"SCINT," a Fortran IV program for the analysis of data for doubly labeled and variably quenched liquid scintillation samples

For some time now, we have been using double label techniques in our laboratory. In our work we generate large numbers of samples containing ¹⁴C and ³H and varying amounts of quenching agents. The analysis of this data led us to develop SCINT, a simple and versatile program written in FORTRAN IV for use on our Control Data 1700 computer facility. We feel that such a program may be of use to the many workers now involved with dual isotope procedures who also have access to similar computer facilities.     

Random sampling of evolution time space and Fourier transform processing

Application of Fourier Transform for processing 3D NMR spectra with random sampling of evolution time space is presented. The 2D FT is calculated for pairs of frequencies, instead of conventional sequence of one-dimensional transforms. Signal to noise ratios and linewidths for different random distributions were investigated by simulations and experiments. The experimental examples include 3D HNCA, HNCACB and ¹⁵N-edited NOESY-HSQC spectra of ¹³C ¹⁵N labeled ubiquitin sample. Obtained results revealed general applicability of proposed method and the significant improvement of resolution in comparison with conventional spectra recorded in the same time.     

Fast acquisition of NMR spectra using Fourier transform of non-equispaced data

Rapid acquisition of high-resolution 2D and 3D NMR spectra is essential for studying biological macromolecules. In order to minimize the experimental time, a non-linear sampling scheme is proposed for the indirect dimensions of multidimensional experiments. These data can be processed using the algorithm proposed by Dutt and Rokhlin (Appl. Comp. Harm. Anal. 1995, 2, 85–100) for fast Fourier transforms of non equispaced data. Examples of ¹H−¹⁵N HSQC spectra are shown, where crowded correlation peaks can be resolved using non-linear acquisition. Simulated data have been used to analyze the artefacts produced by the Lagrange interpolation. As compared to non-linear processing methods, this algorithm is simple and highly robust since no parameters need to be adjusted by the user.     

PRODUCTIVITY AND COMPOSITION OF A BALDCYPRESS-WATER TUPELO SITE AND A BOTTOMLAND HARDWOOD SITE IN A LOUISIANA SWAMP

The productivity and composition of two study sites in a southern Louisiana freshwater swamp were studied from October 1973 to November 1974. Net productivity was determined from measurements of litter-fall, stem growth of woody species, and harvest samples of annual herbaceous understory. Annual stem growth was calculated from biomass estimates on two different dates. The annual increase in stem biomass was 800 g dry wt/m² for a bottomland hardwood site (BLH) and 500 g dry wt/m² for a baldcypress-water tupelo site (CT). Litter-fall was 574 g dry wt/m²/yr for BLH and 620 g dry wt/m²/yr for CT. Harvest samples within the two plots yielded 200 g dry wt/m² and 20 g dry wt/m² for BLH and CT, respectively. Minimum net primary production was calculated as the sum of the three: 1574 g dry wt/m²/ yr for BLH and 1140 g dry wt/m²/yr for CT. Maximum estimates of herbaceous production and insect consumption were made by using values from the literature. Estimated total net primary productivity was 1733 g dry wt/m²/yr for BLH and 1516 g dry wt/m²/yr for CT. Tree composition was determined by the point-centered quarter method. Relative frequency, relative density, absolute density, relative dominance, and importance value (IV) were calculated for the tree species along each transect. In the bottomland hardwood area many woody species exist with Acer rubrum var. drummondii (IV = 23.9) and Nyssa aquatica (IV = 18.4) the most dominant. In the baldcypress-water tupelo area, fewer woody species exist and Taxodium distichum (IV = 39.2) and N. aquatica (IV = 37.6) dominated. Comparison of productivity data from several southeastern swamps indicate that flowing water regimes tend to result in the highest swamp forest productivity.     

Estimating processing time of stream benthic samples

Multiple regression analysis was used to generate equations relating time required to sort and tabulate benthic invertebrates to size characteristics of benthic samples collected from a 5th-order river and a 3rd-order woodland stream. Number of invertebrates in a sample was the primary determinant of sample sorting time. Amount of detritus, occurrence of filamentous algae (Cladophora) and source stream contributed significant but minor additional variability to estimates (cumulativeR ² = 0.95). When number of animals was excluded as a variable, amount of detritus and presence/absence ofCladophora alone could be used to predict sorting time (R ² = 0.81). A typical sample containingCladophora required 29% longer to sort than samples containing equivalent amounts of organic material but noCladophora. The influence of sampler size and subsampling on processing and sorting time are considered. A general equation was derived to provide guidelines for selecting a size of stream sampler that subsequently minimizes total processing time required to estimate density of benthos with acceptable, constant precision. Overall sample processing and sorting time are reduced by using a smaller sampler or by subsampling only if benthic densities of animals are high. Use of regression equations to anticipate processing and sorting time required for a particular sampling program permits development of more efficient designs.     

