Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki ( http://www.codeplex.com/XeO ) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.     

Methods for analysis of unbalanced,longitudinal, growth data

We describe an approach to analysis of growth that does not depend on assumptions about the underlying functional growth pattern and that allows for multiple observations arising from individual-specific, irregularly spaced data. We produce estimated growth curves for predefined subject groups by using LOWESS, a nonparametric smoothing algorithm. We describe how statistical significance of curve features may be evaluated by using the “jackknife,” a sample re-use method; this technique can be used to assess differences between subject groups. We then obtain residuals at each data point by reference to the estimated curve. Consistency of residuals is evaluated as a characteristic of individual subjects, and in the presence of individual consistency, relative size-for-age is then scored by the average residual for each individual. This allows study of relationships between relative size and other individual characteristics such as birth order, dominance rank, or age of maturation. Finally, we indicate flexibility of these methods and alternatives, propose uses related to other questions about growth, and suggest potential applications to variables other than body size. Appendices demonstrate application of the LOWESS and jackknife algorithms to the problem of testing sex differences in growth. © 1992 Wiley-Liss, Inc.     

Molecules and Morphology,Phylogenetics and Genetics

Various explanations can be offered for the incongruence between phylogenetic hypotheses resulting from morphological and molecular data sets. Of these, the possibility that incongruence may result from the mutation of major morphogenetic genes leading to dramatic morphological divergence unaccompanied by equivalent change of the phylogenetic marker molecule(s) used is discussed in detail. As evidence for this hypothesis, several examples for such incongruence are surveyed. It seems possible that in many cases the genetic basis of the morphological characters responsible for the incongruence found may be simple, and that the genes involved may be homologous to genes known from mutant systems. It is suggested that: 1. the systematic documentation of incongruence between molecular and morphological phylogenies may help to assess the frequency of evolutionary change through the mutation of major morphogenetic genes, and that 2. the identification of major morphological characters distinguishing closely related taxa with mutant phenotypes known from mutant systems eventually may allow an experimental approach to the problem of evolutionary change resulting from major genes. Natural taxa suspected to be the result of such processes could be changed morphologically through transformation with the relevant genes.     

Age‐specific,population‐level pedigree of wild black bears provides insights into reproduction,paternity, and maternal effects on offspring apparent survival

Wildlife pedigrees provide insights into ecological and evolutionary processes. DNA obtained from noninvasively collected hair is often used to determine individual identities for pedigrees and other genetic analyses. However, detection rates associated with some noninvasive DNA studies can be relatively low, and genetic data do not provide information on individual birth year. Supplementing hair DNA stations with video cameras should increase the individual detection rate, assuming accurate identification of individuals via video data. Video data can also provide birth year information for individuals captured as young of the year, which can enrich population‐level pedigrees. We placed video cameras at hair stations and combined genetic and video data to reconstruct an age‐specific, population‐level pedigree of wild black bears during 2010–2020. Combining individual birth year with mother–offspring relatedness, we also estimated litter size, interlitter interval, primiparity, and fecundity. We used the Cormack‐Jolly‐Seber model in Program Mark to evaluate the effect of maternal identity on offspring apparent survival. We compared model rankings of apparent survival and parameter estimates based on combined genetic and video data with those based on only genetic data. We observed 42 mother–offspring relationships. Of these, 21 (50%) would not have been detected had we used hair DNA alone. Moreover, video data allowed for the cub and yearling age classes to be determined. Mean annual fecundity was 0.42 (95% CI: 0.27, 0.56). Maternal identity influenced offspring apparent survival, where offspring of one mother experienced significantly lower apparent survival (0.39; SE = 0.15) than that of offspring of four other mothers (0.89–1.00; SE = 0.00–0.06). We video‐documented cub abandonment by the mother whose offspring experienced low apparent survival, indicating individual behaviors (e.g., maternal care) may scale up to affect population‐level parameters (e.g., cub survival). Our findings provide insights into evolutionary processes and are broadly relevant to wildlife ecology and conservation.     

Zero‐modified Poisson model: Bayesian approach,influence diagnostics,and an application to a Brazilian leptospirosis notification data

In this paper, a Bayesian method for inference is developed for the zero‐modified Poisson (ZMP) regression model. This model is very flexible for analyzing count data without requiring any information about inflation or deflation of zeros in the sample. A general class of prior densities based on an information matrix is considered for the model parameters. A sensitivity study to detect influential cases that can change the results is performed based on the Kullback–Leibler divergence. Simulation studies are presented in order to illustrate the performance of the developed methodology. Two real datasets on leptospirosis notification in Bahia State (Brazil) are analyzed using the proposed methodology for the ZMP model.     

