Estimating moose population parameters from aerial surveys

Successful moose management depends on knowledge of population dynamics. The principal parameters required are size, rate of change, recruitment, sex composition, and mortality. Moose management in Alaska has been severely hampered by the lack of good estimates of these parameters, and unfortunately, this lack contributed to the decline of many Alaskan moose populations during the 1970s (e.g., Gasaway et al. 1983). The problems were: (1) population size not adequately estimated, (2) rapid rates of decline not acknowledged until populations were low, (3) meaningful recruitment rates were not available in the absence of good population estimates, and (4) calf and adult mortality rates were grossly underestimated. Frustration of moose managers working with inadequate data led to development of aerial survey procedures that yield minimally biased, sufficiently precise estimates of population parameters for most Alaskan moose management and research. This manual describes these procedures. Development of these procedures would have been impossible without the inspiration, support, advice, and criticism of many colleagues. We thank these colleagues for their contributions. Dale Haggstrom and Dave Kelleyhouse helped develop flight patterns, tested and improved early sampling designs, and as moose managers, put these procedures into routine use. Pilots Bill Lentsch and Pete Haggland were instrumental in developing and testing aerial surveying techniques. Their interest and dedication to improving moose management made them valuable allies. Statisticians Dana Thomas of the University of Alaska and W. Scott Overton of Oregon State University provided advice on variance approximations for the population estimator. Warren Ballard, Sterling Miller, SuzAnne Miller, Doug Larsen, and Wayne Kale tested procedures and provided valuable criticisms and suggestions. Jim Raymond initially programmed a portable calculator to make lengthy calculation simple, fast, and error-free. Angie Babcock, Lisa Ingalls, Vicky Leffingwell, and Laura McManus patiently typed several versions of this manual. John Coady and Oliver Burris provided continuous moral and financial support for a 3-year project that lasted 6 years. Joan Barnett, Rodney Boetje, Steven Peterson, and Wayne Regelin of the Alaska Department of Fish and Game provided helpful editorial suggestions in previous drafts. Finally, we thank referees David Anderson of the Utah Cooperative Wildlife Research Unit, Vincent Schultz of Washington State University, and James Peek, E. "Oz" Garton, and Mike Samuel of the University of Idaho whose comments and suggestions improved this manual. This project was funded by the Alaska Department of Fish and Game through Federal Aid in Wildlife Restoration Projects W-17-9 through W-22-1

Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver

<p>Abstract</p> <p>Background</p> <p>Microarray technology is a powerful and widely accepted experimental technique in molecular biology that allows studying genome wide transcriptional responses. However, experimental data usually contain potential sources of uncertainty and thus many experiments are now designed with repeated measurements to better assess such inherent variability. Many computational methods have been proposed to account for the variability in replicates. As yet, there is no model to output expression profiles accounting for replicate information so that a variety of computational models that take the expression profiles as the input data can explore this information without any modification.</p> <p>Results</p> <p>We propose a methodology which integrates replicate variability into expression profiles, to generate so-called 'true' expression profiles. The study addresses two issues: (i) develop a statistical model that can estimate 'true' expression profiles which are more robust than the average profile, and (ii) extend our previous micro-clustering which was designed specifically for clustering time-series expression data. The model utilizes a previously proposed error model and the concept of 'relative difference'. The clustering effectiveness is demonstrated through synthetic data where several methods are compared. We subsequently analyze <it>in vivo </it>rat data to elucidate circadian transcriptional dynamics as well as liver-specific corticosteroid induced changes in gene expression.</p> <p>Conclusions</p> <p>We have proposed a model which integrates the error information from repeated measurements into the expression profiles. Through numerous synthetic and real time-series data, we demonstrated the ability of the approach to improve the clustering performance and assist in the identification and selection of informative expression motifs.</p

Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures

<p>Abstract</p> <p>Background</p> <p>Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Nevertheless, even in a single tissue different methods of corticosteroid administration can induce different patterns of expression and regulatory control structures. Therefore, rich <it>in vivo </it>datasets of pharmacological time-series with two dosing regimens sampled from rat liver are examined for temporal patterns of changes in gene expression and their regulatory commonalities.</p> <p>Results</p> <p>The study addresses two issues, including (1) identifying significant transcriptional modules coupled with dynamic expression patterns and (2) predicting relevant common transcriptional controls to better understand the underlying mechanisms of corticosteroid adverse effects. Following the orientation of meta-analysis, an extended computational approach that explores the concept of agreement matrix from consensus clustering has been proposed with the aims of identifying gene clusters that share common expression patterns across multiple dosing regimens as well as handling challenges in the analysis of microarray data from heterogeneous sources, e.g. different platforms and time-grids in this study. Six significant transcriptional modules coupled with typical patterns of expression have been identified. Functional analysis reveals that virtually all enriched functions (gene ontologies, pathways) in these modules are shown to be related to metabolic processes, implying the importance of these modules in adverse effects under the administration of corticosteroids. Relevant putative transcriptional regulators (e.g. RXRF, FKHD, SP1F) are also predicted to provide another source of information towards better understanding the complexities of expression patterns and the underlying regulatory mechanisms of those modules.</p> <p>Conclusions</p> <p>We have proposed a framework to identify significant coexpressed clusters of genes across multiple conditions experimented from different microarray platforms, time-grids, and also tissues if applicable. Analysis on rich <it>in vivo </it>datasets of corticosteroid time-series yielded significant insights into the pharmacogenomic effects of corticosteroids, especially the relevance to metabolic side-effects. This has been illustrated through enriched metabolic functions in those transcriptional modules and the presence of GRE binding motifs in those enriched pathways, providing significant modules for further analysis on pharmacogenomic corticosteroid effects.</p

Parasitic Interference in Long Baseline Optical Interferometry: Requirements for Hot Jupiter-like Planet Detection

International audienceThe observable quantities in optical interferometry, which are the modulus and the phase of the complex visibility, may be corrupted by parasitic fringes superimposed on the genuine fringe pattern. These fringes are due to an interference phenomenon occurring from stray light effects inside an interferometric instrument. We developed an analytical approach to better understand this phenomenon when stray light causes cross talk between beams. We deduced that the parasitic interference significantly affects the interferometric phase and thus the associated observables including the differential phase and the closure phase. The amount of parasitic flux coupled to the piston between beams appears to be very influential in this degradation. For instance, considering a point-like source and a piston ranging from λ/500 to λ/5 in the L band (λ = 3.5 μm), a parasitic flux of about 1% of the total flux produces a parasitic phase reaching at most one-third of the intrinsic phase. The piston, which can have different origins (instrumental stability, atmospheric perturbations, etc.), thus amplifies the effect of parasitic interference. According to the specifications of piston correction in space or at ground level (respectively λ/500 ≈ 2 nm and λ/30 ≈ 100 nm), the detection of hot Jupiter-like planets, one of the most challenging aims for current ground-based interferometers, limits parasitic radiation to about 5% of the incident intensity. This was evaluated by considering different types of hot Jupiter synthetic spectra. Otherwise, if no fringe tracking is used, the detection of a typical hot Jupiter-like system with a solar-like star would admit a maximum level of parasitic intensity of 0.01% for piston errors equal to λ/15. If the fringe tracking specifications are not precisely observed, it thus appears that the allowed level of parasitic intensity dramatically decreases and may prevent the detection. In parallel, the calibration of the parasitic phase by a reference star, at this accuracy level, seems very difficult. Moreover, since parasitic phase is an object-dependent quantity, the use of a hypothetical phase abacus, directly giving the parasitic phase from a given parasitic flux level, is also impossible. Some instrumental solutions, implemented at the instrument design stage for limiting or preventing this parasitic interference, appear to be crucial and are presented in this paper

