Variation within teosinte. III. numerical analysis of allozyme data

Principal components analysis of isozyme allele frequencies at 19 loci revealed 133 electrophoretic variants for 77 accessions of annual teosinte and 1 accession each of diploid and tetraploid perennial teosintes. The majority of alleles were found in low frequency, and many were distributed only in specific locations. Zea luxuriansand the annual Mexican teosintes appeared to be the most distantly related of all teosintes. Z. perennisand Z. diploperennisappeared distinct from each other and from all other teosintes. Teosintes of west Guatemala (Huehuetenango) did not appear especially closely related to Balsas teosintes. Several differences were apparent between Chalco and Central Plateau teosintes;however, these differences were not so extreme as those suggested by chromosome knob data. Nobogame teosintes appeared closely related to Chalco and Central Plateau teosintes. Isozyme data reveal teosinte to be a diverse source of germplasm.     

Evaluation and re-evaluation of genetic radiation hazards in man III. Other relevant data and risk assessment

Some of the advances in mammalian radiation genetics, human genetics and cytogenetics that were made during the last 2–3 years and that have either a direct bearing on, or that may be potentially useful in, the evaluation of genetic radiation hazards in man have been examined. Among these are (1) the new data on the incidence of genetic diseases in man; (2) the latest results of the study of mortality rates among children born to survivors of the atomic bombings of Hiroshima and Nagasaki; (3) new data on the radition-induction of reciprocal translocations in human spermatogonia; (4) new results from radiation studies with mice on skeletal mutations, autosomal recessive lethals, sex-chromosome losses, translocation induction and recovery etc., and (5) a re-analysis of the earlier data on dose-rate effects for the induction of specific locus mutations in mouse spermatogonia. Using the pertinent new information as a basis, quantitative estimates are presented employing both a direct method of expressing risks in terms of effects per unit dose of irradiation and the indirect doubling-dose method of expressing these as increments over the load of genetic disorders occuring spontaneously in man.     

Evoked potential measurement and analysis on a small laboratory computer

A program is described for the collection and subsequent analysis of somatosensory evoked potentials using a LINC-8 computer. The program allows simple evoked-potentials analysis in centers where a small laboratory computer may be available but sophisticated instrumentation such as a computer of average transients is not available. This program provides an efficient method of easily obtaining information concerning the conduction pathways of the nervous system as well as the cerebral function; the program can be implemented on small laboratory computers which most hospitals currently own, without the associated cost or complexity of additional hardware in the laboratory. Combining utilization of a small laboratory computer with an easily programmable method provides an approach for evoked potential analysis which is well within the financial and technical scope of most neurophysiology laboratories.     

Computerized topographical analysis of functionally homogeneous neuronal sets.

A computer-assisted analysis of the spatial distribution of neurons having homogeneous characteristics is described in this paper. The camera lucida drawings of sections of a brain nucleus and the points representing the neurons labeled on the basis of a specific behavior of discharge rates were digitized on a personal computer Amiga 2000 or IBM compatible. Our software provided: a) the computerized, stereotaxically oriented reconstruction of the stored sections and of the plotted neurons; b) the identification within each section of the mass center (MC) of the units sharing a given behavior and of the area where the density of such neurons was maximal (MDA). The routine was tested on the spatial distribution of neuronal responses to serotonin in the lateral vestibular nucleus.     

准分子激光屈光性角膜切削术（PRK）治疗近视文献计量分析

通过对近十多年来的ＰＲＫ治疗近视的中外文文献计量分析，以揭示该技术的发展过程、现状及尚存在的问题，进一步科学地预测ＰＲＫ治疗近视的发展趋势。     

Computerized graphic display of physiological data collected during human stereotactic surgery.

An on-line computerized graphic display has been developed for use during stereotactic operations. This depicts in the form of figurine charts and alph-numeric symbols, appropriately oriented on saggital brain diagrams, the results of serial threshold stimulation of the brain. The display facilitates choice of target sites and the data can be stored in a tape library from which search-and-plot programs can be activated for any type or combination of types of response.     

