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PubMed2003

An easy field method for estimating the abundance of culicid larval instars.

A new method is proposed that avoids manual counting of mosquito larvae in order to estimate larval abundance in the field. This method is based on the visual comparison between abundance, in a standardized sampling tray (called an abacus), with 5 (abacus 5) or 10 (abacus 10) diagrammatically prepared abundance classes. Accuracy under laboratory and field conditions and individual bias have been evaluated and both abaci provide a reliable estimation of abundance in both conditions. There is no individual bias, whether people are familiar or not with its use. They could also be used for a quick estimation of larval treatment effectiveness, for the study of population dynamics and spatial distribution.

Animals↗

PubMed2006

ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation.

A profile likelihood algorithm is proposed for quantitative shotgun proteomics to infer the abundance ratios of proteins from the abundance ratios of isotopically labeled peptides derived from proteolysis. Previously, we have shown that the estimation variability and bias of peptide abundance ratios can be predicted from their profile signal-to-noise ratios. Given multiple quantified peptides for a protein, the profile likelihood algorithm probabilistically weighs the peptide abundance ratios by their inferred estimation variability, accounts for their expected estimation bias, and suppresses contribution from outliers. This algorithm yields maximum likelihood point estimation and profile likelihood confidence interval estimation of protein abundance ratios. This point estimator is more accurate than an estimator based on the average of peptide abundance ratios. The confidence interval estimation provides an "error bar" for each protein abundance ratio that reflects its estimation precision and statistical uncertainty. The accuracy of the point estimation and the precision and confidence level of the interval estimation were benchmarked with standard mixtures of isotopically labeled proteomes. The profile likelihood algorithm was integrated into a quantitative proteomics program, called ProRata, freely available at www.MSProRata.org.

Algorithms↗

PubMed1997

Use of feces to estimate isotopic abundance in doubly labeled water studies in reindeer in summer and winter.

The reliance on samples of blood or urine to estimate isotopic abundance in studies of energy metabolism using the doubly labeled water method has restricted application of the technique to animals that are either tame or easy to catch. This is generally not the case with large, free-ranging wild mammals. The use of feces as a source of body water in which to measure the concentration of isotopic markers was investigated in four female reindeer in summer and in winter. (2)H2O and H2(18)O were injected to approximately 160 parts per million excess. Samples of plasma and feces were then collected simultaneously for up to 456 h. Both isotopes were equilibrated with body water at 8 h postdose. There were no significant differences by animal between dilution spaces, rate constants, rates of CO2 production, and total energy expenditure (TEE) calculated based on samples of plasma or feces in any trial. Mean TEE was 3.557 W/kg (SD 0.907, n = 4) in summer and 1.865 W/kg (SD 0.166, n = 4) in winter.

Animals↗

PubMed1986

A review of estimating animal abundance.

During the past 5 years there have been a number of important developments in the estimation of animal abundance and related parameters such as survival rates. Many of the new techniques need to be more widely publicized as they supplant previous methods. The aim of this paper is to review this literature and suggest further avenues for research.

Animals↗

PubMed1997

Metazoan parasites of sika deer from east Hokkaido, Japan and ecological analyses of their abomasal nematodes.

Metazoan parasites of 50 sika deer (Cervus nippon yezoensis) collected in March 1991 in the Ashoro District in east Hokkaido, Japan, were evaluated. Ten species of helminths and three species of ectoparasites were obtained. Estimated abundance of males of two species of abomasal nematodes, Spiculopteragia houdemeri and Rinadia andreevae, were positively correlated with each other, and were overdispersed; S. houdemeri followed Poisson's and R. andreevae followed a negative binomial distribution. No significant relationship was detected between the estimated abundance of males of these two nematode species and nutritional condition of the hosts. Using a general linear model, the fourth-root transformed estimated abundance of male S. houndemeri was influenced by the main effects of host sex and age. This phenomenon was attributable to the ecological and behavioral features of the deer. The low diversity of the abomasal nematode community was regarded as the result of the extinction of some species of nematodes on Hokkaido Island.

