Automation in the Teaching of Descriptive Geometry and CAD. High-Level CAD Templates Using Script Languages

Science.gov (United States)

Moreno, R.; Bazán, A. M.

2017-10-01

The main purpose of this work is to study improvements to the learning method of technical drawing and descriptive geometry through exercises with traditional techniques that are usually solved manually by applying automated processes assisted by high-level CAD templates (HLCts). Given that an exercise with traditional procedures can be solved, detailed step by step in technical drawing and descriptive geometry manuals, CAD applications allow us to do the same and generalize it later, incorporating references. Traditional teachings have become obsolete and current curricula have been relegated. However, they can be applied in certain automation processes. The use of geometric references (using variables in script languages) and their incorporation into HLCts allows the automation of drawing processes. Instead of repeatedly creating similar exercises or modifying data in the same exercises, users should be able to use HLCts to generate future modifications of these exercises. This paper introduces the automation process when generating exercises based on CAD script files, aided by parametric geometry calculation tools. The proposed method allows us to design new exercises without user intervention. The integration of CAD, mathematics, and descriptive geometry facilitates their joint learning. Automation in the generation of exercises not only saves time but also increases the quality of the statements and reduces the possibility of human error.

Utilising scripting language for unmanned and automated guided vehicles operating within row crops

DEFF Research Database (Denmark)

Jørgensen, R. N.; Nørremark, M.; Sørensen, C.G.

2008-01-01

A flexible high-level control language is an important element in the ongoing task of introducing automated guided vehicles (AGV) to new application domains. A new application domain is row crops, where small AGV's will perform weed control around individual crop plants. This paper defines...... is described here as the ‘supervisory field coverage monitor’ (SFCM), which acts to coordinate the behaviours. The applicability of this modified SMR-CL has been successfully demonstrated using a vehicle test in a specially designed artificial row crop field. The analysis of the operational performance...

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology.

Science.gov (United States)

Sadowski, Michael I; Grant, Chris; Fell, Tim S

2016-03-01

Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Phylogeny and subgeneric taxonomy of Aspergillus

DEFF Research Database (Denmark)

Peterson, S.W.; Varga, Janos; Frisvad, Jens Christian

2008-01-01

The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence...

Automated Status Notification System

Science.gov (United States)

2005-01-01

NASA Lewis Research Center's Automated Status Notification System (ASNS) was born out of need. To prevent "hacker attacks," Lewis' telephone system needed to monitor communications activities 24 hr a day, 7 days a week. With decreasing staff resources, this continuous monitoring had to be automated. By utilizing existing communications hardware, a UNIX workstation, and NAWK (a pattern scanning and processing language), we implemented a continuous monitoring system.

Automation of the Jarrell--Ash model 70-314 emission spectrometer

International Nuclear Information System (INIS)

Morris, W.F.; Fisher, E.R.; Taber, L.

1978-01-01

Automation of the Jarrell-Ash 3.4-Meter Ebert direct-reading emission spectrometer with digital scaler readout is described. The readout is interfaced to a Data General NOVA 840 minicomputer. The automation code consists of BASIC language programs for interactive routines, data processing, and report generation. Call statements within the BASIC programs invoke assembly language routines for real-time data acquisition and control. In addition, the automation objectives as well as the spectrometer-computer system functions, coding, and operating instructions are presented

Automating spectral measurements

Science.gov (United States)

Goldstein, Fred T.

2008-09-01

This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

Automation of a problem list using natural language processing

Directory of Open Access Journals (Sweden)

Haug Peter J

2005-08-01

Full Text Available Abstract Background The medical problem list is an important part of the electronic medical record in development in our institution. To serve the functions it is designed for, the problem list has to be as accurate and timely as possible. However, the current problem list is usually incomplete and inaccurate, and is often totally unused. To alleviate this issue, we are building an environment where the problem list can be easily and effectively maintained. Methods For this project, 80 medical problems were selected for their frequency of use in our future clinical field of evaluation (cardiovascular. We have developed an Automated Problem List system composed of two main components: a background and a foreground application. The background application uses Natural Language Processing (NLP to harvest potential problem list entries from the list of 80 targeted problems detected in the multiple free-text electronic documents available in our electronic medical record. These proposed medical problems drive the foreground application designed for management of the problem list. Within this application, the extracted problems are proposed to the physicians for addition to the official problem list. Results The set of 80 targeted medical problems selected for this project covered about 5% of all possible diagnoses coded in ICD-9-CM in our study population (cardiovascular adult inpatients, but about 64% of all instances of these coded diagnoses. The system contains algorithms to detect first document sections, then sentences within these sections, and finally potential problems within the sentences. The initial evaluation of the section and sentence detection algorithms demonstrated a sensitivity and positive predictive value of 100% when detecting sections, and a sensitivity of 89% and a positive predictive value of 94% when detecting sentences. Conclusion The global aim of our project is to automate the process of creating and maintaining a problem

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Automation of Feynman diagram evaluations

International Nuclear Information System (INIS)

Tentyukov, M.N.

1998-01-01

A C-program DIANA (DIagram ANAlyser) for the automation of Feynman diagram evaluations is presented. It consists of two parts: the analyzer of diagrams and the interpreter of a special text manipulating language. This language can be used to create a source code for analytical or numerical evaluations and to keep the control of the process in general

Automated Single Cell Data Decontamination Pipeline

Energy Technology Data Exchange (ETDEWEB)

Tennessen, Kristin [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Pati, Amrita [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2014-03-21

Recent technological advancements in single-cell genomics have encouraged the classification and functional assessment of microorganisms from a wide span of the biospheres phylogeny.1,2 Environmental processes of interest to the DOE, such as bioremediation and carbon cycling, can be elucidated through the genomic lens of these unculturable microbes. However, contamination can occur at various stages of the single-cell sequencing process. Contaminated data can lead to wasted time and effort on meaningless analyses, inaccurate or erroneous conclusions, and pollution of public databases. A fully automated decontamination tool is necessary to prevent these instances and increase the throughput of the single-cell sequencing process

Transitivizing-detransitivizing typology and language family history

Directory of Open Access Journals (Sweden)

Grünthal Riho

2016-12-01

Full Text Available The transitivizing/detransitivizing typology of Nichols et al. 2004 also proves useful to historical linguistics. We focus on language families of northern Eurasia, chiefly the three oldest families (Indo-European, Uralic, Nakh-Daghestanian, some of their daughter branches aged about 2000-3000 years, and one younger family for which we have data on enough daughters to support a family phylogeny (Tungusic. We use the 18-pair wordlist of Nichols et al. 2004, which typologizes each pair of verbs depending on which of the two is derived. We make some improvements in the coding of grammatical properties and the typologization of pairs. NeighborNet trees based on this information reveal family-wide linguistic geography and areal trends. Adding minimal information about the cognacy or non-cognacy of the roots of the wordlist items produces Neighbor- Net trees which approximate well the known phylogeny of the family. Thus very small closed data sets, collected originally for typology, yield rich information about language family history - strikingly, a mere 18 verbs (9 pairs, coded for morphological type and cognacy, yield a very good genealogical tree - while historical methods have also improved the typology.

High-Performance Phylogeny Reconstruction

Energy Technology Data Exchange (ETDEWEB)

Tiffani L. Williams

2004-11-10

Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

Phylogeny mandalas for illustrating the Tree of Life.

Science.gov (United States)

Hasegawa, Masami

2017-12-01

A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates. Copyright © 2016 Elsevier Inc. All rights reserved.

Interoperability between OPC UA and AutomationML

OpenAIRE

Henßen, Robert; Schleipen, Miriam

2014-01-01

OPC UA (OPC Unified Architecture) is a platform-independent standard series (IEC 62541) [1], [2] for communication of industrial automation devices and systems. The OPC Unified Architecture is an advanced communication technology for process control. Certainly the launching costs for the initial information model are quite high. AutomationML (Automation Markup Language) is an upcoming open standard series (IEC 62714) [3], [4] for describing production plants or plant components. The goal of t...

Phonotactic diversity predicts the time depth of the world's language families.

Directory of Open Access Journals (Sweden)

Taraka Rama

Full Text Available The ASJP (Automated Similarity Judgment Program described an automated, lexical similarity-based method for dating the world's language groups using 52 archaeological, epigraphic and historical calibration date points. The present paper describes a new automated dating method, based on phonotactic diversity. Unlike ASJP, our method does not require any information on the internal classification of a language group. Also, the method can use all the available word lists for a language and its dialects eschewing the debate on 'language' vs. 'dialect'. We further combine these dates and provide a new baseline which, to our knowledge, is the best one. We make a systematic comparison of our method, ASJP's dating procedure, and combined dates. We predict time depths for world's language families and sub-families using this new baseline. Finally, we explain our results in the model of language change given by Nettle.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Science.gov (United States)

Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

2007-12-05

Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

Direct maximum parsimony phylogeny reconstruction from genotype data

Directory of Open Access Journals (Sweden)

Ravi R

2007-12-01

Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

Automated Scoring of L2 Spoken English with Random Forests

Science.gov (United States)

Kobayashi, Yuichiro; Abe, Mariko

2016-01-01

The purpose of the present study is to assess second language (L2) spoken English using automated scoring techniques. Automated scoring aims to classify a large set of learners' oral performance data into a small number of discrete oral proficiency levels. In automated scoring, objectively measurable features such as the frequencies of lexical and…

Juvenile morphology in baleen whale phylogeny.

Science.gov (United States)

Tsai, Cheng-Hsiu; Fordyce, R Ewan

2014-09-01

Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

On simulated annealing phase transitions in phylogeny reconstruction.

Science.gov (United States)

Strobl, Maximilian A R; Barker, Daniel

2016-08-01

Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Home automation with Intel Galileo

CERN Document Server

Dundar, Onur

2015-01-01

This book is for anyone who wants to learn Intel Galileo for home automation and cross-platform software development. No knowledge of programming with Intel Galileo is assumed, but knowledge of the C programming language is essential.

Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida).

Science.gov (United States)

Cornils, Astrid; Blanco-Bercial, Leocadio

2013-12-01

The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

Studies in Phylogeny. I. On the relation of Taxonomy, Phylogeny and Biogeography

NARCIS (Netherlands)

Lam, H.J.

1938-01-01

Taxonomy is static, its symbols are therefore two-dimensional, representing 1. differences or resemblances and 2. diversity (eventually are also area). Phylogeny is dynamic and its symbols are three-dimensional, representing 1. Time, 2. differences or resemblances and 3. diversity (eventually also

Automated prototyping tool-kit (APT)

OpenAIRE

Nada, Nader; Shing, M.; Berzins, V.; Luqi

2002-01-01

Automated prototyping tool-kit (APT) is an integrated set of software tools that generate source programs directly from real-time requirements. The APT system uses a fifth-generation prototyping language to model the communication structure, timing constraints, 1/0 control, and data buffering that comprise the requirements for an embedded software system. The language supports the specification of hard real-time systems with reusable components from domain specific component libraries. APT ha...

Ribosomal RNA: a key to phylogeny

Science.gov (United States)

Olsen, G. J.; Woese, C. R.

1993-01-01

As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.

Primate diversification inferred from phylogenies and fossils.

Science.gov (United States)

Herrera, James P

2017-12-01

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Towards an Automated Requirements-driven Development of Smart Cyber-Physical Systems

Directory of Open Access Journals (Sweden)

Jiri Vinarek

2016-03-01

Full Text Available The Invariant Refinement Method for Self Adaptation (IRM-SA is a design method targeting development of smart Cyber-Physical Systems (sCPS. It allows for a systematic translation of the system requirements into the system architecture expressed as an ensemble-based component system (EBCS. However, since the requirements are captured using natural language, there exists the danger of their misinterpretation due to natural language requirements' ambiguity, which could eventually lead to design errors. Thus, automation and validation of the design process is desirable. In this paper, we (i analyze the translation process of natural language requirements into the IRM-SA model, (ii identify individual steps that can be automated and/or validated using natural language processing techniques, and (iii propose suitable methods.

Algorithms For Phylogeny Reconstruction In a New Mathematical Model

NARCIS (Netherlands)

Lenzini, Gabriele; Marianelli, Silvia

1997-01-01

The evolutionary history of a set of species is represented by a tree called phylogenetic tree or phylogeny. Its structure depends on precise biological assumptions about the evolution of species. Problems related to phylogeny reconstruction (i.e., finding a tree representation of information

Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction.

Science.gov (United States)

Soon, Villu; Saarma, Urmas

2011-07-01

The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute

The phylogeny of Arthrotardigrada

DEFF Research Database (Denmark)

Hansen, Jesper Guldberg

2011-01-01

The order Arthrotardigrada, or water bears, constitutes a small group of 160 species of marine, microscopical invertebrates, within the phylum Tardigrada. Although the position of tardigrades in the Animal Kingdom has received much attention focusing on the metazoan phylogeny, the phylogenetic...

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches.

Science.gov (United States)

Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

2009-02-11

Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations

Inference of Large Phylogenies Using Neighbour-Joining

DEFF Research Database (Denmark)

Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm

2011-01-01

The neighbour-joining method is a widely used method for phylogenetic reconstruction which scales to thousands of taxa. However, advances in sequencing technology have made data sets with more than 10,000 related taxa widely available. Inference of such large phylogenies takes hours or days using...... the Neighbour-Joining method on a normal desktop computer because of the O(n^3) running time. RapidNJ is a search heuristic which reduce the running time of the Neighbour-Joining method significantly but at the cost of an increased memory consumption making inference of large phylogenies infeasible. We present...... two extensions for RapidNJ which reduce the memory requirements and \\makebox{allows} phylogenies with more than 50,000 taxa to be inferred efficiently on a desktop computer. Furthermore, an improved version of the search heuristic is presented which reduces the running time of RapidNJ on many data...

Automated identification of wound information in clinical notes of patients with heart diseases: Developing and validating a natural language processing application.

Science.gov (United States)

Topaz, Maxim; Lai, Kenneth; Dowding, Dawn; Lei, Victor J; Zisberg, Anna; Bowles, Kathryn H; Zhou, Li

2016-12-01

Electronic health records are being increasingly used by nurses with up to 80% of the health data recorded as free text. However, only a few studies have developed nursing-relevant tools that help busy clinicians to identify information they need at the point of care. This study developed and validated one of the first automated natural language processing applications to extract wound information (wound type, pressure ulcer stage, wound size, anatomic location, and wound treatment) from free text clinical notes. First, two human annotators manually reviewed a purposeful training sample (n=360) and random test sample (n=1100) of clinical notes (including 50% discharge summaries and 50% outpatient notes), identified wound cases, and created a gold standard dataset. We then trained and tested our natural language processing system (known as MTERMS) to process the wound information. Finally, we assessed our automated approach by comparing system-generated findings against the gold standard. We also compared the prevalence of wound cases identified from free-text data with coded diagnoses in the structured data. The testing dataset included 101 notes (9.2%) with wound information. The overall system performance was good (F-measure is a compiled measure of system's accuracy=92.7%), with best results for wound treatment (F-measure=95.7%) and poorest results for wound size (F-measure=81.9%). Only 46.5% of wound notes had a structured code for a wound diagnosis. The natural language processing system achieved good performance on a subset of randomly selected discharge summaries and outpatient notes. In more than half of the wound notes, there were no coded wound diagnoses, which highlight the significance of using natural language processing to enrich clinical decision making. Our future steps will include expansion of the application's information coverage to other relevant wound factors and validation of the model with external data. Copyright © 2016 Elsevier Ltd. All

Fossils and decapod phylogeny

NARCIS (Netherlands)

Schram, Frederick R.; Dixon, Christopher

2003-01-01

An expanded series of morphological characters developed for a cladistic analysis of extant decapods has yielded a new hypothesis for the phylogeny of the group. Application of this database to selected fossil genera produces some interesting results and demonstrates the feasibility of treating

Sequoyah Foreign Language Translation System - Business Case Analysis

National Research Council Canada - National Science Library

Ong, Wing S. S

2007-01-01

Sequoyah, which is the Department of Defense (DoD)'s Program of Record for automated foreign language translation, is to identify current and developing technologies to meet warfighter requirements for foreign language support...

The automated testing system of programs with the graphic user interface within the context of educational process

OpenAIRE

Sychev, O.; Kiryushkin, A.

2009-01-01

The paper describes the problems of automation of educational process at the course "Programming on high level language. Algorithmic languages". Complexities of testing of programs with the user interface are marked. Existing analogues was considered. Methods of automation of student's jobs testing are offered.

Dependency Grammar in Lithuanian Language Processing

OpenAIRE

Grigonytė, Gintarė

2006-01-01

Lithuanian language is quite in an early stage of language processing. And therefore has a high demand on automated tools like taggers, parsers, word sense disambiguators etc. During the last 10 years only a few researchers were attempting to create a parser for Lithuanian language. However none of them are used in practices nowadays. The process of designing and implementing rule based parser for Lithuanian language is presented in this paper. Rules and constraints of the formal grammar foll...

The phylogeny of Orussidae (Insecta: Hymenoptera) revisited

DEFF Research Database (Denmark)

Vilhelmsen, Lars

2007-01-01

The phylogeny of the parasitic wasp family Orussidae is analyzed with a slightly expanded version of a previously published data set. The basal splitting events in the family between two fossil taxa and the extant members are not unambiguously resolved. Intergeneric relationships in general...... are poorly supported and change under different analytical conditions. This corroborates earlier fi ndings regarding the phylogeny of the family. A resumé of the evolutionary history of the Orussidae is provided. Leptorussus madagascarensis sp.n. is described. Udgivelsesdato: 7/12...

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

Directory of Open Access Journals (Sweden)

Beaulieu Jeremy M

2009-02-01

Full Text Available Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae with 13,533 species and 1,401 sites. Conclusion By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously

Molecular data and phylogeny of family

International Nuclear Information System (INIS)

Shinwari, Z.K.; Shinwari, S.

2010-01-01

Family Smilacaceae's higher order taxonomy remained disputed for many years. It was treated as an order 'Smilacales' and was also placed under Liliales by several taxonomists. Even some considered as part of family Liliacaeae. In present paper, we investigated the family's higher order phylogeny and also compared its rbcL gene sequence data with related taxa to elucidate its phylogeny. The data suggests that its family stature is beyond dispute because of its advanced karyotype, woody climbing habit and DNA sequence data. The data suggest that Smilacaceae may be a sister group of order Liliales and it forms a clear clade with the order. (author)

Connected digit speech recognition system for Malayalam language

Indian Academy of Sciences (India)

A connected digit speech recognition is important in many applications such as automated banking system, catalogue-dialing, automatic data entry, automated banking system, etc. This paper presents an optimum speaker-independent connected digit recognizer for Malayalam language. The system employs Perceptual ...

Plastome phylogeny and early diversification of Brassicaceae.

Science.gov (United States)

Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A; Koch, Marcus A

2017-02-16

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Building a Twig Phylogeny

Science.gov (United States)

Flinn, Kathryn M.

2015-01-01

In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a…

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies.

Science.gov (United States)

Min, Xiaoping; Zhang, Mouzhao; Yuan, Sisi; Ge, Shengxiang; Liu, Xiangrong; Zeng, Xiangxiang; Xia, Ningshao

2017-12-26

In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

Digital-flight-control-system software written in automated-engineering-design language: A user's guide of verification and validation tools

Science.gov (United States)

Saito, Jim

1987-01-01

The user guide of verification and validation (V&V) tools for the Automated Engineering Design (AED) language is specifically written to update the information found in several documents pertaining to the automated verification of flight software tools. The intent is to provide, in one document, all the information necessary to adequately prepare a run to use the AED V&V tools. No attempt is made to discuss the FORTRAN V&V tools since they were not updated and are not currently active. Additionally, the current descriptions of the AED V&V tools are contained and provides information to augment the NASA TM 84276. The AED V&V tools are accessed from the digital flight control systems verification laboratory (DFCSVL) via a PDP-11/60 digital computer. The AED V&V tool interface handlers on the PDP-11/60 generate a Univac run stream which is transmitted to the Univac via a Remote Job Entry (RJE) link. Job execution takes place on the Univac 1100 and the job output is transmitted back to the DFCSVL and stored as a PDP-11/60 printfile.

Bayesian phylogeny analysis via stochastic approximation Monte Carlo

KAUST Repository

Cheon, Sooyoung

2009-11-01

Monte Carlo methods have received much attention in the recent literature of phylogeny analysis. However, the conventional Markov chain Monte Carlo algorithms, such as the Metropolis-Hastings algorithm, tend to get trapped in a local mode in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method is compared with two popular Bayesian phylogeny software, BAMBE and MrBayes, on simulated and real datasets. The numerical results indicate that our method outperforms BAMBE and MrBayes. Among the three methods, SAMC produces the consensus trees which have the highest similarity to the true trees, and the model parameter estimates which have the smallest mean square errors, but costs the least CPU time. © 2009 Elsevier Inc. All rights reserved.

Automated nuclear materials accounting

International Nuclear Information System (INIS)

Pacak, P.; Moravec, J.

1982-01-01

An automated state system of accounting for nuclear materials data was established in Czechoslovakia in 1979. A file was compiled of 12 programs in the PL/1 language. The file is divided into four groups according to logical associations, namely programs for data input and checking, programs for handling the basic data file, programs for report outputs in the form of worksheets and magnetic tape records, and programs for book inventory listing, document inventory handling and materials balance listing. A similar automated system of nuclear fuel inventory for a light water reactor was introduced for internal purposes in the Institute of Nuclear Research (UJV). (H.S.)

Lexical evolution rates derived from automated stability measures

Science.gov (United States)

Petroni, Filippo; Serva, Maurizio

2010-03-01

Phylogenetic trees can be reconstructed from the matrix which contains the distances between all pairs of languages in a family. Recently, we proposed a new method which uses normalized Levenshtein distances among words with the same meaning and averages over all the items of a given list. Decisions about the number of items in the input lists for language comparison have been debated since the beginning of glottochronology. The point is that words associated with some of the meanings have a rapid lexical evolution. Therefore, a large vocabulary comparison is only apparently more accurate than a smaller one, since many of the words do not carry any useful information. In principle, one should find the optimal length of the input lists, studying the stability of the different items. In this paper we tackle the problem with an automated methodology based only on our normalized Levenshtein distance. With this approach, the program of an automated reconstruction of language relationships is completed.

How will XML impact industrial automation?

CERN Multimedia

Pinceti, P

2002-01-01

A working group of the World Wide Web Consortium (W3C) has overcome the limits of both HTML and SGML with the definition of the extensible markup language - XML. This article looks at how XML will affect industrial automation (2 pages).

Language Muse: Automated Linguistic Activity Generation for English Language Learners

Science.gov (United States)

Madnani, Nitin; Burstein, Jill; Sabatini, John; Biggers, Kietha; Andreyev, Slava

2016-01-01

Current education standards in the U.S. require school students to read and understand complex texts from different subject areas (e.g., social studies). However, such texts usually contain figurative language, complex phrases and sentences, as well as unfamiliar discourse relations. This may present an obstacle to students whose native language…

Phylogeny and adaptation shape the teeth of insular mice.

Science.gov (United States)

Ledevin, Ronan; Chevret, Pascale; Ganem, Guila; Britton-Davidian, Janice; Hardouin, Emilie A; Chapuis, Jean-Louis; Pisanu, Benoit; da Luz Mathias, Maria; Schlager, Stefan; Auffray, Jean-Christophe; Renaud, Sabrina

2016-02-10

By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. © 2016 The Author(s).

Leveraging Small-Lexicon Language Models

Science.gov (United States)

2016-12-31

Glottolog/ ... a typical example: ./geo_distance.tsv – geographical distance sets (0 to 500 km, by 100km) ./ety_distance.tsv – genetic distance...normalizing notation affected automated syllabification; while tweaks of language and subbranch-specific syllable-break rubrics affected proper...many languages – an index that points to the forms that are most likely to be genetically related, but still respects semantic variation between

USB port compatible virtual instrument based automation for x-ray diffractometer setup

International Nuclear Information System (INIS)

Jayapandian, J.; Sheela, O.K.; Mallika, R.; Thiruarul, A.; Purniah, B.

2004-01-01

Windows based virtual instrument (VI) programs in graphic language simplify the design automation in R and D laboratories. With minimal hardware and maximum support of software, the automation becomes easier and user friendly. A novel design approach for the automation of SIEMENS make x-ray diffractometer setup is described in this paper. The automation is achieved with an indigenously developed virtual instrument program in labVIEW ver.6.0 and with a simple hardware design using 89C2051 micro-controller compatible with PC's USB port for the total automation of the experiment. (author)

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

Science.gov (United States)

Leduc-Robert, Geneviève; Maddison, Wayne P

2018-02-22

Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti

Improved compliance by BPM-driven workflow automation.

Science.gov (United States)

Holzmüller-Laue, Silke; Göde, Bernd; Fleischer, Heidi; Thurow, Kerstin

2014-12-01

Using methods and technologies of business process management (BPM) for the laboratory automation has important benefits (i.e., the agility of high-level automation processes, rapid interdisciplinary prototyping and implementation of laboratory tasks and procedures, and efficient real-time process documentation). A principal goal of the model-driven development is the improved transparency of processes and the alignment of process diagrams and technical code. First experiences of using the business process model and notation (BPMN) show that easy-to-read graphical process models can achieve and provide standardization of laboratory workflows. The model-based development allows one to change processes quickly and an easy adaption to changing requirements. The process models are able to host work procedures and their scheduling in compliance with predefined guidelines and policies. Finally, the process-controlled documentation of complex workflow results addresses modern laboratory needs of quality assurance. BPMN 2.0 as an automation language to control every kind of activity or subprocess is directed to complete workflows in end-to-end relationships. BPMN is applicable as a system-independent and cross-disciplinary graphical language to document all methods in laboratories (i.e., screening procedures or analytical processes). That means, with the BPM standard, a communication method of sharing process knowledge of laboratories is also available. © 2014 Society for Laboratory Automation and Screening.

Multi-purpose logical device with integrated circuit for the automation of mine water disposal

Energy Technology Data Exchange (ETDEWEB)

Pop, E.; Pasculescu, M.

1980-06-01

After an analysis of the waste water disposal as an object of automation, the author presents a BASIC-language programme established to simulate the automated control system on a digital computer. Then a multi-purpose logical device with integrated circuits for the automation of the mine water disposal is presented. (In Romanian)

Advances in natural language processing.

Science.gov (United States)

Hirschberg, Julia; Manning, Christopher D

2015-07-17

Natural language processing employs computational techniques for the purpose of learning, understanding, and producing human language content. Early computational approaches to language research focused on automating the analysis of the linguistic structure of language and developing basic technologies such as machine translation, speech recognition, and speech synthesis. Today's researchers refine and make use of such tools in real-world applications, creating spoken dialogue systems and speech-to-speech translation engines, mining social media for information about health or finance, and identifying sentiment and emotion toward products and services. We describe successes and challenges in this rapidly advancing area. Copyright © 2015, American Association for the Advancement of Science.

Molecular phylogeny and morphological change in the Psittacula parakeets

OpenAIRE

Groombridge, Jim J.; Jones, Carl G.; Nichols, Richard A.; Carlton, Mark; Bruford, Michael W.

2004-01-01

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800 bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that ext...

Effects of methodology and analysis strategy on robustness of pestivirus phylogeny.

Science.gov (United States)

Liu, Lihong; Xia, Hongyan; Baule, Claudia; Belák, Sándor; Wahlberg, Niklas

2010-01-01

Phylogenetic analysis of pestiviruses is a useful tool for classifying novel pestiviruses and for revealing their phylogenetic relationships. In this study, robustness of pestivirus phylogenies has been compared by analyses of the 5'UTR, and complete N(pro) and E2 gene regions separately and combined, performed by four methods: neighbour-joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI). The strategy of analysing the combined sequence dataset by BI, ML, and MP methods resulted in a single, well-supported tree topology, indicating a reliable and robust pestivirus phylogeny. By contrast, the single-gene analysis strategy resulted in 12 trees of different topologies, revealing different relationships among pestiviruses. These results indicate that the strategies and methodologies are two vital aspects affecting the robustness of the pestivirus phylogeny. The strategy and methodologies outlined in this paper may have a broader application in inferring phylogeny of other RNA viruses.

The shape of mammalian phylogeny

DEFF Research Database (Denmark)

Purvis, Andy; Fritz, Susanne A; Rodríguez, Jesús

2011-01-01

an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions...

A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides).

Science.gov (United States)

Jønsson, Knud Andreas; Fabre, Pierre-Henri; Kennedy, Jonathan D; Holt, Ben G; Borregaard, Michael K; Rahbek, Carsten; Fjeldså, Jon

2016-01-01

The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not. Copyright © 2015 Elsevier Inc. All rights reserved.

Extensible and Efficient Automation Through Reflective Tactics

DEFF Research Database (Denmark)

Malecha, Gregory; Bengtson, Jesper

2016-01-01

Foundational proof assistants simultaneously offer both expressive logics and strong guarantees. The price they pay for this flexibility is often the need to build and check explicit proof objects which can be expensive. In this work we develop a collection of techniques for building reflective...... automation, where proofs are witnessed by verified decision procedures rather than verbose proof objects. Our techniques center around a verified domain specific language for proving, Rtac, written in Gallina, Coq’s logic. The design of tactics makes it easy to combine them into higher-level automation...... that can be proved sound in a mostly automated way. Furthermore, unlike traditional uses of reflection, Rtac tactics are independent of the underlying problem domain. This allows them to be re-tasked to automate new problems with very little effort. We demonstrate the usability of Rtac through several case...