The Effectiveness of Neurofeedback and Stimulant Drugs in Treating AD/HD: Part II. Replication

This study replicated T. R. Rossiter and T. J. La Vaque (1995) with a larger sample, expanded age range, and improved statistical analysis. Thirty-one AD/HD patients who chose stimulant drug (MED) treatment were matched with 31 patients who chose a neurofeedback (EEG) treatment program. EEG patients received either office (n = 14) or home (n = 17) neurofeedback. Stimulants for MED patients were titrated using the Test of Variables of Attention (TOVA). EEG (effect size [ES] = 1.01–1.71) and MED (ES = 0.80–1.80) groups showed statistically and clinically significant improvement on TOVA measures of attention, impulse control, processing speed, and variability in attention. The EEG group demonstrated statistically and clinically significant improvement on behavioral measures (Behavior Assessment System for Children, ES = 1.16–1.78, and Brown Attention Deficit Disorder Scales, ES = 1.59). TOVA gain scores for the EEG and MED groups were not significantly different. More importantly, confidence interval and nonequivalence null hypothesis testing confirmed that the neurofeedback program produced patient outcomes equivalent to those obtained with stimulant drugs. An effectiveness research design places some limitations on the conclusions that can be drawn.     

Examination of the secondary structure of proteins by deconvolved FTIR spectra

Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm^?1 resolution from 1600 to 1700 cm^?1 in deuterium oxide solution. Fourier self-deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well-defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm^?1. The observed components are assigned to helical segments, extended beta-segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta-structure band can vary within a range of approximately 15 cm^?1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss–Newton, iterative curve-fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta-structure for each of 21 globular proteins. The results are in good general agreement with values derived from x-ray data by Levitt and Greer. The RMS deviation between 22 values (alpha- and beta-content of 11 beta-rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.     

Zooplankton biomass and abundance of Antarctic krillEuphausia superba DANA in Indian ocean sector of the southern ocean

Zooplankton sampling was carried out during the first six Indian Scientific Expeditions to Antarctica (1981—1987) to estimate krill abundance in the Indian sector of the southern ocean (between 35° to 70° S and 10° to 52° E). This study aims to understand the distribution of biomass of zooplankton, especially the krill, using the data collected by net sampling techniques. Total zooplankton biomass for all the sampling stations ranged from 9 to 684 ml/1000m³ (x: 143.34±138.61 SD; n=150). Biomass data grouped by 5° latitude interval shows the presence of higher biomass (x: 191 ml/1000 m³;n = 31) in the Antarctic divergence region (between 60° to 65° S). EuphausiidEuphausia superba DANA formed a considerable component of biomass and together with eggs and larvae represented over 60% (n = 39) of mean total zooplankton-biomass in the coastal ice region. The values for population density and biomass of adult-size krill varied between 0 to 4320 individuals and 6 to 305 ml/1000 m³, respectively. The highest values were recorded between 62° to 69° S and between 16° to 30° E. A high density of krill larvae was encountered in the shelf region during January 1987 which was related to chlorophyll concentration. However, the values obtained during six consecutive summers showed that values of adult krill biomass at given location was highly variable and, hence, not comparable on inter-annual basis, during the sampling years.     

Demography and Genetic Structure of a Recovering Grizzly Bear Population

ABSTRACT Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins—Pledger closed mark—recapture models. Our population estimate, Ň = 765 (95% CI = 715–831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2–4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km² in the Northern Continental Divide Ecosystem (NCDE) during 1994–2007, including 10,340 km² beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.     

Structure in solution of protected homo-oligopeptides of L-valine,L-isoleucine,and L-phenylalanine: An infrared absorption study

Monodisperesed, N-and C-Protected homo-oligopeptides [number (n) of resides from 2 to 5] of L -valine, L -isoleucine, and L -phenylalnine were studied by ir absorption spectroscopy between 1200 and 350 cm^?1 at various solvents. The solvents and chain-length effects were examined for non-hydrogen-bonded peptide groups. The frequencies of the self-associated species are consistent with a model derived from the amide data. Self-association species are consistent with a model derived from the amide data. Self-association is favored by higher values of n = 2, the peptide is insoluble when more than two chains are bonded. For n = 3, 4, several chains may be associated by sliding along one another and remain soluble. For n = 2, the peptide is insoluble when more than two chains are bonded. For n = 3, 4, several chains may be associated by sliding along one another and remain slouble. For n = 5, the effect of n is to favour a model in which two chains exactly face each other so that the peptide precipitates at relatively low concentration.     

GFT projection NMR spectroscopy for proteins in the solid state

Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated ‘sampling problem’ and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins.     

