A line transect density index for wolf spiders (Pardosa spp.), and a note on the applicability of catch per unit effort methods to entomological studies

Abstract. 1. A line transect density index for small wolf spiders is described and shown by means of regression analysis to provide adequate accuracy and excellent reproducibility.
2. A review of the literature discloses numerous regression and replication studies of other catch per unit effort methods possessing equal precision and reliability.
3. Such methods, when used judiciously, can provide accuracy and reproducibility as good as those obtainable using the statistical methods now in wider use, and deserve serious consideration in many kinds of sampling situations.     

Morphometry of the heterogenic distribution of tissue components

If the structure elements are distributed unhomogeneously, it is possible that morphometric measurements of single sections lead to data which are in less agreement with the true relations in an organ. In such cases, systematic sampling should be better than random sampling and often a very few sections with approximately equal distances are sufficient for measurements with an acceptable accuracy. This was demonstrated in examples of thyroid and mammary glands, cirrhotic livers and heart biopsies.     

Degrees of divergence in the E. coli genome from correlations between dinucleotide, trinucleotide and codon frequencies

Oligonucleotide and codon frequencies have been determined in published sequences of E. coli DNA totaling 103,100bp with 18,459 reading frame trinucleotides; corresponding to 2.5% of the total genome. Dinucleotide frequencies are in excellent agreement with those determined by nearest neighbor chemical analysis, indicating the computer count of a limited sampling to be a good representation of the overall frequencies in total genomic DNA. The distinctive nonrandom codon pattern is found to be uniformly distributed and contributes to a distinctive nonrandom oligonucleotide pattern; enabling correlations between frequency levels to be extended beyond reading frame sequences. Correlation analysis indicates a surprisingly high degree of correlation everywhere in the genome. Coefficients of correlation between oligonucleotide frequencies overall and those in specific segments vary as follows: primary strands of individual coding sequences greater than 0.9 greater than lambda DNA greater than noncoding, non-RNA greater than phi X174 DNA greater than complementary strands greater than RNA genes congruent to 0.6 greater than transposon-insertion elements greater than T7DNA much greater than eukaryotic sequences congruent to 0. It is concluded that this high degree of oligonucleotide and codon correspondence in E. coli reflects the widespread distribution of remnants of an early and slowly changing codon pattern that has been continually dispersed by duplication-divergence processes, leading to the present genome.     

Testing methods to estimate abundance of Magellanic Penguins Spheniscus magellanicus

Capsule Using simulations in a geographical information system our results showed that systematic sampling with quadrats was the most accurate, precise and cost-effective method to survey Magellanic Penguin colonies.

Aims To determine which sampling method gives better estimations of penguin abundance.

Methods A virtual colony was generated deriving spatial parameters from a real survey and applying Kriging interpolation. Three sampling methods were then applied on this virtual colony: random sampling with quadrats; systematic sampling with quadrats; systematic sampling with fixed-width transects. The estimated abundance for each trial was compared to the abundance of the virtual colony to have a measure of accuracy and precision.

Results Systematic sampling with quadrats estimated penguin abundance better than random or systematic sampling with transects since it achieved 100% accuracy and great precision after sampling only 2.1% of the virtual colony.

Conclusion The use of a simulated colony allowed the comparison of several sampling methods traditionally used in Magellanic Penguin surveys. The results of this study are important in order to standardize sampling protocols for Magellanic Penguins and to have more comparable estimations to detect trends over time. Also, the methodological approach used here could be used to assess sampling methods for other colonial bird species.     