Clinico-genetical studies of colonic cancer. III. Primary multiple malignant neoplasms

The results of clinico-genealogic analysis of 46 patients with primary-multiple malignant neoplasms are given (among them 16 patients with primary-multiple malignant neoplasms of colon cancer and 30 patients with one or more neoplasms in combination with different malignant tumors of other organs). The values of segregation rates obtained for primary-multiple malignant neoplasms are lower than theoretically expected for simple monogeneous types of inheritance. The relation analysis of primary-multiple malignant neoplasms and colon cancer revealed that these tumors are likely to appear among relatives of probands under the influence of the same genetic system of determination. Risk of the colon cancer development for relatives of the patients with primary-multiple malignant neoplasms is higher than for relatives of the patients with colon cancer.     

Computerized analysis of enzyme cascade reactions using continuous rate data obtained with an ELISA reader

Two programs have been written which permit analysis of multiple continuous-rate enzyme-cascade assays conducted with the use of an ELISA spectrophotometer and a synthetic chromogenic substrate. Because the product of the first reaction functions as the enzyme in the second reaction, production of chromophore continuously accelerates and it is the rate of acceleration which serves to measure the rate of the initial reaction in the system. The first program determines the rate of acceleration using linear regression to analyze the reaction curves as a function of the square of time. The second program, using a Simplex algorithm, determines the parameters which establish the assay standard curve by fitting the rate data to the Hill equation. Used together, these programs facilitate the analysis of many kinetic experiments conducted simultaneously.     

The detection and measurement of recombination from sequence data.

There are two types of recombination that we may wish to detect: rare recombinants between members of different populations or species and repeated recombination within a population. Methods appropriate in the former context are inappropriate in the latter because they depend on recognizing the existence of runs of nucleotides with similar ancestry. If recombination is sufficiently frequent, no such runs will be present. Several methods, including the homoplasy test and the incompatibility test, are described that are appropriate for detecting repeated recombination and for measuring its importance, relative to mutation, in causing genetic change. The sensitivity of these tests is investigated by simulating populations with varying frequencies of mutation and recombination and calculating the various statistics on samples.     

Quality assessment of measurement

Assessing the quality of measurements is of interest to organizers of external quality assessment schemes (EQAS, or proficiency testing schemes), laboratory analysts and managers, users of laboratory results and other agencies. Scheme organizers run test programmes, define standards of acceptable and non-acceptable performance, and interact with participants and oversight authorities. Laboratory personnel are responsible for the quality management system and to choose whether to accept the standards set by scheme organizers or to adopt their own. Users receive and act upon the laboratory results.Schemes within the same analytical sector are often organized very differently causing contradictory assessment of performance. The Network of EQAS in occupational and environmental laboratory medicine established collaborative projects designed to enhance assessment of measurement quality and to improve the reliability of laboratory results.To address the issue of variations in assessing the quality of measurements, and in response to comments from some participants, standards derived from biological variation, rather than on the analytical performance of participants have been developed. Evaluation of test materials with respect to homogeneity and stability, and work on methods to give the assigned value to test materials, has also been undertaken. Following from these projects, further collaboration is planned which will provide better quality assessment of measurement to scheme participants and their users.     

Biological assessment of robust noise models in microarray data analysis

MOTIVATION: Although several recently proposed analysis packages for microarray data can cope with heavy-tailed noise, many applications rely on Gaussian assumptions. Gaussian noise models foster computational efficiency. This comes, however, at the expense of increased sensitivity to outlying observations. Assessing potential insufficiencies of Gaussian noise in microarray data analysis is thus important and of general interest. RESULTS: We propose to this end assessing different noise models on a large number of microarray experiments. The goodness of fit of noise models is quantified by a hierarchical Bayesian analysis of variance model, which predicts normalized expression values as a mixture of a Gaussian density and t-distributions with adjustable degrees of freedom. Inference of differentially expressed genes is taken into consideration at a second mixing level. For attaining far reaching validity, our investigations cover a wide range of analysis platforms and experimental settings. As the most striking result, we find irrespective of the chosen preprocessing and normalization method in all experiments that a heavy-tailed noise model is a better fit than a simple Gaussian. Further investigations revealed that an appropriate choice of noise model has a considerable influence on biological interpretations drawn at the level of inferred genes and gene ontology terms. We conclude from our investigation that neglecting the over dispersed noise in microarray data can mislead scientific discovery and suggest that the convenience of Gaussian-based modelling should be replaced by non-parametric approaches or other methods that account for heavy-tailed noise.     