Abomasum↗

PubMed2000

Methodology for estimating the abundance of rare animals: seabird nesting on north east Herald Cay.

We discuss the problem of estimating the number of nests of different species of seabirds on North East Herald Cay based on the data from a 1996 survey of quadrats along transects and data from similar past surveys. We consider three approaches based on different plausible models, namely a conditional negative binomial model that allows for additional zeroes in the data, a weighting approach (based on a heteroscedastic regression model), and a transform-both-sides regression approach. We find that the conditional negative binomial approach and a linear regression approach work well but that the transform-both-sides approach should not be used. We apply the conditional negative binomial and linear regression approaches with poststratification based on data quality and availability to estimate the number of frigatebird nests on North East Herald Cay.

Animals↗

PubMed2001

Rapid PCR-single-strand conformation polymorphism method to differentiate and estimate relative abundance of Pneumocystis carinii special forms infecting rats.

A rapid method that uses PCR-single-strand conformation polymorphism analysis of the intron of the nuclear 26S rRNA gene was shown to differentiate the two Pneumocystis carinii special forms that infect rats, P. carinii f. sp. carinii and P. carinii f. sp. ratti. The method also provides a means for estimation of the relative abundance of the two special forms in the case of a coinfected rat. The results suggest that the method described will help to further standardize the immunosuppressed rat model of P. carinii infection and, thus, contribute to a better understanding of P. carinii infection in humans.

Animals↗

PubMed1990

Heterogeneity of dystrophin expression in patients with Duchenne and Becker muscular dystrophy.

This report documents the results of an integrated biochemical and immunocytochemical investigation into the expression of dystrophin (the protein product of the Duchenne muscular dystrophy gene) in muscle biopsies from 226 patients. It is the first study in which dystrophin has been analysed on blots and on tissue sections in such a large number of patients using the same (monoclonal) antibody. The 140 patients with Xp21 muscular dystrophy who were included in this study represent a continuous spectrum of disease severity and this range was reflected in the heterogeneity of dystrophin expression which was observed with respect to abundance, size and the pattern of tissue localisation. Approximately 40% of biopsies obtained from patients diagnosed as having Duchenne muscular dystrophy (DMD) contained isolated clearly positive fibres and a further 20% had very weak labelling on a large number of fibres. Biopsies from patients with Becker muscular dystrophy (BMD) showed labelling patterns which varied from weak labelling on the majority of fibres to clear labelling on all fibres. Typically, however, there was inter- and intra-fibre variation in labelling intensity. Approximately 85% of the 52 BMD and 54 DMD patients who had unequivocal labelling on blots demonstrated a protein of abnormal size. The remaining 15% had a protein of normal size but reduced abundance. Overall, the estimated abundance of dystrophin correlated well with clinical assessments of the disease severity expressed in patients. We conclude that dystrophin analysis is an essential and dependable technique for the differential diagnosis of patients with Xp21 muscular dystrophy.

Adolescent↗

PubMed2004

Processing deep-sea particle-rich water samples for fluorescence in situ hybridization: consideration of storage effects, preservation, and sonication.

Particles are often regarded as microniches of enhanced microbial production and activities in the pelagic ocean and are vehicles of vertical material transport from the euphotic zone to the deep sea. Fluorescence in situ hybridization (FISH) can be a useful tool to study the microbial community structures associated with these particles, and thus their ecological significance, yet an appropriate protocol for processing deep-sea particle-rich water samples is lacking. Some sample processing considerations are discussed in the present study, and different combinations of existing procedures for preservation, size fractionation sequential filtration, and sonication were tested in conjunction with FISH. Results from this study show that water samples should be filtered and processed within no more than 10 to 12 h after collection, or else preservation is necessary. The commonly used prefiltration formaldehyde fixation was shown to be inadequate for the rRNA targeted by FISH. However, prefiltration formaldehyde fixation followed by immediate freezing and postfiltration paraformaldehyde fixation yielded highly consistent cell abundance estimates even after 96 days or potentially longer storage. Size fractionation sequential filtration and sonication together enhanced cell abundance estimates by severalfold. Size fractionation sequential filtration effectively separated particle-associated microbial communities from their free-living counterparts, while sonication detached cells from particles or aggregates for more-accurate cell counting using epifluorescence microscopy. Optimization in sonication time is recommended for different specific types of samples. These tested and optimized procedures can be incorporated into a FISH protocol for sampling in deep-sea particle-rich waters.

