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At least 433 records · Page 24Linked to original sources

Cognitive modeling with spreadsheets.

Spreadsheet implementations of two different types of cognitive models--a neural network model and a statistical model--are presented. The two examples illustrate how to employ the facilities of spreadsheets, the spreadsheet data structure, array functions, the built-in function library, and the integrated optimizer, for building cognitive models. The two presented models are new extensions of existing models. They are used for simulating data from experiments illustrating that the extended versions are able to explain experimental results that could not be simulated by the original models. The whole simulation study demonstrates that spreadsheets are a handy tool, especially for researchers without programming knowledge who want to build cognitive models and for instructors teaching cognitive modeling.

Algorithms↗

Molecular phylogeny and evolution of unique mud-using territorial behavior in ocypodid crabs (Crustacea: Brachyura: Ocypodidae).

Among crabs of the family Ocypodidae, Ilyoplax has been known to exhibit unique mud-using territorial behavior against neighbors, including neighbor burrow plugging, barricade building, and fence building. To assess the evolution of current behavioral forms observed in Ilyoplax, 1,416-bp nucleotide sequences from the mitochondrial 12S rRNA to 16S rRNA genes of 20 species, representing four recognized subfamilies of Ocypodidae, were analyzed. The resultant phylogenetic tree revealed the subfamily Dotillinae, including Ilyoplax, to be monophyletic, with a sister group relationship with subfamily Camptandriinae. These two subfamilies were branched after Ocypodinae, with Macrophthalminae being most basal. Species of Ilyoplax fell into three different Dotillinae lineages, indicating the genus to be polyphyletic. Crabs in two of the three lineages showed differential geographic distribution and body size. Phylogenetic analyses of behavioral characters demonstrated that mud-using techniques had evolved multiple times and sequentially. From their behavioral similarity and evolutionary occurrence, fence building is hypothesized to have evolved from barricade building, and the latter, from burrow plugging. This scenario also appeared reasonable with respect to behavioral trends observed in the field. The evolution of such territorial behavior is considered to be associated with ecological conditions such as burrow fidelity and substrate condition.

Animals↗

The position end-set tree: a small automaton for word recognition in biological sequences.

We consider the basic function which locates a specific string of symbols within a longer sequence. When one is expecting to do many substring searches it is worthwhile to build an auxiliary index to the sequence to aid in the search. We propose a method to generate a compact index that can be viewed as a small (partial) deterministic finite automaton recognizing the subword structure of a sequence. We present an algorithm for its construction on-line in linear time. Such a data structure permits the efficient localization of subwords in a sequence and can be used in the development of interactive sequence analysis software.

Algorithms↗

Recent speciation in the Formica rufa group ants (Hymenoptera, Formicidae): inference from mitochondrial DNA phylogeny.

This study examines phylogenetic relationships among six species of the Formica rufa group ants (F. polyctena, F. rufa, F. lugubris, F. paralugubris, F. aquilonia, and F. pratensis). The phylogeny based on a 2051bp fragment of mtDNA including cyt b, tRNASer, and ND1 genes supports the division of the group into three major clusters: one with the species F. polyctena and F. rufa, one with F. aquilonia, F. lugubris, and F. paralugubris, and the third one with F. pratensis. The interspecific divergence estimates (mean 0.98 +/- 0.15% for the main phylogenetic groups) imply that radiation took place during the Pleistocene. Comparison of the divergence estimates among the F. rufa group species with divergence estimates among other closely related species of insects suggests that speciation in the group was relatively fast, and the mitochondrial lineages of F. polyctena and F. rufa have not fully separated. The haplotype tree shows also signs of transfer of mtDNA between species through hybridisation. The distribution of polygyny (multiple queens per nest) along the branches of the tree indicates that the social type characterised by highly polygynous societies and large colonial networks, has originated at least three times. The species F. aquilonia and F. paralugubris that build such large supercolonies, cluster tightly together with very little nucleotide variation, suggesting that this type of social organisation could be a factor promoting speciation in the ants.

Animals↗

Using consensus networks to visualize contradictory evidence for species phylogeny.

Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene trees for eight yeast genomes and show that consensus networks have potential for helping to visualize contradictory evidence for species phylogenies.

Genome, Fungal↗

The building block folding model and the kinetics of protein folding.

Here we show that qualitatively, the building blocks folding model accounts for three-state versus the two-state protein folding. Additionally, it is consistent with the faster versus slower folding rates of the two-state proteins. Specifically, we illustrate that the building blocks size, their mode of associations in the native structure, the number of ways they can combinatorially assemble, their population times and the way they are split in the iterative, step-by-step structural dissection which yields the anatomy trees, explain a broad range of folding rates. We further show that proteins with similar general topologies may have different folding pathways, and hence different folding rates. On the other hand, the effect of mutations resembles that of changes in conditions, shifting the population times and hence the energy landscapes. Hence, together with the secondary structure type and the extent of local versus non-local interactions, a coherent, consistent rationale for folding kinetics can be outlined, in agreement with experimental results. Given the native structure of a protein, these guidelines enable a qualitative prediction of the folding kinetics. We further describe these in the context of the protein folding energy landscape. Quantitatively, in principle, the diffusion-collision model for the building block association can be used. However, the folding rates of the building blocks and traps in their formation and association, need to be considered.

Adenylate Kinase↗

Outcomes of care: the use of conceptual models to "see the forest and the trees" in planning outcomes studies.

Outcomes research provides many opportunities to explore how care activities, care processes, and care systems impact on individuals and health care resources. This article discusses clinical outcomes research and its connection to real-life situations. A model-building approach is presented to clarify the process of outcomes research by acknowledging multiple variables and how they interact. The process is illustrated through a hypothetical model addressing coronary artery disease. The usefulness of using conceptual modeling typing related variables together while creating a framework for increased understanding of key variables and their interaction is discussed.

Coronary Artery Disease↗

Decision making by auxiliary nurses to assess postpartum bleeding in a Dominican Republic maternity ward.

OBJECTIVE: To understand the process of decision making by auxiliary nurses regarding postpartum bleeding among women in the Dominican Republic. DESIGN: An ethnographic qualitative design of semistructured interviews and participant observation. PARTICIPANTS: Twenty four auxiliary nurses on a maternity unit of a referral hospital in the Dominican Republic. FINDINGS: Auxiliary nurses use specific criteria and logic to decide if postpartum maternal bleeding is excessive. However, systematic postpartum assessments are not routinely conducted on every woman. MAIN OUTCOME MEASURES: A decision tree that traces how auxiliary nurses evaluate postpartum bleeding indicates that they have knowledge of contemporary obstetric nursing care, but the organization of care delivery is not structured for them to apply it routinely. CONCLUSIONS: A collaboration of U.S. midwives and Dominican nurses will build on the assets of the auxiliary nurses. Rather than focusing the content of educational conferences on current knowledge of labor and delivery, an important next step is modeling woman- and family-centered care. The U.S. midwives and Dominican nurses are committed to finding empowering and effective ways to improve maternity care.

Adult↗

Relationship between foliar chemical parameters measured in Melia azedarach L. and environmental conditions in urban areas.

A diagnostic study was done on Melia azedarach L. in relation to atmospheric pollutants in Córdoba city, Argentina. The study area receives regional pollutants, and it was categorized taking into account traffic level, industrial level, location of the sample point in relation to the corner, treeless condition, building type, topographic level and distance to the river. Water content and Specific Leaf Area (SLA) were calculated; and concentrations of soluble proteins, sulphur, hydroperoxy conjugated dienes (HPCD), chlorophylls (Total Chl) and pheophytins (Total Paeoph) were determined in leaf samples. HPCD correlated positively with industry, topographic level and distance to the river, and with a combination of the environmental variables (ECI); pigments correlated negatively with traffic level and with ECI; Total Phaeoph/Total Chl ratio correlated positively with traffic, building and ECI. On the basis of our results, traffic level, industrial level, building type, topographic level and distance to the river are the environmental variables to bear in mind when selecting analogous sampling points in a passive monitoring program. An approximation to predict tree injury may be obtained by measuring water content, soluble proteins, sulphur, HPCD and pigments as they are responsible for the major variability of data. This study revealed that M. azedarach was sensitive to air pollutants from traffic and industry. Thus, in those sampling sites with the maximum score for traffic level, industrial level and ECI, the highest values of the parameters that indicate foliar damage together with the least pigment concentration were observed.