Behavior research in zoos: Past,present, and future

This paper reviews the historical emphases in zoo behavioral research and the contribution of these studies to animal management and to advancement in the behavioral sciences. Some examples are provided from research conducted at the National Zoological Park and elsewhere. The potential for doing behavior studies of excellence in zoos and aquariums has become more complicated in recent years by 1) changes in the aims and objectives of modern zoological parks, especially the increasing emphasis on conservation, 2) changes in focus in the science of animal behavior itself, and 3) the tendency of trained behaviorists to assume positions as curators and directors without time for research. These issues represent challenges to be overcome so that zoos can continue to be important sites for the study of animal behavior and contribute to the science of animal management and conservation, as well as the advancement of theory in biology. © 1992 Wiley-Liss, Inc.     

Satellite remote sensing,biodiversity research and conservation of the future

Assessing and predicting ecosystem responses to global environmental change and its impacts on human well-being are high priority targets for the scientific community. The potential for synergies between remote sensing science and ecology, especially satellite remote sensing and conservation biology, has been highlighted by many in the past. Yet, the two research communities have only recently begun to coordinate their agendas. Such synchronization is the key to improving the potential for satellite data effectively to support future environmental management decision-making processes. With this themed issue, we aim to illustrate how integrating remote sensing into ecological research promotes a better understanding of the mechanisms shaping current changes in biodiversity patterns and improves conservation efforts. Added benefits include fostering innovation, generating new research directions in both disciplines and the development of new satellite remote sensing products.     

云南兰科植物拾零

报道了云南兰科1个新记录属及4个新记录种,确定了文山石仙桃(PholidotawenshanicaS.C.ChenetZ.H.Tsi)的具体野外产地,并对石仙桃属一种和厚唇兰属一种的文献进行了订正。     

Unusual 28, 29-nor-9, 19 cycloartane triterpenoids from Chinese medical plant Streptocaulon griffithii Hook

Phytochemical investigation of the root of Streptocaulon griffithii Hook (Asclepiadaceae) led to the isolation of three unusual novel triterpenoids, 28, 29-nor-3β, 4β-dihydroxyl-9, 19-cycloartan-26-acid (1), 28, 29-nor-3β, 4β-dihydroxyl-9, 19-cycloartan- 26-acid methylester (2), a 30-nor-lupeol derivative 30-nor-3β-acetoxy-lupan-20-one (3) and five known compounds 4–8. Their structures were established on the basis of physical and spectroscopic analysis, including 1D and 2D NMR (1H, ¹³C, COSY, HSQC, and HMBC), ESI mass spectrometry, and by comparison with the NMR data published in the literature. The cytotoxicities of the isolated compounds against a panel of cultured tumor cell lines (Hela, PC3, SMMC7721, CNE) were evaluated. The new compounds 1 and 2 showed moderate activities with IC₅₀ values of 11.76 ∼ 26.52 μg/mL, respectively. The result showed that triterpenoids are typical compounds of Streptocaulon genus, which could be useful as characteristic markers in chemotaxonomic research and might helpful for explaining the use of S. griffithii in traditional medicine.     

GT-Miner: a graph-theoretic data miner, viewer, and model processor

Inexpensive computational power combined with high-throughput experimental platforms has created a wealth of biological information requiring analytical tools and techniques for interpretation. Graph-theoretic concepts and tools have provided an important foundation for information visualization, integration, and analysis of datasets, but they have often been relegated to background analysis tasks. GT-Miner is designed for visual data analysis and mining operations, interacts with other software, including databases, and works with diverse data types. It facilitates a discovery-oriented approach to data mining wherein exploration of alterations of the data and variations of the visualization is encouraged. The user is presented with a basic iterative process, consisting of loading, visualizing, transforming, and then storing the resultant information. Complex analyses are built-up through repeated iterations and user interactions. The iterative process is optimized by automatic layout following transformations and by maintaining a current selection set of interest for elements modified by the transformations. Multiple visualizations are supported including hierarchical, spring, and force-directed self-organizing layouts. Graphs can be transformed with an extensible set of algorithms or manually with an integral visual editor. GT-Miner is intended to allow easier access to visual data mining for the non-expert.     

Bayesian semiparametric nonlinear mixed-effects joint models for data with skewness, missing responses, and measurement errors in covariates

Summary It is a common practice to analyze complex longitudinal data using semiparametric nonlinear mixed-effects (SNLME) models with a normal distribution. Normality assumption of model errors may unrealistically obscure important features of subject variations. To partially explain between- and within-subject variations, covariates are usually introduced in such models, but some covariates may often be measured with substantial errors. Moreover, the responses may be missing and the missingness may be nonignorable. Inferential procedures can be complicated dramatically when data with skewness, missing values, and measurement error are observed. In the literature, there has been considerable interest in accommodating either skewness, incompleteness or covariate measurement error in such models, but there has been relatively little study concerning all three features simultaneously. In this article, our objective is to address the simultaneous impact of skewness, missingness, and covariate measurement error by jointly modeling the response and covariate processes based on a flexible Bayesian SNLME model. The method is illustrated using a real AIDS data set to compare potential models with various scenarios and different distribution specifications.     