Bacteria↗

PubMed2002

Integrating mark-recapture-recovery and census data to estimate animal abundance and demographic parameters.

In studies of wild animals, one frequently encounters both census and mark-recapture-recovery data. We show how a state-space model for census data in combination with the usual multinomial-based models for ring-recovery data provide estimates of productivity not available from either type of data alone. The approach is illustrated on two British bird species. For the lapwing, we calibrate how its recent decline could be due to a decrease in productivity. For the heron, there is no evidence for a decline in productivity, and the combined analysis increases significantly the strength of logistic regressions of survival on winter severity.

Animals↗

PubMed2001

Model-supported estimation of mortality rates in Baltic cod (Gadus morhua callarias L.) larvae: the varying impact of 'critical periods'.

BACKGROUND: Changes in the survival-rate during the larval phase may strongly influence the recruitment level in marine fish species. During the larval phase different 'critical periods' are discussed, e.g. the hatching period and the first-feeding period. No such information was available for the Baltic cod stock, a commercially important stock showing reproduction failure during the last years. We calculated field-based mortality rates for larval Baltic cod during these phases using basin-wide abundance estimates from two consecutive surveys. Survey information was corrected by three dimensional hydrodynamic model runs. RESULTS: The corrections applied for transport were of variable impact, depending on the prevailing circulation patterns. Especially at high wind forcing scenarios, abundance estimates have the potential to be biased without accounting for transport processes. In May 1988 mortality between hatch and first feeding amounted to approximately 20% per day. Mortality rates during the onset of feeding were considerably lower with only 7% per day. In August 1991 the situation was vice versa: Extremely low mortality rates of 0.08% per day were calculated between hatch and first feeding, while the period between the onset of feeding to the state of an established feeder was more critical with mortality rates of 22% per day. CONCLUSIONS: Mortality rates during the different proposed 'critical periods' were found to be highly variable. Survival rates of Baltic cod are not only influenced by a single 'critical period', but can be limited at different points during the larval phase, depending on several biotic and abiotic factors.

Animals↗

PubMed2005

Comparison of multifrequency acoustic and in situ measurements of zooplankton abundances in Knight Inlet, British Columbia.

An investigation of midwater zooplankton aggregations in a coastal fjord was conducted in November 2002. This study focused on quantitative comparisons between a calibrated, three-frequency (38, 120, and 200 kHz) vessel-based echo-sounder, a multinet towed zooplankton sampler (BIONESS), and a high-resolution underwater camera (ZOOVIS). Daytime layers of euphausiids and amphipods near 70-90-m depth were observed in lower parts of the inlet, especially concentrated by tidal flows around a sill. Quantitative backscatter measurements of euphausiids and amphipods, combined with in situ size and abundance estimates, and using an assumed tilt-angle distribution, were in agreement with averaged fluid-cylinder scattering models produced by Stanton and Chu [ICES J. Mar. Sci. 57, 793-807, (2000)]. Acoustic measurements of physonect siphonophores in the upper inlet were found to have a strong 38-kHz scattering strength, in agreement with a damped bubble scattering model using a diameter of 0.4 mm. In relatively dense euphausiid layers, ZOOVIS abundance estimates were found to be a factor of 2 to 4 higher than the acoustic estimates, potentially due to deviations from assumed euphausiid orientation. Nocturnal near-surface euphausiid scattering exhibited a strong (15 dB) and rapid (seconds) sensitivity to vessel lights, interpreted as due to changing animal orientation.

