic absorbers and devices are needed for fast, high throughput investigations of combinatorial experiments such as the projects carried out for the material genomics programme.
We examined changes to the behaviour of flour beetles, Tribolium confusum, infected with the rodent stomach worm, the spirurid Protospirura muricola, in the context of the ‘Behavioural Manipulation Hypothesis’. Trobolium confusum infected with the third-stage infective larvae of P. muricola showed consistently altered patterns of behaviour. Relative to uninfected beetles, over a measured time period, beetles infected with P. muricola were likely to move over a shorter distance, when moving their speed of movement was slower, they were more likely to stay in the illuminated area of their environment, more likely to emerge from darkened areas into the illuminated areas, and their longevity was significantly shortened. The changes in behaviour, as reflected in effects on speed of movement, were only evident among beetles that actually harboured infective cysts and not among those carrying younger infections when the larvae within their haemocoels would have been at an earlier stage of development and not yet capable of infecting the definitive murine hosts. We discuss whether these changes would have made the beetles more susceptible to predation by rodents, and specifically by the omnivorous eastern spiny mouse, Acomys dimidiatus, the natural definitive host of this parasite in Egypt, from where the P. muricola isolate originated, and whether they support the Behavioural Manipulation Hypothesis or reflect parasite-induced pathology.
We compared serotype distributions of Streptococcus pneumoniae isolates from patients aged <5 and ⩾5 years with invasive pneumococcal disease in New South Wales, Australia, and antibiotic susceptibilities of isolates from the <5 years age group only, before (2002–2004) and after (2005–2009) introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). Overall, there were significant decreases in the mean annual number of referred isolates (770 vs. 515) and the proportion belonging to PCV7 serotypes (74% vs. 38%), but non-PCV7 serotypes, particularly 19A, increased (5% vs. 18%). All changes were more marked in the <5 years age group. Susceptibility testing of isolates from the <5 years age group showed variation in resistance between serotypes, but significant overall increases in penicillin non-susceptibility (23% vs. 31%), ceftriaxone resistance (2% vs. 12%) and multidrug resistance (4% vs. 7%) rates; erythromycin resistance fell (32% vs. 25%). Continued surveillance is needed to monitor changes following the introduction of 13-valent PCV in 2012.
Lyme borreliosis (LB) is the most common arthropod-borne disease of humans in the Northern hemisphere. In Europe, the causative agent, Borrelia burgdorferi sensu lato complex, is principally vectored by Ixodes ricinus ticks. The aim of this study was to identify environmental factors influencing questing I. ricinus nymph abundance and B. burgdorferi s.l. infection in questing nymphs using a large-scale survey across Scotland. Ticks, host dung and vegetation were surveyed at 25 woodland sites, and climatic variables from a Geographical Information System (GIS) were extracted for each site. A total of 2397 10 m2 transect surveys were conducted and 13 250 I. ricinus nymphs counted. Questing nymphs were assayed for B. burgdorferi s.l. and the average infection prevalence was 5·6% (range 0·8–13·9%). More questing nymphs and higher incidence of B. burgdorferi s.l. infection were found in areas with higher deer abundance and in mixed/deciduous compared to coniferous forests, as well as weaker correlations with season, altitude, rainfall and ground vegetation. No correlation was found between nymph abundance and infection prevalence within the ranges encountered. An understanding of the environmental conditions associated with tick abundance and pathogen prevalence may be used to reduce risk of exposure and to predict future pathogen prevalence and distributions under environmental changes.
Monte Carlo simulations of some typical order-disorder ferroelectrics such as TGS, NaNO2 and DKDP nanocrystals were studied using a Transverse Ising Model Hamiltonian with four-spins interactions. The microscopic parameters corresponding to this Hamiltonian were adjusted to fit the experimental polarization-temperature curves for each one of the materials in the bulk phase. Then the dependences of the ferroelectric-paraelectric phase transition temperatures, Tc, on the sizes of those crystals were studied with Monte Carlo simulations of the order-disorder system. We report a weak dependence of Tc on the size of the crystal (d) for these materials above d∼6nm. The addition of surface effects showed that the expected lowtemperature shift of Tc due to size effects, can be reverted.