A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

Chronograms from molecular dating are increasingly being used to infer rates of diversification and their change over time. A major limitation in such analyses is incomplete species sampling that moreover is usually nonrandom. While the widely used γ statistic with the Monte Carlo constant-rates test or the birth-death likelihood analysis with the δ AICrc test statistic are appropriate for comparing the fit of different diversification models in phylogenies with random species sampling, no objective automated method has been developed for fitting diversification models to nonrandomly sampled phylogenies. Here, we introduce a novel approach, CorSiM, which involves simulating missing splits under a constant rate birth-death model and allows the user to specify whether species sampling in the phylogeny being analyzed is random or nonrandom. The completed trees can be used in subsequent model-fitting analyses. This is fundamentally different from previous diversification rate estimation methods, which were based on null distributions derived from the incomplete trees. CorSiM is automated in an R package and can easily be applied to large data sets. We illustrate the approach in two Araceae clades, one with a random species sampling of 52% and one with a nonrandom sampling of 55%. In the latter clade, the CorSiM approach detects and quantifies an increase in diversification rate, whereas classic approaches prefer a constant rate model; in the former clade, results do not differ among methods (as indeed expected since the classic approaches are valid only for randomly sampled phylogenies). The CorSiM method greatly reduces the type I error in diversification analysis, but type II error remains a methodological problem.     

A new optoelectronic measuring device for assessment of leg circumference in comparison with manual measurement]

For compression treatment to be effective in patients with chronic venous insufficiency, it is vital that leg circumference be measured accurately. If compression stockings are custom fit and appropriate for the medical indications, patient compliance will be high. Exact measurements of circumference and length are prerequisites for a good fit. The aim of the present study was to compare an opto-electronic device for the contact-free measurement of calf circumference with the conventional manual method using a tape measure. We investigated the differences between the results obtained with the two methods, and also their reproducibility. Circumferences were measured at defined heights on an anatomically shaped non-yielding leg model and on the leg of a healthy volunteer by 10 different experimenters both with the tape measure and with the opto-electronic device. The calf circumferences measured manually with the tape measure varied significantly more than those measured opto-electronically, both in the leg model and in the leg of the volunteer. A systematic error in the opto-electronic method appears unlikely, since the manual measurements on the leg model were both larger and smaller than those obtained with the opto-electronic device. Reproducibility was exceptionally high with the opto-electronic device (standard deviation 0.11-0.42 cm). The opto-electronic method yields rapid accurate measurements of circumference with excellent intra- and inter-operator reproducibility.     

Flow cytometry and FISH to measure the average length of telomeres (flow FISH)

Telomeres have emerged as crucial cellular elements in aging and various diseases including cancer. To measure the average length of telomere repeats in cells, we describe our protocols that use fluorescent in situ hybridization (FISH) with labeled peptide nucleic acid (PNA) probes specific for telomere repeats in combination with fluorescence measurements by flow cytometry (flow FISH). Flow FISH analysis can be performed using commercially available flow cytometers, and has the unique advantage over other methods for measuring telomere length of providing multi-parameter information on the length of telomere repeats in thousands of individual cells. The accuracy and reproducibility of the measurements is augmented by the automation of most pipetting (aspiration and dispensing) steps, and by including an internal standard (control cells) with a known telomere length in every tube. The basic protocol for the analysis of nucleated blood cells from 22 different individuals takes about 12 h spread over 2-3 days.     

A computer program to simulate multilocus genotype data with spatially autocorrelated allele frequencies

Many models for inference of population genetic parameters are based on the assumption that the data set at hand consists of groups displaying within-group Hardy-Weinberg equilibrium at individual loci and linkage equilibrium between loci. This assumption is commonly violated by the presence of within-group spatial structure arising from nonrandom mating of individuals due to isolation by distance (IBD). This paper proposes a model and simulation method implemented in a computer program to flexibly simulate data displaying such patterns. The program permits displaying of smooth spatial variations of allele frequencies due to IBD and more abrupt variations due to presence of strong barriers to gene flow. It is useful in assessing performance of various statistical inference methods and in designing spatial sampling schemes. This is shown by a simulation study aimed at assessing the extent to which IBD patterns affect accuracy of cluster inferences performed in models assuming panmixia. The program is also used to study the effects of spatial sampling scheme (e.g. sampling individuals in clumps or uniformly across the spatial domain). The accuracy of such inferences is assessed in terms of number of inferred populations, assignment of individuals to populations and location of borders between populations. The effect of spatial sampling was weak while the effect of IBD may be substantial, leading to the inference of spurious populations, especially when IBD was strong with respect to the size of the sampling domain. The model and program are new and have been embedded in the R package Geneland, for user convenience and compliance with existing data formats.     