PR-PR: cross-platform laboratory automation system.

Science.gov (United States)

Linshiz, Gregory; Stawski, Nina; Goyal, Garima; Bi, Changhao; Poust, Sean; Sharma, Monica; Mutalik, Vivek; Keasling, Jay D; Hillson, Nathan J

2014-08-15

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

Whole genome phylogenies for multiple Drosophila species

Directory of Open Access Journals (Sweden)

Seetharam Arun

2012-12-01

Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

Automated Speech Rate Measurement in Dysarthria

Science.gov (United States)

Martens, Heidi; Dekens, Tomas; Van Nuffelen, Gwen; Latacz, Lukas; Verhelst, Werner; De Bodt, Marc

2015-01-01

Purpose: In this study, a new algorithm for automated determination of speech rate (SR) in dysarthric speech is evaluated. We investigated how reliably the algorithm calculates the SR of dysarthric speech samples when compared with calculation performed by speech-language pathologists. Method: The new algorithm was trained and tested using Dutch…

Formal Test Automation: A Simple Experiment

NARCIS (Netherlands)

Belinfante, Axel; Feenstra, J.; de Vries, R.G.; Tretmans, G.J.; Goga, N.; Feijs, Loe; Mauw, Sjouke; Heerink, A.W.; Csopaki, Gyula; Dibuz, Sarolta; Tarnay, Katalin

1999-01-01

In this paper1 we study the automation of test derivation and execution in the area of conformance testing. The test scenarios are derived from multiple specication languages: LOTOS, Promela and SDL. A central theme of this study is the usability of batch-oriented and on-the-fly testing approaches.

Automated bar coding of air samples at Hanford (ABCASH)

International Nuclear Information System (INIS)

Troyer, G.L.; Brayton, D.D.; McNeece, S.G.

1992-10-01

This article describes the basis, main features and benefits of an automated system for tracking and reporting radioactive air particulate samples. The system was developed due to recognized need for improving the quality and integrity of air sample data related to personnel and environmental protection. The data capture, storage, and retrieval of air sample data are described. The automation aspect of the associated and data input eliminates a large potential for human error. The system utilizes personal computers, handheld computers, a commercial personal computer database package, commercial programming languages, and complete documentation to satisfy the system's automation objective

Artificial intelligence programming languages for computer aided manufacturing

Science.gov (United States)

Rieger, C.; Samet, H.; Rosenberg, J.

1979-01-01

Eight Artificial Intelligence programming languages (SAIL, LISP, MICROPLANNER, CONNIVER, MLISP, POP-2, AL, and QLISP) are presented and surveyed, with examples of their use in an automated shop environment. Control structures are compared, and distinctive features of each language are highlighted. A simple programming task is used to illustrate programs in SAIL, LISP, MICROPLANNER, and CONNIVER. The report assumes reader knowledge of programming concepts, but not necessarily of the languages surveyed.

Machine tongues. X. Constraint languages

Energy Technology Data Exchange (ETDEWEB)

Levitt, D.

Constraint languages and programming environments will help the designer produce a lucid description of a problem domain, and then of particular situations and problems in it. Early versions of these languages were given descriptions of real world domain constraints, like the operation of electrical and mechanical parts. More recently, the author has automated a vocabulary for describing musical jazz phrases, using constraint language as a jazz improviser. General constraint languages will handle all of these domains. Once the model is in place, the system will connect built-in code fragments and algorithms to answer questions about situations; that is, to help solve problems. Bugs will surface not in code, but in designs themselves. 15 references.

A six-gene phylogeny provides new insights into choanoflagellate evolution.

Science.gov (United States)

Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

2017-02-01

Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Book review: Insect morphology and phylogeny

Directory of Open Access Journals (Sweden)

Susanne Randolf

2014-05-01

Full Text Available Beutel RG, Friedrich F, Ge S-Q, Yang X-K (2014 Insect Morphology and Phylogeny: A textbook for students of entomology. De Gruyter, Berlin/Boston, 516 pp., softcover. ISBN 978-3-11-026263-6.

“The Naming of Cats”: Automated Genre Classification

Directory of Open Access Journals (Sweden)

Yunhyong Kim

2007-07-01

Full Text Available This paper builds on the work presented at the ECDL 2006 in automated genre classification as a step toward automating metadata extraction from digital documents for ingest into digital repositories such as those run by archives, libraries and eprint services (Kim & Ross, 2006b. We have previously proposed dividing features of a document into five types (features for visual layout, language model features, stylometric features, features for semantic structure, and contextual features as an object linked to previously classified objects and other external sources and have examined visual and language model features. The current paper compares results from testing classifiers based on image and stylometric features in a binary classification to show that certain genres have strong image features which enable effective separation of documents belonging to the genre from a large pool of other documents.

Bayesian inference of the metazoan phylogeny

DEFF Research Database (Denmark)

Glenner, Henrik; Hansen, Anders J; Sørensen, Martin V

2004-01-01

Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has...

Automating quantum experiment control

Science.gov (United States)

Stevens, Kelly E.; Amini, Jason M.; Doret, S. Charles; Mohler, Greg; Volin, Curtis; Harter, Alexa W.

2017-03-01

The field of quantum information processing is rapidly advancing. As the control of quantum systems approaches the level needed for useful computation, the physical hardware underlying the quantum systems is becoming increasingly complex. It is already becoming impractical to manually code control for the larger hardware implementations. In this chapter, we will employ an approach to the problem of system control that parallels compiler design for a classical computer. We will start with a candidate quantum computing technology, the surface electrode ion trap, and build a system instruction language which can be generated from a simple machine-independent programming language via compilation. We incorporate compile time generation of ion routing that separates the algorithm description from the physical geometry of the hardware. Extending this approach to automatic routing at run time allows for automated initialization of qubit number and placement and additionally allows for automated recovery after catastrophic events such as qubit loss. To show that these systems can handle real hardware, we present a simple demonstration system that routes two ions around a multi-zone ion trap and handles ion loss and ion placement. While we will mainly use examples from transport-based ion trap quantum computing, many of the issues and solutions are applicable to other architectures.

An Inference Language for Imaging

DEFF Research Database (Denmark)

Pedemonte, Stefano; Catana, Ciprian; Van Leemput, Koen

2014-01-01

We introduce iLang, a language and software framework for probabilistic inference. The iLang framework enables the definition of directed and undirected probabilistic graphical models and the automated synthesis of high performance inference algorithms for imaging applications. The iLang framewor...

Automating Visualization Service Generation with the WATT Compiler

Science.gov (United States)

Bollig, E. F.; Lyness, M. D.; Erlebacher, G.; Yuen, D. A.

2007-12-01

As tasks and workflows become increasingly complex, software developers are devoting increasing attention to automation tools. Among many examples, the Automator tool from Apple collects components of a workflow into a single script, with very little effort on the part of the user. Tasks are most often described as a series of instructions. The granularity of the tasks dictates the tools to use. Compilers translate fine-grained instructions to assembler code, while scripting languages (ruby, perl) are used to describe a series of tasks at a higher level. Compilers can also be viewed as transformational tools: a cross-compiler can translate executable code written on one computer to assembler code understood on another, while transformational tools can translate from one high-level language to another. We are interested in creating visualization web services automatically, starting from stand-alone VTK (Visualization Toolkit) code written in Tcl. To this end, using the OCaml programming language, we have developed a compiler that translates Tcl into C++, including all the stubs, classes and methods to interface with gSOAP, a C++ implementation of the Soap 1.1/1.2 protocols. This compiler, referred to as the Web Automation and Translation Toolkit (WATT), is the first step towards automated creation of specialized visualization web services without input from the user. The WATT compiler seeks to automate all aspects of web service generation, including the transport layer, the division of labor and the details related to interface generation. The WATT compiler is part of ongoing efforts within the NSF funded VLab consortium [1] to facilitate and automate time-consuming tasks for the science related to understanding planetary materials. Through examples of services produced by WATT for the VLab portal, we will illustrate features, limitations and the improvements necessary to achieve the ultimate goal of complete and transparent automation in the generation of web

Phylogeny of Cirsium spp. in North America: Host Specificity Does Not Follow Phylogeny

Directory of Open Access Journals (Sweden)

Tracey A. Bodo Slotta

2012-10-01

Full Text Available Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native Great Plains Cirsium spp. and other thistles to determine if host specificity follows phylogeny. The monophyly of Cirsium spp. and Carduus within the tribe Cardinae was confirmed with native North American and European lineages of the Cirsium spp. examined. We did not detect interspecific hybridization between the introduced invasive and the native North American Cirsium spp. Selected host-biological control agent interactions were mapped onto the phylogenic tree derived by maximum likelihood analysis to examine the co-occurrence of known hosts with biological control agents. Within Cirsium-Cardueae, the insect biological control agents do not associate with host phylogenetic lines. Thus, more comprehensive testing of species in host-specificity trials, rather than relying on a single representative of a given clade may be necessary; because the assumption that host-specificity follows phylogeny does not necessarily hold. Since the assumption does not always hold, it will also be important to evaluate ecological factors to provide better cues for host specificity.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Science.gov (United States)

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

Explaining evolution via constrained persistent perfect phylogeny

Science.gov (United States)

2014-01-01

Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

A Bayesian approach to the evolution of metabolic networks on a phylogeny.

Directory of Open Access Journals (Sweden)

Aziz Mithani

2010-08-01

Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

Science.gov (United States)

Huang, Zuhao; Tu, Feiyun

2017-07-01

The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

美國研究圖書館資訊網東亞語文圖書資訊系統之發展 The Development of RLIN's Automated System in East Asian Languages Material

Directory of Open Access Journals (Sweden)

Hon-chu Huang

1985-09-01

Full Text Available 無The major problem of data processing for library material in East Asian languages are the design of character set, hardware for inputting, storing, processing, transmitting etc. and MARC Format. RLIN is the first institution to implement online network cataloging system in East Asian Languages. In this paper RLIN's achievement and effort on this area are described and what can we learn from it to develop the Chinese library automation system in the R. O. C. are suggested.

Language-based multimedia information retrieval

NARCIS (Netherlands)

de Jong, Franciska M.G.; Gauvain, J.L.; Hiemstra, Djoerd; Netter, K.

2000-01-01

This paper describes various methods and approaches for language-based multimedia information retrieval, which have been developed in the projects POP-EYE and OLIVE and which will be developed further in the MUMIS project. All of these project aim at supporting automated indexing of video material

A molecular phylogeny of living primates.

Science.gov (United States)

Perelman, Polina; Johnson, Warren E; Roos, Christian; Seuánez, Hector N; Horvath, Julie E; Moreira, Miguel A M; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C; Silva, Artur; O'Brien, Stephen J; Pecon-Slattery, Jill

2011-03-01

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

A Molecular Phylogeny of Living Primates

Science.gov (United States)

Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

2011-01-01

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

A molecular phylogeny of living primates.

Directory of Open Access Journals (Sweden)

Polina Perelman

2011-03-01

Full Text Available Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb from 186 primates representing 61 (~90% of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

Automated Assessment of Patients' Self-Narratives for Posttraumatic Stress Disorder Screening Using Natural Language Processing and Text Mining.

Science.gov (United States)

He, Qiwei; Veldkamp, Bernard P; Glas, Cees A W; de Vries, Theo

2017-03-01

Patients' narratives about traumatic experiences and symptoms are useful in clinical screening and diagnostic procedures. In this study, we presented an automated assessment system to screen patients for posttraumatic stress disorder via a natural language processing and text-mining approach. Four machine-learning algorithms-including decision tree, naive Bayes, support vector machine, and an alternative classification approach called the product score model-were used in combination with n-gram representation models to identify patterns between verbal features in self-narratives and psychiatric diagnoses. With our sample, the product score model with unigrams attained the highest prediction accuracy when compared with practitioners' diagnoses. The addition of multigrams contributed most to balancing the metrics of sensitivity and specificity. This article also demonstrates that text mining is a promising approach for analyzing patients' self-expression behavior, thus helping clinicians identify potential patients from an early stage.

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

Directory of Open Access Journals (Sweden)

Suchard Marc A

2007-03-01

Full Text Available Abstract Background Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments. Results We introduce a novel Markov chain transition kernel that improves computational efficiency by proposing non-local topology rearrangements and by block sampling alignment and topology parameters. In addition, we extend our previous indel model to increase biological realism by placing indels preferentially on longer branches. We demonstrate the ability of indel information to increase phylogenetic resolution in examples drawn from within-host viral sequence samples. We also demonstrate the importance of taking alignment uncertainty into account when using such information. Finally, we show that codon-based substitution models can significantly affect alignment quality and phylogenetic inference by unrealistically forcing indels to begin and end between codons. Conclusion These results indicate that indel information can improve phylogenetic resolution of recently diverged pathogens and that alignment uncertainty should be considered in such analyses.

Air Force Information Workflow Automation through Synchronized Air Power Management (SAPM)

National Research Council Canada - National Science Library

Benkley, Carl; Chang, Irene; Crowley, John; Oristian, Thomas

2004-01-01

.... Implementing Extensible Markup Language (XML) messages, web services, and workflow automation, SAPM expands existing web-based capabilities, enables machine-to-machine interfaces, and streamlines the war fighter kill chain process...

Automated Analysis of Security in Networking Systems

DEFF Research Database (Denmark)

Buchholtz, Mikael

2004-01-01

such networking systems are modelled in the process calculus LySa. On top of this programming language based formalism an analysis is developed, which relies on techniques from data and control ow analysis. These are techniques that can be fully automated, which make them an ideal basis for tools targeted at non...

Molecular phylogeny of Ranunculaceae based on internal ...

African Journals Online (AJOL)

STORAGESEVER

2009-10-19

Oct 19, 2009 ... evidence regarding the systematic classification of Ranunculaceae plants, we used molecular ... Ranunculaceae is a family of flowering plants known as ... and in the analysis of the evolutionary rate for lower level phylogeny ...

Molecular phylogeny and morphological change in the Psittacula parakeets.

Science.gov (United States)

Groombridge, Jim J; Jones, Carl G; Nichols, Richard A; Carlton, Mark; Bruford, Michael W

2004-04-01

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.

A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

Science.gov (United States)

Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

2014-01-01

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean

Automation from pictures

International Nuclear Information System (INIS)

Kozubal, A.J.

1992-01-01

The state transition diagram (STD) model has been helpful in the design of real time software, especially with the emergence of graphical computer aided software engineering (CASE) tools. Nevertheless, the translation of the STD to real time code has in the past been primarily a manual task. At Los Alamos we have automated this process. The designer constructs the STD using a CASE tool (Cadre Teamwork) using a special notation for events and actions. A translator converts the STD into an intermediate state notation language (SNL), and this SNL is compiled directly into C code (a state program). Execution of the state program is driven by external events, allowing multiple state programs to effectively share the resources of the host processor. Since the design and the code are tightly integrated through the CASE tool, the design and code never diverge, and we avoid design obsolescence. Furthermore, the CASE tool automates the production of formal technical documents from the graphic description encapsulated by the CASE tool. (author)

Phylogeny mandalas of birds using the lithographs of John Gould's folio bird books.

Science.gov (United States)

Hasegawa, Masami; Kuroda, Sayako

2017-12-01

The phylogeny mandala, which is a circular phylogeny with photos or drawings of species, is a suitable way to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. In this article, in order to demonstrate the recent progress of avian molecular phylogenetics, six phylogeny mandalas of various taxonomic groups of birds are presented with the lithographs of John Gould's folio bird books; i.e., (1) whole Aves, (2) Passeriformes, (3) Paradisaeidae in Corvoidea (Passeriformes), (4) Meliphagoidea (Passeriformes), (5) Trochili in Apodiformes, and (6) Galliformes. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogeny, diet, and cranial integration in australodelphian marsupials.

Directory of Open Access Journals (Sweden)

Anjali Goswami

2007-10-01

Full Text Available Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Directory of Open Access Journals (Sweden)

David Lee Erickson

2014-11-01

Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

Science.gov (United States)

Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

2004-06-01

A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

Science.gov (United States)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

Science.gov (United States)

Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

2012-11-01

The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. Copyright © 2012 Elsevier Inc. All rights reserved.

One of My Favorite Assignments: Automated Teller Machine Simulation.

Science.gov (United States)

Oberman, Paul S.

2001-01-01

Describes an assignment for an introductory computer science class that requires the student to write a software program that simulates an automated teller machine. Highlights include an algorithm for the assignment; sample file contents; language features used; assignment variations; and discussion points. (LRW)

Automated sensitivity analysis using the GRESS language

International Nuclear Information System (INIS)

Pin, F.G.; Oblow, E.M.; Wright, R.Q.

1986-04-01

An automated procedure for performing large-scale sensitivity studies based on the use of computer calculus is presented. The procedure is embodied in a FORTRAN precompiler called GRESS, which automatically processes computer models and adds derivative-taking capabilities to the normal calculated results. In this report, the GRESS code is described, tested against analytic and numerical test problems, and then applied to a major geohydrological modeling problem. The SWENT nuclear waste repository modeling code is used as the basis for these studies. Results for all problems are discussed in detail. Conclusions are drawn as to the applicability of GRESS in the problems at hand and for more general large-scale modeling sensitivity studies

A human genome-wide library of local phylogeny predictions for whole-genome inference problems

Directory of Open Access Journals (Sweden)

Schwartz Russell

2008-08-01

Full Text Available Abstract Background Many common inference problems in computational genetics depend on inferring aspects of the evolutionary history of a data set given a set of observed modern sequences. Detailed predictions of the full phylogenies are therefore of value in improving our ability to make further inferences about population history and sources of genetic variation. Making phylogenetic predictions on the scale needed for whole-genome analysis is, however, extremely computationally demanding. Results In order to facilitate phylogeny-based predictions on a genomic scale, we develop a library of maximum parsimony phylogenies within local regions spanning all autosomal human chromosomes based on Haplotype Map variation data. We demonstrate the utility of this library for population genetic inferences by examining a tree statistic we call 'imperfection,' which measures the reuse of variant sites within a phylogeny. This statistic is significantly predictive of recombination rate, shows additional regional and population-specific conservation, and allows us to identify outlier genes likely to have experienced unusual amounts of variation in recent human history. Conclusion Recent theoretical advances in algorithms for phylogenetic tree reconstruction have made it possible to perform large-scale inferences of local maximum parsimony phylogenies from single nucleotide polymorphism (SNP data. As results from the imperfection statistic demonstrate, phylogeny predictions encode substantial information useful for detecting genomic features and population history. This data set should serve as a platform for many kinds of inferences one may wish to make about human population history and genetic variation.

Genomes-based phylogeny of the genus Xanthomonas

Directory of Open Access Journals (Sweden)

Rodriguez-R Luis M

2012-03-01

Full Text Available Abstract Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

The role of automation and artificial intelligence

Science.gov (United States)

Schappell, R. T.

1983-07-01

Consideration is given to emerging technologies that are not currently in common use, yet will be mature enough for implementation in a space station. Artificial intelligence (AI) will permit more autonomous operation and improve the man-machine interfaces. Technology goals include the development of expert systems, a natural language query system, automated planning systems, and AI image understanding systems. Intelligent robots and teleoperators will be needed, together with improved sensory systems for the robotics, housekeeping, vehicle control, and spacecraft housekeeping systems. Finally, NASA is developing the ROBSIM computer program to evaluate level of automation, perform parametric studies and error analyses, optimize trajectories and control systems, and assess AI technology.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-01-01

Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-02-01

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

Resolution of ray-finned fish phylogeny and timing of diversification.

Science.gov (United States)

Near, Thomas J; Eytan, Ron I; Dornburg, Alex; Kuhn, Kristen L; Moore, Jon A; Davis, Matthew P; Wainwright, Peter C; Friedman, Matt; Smith, W Leo

2012-08-21

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

KAUST Repository

Díaz-Arce, Natalia

2016-06-07

Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data.

Phylogeny and taxonomy of the Inonotus linteus complex

Czech Academy of Sciences Publication Activity Database

Tian, X.-M.; Yu, H.-Y.; Zhou, L.-W.; Decock, C.; Vlasák, Josef; Dai, Y.C.

2013-01-01

Roč. 58, č. 1 (2013), s. 159-169 ISSN 1560-2745 Institutional support: RVO:60077344 Keywords : Hymenochaetaceae * Phellinus * Phylogeny * ITS Subject RIV: EF - Botanics Impact factor: 6.938, year: 2013

Automated Guidance for Thermodynamics Essays: Critiquing versus Revisiting

Science.gov (United States)

Donnelly, Dermot F.; Vitale, Jonathan M.; Linn, Marcia C.

2015-01-01

Middle school students struggle to explain thermodynamics concepts. In this study, to help students succeed, we use a natural language processing program to analyze their essays explaining the aspects of thermodynamics and provide guidance based on the automated score. The 346 sixth-grade students were assigned to either the critique condition…

Molecular phylogeny of Ranunculaceae based on internal ...

African Journals Online (AJOL)

The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic analysis of 92 ...

Benchmarks of programming languages for special purposes in the space station

Science.gov (United States)

Knoebel, Arthur

1986-01-01

Although Ada is likely to be chosen as the principal programming language for the Space Station, certain needs, such as expert systems and robotics, may be better developed in special languages. The languages, LISP and Prolog, are studied and some benchmarks derived. The mathematical foundations for these languages are reviewed. Likely areas of the space station are sought out where automation and robotics might be applicable. Benchmarks are designed which are functional, mathematical, relational, and expert in nature. The coding will depend on the particular versions of the languages which become available for testing.

Microcomputer automation of the sample probe of an ESCA spectrometer

Energy Technology Data Exchange (ETDEWEB)

Fischer, J W; Downey, R M; Schrawyer, L R; Meisenheimer, R G [California Univ., Livermore (USA). Lawrence Livermore Lab.

1979-06-01

Many of the currently available ESCA spectrometers can be obtained with fully automated control and data acquisition systems as well as a variety of algorithms for data processing. The majority of these computer-controlled functions, however, are directed toward the analysis of a single physical sample. Since many analyses require the collection of data for several hours for the purpose of ensemble averaging to enhance the signal-to-noise ratio, overnight operation is a common practice. It is during these periods that a capability for multiple sample analyses would be most useful. The subject instrument for the automation was a Hewlett-Packard Model 5950A ESCA spectrometer which was supplied with a Hewlett-Packard 5952A Data System consisting of a Hewlett-Packard 2100A small computer and a Hewlett-Packard 85001A Magnetic Tape Cassett I/O unit. A microprocessor based system was used to implement this automation. The system uses the high-level language BASIC for virtually all control functions, thus providing the obvious advantages of rapid programming and ease of software modification over an assembly language although more ROM is required.

STAR - A computer language for hybrid AI applications

Science.gov (United States)

Borchardt, G. C.

1986-01-01

Constructing Artificial Intelligence application systems which rely on both symbolic and non-symbolic processing places heavy demands on the communication of data between dissimilar languages. This paper describes STAR (Simple Tool for Automated Reasoning), a computer language for the development of AI application systems which supports the transfer of data structures between a symbolic level and a non-symbolic level defined in languages such as FORTRAN, C and PASCAL. The organization of STAR is presented, followed by the description of an application involving STAR in the interpretation of airborne imaging spectrometer data.

Cladistic analysis of Bantu languages: a new tree based on combined lexical and grammatical data

Science.gov (United States)

Rexová, Kateřina; Bastin, Yvonne; Frynta, Daniel

2006-04-01

The phylogeny of the Bantu languages is reconstructed by application of the cladistic methodology to the combined lexical and grammatical data (87 languages, 144 characters). A maximum parsimony tree and Bayesian analysis supported some previously recognized clades, e.g., that of eastern and southern Bantu languages. Moreover, the results revealed that Bantu languages south and east of the equatorial forest are probably monophyletic. It suggests an unorthodox scenario of Bantu expansion including (after initial radiation in their homelands and neighboring territories) just a single passage through rainforest areas followed by a subsequent divergence into major clades. The likely localization of this divergence is in the area west of the Great Lakes. It conforms to the view that demographic expansion and dispersal throughout the dry-forests and savanna regions of subequatorial Africa was associated with the acquisition of new technologies (iron metallurgy and grain cultivation).

Specification of real-time automation systems with HybridUML; Spezifikation von Echtzeit-Automatisierungssystemen mit HybridUML

Energy Technology Data Exchange (ETDEWEB)

Berkenkoetter, K.; Bisanz, S.; Hannemann, U.; Peleska, J. [Univ. Bremen (Germany)

2004-07-01

Complex automation systems require specification formalisms supporting the description of real-time requirements with respect to both discrete and time-continuous observables. For this purpose, the authors have designed the HybridUML specification language. Discrete events, communication, and variable assignments are specified by state machines, timers, and invariant conditions. The time-continuous aspects of system behaviour are described by associating differential equations or time-dependent algebraic conditions with system states. The complexity of large systems is controlled by decomposing the specification into parallel components and hierarchical state machines. Instead of inventing a new language syntax, HybridUML is represented as a profile of the Unified Modeling Language UML 2.0. This allows to re-use the syntactic framework of well-accepted graphical UML constructs and development support provided by various UML case tools. The profile is associated with a precise language semantics linking unambiguous meaning to all HybridUML specifications. As a consequence, HybridUML specifications can be compiled into executable code which is suitable for execution in hard realtime on multi-processor computers. This serves both for the development of automation systems and for specification-based testing in real-time. This paper contains an introduction to HybridUML which is illustrated by an example from the field of automated train control. (orig.)

Automation of strategy using IDEF0 — A proof of concept

Directory of Open Access Journals (Sweden)

Gary R. Waissi

2015-12-01

Full Text Available The goal of this interdisciplinary paper is to show that an existing modeling language, Integration Definition for Function Modeling (IDEF0, is applicable for use in strategy modeling and for automation of strategic plan development and implementation. We will show how utilization of the systems modeling language IDEF0 simplifies strategic plan development, and moves strategic planning and management from a static, document-based approach to a model- and software-based approach. A sequence of examples, as a proof-of-concept, is shown to demonstrate the use of IDEF0 to translate document-based strategic plans to model-based plans. The advantages of IDEF0 include: a well-tested language, and comprehensive systems modeling technique. The resulting IDEF0 models are well-defined, well-structured, easy to understand, easy to modify and use, and can be extended to any depth of detail. It is noted, that while the paper focuses on small- and medium manufacturing enterprises (SME, the approach can be used for strategy development and strategy automation of any size company or organization.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

Science.gov (United States)

Helaers, Raphaël; Milinkovitch, Michel C

2010-07-15

The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high

Cultural phylogeography of the Bantu Languages of sub-Saharan Africa.

Science.gov (United States)

Currie, Thomas E; Meade, Andrew; Guillon, Myrtille; Mace, Ruth

2013-07-07

There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees of Bantu languages and map them onto geographical space in order to assess the likely pathway of expansion and test between dispersal scenarios. The results clearly support a scenario in which groups first moved south through the rainforest from a homeland somewhere near the Nigeria-Cameroon border. Emerging on the south side of the rainforest, one branch moved south and west. Another branch moved towards the Great Lakes, eventually giving rise to the monophyletic clade of East Bantu languages that inhabit East and Southeastern Africa. These phylogenies also reveal information about more general processes involved in the diversification of human populations into distinct ethnolinguistic groups. Our study reveals that Bantu languages show a latitudinal gradient in covering greater areas with increasing distance from the equator. Analyses suggest that this pattern reflects a true ecological relationship rather than merely being an artefact of shared history. The study shows how a phylogeographic approach can address questions relating to the specific histories of certain groups, as well as general cultural evolutionary processes.

Bayesian phylogeny analysis via stochastic approximation Monte Carlo

KAUST Repository

Cheon, Sooyoung; Liang, Faming

2009-01-01

in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method

Altered functional connectivity of the language network in ASD: Role of classical language areas and cerebellum☆

Science.gov (United States)

Verly, Marjolein; Verhoeven, Judith; Zink, Inge; Mantini, Dante; Peeters, Ronald; Deprez, Sabine; Emsell, Louise; Boets, Bart; Noens, Ilse; Steyaert, Jean; Lagae, Lieven; De Cock, Paul; Rommel, Nathalie; Sunaert, Stefan

2014-01-01

The development of language, social interaction and communicative skills is remarkably different in the child with autism spectrum disorder (ASD). Atypical brain connectivity has frequently been reported in this patient population. However, the neural correlates underlying their disrupted language development and functioning are still poorly understood. Using resting state fMRI, we investigated the functional connectivity properties of the language network in a group of ASD patients with clear comorbid language impairment (ASD-LI; N = 19) and compared them to the language related connectivity properties of 23 age-matched typically developing children. A verb generation task was used to determine language components commonly active in both groups. Eight joint language components were identified and subsequently used as seeds in a resting state analysis. Interestingly, both the interregional and the seed-based whole brain connectivity analysis showed preserved connectivity between the classical intrahemispheric language centers, Wernicke's and Broca's areas. In contrast however, a marked loss of functional connectivity was found between the right cerebellar region and the supratentorial regulatory language areas. Also, the connectivity between the interhemispheric Broca regions and modulatory control dorsolateral prefrontal region was found to be decreased. This disruption of normal modulatory control and automation function by the cerebellum may underlie the abnormal language function in children with ASD-LI. PMID:24567909

Detection, phylogeny and population dynamics of syntrophic propionate - oxidizing bacteria in anaerobic granular sludge

NARCIS (Netherlands)

Harmsen, H.J.M.

