The future prospects of electronic seed lists

For many botanic gardens worldwide, seed lists have provided a cost-effective means to replace plant losses in their collections for many decades, if not centuries. In seed lists, seeds are offered on the basis of what each garden can manage to collect and considers ‘of interest’ to other botanic gardens, some offering relatively few, while others offer many, or only wild collected seeds. Seed lists have always been printed on paper. With the use of printed seed lists, the amount of information per accession has always been quite limited to keep printing costs low. Over the past few years, electronic seed lists have been rapidly replacing printed seed lists. Since distribution is electronic, there is no longer a direct link between the amount of information provided and the cost per seed list sent out. This now offers new opportunities to share information that is linked to the plant material that botanic gardens exchange. Information is not limited to text, as images can also be included. This situation is beneficial if seed-raised plants are to be used for in situ conservation. Electronic seed lists have other advantages, but there are also some disadvantages. e.g., electronic information offered via websites is quite ephemeral in nature. Some suggestions are made to overcome the several drawbacks.     

Automatic term list generation for entity tagging

MOTIVATION: Many entity taggers and information extraction systems make use of lists of terms of entities such as people, places, genes or chemicals. These lists have traditionally been constructed manually. We show that distributional clustering methods which group words based on the contexts that they appear in, including neighboring words and syntactic relations extracted using a shallow parser, can be used to aid in the construction of term lists. RESULTS: Experiments on learning lists of terms and using them as part of a gene tagger on a corpus of abstracts from the scientific literature show that our automatically generated term lists significantly boost the precision of a state-of-the-art CRF-based gene tagger to a degree that is competitive with using hand curated lists and boosts recall to a degree that surpasses that of the hand-curated lists. Our results also show that these distributional clustering methods do not generate lists as helpful as those generated by supervised techniques, but that they can be used to complement supervised techniques so as to obtain better performance. AVAILABILITY: The code used in this paper is available from http://www.cis.upenn.edu/datamining/software_dist/autoterm/     

A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities

Analysis of multivariate data sets from, for example, microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper, we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward comparison between any 2 lists. It can also be used to generate new more stable gene rankings incorporating more information from the experimental data. Using 2 microarray data sets, we show that the proposed method provides more robust gene rankings than existing methods with respect to sampling variations, without compromising the biological significance of the rankings.     

GeneVenn - A web application for comparing gene lists using Venn diagrams

Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a Venn diagram. Venn diagrams are graphical ways of representing interactions among sets to display information that can be read easily. Here we propose a simple but effective web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI's Entrez Nucleotide database. AVAILABILITY: GeneVenn is available for free at http://mcbc.usm.edu/genevenn/     

Parallel processing data acquisition system for multilaser flow cytometry and cell sorting

This report describes the data acquisition electronics for a flow cytometer. The design differs from most instruments in that the signals from a large number of detectors are processed in parallel. Each of the input channels is capable of autonomously measuring and digitizing the fluorescence signals. The digitized values that belong to one particle are collected by digital circuitry and are presented as a compact data package on a special bus. In addition to the pulse values, the data package contains a time marker, information needed for sort decisions, and an error detection code. Specially designed electronic modules that read the information from the bus can take complex multiparameter sort decisions at a very high speed. All events can also be recorded as data lists by a computer. The lists can be used to reconstruct a sort or analysis run. The raw data lists can also be reduced to kinetic curves and/or (gated) multivariate histograms. As a result of the applied scheme of parallel pulse processing, the dead time of the system is independent of the number of parameters measured and the number and time separation of the excitation beams. The instrument has a cycle time of 5 microseconds, which corresponds to a throughput rate of 2 x 10(5) events/s. At this rate, the incidence of correlation errors is well below 1 in 10(8) analyzed particles. The system has proved to be reliable and convenient to use in a variety of experiments. Its high speed and low error rate make it well suited for high-resolution measurements, rare-event analysis, kinetic measurements, and high-speed cell sorting.     

Folds and activities of peptidoglycan amidases

Bacterial peptidoglycan amidases are a large and diverse group of enzymes. During the last few years, genomic sequence information has accumulated to an extent such that lists of proven or predicted peptidoglycan amidases can now be expected to be fairly complete. Moreover, representative crystal structures for most groups of phylogenetically related peptidoglycan amidases have been solved. Here, sequence and structural information is combined with published biochemical findings to demonstrate that (a) peptidoglycan amidases have evolved for almost every bond that occurs in peptidoglycan, (b) there are enzymes that share the fold, yet cleave different bonds and (c) there are enzymes that have entirely different folds and must have evolved independently, and yet cleave the same peptide bond. It is shown that despite these complications, some rules can be deduced from the available biochemical and structural information that can be useful to predict the specificity of hypothetical peptidoglycan hydrolases, for which only sequence information is available.     