Fluorescence spectroscopy as a tool for monitoring solubility and aggregation behavior of beta-lactoglobulin after heat treatment

Denaturation and aggregation of whey proteins are of interest to the food and pharmaceutical industry due to the importance of final structure in functionality, impact on food texture, and the chemical stability of the final product. In this study, we demonstrate the potential of fluorescence spectrometry combined with multivariate chemometric methods for quantifying solubility and aggregation behavior of beta-lactoglobulin (beta-LG); a major whey protein and a frequent food ingredient. Heat-induced aggregation of beta-LG was studied under different conditions including pH, temperature and heating durations. Results showed very good agreement between the fluorescence-based predictions and measurements obtained by HPLC and gravimetric analysis regardless of the conditions. Standard normal variate (SNV), a signal preprocessing and filtering tool, was found to enhance the predictive accuracy and robustness of the fluorescence-based model.     

Cerebral blood flow in acute mountain sickness

Changes in cerebral blood flow (CBF) were measured using the radioactive xenon technique and were related to the development of acute mountain sickness (AMS). In 12 subjects, ascending from 150 to 3,475 m, CBF was 24% increased at 24 h [45.1 to 55.9 initial slope index (ISI) units] and 4% increased at 6 days (47.1 ISI units). Four subjects had similar increases of CBF when ascending to 3,200 m 3 mo later, indicating the reproducibility of the measurements. In nine subjects, ascending from 3,200 to 4,785-5,430 m, CBF increased to 76.4 ISI units, 53% above estimated sea-level values. CBF and increases in CBF were similar in subjects with or without AMS. In six subjects, CBF was measured before and after therapeutic intervention. At 2 h CBF increased 22% (71.3 to 87.3 ISI units) above pretreatment values in three subjects given 1.5 g acetazolamide, while three subjects given placebo showed no change. Symptoms remained unaltered in all subjects during the 2 h of the study. Overall, the results indicated that increases in CBF were similar in subjects with or without AMS while acetazolamide-provoked increases of CBF in AMS subjects caused no acute change in symptoms. Alterations in CBF cannot be directly implicated in the pathogenesis of AMS.     

Elemental analysis of herbal preparations for traditional medicines by neutron activation analysis with the k0 standardization method

Medicinal herb preparations prescribed for specific treatment purposes were purchased from markets and were analyzed by instrumental neutron activation analysis withk ₀ standardization. Then, 500–700 mg of each sample was pelletized under a pressure of six tones and irradiated together with monitors for a and neutron flux ratio determinations for about 6 h in a thermal flux of 2.29 x 10¹² n/cm²/s. The accuracy of the method was established by analyzing standard reference materials. Twenty-nine elements, Ag, As, Au, Ba, Br, Ca, Ce, Co, Cr, Cs, Eu, Fe, Hf, K, La, Mn, Mo, Na, Rb, Sb, Sc, Se, Sm, Sr, Th, U, Yb, and Zn, were measured in all the samples, and Hg was detected in some samples, with good accuracy and reproducibility. The concentration of elements determined was found to vary depending on the composition of the herbs used. Although the trend linking the element of the medicinal plants to its curative abilities could not be clearly determined, this study showed that the toxic elements found in the samples were below the levels prescribed by health regulations. Nevertheless, such data are important to understand the pharmacological action and the exact mechanisms of action and formation of active constituents for each medicinal plant and to decide the dosage of the herbs used in the final formulation.     

Transect sampling to enhance efficiency of corn rootworm (Coleoptera: Chrysomelidae) monitoring in corn

