Continuous plankton records stand the test of time: evaluation of flow rates, clogging and the continuity of the CPR time-series

The Continuous Plankton Recorder (CPR) survey is one of themost extensive biological time-series in existence and has beenin operation over major regions of the North Atlantic since1932. However, there is little information about the volumeof water filtered through each sample, but rather a generalassumption has persisted that each sample represents 3 m³. Datafrom electromagnetic flowmeters, deployed on CPRs between 1995and 1998, was examined. The mean volume filtered through sampleswas 3.11 m³ and the effect of clogging on filtration efficiencieswas not great. Consequently, even when the likely variationsin flow due to clogging are taken into account, previously identifiedlinks between zooplankton abundance and climatic signals remainstrong.     

Gear ratios at the limb joints of jumping dogs

An increase in gear ratio of the limb extensor muscles during joint extension has been suggested to be a mechanism that facilitates optimal power production by skeletal muscles. The objectives of this study were to: (1) measure gear ratios at the wrist, elbow, shoulder, ankle, knee, and hip joints of jumping dogs, (2) compute the work performed by each of these joints, and (3) measure muscle shortening velocity for a joint exhibiting an increasing gear ratio during joint extension. The gear ratio out-lever was computed by dividing the ground reaction force (GRF) moment by the GRF, whereas the in-lever was directly measured as the perpendicular distance from the joint center to the line of action of the extensor muscle. In addition, changes in fascicle length were measured from the vastus lateralis muscle using sonomicrometry. Of the joints examined, only the gear ratios at the shoulder and knee joints increased during jumping in a manner that could facilitate peak power production of actively shortening muscles. The vastus lateralis was found to shorten at an average velocity of 3.20 muscle lengths per second. This is similar to estimates of shortening velocity that produce peak muscular power in mammals the size of dogs. Additionally, the knee extensors were found to produce a large proportion (26.6%) of the positive external work of the limbs. These observations suggest that dynamic gearing in jumping dogs may allow the extensor muscles of the knee joint to shorten in a way that maximizes their power production.     

Helical nature of sperm swimming affects the fit of fertilization-kinetics models to empirical data

Models of fertilization kinetics rely upon estimates of the swimming velocity of sperm to predict collision rates between egg and sperm. Most investigators measure sperm swimming velocity without accounting for the helical motion of sperm, thereby obtaining an inflated estimate of the velocity with which sperm approach eggs. In turn, models of fertilization predict inflated rates of sperm/egg collision. I observed sea urchin sperm colliding with eggs, quantified the rate of sperm/egg collision, and measured sperm velocity as a component of the helix through which they swim. I also adjusted the "target size" of eggs to reflect the diameter of the helix. My estimate of sperm swimming velocity is an order of magnitude lower than other estimates for the same species. By using helical parameters in fertilization kinetics models and accounting for dead sperm in laboratory trials, I was able to accurately predict lower rates of sperm/egg collision. Moreover, making these adjustments in the model increased the estimated proportion of sperm that initiate fertilization by 6- to 7-fold, suggesting that a better understanding of sperm swimming might lead to a more complete understanding of fertilization biology and natural selection on gamete traits.     

Bacteriophage Transport in Sandy Soil and Fractured Tuff

Bacteriophage transport was investigated in laboratory column experiments using sandy soil, a controlled field study in a sandy wash, and laboratory experiments using fractured rock. In the soil columns, the phage MS-2 exhibited significant dispersion and was excluded from 35 to 40% of the void volume but did not adsorb. Dispersion in the field was similiar to that observed in the laboratory. The phage f2 was largely excluded from the porous matrix of the two fractured-rock cores studied, coming through 1.2 and 2.0 times later than predicted on the basis of fracture flow alone. Because of matrix diffusion, nonsorbing solutes were retarded by over a factor of three relative to fracture flow. The time for a solute tracer to equilibrate with the porous matrix of 6.5-cm-diameter by 25-cm-long cores was measured in days. Results of both granular-medium and fractured-rock experiments illustrate the inability of a solute tracer to provide estimates for dispersion and effective porosity that are applicable to a colloid. Bacteriophage can be used to better estimate the maximum subsurface transport rate of colloidal contaminants through a porous formation.     