1996-01-01

The research described this thesis concerns the diversity and phylogeny of syntrophic propionate-oxidizing bacteria and their ecology in granular sludge, from which they were obtained. 16S rRNA was used as a molecular marker to study both the phylogeny and the ecology of these bacteria.

Resting-State Functional Magnetic Resonance Imaging for Language Preoperative Planning

Science.gov (United States)

Branco, Paulo; Seixas, Daniela; Deprez, Sabine; Kovacs, Silvia; Peeters, Ronald; Castro, São L.; Sunaert, Stefan

2016-01-01

Functional magnetic resonance imaging (fMRI) is a well-known non-invasive technique for the study of brain function. One of its most common clinical applications is preoperative language mapping, essential for the preservation of function in neurosurgical patients. Typically, fMRI is used to track task-related activity, but poor task performance and movement artifacts can be critical limitations in clinical settings. Recent advances in resting-state protocols open new possibilities for pre-surgical mapping of language potentially overcoming these limitations. To test the feasibility of using resting-state fMRI instead of conventional active task-based protocols, we compared results from fifteen patients with brain lesions while performing a verb-to-noun generation task and while at rest. Task-activity was measured using a general linear model analysis and independent component analysis (ICA). Resting-state networks were extracted using ICA and further classified in two ways: manually by an expert and by using an automated template matching procedure. The results revealed that the automated classification procedure correctly identified language networks as compared to the expert manual classification. We found a good overlay between task-related activity and resting-state language maps, particularly within the language regions of interest. Furthermore, resting-state language maps were as sensitive as task-related maps, and had higher specificity. Our findings suggest that resting-state protocols may be suitable to map language networks in a quick and clinically efficient way. PMID:26869899

Emerging Approach of Natural Language Processing in Opinion Mining: A Review

Science.gov (United States)

Kim, Tai-Hoon

Natural language processing (NLP) is a subfield of artificial intelligence and computational linguistics. It studies the problems of automated generation and understanding of natural human languages. This paper outlines a framework to use computer and natural language techniques for various levels of learners to learn foreign languages in Computer-based Learning environment. We propose some ideas for using the computer as a practical tool for learning foreign language where the most of courseware is generated automatically. We then describe how to build Computer Based Learning tools, discuss its effectiveness, and conclude with some possibilities using on-line resources.

Instrument calls and real-time code for laboratory automation

International Nuclear Information System (INIS)

Taber, L.; Ames, H.S.; Yamauchi, R.K.; Barton, G.W. Jr.

1978-01-01

These programs are the result of a joint Lawrence Livermore Laboratory and Environmental Protection Agency project to automate water quality laboratories. They form the interface between the analytical instruments and the BASIC language programs for data reduction and analysis. They operate on Data General NOVA 840's at Cincinnati and Chicago and on a Data General ECLIPSE C330 at Livermore. The operating system consists of unmodified RDOS, Data General's disk operating system, and Data General's multiuser BASIC modified to provide the instrument CALLs and other functions described. Instruments automated at various laboratories include Technicon AutoAnalyzers, atomic absorption spectrophotometers, total organic carbon analyzers, an emission spectrometer, an electronic balance, sample changers, and an optical spectrophotometer. Other instruments may be automated using these same CALLs, or new CALLs may be written as described

Learn AppleScript The Comprehensive Guide to Scripting and Automation on MAC OS X

CERN Document Server

Rosenthal, Hanaan

2009-01-01

AppleScript is an English-like, easy-to-understand scripting language built into every Mac. AppleScript can automate hundreds of AppleScriptable applications, performing tasks both large and small, complex and simple. Learn AppleScript: The Comprehensive Guide to Scripting and Automation on Mac OS X, Third Edition has been completely updated for Mac OS X Snow Leopard. It's all here, with an emphasis on practical information that will help you solve any automation problem-from the most mundane repetitive tasks to highly integrated workflows of complex systems. * Friendly enough for beginners, d

An ultraviolet-visible spectrophotometer automation system. Part 3: Program documentation

Science.gov (United States)

Roth, G. S.; Teuschler, J. M.; Budde, W. L.

1982-07-01

The Ultraviolet-Visible Spectrophotometer (UVVIS) automation system accomplishes 'on-line' spectrophotometric quality assurance determinations, report generations, plot generations and data reduction for chlorophyll or color analysis. This system also has the capability to process manually entered data for the analysis of chlorophyll or color. For each program of the UVVIS system, this document contains a program description, flowchart, variable dictionary, code listing, and symbol cross-reference table. Also included are descriptions of file structures and of routines common to all automated analyses. The programs are written in Data General extended BASIC, Revision 4.3, under the RDOS operating systems, Revision 6.2. The BASIC code has been enhanced for real-time data acquisition, which is accomplished by CALLS to assembly language subroutines. Two other related publications are 'An Ultraviolet-Visible Spectrophotometer Automation System - Part I Functional Specifications,' and 'An Ultraviolet-Visible Spectrophotometer Automation System - Part II User's Guide.'

Asian horses deepen the MSY phylogeny.

Science.gov (United States)

Felkel, S; Vogl, C; Rigler, D; Jagannathan, V; Leeb, T; Fries, R; Neuditschko, M; Rieder, S; Velie, B; Lindgren, G; Rubin, C-J; Schlötterer, C; Rattei, T; Brem, G; Wallner, B

2018-02-01

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages. © 2018 Stichting International Foundation for Animal Genetics.

Automated Generation of OCL Constraints: NL based Approach vs Pattern Based Approach

Directory of Open Access Journals (Sweden)

IMRAN SARWAR BAJWA

2017-04-01

Full Text Available This paper presents an approach used for automated generations of software constraints. In this model, the SBVR (Semantics of Business Vocabulary and Rules based semi-formal representation is obtained from the syntactic and semantic analysis of a NL (Natural Language (such as English sentence. A SBVR representation is easy to translate to other formal languages as SBVR is based on higher-order logic like other formal languages such as OCL (Object Constraint Language. The proposed model endows with a systematic and powerful system of incorporating NL knowledge on the formal languages. A prototype is constructed in Java (an Eclipse plug-in as a proof of the concept. The performance was tested for a few sample texts taken from existing research thesis reports and books

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

OpenAIRE

Marx, Felix G.; Fordyce, R. Ewan

2015-01-01

A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36?30?Ma), a shift towards bulk filter-feeding (30?23?Ma) and a climate-driven diversity loss around 3?Ma. Evolutionary rates and...

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

Science.gov (United States)

Vélez-Zuazo, Ximena; Agnarsson, Ingi

2011-02-01

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

Altered functional connectivity of the language network in ASD: Role of classical language areas and cerebellum

Directory of Open Access Journals (Sweden)

Marjolein Verly

2014-01-01

Full Text Available The development of language, social interaction and communicative skills is remarkably different in the child with autism spectrum disorder (ASD. Atypical brain connectivity has frequently been reported in this patient population. However, the neural correlates underlying their disrupted language development and functioning are still poorly understood. Using resting state fMRI, we investigated the functional connectivity properties of the language network in a group of ASD patients with clear comorbid language impairment (ASD-LI; N = 19 and compared them to the language related connectivity properties of 23 age-matched typically developing children. A verb generation task was used to determine language components commonly active in both groups. Eight joint language components were identified and subsequently used as seeds in a resting state analysis. Interestingly, both the interregional and the seed-based whole brain connectivity analysis showed preserved connectivity between the classical intrahemispheric language centers, Wernicke's and Broca's areas. In contrast however, a marked loss of functional connectivity was found between the right cerebellar region and the supratentorial regulatory language areas. Also, the connectivity between the interhemispheric Broca regions and modulatory control dorsolateral prefrontal region was found to be decreased. This disruption of normal modulatory control and automation function by the cerebellum may underlie the abnormal language function in children with ASD-LI.

Shortest triplet clustering: reconstructing large phylogenies using representative sets

Directory of Open Access Journals (Sweden)

Sy Vinh Le

2005-04-01

Full Text Available Abstract Background Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. Results We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC, to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2 time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at http://www.bi.uni-duesseldorf.de/software/stc/. Conclusion The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy.

Phylogenies support out-of-equilibrium models of biodiversity.

Science.gov (United States)

Manceau, Marc; Lambert, Amaury; Morlon, Hélène

2015-04-01

There is a long tradition in ecology of studying models of biodiversity at equilibrium. These models, including the influential Neutral Theory of Biodiversity, have been successful at predicting major macroecological patterns, such as species abundance distributions. But they have failed to predict macroevolutionary patterns, such as those captured in phylogenetic trees. Here, we develop a model of biodiversity in which all individuals have identical demographic rates, metacommunity size is allowed to vary stochastically according to population dynamics, and speciation arises naturally from the accumulation of point mutations. We show that this model generates phylogenies matching those observed in nature if the metacommunity is out of equilibrium. We develop a likelihood inference framework that allows fitting our model to empirical phylogenies, and apply this framework to various mammalian families. Our results corroborate the hypothesis that biodiversity dynamics are out of equilibrium. © 2015 John Wiley & Sons Ltd/CNRS.

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

OpenAIRE

Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

2009-01-01

Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylog...

Designing Automated Guidance to Promote Productive Revision of Science Explanations

Science.gov (United States)

Tansomboon, Charissa; Gerard, Libby F.; Vitale, Jonathan M.; Linn, Marcia C.

2017-01-01

Supporting students to revise their written explanations in science can help students to integrate disparate ideas and develop a coherent, generative account of complex scientific topics. Using natural language processing to analyze student written work, we compare forms of automated guidance designed to motivate productive revision and help…

Molecular phylogeny of Eriocaulon (Eriocaulaceae)

DEFF Research Database (Denmark)

Ito, Yu; Tanaka, Norio; Barfod, Anders

Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an Africa...... the genus. In this talk, we provide preliminary results of our molecular phylogenetic analysis of the genus aiming to i) assess the biogeographic origin, ii) explore phylogenetic origins of submerged species, and iii) address the evolutionary role of polyploids.......Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an African...... origin for Eriocaulon as a sister relationship between the genus and an African endemic one was recovered. The species of Eriocaulon primarily grow in wetlands while some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. Polyploidy is known from...

A novel molecular marker for the study of Neotropical cichlid phylogeny.

Science.gov (United States)

Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J

2015-12-22

The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising.

Driving Under the Influence (of Language).

Science.gov (United States)

Barrett, Daniel Paul; Bronikowski, Scott Alan; Yu, Haonan; Siskind, Jeffrey Mark

2017-06-09

We present a unified framework which supports grounding natural-language semantics in robotic driving. This framework supports acquisition (learning grounded meanings of nouns and prepositions from human sentential annotation of robotic driving paths), generation (using such acquired meanings to generate sentential description of new robotic driving paths), and comprehension (using such acquired meanings to support automated driving to accomplish navigational goals specified in natural language). We evaluate the performance of these three tasks by having independent human judges rate the semantic fidelity of the sentences associated with paths. Overall, machine performance is 74.9%, while the performance of human annotators is 83.8%.

Automated information retrieval system for radioactivation analysis

International Nuclear Information System (INIS)

Lambrev, V.G.; Bochkov, P.E.; Gorokhov, S.A.; Nekrasov, V.V.; Tolstikova, L.I.

1981-01-01

An automated information retrieval system for radioactivation analysis has been developed. An ES-1022 computer and a problem-oriented software ''The description information search system'' were used for the purpose. Main aspects and sources of forming the system information fund, characteristics of the information retrieval language of the system are reported and examples of question-answer dialogue are given. Two modes can be used: selective information distribution and retrospective search [ru

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada, Tardigrada)

DEFF Research Database (Denmark)

Fujimoto, Shinta; Jørgensen, Aslak; Hansen, Jesper Guldberg

2017-01-01

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phy...... of the inferred phylogeny....

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

Science.gov (United States)

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

An Experiment on Creating Enterprise Specific BPM Languages and Tools

DEFF Research Database (Denmark)

Brahe, Steen

Many enterprises use their own domain concepts in modeling business process and use technology in specialized ways when they implement them in a Business Process Management (BPM) system.In contrast, BPM tools used for modeling and implementing business processes often provide a standard modeling...... and automation to BPM tools through a tool experiment in Danske Bank, a large financial institute; We develop business process modeling languages, tools and transformations that capture Danske Banks specific modeling concepts and use of technology, and which automate the generation of code. An empirical...... language, a standard implementation technology and a fixed transformation that may generate the implementation from the model. This makes the tools inflexible and difficult to use.This paper presents another approach. It applies the basic model driven development principles of direct representation...

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades.

Science.gov (United States)

Arnold, E N

1990-05-22

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown

LAVA: a conceptual framework for automated risk assessment

International Nuclear Information System (INIS)

Smith, S.T.; Brown, D.C.; Erkkila, T.H.; FitzGerald, P.D.; Lim, J.J.; Massagli, L.; Phillips, J.R.; Tisinger, R.M.

1986-01-01

At the Los Alamos National Laboratory we are developing the framework for generating knowledge-based systems that perform automated risk analyses on an organization's assets. An organization's assets can be subdivided into tangible and intangible assets. Tangible assets include facilities, materiel, personnel, and time, while intangible assets include such factors as reputation, employee morale, and technical knowledge. The potential loss exposure of an asset is dependent upon the threats (both static and dynamic), the vulnerabilities in the mechanisms protecting the assets from the threats, and the consequences of the threats successfully exploiting the protective systems vulnerabilities. The methodology is based upon decision analysis, fuzzy set theory, natural-language processing, and event-tree structures. The Los Alamos Vulnerability and Risk Assessment (LAVA) methodology has been applied to computer security. LAVA is modeled using an interactive questionnaire in natural language and is fully automated on a personal computer. The program generates both summary reports for use by both management personnel and detailed reports for use by operations staff. LAVA has been in use by the Nuclear Regulatory Commission and the National Bureau of Standards for nearly two years and is presently under evaluation by other governmental agencies. 7 refs

Phylogeny and Species Diversity of Gulf of California Oysters

Data.gov (United States)

U.S. Environmental Protection Agency — Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North...

Automation of Educational Tasks for Academic Radiology.

Science.gov (United States)

Lamar, David L; Richardson, Michael L; Carlson, Blake

2016-07-01

The process of education involves a variety of repetitious tasks. We believe that appropriate computer tools can automate many of these chores, and allow both educators and their students to devote a lot more of their time to actual teaching and learning. This paper details tools that we have used to automate a broad range of academic radiology-specific tasks on Mac OS X, iOS, and Windows platforms. Some of the tools we describe here require little expertise or time to use; others require some basic knowledge of computer programming. We used TextExpander (Mac, iOS) and AutoHotKey (Win) for automated generation of text files, such as resident performance reviews and radiology interpretations. Custom statistical calculations were performed using TextExpander and the Python programming language. A workflow for automated note-taking was developed using Evernote (Mac, iOS, Win) and Hazel (Mac). Automated resident procedure logging was accomplished using Editorial (iOS) and Python. We created three variants of a teaching session logger using Drafts (iOS) and Pythonista (iOS). Editorial and Drafts were used to create flashcards for knowledge review. We developed a mobile reference management system for iOS using Editorial. We used the Workflow app (iOS) to automatically generate a text message reminder for daily conferences. Finally, we developed two separate automated workflows-one with Evernote (Mac, iOS, Win) and one with Python (Mac, Win)-that generate simple automated teaching file collections. We have beta-tested these workflows, techniques, and scripts on several of our fellow radiologists. All of them expressed enthusiasm for these tools and were able to use one or more of them to automate their own educational activities. Appropriate computer tools can automate many educational tasks, and thereby allow both educators and their students to devote a lot more of their time to actual teaching and learning. Copyright © 2016 The Association of University Radiologists

An automation model of Effluent Treatment Plant

Directory of Open Access Journals (Sweden)

Luiz Alberto Oliveira Lima Roque

2012-07-01

Full Text Available Population growth and intensification of industrial activities have increased the deterioration of natural resources. Industrial, hospital and residential wastes are dumped directly into landfills without processing, polluting soils. This action will have consequences later, because the liquid substance resulting from the putrefaction of organic material plows into the soil to reach water bodies. Cities arise without planning, industrial and household wastes are discharged into rivers, lakes and oceans without proper treatment, affecting water resources. It is well known that in the next century there will be fierce competition for fresh water on the planet, probably due to the scarcity of it. Demographic expansion has occurred without proper health planning, degrading oceans, lakes and rivers. Thus, a large percentage of world population suffers from diseases related to water pollution. Accordingly, it can be concluded that sewage treatment is essential to human survival, to preserve rivers, lakes and oceans. An Effluent Treatment Plant (ETP treats wastewater to reduce its pollution to acceptable levels before sending them to the oceans or rivers. To automate the operation of an ETP, motors, sensors and logic blocks, timers and counters are needed. These functions are achieved with programmable logic controllers (PLC and Supervisory Systems. The Ladder language is used to program controllers and is a pillar of the Automation and Control Engineering. The supervisory systems allow process information to be monitored, while the PLC are responsible for control and data acquisition. In the age we live in, process automation is used in an increasing scale in order to provide higher quality, raise productivity and improve the proposed activities. Therefore, an automatic ETP will improve performance and efficiency to handle large volumes of sewage. Considering the growing importance of environmental awareness with special emphasis

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

Science.gov (United States)

Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

2011-10-01

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of

Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.

Science.gov (United States)

Kropáčková, Lucie; Těšický, Martin; Albrecht, Tomáš; Kubovčiak, Jan; Čížková, Dagmar; Tomášek, Oldřich; Martin, Jean-François; Bobek, Lukáš; Králová, Tereza; Procházka, Petr; Kreisinger, Jakub

2017-10-01

Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM. © 2017 John Wiley & Sons Ltd.

Use of the MCL dialog language for autonomous multi-channel analyzer automation

International Nuclear Information System (INIS)

Gyunter, Z.; Lebner, M.; Mikhaehlis, B.; Shvenkner, V.; Shul'tts, K.-Kh.

1985-01-01

The structure and software of a time-of-flight multichannel analyzer are considered. The analyzer is a subsystem of the measuring module of the SPN-1 polarized neutron spectrometer used in experiments at the IBR-2 reactor. The analyzer operates having several structures differing from one another by a timing coder. The MCL (MULTI-CONTROL-LANGUAGE) system is developed for control of the spectrometer. The system ensures the computer-user conversation and interfacing the computer and the experimental equipment. The MCL language is similar to that of the BASIC or the BAMBI. It has modular structure. The language interpreter and operating system have about 2 kbyte memory. The considered analyser is successfully used already during 6 months. The number of detector inputs of the analyser increased. Expenditures for alternations of programs are negligible due to modular structure of the system. Realization of new commads does not require comprehensive knowledge of the MCL language

Gene structure, phylogeny and expression profile of the sucrose ...

Indian Academy of Sciences (India)

Gene structure, phylogeny and expression profile of the sucrose synthase gene family in .... 24, 701–713. Bate N. and Twell D. 1998 Functional architecture of a late pollen .... Manzara T. and Gruissem W. 1988 Organization and expression.

The genus Gloriosa (Colchicaceae) : ethnobotany, phylogeny and taxonomy

NARCIS (Netherlands)

Maroyi, A.

2012-01-01

This thesis focuses on the ethnobotany, phylogeny and taxonomy of the genus Gloriosa L. over its distributional range. Some Gloriosa species are known to have economic and commercial value, but the genus is also well known for its complex alpha taxonomy. An appropriate taxonomy for this group is of

Making progress with the automation of systematic reviews: principles of the International Collaboration for the Automation of Systematic Reviews (ICASR).

Science.gov (United States)

Beller, Elaine; Clark, Justin; Tsafnat, Guy; Adams, Clive; Diehl, Heinz; Lund, Hans; Ouzzani, Mourad; Thayer, Kristina; Thomas, James; Turner, Tari; Xia, Jun; Robinson, Karen; Glasziou, Paul

2018-05-19

Systematic reviews (SR) are vital to health care, but have become complicated and time-consuming, due to the rapid expansion of evidence to be synthesised. Fortunately, many tasks of systematic reviews have the potential to be automated or may be assisted by automation. Recent advances in natural language processing, text mining and machine learning have produced new algorithms that can accurately mimic human endeavour in systematic review activity, faster and more cheaply. Automation tools need to be able to work together, to exchange data and results. Therefore, we initiated the International Collaboration for the Automation of Systematic Reviews (ICASR), to successfully put all the parts of automation of systematic review production together. The first meeting was held in Vienna in October 2015. We established a set of principles to enable tools to be developed and integrated into toolkits.This paper sets out the principles devised at that meeting, which cover the need for improvement in efficiency of SR tasks, automation across the spectrum of SR tasks, continuous improvement, adherence to high quality standards, flexibility of use and combining components, the need for a collaboration and varied skills, the desire for open source, shared code and evaluation, and a requirement for replicability through rigorous and open evaluation.Automation has a great potential to improve the speed of systematic reviews. Considerable work is already being done on many of the steps involved in a review. The 'Vienna Principles' set out in this paper aim to guide a more coordinated effort which will allow the integration of work by separate teams and build on the experience, code and evaluations done by the many teams working across the globe.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

Directory of Open Access Journals (Sweden)

Stajich Jason E

2006-11-01

Full Text Available Abstract Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available. Results A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD, and their close

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

Directory of Open Access Journals (Sweden)

Milinkovitch Michel C

2010-07-01

Full Text Available Abstract Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood, including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these

Finding Relevant Data in a Sea of Languages

Science.gov (United States)

2016-04-26

and information retrieval to automate language processing tasks so that the limited number of linguists available for analyzing text and spoken...HLT literature that a research team would do a study and stop short,” says Williams. “Each study was trying to solve a very specific problem. No

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

Science.gov (United States)

Zhang, Yan-Cong; Lin, Kui

2015-01-01

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

Science.gov (United States)

Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

Genes, language, cognition, and culture: towards productive inquiry.

Science.gov (United States)

Fitch, W Tecumseh

2011-04-01

The Queen Mary conference on “Integrating Genetic and Cultural Evolutionary Approaches to Language,” and the papers in this special issue, clearly illustrate the excitement and potential of trans-disciplinary approaches to language as an evolved biological capacity (phylogeny) and an evolving cultural entity (glossogeny). Excepting the present author, the presenters/authors are mostly young rising stars in their respective fields, and include scientists with backgrounds in linguistics, animal communication, neuroscience, evolutionary biology, anthropology, and computer science. On display was a clear willingness to engage with different approaches and terminology and a commitment to shared standards of scientific rigor, empirically driven theory, and logical argument. Because the papers assembled here, together with the introduction, speak for themselves, I will focus in this “extro-duction” on some of the terminological and conceptual difficulties which threaten to block this exciting wave of scientific progress in understanding language evolution, in both senses of that term. In particular I will first argue against the regrettably widespread practice of opposing cultural and genetic explanations of human cognition as if they were dichotomous. Second, I will unpack the debate concerning “general-purpose” and “domain-specific” mechanisms, which masquerades as a debate about nativism but is nothing of the sort. I believe that framing discussions of language in these terms has generated more heat than light, and that a modern molecular understanding of genes, development, behavior, and evolution renders many of the assumptions underlying this debate invalid.

Natural language processing in psychiatry. Artificial intelligence technology and psychopathology.

Science.gov (United States)

Garfield, D A; Rapp, C; Evens, M

1992-04-01

The potential benefit of artificial intelligence (AI) technology as a tool of psychiatry has not been well defined. In this essay, the technology of natural language processing and its position with regard to the two main schools of AI is clearly outlined. Past experiments utilizing AI techniques in understanding psychopathology are reviewed. Natural language processing can automate the analysis of transcripts and can be used in modeling theories of language comprehension. In these ways, it can serve as a tool in testing psychological theories of psychopathology and can be used as an effective tool in empirical research on verbal behavior in psychopathology.

Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances

Directory of Open Access Journals (Sweden)

Jose L. Horreo

2017-09-01

Full Text Available The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

Interactions between working memory and language in young children with specific language impairment (SLI).

Science.gov (United States)

Vugs, Brigitte; Knoors, Harry; Cuperus, Juliane; Hendriks, Marc; Verhoeven, Ludo

2016-01-01

The underlying structure of working memory (WM) in young children with and without specific language impairment (SLI) was examined. The associations between the components of WM and the language abilities of young children with SLI were then analyzed. The Automated Working Memory Assessment and four linguistic tasks were administered to 58 children with SLI and 58 children without SLI, aged 4-5 years. The WM of the children was best represented by a model with four separate but interacting components of verbal storage, visuospatial storage, verbal central executive (CE), and visuospatial CE. The associations between the four components of WM did not differ significantly for the two groups of children. However, the individual components of WM showed varying associations with the language abilities of the children with SLI. The verbal CE component of WM was moderately to strongly associated with all the language abilities in children with SLI: receptive vocabulary, expressive vocabulary, verbal comprehension, and syntactic development. These results show verbal CE to be involved in a wide range of linguistic skills; the limited ability of young children with SLI to simultaneously store and process verbal information may constrain their acquisition of linguistic skills. Attention should thus be paid to the language problems of children with SLI, but also to the WM impairments that can contribute to their language problems.

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

Science.gov (United States)

Longdon, Ben; Hadfield, Jarrod D.; Webster, Claire L.

2011-01-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts. PMID:21966271

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

Directory of Open Access Journals (Sweden)

Rønsted Nina

2012-09-01

Full Text Available Abstract Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE and binding to the serotonin reuptake transporter (SERT are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.

Mixed deep learning and natural language processing method for fake-food image recognition and standardization to help automated dietary assessment.

Science.gov (United States)

Mezgec, Simon; Eftimov, Tome; Bucher, Tamara; Koroušić Seljak, Barbara

2018-04-06

The present study tested the combination of an established and a validated food-choice research method (the 'fake food buffet') with a new food-matching technology to automate the data collection and analysis. The methodology combines fake-food image recognition using deep learning and food matching and standardization based on natural language processing. The former is specific because it uses a single deep learning network to perform both the segmentation and the classification at the pixel level of the image. To assess its performance, measures based on the standard pixel accuracy and Intersection over Union were applied. Food matching firstly describes each of the recognized food items in the image and then matches the food items with their compositional data, considering both their food names and their descriptors. The final accuracy of the deep learning model trained on fake-food images acquired by 124 study participants and providing fifty-five food classes was 92·18 %, while the food matching was performed with a classification accuracy of 93 %. The present findings are a step towards automating dietary assessment and food-choice research. The methodology outperforms other approaches in pixel accuracy, and since it is the first automatic solution for recognizing the images of fake foods, the results could be used as a baseline for possible future studies. As the approach enables a semi-automatic description of recognized food items (e.g. with respect to FoodEx2), these can be linked to any food composition database that applies the same classification and description system.

Monitoring the Performance of Human and Automated Scores for Spoken Responses

Science.gov (United States)

Wang, Zhen; Zechner, Klaus; Sun, Yu

2018-01-01

As automated scoring systems for spoken responses are increasingly used in language assessments, testing organizations need to analyze their performance, as compared to human raters, across several dimensions, for example, on individual items or based on subgroups of test takers. In addition, there is a need in testing organizations to establish…

The phylogeny of amphibian metamorphosis.

Science.gov (United States)

Reiss, John O

2002-01-01

Frogs have one of the most extreme metamorphoses among vertebrates. How did this metamorphosis evolve? By combining the methods previously proposed by Mabee and Humphries (1993) and Velhagen (1997), I develop a phylogenetic method suited for rigorous analysis of this question. In a preliminary analysis using 12 transformation sequence characters and 36 associated event sequence characters, all drawn from the osteology of the skull, the evolution of metamorphosis is traced on an assumed phylogeny. This phylogeny has lissamphibians (frogs, salamanders, and caecilians) monophyletic, with frogs the sister group of salamanders. Successive outgroups used are temnospondyls and discosauriscids, both of which are fossil groups for which ontogenetic data are available. In the reconstruction of character evolution, an unambiguous change (synapomorphy) along the branch leading to lissamphibians is a delay in the lengthening of the maxilla until metamorphosis, in accordance with my previous suggestion (Reiss, 1996). However, widening of the interpterygoid vacuity does not appear as a synapomophy of lissamphibians, due to variation in the character states in the outgroups. From a more theoretical perspective, the reconstructed evolution of amphibian metamorphosis involves examples of heterochrony, through the shift of ancestral premetamorphic events to the metamorphic period, caenogenesis, through the origin of new larval features, and terminal addition, through the origin of new adult features. Other changes don't readily fit these categories. This preliminary study provides evidence that metamorphic changes in frogs arose as further modifications of changes unique to lissamphibians, as well as a new method by which such questions can be examined.

A supertree approach to shorebird phylogeny

Directory of Open Access Journals (Sweden)

Thomas Gavin H

2004-08-01

Full Text Available Abstract Background Order Charadriiformes (shorebirds is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree. Results Three main lineages are revealed: i the plovers and allies; ii the gulls and allies; and iii the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny. Conclusion The supertree hypothesis presented herein is (to our knowledge the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion, we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.

The symbol coding language for the BUTs processor of in-core reactor control systems

International Nuclear Information System (INIS)

Vorob'ev, D.M.; Golovanov, M.N.; Levin, G.L.; Parfenova, T.K.; Filatov, V.P.

