Basic strategies for valid cytometry using image analysis

The present review provides a starting point for setting up an image analysis system for quantitative densitometry and absorbance or fluorescence measurements in cell preparations, tissue sections or gels. Guidelines for instrumental settings that are essential for the valid application of image analysis in cytophotometry and cytofluorometry are described. The general principles of the working mechanism of CCD cameras in combination with general methods to improve the behaviour of the cameras are presented. Optimization of illumination of microscopical and macroscopical objects receives special attention because of its importance for valid cytometry. Sources of errors in quantitative measurements are listed and step-by-step charts for tuning the CCD camera, frame grabber and illumination for the optimal use of the systems are described. Suggestions are given for improvement of image arithmetics in difficult imaging situations, such as low fluorescence signals and high absorbance signals. This revised version was published online in November 2006 with corrections to the Cover Date.     

Result verification, code verification and computation of support values in phylogenetics

Verification in phylogenetics represents an extremely difficult subject. Phylogenetic analysis deals with the reconstruction of evolutionary histories of species, and as long as mankind is not able to travel in time, it will not be possible to verify deep evolutionary histories reconstructed with modern computational methods. Here, we focus on two more tangible issues that are related to verification in phylogenetics (i) the inference of support values on trees that provide some notion about the 'correctness' of the tree within narrow limits and, more importantly; (ii) issues pertaining to program verification, especially with respect to codes that rely heavily on floating-point arithmetics. Program verification represents a largely underestimated problem in computational science that can have fatal effects on scientific conclusions.     

Does the weight of the brain depend on the body height?]

Brains of 1664 subjects (895 males and 769 females) aged from 20 to 89 years have been studied. The whole material being investigated was divided, within sex groups, into body-height classes and age classes. The class interval within the age classes was 10 years, that in height classes 5 cm. Mean arithmetics, standard deviations, standard error as well as coefficients of variation and correlation for respective classes have been calculated. It has been ascertained that the brain weight depends on the body height. In tall subjects no brains of extremely low absolute weight are encountered and, adversely, high brain weight is seldom met in short individuals. The body height also exerts certain influence upon the relative weight of the brain. More favourable proportion between the brain weight and the body length has been revealed in short subjects. Tall individuals are characterized by a low relative weight of the brain. It should be supposed that the spinal cord weight is higher in the latter subjects. The differences between the mean absolute weight of women's brains and that in men of the same age class are conditioned by the difference in the body length. A constant magnitude of difference in the mean brain weight in subjects of the same body height claims 100 g. The paper provides 2 enclosed tables representing obtained results for arithmetic mean of the absolute brain weight both in the age classes and body height classes. The differences between the mean weights of brains in women as well as in men are not significant. The coefficient of correlation between the brain weight and the body height is for men r male1 = 0.2008 for women r female1 = 0.2630, wherease the coefficient of regression for the brain weight is r male2 = 3.67 and r female2 = 3.906 respectively.     

Determination of kerosene and #2 diesel in soil by purge and trap vs. extraction procedure

Low‐ to medium‐boiling‐point hydrocarbons, which include the full range of gasoline (C4‐C12), are routinely analyzed by using headspace or purge and trap with gas chromatography techniques. Some of the higher boiling point hydrocarbons, including diesel motor fuels (C9‐C22) and kerosene (C10‐C16), are normally analyzed by using sonication extraction with gas chromatography technique. However, since both of these groups are medium range in numbers of hydrocarbons as well as boiling point, analysis by elevated temperature purge and trap (85°C) may prove to be an accurate and time‐saving method of analysis. Testing by purge and trap may prove successful for both kerosene (b.p. 175 to 328°C) and #2 diesel (b.p. 179 to 360°C). This research is designed to compare data using the high‐temperature purge and trap technique to the data obtained by the sonication extraction technique.     