Ferroelectric Pb(Zr1划xTix)O3 (PZT) films have been extensively studied for active components in microelectromechanical systems. The properties of PZT films depend on many parameters, including composition, orientation, film thickness and microstructure. In this study, the effects of crystallographic orientation on the dielectric and transverse piezoelectric properties of Pb(Zr0.52Ti0.48)O3 (PZT 52/48) films are reported. Crack free random and highly (100) oriented PZT(52/48) films up to ∼ 7 μm thick were deposited using a sol-gel process on Pt (111)/Ti/SiO2/Si and Pt(100)/SiO2/Si substrates, respectively. The dielectric permittivity (at 1kHz) for the (100) oriented films was 980-1000, and for the random films ∼ 930-950. In both cases, tanä was less than 0.03. The remanent polarization (∼ 30 μC/cm2) of random PZT films was larger than that of (100) oriented PZT films. The transverse piezoelectric coefficient (d31(eff)) of PZT films was measured by the wafer flexure method. The d31(eff) coefficient of random PZT thick films (-80pC/N) was larger than that of (100) oriented films (-60pC/N) when poled at 80 kV/cm for 15 min.
We report on the performance of a planetary multi-wafer MOCVD reactor which handles 5 six inch wafers simultaneously. The reactor is combined with a liquid delivery system which mixes the liquid precursors from three different sources: 0.35 molar solutions of Ba(thd)2 and Sr(thd)2 and a 0.4 molar solution of Ti(O-i-Pr)2(thd)2. The microstructure and the film stress were investigated by X-ray diffraction and the composition of the films was determined by X-ray fluorescence analysis. As a direct consequence of the reactor design we obtain a high uniformity of the films over 6 inch wafers, as well as high efficiencies for the precursor incorporation. Film growth is discussed within a wide parameter field and the finally achieved electrical properties, e.g., permittivity, loss tangent, leakage current, are discussed in relation to the microstructural properties.
Due to its resistance to oxidation, TaSiN is a promising candidate as an electrically conductive barrier layer for integration of high permittivity oxides in advanced memory devices. In this study we report on the properties and the resistance to oxidation of TaSiN thin films deposited by reactive magnetron sputtering and processed by rapid thermal annealing (RTA) in 18O2 at 650°C. In order to determine the composition, RBS (Rutherford Backscattering Spectroscopy) and NRA (Nuclear Reaction Analysis) techniques have been used. 18O depth profile concentrations were measured after RTA using the narrow (fwhm=100eV) resonance at 151 keV in the nuclear reaction 18O(p,α)15N.
The Thermally Stimulated Depolarization Current (TSDC) and pyroelectric properties of the modified SBN ferroelectric ceramic system were studied for different lanthanum and titanium doping concentrations. The TSDC measurements show the pyroelectric peak for all compositions while a second smaller peak at higher temperature, possibly associated to induced vacancy-impurity dipoles, is also observed in all cases. The second peak contribution was experimentally and mathematically eliminated to determine the remanent polarization and pyroelectric coefficient, both associated only to permanent ferroelectric dipoles. The figures of merit for sensor devices are determined for all compositions and compared with those of other pyroelectric systems. The La0.03Sr0.255Ba0.7 Nb1.95Ti0.05O5.975 sample, in particular, has excellent pyroelectric response, making this material very suitable for pyroelectricity-derived applications.
We describe a method based on single molecule probing of acid concentration to measure the profiles of photogenerated acid patterns in chemically amplified resist films. We further present preliminary data which demonstrates the viability of this method.
We have successfully grown SrTiO3 films on LaAlO3 and MgO substrates up to 2” in diameter using the deposition technique of reactive coevaporation. We have explored a wide range of deposition temperatures, oxygen pocket pressures, and compositions in order to determine the optimal growth process window. X-ray diffraction analyses indicate that the process window for growth on MgO substrates is narrower than for LaAlO3 substrates. Dielectric property measurements show that samples near stoichiometry have higher tunability, but their peak loss tangents are also high (∼0.02). The slightly Sr-poor samples (46-48 at.%) show a reduced loss tangent (<0.01) while maintaining an acceptable tunability (∼50%) at an average electric field of 1.7 V/μm.
We present evidence that the microstructure of the metastable fluorite phase Pb2(Zr,Ti)2O6, which forms during the pyrolysis treatment of sol-gel PZT layers by homogeneous nucleation throughout the film, has a larger impact on orientation selection than has previously been realized. Elaborate TEM studies demonstrate that by varying the pyrolysis time, temperature and duration, the crystallinity of the transient fluorite phase can be greatly influenced. Pyrolysis at 350°C leads to the formation of a well crystallized fluorite phase with a cubic structure (Fd3m space group) and a= 10.5-10.6 Å. Rapid crystallization of the transient fluorite phase is attributed to the low oxygen partial pressure conditions, prevailing during burnoff of acetate groups originating from the lead starting compound. A possible connection between the fluorite formation kinetics and orientation selection in the layers is discussed.