A generic, object-oriented data model for life cycle analysis applications

Life Cycle Analysis (LCA) requires the manipulation of a large amount of both quantitative and qualitative data. It is also a continuous and iterative process in which the knowledge of previous steps is always necessary for the realization and understanding of subsequent stages. Current LCA data models are mostly organized as lists from which quantitative data can be extracted and manipulated, subsequently leading to lists of numerical results. Performing an LCA can benefit from more flexible structures that allow for complete or partial treatments and provides links between the successive transformations of various types of information. A generic, object-oriented model is presented, written in ISO/STEP EXPRESS, using the STEP principles.     

An interdisciplinary evaluation of the status and health of African lake fisheries using a rapid appraisal technique

Data from biological, economic, sociological, and technological attribute lists for 32 African lake fisheries were analysed with multivariate statistics. Multidimensional scaling (MDS) was used to create two-dimensional graphic ordinations of the fisheries for each of these four attributes lists. An overall MDS ordination was also generated, based on the fisheries' scores in the four ordinations. Groupings in each MDS ordination were achieved through cluster analysis. Multiple correlations was used to help determine the attributes which were most important in creating the MDS ordinations. This work showed that relatively fast and simple assessments of the status of African lake and other fisheries can be achieved. The technique also provided insight to help resolve the confounding information often associated with fisheries assessment. Diagnostic information may also be a product of such investigations as this research identified African lake fisheries at risk of declining standards. Indeed, many of the fisheries studied demonstrated similar interdisciplinary symptoms of fisheries decline as other small-scale tropical fisheries.     

Peakmatch: a simple and robust method for peak list matching

Peak lists are commonly used in NMR as input data for various software tools such as automatic assignment and structure calculation programs. Inconsistencies of chemical shift referencing among different peak lists or between peak and chemical shift lists can cause severe problems during peak assignment. Here we present a simple and robust tool to achieve self-consistency of the chemical shift referencing among a set of peak lists. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned. The chemical shift referencing offset between two peak lists is determined by optimizing an assignment-free match score function using either a complete grid search or downhill simplex optimization. It is shown that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. Using a simulated peak list, the Peakmatch algorithm can also be used to obtain the optimal agreement between a chemical shift list and experimental peak lists. Combining these features makes Peakmatch a useful tool that can be applied routinely before automatic assignment or structure calculation in order to obtain an optimized input data set.     

Comprehensive restriction enzyme lists to update any DNA sequence computer program

Restriction enzyme lists are presented for the practical working geneticist to update any DNA computer program. These lists combine formerly scattered information and contain all presently known restriction enzymes with a unique recognition sequence, a cut site, or methylation (in)sensitivity. The lists are in the shortest possible form to also be functional with small DNA computer programs, and will produce clear restriction maps without any redundancy or loss of information. The lists discern between commercial and noncommercial enzymes, and prototype enzymes and different isoschizomers are cross-referenced. Differences in general methylation sensitivities and (in)sensitivities against Dam and Dcm methylases of Escherichia coli are indicated. Commercial methylases and intron-encoded endonucleases are included. An address list is presented to contact commercial suppliers. The lists are constantly updated and available in electronic form as pure US ASCII files, and in formats for the DNA computer programs DNA-Strider for Apple Macintosh, and DNAsis for IBM personal computers or compatibles via e-mail from the internet address: netservembl-heidelberg.de by sending only the message help relibrary.     

Problematic character coding methods in morphology and their effects

The effects of different coding practices in morphological phylogenetic analysis are well documented. In many cases, we can determine that certain practices can be regarded as undesirable and should be avoided. Certain coding practices do not correctly translate the expected information to the cladistic algorithm. It may go unnoticed that expressions of character information in character lists, which may be entirely logical to any reader, do not necessarily reflect the mathematics employed by a phylogenetic algorithm. Despite a wealth of literature on coding procedures and documentation of these issues, problematic character coding practices are still common. A review is provided of different coding and character formulation practices, particularly relating to multistate character information that may either: (1) lead to a failure to capture grouping information implied in the character list; (2) cause problematic weighting or spuriously high certainty in particular optimizations; and (3) impose congruence artificially, by linking more than one variable character to a particular state. Each of these is reviewed and presented with a hypothetical example. Recommendations for avoiding these pitfalls are described in light of how parsimony algorithms work with character data. Character lists must be drawn up not only to present character variation logically, but also with consideration for how computer algorithms implement cladistic logic. The widespread use of problematic character coding procedures may account for some of the perceived problems with morphological data. Therefore, an exploration of the effects of these methods and standardization of methods should be a goal for the very near future. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 489–498.     

AUTOMATED HABITAT ANNOTATION OF BIRD SPECIES LISTS-AN AID IN ENVIRONMENTAL CONSULTANCY

Harrison, J.A., Allan, D.G. & Van Hensbergen, H.J. 1994 Automated habitat annotation of bird species lists - an aid in environmental consultancy. Ostrich 65: 316–328.

The Southern African Bird Atlas Project (SABAP) has compiled a comprehensive distributional database for birds. This information is potentially valuable to environmental consultants, planners and managers. A computer-based routine was developed to enhance the usefulness of the information to this user group. The routine produces habitat-specific species lists and includes annotations on endemism, Red Data status and other relevant information. A hierarchical system of habitat categories and indicator and associate species statuses was designed to maximize the information which can be derived from the databank. The report was designed to facilitate prioritization and decision-making. The approach is novel in its use of a species list to generate information on habitat.     

The fungi of Scottish Western oakwoods

Summary

Unfortunately the Atlantic oakwoods of Scotland have never been targeted by mycologists and information is very patchy. The best data lie in the lists of fungi from the Inner Hebridean oakwoods and it is on these records which go back to the end of the 19th century, and limited information from the mainland that a potential picture is offered. There appear to be no fungi specific to Western oakwoods and there are few differences between eastern and western oak communities in Scotland. Emphasis is placed on the need for more funding for those who can identify and recognise potential indicator species so that progress can be made.     

FiRe and microarrays: a fast answer to burning questions

FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .     

Information Retrieval during Free Listing Is Biased by Memory: Evidence from Medicinal Plants

Free listing is a methodological tool that is widely used in various scientific disciplines. A typical assumption of this approach is that individual lists reflect a subset of total knowledge and that the first items listed are the most culturally important. However, little is known about how cognitive processes influence free lists. In this study, we assess how recent memory of use, autonoetic and anoetic memory, and long-term associative memory can affect the composition and order of items in free lists and evaluate whether free lists indicate the most important items. Based on a model of local knowledge about medicinal plants and their therapeutic targets, which was collected via individual semi-structured interviews, we classify each item recorded in free lists according to the last time that the item was used by the informant (recently or long ago), the type of relevant memory (autonoetic or anoetic memory) and the existing associations between therapeutic targets (similar or random). We find that individuals have a tendency to recall information about medicinal plants used during the preceding year and that the recalled plants were also the most important plants during this period. However, we find no trend in the recall of plants from long-term associative memory, although this phenomenon is well established in studies on cognitive psychology. We suggest that such evidence should be considered in studies that use lists of medicinal plants because this temporal cognitive limit on the retrieval of knowledge affects data interpretation.     

A comparison of methods for selecting non-target species for risk assessment of the biological control agent <Emphasis Type="Italic">Cotesia urabae</Emphasis>

A computer-based tool called PRONTI (priority ranking of non-target invertebrates) has been developed to aid the selection of non-target species (NTS) for pre-release testing with entomophagous biological control agents. To test whether PRONTI can improve NTS selection, we used it to produce a prioritised list of NTS for the agent Cotesia urabae Austin & Allen (Hymenoptera: Braconidae), and compared it with the original list that was produced before this species was released in New Zealand in 2011. While the two lists were similar, with five NTS occurring in the top nine of both lists, the remaining four NTS in the top nine of each list were different, primarily because the selection criteria used by the two methods were weighted differently (e.g., PRONTI put more weight on the likelihood of a NTS being exposed to the agent). Post-release testing has demonstrated that C. urabae is able to oviposit in two NTS that were ranked highly on both lists, suggesting both methods are useful for species selection. The main advantages of PRONTI were considered to be its ability to rank hundreds of NTS simultaneously, and to provide a body of information that can be used to both understand each NTS’ ranking and to justify more objectively the selection of NTS for pre-release testing.     