Digital radiography for target point evaluation in stereotactic neurosurgery

Today, the usual target point evaluation during stereotactic operations using planar X-ray films can be supplemented by digital video storage. The picture-delivering system is a digital X-ray video chain which replaces the X-ray film. Evaluation of target point coordinates as well as parameters of electrode approach and positioning are determined by a microcomputer. Such an inexpensive system is described.     

Exciton interactions in synthetic porphyrin dimers

The Soret absorption spectra of six synthetic rigid porphyrin dimers whose crystal structures have been determined are simulated using simple exciton theory. The objective is to test the validity of the point dipole and associated approximations; the electronic interaction parameters are thus calculated using data obtained from the monomer spectra, with no adjustable parameters. Satisfactory agreement between theory and experiment is obtained for one class of dimers but not for a second. This poses a challenge for semiempirical electronic structure methods as to whether improvements over the point dipole calculations can be obtained.     

A point process driven multiple change point model: A robust resistant approach

Helicases are a class of enzymes involved in Ribonucleic Acid (RNA) metabolism. In this work a statistical method is proposed to analyze the individual mechanistic cycle of these motor proteins which are crucial to the understanding of their cellular functions. The RNA unwinding by NS3 helicase is hypothesized to occur in a series of discrete steps and the steps themselves occurring in accordance to an underlying point process. A point process driven multiple change point model is proposed to model the RNA unwinding mechanism. The methods are portable to other areas of applications as well. Algorithms based on robust-resistant statistical procedures are proposed to detect the change points. Both sequential and a posteriori change point models are considered. The relevant parameters of interest are estimated using a maximum likelihood approach. Simulations are performed to assess the performance of the methodology.     

Three-Dimensional Geometrical Modelling of Wild Boar Head by Reverse Engineering Technology

In this paper, a wild boar head was taken as the bionic research object for the development of new ridgers, a kind of plough. The reverse engineering technology was adopted to obtain the surface geometrical information of the head. Several three-dimensional （3D） point clouds of the head were captured first using a non-touch laser scanner, and an integrated point cloud was generated by aligning these point clouds using UG/Imageware. Then, the digital surface model of the head was rebuilt by means of CATIA. The characteristic curves of the surface model were analyzed. The results show that the average error between the rebuilt surface and the point cloud is -0.431 ram. The max curvature of the ridge on the neb of the head is 0.187 mm^-1, and the max and rain Gauss curvatures on the surface are 0.008 mm^-2 and -0.002 mm^-2. These geometrical information are the essential parameters for biomimetics study of the ridger.     

Comparative evaluation of three sampling methods to estimate detection probability of American red squirrels (Tamiasciurus hudsonicus)

Measuring changes in species distribution and understanding factors influencing site occupancy are recurring goals in wildlife studies. Imperfect detection of species hinders such studies, resulting in the underestimation of the number of sites occupied by the species of interest. American red squirrels (Tamiasciurus hudsonicus) are sampled traditionally with live-traps that require substantial resources to deploy and monitor. Here, we assessed whether auditory methods yield similar detection probabilities. We compared the detection probability of American red squirrels in boreal forest using point counts, playback counts, and live-trapping. Over the summer of 2014, we conducted three trapping sessions in 60 sites within black spruce forests of northwestern Quebec, Canada. We also conducted 10 min point counts in the same sites, together with playback counts using recordings of American red squirrel alarm and territorial calls. Using dynamic occupancy models to analyse three primary periods, all composed of three secondary periods, we found that the detection probability of squirrels from point counts was as high as with live-trapping. Our results thus highlight the value of the point count method in measuring American red squirrel occupancy.     