Air Pollutants↗

Causality and pathway search in microarray time series experiment.

MOTIVATION: Interaction among time series can be explored in many ways. All the approach has the usual problem of low power and high dimensional model. Here we attempted to build a causality network among a set of time series. The causality has been established by Granger causality, and then constructing the pathway has been implemented by finding the Minimal Spanning Tree within each connected component of the inferred network. False discovery rate measurement has been used to identify the most significant causalities. RESULTS: Simulation shows good convergence and accuracy of the algorithm. Robustness of the procedure has been demonstrated by applying the algorithm in a non-stationary time series setup. Application of the algorithm in a real dataset identified many causalities, with some overlap with previously known ones. Assembled network of the genes reveals features of the network that are common wisdom about naturally occurring networks.

Algorithms↗

Advances in Plant Health Management in the Twentieth Century.

▪ Abstract Plant health management is the science and practice of understanding and overcoming the succession of biotic and abiotic factors that limit plants from achieving their full genetic potential as crops, ornamentals, timber trees, or other uses. Although practiced as long as agriculture itself, as a science-based concept, plant heath management is even younger than integrated pest management (IPM), and includes and builds upon but is not a replacement for IPM. Probably the greatest collection of success stories for plant health management is the number of diseases managed by cleaning up the planting material. The record for root health management is more mixed, with the loss or phase-out of soil fumigants, and practices such as crop rotation and clean tillage being replaced with more intensive cropping and less or no tillage. Perhaps the greatest scientific and technical advances for plant health management have come from the work aimed at management of the pathogens, pests, and other hazards that arrive by air. Flor's work on flax rust, which produced the gene-for-gene model, is possibly the most significant contribution of plant pathology to the life sciences in the twentieth century. Research aimed at the management of foliar pathogens is also the basis for modern theory on epidemiology, population biology, aerobiology, and disease prediction and decision-support systems. Even IPM arose mainly in response to the need to protect crops from pests that arrive by air. If the definition of biological control includes the plant induced or genetically modified to defend itself, as it should, then biological control has been the most significant approach to plant health management during the twentieth century and promises through modern biotechnology to be even more significant in the twenty-first century. Rather than "reducing losses," the advances are discussed here within the simple framework of achieving the attainable yield by increasing the actual and/or affordable and hence the average yield. Each of these four benchmark yields, as well as the absolute yield for crops, and their significance to the goals and achievements of plant health management are defined. Plant health management is a moving target, which I discuss metaphorically like an American football game, where one team is science and technology and the other is nature, where the S & T team is only beginning to know nature's rules while playing itself with the three sets of rules written to, respectively, satisfy the laws of economics, protect the environment, and gain social acceptance.

Journal Article↗

Documenting nursing practice by using ICNP on the Web.

This paper presents the design and implementation of an internet based nursing care planning system which helps nursing professionals and students to study ICNP beta 2 version and to create nursing diagnoses, interventions and outcomes by selecting relevant terms from ICNP. This advanced web-based ICNP browser enables the authentication of the user, and the creation of a type of nursing care plan through the use of ICNP. It provides different ways for creating nursing diagnoses, interventions and outcomes, by selecting relevant ICNP terms through the tree-structure view, index and search components of the tool. The created diagnoses, interventions and outcomes are stored to a secured database. The system provides to the user the facility to build and manage nursing care plans by using both the English and the translated Greek ICNP versions. The first results of the implementation of this internet based nursing care planning system are presented.

Database Management Systems↗

Air pollution--adverse effects of sulfur dioxide.

Among air pollutants, sulfur dioxide has been found to be very injurious. The present article deals with the adverse effects of sulfur dioxide gas on metals, metal alloys, buildings and plants, animals and human beings.

Air Pollutants↗

Expression patterns and subcellular localization of the Down syndrome candidate protein MNB/DYRK1A suggest a role in late neuronal differentiation.

The Minibrain (Mnb) gene belongs to a new protein kinase family, which is evolutionarily conserved, and probably plays several roles during brain development and in adulthood. In Drosophila, mnb is involved in postembryonic neurogenesis and in learning/memory. In humans, MNB has been mapped within the Down syndrome critical region of chromosome 21 and is overexpressed in the Down syndrome embryonic brain. It has been widely proposed that MNB is involved in the neurobiological alterations associated with Down syndrome. Nevertheless, little is known about the functional role that MNB plays in vertebrate brain development. We have recently shown [Hämmerle et al. (2002) Dev. Biol., 246, 259-273] that in early vertebrate embryos, Mnb is transiently expressed in neural progenitor cells during the transition from proliferating to neurogenic divisions. Here we have studied in detail a second wave of Mnb expression, which takes place in the brain of intermediate and late vertebrate embryos. In these stages, MNB seems to be restricted to certain populations of neurons, as no consistent expression was detected in astroglial or oligodendroglial cells. Interestingly, MNB expression takes place at the time of dendritic tree differentiation and is initiated by a transient translocation from the cytoplasm to the nucleus. Afterwards, MNB protein is transported to the growing dendritic tree, where it colocalizes with Dynamin 1, a putative substrate of MNB kinases. We propose that MNB kinase is involved in the signalling mechanisms that regulate dendrite differentiation. This functional role helps to build a new hypothesis for the implication of MNB/DYRK1A in the developmental aetiology of Down syndrome neuropathologies.

Aging↗

PAQ: Partition Analysis of Quasispecies.

MOTIVATION: The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups. RESULTS: We have developed an intuitive exploratory program, Partition Analysis of Quasispecies (PAQ), which utilizes a non-hierarchical technique to partition sequences that are genetically similar. PAQ was used to analyze a data set of human immunodeficiency virus type 1 (HIV-1) envelope sequences isolated from different regions of the brain and another data set consisting of the equine infectious anemia virus (EIAV) regulatory gene rev. Analysis of the HIV-1 data set by PAQ was consistent with phylogenetic analysis of the same data, and the EIAV rev variants were partitioned into two overlapping groups. PAQ provides an additional tool which can be used to glean information from genetic data and can be used in conjunction with other tools to study genetic similarities and genetic evolution of viral quasispecies.

Algorithms↗

Vienna's biowaste compost--quality development and effects of input materials.

Extensive chemical analyses were conducted during the last decade to assess the heavy metal content of the finished compost as well as of biowaste and other input materials. Twenty six percent of the compost lots were class I according to ONORM S2200, 70% class II and 4% did not reach class II. If the compost lots were classified according to the new Austrian compost ordinance, 22% would conform to class A+ and 78% to class A. These data are put into relation with heavy metal contents of soil, of yard wastes and of biowastes without contaminants. In the soil samples particularly nickel and lead exceeded the limits for class A+ (compost ordinance). In the yard wastes, more than 90% of the samples met the limits for all heavy metals. Biowaste without contaminants conformed to class A+ on average. In biowaste without contaminants no influence of the housing structure on the heavy metal content was observed. The compost produced only from biowaste from areas with high building density, after undergoing the normal process of metal removal, however, was significantly higher contaminated than that of compost of the whole city of Vienna. The impact of specific input materials, such as Christmas trees or wooden crates, was investigated by chemical analyses before and after controlled composting experiments with those materials. In both experiments the compost quality did not reach the limits for heavy metals of class I (ONORM S2200).

Austria↗

Metabolic pathways variability and sequence/networks comparisons.

BACKGROUND: In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. RESULTS: We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microorganisms and the strong correlation between the metabolic network wiring and involved enzymes sequence space. CONCLUSION: The method represents a valuable tool for the investigation of genotype/phenotype correlations allowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolic network space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process.

Algorithms↗