A New Method to Estimate the Population Size of Coconut Mite, Aceria Guerreronis, on a Coconut

Studies of the coconut mite, Aceria guerreronis, often require accurate assessment of the population density on individual infested coconuts. Here an efficient and accurate method was developed to estimate its population density on an infested coconut. The coconut mites were removed by washing the bracts and surface of an infested coconut with 30 ml of a detergent solution. Shaking the wash for 5 s allowed the mites to distribute uniformly. The number of mites in the first 1 ml of the first wash (X) yielded a very accurate predictor of the total number of mites on a coconut (Y): Y = 30.1X (R² = 0.99; p <0.0001), also confirming that the wash was indeed homogeneous. The advantages and disadvantages of this method are discussed.     

Measuring Evolutionary Constraints Through the Dimensionality of the Phenotype: Adjusted Bootstrap Method to Estimate Rank of Phenotypic Covariance Matrices

The potential and direction of phenotypic evolution is constrained by the distribution of genetic variation for the traits as described by the phenotypic (P) and genetic covariance matrices (G). The rank of the covariance matrix reflects the number of independent variational dimensions of the phenotype. Covariance matrices with less than full rank indicate lack of variation in some directions of the phenotype space and thus are an indication of absolute evolutionary constraints. Because selection acts upon phenotypic variation, the rank of P represents the upper limit of the dimensionality in G, relevant for selection response. The limitations of current methods to estimate matrix rank motivated us to analyze and adjust a bootstrap method and evaluate its performance by simulation. The results show that the modified bootstrap method (ABRE) gives reliable and rather conservative rank estimates when the sample size is sufficient for the number of variables studied (the sample size is at least five-fold the number of variables). Applying the method to various datasets suggests high phenotypic dimensionality in all cases. The analysis thus provides no evidence for absolute evolutionary constraints. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The Extratropical Northern Hemisphere Temperature Reconstruction during the Last Millennium Based on a Novel Method

Large-scale climate history of the past millennium reconstructed solely from tree-ring data is prone to underestimate the amplitude of low-frequency variability. In this paper, we aimed at solving this problem by utilizing a novel method termed “MDVM”, which was a combination of the ensemble empirical mode decomposition (EEMD) and variance matching techniques. We compiled a set of 211 tree-ring records from the extratropical Northern Hemisphere (30–90°N) in an effort to develop a new reconstruction of the annual mean temperature by the MDVM method. Among these dataset, a number of 126 records were screened out to reconstruct temperature variability longer than decadal scale for the period 850–2000 AD. The MDVM reconstruction depicted significant low-frequency variability in the past millennium with evident Medieval Warm Period (MWP) over the interval 950–1150 AD and pronounced Little Ice Age (LIA) cumulating in 1450–1850 AD. In the context of 1150-year reconstruction, the accelerating warming in 20^th century was likely unprecedented, and the coldest decades appeared in the 1640s, 1600s and 1580s, whereas the warmest decades occurred in the 1990s, 1940s and 1930s. Additionally, the MDVM reconstruction covaried broadly with changes in natural radiative forcing, and especially showed distinct footprints of multiple volcanic eruptions in the last millennium. Comparisons of our results with previous reconstructions and model simulations showed the efficiency of the MDVM method on capturing low-frequency variability, particularly much colder signals of the LIA relative to the reference period. Our results demonstrated that the MDVM method has advantages in studying large-scale and low-frequency climate signals using pure tree-ring data.     

Method to Estimate Activity of Subcutaneous Thermogenic Structures on Exposure to Stimuli of Different Modalities

A method to estimate activity of subcutaneous thermogenic structures was developed on the basis of dynamical infrared thermography. The gist is comparing the dynamics of skin temperature changes for different body sites on exposure to factors evoking metabolic responses. The method can be used for investigating the mechanisms of changes in body temperature in response to various disturbing factors and, in certain cases, can help to differentiate metabolic and vascular responses.     