Known unknowns,Google Earth,plate tectonics and Mt?Bellenden Ker: some thoughts on locality data

Latitude/longitude data in locality records should be published with spatial uncertainties, datum(s) used and indications of how the data were obtained. Google Earth can be used to locate sampling sites, but the underlying georegistration of the satellite image should be checked. The little-known relabelling of a set of landmarks on Mt Bellenden Ker, a scientifically important collecting locality in tropical north Queensland, Australia, is documented as an example of the importance of checking records not accompanied by appropriately accurate latitude/longitude data.     

From a textual checklist to an information system: The case study of ITALIC,the Information System on Italian Lichens

Abstract

Checklists are fundamental for accessing information about organisms known to occur in a given area. It is possible to convert textual, paper-printed checklists into structured digital formats. This process can eventually lead to the development of digital information systems, for which the output can be far more complex than a list of taxa. Digital information systems can be continuously updated by a constant flow of information, and their content can be exported in many other different formats, hence not only mobilising, but also making biodiversity data reusable on different platforms. The conversion of the Checklist of Italian Lichens into an information system is discussed, in order to provide some general guidelines of such a process.     

Structural Diversity,Spectral Data,and Pharmacological Effects of Genus Nigella

Nigella is one of the most studied plants because of its pharmacological properties like anti-parasitic, anti-inflammatory, neuro-protective, hepatoprotective, and anti-cancerous. In this study, about 20 species of the genus Nigella were reviewed and among them, N. damascene, N. glandulifera, and N. sativa are widely studied for their phytochemical and pharmacological effects. This review describes the phytochemical composition of the genus Nigella, which constitutes many of the compounds including alkaloids, flavonoids, saponins, and terpenoids. The extracts produced by using different solvents and the isolated compounds displayed a wide range of biological activity. These compounds were identified by different spectral techniques. The spectral detail of some advanced techniques including EIS-MS, UV/VIS, IR, ¹³C-NMR, and ¹H-NMR of some important phytoconstituents of Nigella spp. has been compiled for the first time in this review which will be helpful to explore and further investigate the chemical composition of this genus.     

Theoretical studies on tetrahedral oxoanions MO4 (n=2, 3, 4; M=Cr, Mo, W)

The structure and bonding in MO₄ ⁿ⁻ (n=2, 3, 4; M=Cr, Mo, W) tetrahedral oxoanions have been investigated using density-functional methods. Good computational-experimental agreement for the geometrical parameters of the known species has been obtained which allowed the prediction of the cited parameters for those species that have not yet been isolated. The molecular-orbital analysis indicates that the chemical bonds mainly have d functions of the metal and p functions of oxygen. The electron affinities for the process MO₄ ⁿ⁻ + 1e → MO₄ ^(n + 1)− have also been calculated and their importance in relation with the preparation of the oxoanions MO₄ ⁿ⁻ (M=Mo, W; n=3, 4) not reported in the bibliography is discussed. Comparative studies of the electronic structures of oxoanions allow to explain their reactivities against nucleophilic and electrophilic attacks. The vibrational frequencies have been calculated and compared with the experimental values and the different relationships between the symmetric-stretching and antisymmetric-bending frequencies allow to confirm the assignations of the calculated spectra.     

Phylogenetic relationships in the genus Agathemera (Insecta: Phasmatodea) inferred from the genes 16S,COI and H3

We present a phylogenetic analysis that includes all known species of Agathemera, using as outgroup four species of the genera Heteronemia, Spinonemia, Monticomorpha, and Anisomorpha. Phylogenetic inference was based on three genes, 16S, COI (mitochondrial markers) and H3 (nuclear marker), based on the maximum‐parsimony, maximum‐likelihood and Bayesian inference methods. Our results show that the genus Agathemera is monophyletic; six of its eight species showed phylogenetic support, while the group A. claraziana + A. millepunctata was not resolved. The resulting topology shows two major clades, the first with A. maculafulgens, A. luteola, A. crassa, A. millepunctata, and A. claraziana, and the second including A. grylloidea, A. mesoauriculae, and A. elegans. Species of the first clade have large mesonotal processes and are found mainly east of the Andes, except for A. crassa. Members of the second clade have small or absent mesonotal processes and are distributed mainly to the west of the Andes. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 63–72.     

The Thermometer and the Calorimeter,or the Best Choice for Data Acquisition in the Sampling of Biological Rhythms

The comparison between measurements effected by different apparati shows that a given class of instruments provides an integral set of measurements. This characteristic has a certain disadvantage: the modification of the spectral bandwidth is limited to an attenuation of 3 dB. However, it also has certain advantages. The integral measurement (or the counting measurement) makes it possible to satisfy Shannon's sampling criteria by avoiding the necessary anti-aliasing filtering which is commonly impossible to realize on measurements of a biological nature. A second advantage is linked to the reduction of the background noise on the band.