1978-01-01

A symbolic coding language is described; it has been developed for automation of making up programs for in-core control systems. The systems use the ideology of the CAMAC-VECTOR system and include the BUTs-20 processor. The symbolic coding language has been developed as a programming language of the ASSEMBLER type. Operators of instructions and pseudo-instructions, the rules of reading in the text of the source program, and operator record formats are considered

Rules-based analysis with JBoss Drools: adding intelligence to automation

International Nuclear Information System (INIS)

Ley, E. de; Jacobs, D.

2012-01-01

Rule engines are specialized software systems for applying conditional actions (if/then rules) on data. They are also known as 'production rule systems'. Rules engines are less-known as software technology than the traditional procedural, object-oriented, scripting or dynamic development languages. This is a pity, as their usage may offer an important enrichment to a development toolbox. JBoss Drools is an open-source rules engine that can easily be embedded in any Java application. Through an integration in our Passerelle process automation suite, we have been able to provide advanced solutions for intelligent process automation, complex event processing, system monitoring and alarming, automated repair etc. This platform has been proven for many years as an automated diagnosis and repair engine for Belgium's largest telecom provider, and it is being piloted at Synchrotron Soleil for device monitoring and alarming. After an introduction to rules engines in general and JBoss Drools in particular, we will present its integration in a solution platform, some important principles and a practical use case. (authors)

Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies.

Science.gov (United States)

Hagen, Oskar; Andermann, Tobias; Quental, Tiago B; Antonelli, Alexandre; Silvestro, Daniele

2018-05-01

The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more

Planning representation for automated exploratory data analysis

Science.gov (United States)

St. Amant, Robert; Cohen, Paul R.

1994-03-01

Igor is a knowledge-based system for exploratory statistical analysis of complex systems and environments. Igor has two related goals: to help automate the search for interesting patterns in data sets, and to help develop models that capture significant relationships in the data. We outline a language for Igor, based on techniques of opportunistic planning, which balances control and opportunism. We describe the application of Igor to the analysis of the behavior of Phoenix, an artificial intelligence planning system.

Automated evolutionary restructuring of workflows to minimise errors via stochastic model checking

DEFF Research Database (Denmark)

Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

2014-01-01

This paper presents a framework for the automated restructuring of workflows that allows one to minimise the impact of errors on a production workflow. The framework allows for the modelling of workflows by means of a formalised subset of the Business Process Modelling and Notation (BPMN) language...

Automating tasks in protein structure determination with the clipper python module.

Science.gov (United States)

McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M; Hoh, Soon Wen; Jenkins, Huw T; Dodson, Eleanor; Cowtan, Kevin; Agirre, Jon

2018-01-01

Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Artificial intelligence, expert systems, computer vision, and natural language processing

Science.gov (United States)

Gevarter, W. B.

1984-01-01

An overview of artificial intelligence (AI), its core ingredients, and its applications is presented. The knowledge representation, logic, problem solving approaches, languages, and computers pertaining to AI are examined, and the state of the art in AI is reviewed. The use of AI in expert systems, computer vision, natural language processing, speech recognition and understanding, speech synthesis, problem solving, and planning is examined. Basic AI topics, including automation, search-oriented problem solving, knowledge representation, and computational logic, are discussed.

On the emergence of pervasive home automation

DEFF Research Database (Denmark)

Torbensen, Rune Sonnich

2012-01-01

bridges and expandable via USB modules so that new data-communication technologies can be connected to cover the whole residence. An ’IHAP ready’ flexible communication software framework that supports wireless end-device development is proposed. The idea is to bootstrap this new market with open source...... end-devices via the Open Device Service Description Language, which employs abstract service types to describe transformations to the simple end-device application protocols used in home automation. A security system called Trusted Domain grants access for remote control of home automation devices...... by smartphones, M2M applications, and service providers. These Internet nodes and home gateways become the trusted members of a home network capable of spanning several network segments. To include new members, both locally and remotely, a new user-friendly method for establishing trust between remote devices...

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Science.gov (United States)

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes).

Science.gov (United States)

Marki, Petter Z; Jønsson, Knud A; Irestedt, Martin; Nguyen, Jacqueline M T; Rahbek, Carsten; Fjeldså, Jon

2017-02-01

With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3Mya, 95% HPD 25.2-38.2Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change. Copyright © 2016 Elsevier Inc. All rights reserved.

Maneuver Automation Software

Science.gov (United States)

Uffelman, Hal; Goodson, Troy; Pellegrin, Michael; Stavert, Lynn; Burk, Thomas; Beach, David; Signorelli, Joel; Jones, Jeremy; Hahn, Yungsun; Attiyah, Ahlam;

galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

Science.gov (United States)

Nilsson, R Henrik; Larsson, Karl-Henrik; Ursing, Björn M

2004-06-12

The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable. A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

Automated detection of unfilled pauses in speech of healthy and brain-damaged individuals

NARCIS (Netherlands)

Ossewaarde, Roelant; Jonkers, Roel; Jalvingh, Fedor; Bastiaanse, Yvonne

Automated detection of un lled pauses in speech of healthy and brain-damaged individuals Roelant Ossewaardea,b, Roel Jonkersa, Fedor Jalvingha,c, Roelien Bastiaansea aCenter for Language and Cognition, University of Groningen; bInstitute for ICT, HU University of Applied Science, Utrecht; cSt.

Molecular phylogeny and evolution of mosquito parasitic Microsporidia (Microsporidia: Amblyosporidae)

Czech Academy of Sciences Publication Activity Database

Vossbrinck, C. R.; Andreadis, T.; Vávra, Jiří; Becnel, J. J.

2004-01-01

Roč. 51, č. 1 (2004), s. 88-95 ISSN 1066-5234 Institutional research plan: CEZ:AV0Z6022909 Keywords : Microsporidia * molecular phylogeny * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.403, year: 2004

A systematic literature review of automated clinical coding and classification systems.

Science.gov (United States)

Stanfill, Mary H; Williams, Margaret; Fenton, Susan H; Jenders, Robert A; Hersh, William R

2010-01-01

Clinical coding and classification processes transform natural language descriptions in clinical text into data that can subsequently be used for clinical care, research, and other purposes. This systematic literature review examined studies that evaluated all types of automated coding and classification systems to determine the performance of such systems. Studies indexed in Medline or other relevant databases prior to March 2009 were considered. The 113 studies included in this review show that automated tools exist for a variety of coding and classification purposes, focus on various healthcare specialties, and handle a wide variety of clinical document types. Automated coding and classification systems themselves are not generalizable, nor are the results of the studies evaluating them. Published research shows these systems hold promise, but these data must be considered in context, with performance relative to the complexity of the task and the desired outcome.

Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.

Science.gov (United States)

Bourlat, Sarah J; Nielsen, Claus; Economou, Andrew D; Telford, Maximilian J

2008-10-01

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.

Knowledge-based requirements analysis for automating software development

Science.gov (United States)

Markosian, Lawrence Z.

1988-01-01

We present a new software development paradigm that automates the derivation of implementations from requirements. In this paradigm, informally-stated requirements are expressed in a domain-specific requirements specification language. This language is machine-understable and requirements expressed in it are captured in a knowledge base. Once the requirements are captured, more detailed specifications and eventually implementations are derived by the system using transformational synthesis. A key characteristic of the process is that the required human intervention is in the form of providing problem- and domain-specific engineering knowledge, not in writing detailed implementations. We describe a prototype system that applies the paradigm in the realm of communication engineering: the prototype automatically generates implementations of buffers following analysis of the requirements on each buffer.

Host phylogeny determines viral persistence and replication in novel hosts.

Directory of Open Access Journals (Sweden)

Ben Longdon

2011-09-01

Full Text Available Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

Mitogenomic perspectives on the origin and phylogeny of living amphibians.

Science.gov (United States)

Zhang, Peng; Zhou, Hui; Chen, Yue-Qin; Liu, Yi-Fei; Qu, Liang-Hu

2005-06-01

Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for "missing" fossils, and can benefit comparative studies of amphibian evolution.

The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes).

Science.gov (United States)

Amaral, Cesar R L; Pereira, Filipe; Silva, Dayse A; Amorim, António; de Carvalho, Elizeu F

2017-09-20

Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all over the world's seas, including some of the ocean's largest fishes. The group dates back about 400 million years near the Devonian-Silurian boundary, being nowadays represented by several derivative lineages, mainly related to Mesozoic forms. Although considered of ecological, commercial and conservation importance, the phylogeny of this old group is poorly studied and still under debate. Here we apply a molecular systematic approach on 82 complete mitochondrial genomes to investigate the phylogeny of the Elasmobranchii. By using maximum likelihood (ML) and Bayesian analyses, we found a clear separation within the shark clade between the Galeomorphii and the Squalomorphii, as well as sister taxa relationships between the Carcharhiniformes and the Lamniformes. Moreover, we found that Pristoidei clusters within the Rhinobatoidei, having been recovered as the sister taxon of the Rhinobatos genus in a clade which also includes the basal Zapteryx. Our results also reject the Hypnosqualea hypothesis, which proposes that the Batoidea should be placed within the Selachii.

Phylogeny and species traits predict bird detectability

Science.gov (United States)

Solymos, Peter; Matsuoka, Steven M.; Stralberg, Diana; Barker, Nicole K. S.; Bayne, Erin M.

2018-01-01

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.

Whole genome association mapping by incompatibilities and local perfect phylogenies

DEFF Research Database (Denmark)

Mailund, Thomas; Besenbacher, Søren; Schierup, Mikkel Heide

2006-01-01

around each marker that is compatible with a single phylogenetic tree. This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree. The rationale for this is that the perfect phylogeny near a disease affecting mutation should...... a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls. The method searches for significant clustering of case chromosomes in the "perfect" phylogenetic tree defined by the largest region...... provide more information about the affected/unaffected classification than random trees. If regions of compatibility contain few markers, due to e.g. large marker spacing, the algorithm can allow the inclusion of incompatibility markers in order to enlarge the regions prior to estimating their phylogeny...

A large phylogeny of turtles (Testudines) using molecular data

NARCIS (Netherlands)

Guillon, J.-M.; Guéry, L.; Hulin, V.; Girondot, M.

2012-01-01

Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA

Phylogeny of not-yet-cultured spirochetes from termite guts

DEFF Research Database (Denmark)

Paster, B.J.; Dewhirst, F.E.; Cooke, S.M.

1996-01-01

Comparisons of 16S rDNA sequences were used to determine the phylogeny of not-yet-cultured spirochetes from hindguts of the African higher termite, Nasutitermes lujae (Wasmann). The 16S rRNA genes were amplified directly from spirochete-rich hindguts by using universal primers, and the amplified...

Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

Science.gov (United States)

Gendrault, Yves; Madec, Morgan; Lallement, Christophe; Haiech, Jacques

2014-04-01

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

HAUTO: Automated composition of convergent services based in HTN planning

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Armando Ordoñez

2014-01-01

Full Text Available This paper presents HAUTO, a framework able to compose convergent services automatically. HAUTO is based in HTN (hierarchical task networks Automated Planning and is composed of three modules: a request processing module that transforms natural language and context information into a planning instance, the automated composition module based on HTN planning and the execution environment for convergent (Web and telecom services. The integration of a planning component provides two basic functionalities: the possibility of customizing the composition of services using the user context information and a middleware level that integrates the execution of services in high performance telecom environments. Finally, a prototype in environmental early warning management is presented as a test case.

A Transcription Scheme for Languages Employing the Arabic Script Motivated by Speech Processing Application

National Research Council Canada - National Science Library

Ganjavi, Shadi; Georgiou, Panayiotis G; Narayanan, Shrikanth

2004-01-01

... (The DARPA Babylon Program; Narayanan, 2003). In this paper, we discuss transcription systems needed for automated spoken language processing applications in Persian that uses the Arabic script for writing...

Relationships of Reproductive Traits with the Phylogeny of the African Noctuid Stem Borers

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Paul-André Calatayud

2016-01-01

Full Text Available The display of the reproductive behavior in most noctuid Lepidoptera follows a diel periodicity and is limited to a precise period of either the day or the night. These behavioral traits and the sex pheromone chemistry can be species specific and thus might be linked to the phylogeny. The objective of this study was to test the relationship of these reproductive traits with phylogeny. The study was undertaken using eight closely related species of noctuid stem borers, which are easy to rear under artificial conditions, namely, Busseola fusca, B. nairobica, B . sp. nr. segeta, Manga melanodonta, M . sp. nr. nubifera, Pirateolea piscator, Sesamia calamistis , and S. nonagrioides . For each species, the adult emergence period, the mating time, and the oviposition period were estimated, referred as biological traits. The components of the sex pheromones emitted by the females of each species were also analyzed by gas chromatography–mass spectrometry. Among the biological traits measured, only those linked to the oviposition pattern (timing and egg loads per night were significantly correlated with the phylogeny of these species. For the sex pheromone components, among the 13 components identified in all species, only four, namely, Z9-tetradecenyl acetate (Z9-TDA, Z11-TDA, E11-TDA, and Z11-hexadecenyl acetate (Z11-HDA, showed the highest significant correlations with the phylogeny. These results suggest that among the different reproductive traits evaluated, only few are phylogenetically constrained. Their involvement in the reinforcement of ecological speciation in noctuid stem borers is discussed.

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

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Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).

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Schmidt, Ray C; Bart, Henry L; Nyingi, Wanja Dorothy

2017-06-01

The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa. Copyright © 2017 Elsevier Inc. All rights reserved.

Ontogeny and Phylogeny from an Epigenetic Point of View.

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Lovtrup, Soren

1984-01-01

The correlation between ontogeny and phylogeny is analyzed through the discussion of four theories on the reality, history, epigenetic, and ecological aspects of the mechanism of evolution. Also discussed are historical and creative aspects of evolution and three epigenetic mechanisms instantiated in the case of the amphibian embryo. (Author/RH)

Host and parasite morphology influence congruence between host and parasite phylogenies.

Science.gov (United States)

Sweet, Andrew D; Bush, Sarah E; Gustafsson, Daniel R; Allen, Julie M; DiBlasi, Emily; Skeen, Heather R; Weckstein, Jason D; Johnson, Kevin P

2018-03-23

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution. Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

On the Accuracy of Language Trees

Science.gov (United States)

Pompei, Simone; Loreto, Vittorio; Tria, Francesca

2011-01-01

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic) features or characters for many different languages: a set of parallel corpora whose compilation represents a paramount achievement in linguistics. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve it. PMID:21674034

On the accuracy of language trees.

Directory of Open Access Journals (Sweden)

Simone Pompei

Full Text Available Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic features or characters for many different languages: a set of parallel corpora whose compilation represents a paramount achievement in linguistics. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve

Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization

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Blanc Michel

2007-01-01

Full Text Available Abstract Background The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and breed in empty gastropod shells is probably the most peculiar. Although shell-breeding arose several times in the evolutionary history of the lamprologines, all obligatory and most facultative shell-breeders belong to the so called "ossified group", a monophyletic lineage within the lamprologine cichlids. Since their distinctive life style enables these species to live and breed in closest vicinity, we hypothesized that these cichlids might be particularly prone to accidental hybridization, and that introgression might have affected the evolutionary history of this cichlid lineage. Results Our analyses revealed discrepancies between phylogenetic hypotheses based on mitochondrial and nuclear (AFLP data. While the nuclear phylogeny was congruent with morphological, behavioral and ecological characteristics, several species – usually highly specialized shell-breeders – were placed at contradicting positions in the mitochondrial phylogeny. The discordant phylogenies strongly suggest repeated incidents of introgressive hybridization between several distantly related shell-breeding species, which reticulated the phylogeny of this group of cichlids. Long interior branches and high bootstrap support for many interior nodes in the mitochondrial phylogeny argue against a major effect of ancient incomplete lineage sorting on the phylogenetic reconstruction. Moreover, we provide morphological and genetic (mtDNA and microsatellites evidence for ongoing hybridization among distantly related shell-breeders. In these cases, the territorial males of the inferred paternal species are too large to enter the shells of their mate, such that they have to release their sperm over the entrance of the shell to fertilize the eggs. With sperm

Automated Classification of Consumer Health Information Needs in Patient Portal Messages.

Science.gov (United States)

Cronin, Robert M; Fabbri, Daniel; Denny, Joshua C; Jackson, Gretchen Purcell

2015-01-01

Patients have diverse health information needs, and secure messaging through patient portals is an emerging means by which such needs are expressed and met. As patient portal adoption increases, growing volumes of secure messages may burden healthcare providers. Automated classification could expedite portal message triage and answering. We created four automated classifiers based on word content and natural language processing techniques to identify health information needs in 1000 patient-generated portal messages. Logistic regression and random forest classifiers detected single information needs well, with area under the curves of 0.804-0.914. A logistic regression classifier accurately found the set of needs within a message, with a Jaccard index of 0.859 (95% Confidence Interval: (0.847, 0.871)). Automated classification of consumer health information needs expressed in patient portal messages is feasible and may allow direct linking to relevant resources or creation of institutional resources for commonly expressed needs.

Restructuring of workflows to minimise errors via stochastic model checking: An automated evolutionary approach

DEFF Research Database (Denmark)

Herbert, Luke Thomas; Hansen, Zaza Nadja Lee

2016-01-01

This article presents a framework for the automated restructuring of stochastic workflows to reduce the impact of faults. The framework allows for the modelling of workflows by means of a formalised subset of the BPMN workflow language. We extend this modelling formalism to describe faults...

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

Directory of Open Access Journals (Sweden)

Ó'Fágáin Ciarán

2008-03-01

Full Text Available Abstract Background The mammalian heme peroxidases (MHPs are a medically important group of enzymes. Included in this group are myeloperoxidase, eosinophil peroxidase, lactoperoxidase, and thyroid peroxidase. These enzymes are associated with such diverse diseases as asthma, Alzheimer's disease and inflammatory vascular disease. Despite much effort to elucidate a clearer understanding of the function of the 4 major groups of this multigene family, we still do not have a clear understanding of their relationships to each other. Results Sufficient signal exists for the resolution of the evolutionary relationships of this family of enzymes. We demonstrate, using a root mean squared deviation statistic, how the removal of the fastest evolving sites aids in the minimisation of the effect of long branch attraction and the generation of a highly supported phylogeny. Based on this phylogeny we have pinpointed the amino acid positions that have most likely contributed to the diverse functions of these enzymes. Many of these residues are in close proximity to sites implicated in protein misfolding, loss of function or disease. Conclusion Our analysis of all available genomic sequence data for the MHPs from all available completed mammalian genomes, involved sophisticated methods of phylogeny reconstruction and data treatment. Our study has (i fully resolved the phylogeny of the MHPs and the subsequent pattern of gene duplication, and (ii, we have detected amino acids under positive selection that have most likely contributed to the observed functional shifts in each type of MHP.

Live phylogeny with polytomies: Finding the most compact parsimonious trees.

Science.gov (United States)

Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

2017-08-01

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii as a case study

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Zhang Gong

2007-03-01

Full Text Available Abstract Background Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the ray-finned fishes – the largest vertebrate clade in need of phylogenetic resolution. Results A total of 154 candidate molecular markers – relatively well conserved, putatively single-copy gene fragments with long, uninterrupted exons – were obtained by comparing whole genome sequences of two model organisms, Danio rerio and Takifugu rubripes. Experimental tests of 15 of these (randomly picked markers on 36 taxa (representing two-thirds of the ray-finned fish orders demonstrate the feasibility of amplifying by PCR and directly sequencing most of these candidates from whole genomic DNA in a vast diversity of fish species. Preliminary phylogenetic analyses of sequence data obtained for 14 taxa and 10 markers (total of 7,872 bp for each species are encouraging, suggesting that the markers obtained will make significant contributions to future fish phylogenetic studies. Conclusion We present a practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny. Our method is an improvement over traditional approaches (e.g., manually picking genes for testing because it uses genomic information and automates the process to identify large numbers of candidate makers. This approach is shown here to be successful for fishes

Techniques for Automated Testing of Lola Industrial Robot Language Parser

Directory of Open Access Journals (Sweden)

M. M. Lutovac

2014-06-01

Full Text Available The accuracy of parsing execution directly affects the accuracy of semantic analysis, optimization and object code generation. Therefore, parser testing represents the basis of compiler testing. It should include tests for correct and expected, but also for unexpected and invalid cases. Techniques for testing the parser, as well as algorithms and tools for test sentences generation, are discussed in this paper. The methodology for initial testing of a newly developed compiler is proposed. Generation of negative test sentences by modifying the original language grammar is described. Positive and negative test cases generated by Grow, Purdom’s algorithm with and without length control, CDRC-P algorithm and CDRC-P algorithm with length control are applied to the testing of L-IRL robot programming language. For this purpose two different tools for generation of test sentences are used. Based on the presented analysis of possible solutions, the appropriate method can be chosen for testing the parser for smaller grammars with many recursive rules.

Applications of Natural Language Processing in Biodiversity Science

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Anne E. Thessen

2012-01-01

A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters, but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science.

Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

Science.gov (United States)

Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K

2012-09-01

The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates. Published by Elsevier Inc.

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.

Science.gov (United States)

Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin; Blattner, Frank R

2017-06-16

Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

Automating with SIMATIC S7-1500 configuring, programming and testing with STEP 7 Professional

CERN Document Server

Berger, Hans

2014-01-01

With many innovations, the SIMATIC S7-1500 programmable logic controller (PLC) sets new standards in productivity and efficiency in control technology. By its outstanding system performance and with PROFINET as the standard interface, it ensures extremely short system response times and the highest control quality with a maximum of flexibility for most demanding automation tasks. The engineering software STEP 7 Professional operates inside TIA Portal, a user interface that is designed for intuitive operation. Functionality includes all aspects of Automation: from the configuration of the controllers via the programming in the IEC languages ¿¿LAD, FBD, STL, and SCL up to the program test. In the book, the hardware components of the automation system S7-1500 are presented including the description of their configuration and parameterization. A comprehensive introduction into STEP 7 Professional illustrates the basics of programming and troubleshooting. Beginners learn the basics of automation with Simatic...

Studies in using a universal exchange and inference language for evidence based medicine. Semi-automated learning and reasoning for PICO methodology, systematic review, and environmental epidemiology.

Science.gov (United States)

Robson, Barry

2016-12-01

The Q-UEL language of XML-like tags and the associated software applications are providing a valuable toolkit for Evidence Based Medicine (EBM). In this paper the already existing applications, data bases, and tags are brought together with new ones. The particular Q-UEL embodiment used here is the BioIngine. The main challenge is one of bringing together the methods of symbolic reasoning and calculative probabilistic inference that underlie EBM and medical decision making. Some space is taken to review this background. The unification is greatly facilitated by Q-UEL's roots in the notation and algebra of Dirac, and by extending Q-UEL into the Wolfram programming environment. Further, the overall problem of integration is also a relatively simple one because of the nature of Q-UEL as a language for interoperability in healthcare and biomedicine, while the notion of workflow is facilitated because of the EBM best practice known as PICO. What remains difficult is achieving a high degree of overall automation because of a well-known difficulty in capturing human expertise in computers: the Feigenbaum bottleneck. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recapitulating phylogenies using k-mers: from trees to networks.

Science.gov (United States)

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Antifungal susceptibility and phylogeny of opportunistic members of the order mucorales.

NARCIS (Netherlands)

Vitale, R.G.; Hoog, G.S. de; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; Sande, W.W. van de; Dolatabadi, S.; Meis, J.F.G.M.; Walther, G.

2012-01-01

The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales

NARCIS (Netherlands)

R.G. Vitale (Roxana); G.S. de Hoog; P. Schwarz (Peter); E. Dannaoui (Eric); S. Deng (Shuwen); M. Machouart (Marie); K. Voigt (Kerstin); W.W.J. van de Sande (Wendy); S. Dolatabadi (Somayeh); J.F. Meis; G. Walther

2012-01-01

textabstractThe in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the

Antifungal Susceptibility and Phylogeny of Opportunistic Members of the Order Mucorales

NARCIS (Netherlands)

Vitale, R.G.; de Hoog, G.S.; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; de Sande, W.W.J.v.; Dolatabadi, S.; Meis, J.F.; Walther, G.

2012-01-01

The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

Science.gov (United States)

Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

2017-04-01

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. Copyright © 2016 Elsevier GmbH. All rights reserved.

The AVANTSSAR Platform for the Automated Validation of Trust and Security of Service-Oriented Architectures

DEFF Research Database (Denmark)

Armando, Alessandro; Arsac, Wihem; Avanesov, Tigran

2012-01-01

The AVANTSSAR Platform is an integrated toolset for the formal specification and automated validation of trust and security of service-oriented architectures and other applications in the Internet of Services. The platform supports application-level specification languages (such as BPMN and our...

Automation of Publications in Official Statistics using R

Directory of Open Access Journals (Sweden)

Guido Schulz

2018-03-01

Full Text Available A key task of official statistical authorities is to collect and disseminate indicators periodically. Automation using a wide range of R packages bears massive potential to cut down the resources necessary for the creation of publications. Furthermore, automation in R has the potential to improve transparency, punctuality and coherence of statistical products. The dynamic reporting engine knitr in particular allows for an efficient combination of R’s functionalities of data retrieval, data manipulation and customizable plotting on the one hand, and the layout and typesetting flexibility of LaTex or other markup languages on the other. This allows official statistical authorities to produce either ready-to-print PDFs or interactive websites while adhering to their corporate design requirements. Furthermore, dynamic reporting makes it possible to update periodic publications automatically. A work in progress example of automated statistical country profiles – a product the German Federal Statistical Office regularly publishes based on a wide range of official international sources – will be presented to illustrate both advantages and challenges in the practical use of dynamic reporting using R and knitr in particular.

Archaebacterial phylogeny: perspectives on the urkingdoms

Science.gov (United States)

Woese, C. R.; Olsen, G. J.

1986-01-01

Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

Directory of Open Access Journals (Sweden)

W John Kress

2010-11-01

Full Text Available Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

Science.gov (United States)

Kang, Hahk-Soo

2017-02-01

Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

Automated screening for retinopathy

Directory of Open Access Journals (Sweden)

A. S. Rodin

2014-07-01

Full Text Available Retinal pathology is a common cause of an irreversible decrease of central vision commonly found amongst senior population. Detection of the earliest signs of retinal diseases can be facilitated by viewing retinal images available from the telemedicine networks. To facilitate the process of retinal images, screening software applications based on image recognition technology are currently on the various stages of development.Purpose: To develop and implement computerized image recognition software that can be used as a decision support technologyfor retinal image screening for various types of retinopathies.Methods: The software application for the retina image recognition has been developed using C++ language. It was tested on dataset of 70 images with various types of pathological features (age related macular degeneration, chorioretinitis, central serous chorioretinopathy and diabetic retinopathy.Results: It was shown that the system can achieve a sensitivity of 73 % and specificity of 72 %.Conclusion: Automated detection of macular lesions using proposed software can significantly reduce manual grading workflow. In addition, automated detection of retinal lesions can be implemented as a clinical decision support system for telemedicine screening. It is anticipated that further development of this technology can become a part of diagnostic image analysis system for the electronic health records.

Altering user' acceptance of automation through prior automation exposure.

Science.gov (United States)

Bekier, Marek; Molesworth, Brett R C

2017-06-01

Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

Science.gov (United States)

Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

2014-04-01

Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

Automated Formal Verification for PLC Control Systems

CERN Multimedia

Fernández Adiego, Borja

2014-01-01

Programmable Logic Controllers (PLCs) are widely used devices used in industrial control systems. Ensuring that the PLC software is compliant with its specification is a challenging task. Formal verification has become a recommended practice to ensure the correctness of the safety-critical software. However, these techniques are still not widely applied in industry due to the complexity of building formal models, which represent the system and the formalization of requirement specifications. We propose a general methodology to perform automated model checking of complex properties expressed in temporal logics (e.g. CTL, LTL) on PLC programs. This methodology is based on an Intermediate Model (IM), meant to transform PLC programs written in any of the languages described in the IEC 61131-3 standard (ST, IL, etc.) to different modeling languages of verification tools. This approach has been applied to CERN PLC programs validating the methodology.

A Domain Specific Language for Performance Evaluation of Medical Imaging Systems

NARCIS (Netherlands)

van den Berg, Freek; Remke, Anne Katharina Ingrid; Haverkort, Boudewijn R.H.M.; Turau, Volker; Kwiatkowska, Marta; Mangharam, Rahul; Weyer, Christoph

2014-01-01

We propose iDSL, a domain specific language and toolbox for performance evaluation of Medical Imaging Systems. iDSL provides transformations to MoDeST models, which are in turn converted into UPPAAL and discrete-event MODES models. This enables automated performance evaluation by means of model

Measures of lexical distance between languages

Science.gov (United States)

Petroni, Filippo; Serva, Maurizio

2010-06-01

The idea of measuring distance between languages seems to have its roots in the work of the French explorer Dumont D’Urville (1832) [13]. He collected comparative word lists for various languages during his voyages aboard the Astrolabe from 1826 to 1829 and, in his work concerning the geographical division of the Pacific, he proposed a method for measuring the degree of relation among languages. The method used by modern glottochronology, developed by Morris Swadesh in the 1950s, measures distances from the percentage of shared cognates, which are words with a common historical origin. Recently, we proposed a new automated method which uses the normalized Levenshtein distances among words with the same meaning and averages on the words contained in a list. Recently another group of scholars, Bakker et al. (2009) [8] and Holman et al. (2008) [9], proposed a refined version of our definition including a second normalization. In this paper we compare the information content of our definition with the refined version in order to decide which of the two can be applied with greater success to resolve relationships among languages.