The Application of Optical Coherence Tomography to Image Subsurface Tissue Structure of Antarctic Krill Euphausia superba

Many small open ocean animals, such as Antarctic krill, are an important part of marine ecosystems. To discover what will happen to animals such as krill in a changing ocean, experiments are run in aquaria where conditions can be controlled to simulate water characteristics predicted to occur in the future. The response of individual animals to changing water conditions can be hard to observe, and with current observation techniques it is very difficult to follow the progress of an individual animal through its life. Optical coherence tomography (OCT) is an optical imaging technique that allows images at high resolution to be obtained from depths up to a few millimeters inside biological specimens. It is compatible with in vivo imaging and can be used repeatedly on the same specimens. In this work, we show how OCT may be applied to post mortem krill samples and how important physiological data such as shell thickness and estimates of organ volume can be obtained. Using OCT we find an average value for the thickness of krill exoskeleton to be (30±4) µm along a 1 cm length of the animal body. We also show that the technique may be used to provide detailed imagery of the internal structure of a pleopod joint and provide an estimate for the heart volume of (0.73±0.03) mm³.     

Cryptosporidium and giardia recoveries in natural waters by using environmental protection agency method 1623

Relatively few studies have examined recoveries from source waters by using Environmental Protection Agency method 1623 with organism spike doses that are environmentally realistic and at turbidity levels commonly found in surface waters. In this study, we evaluated the filtration capacities and recovery efficiencies of the Gelman Envirochek (standard filter) and the Gelman Envirochek high-volume (HV) sampling capsules under environmental conditions. We also examined the performance of method 1623 under ambient conditions with matrix spike experiments using 10 organisms/liter. Under turbid conditions, the HV capsule filtered approximately twice the volume filtered by the standard filter, but neither could filter 10 liters without clogging. In low-turbidity waters, oocyst, but not cyst, recoveries were significantly higher when the HV capsule was used. In turbid waters, organism recoveries were lower than those in nonturbid waters and were not significantly different for the different filters. When the HV capsule was used, Cryptosporidium recoveries ranged from 36 to 75%, and Giardia recoveries ranged from 0.5 to 53%. For both organisms, recoveries varied significantly by site. Turbidity could explain variation in Giardia recoveries (r(2) = 0.80) but not variation in Cryptosporidium recoveries (r(2) = 0.16). The inconsistent recoveries across sites suggested that the background matrix of the ambient water affected recovery by method 1623. A control sample collected at the height of the winter rainy season detected one organism, highlighting the difficulty of using this method to accurately measure pathogen abundance under natural conditions. Our findings support the use of the HV filter under field conditions but suggest that designing a cost-effective and statistically valid monitoring program to evaluate sources and loads of protozoan pathogens may be difficult.     

Behavioral responses of minke whales (Balaenoptera acutorostrata) to experimental fishing gear in a coastal environment

Whale entanglement in fishing gear is a global problem, and underwater ropes associated with this gear are often the cause of injuries that can lead to fatalities. Minke whales (Balaenoptera acutorostrata) are especially at risk because they are relatively small, widely distributed, and often occur in coastal habitats where many types of fishing gear are deployed. It is unknown whether minke whales can detect and avoid ropes associated with fishing gear. To address this question we conducted a series of field experiments to measure behavioral responses of nearshore minke whales to underwater ropes simulating crab and whelk fishing gear. We also investigated correlations between whale behaviors and specific environmental variables. Our methods involved both visual and acoustic monitoring of whale behaviors near experimental ropes and buoys of different colors. A remote sensing system was also used to simultaneously monitor oceanographic conditions, record underwater sounds, and capture underwater video of whales swimming near ropes. Minke whales (N = 42) decreased their swimming velocity and altered their bearing when passing near experimental ropes, especially during trials with white and black ropes. Some minkes (N = 7) also altered their underwater swimming trajectories when passing near ropes, and often appeared to produce low-frequency vocalizations. Collectively this information provides strong evidence that minke whales detect and react behaviorally to the presence of underwater ropes that simulate fishing gear in nearshore areas. We hypothesize that visual and perhaps passive acoustic sensory abilities may be the mechanisms behind these rope avoidance behaviors. We recommend that high contrast ropes (white and black) be used with fishing gear in coastal areas to help minimize entanglements of minke and perhaps other whale species.     