A New Approach to Segment Both Main and Peripheral Retinal Vessels Based on Gray-Voting and Gaussian Mixture Model

Vessel segmentation in retinal fundus images is a preliminary step to clinical diagnosis for some systemic diseases and some eye diseases. The performances of existing methods for segmenting small vessels which are usually of more importance than the main vessels in a clinical diagnosis are not satisfactory in clinical use. In this paper, we present a method for both main and peripheral vessel segmentation. A local gray-level change enhancement algorithm called gray-voting is used to enhance the small vessels, while a two-dimensional Gabor wavelet is used to extract the main vessels. We fuse the gray-voting results with the 2D-Gabor filter results as pre-processing outcome. A Gaussian mixture model is then used to extract vessel clusters from the pre-processing outcome, while small vessels fragments are obtained using another gray-voting process, which complements the vessel cluster extraction already performed. At the last step, we eliminate the fragments that do not belong to the vessels based on the shape of the fragments. We evaluated the approach with two publicly available DRIVE (Staal et al., 2004) and STARE (Hoover et at., 2000) datasets with manually segmented results. For the STARE dataset, when using the second manually segmented results which include much more small vessels than the first manually segmented results as the “gold standard,” this approach achieved an average sensitivity, accuracy and specificity of 65.0%, 92.1% and 97.0%, respectively. The sensitivities of this approach were much higher than those of the other existing methods, with comparable specificities; these results thus demonstrated that this approach was sensitive to detection of small vessels.     

The Impact of Iterative Reconstruction on Computed Tomography Radiation Dosimetry: Evaluation in a Routine Clinical Setting

Purpose

To evaluate the effect of introduction of iterative reconstruction as a mandated software upgrade on radiation dosimetry in routine clinical practice over a range of computed tomography examinations.

Methods

Random samples of scanning data were extracted from a centralised Picture Archiving Communication System pertaining to 10 commonly performed computed tomography examination types undertaken at two hospitals in Western Australia, before and after the introduction of iterative reconstruction. Changes in the mean dose length product and effective dose were evaluated along with estimations of associated changes to annual cancer incidence.

Results

We observed statistically significant reductions in the effective radiation dose for head computed tomography (22–27%) consistent with those reported in the literature. In contrast the reductions observed for non-contrast chest (37–47%); chest pulmonary embolism study (28%), chest/abdominal/pelvic study (16%) and thoracic spine (39%) computed tomography. Statistically significant reductions in radiation dose were not identified in angiographic computed tomography. Dose reductions translated to substantial lowering of the lifetime attributable risk, especially for younger females, and estimated numbers of incident cancers.

Conclusion

Reduction of CT dose is a priority Iterative reconstruction algorithms have the potential to significantly assist with dose reduction across a range of protocols. However, this reduction in dose is achieved via reductions in image noise. Fully realising the potential dose reduction of iterative reconstruction requires the adjustment of image factors and forgoing the noise reduction potential of the iterative algorithm. Our study has demonstrated a reduction in radiation dose for some scanning protocols, but not to the extent experimental studies had previously shown or in all protocols expected, raising questions about the extent to which iterative reconstruction achieves dose reduction in real world clinical practice.     

An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values

Interspecific comparisons have played a prominent role in evolutionarybiology at least since the time of Charles Darwin. Since 1985,the "comparative method" has been revitalized by new analyticaltechniques that use phylogenetic information and by increasedavailability of phytogenies (often from molecular data sets).Because species descend from common ancestors in a hierarchicalfashion, related species tend to resemble each other (elephantslook like elephants); therefore, cross-species data sets generallydo not comprise independent and identically distributed datapoints. Phylogenetically based statistical methods attempt toaccount for this fact. Phylogenetic methods allow traditionaltopics in comparative and ecological physiology to be addressedwith greater rigor, including the form of allometric relationshipsand whether physiological phenotypes vary predictably in relationto behavior, ecology or environmental characteristics, whichprovides evidence about adaptation. They can also address newtopics, such as whether rates of physiological evolution havediffered among lineages (clades), and where and when a phenotypefirst evolved. We present brief overviews of three phylogeneticallybased statistical methods: phylogenetically independent contrasts,Monte Carlo computer simulations to obtain null distributionsof test statistics, and phylogenetic autocorrelation. In a newresult, we show analytically how to use independent contraststo estimate ancestral values and confidence intervals aboutthem. These confidence intervals often exceed the range of variationobserved among extant species, which points out the relativelygreat uncertainty inherent in such inferences. The use of phytogeniesshould become as common as the use of body size and scalingrelationships in the analysis of physiological diversity.     