Crop monitoring for adult corn rootworms, Diabrotica virgifera virgifera LeConte and Diabrotica barberi Smith and Lawrence, remains the best means to assess fields at risk from this pest if replanted to corn, Zea mays (L.). Improvements in sampling methodology, including the development of a sequential sampling plan, have reduced the minimum sampling time required to make a management decision to 20 min or less per field per visit. However, many growers and crop consultants still find this time commitment a constraint to repeated scouting. A common currently used sampling method involves systematically covering most of the field following a "W" pattern. The feasibility of replacing the current sampling pattern with a simpler and less time-consuming transect (straight line) pattern was assessed. When sampling methods were compared, computer simulations demonstrated that treatment decisions based on transect sampling would have an acceptably low error rate averaging 10% over a range of realistic corn rootworm densities (0-2 adults per plant). This error rate represented a decrease in accuracy of <1% compared with systematic sampling. Field trials using transect, systematic, and random sampling in each field were used to compare the categorization of adult corn rootworm densities into "above" or "below" threshold with a sequential sampling plan. Efficiency measured in time to reach a decision, number of corn plants evaluated, and time divided by plants observed were compared between sampling methods. The three methods did not differ significantly in the number of plants evaluated or in the categorization of corn rootworm populations. Transect sampling resulted in a significantly shorter time divided by plants observed (38 s), than either systematic (78 s), or random sampling methods (166 s). Based on these results transect sampling reduces sampling time 51% compared with systematic sampling and thus could be used to reduce total sampling times substantially.     

Blood flow in exercising muscles by xenon clearance and by microsphere trapping

The accuracy of muscle blood flow measurement by the 133Xe clearance method (QXe) was assessed against direct venous outflow (Qv) and microsphere trapping flow (Q mu) determinations in isolated perfused dog gastrocnemius both at rest and during graded stimulation [O2 consumption (VO2) up to 12 ml X 100 g-1 X min-1] and in the gastrocnemius, vastus lateralis, and triceps of intact dogs at rest and while running on a treadmill at varied speeds up to maximum VO2. In 29 measurements performed in 11 isolated muscles, Q mu was in good agreement with Qv at rest and at all stimulation levels (Q mu/Qv = 1.0; r = 0.98). 133Xe clearance yielded much lower blood flows than the venous outflow and the microsphere trapping methods. In 43 measurements in 11 muscles, the mean QXe/Qv ratio was 0.57 +/- 0.03 (SE), independent of blood flow. Similarly, in 65 measurements in 2 intact dogs, the mean QXe/Q mu ratio in all tested muscles was 0.49 +/- 0.02 (SE), independent of blood flow. These results show that the 133Xe clearance method considerably underestimates blood flow in dog muscles.     

Radionuclide plethysmography for noninvasive evaluation of peripheral arterial blood flow

We validated a noninvasive radionuclide plethysmography technique to evaluate peripheral arterial blood flow during reactive hyperemia. This method, based on the measurement of blood volume variations during repetitive venous occlusions, was compared with strain-gauge venous impedance plethysmography. The technique uses 99mTc-labeled autologous red blood cells scintigraphy to determine the rate of change of forearm scintigraphic counts during venous occlusion. Thirteen subjects were simultaneously evaluated with radionuclide and impedance plethysmography. Six baseline flow measurements were performed to evaluate the reproducibility of each method. Twenty-seven serial measurements were then made to evaluate flow variation during forearm reactive hyperemia. After 30 min of recovery, resting forearm blood flows were again evaluated. Impedance and radionuclide methods showed excellent reproducibility with intraclass correlation coefficients of 0.96 and 0.93, respectively. There was also good correlation of flows between both methods during reactive hyperemia (r = 0.87). Resting flows at 30 min after reactive hyperemia were slightly lower than at baseline with both methods. We conclude that radionuclide plethysmography could be used for the noninvasive evaluation of forearm blood flow and its dynamic variations during reactive hyperemia.     

Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation.

The human androgen-receptor gene (HUMARA; GenBank) contains a highly polymorphic trinucleotide repeat in the first exon. We have found that the methylation of HpaII and HhaI sites less than 100 bp away from this polymorphic short tandem repeat (STR) correlates with X inactivation. The close proximity of the restriction-enzyme sites to the STR allows the development of a PCR assay that distinguishes between the maternal and paternal alleles and identifies their methylation status. The accuracy of this assay was tested on (a) DNA from hamster/human hybrid cell lines containing either an active or inactive human X chromosome; (b) DNA from normal males and females; and (c) DNA from females showing nonrandom patterns of X inactivation. Data obtained using this assay correlated substantially with those obtained using the PGK, HPRT, and M27 beta probes, which detect X inactivation patterns by Southern blot analysis. In order to demonstrate one application of this assay, we examined X inactivation patterns in the B lymphocytes of potential and obligate carriers of X-linked agammaglobulinemia.     