External cross-validation for unbiased evaluation of protein family detectors: application to allergens

Key issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10-fold cross-validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held-out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected.     

Application of data consistency tests and new parameter estimation methods to microbial growth on corn dust in batch culture

The microorganism Candida utilis was grown on both filtered and unfiltered substrate obtained from enzymatic hydrolysis of starch in corn dust. For growth on filtered substrate, the average integrated biomass energetic yield value based on biomass-substrate data was η = 0.55 and for growth on unfiltered substrate an average yield value of η = 0.59 was obtained. Material and energy balances showed that the presence of unfiltered corn residue in the media had no significant effect on the yields. Statistical methods were developed and used to obtain best estimates of the growth parameters. Values of the biomass energetic yield corrected for maintenance (η_max = 0.619) and the maintenance coefficient (m_e = 0.043) were obtained for growth on filtered substrate. Values of η_max = 0.741 and m_e = 0.142 were obtained for the growth on unfiltered substrate. The consistency of data and parameter estimates was relatively good for filtered substrate; however, parameter estimates for unfiltered substrate were not consistent. Growth experiments without filtration of the products of starch hydrolysis resulted in protein-enriched products with about 39.73% protein.     

On the measurement of cytokinetics by continuous labeling with bromodeoxyuridine with applications to chick wing buds.

The cytokinetic properties, specifically the phase-transit times, TG1, TS, and TG2+M, of chick wing bud cells were estimated using data obtained from continuous labeling of stage 20 embryos with bromodeoxyuridine (BrdUrd). The presence of BrdUrd was detected with monoclonal antibodies, and the amount of DNA in the cells was determined with propidium iodide. The fraction of cells in each cell cycle phase, the fraction of labeled cells, and the relative movement, a measure of the mean DNA content, of all labeled cells were evaluated using bivariate flow cytometry at successive times following introduction of the label. Equations are presented to describe the fraction of unlabeled cells in G2 + M, which gives a direct estimate of TG2+M; the fraction of all labeled cells, which can then be used to estimate TG1; and, finally, the relative movement, which provides an estimate of TS. Thus, the data measured in these experiments together provide estimates of the progression through the cell cycle of limb mesoderm cells.     

Relationship between the 4 mmol running velocity, the time-distance relationship and the Léger-Boucher's test

The relationship between distance and best time is roughly linear for distances between 1500 and 5000 m. The slope of this relationship has the dimension of a velocity (Vlim) which can be sustained during a long time. The individual time-distance relationships and the resulting Vlim have been studied in 32 subjects practicing different athletic activities by measuring exhaustion time for 2 to 4 constant-velocity running exercises performed to exhaustion. The velocity corresponding to 4 mmol.l-1 of blood lactate (V4 mmol) has been compared with Vlim. As maximal oxygen uptake is a major factor determining V4 mmol, Vlim and V4 mmol have also been correlated with the result of a field test which is assumed to measure maximal aerobic power (Léger-Boucher's test). This test consists in running until exhaustion at a velocity which increases every two minutes. The higher the velocity at exhaustion (Vléger) is, the higher the maximal oxygen uptake is assumed. Both Vlim and Vléger were very well correlated with V4 mmol (r greater than 0.90) and the average value of Vlim was almost equal to the average value of V4 mmol (13.89 vs 13.71 km.h-1). However, it was not possible to estimate V4 mmol accurately from the values of Vlim or Vléger because the standard errors of estimates were too large.     

Measurement of magnetically induced electric fields in conductive media near a 60 Hz current-carrying wire.

Electric fields induced in a conductive body by the magnetic field of a current-carrying wire were analyzed theoretically and experimentally to assess the dosimetric importance of highly nonuniform, field-exposure conditions. Experimentation revealed that a 60-Hz magnetic field was inversely proportional to the radius of a wire bundle carrying 100 A within a 0.5-m2 test area. A miniaturized electric field probe was used to measure the electric fields induced in 5-cm-deep, saline-filled models. In the theoretical analysis, numerical estimates of induced fields were made by a spreadsheet method. The theoretical calculations and the measured values of induced electric fields were generally in good agreement. The induced fields were in a plane perpendicular to a vertically incident magnetic field; the maximally induced fields were in areas nearest the wire bundle. The strength of the induced field increased with model size: from 96 microV/cm in a 10 x 10 cm model to 176 microV/cm in a 40 x 40 cm model. The strength of the field induced in a 20 x 20 cm model decreased with increasing model-to-wire spacing: from 132 microV/cm for a 1-cm spacing (2-mT maximum, incident field) to 50 microV/cm for a 6-cm spacing (0.33-mT maximum). The results indicate that increases in local values of nonuniformly incident fields produce relatively small increases in induced electric fields. This finding may be important in dosimetric consideration of circumstances, such as use of electric blankets, in which fields of low average strength are accompanied by intense local fields.     