Modeling of Actual Eukaryotic Control Gene Subnetworks Based on the Method of Generalized Threshold Models

Mathematical and computational means are developed that take into consideration the specifics of control processes at the molecular level and allow one to obtain both qualitative and quantitative patterns of gene network dynamics. Using the method of generalized threshold models, models are constructed for the Arabidopsis thalianaflower morphogenesis control subsystem and gene subnetwork controlling the Drosophila melanogasterearly ontogeny. The dynamics of these systems are investigated: kinetic curves are computed for molecular components (RNA, proteins), possible modes of functioning and steady states of the nets are revealed and biologically interpreted. The models are shown to be adequate to the real processes. The effectiveness of the generalized threshold model method is evaluated in the analysis of the actual eukaryotic gene networks.     

Identification of a New Rice Low-Tiller Mutant and Association Analyses Based on the SLAF-seq Method

By studying the regulatory mechanism by which rice tillers are controlled, many rice mutants were described as providing important insights into the investigation of tillering control. In this study, we surveyed a new rice mutant produced by ethyl methane sulfonate induction, designated as Oryza sativa low-tiller 1 (oslt1), which had been planted to the fourth generation and proved to stably inherit the low-tillering trait. The statistical analysis of the number of tillers in oslt1 showed that there was a significant lack of tillering in the mutant lines, with the average number being 2.33 as opposed to 8.00 in wild-type plants. The data from a series of crossed populations, including F₂ populations produced by selfing of the offspring of oslt1?×?ptb and backcross populations of the F₁ generation?×?oslt1, indicated that a single recessive gene controlled the low-tillering trait. To locate the recessive gene, the crossed population in the F₂ generation from two parents, oslt1 and Peiai 64, was constructed and the population was used for bulked segregate analysis based on specific locus amplified fragment-sequencing (SLAF-seq) method. The results showed that approximately 100 differential markers were procured by analyzing 7437 polymorphic SLAFs and 1 primary region associated with low-tillering characteristics located on Chr12. In the associated regions, there were 34 candidate genes of 0.24 Mb that might be related to the number of low tillers in oslt1 plants. All of these results are necessary for further fine mapping for this low tillering-related gene. In addition, these identified SLAF-tags will be valuable for marker-assisted selection in rice breeding.     

Note on a New Method of Dye Analysis

Positive and negative dye ions may be titrated with one another conductometrically. The method appears to give values reproducible to about one percent. Difficulty has been experienced in preparing a satisfactory primary standard, so that data on the quantitative analysis of stains are not at present available.     

A New Method of Regression of Time-series Based on a Mathematical Connection Between Path and Compartmental Analyses

In the regression analysis of time-series the error terms may be serially correlated with the results. In this case the possibility arises that the expectations and adjustment processes are themselves mis-specifications of the correct behavioural relationships. In this paper an analogy is pointed out between the compartmental-analysis and the path analysis by the author. It will be argued that the time-series of the standardized partial regression coefficients (path coefficients or beta weights) computed from the cross-sectional data, have to be analysed instead of applying ordinary least squares directly to the timeseries. An application of the new method is briefly discussed.     