The Arabidopsis SeedGenes Project

The SeedGenes database (http://www.seedgenes.org) presents molecular and phenotypic information on essential, non-redundant genes of Arabidopsis that give a seed phenotype when disrupted by mutation. Experimental details are synthesized for efficient use by the community and organized into two major sections in the database, one dealing with genes and the other with mutant alleles. The database can be queried for detailed information on a single gene to create a SeedGenes Profile. Queries can also generate lists of genes or mutants that fit specified criteria. The long-term goal is to establish a complete collection of Arabidopsis genes that give a knockout phenotype. This information is needed to focus attention on genes with important cellular functions in a model plant and to assess from a genetic perspective the extent of functional redundancy in the Arabidopsis genome.     

Network selection: a method for ranked lists selection

We consider the problem of finding the set of rankings that best represents a given group of orderings on the same collection of elements (preference lists). This problem arises from social choice and voting theory, in which each voter gives a preference on a set of alternatives, and a system outputs a single preference order based on the observed voters' preferences. In this paper, we observe that, if the given set of preference lists is not homogeneous, a unique true underling ranking might not exist. Moreover only the lists that share the highest amount of information should be aggregated, and thus multiple rankings might provide a more feasible solution to the problem. In this light, we propose Network Selection, an algorithm that, given a heterogeneous group of rankings, first discovers the different communities of homogeneous rankings and then combines only the rank orderings belonging to the same community into a single final ordering. Our novel approach is inspired by graph theory; indeed our set of lists can be loosely read as the nodes of a network. As a consequence, only the lists populating the same community in the network would then be aggregated. In order to highlight the strength of our proposal, we show an application both on simulated and on two real datasets, namely a financial and a biological dataset. Experimental results on simulated data show that Network Selection can significantly outperform existing related methods. The other way around, the empirical evidence achieved on real financial data reveals that Network Selection is also able to select the most relevant variables in data mining predictive models, providing a clear superiority in terms of predictive power of the models built. Furthermore, we show the potentiality of our proposal in the bioinformatics field, providing an application to a biological microarray dataset.     

Modified genetic algorithm resolves ambiguous NOE restraints and reduces unsightly NOE violations

In an ideal world, every NOE cross peak would have a unique assignment. However, the interpretation of NOE peaks is frequently complicated by overlapping resonances. In theory, ambiguous assignments could be resolved by performing separate structure calculations with each possible interpretation. Unfortunately, this would require an astronomical amount of computing time. A modified genetic algorithm has been developed that efficiently resolves hundreds of ambiguous restraints in parallel. Each NOE assignment becomes a gene that can be passed on to a new generation. New individuals are constructed by making a constraint lists from a subset of the genes. The constraint lists are then tested for self-consistency by using molecular dynamics to generate new structures for each list. To a first-degree approximation, there is enough information retained in each list to determine the global fold of the protein. Self-consistent constraint lists receive higher scores and their genes (or NOEs) stand a better chance of surviving into the next generation. The process selects NOEs that are consistent with the global fold. Under normal conditions, the program converges in 3 to 8 generations using 70 structures per generation. The final constraints are self-consistent and contain almost no residual NOE violations.     

Using simple species lists to monitor trends in animal populations: new methods and a comparison with independent data

There is an urgent need to develop simple and inexpensive methods for monitoring wildlife populations in resource-poor countries. List-based methods have been advocated as simple yet potentially useful biodiversity monitoring tools, and systems have recently been launched in a number of countries to collect species lists. We attempt to advance the use of systematic list-based monitoring by (1) suggesting improvements to the way in which list reporting rates are calculated; (2) assessing the extent to which degrading effort-corrected measures of abundance into simple species lists results in loss of information on population trends; (3) comparing long-term trends in list reporting rates with population trends from a wholly independent monitoring scheme. Daily species lists of birds were derived from regular trapping at a nature reserve in southern England. Most species showed a strong correlation across years between the proportion of lists on which they occurred, adjusted for list length (adjusted list reporting rate; ALRR), and an effort-corrected measure of abundance (captures per unit effort; CPUE). ALRR revealed almost as much about annual variation in abundance as CPUE for all but the most frequently captured species. Long-term (>20 years) trends in ALRRs at the nature reserve were positively correlated with UK national population trends recorded over the same period by an independent, labour-intensive monitoring scheme that counted birds at a large number of widely spread sites. Our results support previous claims that simple species lists could generate data useful for monitoring long-term population trends, particularly where such lists are collected systematically. However, further research on the efficiency of list reporting rates relative to more sophisticated methods is necessary, before list-based methods can be advocated for dedicated monitoring schemes in resource-poor regions.