Analysis of regurgitant jets in natural and bio-prosthetic heart valves.

Artificial bio-prosthetic heart valves are prone to fatigue tearing, having a 50% failure rate in ten years. Tears in valves give rise to pulsing reverse flow back through the valve. This is termed regurgitant flow and the resultant jet of blood a regurgitant jet. The regurgitant volume of the jet during the pulsing cycle gives a measure of the severity of the valve defect and clinical significance. Hence, it is important for the cardiologists to be able to quantify this volume. Although the velocity of the regurgitant jet can be determined using Doppler ultrasound, the dimensions of the heart valve lesion cannot be measured directly; hence, the volumetric flow rate cannot be quantified accurately. At present the severity of the regurgitant jet is assessed qualitatively from the intrusion of the jet into the cardiac chamber. In the present study, classical mathematical theories of turbulent jets have been used to describe the velocity distributions for the types of jets expected in defective heart valves and these distributions have been verified experimentally. One of these models has been developed to enable the regurgitant volumetric flow through an axisymmetric orifice of unknown radius to be calculated from the velocity distribution of the jet. This relationship may be used in conjunction with ultrasound techniques to quantify the regurgitant volume within defective artificial heart valve implants. The present study shows that there is a significant difference in the velocity distributions in jets emanating from axisymmetric and high aspect ratio slots.(ABSTRACT TRUNCATED AT 250 WORDS)     

Effect of the electron drift in a transverse electric field on the width of spark channels in a multichannel sliding discharge

The effect of electron drift on the transverse size of the spark channels in a multichannel sliding discharge on a dielectric surface is considered in a semianalytic approximation. The strength of an electric field transverse to the channel axis is estimated by the mirror image method. The estimate obtained is used to analyze the differential equation for the density of electrons with allowance for their drift from the channel into the surrounding layers. It is shown that the channel expands to a certain steady-state radius at which an increase in the local electron density due to the ionization of atoms is balanced by its decrease due to the electron drift from the surface channel layer into the surrounding layers. Numerical estimates are carried out for the conditions of earlier experiments with discharges in He, Ne, Ar, and Xe. The analysis applies to the initial nanosecond stage of the spark development, when the hydrodynamic expansion of the channels is still insignificant.     

Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis elegans

We develop a maximum-likelihood (ML) approach to estimate genomic mutation rates (U) and average homozygous mutation effects (s) from mutation-accumulation (MA) experiments in which phenotypic assays are carried out in several generations. We use simulations to compare the procedure's performance with the method of moments traditionally used to analyze MA data. Similar precision is obtained if mutation effects are small relative to the environmental standard deviation, but ML can give estimates of mutation parameters that have lower sampling variances than those obtained by the method of moments if mutations with large effects have accumulated. The inclusion of data from intermediate generations may improve the precision. We analyze life-history trait data from two Caenorhabditis elegans MA experiments. Under a model with equal mutation effects, the two experiments provide similar estimates for U of approximately 0.005 per haploid, averaged over traits. Estimates of s are more divergent and average at -0.51 and -0.13 in the two studies. Detailed analysis shows that changes of mean and variance of genetic values of MA lines in both C. elegans experiments are dominated by mutations with large effects, but the analysis does not rule out the presence of a large class of deleterious mutations with very small effects.     