Evaluation of the Quantitative Accuracy of 3D Reconstruction of Edentulous Jaw Models with Jaw Relation Based on Reference Point System Alignment

ObjectivesTo apply contact measurement and reference point system (RPS) alignment techniques to establish a method for 3D reconstruction of the edentulous jaw models with centric relation and to quantitatively evaluate its accuracy.MethodsUpper and lower edentulous jaw models were clinically prepared, 10 pairs of resin cylinders with same size were adhered to axial surfaces of upper and lower models. The occlusal bases and the upper and lower jaw models were installed in the centric relation position. Faro Edge 1.8m was used to directly obtain center points of the base surface of the cylinders (contact method). Activity 880 dental scanner was used to obtain 3D data of the cylinders and the center points were fitted (fitting method). 3 pairs of center points were used to align the virtual model to centric relation. An observation coordinate system was interactively established. The straight-line distances in the X (horizontal left/right), Y (horizontal anterior/posterior), and Z (vertical) between the remaining 7 pairs of center points derived from contact method and fitting method were measured respectively and analyzed using a paired t-test.ResultsThe differences of the straight-line distances of the remaining 7 pairs of center points between the two methods were X: 0.074 ± 0.107 mm, Y: 0.168 ± 0.176 mm, and Z: −0.003± 0.155 mm. The results of paired t-test were X and Z: p >0.05, Y: p <0.05.ConclusionBy using contact measurement and the reference point system alignment technique, highly accurate reconstruction of the vertical distance and centric relation of a digital edentulous jaw model can be achieved, which meets the design and manufacturing requirements of the complete dentures. The error of horizontal anterior/posterior jaw relation was relatively large.     

Use of the 'Food Vacuole Content' Method to Estimate Grazing by the Mixotrophic Dinoflagellate Gyrodinium Galatheanum on Cryptophytes

We measured in situ grazing rates of the mixotrophic dinoflagellateGyrodinium galatheanum (Braarud) Taylor 1995 on populationsof phycoerythrin-containing cryptophytes in Chesapeake Bay.Rates were estimated from instantaneous food vacuole contents,in situ temperatures, cryptophyte abundances and experimentallydetermined digestion rates. Laboratory digestion experimentsshowed that specific digestion rate constants increased sigmoidallywith temperature, but were unrelated to the initial food vacuolecontent when it was <0.46 cryptophytes dinoflagellate^–1.These results allowed us to establish an empirical model toestimate in situ ingestion of cryptophyte prey by G. galatheanum.The estimated rates ranged from 0 to 0.26 cryptophytes dinoflagellate^–1day^–1, corresponding to daily ingestion of 0–12.29pg carbon, 0–2.48 pg nitrogen and 0–0.34 pg phosphorusdinoflagellate^–1. Estimated daily consumption of cryptophytebiomass by G. galatheanum was equivalent to 0–12% of bodycarbon, 0–13% of body nitrogen and 0–21% of bodyphosphorus. Estimated in situ clearance rates for cryptophytesranged from 0 to 0.27 µl dinoflagellate^–1 day^–1,representing daily removal of 0–4% of the cryptophytestanding stock. Although G. galatheanum may increase its growthrate through phagotrophy, it appears to have little grazingimpact on cryptophyte prey populations.     

Hemodynamic Changes Caused by Flow Diverters in Rabbit Aneurysm Models: Comparison of Virtual and Realistic FD Deployments Based on Micro-CT Reconstruction

Adjusting hemodynamics via flow diverter (FD) implantation is emerging as a novel method of treating cerebral aneurysms. However, most previous FD-related hemodynamic studies were based on virtual FD deployment, which may produce different hemodynamic outcomes than realistic (in vivo) FD deployment. We compared hemodynamics between virtual FD and realistic FD deployments in rabbit aneurysm models using computational fluid dynamics (CFD) simulations. FDs were implanted for aneurysms in 14 rabbits. Vascular models based on rabbit-specific angiograms were reconstructed for CFD studies. Real FD configurations were reconstructed based on micro-CT scans after sacrifice, while virtual FD configurations were constructed with SolidWorks software. Hemodynamic parameters before and after FD deployment were analyzed. According to the metal coverage (MC) of implanted FDs calculated based on micro-CT reconstruction, 14 rabbits were divided into two groups (A, MC >35%; B, MC <35%). Normalized mean wall shear stress (WSS), relative residence time (RRT), inflow velocity, and inflow volume in Group A were significantly different (P<0.05) from virtual FD deployment, but pressure was not (P>0.05). The normalized mean WSS in Group A after realistic FD implantation was significantly lower than that of Group B. All parameters in Group B exhibited no significant difference between realistic and virtual FDs. This study confirmed MC-correlated differences in hemodynamic parameters between realistic and virtual FD deployment.     