Final Report A Multi-Language Environment For Programmable Code Optimization and Empirical Tuning

Energy Technology Data Exchange (ETDEWEB)

Yi, Qing [Univ. of Colorado, Colorado Springs, CO (United States); Whaley, Richard Clint [Univ. of Texas, San Antonio, TX (United States); Qasem, Apan [Texas State Univ., San Marcos, TX (United States); Quinlan, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2013-11-23

This report summarizes our effort and results of building an integrated optimization environment to effectively combine the programmable control and the empirical tuning of source-to-source compiler optimizations within the framework of multiple existing languages, specifically C, C++, and Fortran. The environment contains two main components: the ROSE analysis engine, which is based on the ROSE C/C++/Fortran2003 source-to-source compiler developed by Co-PI Dr.Quinlan et. al at DOE/LLNL, and the POET transformation engine, which is based on an interpreted program transformation language developed by Dr. Yi at University of Texas at San Antonio (UTSA). The ROSE analysis engine performs advanced compiler analysis, identifies profitable code transformations, and then produces output in POET, a language designed to provide programmable control of compiler optimizations to application developers and to support the parameterization of architecture-sensitive optimizations so that their configurations can be empirically tuned later. This POET output can then be ported to different machines together with the user application, where a POET-based search engine empirically reconfigures the parameterized optimizations until satisfactory performance is found. Computational specialists can write POET scripts to directly control the optimization of their code. Application developers can interact with ROSE to obtain optimization feedback as well as provide domain-specific knowledge and high-level optimization strategies. The optimization environment is expected to support different levels of automation and programmer intervention, from fully-automated tuning to semi-automated development and to manual programmable control.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

Science.gov (United States)

2013-01-01

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.

Directory of Open Access Journals (Sweden)

Emmanuelle Lerat

2003-10-01

Full Text Available The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205 of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.

The Weapons Laboratory Technical Library: Automating with ’Stilas’

Science.gov (United States)

1990-03-01

version of the system to LC in October 1988. -X- A small business specializing in library automation, SIRSI was founded in 1979 by library and...computer specialists, and has a strong reputation based upon the success of their UNIX-based Unicorn Collection Management System. SIRSI offers a complete...system based on the Unicorn and BRS/ Search systems. The contracted STILAS package includes UNISYS hardware, software written in the C language

Domain Specific Language Support for Exascale

Energy Technology Data Exchange (ETDEWEB)

Mellor-Crummey, John [Rice Univ., Houston, TX (United States)

2017-10-20

A multi-institutional project known as D-TEC (short for “Domain- specific Technology for Exascale Computing”) set out to explore technologies to support the construction of Domain Specific Languages (DSLs) to map application programs to exascale architectures. DSLs employ automated code transformation to shift the burden of delivering portable performance from application programmers to compilers. Two chief properties contribute: DSLs permit expression at a high level of abstraction so that a programmer’s intent is clear to a compiler and DSL implementations encapsulate human domain-specific optimization knowledge so that a compiler can be smart enough to achieve good results on specific hardware. Domain specificity is what makes these properties possible in a programming language. If leveraging domain specificity is the key to keep exascale software tractable, a corollary is that many different DSLs will be needed to encompass the full range of exascale computing applications; moreover, a single application may well need to use several different DSLs in conjunction. As a result, developing a general toolkit for building domain-specific languages was a key goal for the D-TEC project. Different aspects of the D-TEC research portfolio were the focus of work at each of the partner institutions in the multi-institutional project. D-TEC research and development work at Rice University focused on on three principal topics: understanding how to automate the tuning of code for complex architectures, research and development of the Rosebud DSL engine, and compiler technology to support complex execution platforms. This report provides a summary of the research and development work on the D-TEC project at Rice University.

Automated Classification of Consumer Health Information Needs in Patient Portal Messages

Science.gov (United States)

Cronin, Robert M.; Fabbri, Daniel; Denny, Joshua C.; Jackson, Gretchen Purcell

2015-01-01

Patients have diverse health information needs, and secure messaging through patient portals is an emerging means by which such needs are expressed and met. As patient portal adoption increases, growing volumes of secure messages may burden healthcare providers. Automated classification could expedite portal message triage and answering. We created four automated classifiers based on word content and natural language processing techniques to identify health information needs in 1000 patient-generated portal messages. Logistic regression and random forest classifiers detected single information needs well, with area under the curves of 0.804–0.914. A logistic regression classifier accurately found the set of needs within a message, with a Jaccard index of 0.859 (95% Confidence Interval: (0.847, 0.871)). Automated classification of consumer health information needs expressed in patient portal messages is feasible and may allow direct linking to relevant resources or creation of institutional resources for commonly expressed needs. PMID:26958285

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada, Heterotardigrada)

DEFF Research Database (Denmark)

Guil, Noemi; Jørgensen, Aslak; Giribet, Gonzalo

2013-01-01

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ...

SCDU Testbed Automated In-Situ Alignment, Data Acquisition and Analysis

Science.gov (United States)

Werne, Thomas A.; Wehmeier, Udo J.; Wu, Janet P.; An, Xin; Goullioud, Renaud; Nemati, Bijan; Shao, Michael; Shen, Tsae-Pyng J.; Wang, Xu; Weilert, Mark A.;

Molecular phylogeny of Neotropical monogeneans (Platyhelminthes: Monogenea) from catfishes (Siluriformes)

Czech Academy of Sciences Publication Activity Database

Mendoza-Palmero, Carlos Alonso; Blasco-Costa, I.; Scholz, Tomáš

2015-01-01

Roč. 8, MAR 18 2015 (2015), s. 164 ISSN 1756-3305 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Phylogeny * Monogenea * Dactylogyridae * Neotropical region * Diversity * Siluriformes * 28S rRNA Subject RIV: EG - Zoology Impact factor: 3.234, year: 2015

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

Science.gov (United States)

Ahrenfeldt, Johanne; Skaarup, Carina; Hasman, Henrik; Pedersen, Anders Gorm; Aarestrup, Frank Møller; Lund, Ole

2017-01-05

Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods. Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator strain grow in the lab for 8 consecutive days, each day splitting the culture in two while also collecting samples for sequencing. The result is a data set consisting of 101 whole genome sequences with known phylogenetic relationship. Among the sequenced samples 51 correspond to internal nodes in the phylogeny because they are ancestral, while the remaining 50 correspond to leaves. We also used the newly created data set to compare three different online available methods that infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and REALPHY. One complication when comparing the output of these methods with the known phylogeny is that phylogenetic methods typically build trees where all observed sequences are placed as leafs, even though some of them are in fact ancestral. We therefore devised a method for post processing the inferred trees by collapsing short branches (thus relocating some leafs to internal nodes), and also present two new measures of tree similarity that takes into account the identity of both internal and leaf nodes. Based on this analysis we find that, among the investigated methods, CSI Phylogeny had the best performance, correctly identifying 73% of all branches in the

Phylogeny of Selaginellaceae: There is value in morphology after all!

Science.gov (United States)

Weststrand, Stina; Korall, Petra

2016-12-01

The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian-Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

What Does Corpus Linguistics Have to Offer to Language Assessment?

Science.gov (United States)

Xi, Xiaoming

2017-01-01

In recent years, continuing advances in technology have increased the capacity to automate the extraction of a range of linguistic features of texts and thus have provided the impetus for the substantial growth of corpus linguistics. While corpus linguistic tools and methods have been used extensively in second language learning research, they…

Molecular Phylogeny of the Bamboo Sharks (Chiloscyllium spp.

Directory of Open Access Journals (Sweden)

Noor Haslina Masstor

2014-01-01

Full Text Available Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences’ lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate that can clearly be used to differentiate each species.

Complacency and Automation Bias in the Use of Imperfect Automation.

Science.gov (United States)

Wickens, Christopher D; Clegg, Benjamin A; Vieane, Alex Z; Sebok, Angelia L

2015-08-01

We examine the effects of two different kinds of decision-aiding automation errors on human-automation interaction (HAI), occurring at the first failure following repeated exposure to correctly functioning automation. The two errors are incorrect advice, triggering the automation bias, and missing advice, reflecting complacency. Contrasts between analogous automation errors in alerting systems, rather than decision aiding, have revealed that alerting false alarms are more problematic to HAI than alerting misses are. Prior research in decision aiding, although contrasting the two aiding errors (incorrect vs. missing), has confounded error expectancy. Participants performed an environmental process control simulation with and without decision aiding. For those with the aid, automation dependence was created through several trials of perfect aiding performance, and an unexpected automation error was then imposed in which automation was either gone (one group) or wrong (a second group). A control group received no automation support. The correct aid supported faster and more accurate diagnosis and lower workload. The aid failure degraded all three variables, but "automation wrong" had a much greater effect on accuracy, reflecting the automation bias, than did "automation gone," reflecting the impact of complacency. Some complacency was manifested for automation gone, by a longer latency and more modest reduction in accuracy. Automation wrong, creating the automation bias, appears to be a more problematic form of automation error than automation gone, reflecting complacency. Decision-aiding automation should indicate its lower degree of confidence in uncertain environments to avoid the automation bias. © 2015, Human Factors and Ergonomics Society.

PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

Directory of Open Access Journals (Sweden)

Fredslund Jakob

2006-06-01

Full Text Available Abstract Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates". The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go

Software complex for developing dynamically packed program system for experiment automation

International Nuclear Information System (INIS)

Baluka, G.; Salamatin, I.M.

1985-01-01

Software complex for developing dynamically packed program system for experiment automation is considered. The complex includes general-purpose programming systems represented as the RT-11 standard operating system and specially developed problem-oriented moduli providing execution of certain jobs. The described complex is realized in the PASKAL' and MAKRO-2 languages and it is rather flexible to variations of the technique of the experiment

A Simple Take on Typed Abstract Syntax in Haskell-Like Languages

DEFF Research Database (Denmark)

Danvy, Olivier; Rhiger, Morten

2000-01-01

We present a simple way to program typed abstract syntax in a language following a Hindley-Milner typing discipline, such as Haskell and ML, and we apply it to automate two proofs about normalization functions as embodied in type-directed partial evaluation for the simply typed lambda calculus...

A molecular phylogeny of selected species of genus Prunus L ...

African Journals Online (AJOL)

(Syn. Prunus amygdalus) and Prunus cornuta (Wall. ex. Royle) Steudel. These are indigenous to Pakistan. In the ITS strict consensus results for example, the clade consisting of Laurocerasus, Padus and Cerasus subgenera are sister to the rest of the clades in the phylogenetic tree. Key words: Phylogeny, Prunus, Pakistan, ...

Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

Science.gov (United States)

D. Jean Lodge; Mahajabeen Padamsee; P. Brandon Matheny; M. Catherine Aime; Sharon A. Cantrell; David Boertmann; Alexander Kovalenko; Alfredo Vizzini; Bryn T.M. Dentinger; Paul M. Kirk; A. Martin Ainsworth; Jean-Marc Moncalvo; Rytas Vilgalys; Ellen Larsson; Robert Lucking; Gareth W. Griffith; Matthew E. Smith; Lorilei L. Norvell; Dennis E. Desjardin; Scott A. Redhead; Clark L. Ovrebo; Edgar B. Lickey; Enrico Ercole; Karen W. Hughes; Regis Courtecuisse; Anthony Young; Manfred Binder; Andrew M. Minnis; Daniel L. Lindner; Beatriz Ortiz-Santana; John Haight; Thomas Laessoe; Timothy J. Baroni; Jozsef Geml; Tsutomu Hattori

2013-01-01

Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe,...

An automated methodology development. [software design for combat simulation

Science.gov (United States)

Hawley, L. R.

1985-01-01

The design methodology employed in testing the applicability of Ada in large-scale combat simulations is described. Ada was considered as a substitute for FORTRAN to lower life cycle costs and ease the program development efforts. An object-oriented approach was taken, which featured definitions of military targets, the capability of manipulating their condition in real-time, and one-to-one correlation between the object states and real world states. The simulation design process was automated by the problem statement language (PSL)/problem statement analyzer (PSA). The PSL/PSA system accessed the problem data base directly to enhance the code efficiency by, e.g., eliminating non-used subroutines, and provided for automated report generation, besides allowing for functional and interface descriptions. The ways in which the methodology satisfied the responsiveness, reliability, transportability, modifiability, timeliness and efficiency goals are discussed.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

KAUST Repository

Dí az-Arce, Natalia; Arrizabalaga, Haritz; Murua, Hilario; Irigoien, Xabier; Rodrí guez-Ezpeleta, Naiara

2016-01-01

conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough

Phantoms of Gondwana?-phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

DEFF Research Database (Denmark)

Frick, Holger; Scharff, Nikolaj

2014-01-01

This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiin...

Automation of radiation dosimetry using PTW dosemeter and LabVIEWTM

International Nuclear Information System (INIS)

Weiss, C.; Al-Frouh, K.; Anjak, O.

2011-01-01

Automation of UNIDOS 'Dosemeter' using personal computer (PC) is discussed in this paper. In order to save time and eliminate human operation errors during the radiation dosimetry, suitable software, using LabVIEW TM graphical programming language, was written to automate and facilitate the processes of measurements, analysis and data storage. The software calculates the calibration factor of the ionization chamber in terms of air kerma or absorbed dose to water according to IAEA dosimetry protocols. It also has the ability to print a calibration certificate. The obtained results using this software are found to be more reliable and flexible than those obtained by manual methods previously employed. Using LabVIEW TM as a development tool is extremely convenient to make things easier when software modifications and improvements are needed.

Automation, communication and cybernetics in science and engineering 2013/2014

CERN Document Server

Isenhardt, Ingrid; Hees, Frank; Henning, Klaus

2014-01-01

This book continues the tradition of its predecessors “Automation, Communication and Cybernetics in Science and Engineering 2009/2010 and 2011/2012” and includes a representative selection of scientific publications from researchers at the institute cluster IMA/ZLW & IfU.   IMA - Institute of Information Management in Mechanical Engineering
 ZLW - Center for Learning and Knowledge Management
 IfU - Associated Institute for Management Cybernetics e.V.
Faculty of Mechanical Engineering, RWTH Aachen University   The book presents a range of innovative fields of application, including: cognitive systems, cyber-physical production systems, robotics, automation technology, machine learning, natural language processing, data mining, predictive data analytics, visual analytics, innovation and diversity management, demographic models, virtual and remote laboratories, virtual and augmented realities, multimedia learning environments, organizational development and management cybernetics. The contributio...

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

Science.gov (United States)

Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

2015-10-01

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

Directory of Open Access Journals (Sweden)

Holland Barbara R

2006-07-01

Full Text Available Abstract Background Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. Results Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. Conclusion Using the most treelike distance matrices, as

Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction

Czech Academy of Sciences Publication Activity Database

Pečnerová, P.; Martínková, Natália

2012-01-01

Roč. 41, č. 3 (2012), s. 211-219 ISSN 0300-3256 Institutional research plan: CEZ:AV0Z60930519 Keywords : phylogeny * Sciurus * biogeography * colonisation Subject RIV: EG - Zoology Impact factor: 2.793, year: 2012

Model Problems in Technologies for Interoperability: OWL Web Ontology Language for Services (OWL-S)

National Research Council Canada - National Science Library

Metcalf, Chris; Lewis, Grace A

2006-01-01

.... The OWL Web Ontology Language for Services (OWL-S) is a language to describe the properties and capabilities of Web Services in such a way that the descriptions can be interpreted by a computer system in an automated manner. This technical note presents the results of applying the model problem approach to examine the feasibility of using OWL-S to allow applications to automatically discover, compose, and invoke services in a dynamic services-oriented environment.

Chromosomal phylogeny of Lagothrix, Brachyteles, and Cacajao.

Science.gov (United States)

Viegas Péquignot, E; Koiffmann, C P; Dutrillaux, B

1985-01-01

Based on a comparison of the karyotypes of two Plathyrrhini species, Cacajao melanocephalus (Pitheciinae) and Brachyteles arachnoides (Atelinae), with those of two previously studied species, Lagothrix lagothrica (Atelinae) and C calvus rubicundus (Pitheciinae), it appears that the two Cacajao species have undergone the same number of chromosome rearrangements since they diverged from their common ancestor and that the karyotype of Brachyteles is ancestral to that of Lagothrix. The chromosomal phylogeny of these four species is proposed. A Y-autosome translocation is present in the karyotypes of the two Cacajao species.

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

Directory of Open Access Journals (Sweden)

Strassmann Joan E

2004-03-01

Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

An innovative approach for modeling and simulation of an automated industrial robotic arm operated electro-pneumatically

Science.gov (United States)

Popa, L.; Popa, V.

2017-08-01

The article is focused on modeling an automated industrial robotic arm operated electro-pneumatically and to simulate the robotic arm operation. It is used the graphic language FBD (Function Block Diagram) to program the robotic arm on Zelio Logic automation. The innovative modeling and simulation procedures are considered specific problems regarding the development of a new type of technical products in the field of robotics. Thus, were identified new applications of a Programmable Logic Controller (PLC) as a specialized computer performing control functions with a variety of high levels of complexit.

Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.

Science.gov (United States)

Kreipe, Victoria; Corral-Hernández, Elena; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

2015-06-01

Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

Automated electronic filter design

CERN Document Server

Banerjee, Amal

2017-01-01

This book describes a novel, efficient and powerful scheme for designing and evaluating the performance characteristics of any electronic filter designed with predefined specifications. The author explains techniques that enable readers to eliminate complicated manual, and thus error-prone and time-consuming, steps of traditional design techniques. The presentation includes demonstration of efficient automation, using an ANSI C language program, which accepts any filter design specification (e.g. Chebyschev low-pass filter, cut-off frequency, pass-band ripple etc.) as input and generates as output a SPICE(Simulation Program with Integrated Circuit Emphasis) format netlist. Readers then can use this netlist to run simulations with any version of the popular SPICE simulator, increasing accuracy of the final results, without violating any of the key principles of the traditional design scheme.

Developing Formal Correctness Properties from Natural Language Requirements

Science.gov (United States)

Nikora, Allen P.

2006-01-01

This viewgraph presentation reviews the rationale of the program to transform natural language specifications into formal notation.Specifically, automate generation of Linear Temporal Logic (LTL)correctness properties from natural language temporal specifications. There are several reasons for this approach (1) Model-based techniques becoming more widely accepted, (2) Analytical verification techniques (e.g., model checking, theorem proving) significantly more effective at detecting types of specification design errors (e.g., race conditions, deadlock) than manual inspection, (3) Many requirements still written in natural language, which results in a high learning curve for specification languages, associated tools and increased schedule and budget pressure on projects reduce training opportunities for engineers, and (4) Formulation of correctness properties for system models can be a difficult problem. This has relevance to NASA in that it would simplify development of formal correctness properties, lead to more widespread use of model-based specification, design techniques, assist in earlier identification of defects and reduce residual defect content for space mission software systems. The presentation also discusses: potential applications, accomplishments and/or technological transfer potential and the next steps.

Automation of the control scheme for IUAC Linac

International Nuclear Information System (INIS)

Sahu, B.K.; Dutt, R.N.; Antony, J.; Mathuria, D.S.; Pandey, A.; Singh, K.; Ahuja, R.; Chowdhury, G.K.; Rai, A.; Patra, P.; Ghosh, S.; Ajithkumar, B.P.; Kanjilal, D.; Roy, A.

2011-01-01

Improvement of the Linac control scheme is undertaken for automation with minimum human intervention during beam acceleration. Python language interface with the present control scheme is used in writing automation routines to monitor the status of the phase/amplitude lock during operation and shut-down the locking mechanism to reduce the RF power, if required. Simultaneous pulse conditioning of the resonators is made possible by using dedicated hardware interfaced and Python based client interface. Movement of the drive coupler is enabled from operation console with position read back. The manual control of the slow-tuner electronics module to bring the frequency close to reference during phase locking is interfaced with the present control scheme for remote operation. Monitoring of amplitude and absolute phase of each cavity is made possible from operation console. An alternate tuning mechanism using piezoelectric actuator and stepper motor combination has been successfully tested in the test cryostat. (author)

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

Science.gov (United States)

Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae

Directory of Open Access Journals (Sweden)

Francisco Perfectti

2017-10-01

Full Text Available Background The phylogeny of tribe Brassiceae (Brassicaceae has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established. Methods Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region. We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca. Results The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis. Discussion We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic

Improving the driver-automation interaction: an approach using automation uncertainty.

Science.gov (United States)

Beller, Johannes; Heesen, Matthias; Vollrath, Mark

2013-12-01

The aim of this study was to evaluate whether communicating automation uncertainty improves the driver-automation interaction. A false system understanding of infallibility may provoke automation misuse and can lead to severe consequences in case of automation failure. The presentation of automation uncertainty may prevent this false system understanding and, as was shown by previous studies, may have numerous benefits. Few studies, however, have clearly shown the potential of communicating uncertainty information in driving. The current study fills this gap. We conducted a driving simulator experiment, varying the presented uncertainty information between participants (no uncertainty information vs. uncertainty information) and the automation reliability (high vs.low) within participants. Participants interacted with a highly automated driving system while engaging in secondary tasks and were required to cooperate with the automation to drive safely. Quantile regressions and multilevel modeling showed that the presentation of uncertainty information increases the time to collision in the case of automation failure. Furthermore, the data indicated improved situation awareness and better knowledge of fallibility for the experimental group. Consequently, the automation with the uncertainty symbol received higher trust ratings and increased acceptance. The presentation of automation uncertaintythrough a symbol improves overall driver-automation cooperation. Most automated systems in driving could benefit from displaying reliability information. This display might improve the acceptance of fallible systems and further enhances driver-automation cooperation.

Phylogeny and Evolution of Bracts and Bracteoles in Tacca (Dioscoreaceae)

Institute of Scientific and Technical Information of China (English)

Ling Zhang; Hong-Tao Li; Lian-Ming Gao; Jun-Bo Yang; De-Zhu Li; Charles H. Cannon; Jin Chen; Qing-Jun Li

2011-01-01

Most species in the genus Tacca (Dioscoreaceae) feature green to black purple,conspicuous inflorescence involucral bracts with variable shapes,motile filiform appendages (bracteoles),and diverse types of inflorescence morphology.To infer the evolution of these inflorescence traits,we reconstructed the molecular phylogeny of the genus,using DNA sequences from one nuclear,one mitochondrial,and three plastid loci (Internal Transcribed Spacer (ITS),atpA,rbcL,trnL-F,and trnH-psbA).Involucres and bracteoles characters were mapped onto the phylogeny to analyze the sequence of inflorescence trait evolution.In all analyses,species with showy involucres and bracteoles formed the most derived clade,while ancestral Tacca had small and plain involucres and short bracteoles,namely less conspicuous inflorescence structures.Two of the species with the most elaborate inflorescence morphologies (T.chantrieri in southeast China and T.integrifolia in Tibet),are predominantly self-pollinated,indicating that these conspicuous floral displays have other functions rather than pollinator attraction.We hypothesize that the motile bracteoles and involucres may facilitate selfing; display photosynthesis in the dim understory,and protect flowers from herbivory.

Identification and phylogeny of the tomato receptor-like proteins family

Directory of Open Access Journals (Sweden)

Ermis Yanes-Paz

2017-03-01

Full Text Available The receptor-like proteins (RLPs play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L. using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between related proteins of different species. Indeed, the functionally characterized CLAVATA2 (CLV2, the maize ortholog FASCIATED EAR2 (FEA2 and a putative tomato CLV2 described in Uniprot clustered together, which validates the approach. Using this approach Solyc12g042760.1.1 was identified as the putative tomato homologue of TOO MANY MOUTHS (TMM. It was shown that proteins in the same cluster of the phylogenetic tree share functional relations since several clusters of functionally related proteins i.e. the Ve cluster, the Cf cluster, and the Eix clade were formed.   Keywords: phylogeny, receptors, RLP, tomato

Automated Microscopy: Macro Language Controlling a Confocal Microscope and its External Illumination: Adaptation for Photosynthetic Organisms.

Science.gov (United States)

Steinbach, Gábor; Kaňa, Radek

2016-04-01

Photosynthesis research employs several biophysical methods, including the detection of fluorescence. Even though fluorescence is a key method to detect photosynthetic efficiency, it has not been applied/adapted to single-cell confocal microscopy measurements to examine photosynthetic microorganisms. Experiments with photosynthetic cells may require automation to perform a large number of measurements with different parameters, especially concerning light conditions. However, commercial microscopes support custom protocols (through Time Controller offered by Olympus or Experiment Designer offered by Zeiss) that are often unable to provide special set-ups and connection to external devices (e.g., for irradiation). Our new system combining an Arduino microcontroller with the Cell⊕Finder software was developed for controlling Olympus FV1000 and FV1200 confocal microscopes and the attached hardware modules. Our software/hardware solution offers (1) a text file-based macro language to control the imaging functions of the microscope; (2) programmable control of several external hardware devices (light sources, thermal controllers, actuators) during imaging via the Arduino microcontroller; (3) the Cell⊕Finder software with ergonomic user environment, a fast selection method for the biologically important cells and precise positioning feature that reduces unwanted bleaching of the cells by the scanning laser. Cell⊕Finder can be downloaded from http://www.alga.cz/cellfinder. The system was applied to study changes in fluorescence intensity in Synechocystis sp. PCC6803 cells under long-term illumination. Thus, we were able to describe the kinetics of phycobilisome decoupling. Microscopy data showed that phycobilisome decoupling appears slowly after long-term (>1 h) exposure to high light.

Automated analysis of instructional text

Energy Technology Data Exchange (ETDEWEB)

Norton, L.M.

1983-05-01

The development of a capability for automated processing of natural language text is a long-range goal of artificial intelligence. This paper discusses an investigation into the issues involved in the comprehension of descriptive, as opposed to illustrative, textual material. The comprehension process is viewed as the conversion of knowledge from one representation into another. The proposed target representation consists of statements of the prolog language, which can be interpreted both declaratively and procedurally, much like production rules. A computer program has been written to model in detail some ideas about this process. The program successfully analyzes several heavily edited paragraphs adapted from an elementary textbook on programming, automatically synthesizing as a result of the analysis a working Prolog program which, when executed, can parse and interpret let commands in the basic language. The paper discusses the motivations and philosophy of the project, the many kinds of prerequisite knowledge which are necessary, and the structure of the text analysis program. A sentence-by-sentence account of the analysis of the sample text is presented, describing the syntactic and semantic processing which is involved. The paper closes with a discussion of lessons learned from the project, possible alternative approaches, and possible extensions for future work. The entire project is presented as illustrative of the nature and complexity of the text analysis process, rather than as providing definitive or optimal solutions to any aspects of the task. 12 references.

Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

Science.gov (United States)

The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

Using genomic data to unravel the root of the placental mammal phylogeny.

Science.gov (United States)

Murphy, William J; Pringle, Thomas H; Crider, Tess A; Springer, Mark S; Miller, Webb

2007-04-01

The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

Science.gov (United States)

Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

2017-03-01

Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

A catalog of automated analysis methods for enterprise models.

Science.gov (United States)

Florez, Hector; Sánchez, Mario; Villalobos, Jorge

2016-01-01

Enterprise models are created for documenting and communicating the structure and state of Business and Information Technologies elements of an enterprise. After models are completed, they are mainly used to support analysis. Model analysis is an activity typically based on human skills and due to the size and complexity of the models, this process can be complicated and omissions or miscalculations are very likely. This situation has fostered the research of automated analysis methods, for supporting analysts in enterprise analysis processes. By reviewing the literature, we found several analysis methods; nevertheless, they are based on specific situations and different metamodels; then, some analysis methods might not be applicable to all enterprise models. This paper presents the work of compilation (literature review), classification, structuring, and characterization of automated analysis methods for enterprise models, expressing them in a standardized modeling language. In addition, we have implemented the analysis methods in our modeling tool.

CSS Preprocessing: Tools and Automation Techniques

Directory of Open Access Journals (Sweden)

Ricardo Queirós

2018-01-01

Full Text Available Cascading Style Sheets (CSS is a W3C specification for a style sheet language used for describing the presentation of a document written in a markup language, more precisely, for styling Web documents. However, in the last few years, the landscape for CSS development has changed dramatically with the appearance of several languages and tools aiming to help developers build clean, modular and performance-aware CSS. These new approaches give developers mechanisms to preprocess CSS rules through the use of programming constructs, defined as CSS preprocessors, with the ultimate goal to bring those missing constructs to the CSS realm and to foster stylesheets structured programming. At the same time, a new set of tools appeared, defined as postprocessors, for extension and automation purposes covering a broad set of features ranging from identifying unused and duplicate code to applying vendor prefixes. With all these tools and techniques in hands, developers need to provide a consistent workflow to foster CSS modular coding. This paper aims to present an introductory survey on the CSS processors. The survey gathers information on a specific set of processors, categorizes them and compares their features regarding a set of predefined criteria such as: maturity, coverage and performance. Finally, we propose a basic set of best practices in order to setup a simple and pragmatic styling code workflow.

Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera

Czech Academy of Sciences Publication Activity Database

Han, M.L.; Chen, Y.-Y.; Shen, L.-L.; Song, J.; Vlasák, Josef; Dai, Y.-C.; Cui, B.-K.

2016-01-01

Roč. 80, č. 1 (2016), s. 343-373 ISSN 1560-2745 Institutional support: RVO:60077344 Keywords : Fomitopsidaceae * Multi-marker analysis * Phylogeny Subject RIV: EF - Botanics Impact factor: 13.465, year: 2016

Molecular phylogeny of extant Holothuroidea (Echinodermata).

Science.gov (United States)

Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

2017-06-01

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown

A multi gene sequence-based phylogeny of the Musaceae (banana) family

Czech Academy of Sciences Publication Activity Database

Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; De Langhe, E.; Doležel, Jaroslav

2011-01-01

Roč. 11, č. 103 (2011), s. 1-13 ISSN 1471-2148 R&D Projects: GA AV ČR IAA600380703 Institutional research plan: CEZ:AV0Z50380511 Keywords : MOLECULAR PHYLOGENY * FLOWERING PLANTS * RIBOSOMAL DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.521, year: 2011

Complex phylogenetic placement of ilex species (aquifoliaceae): a case study of molecular phylogeny

International Nuclear Information System (INIS)

Yi, F.; Sun, L.; Xiao, P.G.; Hao, D.C.

2017-01-01

To investigate the phylogenetic relationships among Ilex species distributed in China, we analyzed two alignments including 4,698 characters corresponding to six plastid sequences (matK, rbcL, atpB-rbcL, trnL-F, psbA-trnH, and rpl32-trnL) and 1,748 characters corresponding to two nuclear sequences (ITS and nepGS). Using different partitioning strategies and approaches (i.e., Bayesian inference, maximum likelihood, and maximum parsimony) for phylogeny reconstruction, different topologies and clade supports were determined. A total of 18 Ilex species was divided into two major groups (group I and II) in both plastid and nuclear phylogenies with some incongruences. Potential hybridization events may account, in part, for those phylogenetic uncertainties. The analyses, together with previously identified sequences, indicated that all 18 species were recovered within Eurasia or Asia/North America groups based on plastid data. Meanwhile, the species in group II in the nuclear phylogeny were placed in the Aquifolium clade, as inferred from traditional classification, whereas the species in group I belonged to several other clades. The divergence time of most of the 18 Ilex species was estimated to be not more than 10 million years ago. Based on the results of this study, we concluded that paleogeographical events and past climate changes during the same period might have played important roles in these diversifications. (author)

Cassini Tour Atlas Automated Generation

Science.gov (United States)

Grazier, Kevin R.; Roumeliotis, Chris; Lange, Robert D.

2011-01-01

During the Cassini spacecraft s cruise phase and nominal mission, the Cassini Science Planning Team developed and maintained an online database of geometric and timing information called the Cassini Tour Atlas. The Tour Atlas consisted of several hundreds of megabytes of EVENTS mission planning software outputs, tables, plots, and images used by mission scientists for observation planning. Each time the nominal mission trajectory was altered or tweaked, a new Tour Atlas had to be regenerated manually. In the early phases of Cassini s Equinox Mission planning, an a priori estimate suggested that mission tour designers would develop approximately 30 candidate tours within a short period of time. So that Cassini scientists could properly analyze the science opportunities in each candidate tour quickly and thoroughly so that the optimal series of orbits for science return could be selected, a separate Tour Atlas was required for each trajectory. The task of manually generating the number of trajectory analyses in the allotted time would have been impossible, so the entire task was automated using code written in five different programming languages. This software automates the generation of the Cassini Tour Atlas database. It performs with one UNIX command what previously took a day or two of human labor.

Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

NARCIS (Netherlands)

Bokma, Folmer

2006-01-01

Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because. recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process,

Testing Automation of Context-Oriented Programs Using Separation Logic

Directory of Open Access Journals (Sweden)

Mohamed A. El-Zawawy

2014-01-01

Full Text Available A new approach for programming that enables switching among contexts of commands during program execution is context-oriented programming (COP. This technique is more structured and modular than object-oriented and aspect-oriented programming and hence more flexible. For context-oriented programming, as implemented in COP languages such as ContextJ* and ContextL, this paper introduces accurate operational semantics. The language model of this paper uses Java concepts and is equipped with layer techniques for activation/deactivation of layer contexts. This paper also presents a logical system for COP programs. This logic is necessary for the automation of testing, developing, and validating of partial correctness specifications for COP programs and is an extension of separation logic. A mathematical soundness proof for the logical system against the proposed operational semantics is presented in the paper.

Formal verification of automated teller machine systems using SPIN

Science.gov (United States)

Iqbal, Ikhwan Mohammad; Adzkiya, Dieky; Mukhlash, Imam

2017-08-01

Formal verification is a technique for ensuring the correctness of systems. This work focuses on verifying a model of the Automated Teller Machine (ATM) system against some specifications. We construct the model as a state transition diagram that is suitable for verification. The specifications are expressed as Linear Temporal Logic (LTL) formulas. We use Simple Promela Interpreter (SPIN) model checker to check whether the model satisfies the formula. This model checker accepts models written in Process Meta Language (PROMELA), and its specifications are specified in LTL formulas.

Effects of phylogeny, leaf traits, and the altitudinal distribution of host plants on herbivore assemblages on congeneric Acer species.

Science.gov (United States)

Nakadai, Ryosuke; Murakami, Masashi; Hirao, Toshihide

2014-08-01

Historical, niche-based, and stochastic processes have been proposed as the mechanisms that drive community assembly. In plant-herbivore systems, these processes can correspond to phylogeny, leaf traits, and the distribution of host plants, respectively. Although patterns of herbivore assemblages among plant species have been repeatedly examined, the effects of these factors among co-occurring congeneric host plant species have rarely been studied. Our aim was to reveal the process of community assembly for herbivores by investigating the effects of phylogeny, leaf traits, and the altitudinal distribution of closely related host plants of the genus Acer. We sampled leaf functional traits for 30 Acer species in Japan. Using a newly constructed phylogeny, we determined that three of the six measured leaf traits (leaf thickness, C/N ratio, and condensed tannin content) showed a phylogenetic signal. In a field study, we sampled herbivore communities on 14 Acer species within an elevation gradient and examined relationships between herbivore assemblages and host plants. We found that herbivore assemblages were significantly correlated with phylogeny, leaf traits, phylogenetic signals, and the altitudinal distribution of host plants. Our results indicate that the interaction between historical and current ecological processes shapes herbivore community assemblages.

Syntactic Complexity Metrics and the Readability of Programs in a Functional Computer Language

NARCIS (Netherlands)

van den Berg, Klaas; Engel, F.L.; Bouwhuis, D.G.; Bosser, T.; d'Ydewalle, G.

This article reports on the defintion and the measutement of the software complexity metrics of Halstead and McCabe for programs written in the functional programming language Miranda. An automated measurement of these metrics is described. In a case study, the correlation is established between the

Mixed integer linear programming for maximum-parsimony phylogeny inference.

Science.gov (United States)

Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

2008-01-01

Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language

Science.gov (United States)

Friedman, Carol; Hripcsak, George; Shagina, Lyuda; Liu, Hongfang

1999-01-01

Objective: To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. Methods: A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. Results: The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. Conclusions: Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available. PMID:9925230

Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats

DEFF Research Database (Denmark)

Fabre, Pierre-Henri; Upham, Nathan S.; Emmons, Louise H.

2017-01-01

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorina...... Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes....

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

Science.gov (United States)

Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

2003-01-01

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

A methodology to annotate systems biology markup language models with the synthetic biology open language.

Science.gov (United States)

Roehner, Nicholas; Myers, Chris J

2014-02-21

Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae

Directory of Open Access Journals (Sweden)

Kingston Sarah E

2009-10-01

Full Text Available Abstract Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

Automation and Control of an Imaging Internal Laser Desorption Fourier Transform Mass Spectrometer (I2LD-FTMS)

Energy Technology Data Exchange (ETDEWEB)

McJunkin, Timothy R; Tranter, Troy Joseph; Scott, Jill Rennee

2002-06-01

This paper describes the automation of an imaging internal source laser desorption Fourier transform mass spectrometer (I2LD-FTMS). The I2LD-FTMS consists of a laser-scanning device [Scott and Tremblay, Rev. Sci. Instrum. 2002, 73, 1108–1116] that has been integrated with a laboratory-built FTMS using a commercial data acquisition system (ThermoFinnigan FT/MS, Bremen, Germany). A new user interface has been developed in National Instrument's (Austin, Texas) graphical programming language LabVIEW to control the motors of the laser positioning system and the commercial FTMS data acquisition system. A feature of the FTMS software that allows the user to write macros in a scripting language is used creatively to our advantage in creating a mechanism to control the FTMS from outside its graphical user interface. The new user interface also allows the user to configure target locations. Automation of the data analysis along with data display using commercial graphing software is also described.

Low cost automation

International Nuclear Information System (INIS)

1987-03-01

This book indicates method of building of automation plan, design of automation facilities, automation and CHIP process like basics of cutting, NC processing machine and CHIP handling, automation unit, such as drilling unit, tapping unit, boring unit, milling unit and slide unit, application of oil pressure on characteristics and basic oil pressure circuit, application of pneumatic, automation kinds and application of process, assembly, transportation, automatic machine and factory automation.

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea)

Czech Academy of Sciences Publication Activity Database

Tkach, V.V.; Kudlai, Olena; Kostadinova, Aneta

2016-01-01

Roč. 46, č. 3 (2016), s. 171-185 ISSN 0020-7519 R&D Projects: GA ČR(CZ) GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Echinostomatoidea * Molecular phylogeny * Systematics * Echinostomatidae (sensu stricto) * Caballerotrematidae n. fam. * Himasthlidae * Echinochasmidae * Host associations Subject RIV: EG - Zoology Impact factor: 3.730, year: 2016

A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

Science.gov (United States)

Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

2012-01-01

Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

Directory of Open Access Journals (Sweden)

Nan Song

Full Text Available Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha,Cicadomorpha,Heteroptera, and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

Phylogeny of the Gondwanan beetle family Ulodidae (Tenebrionoidea).

Science.gov (United States)

Leschen, Richard A B; Escalona, Hermes E; Elgueta, Mario

2016-07-18

Ulodidae is a small family of saproxylic and fungus feeding beetles restricted to New Zealand, Australia, Chile and New Caledonia. The phylogeny of this family is presented for the first time, based on a cladistic analysis of 53 adult characters from 16 ulodid genera, rooted with Parahelops Waterhouse (Promecheilidae). The topology shows Arthopus Sharp at the base of the tree and confirms the placement of Meryx Latreille as a member of Ulodidae and closely related to the Chilean genus Trachyderas Philippi & Philippi. The extinct New Zealand genus Waitomophylax Leschen & Rhode was placed among a clade consisting of Brouniphylax Strand, Exohadrus Broun, and Pteroderes Germain. Two new genera and two new species are described: Ulobostrichus gen. n. (type species: Ulobostrichus monteithi sp. n.) and Ulocyphaleus gen. n. (type species: Cyphaleus valdivianus Philippi & Philippi, 1864, now U. valdivianus (Philippi & Philippi) n. comb.; U. laetus sp. n.). Dipsaconia pyritosa Pascoe is designated as the type species of Dipsaconia Pascoe and a lectotype was designated for C. valdivianus. A fully illustrated key to the genera and a checklist of the 16 genera and 42 species is included. Based on the phylogeny, the following characters are derived in the family: tuberculate body surface and the presence of scales and /or encrustations. The presence of pore-fields in the abdominal cuticle has evolved at least three times in Meryx Latreille (Australia), Syrphetodes Pascoe (New Zealand) and Trachyderastes Kaszab (New Caledonia).

An Expedient Study on Back-Propagation (BPN) Neural Networks for Modeling Automated Evaluation of the Answers and Progress of Deaf Students' That Possess Basic Knowledge of the English Language and Computer Skills

Science.gov (United States)

Vrettaros, John; Vouros, George; Drigas, Athanasios S.

This article studies the expediency of using neural networks technology and the development of back-propagation networks (BPN) models for modeling automated evaluation of the answers and progress of deaf students' that possess basic knowledge of the English language and computer skills, within a virtual e-learning environment. The performance of the developed neural models is evaluated with the correlation factor between the neural networks' response values and the real value data as well as the percentage measurement of the error between the neural networks' estimate values and the real value data during its training process and afterwards with unknown data that weren't used in the training process.

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Science.gov (United States)

Hale, Vanessa L; Tan, Chia L; Niu, Kefeng; Yang, Yeqin; Knight, Rob; Zhang, Qikun; Cui, Duoying; Amato, Katherine R

2018-02-01

Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.

Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny.

Science.gov (United States)

Zhang, Junxia; Maddison, Wayne P

2015-03-27

Morphological traits of euophryine jumping spiders were studied to clarify generic limits in the Euophryinae and to permit phylogenetic classification of genera lacking molecular data. One hundred and eight genera are recognized within the subfamily. Euophryine generic groups and the delimitation of some genera are reviewed in detail. In order to explore the effect of adding formal morphological data to previous molecular phylogenetic studies, and to find morphological synapomorphies, eighty-two morphological characters were scored for 203 euophryine species and seven outgroup species. The morphological dataset does not perform as well as the molecular dataset (genes 28S, Actin 5C; 16S-ND1, COI) in resolving the phylogeny of Euophryinae, probably because of frequent convergence and reversal. The formal morphological data were mapped on the phylogeny in order to seek synapomorphies, in hopes of extending the phylogeny to include taxa for which molecular data are not available. Because of homoplasy, few globally-applicable morphological synapomorphies for euophryine clades were found. However, synapomorphies that are unique locally in subclades still help to delimit euophryine generic groups and genera. The following synonyms of euophryine genera are proposed: Maeotella with Anasaitis; Dinattus with Corythalia; Paradecta with Compsodecta; Cobanus, Chloridusa and Wallaba with Sidusa; Tariona with Mopiopia; Nebridia with Amphidraus; Asaphobelis and Siloca with Coryphasia; Ocnotelus with Semnolius; Palpelius with Pristobaeus; Junxattus with Laufeia; Donoessus with Colyttus; Nicylla, Pselcis and Thianitara with Thiania. The new genus Saphrys is erected for misplaced species from southern South America.

Language ENvironment Analysis (LENA) in Phelan-McDermid Syndrome: Validity and Suggestions for Use in Minimally Verbal Children with Autism Spectrum Disorder

Science.gov (United States)

Rankine, Jacquelin; Li, Erin; Lurie, Stacey; Rieger, Hillary; Fourie, Emily; Siper, Paige M.; Wang, A. Ting; Buxbaum, Joseph D.; Kolevzon, Alexander

2017-01-01

Phelan-McDermid syndrome (PMS) is a single-locus cause of developmental delay, autism spectrum disorder, and minimal verbal abilities. There is an urgent need to identify objective outcome measures of expressive language for use in this and other minimally verbal populations. One potential tool is an automated language processor called Language…

The co phylogeny reconstruction problem is NP-complete.

Science.gov (United States)

Ovadia, Y; Fielder, D; Conow, C; Libeskind-Hadas, R

2011-01-01

The co phylogeny reconstruction problem is that of finding minimum cost explanations of differences between historical associations. The problem arises in parasitology, molecular systematics, and biogeography. Existing software tools for this problem either have worst-case exponential time or use heuristics that do not guarantee optimal solutions. To date, no polynomial time optimal algorithms have been found for this problem. In this article, we prove that the problem is NP-complete, suggesting that future research on algorithms for this problem should seek better polynomial-time approximation algorithms and heuristics rather than optimal solutions.

Autonomy and Automation

Science.gov (United States)

Shively, Jay

2017-01-01

A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

Visual Iconicity Across Sign Languages: Large-Scale Automated Video Analysis of Iconic Articulators and Locations

Science.gov (United States)

Östling, Robert; Börstell, Carl; Courtaux, Servane

2018-01-01

We use automatic processing of 120,000 sign videos in 31 different sign languages to show a cross-linguistic pattern for two types of iconic form–meaning relationships in the visual modality. First, we demonstrate that the degree of inherent plurality of concepts, based on individual ratings by non-signers, strongly correlates with the number of hands used in the sign forms encoding the same concepts across sign languages. Second, we show that certain concepts are iconically articulated around specific parts of the body, as predicted by the associational intuitions by non-signers. The implications of our results are both theoretical and methodological. With regard to theoretical implications, we corroborate previous research by demonstrating and quantifying, using a much larger material than previously available, the iconic nature of languages in the visual modality. As for the methodological implications, we show how automatic methods are, in fact, useful for performing large-scale analysis of sign language data, to a high level of accuracy, as indicated by our manual error analysis.

Automated information retrieval using CLIPS

Science.gov (United States)

Raines, Rodney Doyle, III; Beug, James Lewis

1991-01-01

Expert systems have considerable potential to assist computer users in managing the large volume of information available to them. One possible use of an expert system is to model the information retrieval interests of a human user and then make recommendations to the user as to articles of interest. At Cal Poly, a prototype expert system written in the C Language Integrated Production System (CLIPS) serves as an Automated Information Retrieval System (AIRS). AIRS monitors a user's reading preferences, develops a profile of the user, and then evaluates items returned from the information base. When prompted by the user, AIRS returns a list of items of interest to the user. In order to minimize the impact on system resources, AIRS is designed to run in the background during periods of light system use.

Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

Directory of Open Access Journals (Sweden)

Michelle Klein Sercundes

2016-03-01

Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

Phylogeny of European bat Lyssavirus 1 in Eptesicus isabellinus bats, Spain.

Science.gov (United States)

Vázquez-Moron, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M; Echevarria, Juan E

2011-03-01

To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

Phylogeny of European Bat Lyssavirus 1 in Eptesicus isabellinus Bats, Spain

OpenAIRE

Vázquez-Morón, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M.; Echevarría, Juan E.

2011-01-01

To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

Development of automation and robotics for space via computer graphic simulation methods

Science.gov (United States)

Fernandez, Ken

1988-01-01

A robot simulation system, has been developed to perform automation and robotics system design studies. The system uses a procedure-oriented solid modeling language to produce a model of the robotic mechanism. The simulator generates the kinematics, inverse kinematics, dynamics, control, and real-time graphic simulations needed to evaluate the performance of the model. Simulation examples are presented, including simulation of the Space Station and the design of telerobotics for the Orbital Maneuvering Vehicle.

Automated Item Generation with Recurrent Neural Networks.

Science.gov (United States)

von Davier, Matthias

2018-03-12

Utilizing technology for automated item generation is not a new idea. However, test items used in commercial testing programs or in research are still predominantly written by humans, in most cases by content experts or professional item writers. Human experts are a limited resource and testing agencies incur high costs in the process of continuous renewal of item banks to sustain testing programs. Using algorithms instead holds the promise of providing unlimited resources for this crucial part of assessment development. The approach presented here deviates in several ways from previous attempts to solve this problem. In the past, automatic item generation relied either on generating clones of narrowly defined item types such as those found in language free intelligence tests (e.g., Raven's progressive matrices) or on an extensive analysis of task components and derivation of schemata to produce items with pre-specified variability that are hoped to have predictable levels of difficulty. It is somewhat unlikely that researchers utilizing these previous approaches would look at the proposed approach with favor; however, recent applications of machine learning show success in solving tasks that seemed impossible for machines not too long ago. The proposed approach uses deep learning to implement probabilistic language models, not unlike what Google brain and Amazon Alexa use for language processing and generation.

A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity.

Science.gov (United States)

Milla, Liz; van Nieukerken, Erik J; Vijverberg, Ruben; Doorenweerd, Camiel; Wilcox, Stephen A; Halsey, Mike; Young, David A; Jones, Therésa M; Kallies, Axel; Hilton, Douglas J

2018-03-01

Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A synthetic phylogeny of freshwater crayfish: insights for conservation

Science.gov (United States)

Owen, Christopher L.; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A.

2015-01-01

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

Freud e a filogenia anímica Freud and the animic phylogeny

Directory of Open Access Journals (Sweden)

Monah Winograd

2007-01-01

Full Text Available Este ensaio investiga a presença, na obra de Freud, da idéia de uma filogenia anímica paralela, concomitante e dependente da filogenia somática descrita pelos teóricos da evolução. Objetivamos mostrar como se forma esta vizinhança da psicanálise com a biologia evolutiva, sublinhando que na filogenia esboçada por Freud, formas psíquicas típicas se sucedem na história da espécie humana, sendo repetidas por cada indivíduo em sua ontogenia singular. Tal como ocorre no plano somático, tempo e forma se associam intimamente na espécie e nos indivíduos. A presença desta idéia no pensamento freudiano abriu um debate sobre sua filiação lamarckista ou darwinista.This essay investigates the presence, in Freud´s work, of the idea of an animic phylogeny parallel, concomitant and dependent of the somatic phylogeny that the theoreticians of evolution describe. Our objective is to show how this neighborhood between psychoanalysis and evolutionary theory is formed. To do so, we stress that, in the phylogeny theory that Freud sketches, typical psychic forms occurs in the history of the human kind in a way that each individual repeats it in its singular ontogeny. As it happens in the somatic level, time and form are intimately associated in the species and in the individuals. The presence of that idea in Freud´s work has opened a debate about his Darwinist or Lamarckist inspiration.

Control system and automation of the spectrum acquisition for a perturbed gamma-gamma angular correlation spectrometer

International Nuclear Information System (INIS)

Stachowski, Ademir F.A.; Lapolli, André L.; Carbonari, Artur W.; Saxena, Rajendra N.

2017-01-01

This work reports results from the automation of data acquisition for a gamma-gamma perturbed angular correlation (PAC) spectrometer located in the hyperfine interactions laboratory (LIH) of IPEN. A PAC spectrometer comprises usually four scintillation detectors (BaF_3 for example) and carries out time measurements from gamma rays of any two combinations of detectors in coincidence. Gamma rays come from the decay of probe nuclei embedded into the material to be studied. Measurements are generally performed as a function of temperature. The fourth-detectors PAC spectrometer was automated in Java language because it is a multi platform and object oriented programming language, having, therefore, portability and longer lifetime due to the ease of implementation of peripherals. Finally, the software has a friendly and intuitive interface with the user being able to operate the hardware manually or automatically with time acquisitions up to 100 consecutive hours. Before each acquisition, the software sets the temperature, waits for temperature stability and records data in different files. Moreover, the software also saves in a file all information of relevant parameters during acquisition. (author)

Control system and automation of the spectrum acquisition for a perturbed gamma-gamma angular correlation spectrometer

Energy Technology Data Exchange (ETDEWEB)

Stachowski, Ademir F.A.; Lapolli, André L.; Carbonari, Artur W.; Saxena, Rajendra N., E-mail: alapolli@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2017-11-01

This work reports results from the automation of data acquisition for a gamma-gamma perturbed angular correlation (PAC) spectrometer located in the hyperfine interactions laboratory (LIH) of IPEN. A PAC spectrometer comprises usually four scintillation detectors (BaF{sub 3} for example) and carries out time measurements from gamma rays of any two combinations of detectors in coincidence. Gamma rays come from the decay of probe nuclei embedded into the material to be studied. Measurements are generally performed as a function of temperature. The fourth-detectors PAC spectrometer was automated in Java language because it is a multi platform and object oriented programming language, having, therefore, portability and longer lifetime due to the ease of implementation of peripherals. Finally, the software has a friendly and intuitive interface with the user being able to operate the hardware manually or automatically with time acquisitions up to 100 consecutive hours. Before each acquisition, the software sets the temperature, waits for temperature stability and records data in different files. Moreover, the software also saves in a file all information of relevant parameters during acquisition. (author)

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

Science.gov (United States)

2013-01-01

Background Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set H of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of distinct haplotypes hi,hj∈H, the sum of the edge weights belonging to the path from hi to hj in T∗ is not smaller than the observed number of changes between hi and hj. Finding the most parsimonious phylogeny for H involves solving an optimization problem, called the Most Parsimonious Phylogeny Estimation Problem (MPPEP), which is NP-hard in many of its versions. Results In this article we investigate a recent version of the MPPEP that arises when input data consist of single nucleotide polymorphism haplotypes extracted from a population of individuals on a common genomic region. Specifically, we explore the prospects for improving on the implicit enumeration strategy of implicit enumeration strategy used in previous work using a novel problem formulation and a series of strengthening valid inequalities and preliminary symmetry breaking constraints to more precisely bound the solution space and accelerate implicit enumeration of possible optimal phylogenies. We present the basic formulation and then introduce a series of provable valid constraints to reduce the solution space. We then prove

Automated acoustic analysis in detection of spontaneous swallows in Parkinson's disease.

Science.gov (United States)

Golabbakhsh, Marzieh; Rajaei, Ali; Derakhshan, Mahmoud; Sadri, Saeed; Taheri, Masoud; Adibi, Peyman

2014-10-01

Acoustic monitoring of swallow frequency has become important as the frequency of spontaneous swallowing can be an index for dysphagia and related complications. In addition, it can be employed as an objective quantification of ingestive behavior. Commonly, swallowing complications are manually detected using videofluoroscopy recordings, which require expensive equipment and exposure to radiation. In this study, a noninvasive automated technique is proposed that uses breath and swallowing recordings obtained via a microphone located over the laryngopharynx. Nonlinear diffusion filters were used in which a scale-space decomposition of recorded sound at different levels extract swallows from breath sounds and artifacts. This technique was compared to manual detection of swallows using acoustic signals on a sample of 34 subjects with Parkinson's disease. A speech language pathologist identified five subjects who showed aspiration during the videofluoroscopic swallowing study. The proposed automated method identified swallows with a sensitivity of 86.67 %, a specificity of 77.50 %, and an accuracy of 82.35 %. These results indicate the validity of automated acoustic recognition of swallowing as a fast and efficient approach to objectively estimate spontaneous swallow frequency.

Adipokinetic hormones provide inference for the phylogeny of Odonata

Czech Academy of Sciences Publication Activity Database

Gäde, G.; Šimek, Petr; Fescemyer, H. W.

2011-01-01

Roč. 57, č. 1 (2011), s. 174-178 ISSN 0022-1910 R&D Projects: GA ČR GA203/09/2014 Grant - others:University of Cape Town for a Block grant(ZA) IFR 2008071500048; National Research Foundation, Pretoria(ZA) FA 2007021300002; USDA, ARS Specific Cooperative Agreement(US) 58-6402-5-066; US National Science Foundation(US) EF-0412651 Institutional research plan: CEZ:AV0Z50070508 Keywords : phylogeny of Odonata * Libellulidae * Corduliidae Subject RIV: ED - Physiology Impact factor: 2.236, year: 2011

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

Science.gov (United States)

Giribet, Gonzalo; Edgecombe, Gregory D.; Wheeler, Ward C.; Babbitt, Courtney

2002-01-01

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. c2002 The Willi Hennig Society.

Towards improving searches for optimal phylogenies.

Science.gov (United States)

Ford, Eric; St John, Katherine; Wheeler, Ward C

2015-01-01

Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be "tree-like" and focusing on the maximum-parsimony optimality criterion. This has led to much work on using heuristic tree searches to find approximate solutions. We present an approach for finding exact optimal solutions that employs and complements the current heuristic methods for finding optimal trees. Given a set of taxa and a set of aligned sequences of characters, there may be subsets of characters that are compatible, and for each such subset there is an associated (possibly partially resolved) phylogeny with edges corresponding to each character state change. These perfect phylogenies serve as anchor trees for our constrained search space. We show that, for sequences with compatible sites, the parsimony score of any tree [Formula: see text] is at least the parsimony score of the anchor trees plus the number of inferred changes between [Formula: see text] and the anchor trees. As the maximum-parsimony optimality score is additive, the sum of the lower bounds on compatible character partitions provides a lower bound on the complete alignment of characters. This yields a region in the space of trees within which the best tree is guaranteed to be found; limiting the search for the optimal tree to this region can significantly reduce the number of trees that must be examined in a search of the space of trees. We analyze this method empirically using four different biological data sets as well as surveying 400 data sets from the TreeBASE repository, demonstrating the effectiveness of our technique in reducing the number of steps in exact heuristic searches for trees under the maximum-parsimony optimality criterion. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evolution of electric communication signals in the South American ghost knifefishes (Gymnotiformes: Apteronotidae): A phylogenetic comparative study using a sequence-based phylogeny.

Science.gov (United States)

Smith, Adam R; Proffitt, Melissa R; Ho, Winnie W; Mullaney, Claire B; Maldonado-Ocampo, Javier A; Lovejoy, Nathan R; Alves-Gomes, José A; Smith, G Troy

2016-10-01

The electric communication signals of weakly electric ghost knifefishes (Gymnotiformes: Apteronotidae) provide a valuable model system for understanding the evolution and physiology of behavior. Apteronotids produce continuous wave-type electric organ discharges (EODs) that are used for electrolocation and communication. The frequency and waveform of EODs, as well as the structure of transient EOD modulations (chirps), vary substantially across species. Understanding how these signals have evolved, however, has been hampered by the lack of a well-supported phylogeny for this family. We constructed a molecular phylogeny for the Apteronotidae by using sequence data from three genes (cytochrome c oxidase subunit 1, recombination activating gene 2, and cytochrome oxidase B) in 32 species representing 13 apteronotid genera. This phylogeny and an extensive database of apteronotid signals allowed us to examine signal evolution by using ancestral state reconstruction (ASR) and phylogenetic generalized least squares (PGLS) models. Our molecular phylogeny largely agrees with another recent sequence-based phylogeny and identified five robust apteronotid clades: (i) Sternarchorhamphus+Orthosternarchus, (ii) Adontosternarchus, (iii) Apteronotus+Parapteronotus, (iv) Sternarchorhynchus, and (v) a large clade including Porotergus, 'Apteronotus', Compsaraia, Sternarchogiton, Sternarchella, and Magosternarchus. We analyzed novel chirp recordings from two apteronotid species (Orthosternarchus tamandua and Sternarchorhynchus mormyrus), and combined data from these species with that from previously recorded species in our phylogenetic analyses. Some signal parameters in O. tamandua were plesiomorphic (e.g., low frequency EODs and chirps with little frequency modulation that nevertheless interrupt the EOD), suggesting that ultra-high frequency EODs and "big" chirps evolved after apteronotids diverged from other gymnotiforms. In contrast to previous studies, our PGLS analyses using the

Home Automation

OpenAIRE

Ahmed, Zeeshan

2010-01-01

In this paper I briefly discuss the importance of home automation system. Going in to the details I briefly present a real time designed and implemented software and hardware oriented house automation research project, capable of automating house's electricity and providing a security system to detect the presence of unexpected behavior.

PHY∙FI: fast and easy online creation and manipulation of phylogeny color figures

DEFF Research Database (Denmark)

Fredslund, Jakob

2006-01-01

the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create...... types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing...... a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus...

KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

Science.gov (United States)

Wang, Dapeng; Xu, Jiayue; Yu, Jun

2015-09-16

The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

On Verification of PLC-Programs Written in the LD-Language

Directory of Open Access Journals (Sweden)

E. V. Kuzmin

2012-01-01

Full Text Available We discuss some questions connected with the construction of a technology of analysing correctness of Programmable Logic Controller programs. We consider an example of modeling and automated verification of PLC-programs written in the Ladder Diagram language (including timed function blocks of the IEC 61131-3 standard. We use the Cadence SMV for symbolic model checking. Program properties are written in the linear-time temporal logic LTL.

Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era.

Science.gov (United States)

Larmuseau, Maarten H D; Van Geystelen, Anneleen; Kayser, Manfred; van Oven, Mannis; Decorte, Ronny

2015-03-01

Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives.

Science.gov (United States)

Schröder, Christiane; Bleidorn, Christoph; Hartmann, Stefanie; Tiedemann, Ralph

2009-12-15

Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (dog-like carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony-informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.

Phylogeny of economically important insect pests that infesting several crops species in Malaysia

Science.gov (United States)

Ghazali, Siti Zafirah; Zain, Badrul Munir Md.; Yaakop, Salmah

2014-09-01

This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the fern's pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabola's order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage.

Science.gov (United States)

Teske, Peter R; Hamilton, Healy; Matthee, Conrad A; Barker, Nigel P

2007-08-15

The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns. Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to diverge. This suggests that their

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage

Directory of Open Access Journals (Sweden)

Matthee Conrad A

2007-08-01

Full Text Available Abstract Background The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses, as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns. Results Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to

Optimization of automation: I. Estimation method of cognitive automation rates reflecting the effects of automation on human operators in nuclear power plants

International Nuclear Information System (INIS)

Lee, Seung Min; Kim, Jong Hyun; Seong, Poong Hyun

2014-01-01

Highlights: • We propose an estimation method of the automation rate by taking the advantages of automation as the estimation measures. • We conduct the experiments to examine the validity of the suggested method. • The higher the cognitive automation rate is, the greater the decreased rate of the working time will be. • The usefulness of the suggested estimation method is proved by statistical analyses. - Abstract: Since automation was introduced in various industrial fields, the concept of the automation rate has been used to indicate the inclusion proportion of automation among all work processes or facilities. Expressions of the inclusion proportion of automation are predictable, as is the ability to express the degree of the enhancement of human performance. However, many researchers have found that a high automation rate does not guarantee high performance. Therefore, to reflect the effects of automation on human performance, this paper proposes a new estimation method of the automation rate that considers the effects of automation on human operators in nuclear power plants (NPPs). Automation in NPPs can be divided into two types: system automation and cognitive automation. Some general descriptions and characteristics of each type of automation are provided, and the advantages of automation are investigated. The advantages of each type of automation are used as measures of the estimation method of the automation rate. One advantage was found to be a reduction in the number of tasks, and another was a reduction in human cognitive task loads. The system and the cognitive automation rate were proposed as quantitative measures by taking advantage of the aforementioned benefits. To quantify the required human cognitive task loads and thus suggest the cognitive automation rate, Conant’s information-theory-based model was applied. The validity of the suggested method, especially as regards the cognitive automation rate, was proven by conducting

A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach.

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Faurby, Søren; Svenning, Jens-Christian

2015-03-01

Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups. Copyright © 2014 Elsevier Inc. All rights reserved.

Phylogeny and micro-habitats utilized by lizards determine the composition of their endoparasites in the semiarid Caatinga of Northeast Brazil.

Science.gov (United States)

Brito, S V; Corso, G; Almeida, A M; Ferreira, F S; Almeida, W O; Anjos, L A; Mesquita, D O; Vasconcellos, A

2014-11-01

Trophic networks can have architectonic configurations influenced by historical and ecological factors. The objective of this study was to analyze the architecture of networks between lizards, their endoparasites, diet, and micro-habitat, aiming to understand which factors exert an influence on the composition of the species of parasites. All networks showed a compartmentalized pattern. There was a positive relation between diet and the diversity of endoparasites. Our analyses also demonstrated that phylogeny and the use of micro-habitat influenced the composition of species of endoparasites and diet pattern of lizards. The principal factor that explained the modularity of the network was the foraging strategy, with segregation between the "active foragers" and "sit-and-wait" lizards. Our analyses also demonstrated that historical (phylogeny) and ecological factors (use of micro-habitat by the lizards) influenced the composition of parasite communities. These results corroborate other studies with ectoparasites, which indicate phylogeny and micro-habitat as determinants in the composition of parasitic fauna. The influence of phylogeny can be the result of coevolution between parasites and lizards in the Caatinga, and the influence of micro-habitat should be a result of adaptations of species of parasites to occupy the same categories of micro-habitats as hosts, thus favoring contagion.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

Science.gov (United States)

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

Automated guided vehicle systems a primer with practical applications

CERN Document Server

Ullrich, Günter

2015-01-01

This primer is directed at experts and practitioners in intralogistics who are concerned with optimizing material flows. The presentation is comprehensive covering both, practical and theoretical aspects with a moderate degree of specialization, using clear and concise language. Areas of operation as well as technical standards of all relevant components and functions are described. Recent developments in technology and in the markets are taken into account. The goal of this book is to further stronger use of automated guided transport systems and the enhancement of their future performance.

Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria

Directory of Open Access Journals (Sweden)

Laura J. May-Collado

2015-02-01

Full Text Available Marsupials or metatherians are a group of mammals that are distinct in giving birth to young at early stages of development and in having a prolonged investment in lactation. The group consists of nearly 350 extant species, including kangaroos, koala, possums, and their relatives. Marsupials are an old lineage thought to have diverged from early therian mammals some 160 million years ago in the Jurassic, and have a remarkable evolutionary and biogeographical history, with extant species restricted to the Americas, mostly South America, and to Australasia. Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. Here we present the first Methaterian species-level phylogeny to include 80% of the extant marsupial species and five nuclear and five mitochondrial markers obtained from Genbank and a recently published retroposon matrix. Our primary goal is to provide a summary phylogeny that will serve as a tool for comparative research. We evaluate the extent to which the phylogeny recovers current phylogenetic knowledge based on the recovery of “benchmark clades” from prior studies—unambiguously supported key clades and undisputed traditional taxonomic groups. The Bayesian phylogenetic analyses recovered nearly all benchmark clades but failed to find support for the suborder Phalagiformes. The most significant difference with previous published topologies is the support for Australidelphia as a group containing Microbiotheriidae, nested within American marsupials. However, a likelihood ratio test shows that alternative topologies with monophyletic Australidelphia and Ameridelphia are not significantly different than the preferred tree. Although further data are needed to solidify understanding of Methateria phylogeny, the new phylogenetic hypothesis provided here offers a well

Molecular phylogeny of Systellognatha (Plecoptera: Arctoperlaria) inferred from mitochondrial genome sequences.

Science.gov (United States)

Chen, Zhi-Teng; Zhao, Meng-Yuan; Xu, Cheng; Du, Yu-Zhou

2018-05-01

The infraorder Systellognatha is the most species-rich clade in the insect order Plecoptera and includes six families in two superfamilies: Pteronarcyoidea (Pteronarcyidae, Peltoperlidae, and Styloperlidae) and Perloidea (Perlidae, Perlodidae, and Chloroperlidae). To resolve the debatable phylogeny of Systellognatha, we carried out the first mitochondrial phylogenetic analysis covering all the six families, including three newly sequenced mitogenomes from two families (Perlodidae and Peltoperlidae) and 15 published mitogenomes. The three newly reported mitogenomes share conserved mitogenomic features with other sequenced stoneflies. For phylogenetic analyses, we assembled five datasets with two inference methods to assess their influence on topology and nodal support within Systellognatha. The results indicated that inclusion of the third codon positions of PCGs, exclusion of rRNA genes, the use of nucleotide datasets and Bayesian inference could improve the phylogenetic reconstruction of Systellognatha. The monophyly of Perloidea was supported in the mitochondrial phylogeny, but Pteronarcyoidea was recovered as paraphyletic and remained controversial. In this mitochondrial phylogenetic study, the relationships within Systellognatha were recovered as (((Perlidae + (Perlodidae + Chloroperlidae)) + (Pteronarcyidae + Styloperlidae)) + Peltoperlidae). Copyright © 2018 Elsevier B.V. All rights reserved.

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences.

Science.gov (United States)

Lyra, Goia de M; Costa, Emmanuelle da S; de Jesus, Priscila B; de Matos, João Carlos G; Caires, Taiara A; Oliveira, Mariana C; Oliveira, Eurico C; Xi, Zhenxiang; Nunes, José Marcos de C; Davis, Charles C

2015-04-01

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well-supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae. © 2015 Phycological Society of America.

Process automation

International Nuclear Information System (INIS)

Moser, D.R.

1986-01-01

Process automation technology has been pursued in the chemical processing industries and to a very limited extent in nuclear fuel reprocessing. Its effective use has been restricted in the past by the lack of diverse and reliable process instrumentation and the unavailability of sophisticated software designed for process control. The Integrated Equipment Test (IET) facility was developed by the Consolidated Fuel Reprocessing Program (CFRP) in part to demonstrate new concepts for control of advanced nuclear fuel reprocessing plants. A demonstration of fuel reprocessing equipment automation using advanced instrumentation and a modern, microprocessor-based control system is nearing completion in the facility. This facility provides for the synergistic testing of all chemical process features of a prototypical fuel reprocessing plant that can be attained with unirradiated uranium-bearing feed materials. The unique equipment and mission of the IET facility make it an ideal test bed for automation studies. This effort will provide for the demonstration of the plant automation concept and for the development of techniques for similar applications in a full-scale plant. A set of preliminary recommendations for implementing process automation has been compiled. Some of these concepts are not generally recognized or accepted. The automation work now under way in the IET facility should be useful to others in helping avoid costly mistakes because of the underutilization or misapplication of process automation. 6 figs

Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea).

Science.gov (United States)

Brady, Seán G; Litman, Jessica R; Danforth, Bryan N

2011-09-01

The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when using outgroup versus paralogous rooting. Fifty-two taxa representing each of the seven bee families were sequenced for both copies of EF-1α. Two datasets were analyzed. In the first (the "concatenated" dataset), the F1 and F2 copies for each species were concatenated and the tree was rooted using appropriate outgroups (sphecid and crabronid wasps). In the second dataset (the "duplicated" dataset), the F1 and F2 copies were aligned to each another and each copy for all taxa were treated as separate terminals. In this dataset, the root was placed between the F1 and F2 copies (e.g., paralog rooting). Bayesian analyses demonstrate that the outgroup rooting approach outperforms paralog rooting, recovering deeper clades and showing stronger support for groups well established by both morphological and other molecular data. Sequence characteristics of the two copies were compared at the amino acid level, but little evidence was found to suggest that one copy is more functionally conserved. Although neither approach yields an unambiguous root to the tree, both approaches strongly indicate that the root of bee phylogeny does not fall near Colletidae, as has been previously proposed. We discuss paralog rooting as a general strategy and why this approach performs relatively poorly with our particular dataset. Copyright © 2011 Elsevier Inc. All rights reserved.

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

Science.gov (United States)

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Phylogenetic analysis of pelecaniformes (aves based on osteological data: implications for waterbird phylogeny and fossil calibration studies.

Directory of Open Access Journals (Sweden)

Nathan D Smith

2010-10-01

Full Text Available Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group's fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving and temporal diversification (e.g., the origins of modern families. Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification.Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae, Prophaethon and Lithoptila (successive sister taxa to Phaethontidae, and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae. These relationships are invariant when 'backbone' constraints based on recent avian phylogenies are imposed.Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though

Use of Automated Scoring in Spoken Language Assessments for Test Takers with Speech Impairments. Research Report. ETS RR-17-42

Science.gov (United States)

Loukina, Anastassia; Buzick, Heather

2017-01-01

This study is an evaluation of the performance of automated speech scoring for speakers with documented or suspected speech impairments. Given that the use of automated scoring of open-ended spoken responses is relatively nascent and there is little research to date that includes test takers with disabilities, this small exploratory study focuses…

Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes, Cobitidae)

Czech Academy of Sciences Publication Activity Database

Bohlen, Jörg; Šlechtová, Vendula; Tan, H. H.; Britz, R.

2011-01-01

Roč. 61, č. 3 (2011), s. 854-865 ISSN 1055-7903 R&D Projects: GA ČR GA206/05/2556; GA ČR GA206/08/0637; GA AV ČR IAA600450508; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : pangio * eel loaches * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.609, year: 2011

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

Science.gov (United States)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (lepidoptera: papilionoidea: nymphalidae).

Science.gov (United States)

Shi, Qing-Hui; Sun, Xiao-Yan; Wang, Yun-Liang; Hao, Jia-Sheng; Yang, Qun

2015-01-01

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).

Hardware synthesis from DDL. [Digital Design Language for computer aided design and test of LSI

Science.gov (United States)

Shah, A. M.; Shiva, S. G.

1981-01-01

The details of the digital systems can be conveniently input into the design automation system by means of Hardware Description Languages (HDL). The Computer Aided Design and Test (CADAT) system at NASA MSFC is used for the LSI design. The Digital Design Language (DDL) has been selected as HDL for the CADAT System. DDL translator output can be used for the hardware implementation of the digital design. This paper addresses problems of selecting the standard cells from the CADAT standard cell library to realize the logic implied by the DDL description of the system.

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea).

Science.gov (United States)

Tkach, Vasyl V; Kudlai, Olena; Kostadinova, Aneta

2016-03-01

The Echinostomatoidea is a large, cosmopolitan group of digeneans currently including nine families and 105 genera, the vast majority parasitic, as adults, in birds with relatively few taxa parasitising mammals, reptiles and, exceptionally, fish. Despite the complex structure, diverse content and substantial species richness of the group, almost no attempt has been made to elucidate its phylogenetic relationships at the suprageneric level based on molecules due to the lack of data. Herein, we evaluate the consistency of the present morphology-based classification system of the Echinostomatoidea with the phylogenetic relationships of its members based on partial sequences of the nuclear lsrRNA gene for a broad diversity of taxa (80 species, representing eight families and 40 genera), including representatives of five subfamilies of the Echinostomatidae, which currently exhibits the most complex taxonomic structure within the superfamily. This first comprehensive phylogeny for the Echinostomatoidea challenged the current systematic framework based on comparative morphology. A morphology-based evaluation of this new molecular framework resulted in a number of systematic and nomenclatural changes consistent with the phylogenetic estimates of the generic and suprageneric boundaries and a new phylogeny-based classification of the Echinostomatoidea. In the current systematic treatment: (i) the rank of two family level lineages, the former Himasthlinae and Echinochasminae, is elevated to full family status; (ii) Caballerotrema is distinguished at the family level; (iii) the content and diagnosis of the Echinostomatidae (sensu stricto) (s. str.) are revised to reflect its phylogeny, resulting in the abolition of the Nephrostominae and Chaunocephalinae as synonyms of the Echinostomatidae (s. str.); (iv) Artyfechinostomum, Cathaemasia, Rhopalias and Ribeiroia are re-allocated within the Echinostomatidae (s. str.), resulting in the abolition of the Cathaemasiidae, Rhopaliidae

Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

Directory of Open Access Journals (Sweden)

Ferla Matteo P

2009-01-01

Full Text Available Abstract Background The phylogeny of Eumalacostraca (Crustacea remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders has either combined evidence from multiple loci, or combined molecular and morphological evidence. Results We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades. Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed

Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

Directory of Open Access Journals (Sweden)

Tellier Laurent C

2010-03-01

Full Text Available Abstract Background Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae. Results We identified 347 single nucleotide polymorphisms (SNPs in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication. Conclusions We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.

Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae

Czech Academy of Sciences Publication Activity Database

Dogga, S.K.; Bartošová-Sojková, Pavla; Lukeš, Julius; Soldati-Favre, D.

2015-01-01

Roč. 166, č. 6 (2015), s. 659-676 ISSN 1434-4610 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Apicomplexa * Coccidia * Goussia janae * phylogeny * ultrastructure * invasion * central carbon metabolism. Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed

Czech Academy of Sciences Publication Activity Database

Maslov, D. A.; Votýpka, Jan; Yurchenko, V.; Lukeš, Julius

2013-01-01

Roč. 29, č. 1 (2013), s. 43-52 ISSN 1471-4922 R&D Projects: GA ČR GA204/09/1667 Institutional support: RVO:60077344 Keywords : biodiversity * Kinetoplastea * insect trypanosomatids * monoxenous parasites * phylogeny * taxonomy * Trypanosomatidae Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.217, year: 2013

Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

Czech Academy of Sciences Publication Activity Database

Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

2017-01-01

Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

Identification and phylogeny of the tomato receptor-like proteins family

OpenAIRE

Ermis Yanes-Paz; Gioser María Ramos-Echazábal; Glay Chinea; Yanelis Capdesuñer Ruiz; Ramón Santos Bermúdez

2017-01-01

The receptor-like proteins (RLPs) play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L.) using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between...

EpHLA: an innovative and user-friendly software automating the HLAMatchmaker algorithm for antibody analysis.

Science.gov (United States)

Sousa, Luiz Cláudio Demes da Mata; Filho, Herton Luiz Alves Sales; Von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; Neto, Pedro de Alcântara dos Santos; de Castro, José Adail Fonseca; do Monte, Semíramis Jamil Hadad

2011-12-01

The global challenge for solid organ transplantation programs is to distribute organs to the highly sensitized recipients. The purpose of this work is to describe and test the functionality of the EpHLA software, a program that automates the analysis of acceptable and unacceptable HLA epitopes on the basis of the HLAMatchmaker algorithm. HLAMatchmaker considers small configurations of polymorphic residues referred to as eplets as essential components of HLA-epitopes. Currently, the analyses require the creation of temporary files and the manual cut and paste of laboratory tests results between electronic spreadsheets, which is time-consuming and prone to administrative errors. The EpHLA software was developed in Object Pascal programming language and uses the HLAMatchmaker algorithm to generate histocompatibility reports. The automated generation of reports requires the integration of files containing the results of laboratory tests (HLA typing, anti-HLA antibody signature) and public data banks (NMDP, IMGT). The integration and the access to this data were accomplished by means of the framework called eDAFramework. The eDAFramework was developed in Object Pascal and PHP and it provides data access functionalities for software developed in these languages. The tool functionality was successfully tested in comparison to actual, manually derived reports of patients from a renal transplantation program with related donors. We successfully developed software, which enables the automated definition of the epitope specificities of HLA antibodies. This new tool will benefit the management of recipient/donor pairs selection for highly sensitized patients. Copyright © 2011 Elsevier B.V. All rights reserved.

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

Science.gov (United States)

Sims, Gregory E.; Kim, Sung-Hou

2011-01-01

A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (∼0.56 million features), which account for ∼69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup. PMID:21536867

A mitochondrial DNA phylogeny of the endangered vipers of the Vipera ursinii complex

Czech Academy of Sciences Publication Activity Database

Gvoždík, Václav; Jandzik, D.; Cordos, B.; Řehák, I.; Kotlík, Petr

2012-01-01

Roč. 62, č. 3 (2012), s. 1019-1024 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : Conservation * Meadow viper * Phylogeny * Steppe viper * Systematics * Vipera ursinii complex Subject RIV: EH - Ecology, Behaviour Impact factor: 4.066, year: 2012

Automated Verification of Quantum Protocols using MCMAS

Directory of Open Access Journals (Sweden)

F. Belardinelli

2012-07-01

Full Text Available We present a methodology for the automated verification of quantum protocols using MCMAS, a symbolic model checker for multi-agent systems The method is based on the logical framework developed by D'Hondt and Panangaden for investigating epistemic and temporal properties, built on the model for Distributed Measurement-based Quantum Computation (DMC, an extension of the Measurement Calculus to distributed quantum systems. We describe the translation map from DMC to interpreted systems, the typical formalism for reasoning about time and knowledge in multi-agent systems. Then, we introduce dmc2ispl, a compiler into the input language of the MCMAS model checker. We demonstrate the technique by verifying the Quantum Teleportation Protocol, and discuss the performance of the tool.

Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.

Science.gov (United States)

Qiu, Dajun; Huang, Liangmin; Liu, Sheng; Zhang, Huan; Lin, Senjie

2013-01-01

Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.

Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.

Directory of Open Access Journals (Sweden)

Dajun Qiu

Full Text Available Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium. Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.

Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family.

Science.gov (United States)

Germot, A; Philippe, H

1999-01-01

Trichomonads, together with diplomonads and microsporidia, emerge at the base of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny. However, phylogenies based on protein sequences such as tubulin are markedly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could be a reliable phylogenetic marker. In eukaryotes, HSP70s are found in cytosol, endoplasmic reticulum, and organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly complete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitochondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters considered. Almost all the undoubtedly monophyletic groups, defined by ultrastructural characters, were recovered. However, due to the long branch attraction phenomenon, the evolutionary rates were the main factor determining the position of species, even with the use of a close outgroup, which is an important advantage of HSP70 with respect to many other markers. Numerous variable sites are peculiar to Trichomonas and probably generated the artefactual placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of species; and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.

AUTOMATING THE DATA SECURITY PROCESS

Directory of Open Access Journals (Sweden)

Florin Ogigau-Neamtiu

2017-11-01

Full Text Available Contemporary organizations face big data security challenges in the cyber environment due to modern threats and actual business working model which relies heavily on collaboration, data sharing, tool integration, increased mobility, etc. The nowadays data classification and data obfuscation selection processes (encryption, masking or tokenization suffer because of the human implication in the process. Organizations need to shirk data security domain by classifying information based on its importance, conduct risk assessment plans and use the most cost effective data obfuscation technique. The paper proposes a new model for data protection by using automated machine decision making procedures to classify data and to select the appropriate data obfuscation technique. The proposed system uses natural language processing capabilities to analyze input data and to select the best course of action. The system has capabilities to learn from previous experiences thus improving itself and reducing the risk of wrong data classification.

Models, Languages and Logics for Concurrent Distributed Systems

DEFF Research Database (Denmark)

The EEC Esprit Basic Research Action No 3011, Models, Languages and Logics for Con current Distributed Systems, CEDISYS, held its second workshop at Aarhus University in May, l991, following the successful workshop in San Miniato in 1990. The Aarhus Workshop was centered around CEDISYS research...... activities, and the selected themes of Applications and Automated Tools in the area of Distributed Systerns. The 24 participants were CEDISYS partners, and invited guests with expertise on the selected themes. This booklet contains the program of the workshop, short abstracts for the talks presented...

High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses

NARCIS (Netherlands)

Barry, A.F.; Durães-Carvalho, R.; Oliveira-Filho, Edmilson F.; Alfieri, A.; Poel, Van der W.H.M.

2017-01-01

The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses

Phylogeny and resistance profiles of HIV-1 POL sequences from rectal biopsies and blood

DEFF Research Database (Denmark)

Katzenstein, Terese Lea; Petersen, A B; Storgaard, M

2010-01-01

The phylogeny and resistance profiles of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) sequences were compared among six patients with HIV-1 who had received numerous treatments. RNA and DNA fractions were obtained from concurrent blood and rectal biopsy...

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.

Science.gov (United States)

Chen, Meng-Yun; Liang, Dan; Zhang, Peng

2015-11-01

Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bootstrapping phylogenies inferred from rearrangement data

Directory of Open Access Journals (Sweden)

Lin Yu

2012-08-01

Full Text Available Abstract Background Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. Results We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Conclusions Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its

Bootstrapping phylogenies inferred from rearrangement data.

Science.gov (United States)

Lin, Yu; Rajan, Vaibhav; Moret, Bernard Me

2012-08-29

Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver

Text mining from ontology learning to automated text processing applications

CERN Document Server

Biemann, Chris

2014-01-01

This book comprises a set of articles that specify the methodology of text mining, describe the creation of lexical resources in the framework of text mining and use text mining for various tasks in natural language processing (NLP). The analysis of large amounts of textual data is a prerequisite to build lexical resources such as dictionaries and ontologies and also has direct applications in automated text processing in fields such as history, healthcare and mobile applications, just to name a few. This volume gives an update in terms of the recent gains in text mining methods and reflects

Sistema de resum automàtic accessible via web service

OpenAIRE

Pedrajas Pérez, Samuel

2015-01-01

En este proyecto se presenta un sistema de resumen automático que utiliza el método de las cadenas léxicas. Se ha implementado como un módulo para FreeLing, que es una librería open source de análisis lingüístico, y hecho accesible vía web service en TextServer, la plataforma de webservices de TALP. In this project an automatic summarization system which uses the lexical chain method is shown. It has been implemented as a module for FreeLing, an open source language analysis tool suite, an...

CULTURE AND TECHNOLOGY: AUTOMATION IN THE CREATIVE PROCESSES OF NARRATIVE

Directory of Open Access Journals (Sweden)

Fernando Fogliano

2013-12-01

Full Text Available The objective here is to think on the problem raised by the progressively opaque presence of technology in the contemporary artistic production. Automation is the most evident aspect of technology of devices used for production, post-production and dissemination of this cultural activity. Along the text the philosophers Vilém Flusser and Gilbert Simon are put in confrontation so that a more profound insight can be obtained. Language is considered here as the integrative factor in the search for a new convergent conceptual scenario that enable us understand the consequences of the technological convergence

Lean automation development : applying lean principles to the automation development process

OpenAIRE

Granlund, Anna; Wiktorsson, Magnus; Grahn, Sten; Friedler, Niklas

2014-01-01

By a broad empirical study it is indicated that automation development show potential of improvement. In the paper, 13 lean product development principles are contrasted to the automation development process and it is suggested why and how these principles can facilitate, support and improve the automation development process. The paper summarises a description of what characterises a lean automation development process and what consequences it entails. Main differences compared to current pr...

Automated Narratives and Journalistic Text Generation: The Lead Organization Structure Translated into Code.

Directory of Open Access Journals (Sweden)

Márcio Carneiro dos Santos

2016-07-01

Full Text Available It describes the experiment of building a software capable of generating leads and newspaper titles in an automated fashion from information obtained from the Internet. The theoretical possibility Lage already provided by the end of last century is based on relatively rigid and simple structure of this type of story construction, which facilitates the representation or translation of its syntax in terms of instructions that the computer can execute. The paper also discusses the relationship between society, technique and technology, making a brief history of the introduction of digital solutions in newsrooms and their impacts. The development was done with the Python programming language and NLTK- Natural Language Toolkit library - and used the results of the Brazilian Soccer Championship 2013 published on an internet portal as a data source.

Automated [inservice testing] IST program

International Nuclear Information System (INIS)

Wright, W.M.

1990-01-01

There are two methods used to manage a Section XI program: Manual and Automated. The manual method usually consists of hand written records of test results and scheduling requirements. This method while initially lower in cost, results in problems later on in the life of a plant as data continues to accumulate. Automation allows instant access to forty years of test results. Due to the lower cost and higher performance of todays' personal computers, an automated method via a computer program provides an excellent method for managing the vast amount of data that accumulates over the forty year life of a plant. Through the use of a computer, special functions involving this data are available, which through a manual method would not be practical. This paper will describe some of the advantages in using a computer program to manage the Section XI 1ST program. The ISTBASE consists of program code and numerous databases. The source code is written and complied in CLIPPER (tm) language. Graphing routines are performed by dGE (tm) graphics library. Graphs are displayed in EGA form. Since it was estimated that the total complied code, would exceed 640K of ram, overlays through the use of modular programming were used to facilitate the DOS restrictions of 640K ram. The use of overlays still require the user to gain access to ISTBASE through the PASSWORD module. The database files are designed to be compatible with dBASE III+ (tm) data structure. This allows transfer of data between ISTBASE and other database managers/applications. A math co-processor is utilized to speed up calculations on graphs and other mathematical calculations. Program code and data files require a hard disk drive with at least 28 Meg capacity. While ISTBASE will execute on a 8088 based computer, an 80286 computer with a 12 MHz operating speed should be considered the minimum system configuration

Both Automation and Paper.