The semicircular canals of the hagfish Myxine glutinosa

The internal radius (r) and radius of curvature (R) of the single semicircular canals of Myxine glutinosa have unusual dimensions. In mammals and fish the increase in dimension of r and R with respect to body weight is small; in fish r is larger than in mammals of equivalent weight in order to increase the sensitivity of the canals to angular rotation and R increases correspondingly (Jones & Spells, 1963). In Myxine r is larger than in fish or mammals yet R is smaller. It is argued that the large internal radius is the result of the need to increase the sensitivity of a single canal which has to signal rotation in three planes while the small radius of curvature follows from the absence of a cupula. In order to verify that the cristae of the canals do respond to rotational velocity, recordings were obtained from the nerves serving the canals during rotation in the horizontal plane. The frequency response of several afferents recorded simultaneously at sinusoidal rotations between 0.25 and 2.0 Hz was in the form of a sine wave 90 in advance of head position, as would be expected of a velocity transducer. The gain of single afferents was an order of magnitude less than those reported for other vertebrates.     

Maximizing quantitative accuracy of lung airway lumen and wall measures obtained from X-ray CT imaging.

To objectively quantify airway geometry from three-dimensional computed tomographic (CT) images, an idealized (circular cross section) airway model is parameterized by airway luminal caliber, wall thickness, and tilt angle. Using a two-dimensional CT slice, an initial guess for the airway center, and the full-width-half-maximum principle, we form an estimate of inner and outer airway wall locations. We then fit ellipses to the inner and outer airway walls via a direct least squares fit and use the major and minor axes of the ellipses to estimate the tilt and in-plane rotation angles. Convolving the airway model, initialized with these estimates, with the three-dimensional scanner point-spread function forms the predicted image. The difference between predicted and actual images is minimized by refining the model parameter estimates via a multidimensional, unconstrained, nonlinear minimization routine. When optimization converges, airway model parameters estimate the airway inner and outer radii and tilt angle. Results using a Plexiglas phantom show that tilt angle is estimated to within +/-4 degrees and both inner and outer radii to within one-half pixel when a "standard" CT reconstruction kernel is used. By opening up the ability to measure airways that are not oriented perpendicular to the scanning plane, this method allows evaluation of a greater sampling of airways in a two-dimensional CT slice than previously possible. In addition, by combining the tilt-angle compensation with the deconvolution method, we provide significant improvement over the previous full-width-half-maximum method for assessing location of the luminal edge but not the outer edge of the airway wall.     

Thermal fluctuations in membranes and the problem of mechanoreception

In order to estimate thermal fluctuations in erythrocyte and mechanoreceptor membranes the transverse fluctuations of plane and spherical bilayer membranes and the fluctuations of the surface of a part of such a membrane, possessing disc shape of the radius R are calculated. The obtained values of the transverse fluctuations are two orders smaller than in the paper [5]. Total plane fluctuations of the disc with R=5.10(-7) cm are some orders higher than the threshold values epsilonpi of relative deformation in mechanoreceptor membranes, but their value in the frequency range of 0 dividied by 20 kHz is of the same order as epsilonpi. The estimates of fluctuations are also produced for Pacinian corpuscle membrane and for the globular protein molecule. The conditions necessary for high sensitivity of mechanoreceptor membranes are the large value of Young modulus E and low membrane viscosity eta.     

Continuous Plankton Recorder flow rates revisited: clogging, ship speed and flow meter design

The factors affecting the volume of water filtered by a TypeII Mark III Continuous Plankton Recorder (CPR) were investigatedin eastern Antarctica in February/March 2003. Three tows wereconducted, one each using 270-, 224- and 125-µm nylonmesh. Volume filtered was measured at 3-s intervals with a Valeportelectromagnetic flow meter, while ship speed, photosyntheticallyactive radiation (PAR) and fluorescence were measured everyminute. Substantial variation in measured volume filtered (MVF)was recorded on each transect. Ship speed was positively correlatedwith MVF and caused up to 30% reductions in MVF while clogging,predominantly by phytoplankton, resulted in up to 60% reductionsin MVF. A maximum 78% reduction in MVF resulted from the combinedeffects of clogging and ship speed. The substantial impact ofclogging on observed zooplankton densities highlights the needfor flow meter measurements to quantify CPR data. However, observationsfrom this study show that the CPR flow meter currently in usemay itself have caused the positive correlation between MVFand ship speed, indicating the need for improved flow meterdesign. Continuing miniaturization and improved resolution ofdistance loggers for attachment to marine vertebrate predatorsholds promise in this area.