Analysis of Square Contingency Tables with Ordered Categories by a New Method of Applying the 1-Weight Modified Marginal Homogeneity Models

For square contingency tables with ordered categories, this note proposes a new method of applying Tomizawa's (1987) 1-weight modified marginal homogeneity models and applies to the 4×4 tables on unaided vision analysed by Tomizawa (1987) and by Stuart (1955). A possible explanation which is derived from fitting those models is first obtained using this new method.     

Development of a New Method to Track Multiple Honey Bees with Complex Behaviors on a Flat Laboratory Arena

A computer program that tracks animal behavior, thereby revealing various features and mechanisms of social animals, is a powerful tool in ethological research. Because honeybee colonies are populated by thousands of bees, individuals co-exist in high physical densities and are difficult to track unless specifically tagged, which can affect behavior. In addition, honeybees react to light and recordings must be made under special red-light conditions, which the eyes of bees perceive as darkness. The resulting video images are scarcely distinguishable. We have developed a new algorithm, K-Track, for tracking numerous bees in a flat laboratory arena. Our program implements three main processes: (A) The object (bee''s) region is detected by simple threshold processing on gray scale images, (B) Individuals are identified by size, shape and spatiotemporal positional changes, and (C) Centers of mass of identified individuals are connected through all movie frames to yield individual behavioral trajectories. The tracking performance of our software was evaluated on movies of mobile multi-artificial agents and of 16 bees walking around a circular arena. K-Track accurately traced the trajectories of both artificial agents and bees. In the latter case, K-track outperformed Ctrax, well-known software for tracking multiple animals. To investigate interaction events in detail, we manually identified five interaction categories; ‘crossing’, ‘touching’, ‘passing’, ‘overlapping’ and ‘waiting’, and examined the extent to which the models accurately identified these categories from bee''s interactions. All 7 identified failures occurred near a wall at the outer edge of the arena. Finally, K-Track and Ctrax successfully tracked 77 and 60 of 84 recorded interactive events, respectively. K-Track identified multiple bees on a flat surface and tracked their speed changes and encounters with other bees, with good performance.     

A New Extraction Method of Loess Shoulder-Line Based on Marr-Hildreth Operator and Terrain Mask

Loess shoulder-lines are significant structural lines which divide the complicated loess landform into loess interfluves and gully-slope lands. Existing extraction algorithms for shoulder-lines mainly are based on local maximum of terrain features. These algorithms are sensitive to noise for complicated loess surface and the extraction parameters are difficult to be determined, making the extraction results usually inaccurate. This paper presents a new extraction approach for loess shoulder-lines, in which Marr-Hildreth edge operator is employed to construct initial shoulder-lines. Then the terrain mask for confining the boundary of shoulder-lines is proposed based on slope degree classification and morphology methods, avoiding interference from non-valley area and modify the initial loess shoulder-lines. A case study is conducted in Yijun located in the northern Shanxi Loess Plateau of China. The Digital Elevation Models with a grid size of 5 m is applied as original data. To obtain optimal scale parameters, the Euclidean Distance Offset Percentages between shoulder-lines is calculated by the Marr-Hildreth operator and the manual delineations. The experimental results show that the new method could achieve the highest extraction accuracy when σ = 5 in Gaussian smoothing. According to the accuracy assessment, the average extraction accuracy is about 88.5%, which indicates that the proposed method is applicable for the extraction of loess shoulder-lines in the loess hilly and gully areas.