Extraction and PCR of DNA From Parasitoid Wasps That Have Been Chemically Dried

Two species of parasitic wasp, Venturia canescens and Leptomastix dactylopii , were dried from alcohol using a range of methods proposed as chemical alternatives to critical point drying, i.e. hexamethyldisilazane (HMDS), amyl acetate, xylene, methyl cellusolve and acetone vapour. Also, fresh specimens of V. canescens were dried using acetone vapour, first as a fixative and then as a drying agent. Total genomic DNA was subsequently extracted and a 524 bp fragment of the mitochondrial 16S ribosomal RNA gene amplified by PCR. This indicated that all of these drying techniques yielded high-quality DNA which was amenable to PCR. the success of chemicals like HMDS as alternate rapid drying methods for wasps and other insects means that they are likely to replace critical point drying (CPD) of museum specimens in the near future. Importantly, the results from this study show that specimens, dried from alcohol using chemical techniques, are a good potential source of DNA for molecular systematics projects.     

Fast and Accurate Registration of the Proximal Femurs in Bilateral Hip Joint Images by Using the Random Sub-Sample Points

Background and ObjectiveAs is known, point clouds representing the objects are frequently used in object registration. Although the objects can be registered by using all the points in the corresponding point clouds of the objects, the registration process can also be achieved with a smaller number of the landmark points selected from the entire point clouds of the objects. This paper introduces a research study focusing on the fast and accurate rigid registration of the bilateral proximal femurs in bilateral hip joint images by using the random sub-sample points. For this purpose, Random Point Sub-sampling (RPS) was analyzed and the reduced point sets were used for an accurate registration of the bilateral proximal femurs in coronal hip joint magnetic resonance imaging (MRI) slices.MethodsIn registration, bilateral proximal femurs in MRI slices were registered rigidly by performing a process consisting of three main phases named as MR image preprocessing, proximal femur registration over the random sub-sample points and MR image postprocessing. In the stage of the MR image preprocessing, segmentation maps of the bilateral proximal femurs are obtained as region of interest (RoI) images from the entire MRI slices and then, the edge maps of the segmented proximal femurs are extracted. In the registration phase, the edge maps describing the proximal femur surfaces are represented as point clouds initially. Thereafter, the RPS is performed on the proximal femur point clouds and the number of points representing the proximal femurs is reduced at different ratios. For the registration of the point clouds, the Iterative Closest Point (ICP) algorithm is performed on the reduced sets of points. Finally, the registration procedures are completed by performing MR image postprocessing on the registered proximal femur images.ResultsIn performance evaluation tests performed on healthy and pathological proximal femurs in 13 bilateral coronal hip joint MRI slices of 13 Legg-Calve-Perthes disease (LCPD) patients, bilateral proximal femurs were successfully registered with very small error rates by using the reduced set of points obtained via the RPS and promising results were achieved. The minimum error rate was observed at RPS rate of 30% as the value of 0.41 (±0.31)% on all over the bilateral proximal femurs evaluated. When the range of RPS rate of 20-30% is considered as the reference, the elapsed time in registration can be reduced by almost 30-40% compared to the case where all the proximal femur points were included in registration. Additionally, it was observed that the RPS rate should be selected as at least 25% to achieve a successful registration with an error rate below 1%.ConclusionIt was concluded from the observed results that a more successful and faster registration can be accomplished by selecting fewer points randomly from the point sets of proximal femurs instead of using all the points describing the proximal femurs. Not only an accurate registration with low error rates was performed, but also a faster registration process was performed by means of the limited number of points that are sub-sampled randomly from the whole point sets.     

Multitype spatial point patterns with hierarchical interactions

Multitype spatial point patterns with hierarchical interactions are considered. Here hierarchical interaction means directionality: points on a higher level of hierarchy affect the locations of points on the lower levels, but not vice versa. Such relations are common, for example, in ecological communities. Interacting point patterns are often modeled by Gibbs processes with pairwise interactions. However, these models are inherently symmetric, and the hierarchy can be acknowledged only when interpreting the results. We suggest the following in allowing the inclusion of the hierarchical structure in the model. Instead of regarding the pattern as a realization of a stationary multivariate point process, we build the pattern one type at a time according to the order of the hierarchy by using nonstationary univariate processes. As interactions connected to points x on a certain level are considered, the effect of the higher levels is interpreted as heterogeneity of the pattern x, and the points on the lower levels are neglected because of the hierarchical structure.     

A plasmid rescue technique for the recovery of plant DNA disrupted by T-DNA insertion

Arabidopsis mutants generated by insertion of the T-DNA from Ti plasmid 3850∶1003 serve as a starting point for the isolation of novel genes. The disrupted plant DNA can be recovered using a plasmid rescue technique utilizing high efficiency electroporation. Rescued plasmids are resistant to ampicillin and contain an origin of replication from pBR322. Plasmids generated from either the left or right border of the T-DNA that carry flanking DNA sequences can be identified by analyzing the products of restriction enzyme digests on agarose gels. The plasmids with flanking sequences can then serve as a starting point for cloning plant sequences that share homology to the DNA at the point of T-DNA insertion.     

RNAmute: RNA secondary structure mutation analysis tool

Background  

RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation.     

Determination of Relative Bacterial Levels on Carcasses and Meats—a New Quick Method

A new method for bacterial surface sampling meats is described. Using a cotton wool swab stick, bacteria are transferred directly to the surface of a segment (= 1/6) of an agar plate. After incubation, the number of colonies is estimated using a comparator disc, giving the result in point values of 1/3 of a log₁₀-unit. The average point value is then converted into the average number of colonies per segment using a Table. In order to emphasize that the results should be regarded as relative levels rather than actual bacterial counts, the result should be recorded as 'bacteria/sample'—not 'bacteria/cm^2'.     

The minimal model of the hypothalamic–pituitary–adrenal axis

This paper concerns ODE modeling of the hypothalamic–pituitary– adrenal axis (HPA axis) using an analytical and numerical approach, combined with biological knowledge regarding physiological mechanisms and parameters. The three hormones, CRH, ACTH, and cortisol, which interact in the HPA axis are modeled as a system of three coupled, nonlinear differential equations. Experimental data shows the circadian as well as the ultradian rhythm. This paper focuses on the ultradian rhythm. The ultradian rhythm can mathematically be explained by oscillating solutions. Oscillating solutions to an ODE emerges from an unstable fixed point with complex eigenvalues with a positive real parts and a non-zero imaginary parts. The first part of the paper describes the general considerations to be obeyed for a mathematical model of the HPA axis. In this paper we only include the most widely accepted mechanisms that influence the dynamics of the HPA axis, i.e. a negative feedback from cortisol on CRH and ACTH. Therefore we term our model the minimal model. The minimal model, encompasses a wide class of different realizations, obeying only a few physiologically reasonable demands. The results include the existence of a trapping region guaranteeing that concentrations do not become negative or tend to infinity. Furthermore, this treatment guarantees the existence of a unique fixed point. A change in local stability of the fixed point, from stable to unstable, implies a Hopf bifurcation; thereby, oscillating solutions may emerge from the model. Sufficient criteria for local stability of the fixed point, and an easily applicable sufficient criteria guaranteeing global stability of the fixed point, is formulated. If the latter is fulfilled, ultradian rhythm is an impossible outcome of the minimal model and all realizations thereof. The second part of the paper concerns a specific realization of the minimal model in which feedback functions are built explicitly using receptor dynamics. Using physiologically reasonable parameter values, along with the results of the general case, it is demonstrated that un-physiological values of the parameters are needed in order to achieve local instability of the fixed point. Small changes in physiologically relevant parameters cause the system to be globally stable using the analytical criteria. All simulations show a globally stable fixed point, ruling out periodic solutions even when an investigation of the ‘worst case parameters’ is performed.     

Establishment of a screening system for essential genes from the pathogenic yeast Candida glabrata: identification of a putative TEM1 homologue

Aims:  To establish a system for screening and identification of essential genes from the pathogenic haploid yeast Candida glabrata by using temperature-sensitive (ts) mutants.
Methods and Results:  Based on the general concepts that ts mutations are generated within essential genes in the genome by virtue of point mutation, we attempted to establish a system where essential genes were screened and identified from the C. glabrata genomic DNA library by the complementation of ts point mutations. By using this system, we successfully identified a putative TEM1 homologue as an essential gene by the complementation of a point mutation (- G AT-/- A AT- corresponding to Asp-143/Asn substitution) within its coding region in a ts mutant, T-3.
Conclusions:  We were able to establish a system for screening and identification of the essential genes, such as the TEM1 homologue, from the pathogenic yeast C. glabrata, as the gene that complements ts mutation.
Significance and Impact of the Study:  The identification of essential genes, by using the present system, may provide novel potential antifungal targets.     

Using soundscape recordings to estimate bird species abundance, richness, and composition

ABSTRACT Point counts are the most frequently used technique for sampling bird populations and communities, but have well‐known limitations such as inter‐ and intraobserver errors and limited availability of expert field observers. The use of acoustic recordings to survey birds offers solutions to these limitations. We designed a Soundscape Recording System (SRS) that combines a four‐channel, discrete microphone system with a quadraphonic playback system for surveying bird communities. We compared the effectiveness of SRS and point counts for estimating species abundance, richness, and composition of riparian breeding birds in California by comparing data collected simultaneously using both methods. We used the temporal‐removal method to estimate individual bird detection probabilities and species abundances using the program MARK. Akaike's Information Criterion provided strong evidence that detection probabilities differed between the two survey methods and among the 10 most common species. The probability of detecting birds was higher when listening to SRS recordings in the laboratory than during the field survey. Additionally, SRS data demonstrated a better fit to the temporal‐removal model assumptions and yielded more reliable estimates of detection probability and abundance than point‐count data. Our results demonstrate how the perceptual constraints of observers can affect temporal detection patterns during point counts and thus influence abundance estimates derived from time‐of‐detection approaches. We used a closed‐population capture–recapture approach to calculate jackknife estimates of species richness and average species detection probabilities for SRS and point counts using the program CAPTURE. SRS and point counts had similar species richness and detection probabilities. However, the methods differed in the composition of species detected based on Jaccard's similarity index. Most individuals (83%) detected during point counts vocalized at least once during the survey period and were available for detection using a purely acoustic technique, such as SRS. SRS provides an effective method for surveying bird communities, particularly when most species are detected by sound. SRS can eliminate or minimize observer biases, produce permanent records of surveys, and resolve problems associated with the limited availability of expert field observers.     

A review on data mining and continuous optimization applications in computational biology and medicine

An emerging research area in computational biology and biotechnology is devoted to mathematical modeling and prediction of gene‐expression patterns; it nowadays requests mathematics to deeply understand its foundations. This article surveys data mining and machine learning methods for an analysis of complex systems in computational biology. It mathematically deepens recent advances in modeling and prediction by rigorously introducing the environment and aspects of errors and uncertainty into the genetic context within the framework of matrix and interval arithmetics. Given the data from DNA microarray experiments and environmental measurements, we extract nonlinear ordinary differential equations which contain parameters that are to be determined. This is done by a generalized Chebychev approximation and generalized semi‐infinite optimization. Then, time‐discretized dynamical systems are studied. By a combinatorial algorithm which constructs and follows polyhedra sequences, the region of parametric stability is detected. In addition, we analyze the topological landscape of gene‐environment networks in terms of structural stability. As a second strategy, we will review recent model selection and kernel learning methods for binary classification which can be used to classify microarray data for cancerous cells or for discrimination of other kind of diseases. This review is practically motivated and theoretically elaborated; it is devoted to a contribution to better health care, progress in medicine, a better education, and more healthy living conditions. Birth Defects Research (Part C) 87:165–181, 2009. © 2009 Wiley‐Liss, Inc.