Critical assessment of microarray data analysis: the 2001 challenge

We initiated the Critical Assessment of Microarray Data Analysis (CAMDA) conference to stimulate and evaluate the development of advanced data analysis techniques for microarrays. A standard data set has been released for this data analysis challenge. The goal of this challenge is to assess the performance of different analytical methods and at the same time to determine how such methods should be evaluated. We hope this effort will catalyze the discussion of microarray data analysis among the research community of biologists, statisticians, mathematicians, and computer scientists. AVAILABILITY: http://camda.duke.edu.     

Predicting gene function through systematic analysis and quality assessment of high-throughput data

MOTIVATION: Determining gene function is an important challenge arising from the availability of whole genome sequences. Until recently, approaches based on sequence homology were the only high-throughput method for predicting gene function. Use of high-throughput generated experimental data sets for determining gene function has been limited for several reasons. RESULTS: Here a new approach is presented for integration of high-throughput data sets, leading to prediction of function based on relationships supported by multiple types and sources of data. This is achieved with a database containing 125 different high-throughput data sets describing phenotypes, cellular localizations, protein interactions and mRNA expression levels from Saccharomyces cerevisiae, using a bit-vector representation and information content-based ranking. The approach takes characteristic and qualitative differences between the data sets into account, is highly flexible, efficient and scalable. Database queries result in predictions for 543 uncharacterized genes, based on multiple functional relationships each supported by at least three types of experimental data. Some of these are experimentally verified, further demonstrating their reliability. The results also generate insights into the relative merits of different data types and provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: f.c.p.holstege@med.uu.nl SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network.     

Spatio-temporal gap analysis of OBIS-SEAMAP project data: assessment and way forward

The OBIS-SEAMAP project has acquired and served high-quality marine mammal, seabird, and sea turtle data to the public since its inception in 2002. As data accumulated, spatial and temporal biases resulted and a comprehensive gap analysis was needed in order to assess coverage to direct data acquisition for the OBIS-SEAMAP project and for taxa researchers should true gaps in knowledge exist. All datasets published on OBIS-SEAMAP up to February 2009 were summarized spatially and temporally. Seabirds comprised the greatest number of records, compared to the other two taxa, and most records were from shipboard surveys, compared to the other three platforms. Many of the point observations and polyline tracklines were located in northern and central Atlantic and the northeastern and central-eastern Pacific. The Southern Hemisphere generally had the lowest representation of data, with the least number of records in the southern Atlantic and western Pacific regions. Temporally, records of observations for all taxa were the lowest in fall although the number of animals sighted was lowest in the winter. Oceanographic coverage of observations varied by platform for each taxa, which showed that using two or more platforms represented habitat ranges better than using only one alone. Accessible and published datasets not already incorporated do exist within spatial and temporal gaps identified. Other related open-source data portals also contain data that fill gaps, emphasizing the importance of dedicated data exchange. Temporal and spatial gaps were mostly a result of data acquisition effort, development of regional partnerships and collaborations, and ease of field data collection. Future directions should include fostering partnerships with researchers in the Southern Hemisphere while targeting datasets containing species with limited representation. These results can facilitate prioritizing datasets needed to be represented and for planning research for true gaps in space and time.     

A kinetic analysis of the electrogenic pump ofChara corallina: III. Pump activity during action potential

Summary The current-voltage curve (I–V curve) of theChara membrane was obtained by applying a slow ramp hyper- and depolarization by use of voltage clamp. By inhibiting the electrogenic pump with 50m DCCD (dicyclohexylcarbodiimide), theI–V curve approached a steadyI–V curve within two hours, which gave thei _d -V curve of the passive diffusion channel. Thei _p -V curve of the electrogenic pump channel was obtained by subtracting the latter from the former. The sigmoidali _p -V curve could be simulated satisfactorily with a simple reaction kinetic model which assumes a stoichiometric ratio of 2. The emf of the pump (E _p ) is given as the voltage at which the pump current changes its sign. The conductance of the pump (g _p ) can be calculated as the chord conductance from thei _p -V curve, which is highly voltage dependent having a peak at a definite voltage. The changes of emf and conductance during excitation were determined by use of the current clamp (I=0). Since theE _p andg _p (V) are known, the changes, during excitation, of emf (E _d ) and conductance (g _d ) of the passive diffusion channel can be calculated. The marked increase of the membrane conductance and the large depolarization during the action potential are caused by the marked increase of the conductance of the passive diffusion channel and the large depolarization of its emf. The conductance of the electrogenic pump decreases to about half at the peak of action potential, while the pump current increases almost to a saturated level.