Neutron activation analysis: A powerful tool for assay of rare-earth elements in terrestrial materials

Neutron activation analysis methods for determination of rare-earth elements in different matrices have been developed at the University of Pavia using the 250 Kw TRIGA Mark II reactor. A critical review of both instrumental and destructive methods is presented, as well as the indication of the best working conditions for irradiation, counting and radiochemical separations. The optimized procedures were utilized in the determination of rare-earth elements in standard reference materials of both mineral and biological origin. The adopted radiochemical procedure is based on the separation of the rare-earth element group by fluoride precipitation.Results, given as the average of six independent determinations and relative standard deviations, are reported and discussed. Precision of the methods can be deduced from the reproducibility of data, whereas accuracy is evaluated by comparison with existing values in the literature. Sensitivity limits under the described operational conditions are also reported, as are trends and correlations among data.     

Measurement of ¹⁵N relaxation rates in perdeuterated proteins by TROSY-based methods

While extracting dynamics parameters from backbone (15)N relaxation measurements in proteins has become routine over the past two decades, it is increasingly recognized that accurate quantitative analysis can remain limited by the potential presence of systematic errors associated with the measurement of (15)N R(1) and R(2) or R(1ρ) relaxation rates as well as heteronuclear (15)N-{(1)H} NOE values. We show that systematic errors in such measurements can be far larger than the statistical error derived from either the observed signal-to-noise ratio, or from the reproducibility of the measurement. Unless special precautions are taken, the problem of systematic errors is shown to be particularly acute in perdeuterated systems, and even more so when TROSY instead of HSQC elements are used to read out the (15)N magnetization through the NMR-sensitive (1)H nucleus. A discussion of the most common sources of systematic errors is presented, as well as TROSY-based pulse schemes that appear free of systematic errors to the level of <1 %. Application to the small perdeuterated protein GB3, which yields exceptionally high S/N and therefore is an ideal test molecule for detection of systematic errors, yields relaxation rates that show considerably less residue by residue variation than previous measurements. Measured R(2)'/R(1)' ratios fit an axially symmetric diffusion tensor with a Pearson's correlation coefficient of 0.97, comparable to fits obtained for backbone amide RDCs to the Saupe matrix.     

Reproducibility of coccolith morphometry: Evaluation of spraying and smear slide preparation techniques

It is of great importance to assess the internal accuracy and reproducibility of coccolith morphometry, and to understand any systematic differences between various sample preparation techniques, so that data obtained with different methods can be adequately compared. Here, we performed a comparative study between two techniques regularly used to prepare nannofossil microscope slides, the standard smear slide and spraying methods. With each technique, ten replicate slides were prepared and morphometric measurements were carried out on the coccolith genus Calcidiscus as well as full assemblage counts to determine the reproducibility of coccolith size measurements and relative species abundances for each method.For either method, two significant sources of variance are related to the morphometric data, the variance between replicate slides and the variance within slides. Thus, in order to reduce the total variance of the estimate of mean coccolith size, it is beneficial to increase the number of replicate slides as well as the number of measurements on each slide. If the aim of the morphometric study is to address the mean size of a coccolith taxon or species complex (a group of closely related sub-species), one could rely on either preparation technique, since no significant difference in (log-normalised) mean size between the two tested methodologies was found. Likewise, the 10th percentiles are statistically equal for both methods. However, the 90th percentile values are significantly larger in the sprayed slides than in the smear slides, indicating that the spraying method may either favour larger coccoliths or better resolve the full extent of size variability present in the sample. Future tests are needed to investigate whether, and if so, how, size-fractionation may occur when using the spraying method. Nevertheless, the spraying method is preferred based on the reproducibility of proportion estimates since no significant difference between replicate samples was observed, in stark contrast to the smear slide series with 3–4 times higher variance. It appears that information gained from one sprayed slide requires counting at least three replicate smear slides.