Circadian signatures in rat liver: from gene expression to pathways

<p>Abstract</p> <p>Background</p> <p>Circadian rhythms are 24 hour oscillations in many behavioural, physiological, cellular and molecular processes that are controlled by an endogenous clock which is entrained to environmental factors including light, food and stress. Transcriptional analyses of circadian patterns demonstrate that genes showing circadian rhythms are part of a wide variety of biological pathways.</p> <p>Pathway activity method can identify the significant pattern of the gene expression levels within a pathway. In this method, the overall gene expression levels are translated to a reduced form, pathway activity levels, via singular value decomposition (SVD). A given pathway represented by pathway activity levels can then be as analyzed using the same approaches used for analyzing gene expression levels. We propose to use pathway activity method across time to identify underlying circadian pattern of pathways.</p> <p>Results</p> <p>We used synthetic data to demonstrate that pathway activity analysis can evaluate the underlying circadian pattern within a pathway even when circadian patterns cannot be captured by the individual gene expression levels. In addition, we illustrated that pathway activity formulation should be coupled with a significance analysis to distinguish biologically significant information from random deviations. Next, we performed pathway activity level analysis on a rich time series of transcriptional profiling in rat liver. The over-represented five specific patterns of pathway activity levels, which cannot be explained by random event, exhibited circadian rhythms. The identification of the circadian signatures at the pathway level identified 78 pathways related to energy metabolism, amino acid metabolism, lipid metabolism and DNA replication and protein synthesis, which are biologically relevant in rat liver. Further, we observed tight coordination between cholesterol biosynthesis and bile acid biosynthesis as well as between folate biosynthesis, one carbon pool by folate and purine-pyrimidine metabolism. These coupled pathways are parts of a sequential reaction series where the product of one pathway is the substrate of another pathway.</p> <p>Conclusions</p> <p>Rather than assessing the importance of a single gene beforehand and map these genes onto pathways, we instead examined the orchestrated change within a pathway. Pathway activity level analysis could reveal the underlying circadian dynamics in the microarray data with an unsupervised approach and biologically relevant results were obtained.</p

Comparison of Pittsburgh compound B and florbetapir in cross-sectional and longitudinal studies.

IntroductionQuantitative in vivo measurement of brain amyloid burden is important for both research and clinical purposes. However, the existence of multiple imaging tracers presents challenges to the interpretation of such measurements. This study presents a direct comparison of Pittsburgh compound B-based and florbetapir-based amyloid imaging in the same participants from two independent cohorts using a crossover design.MethodsPittsburgh compound B and florbetapir amyloid PET imaging data from three different cohorts were analyzed using previously established pipelines to obtain global amyloid burden measurements. These measurements were converted to the Centiloid scale to allow fair comparison between the two tracers. The mean and inter-individual variability of the two tracers were compared using multivariate linear models both cross-sectionally and longitudinally.ResultsGlobal amyloid burden measured using the two tracers were strongly correlated in both cohorts. However, higher variability was observed when florbetapir was used as the imaging tracer. The variability may be partially caused by white matter signal as partial volume correction reduces the variability and improves the correlations between the two tracers. Amyloid burden measured using both tracers was found to be in association with clinical and psychometric measurements. Longitudinal comparison of the two tracers was also performed in similar but separate cohorts whose baseline amyloid load was considered elevated (i.e., amyloid positive). No significant difference was detected in the average annualized rate of change measurements made with these two tracers.DiscussionAlthough the amyloid burden measurements were quite similar using these two tracers as expected, difference was observable even after conversion into the Centiloid scale. Further investigation is warranted to identify optimal strategies to harmonize amyloid imaging data acquired using different tracers

The Influence of Molecular Adsorption on Elongating Gold Nanowires

Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remains relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains and helical structures possessing mechanical stability in excess of what we observe in vacuum. Conversely, we find that a molecular species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry