A Test for the Equality of Variances in the Paired Case with Incomplete Data

A modification of the numbers of degrees of freedom which makes the F ratio test of the equality of two variances applicable also in the paired case with incomplete data is suggested. Monte Carlo simulation studies indicate that the suggested test is reasonably powerful in many cases.     

A computer system for real-time data acquisition and analysis of biopotentials and quantal content at the neuromuscular junction

A computerized data acquisition system for on-line analysis of the parameters of neuromuscular transmission is described. Both hardware usage and software methodologies are discussed with regard to sampling in real-time and analyzing miniature end-plate potentials (MEPPs), end-plate potentials (EPPs) and quantal content of the evoked transmitter release. Significant features of the program include: (1) automatic threshold determination for MEPP detection; (2) the use of a circular buffer to give pre-trigger information; (3) real-time noise spike rejection; (4) an automatic procedure for EPP failure detection; (5) rapid quantal content determinations by several methods as well as complete MEPP and EPP waveform analysis. The system has proven both accurate and reliable during more than two years of use. Advantages of the system over conventional methods include: (1) increased accuracy and efficiency in data analysis; (2) immediate availability of results; (3) conventional data storage; (4) flexibility to meet changing requirements.     

A sampling study of the size and power of tests for paired survival data

The paired-t, sign, and signed rank tests were compared for samples from a bivariate exponential distribution. Each is a valid α-level test. One test was not uniformly more powerful than the others for all sample sizes, α levels, correlations, and alternative hypotheses considered, but the signed rank test did well consistently. It was always preferable to the sign test and never was appreciably worse than the paired-t test. The relative performance of the tests depends on α as well as the sample size.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment

The dynamics of a proteome can only be addressed with large-scale, high-throughput methods. To cope with the inherent complexity, techniques based on targeted quantification using proteotypic peptides are arising. This is an essential systems biology approach; however, for the exploratory discovery of unexpected markers, nontargeted detection of proteins, and protein modifications is indispensable. We present a rapid label-free shotgun proteomics approach that extracts relevant phenotype-specific peptide product ion spectra in an automated workflow without prior identification. These product ion spectra are subsequently sequenced with database search and de novo prediction algorithms. We analyzed six potato tuber cultivars grown on three plots of two geographically separated fields in Germany. For data mining about 1.5 million spectra from 107 analyses were aligned and statistically examined in approximately 1 day. Several cultivar-specific protein markers were detected. Based on de novo-sequencing a dominant protein polymorphism not detectable in the available EST-databases was assigned exclusively to a specific potato cultivar. The approach is applicable to organisms with unsequenced or incomplete genomes and to the automated extraction of relevant mass spectra that potentially cannot be identified by genome/EST-based search algorithms.     

The circulatory system in Phreatoicidea: implications for the isopod ground pattern and peracarid phylogeny

The circulatory systems of four species of Phreatoicidea and two species of Oniscidea were studied on the basis of serial semi-thin sections and a corrosion cast method. A 3D computer reconstruction was used to visualize the circulatory organs in the head of the Phreatoicidea. In the Phreatoicidea, the circulatory system consists of a longitudinal dorsal heart extending from the third thoracic to the border between the fourth and fifth pleonal segments. It is equipped with two pairs of asymmetrically arranged ostia, while five pairs of lateral cardiac arteries and an unpaired anterior aorta extend from the heart. Entering the head, the aorta is accompanied by the two first lateral arteries, which supply the muscles of the mandibles. Four pairs of arteries branch off the aorta to supply both pairs of antennae, the eyes, and sinuses in the head. In addition, several minute capillaries extend from the aorta to supply the brain. The two oniscidean species were re-investigated with regard to some characters which have been controversially discussed. In these species, the heart extends from the border between the fifth and sixth thoracic segments to the fifth pleonal segment. Five pairs of lateral cardiac arteries and the unpaired anterior aorta lead off the heart. A ventral vessel was not observed. The ground pattern of the circulatory system in isopods is reconstructed with greater reliability through optimisation of its characters based on proposed phylogenetic relationships. The results do not support a phylogenetic position of the Isopoda as basal Peracarida or even basal Eumalacostraca.     

NMR View: A computer program for the visualization and analysis of NMR data

Summary NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak analysis features are included to aid in the assignment of complex NMR spectra. NMR View provides structure analysis features and data transfer to and from structure generation programs, allowing for a tight coupling between spectral analysis and structure generation. Visual correlation between structures and spectra can be done with the Molecular Data Viewer, a molecular graphics program with bidirectional communication to NMR View. The user interface can be customized and a command language is provided to allow for the automation of various tasks.Inquiries concerning the availability of NMR View and the Molecular Data Viewer should be sent via email to johnsonb@merck.com or to Bruce A. Johnson, Merck Research Laboratories, RY80Y-103, P.O. Box 2000, Rahway, NJ 07065, U.S.A.     

The use of climatic parameters and indices in vegetation distribution. A case study in the Spanish Sistema Central

In this study, over 100 phytoclimatic indices and other climatic parameters were calculated using the climatic data from 260 meteorological stations in a Mediterranean territory located in the centre of the Iberian Peninsula. The nature of these indices was very different; some of them expressed general climatic features (e.g. continentality), while others were formulated for different Mediterranean territories and included particular limits of those indices that expressed differences in vegetation distribution. We wanted to know whether all of these indices were able to explain changes in vegetation on a spatial scale, and whether their boundaries worked similarly to the original territory. As they were so numerous, we investigated whether any of them were redundant. To relate vegetation to climate parameters we preferred to use its hierarchical nature, in discrete units (characterized by one or more dominant or co-dominant species), although it is known to vary continuously. These units give clearer results in this kind of phytoclimatic study. We have therefore used the main communities that represent natural potential vegetation. Multivariate and estimative analyses were used as statistical methods. The classification showed different levels of correlation among climatic parameters, but all of them were over 0.5. One hundred and eleven parameters were grouped into five larger groups: temperature (T), annual pluviothermic indices (PTY), summer pluviothermic indices (SPT), winter potential evapotranspiration (WPET) and thermal continentality indices (K). The remaining parameters showed low correlations with these five groups; some of them revealed obvious spatial changes in vegetation, such as summer hydric parameters that were zero in most vegetation types but not in high mountain vegetation. Others showed no clear results. For example, the Kerner index, an index of thermal continentality, showed lower values than expected for certain particular types of vegetation. Parameters relating to the water balance turned out to be very discriminative for separating vegetation types according to the season or the month when water begins to be scarce. Thus, water availability in soils is a limiting factor for the development of vegetation in spring or autumn as well as in summer. As expected, precipitation and temperature discriminated the altitudinal levels of vegetation. Finally, these index limits only worked in the territories where they were formulated, or in nearby areas.     

Morphological cladistic analysis of eight popular Olive (Olea europaea L.) cultivars grown in Saudi Arabia using Numerical Taxonomic System for personal computer to detect phyletic relationship and their proximate fruit composition

Varietal identification of olives is an intrinsic and empirical exercise owing to the large number of synonyms and homonyms, intensive exchange of genotypes, presence of varietal clones and lack of proper certification in nurseries. A comparative study of morphological characters of eight olive cultivars grown in Saudi Arabia was carried out and analyzed using NTSYSpc (Numerical Taxonomy System for personal computer) system segregated smaller fruits in one clade and the rest in two clades. Koroneiki, a Greek cultivar with a small sized fruit shared arm with Spanish variety Arbosana. Morphologic analysis using NTSYSpc revealed that biometrics of leaves, fruits and seeds are reliable morphologic characters to distinguish between varieties, except for a few morphologically very similar olive cultivars. The proximate analysis showed significant variations in the protein, fiber, crude fat, ash and moisture content of different cultivars. The study also showed that neither the size of fruit nor the fruit pulp thickness is a limiting factor determining crude fat content of olives.