MUNIN: A new approach to multi-dimensional NMR spectra interpretation

A new method, MUNIN (Multi-dimensional NMR spectra interpretation), is introduced for the automated interpretation of three-dimensional NMR spectra. It is based on a mathematical concept referred to as three-way decomposition. An NMR spectrum is decomposed into a sum of components, with each component corresponding to one or a group of peaks. Each component is defined as the direct product of three one-dimensional shapes. A consequence is reduction in dimensionality of the spectral data used in further analysis. The decomposition may be applied to frequency-domain or time-domain data, or to a mixture of these. Features of MUNIN include good resolution in crowded regions and the absence of assumptions about line shapes. Uniform sampling of time-domain data, a prerequisite for discrete Fourier transform, is not required. This opens an avenue for the processing of NMR data that do not follow oscillating behaviour, e.g. from relaxation measurements. The application of MUNIN is illustrated for a ¹H-¹⁵N-NOESY-HSQC, where each component is defined as the set of all NOE peaks formed by a given amide group. As a result, the extraction of structural information simply consists of one-dimensional peak picking of the shape along the NOE-axis obtained for each amide group.     

Simulated Sampling Strategies for Nematodes Distributed According to a Negative Binomial Model

A FORTRAN computer program was developed to simulate nematode soil sampling strategies consisting of various numbers of samples per field, with each sample consisting of various numbers of soil cores. The program assumes that the nematode species involved fit a negative binomial distribution. Required input data are estimates of the mean and k values, the number of samples per field and cores per sample in the strategy to be investigated, and the number of times the simulation is to be replicated. Output consists of simulated values of the relative deviation from the mean and standard error to mean ratio, both averaged over all replications. The program was used to compare 150 simulated sampling strategies for Meloidogyne incognita, involving all combinations of two mean values (2.0 and 10.0 la.rvae/10 cm³ soil), three k values (1.35, 0.544, and 0.294), five different numbers of samples per field (1, 2, 4. 10, 20), and five different numbers of cores per sample (1, 2, 4, 10, 20). Simulations resulting from different mean values were similar, but best results were obtained with higher k values and 20 cores per sample. Relatively few 20-core samples were needed to obtain average deviations from the mean of 20-25%.     

Leaf area estimation in a sugar beet cultivar by linear models

An indirect method of leaf area measurement for Rizor sugar beet cultivar was tested. Leaves were sampled during two growing seasons in a Randomised Complete Block Design experiment. For 2002 samplings, leaf area [cm²] was linearly correlated with maximum leaf width [cm] using all leaf samples (r ² = 0.83, p < 0.001) or using the means of the 8 sampling occasions (r ² = 0.97, p < 0.001). Correlations between leaf area and leaf mid vein length [cm] were weaker (r ² = 0.75, p < 0.001 and r ² = 0.93, p < 0. 001, respectively). For 2003 samplings, the area estimated by the equations was highly correlated to the measured leaf area.     

Soluble CD23 in Human Immunodeficiency Virus Type 1 Infected Patients

The level of sCD23 produced in the course of human immunodeficiency virus (HIV) infection was measured in patients grouped according to the Centers for Disease Control by using an immunoradiometric assay. Soluble CD23 was evaluated in supernatants of peripheral blood mononuclear cell (PBMC) (10⁶ cells/ml) stimulated by phytohemagglutinin (PHA). Compared with healthy controls (m±S.D. = 1.0 ±0.34 U/ml, n = 7), higher values were observed in some of the patients of group II (asymptomatic) (m±S.D. = 2±1.33, n = 9) and some of the patients of group IV (AIDS) (m±S.D. = 1.3 ±1.40, n = 8). Those results prompted us to compare the plasma levels of sCD23 in group II and group IV HIV-infected patients and in healthy individuals. Soluble CD23 plasma levels in healthy patients (n = 42) ranged from 0 to 1.5 U/ml (m±S.D. = 0.9±0.33), in group II patients (n = 17) from 0 to 3 U/ml (m±S.D. = 0.92±0.83) and in group IV patients (n =73) from 0 to 2.9 U/ml (m±S.D. = 1.15±0.71). The differences between the patients and the healthy individuals were not statistically significant but individual sCD23 values higher than 2 U/ml were obtained in 6% of the group II patients and 16.7% of the group IV patients. Increased values of sCD23 were obtained in plasma from patients with secondary infectious diseases (groups IV-C1 and IV-C2) and from patients without secondary infectious diseases (group II, group IV-A and group IV-B). Elevated values of sCD23 were detected even in patients with low counts of CD4⁺ T cells and CD8⁺ T cells in their peripheral blood. sCD23 has numerous activities including control of IgE synthesis and cytokine-like properties. Our results show a disarray of sCD23 in HIV-infected patients which could be involved in drug reactions, allergic manifestations and the IgE-level increase. Further investigations should attempt to define the role of sCD23 in clinical manifestations of HIV infection.     