Journal Article↗

PubMedDate not supplied

Epidemiological study on porcine circovirus type 2 (PCV2) infection in the European wild boar (Sus scrofa).

Porcine circovirus type 2 (PCV2) is considered as the causative agent of postweaning multisystemic wasting syndrome (PMWS) in domestic pigs, where the virus is ubiquitous as evidenced by serological surveys. We present the results of the first nationwide sero-survey on the presence of PCV2 antibodies in European wild boars, and report the first PMWS case in a wild boar from Spain. Sera from 656 hunter harvested wild boars from 45 different geographical sites and 22 additional imported animals were analysed by means of an immunoperoxidase monolayer assay (IPMA). We also examined the tissues from 55 healthy and one diseased wild boars for the presence of PCV2 nucleic acid and PMWS lesions by in situ hybridisation and histopathology, respectively. Additionally, abundance estimates of wild boars and field interviews were carried out on 30 sampling sites. The prevalence of medium to high PCV2 serological titres among the examined wild boars was 47.89 +/- 1.9%. Seropositive wild boars appeared in all but one of the geographical regions analysed. Seroprevalence and titre of PCV2 antibodies were closely related to the management of the wild boar populations. Wild boars from intensively managed, farm-like populations had higher prevalence than wild boars living in more natural situations. The effect of wild boar abundance and management on PCV2 antibody prevalence was further evidenced by the high correlation existing between the relative abundance estimates of animals and the percentage of wild boars with medium to high levels of PCV2 antibodies. PCV2 nucleic acid was detected in the tissues of three wild boars. One of these was diagnosed as PMWS. The results, in addition to information on piglet mortalities, suggest a potential role of PMWS in piglet mortality in intensively managed wild boar populations.

Animals↗

PubMed2004

Effect of aggregation of horn fly populations within cattle herds and consequences for sampling to obtain unbiased estimates of abundance.

Reanalysis of counts of horn fly, Hematobia irritans (L.), obtained from a variety of cattle herds indicated that aggregation of the flies within herds decreased as mean fly density increased. Aggregation was also related to the proportion of fly-resistant and fly-susceptible cattle in a herd. Herds were grouped according to their degree of horn fly aggregation. Low aggregation herds included larger framed Angus, Horned Hereford, Polled Hereford, and Red Poll breeds. Moderate aggregation occurred with Brahman, Charolais, small-framed Angus, mixed cows, and Hereford x Charolais cross. High aggregation occurred with Chianina and mixed herds. Relationships between the sample means and variances varied among aggregation groups. A resampling approach was used to determine the influence of random sampling of a herd on the proportion of horn fly population estimates within fixed percentages of the true mean. The proportion of sample means within +/- 5, 10, 15, and 20% of the true means varied with the proportion of the herd sampled, the mean and variance of fly density, and herd size. Recommendations for obtaining sample size to estimate fly density within a fixed percentage of the true mean are given.

Alberta↗

PubMed2006

Impact of trap elevation on estimates of abundance, parity rates, and body size of Culex pipiens and Culex restuans (Diptera: Culicidae).

Trapping success, abundance, parity rate, and body size indices of Culex pipiens (L.) and Culex restuans Theobald, important vectors of West Nile virus (family Flaviviridae, genus Flavivirus, WNV), were determined for specimens captured from both ground level (approximately 1-m) and elevated (approximately 6- to 7-m) CO2-baited CDC miniature light traps. Mosquitoes were collected from six study sites in Albany County, New York, from mid-May to mid-October 2004. There was no significant difference in abundance or mean parity for either Cx. pipiens or Cx. restuans between the elevated and the ground-level traps. Mosquitoes collected in elevated traps tended to be larger than mosquitoes collected at ground level. Elevated traps captured significantly fewer mosquitoes per trap-night than did ground traps, but a greater proportion of those captured were Culex spp. Therefore, elevated traps more efficiently captured Cx. pipiens and Cx. restuans with similar reproductive status and body size and reduced the time necessary to sort and identify collections. These findings may be beneficial to researchers or surveillance programs focusing on Cx. pipiens or Cx. restuans.