A Modified-Whittaker nested vegetation sampling method

A standardized sampling technique for measuring plant diversity is needed to assist in resource inventories and for monitoring long-term trends in vascular plant species richness. The widely used Whittaker plot (Shmida 1984) collects species richness data at multiple spatial scales, using 1 m², 10 m², and 100 m² subplots within a 20 m × 50 m (1000 m²) plot, but it has three distinct design flaws involving the shape and placement of subplots. We modified and tested a comparable sampling design (Modified-Whittaker plot) that minimizes the problems encountered in the original Whittaker design, while maintaining many of its attractive attributes. We overlaid the two sampling methods in forest and prairie vegetation types in Larimer County, Colorado, USA (n=13 sites) and Wind Cave National Park, South Dakota, USA (n=19 sites) and showed that the modified design often returned significantly higher (p<0.05) species richness values in the 1 m², 10 m², and 100 m² subplots. For all plots, except seven ecotone plots, there was a significant difference (p<0.001) between the Whittaker plot and the Modified-Whittaker plot when estimating the total number of species in the 1000 m² plots based on linear regressions of the subplot data: the Whittaker plot method, on average, underestimated plant species richness by 34%. Species-area relationships, using the Modified-Whittaker design, conformed better to published semilog relationships, explaining, on average, 92% of the variation. Using the original Whittaker design, the semilog species-area relationships were not as strong, explaining only 83% of the variation, on average. The Modified-Whittaker plot design may allow for better estimates of mean species cover, analysis of plant diversity patterns at multiple spatial scales, and trend analysis from monitoring a series of strategically-placed, long-term plots.     

Ecomorphology ofCrassostrea cucullata (Born, 1778) (Ostreidae) in a mangrove creek (Gazi,Kenya)

Variations of shell form and shell length were studied for oysters growing in the mangroves of Gazi Creek, Kenya, and related to different environmental factors.For the study of the form, Fourier analysis was performed on the circumference of 85 oysters. The resulting coefficients were compared among specimens using cluster analysis. The correspondence between this classification and substrate diameter is virtually perfect (only one misclassification out of 85 oysters). For the clusters based on height above chart datum, 9 specimens, all on intermediate height levels, were misclassified. Orientation with respect to tidal current had 13 misclassifications. Mangrove species seemed to influence form only marginally, if at all.In the study of the size ofCrassostrea cucullata, the length of 956 oysters, growing along two transects were measured, and correlated with several environmental factors. Oyster length was not related to substrate diameter or its orientation with respect to the main current. Length was not influenced by density up to a cover of 70%. For densities higher than 70%, there was a fairly strong negative correlation (r ² = 0.634,n = 217). Length was not correlated with height above bottom (base of the tree) for heights lower than 20 cm, while oysters growing closer to the bottom were smaller. The correlation with height above chart datum was negative but very low (r ² = 0.060,n = 957). However, if all measurements of oysters closer than 20 cm to the bottom, and all from a density of more than 70% cover are deleted from the data set, the correlation with height increased dramatically, the slope still being negative (r ² = 0.859,n = 543).     

A new method for analysis of heart rate variability: counting statistics of 1/f fluctuations

1/f fluctuations in heart rate are usually measured by spectral analysis using Fast Fourier Transform. Here, we introduce a new method based on counting the number of QRS complexes in time intervals t of various length. For a 1/f ^b spectrum the variance of counts in t follows a power-law as gDt ^1+b. This method is applied to analyze long term fluctuations in heart rate variability in 10 healthy men. The results show periods of 1/f fluctuations with interpolated periods of white noise during night hours.     

Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments

A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.     

Population biology and status of exploitation of introduced garfish Belone belone euxini (Günther, 1866) in the Black Sea

The garfish Belone belone euxini (Günther, 1866) is a commercially important pelagic fish species in Sinop artisanal fishery, which is showing a decreasing trend in catch results. As a basis for fisheries management a sampling program was carried out between October 2000 and September 2001 along the Turkish coast of the Black Sea, to study the population structure, growth, and reproduction cycle of garfish in the area, and to achieve a rough estimate of exploitation. The length–weight relationship and von Bertalanffy growth parameters were estimated as W = 0.00076 L^3.137, L_∞ = 74.64 cm, K = 0.13 year^?1, t_o = ?3.67, respectively. First sexual maturity was estimated at age 2 and at a total length of 38.8 cm for females. The spawning period was from May to September. The total fecundity–length relationship was estimated as F = 0.0041 L^4.1086 (r² = 0.92). Mortality rates were Z = 1.24 year^?1, M = 0.23 year^?1and F = 1.01 year^?1 for total, natural, and fishing mortality, respectively. The exploitation ratio E = 0.81 indicates that the population is heavily exploited.