Animals↗

PubMed2006

Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics.

The abundance ratio between the light and heavy isotopologues of an isotopically labeled peptide can be estimated from their selected ion chromatograms. However, quantitative shotgun proteomics measurements yield selected ion chromatograms at highly variable signal-to-noise ratios for tens of thousands of peptides. This challenge calls for algorithms that not only robustly estimate the abundance ratios of different peptides but also rigorously score each abundance ratio for the expected estimation bias and variability. Scoring of the abundance ratios, much like scoring of sequence assignment for tandem mass spectra by peptide identification algorithms, enables filtering of unreliable peptide quantification and use of formal statistical inference in the subsequent protein abundance ratio estimation. In this study, a parallel paired covariance algorithm is used for robust peak detection in selected ion chromatograms. A peak profile is generated for each peptide, which is a scatterplot of ion intensities measured for the two isotopologues within their chromatographic peaks. Principal component analysis of the peak profile is proposed to estimate the peptide abundance ratio and to score the estimation with the signal-to-noise ratio of the peak profile (profile signal-to-noise ratio). We demonstrate that the profile signal-to-noise ratio is inversely correlated with the variability and bias of peptide abundance ratio estimation.

Algorithms↗

PubMed2004

Estimation of fish abundance indices based on scientific research trawl surveys.

The fish abundance index over an ocean region is defined here to be the integral of expected catch per unit effort (CPUE), approximated by the sum of expected CPUE over grid squares. When trawl surveys are done within grid squares selected according to a probability sampling design, several other sources of variation such as the fish population dynamics and the catching process are also involved. In such situations model-assisted methods for estimating abundance, assessed under both design and model perspectives, have some advantages over purely design-based methods such as the Horvitz-Thompson (HT) estimator or purely model-based prediction approaches. This article develops model-assisted empirical likelihood (EL) methods via loglinear regression and nonparametric smoothing. The methods are applied to grid surveys of the Grand Bank region carried out annually by Fishery Products International from 1996 through 2002. The HT and EL methods produce similar point estimates of abundance indices. Simulation results, however, indicate that the EL estimator under local linear smoothing is associated with smaller standard errors.

Animals↗

PubMed2005

Multi-stage sampling for large scale natural resources surveys: a case study of rice and waterfowl.

Large-scale sample surveys to estimate abundance and distribution of organisms and their habitats are increasingly important in ecological studies. Multi-stage sampling (MSS) is especially suited to large-scale surveys because of the natural clustering of resources. To illustrate an application, we: (1) designed a stratified MSS to estimate late autumn abundance (kg/ha) of rice seeds in harvested fields as food for waterfowl wintering in the Mississippi Alluvial Valley (MAV); (2) investigated options for improving the MSS design; and (3) compared statistical and cost efficiency of MSS to simulated simple random sampling (SRS). During 2000-2002, we sampled 25-35 landowners per year, 1 or 2 fields per landowner per year, and measured seed mass in 10 soil cores collected within each field. Analysis of variance components and costs for each stage of the survey design indicated that collecting 10 soil cores per field was near the optimum of 11-15, whereas sampling >1 field per landowner provided few benefits because data from fields within landowners were highly correlated. Coefficients of variation (CV) of annual estimates of rice abundance ranged from 0.23 to 0.31 and were limited by variation among landowners and the number of landowners sampled. Design effects representing the statistical efficiency of MSS relative to SRS ranged from 3.2 to 9.0, and simulations indicated SRS would cost, on average, 1.4 times more than MSS because clustering of sample units in MSS decreased travel costs. We recommend MSS as a potential sampling strategy for large-scale natural resource surveys and specifically for future surveys of the availability of rice as food for waterfowl in the MAV and similar areas.

Animals↗