Science.gov (United States)

Purcell, Royal

1988-01-01

Discusses the concept of a paperless society and the current situation in library automation. Various applications of automation and telecommunications are addressed, and future library automation is considered. Automation at the Monroe County Public Library in Bloomington, Indiana, is described as an example. (MES)

Representing and computing regular languages on massively parallel networks

Energy Technology Data Exchange (ETDEWEB)

Miller, M.I.; O' Sullivan, J.A. (Electronic Systems and Research Lab., of Electrical Engineering, Washington Univ., St. Louis, MO (US)); Boysam, B. (Dept. of Electrical, Computer and Systems Engineering, Rensselaer Polytechnic Inst., Troy, NY (US)); Smith, K.R. (Dept. of Electrical Engineering, Southern Illinois Univ., Edwardsville, IL (US))

1991-01-01

This paper proposes a general method for incorporating rule-based constraints corresponding to regular languages into stochastic inference problems, thereby allowing for a unified representation of stochastic and syntactic pattern constraints. The authors' approach first established the formal connection of rules to Chomsky grammars, and generalizes the original work of Shannon on the encoding of rule-based channel sequences to Markov chains of maximum entropy. This maximum entropy probabilistic view leads to Gibb's representations with potentials which have their number of minima growing at precisely the exponential rate that the language of deterministically constrained sequences grow. These representations are coupled to stochastic diffusion algorithms, which sample the language-constrained sequences by visiting the energy minima according to the underlying Gibbs' probability law. The coupling to stochastic search methods yields the all-important practical result that fully parallel stochastic cellular automata may be derived to generate samples from the rule-based constraint sets. The production rules and neighborhood state structure of the language of sequences directly determines the necessary connection structures of the required parallel computing surface. Representations of this type have been mapped to the DAP-510 massively-parallel processor consisting of 1024 mesh-connected bit-serial processing elements for performing automated segmentation of electron-micrograph images.

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

Science.gov (United States)

Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

2016-01-01

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

Automated Groundwater Screening

International Nuclear Information System (INIS)

Taylor, Glenn A.; Collard, Leonard B.

2005-01-01

The Automated Intruder Analysis has been extended to include an Automated Ground Water Screening option. This option screens 825 radionuclides while rigorously applying the National Council on Radiation Protection (NCRP) methodology. An extension to that methodology is presented to give a more realistic screening factor for those radionuclides which have significant daughters. The extension has the promise of reducing the number of radionuclides which must be tracked by the customer. By combining the Automated Intruder Analysis with the Automated Groundwater Screening a consistent set of assumptions and databases is used. A method is proposed to eliminate trigger values by performing rigorous calculation of the screening factor thereby reducing the number of radionuclides sent to further analysis. Using the same problem definitions as in previous groundwater screenings, the automated groundwater screening found one additional nuclide, Ge-68, which failed the screening. It also found that 18 of the 57 radionuclides contained in NCRP Table 3.1 failed the screening. This report describes the automated groundwater screening computer application

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.

Science.gov (United States)

Zeng, Liping; Zhang, Ning; Zhang, Qiang; Endress, Peter K; Huang, Jie; Ma, Hong

2017-05-01

Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity.

Science.gov (United States)

Marx, Felix G; Fordyce, R Ewan

2015-04-01

A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36-30 Ma), a shift towards bulk filter-feeding (30-23 Ma) and a climate-driven diversity loss around 3 Ma. Evolutionary rates and disparity were high following the origin of mysticetes around 38 Ma, coincident with global cooling, abrupt Southern Ocean eutrophication and the development of the Antarctic Circumpolar Current (ACC). Subsequently, evolutionary rates and disparity fell, becoming nearly constant after approximately 23 Ma as the ACC reached its full strength. By contrast, species diversity rose until 15 Ma and then remained stable, before dropping sharply with the onset of Northern Hemisphere glaciation. This decline coincided with the final establishment of modern mysticete gigantism and may be linked to glacially driven variability in the distribution of shallow habitats or an increased need for long-distance migration related to iron-mediated changes in glacial marine productivity.

Phylogeny of Bembidion and related ground beetles (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidiina).

Science.gov (United States)

Maddison, David R

2012-06-01

The phylogeny of the large genus Bembidion and related genera is inferred from four nuclear protein-coding genes (CAD, wingless, arginine kinase, and topoisomerase I), ribosomal DNA (28S and 18S), and the mitochondrial gene cytochrome oxidase I (COI). 230 of the more than 1200 species of Bembidion are sampled, as well as 26 species of five related genera, and 14 outgroups. Nuclear copies (numts) of COI were found sparsely scattered through sampled species. The resulting phylogeny, based upon individual gene analyses and combined analyses using maximum likelihood and parsimony, is very well supported at most nodes. Additional analyses explored the evidence, and corroborate the phylogeny. Seven analyses, each with one of the seven genes removed from the combined matrix, were also conducted, and yielded maximum likelihood bootstrap trees sharing over 92% of their nodes with the original, well-resolved bootstrap trees based on the complete set of seven genes. All key nodes were present in all seven analyses missing a single gene, indicating that support for these nodes comes from at least two genes. In addition, the inferred maximum likelihood tree based on the combined matrix is well-behaved and self-predicting, in that simulated evolution of sequences on the inferred tree under the inferred model of evolution yields a matrix from which all but one of the model tree's clades are recovered with bootstrap value >50, suggesting that internal branches in the tree may be of a length to yield sequences sufficient to allow their inference. All likelihood analyses were conducted under both a proportion-invariable plus gamma site-to-site rate variation model, as well as a simpler gamma model. The choice of model did not have a major effect on inferred phylogenies or their bootstrap values. The inferred phylogeny shows that Bembidarenas is not closely related to Bembidiina, and Phrypeus is likely distant as well; the remaining genera of Bembidiina form a monophyletic group

Haemoprotozoa: Making biological sense of molecular phylogenies

Directory of Open Access Journals (Sweden)

Peter O'Donoghue

2017-12-01

Full Text Available A range of protistan parasites occur in the blood of vertebrates and are transmitted by haematophagous invertebrate vectors. Some 48 genera are recognized in bood primarily on the basis of parasite morphology and host specificity; including extracellular kinetoplastids (trypanosomatids and intracellular apicomplexa (haemogregarines, haemococcidia, haemosporidia and piroplasms. Gene sequences are available for a growing number of species and molecular phylogenies often link parasite and host or vector evolution. This review endeavours to reconcile molecular clades with biological characters. Four major trypanosomatid clades have been associated with site of development in the vector: salivarian or stercorarian for Trypanosoma, and supra- or peri-pylorian for Leishmania. Four haemogregarine clades have been associated with acarine vectors (Hepatozoon A and B, Karyolysus, Hemolivia and another two with leeches (Dactylosoma, Haemogregarina sensu stricto. Two haemococcidian clades (Lankesterella, Schellackia using leeches and mosquitoes (as paratenic hosts! were paraphyletic with monoxenous enteric coccidia. Two major haemosporidian clades have been associated with mosquito vectors (Plasmodium from mammals, Plasmodium from birds and lizards, two with midges (Hepatocystis from bats, Parahaemoproteus from birds and two with louse-flies and black-flies (Haemoproteus and Leucocytozoon from birds. Three major piroplasm clades were recognized: one associated with transovarian transmission in ticks (Babesia sensu stricto; one with pre-erythrocytic schizogony in vertebrates (Theileria/Cytauxzoon; and one with neither (Babesia sensu lato. Broad comparative studies with allied groups suggest that trypanosomatids and haemogregarines evolved first in aquatic and then terrestrial environments, as evidenced by extant lineages in invertebrates and their radiation in vertebrates. In contrast, haemosporidia and haemococcidia are thought to have evolved first in

Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

Czech Academy of Sciences Publication Activity Database

Doležalová, J.; Vallo, Peter; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, M.; Lukeš, J.; Scholz, T.; Modrý, D.

2015-01-01

Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA ČR GA524/06/0264; GA ČR GA206/09/0927 Institutional support: RVO:68081766 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

New insights in Russula subsect. Rubrinae: phylogeny and the quest for synapomorphic characters

Czech Academy of Sciences Publication Activity Database

Caboň, M.; Eberhardt, U.; Looney, B.; Hampe, F.; Kolařík, Miroslav; Jančovičová, S.; Verbeken, A.; Adamčík, S.

2017-01-01

Roč. 16, č. 9 (2017), s. 877-892 ISSN 1617-416X Grant - others:AV ČR(CZ) SAV-16-06 Program:Bilaterální spolupráce Institutional support: RVO:61388971 Keywords : Sulphovanillin * Incrustations * Multi-locus phylogeny Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.616, year: 2016

BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

Directory of Open Access Journals (Sweden)

Lin Kui

2007-07-01

Full Text Available Abstract Background Overlapping genes (OGs in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest. Description BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ and Unweighted Pair-Group Method using Arithmetic averages (UPGMA. Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint. Conclusion BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by

Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae).

Science.gov (United States)

Martin, Gavin J; Branham, Marc A; Whiting, Michael F; Bybee, Seth M

2017-02-01

Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis. Copyright © 2016 Elsevier Inc. All rights reserved.

A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation.

Science.gov (United States)

Russello, Michael A; Amato, George

2004-02-01

Amazon parrots (Genus Amazona) are among the most recognizable and imperiled of all birds. Several hypotheses regarding the evolutionary history of Amazona are investigated using a combined phylogenetic analysis of DNA sequence data from six partitions including mitochondrial (COI, 12S, and 16S) and nuclear (beta-fibint7, RP40, and TROP) regions. The results demonstrate that Amazona is not monophyletic with respect to the placement of the Yellow-faced parrot (Amazona xanthops), as first implied by. In addition, the analysis corroborates previous studies suggesting a Neotropical short-tailed parrot genus as sister to Amazona. At a finer level, the phylogeny resolves the Greater Antillean endemic species as constituting a monophyletic group, including the Central American Amazona albifrons, while further revealing a paraphyletic history for the extant Amazon species of the Lesser Antilles. The reconstructed phylogeny provides further insights into the mainland sources of the Antillean Amazona, reveals areas of taxonomic uncertainty within the genus, and presents historical information that may be included in conservation priority-setting for Amazon parrots.

Applications of Dynamic Deployment of Services in Industrial Automation

Science.gov (United States)

Candido, Gonçalo; Barata, José; Jammes, François; Colombo, Armando W.

Service-oriented Architecture (SOA) is becoming a de facto paradigm for business and enterprise integration. SOA is expanding into several domains of application envisioning a unified solution suitable across all different layers of an enterprise infrastructure. The application of SOA based on open web standards can significantly enhance the interoperability and openness of those devices. By embedding a dynamical deployment service even into small field de- vices, it would be either possible to allow machine builders to place built- in services and still allow the integrator to deploy on-the-run the services that best fit his current application. This approach allows the developer to keep his own preferred development language, but still deliver a SOA- compliant application. A dynamic deployment service is envisaged as a fundamental framework to support more complex applications, reducing deployment delays, while increasing overall system agility. As use-case scenario, a dynamic deployment service was implemented over DPWS and WS-Management specifications allowing designing and programming an automation application using IEC61131 languages, and deploying these components as web services into devices.

An alu-based phylogeny of lemurs (infraorder: Lemuriformes.

Directory of Open Access Journals (Sweden)

Adam T McLain

Full Text Available LEMURS (INFRAORDER: Lemuriformes are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55-60 million years ago (mya. Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs, to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the

Neural systems language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity.

Science.gov (United States)

Brown, Ramsay A; Swanson, Larry W

2013-09-01

Systematic description and the unambiguous communication of findings and models remain among the unresolved fundamental challenges in systems neuroscience. No common descriptive frameworks exist to describe systematically the connective architecture of the nervous system, even at the grossest level of observation. Furthermore, the accelerating volume of novel data generated on neural connectivity outpaces the rate at which this data is curated into neuroinformatics databases to synthesize digitally systems-level insights from disjointed reports and observations. To help address these challenges, we propose the Neural Systems Language (NSyL). NSyL is a modeling language to be used by investigators to encode and communicate systematically reports of neural connectivity from neuroanatomy and brain imaging. NSyL engenders systematic description and communication of connectivity irrespective of the animal taxon described, experimental or observational technique implemented, or nomenclature referenced. As a language, NSyL is internally consistent, concise, and comprehensible to both humans and computers. NSyL is a promising development for systematizing the representation of neural architecture, effectively managing the increasing volume of data on neural connectivity and streamlining systems neuroscience research. Here we present similar precedent systems, how NSyL extends existing frameworks, and the reasoning behind NSyL's development. We explore NSyL's potential for balancing robustness and consistency in representation by encoding previously reported assertions of connectivity from the literature as examples. Finally, we propose and discuss the implications of a framework for how NSyL will be digitally implemented in the future to streamline curation of experimental results and bridge the gaps among anatomists, imagers, and neuroinformatics databases. Copyright © 2013 Wiley Periodicals, Inc.

IFLA General Conference, 1986. Pre-Conference Seminar on Automated Systems for Access to Multilingual and Multiscript Library materials: Problems and Solutions. Papers.

Science.gov (United States)

International Federation of Library Associations and Institutions, The Hague (Netherlands).

A seminar which considered problems and solutions regarding automated systems for access to multilingual and multiscript library materials was held as a pre-session before the IFLA general conference in 1986. Papers presented include: (1) "Romanized and Transliterated Databases of Asian Language Materials--History, Problems, and…

A dated phylogeny complements macroecological analysis to explain the diversity patterns in Geonoma (Arecaceae)

DEFF Research Database (Denmark)

Roncal, Julissa; Overgaard, Anne Blach; Borchsenius, Finn

2011-01-01

pattern. To test for a time-for-diversification effect, we correlated four different species richness measures with the diversification time of the earliest large lineage that is characteristic of each cluster. In support of this hypothesis, we found that geographic areas with higher richness contained...... coherent floristic clusters. We then evaluated the extent to which the spatial variation in species composition reflects present-day environmental variation vs. nonenvironmental spatial effects, as expected if the pattern reflects historical biogeography. We also examined the degree of geographic structure...... in the Geonoma phylogeny. Finally, we used a dated phylogeny to assess whether species richness within the floristic clusters was constrained by a specific historical biogeographic driver, namely time-for-diversification. A cluster analysis identified six spatially coherent floristic clusters, four of which were...

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

Science.gov (United States)

Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

2017-04-01

Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

[Understand the neurodevelopment of language: a necessity to prevent learning disabilities in children].

Science.gov (United States)

Charollais, A; Marret, S; Stumpf, M-H; Lemarchand, M; Delaporte, B; Philip, E; Monom-Diverre; Guillois, B; Datin-Dorriere, V; Debillon, T; Simon, M-J; De Barace, C; Pasquet, F; Saliba, E; Zebhib, R

2013-09-01

Clinical and radiological knowledge of language development in the former premature infant compared to the newborn allows us to argue for exploration of the sensorimotor co-factors required for proper language development. There are early representations of the maternal language in the infant's visual, auditory, and sensorimotor areas, activated or stabilized by orofacial and articulatory movements. The functional architecture of language is different for vulnerable children such as premature infants. We have already mentioned the impact of early dysfunction of the facial praxis fine motor skills in this population presenting comprehension disorders. A recent meta-analysis confirms the increasing difficulty of understanding between 3 and 12 years, questioning the quality of the initial linguistic processes. A precise analysis of language, referenced from 3 years of age, should be completed by sensorimotor tests to assess possible constraints in automating neurolinguistic foundations. The usual assessment at this age can exclude sensory disturbances and communication and offers guidance and socialization. However, a recent study shows the ineffectiveness of "language-reinforced immersion" at 2 and 3 years in a population of vulnerable children. The LAMOPRESCO study of language and motor skills in the premature infant (National PHRC 2010) has assessed language and sensorimotor skills of preterm-born (theory of speech perception." Early and accurate assessment of language and the patient's constraints should differentiate and specify management strategies for all children, whatever their background and pathologies. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Using the Language Environment Analysis (LENA) system in preschool classrooms with children with autism spectrum disorders.

Science.gov (United States)

Dykstra, Jessica R; Sabatos-Devito, Maura G; Irvin, Dwight W; Boyd, Brian A; Hume, Kara A; Odom, Sam L

2013-09-01

This study describes the language environment of preschool programs serving children with autism spectrum disorders (ASDs) and examines relationships between child characteristics and an automated measure of adult and child language in the classroom. The Language Environment Analysis (LENA) system was used with 40 children with ASD to collect data on adult and child language. Standardized assessments were administered to obtain language, cognitive, and autism severity scores for participants. With a mean of over 5 hours of recording across two days several months apart, there was a mean of 3.6 child vocalizations per minute, 1.0 conversational turns (in which either the adult or child respond to the other within 5 seconds) per minute, and 29.2 adult words per minute. Two of the three LENA variables were significantly correlated with language age-equivalents. Cognitive age-equivalents were also significantly correlated with two LENA variables. Autism Diagnostic Observation Schedule severity scores and LENA variables were not significantly correlated. Implications for using the LENA system with children with ASD in the school environment are discussed.

Higher-level molecular phylogeny of the water mites (Acariformes: Prostigmata: Parasitengonina: Hydrachnidiae).

Science.gov (United States)

Dabert, Miroslawa; Proctor, Heather; Dabert, Jacek

2016-08-01

With nearly 6000 named species, water mites (Hydrachnidiae) represent the largest group of arachnids to have invaded and extensively diversified in freshwater habitats. Water mites together with three other lineages (the terrestrial Erythraiae and Trombidiae, and aquatic Stygothrombiae), make up the hyporder Parasitengonina, which is characterized by having parasitic larvae and predatory nymphs and adults. Relationships between the Hydrachnidiae and other members of the Parasitengonina are unclear, as are relationships among the major lineages of water mites. Monophyly of water mites has been asserted, with the possible exception of the morphologically distinctive Hydrovolzioidea. Here we infer the phylogeny of water mites using multiple molecular markers and including representatives of all superfamilies of Hydrachnidiae and of almost all other Parasitengonina. Our results support a monophyletic Parasitengonina including Trombidiae, Stygothrombiae, and Hydrachnidiae. A monophyletic Hydrachnidiae, including Hydrovolzioidea, is strongly supported. Terrestrial Parasitengonina do not form a monophyletic sister group to water mites. Stygothrombiae is close to water mites but is not nested within this clade. Water mites appear to be derived from ancestors close to Stygothrombiae or the erythraoid group Calyptostomatoidea; however, this relationship is not clear because of extremely short branches in this part of the parasitengonine tree. We recovered with strong support all commonly accepted water mite superfamilies except for Hydryphantoidea, which is clearly paraphyletic. Our data support the previously proposed clades Protohydrachnidia (Hydrovolzioidea and Eylaoidea), Euhydrachnidia (all remaining superfamilies), and the euhydrachnid subclade Neohydrachnidia (Lebertioidea, Hydrachnoidea, Hygrobatoidea, and Arrenuroidea). We found that larval leg structure and locomotory behavior are strongly congruent with the molecular phylogeny. Other morphological and behavioral

Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

Czech Academy of Sciences Publication Activity Database

Doležalová, J.; Vallo, P.; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, Milan; Lukeš, Julius; Scholz, Tomáš; Modrý, David

2015-01-01

Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR GA206/09/0927 Institutional support: RVO:60077344 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

Automated model building

CERN Document Server

Caferra, Ricardo; Peltier, Nicholas

2004-01-01

This is the first book on automated model building, a discipline of automated deduction that is of growing importance Although models and their construction are important per se, automated model building has appeared as a natural enrichment of automated deduction, especially in the attempt to capture the human way of reasoning The book provides an historical overview of the field of automated deduction, and presents the foundations of different existing approaches to model construction, in particular those developed by the authors Finite and infinite model building techniques are presented The main emphasis is on calculi-based methods, and relevant practical results are provided The book is of interest to researchers and graduate students in computer science, computational logic and artificial intelligence It can also be used as a textbook in advanced undergraduate courses

Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

Science.gov (United States)

Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

2015-10-30

Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

DISTRIBUTION, MORPHOLOGY, AND PHYLOGENY OF KLEBSORMIDIUM (KLEBSORMIDIALES, CHAROPHYCEAE) IN URBAN ENVIRONMENTS IN EUROPE(1).

Science.gov (United States)

Rindi, Fabio; Guiry, Michael D; López-Bautista, Juan M

2008-12-01

Klebsormidium is a cosmopolitan genus of green algae, widespread in terrestrial and freshwater habitats. The classification of Klebsormidium is entirely based on morphological characters, and very little is understood about its phylogeny at the species level. We investigated the diversity and phylogenetic relationships of Klebsormidium in urban habitats in Europe by a combination of approaches including examination of field-collected material, culture experiments conducted in many different combinations of factors, and phylogenetic analyses of the rbcL gene. Klebsormidium in European cities mainly occurs at the base of old walls, where it may produce green belts up to several meters in extent. Specimens from different cities showed a great morphological uniformity, consisting of long filaments 6-9 μm in width, with thin-walled cylindrical cells and smooth wall, devoid of false branches, H-shaped pieces, and biseriate parts. Conversely, the rbcL phylogeny showed a higher genetic diversity than expected from morphology. The strains were separated in four different clades supported by high bootstrap values and posterior probabilities. In culture, these clades differed in several characters, such as production of a superficial hydro-repellent layer, tendency to break into short fragments, and inducibility of zoosporulation. On the basis of the taxonomic information available in the literature, most strains could not be identified unambiguously at the species level. The rbcL phylogeny showed no correspondence with classification based on morphology and suggested that the identity of many species, in particular the type species K. flaccidum (kütz.) P.C. Silva, Mattox et W. H. Blackw., needs critical reassessment. © 2008 Phycological Society of America.

Chromosome phylogenies of man, great apes, and Old World monkeys.

Science.gov (United States)

De Grouchy, J

1987-08-31

The karyotypes of man and of the closely related Pongidae--chimpanzee, gorilla, and orangutan--differ by a small number of well known rearrangements, mainly pericentric inversions and one fusion which reduced the chromosome number from 48 in the Pongidae to 46 in man. Dutrillaux et al. (1973, 1975, 1979) reconstructed the chromosomal phylogeny of the entire primate order. More and more distantly related species were compared thus moving backward in evolution to the common ancestors of the Pongidae, of the Cercopithecoidae, the Catarrhini, the Platyrrhini, the Prosimians, and finally the common ancestor of all primates. Descending the pyramid it becomes possible to assign the rearrangements that occurred in each phylum, and the one that led to man in particular. The main conclusions are that this phylogeny is compatible with the occurrence during evolution of simple chromosome rearrangements--inversions, fusions, reciprocal translocation, acquisition or loss of heterochromatin--and that it is entirely consistent with the known primate phylogeny based on physical morphology and molecular evolution. If heterochromatin is not taken into account, man has in common with the other primates practically all of his chromosomal material as determined by chromosome banding. However, it is arranged differently, according to species, on account of chromosome rearrangements. This interpretation has been confirmed by comparative gene mapping, which established that the same chromosome segments, identified by banding, carry the same genes (Finaz et al., 1973; Human Gene Mapping 8, 1985). A remarkable observation made by Dutrillaux is that different primate phyla seem to have adopted different chromosome rearrangements in the course of evolution: inversions for the Pongidae, Robertsonian fusions for the lemurs, etc. This observation may raise many questions, among which is that of an organized evolution. Also, the breakpoints of chromosomal rearrangements observed during evolution

Language Teachers' Target Language Project: Language for Specific Purposes of Language Teaching

Science.gov (United States)

Korenev, Alexey; Westbrook, Carolyn; Merry, Yvonne; Ershova, Tatiana

2016-01-01

The Language Teachers' Target Language project (LTTL) aims to describe language teachers' target language use domain (Bachman & Palmer 2010) and to develop a language test for future teachers of English. The team comprises four researchers from Moscow State University (MSU) and Southampton Solent University.

Application of the informational reference system OZhUR to the automated processing of data from satellites of the Kosmos series

Science.gov (United States)

Pokras, V. M.; Yevdokimov, V. P.; Maslov, V. D.

1978-01-01

The structure and potential of the information reference system OZhUR designed for the automated data processing systems of scientific space vehicles (SV) is considered. The system OZhUR ensures control of the extraction phase of processing with respect to a concrete SV and the exchange of data between phases.The practical application of the system OZhUR is exemplified in the construction of a data processing system for satellites of the Cosmos series. As a result of automating the operations of exchange and control, the volume of manual preparation of data is significantly reduced, and there is no longer any need for individual logs which fix the status of data processing. The system Ozhur is included in the automated data processing system Nauka which is realized in language PL-1 in a binary one-address system one-state (BOS OS) electronic computer.

Data partitions, Bayesian analysis and phylogeny of the zygomycetous fungal family Mortierellaceae, inferred from nuclear ribosomal DNA sequences.

Directory of Open Access Journals (Sweden)

Tamás Petkovits

Full Text Available Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values, implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae.

Directory of Open Access Journals (Sweden)

C Haris Saslis-Lagoudakis

Full Text Available The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae. We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae).

Science.gov (United States)

Saslis-Lagoudakis, C Haris; Klitgaard, Bente B; Forest, Félix; Francis, Louise; Savolainen, Vincent; Williamson, Elizabeth M; Hawkins, Julie A

2011-01-01

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce. In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships. This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into

78 FR 53466 - Modification of Two National Customs Automation Program (NCAP) Tests Concerning Automated...

Science.gov (United States)

2013-08-29

... Customs Automation Program (NCAP) Tests Concerning Automated Commercial Environment (ACE) Document Image... National Customs Automation Program (NCAP) tests concerning document imaging, known as the Document Image... the National Customs Automation Program (NCAP) tests concerning document imaging, known as the...

Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

Science.gov (United States)

Herrera, James P; Dávalos, Liliana M

2016-09-01

Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Molecular phylogeny of Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae).

Science.gov (United States)

Wells, J D; Sperling, F A

1999-05-01

Mitochondrial DNA was used to infer the phylogeny and genetic divergences of Chrysomya albiceps (Wiedemann) and C. rufifacies (Maquart) specimens from widely separated localities in the Old and New World. Analyses based on a 2.3-kb region including the genes for cytochrome oxidase subunits I and II indicated that the 2 species were separate monophyletic lineages that have been separated for > 1 million years. Analysis of DNA, in the form of either sequence or restriction fragment-length polymorphism (RFLP) data, will permit the identification of problematic specimens.

Optimization of automation: III. Development of optimization method for determining automation rate in nuclear power plants

International Nuclear Information System (INIS)

Lee, Seung Min; Kim, Jong Hyun; Kim, Man Cheol; Seong, Poong Hyun

2016-01-01

Highlights: • We propose an appropriate automation rate that enables the best human performance. • We analyze the shortest working time considering Situation Awareness Recovery (SAR). • The optimized automation rate is estimated by integrating the automation and ostracism rate estimation methods. • The process to derive the optimized automation rate is demonstrated through case studies. - Abstract: Automation has been introduced in various industries, including the nuclear field, because it is commonly believed that automation promises greater efficiency, lower workloads, and fewer operator errors through reducing operator errors and enhancing operator and system performance. However, the excessive introduction of automation has deteriorated operator performance due to the side effects of automation, which are referred to as Out-of-the-Loop (OOTL), and this is critical issue that must be resolved. Thus, in order to determine the optimal level of automation introduction that assures the best human operator performance, a quantitative method of optimizing the automation is proposed in this paper. In order to propose the optimization method for determining appropriate automation levels that enable the best human performance, the automation rate and ostracism rate, which are estimation methods that quantitatively analyze the positive and negative effects of automation, respectively, are integrated. The integration was conducted in order to derive the shortest working time through considering the concept of situation awareness recovery (SAR), which states that the automation rate with the shortest working time assures the best human performance. The process to derive the optimized automation rate is demonstrated through an emergency operation scenario-based case study. In this case study, four types of procedures are assumed through redesigning the original emergency operating procedure according to the introduced automation and ostracism levels. Using the

Fully automatic multi-language translation with a catalogue of phrases – successful employment for the Swiss avalanche bulletin

NARCIS (Netherlands)

Winkler, K.; Kuhn, T.

2016-01-01

The Swiss avalanche bulletin is produced twice a day in four languages. Due to the lack of time available for manual translation, a fully automated translation system is employed, based on a catalogue of predefined phrases and predetermined rules of how these phrases can be combined to produce

What do we know about the phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha)?

DEFF Research Database (Denmark)

Damgaard, Jakob

2012-01-01

The present study summarizes knowledge about phylogenetic relationships of the heteropteran infraorder Gerromorpha. A phylogeny for all families and subfamilies, and for all genera but those assigned to the two most diverse families, Veliidae and Gerridae, is compiled from the many studies by the...

Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Czech Academy of Sciences Publication Activity Database

Haddad, S.; Shin, S.; Lemmon, A. R.; Lemmon, E. M.; Švácha, Petr; Farrell, B.; Ślipiński, A.; Windsor, D.; McKenna, D. D.

2018-01-01

Roč. 43, č. 1 (2018), s. 68-89 ISSN 0307-6970 Institutional support: RVO:60077344 Keywords : Chrysomeloidea * Cerambycidae * molecular phylogeny Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 4.474, year: 2016 http://onlinelibrary.wiley.com/doi/10.1111/syen.12257/abstract

Automated Smoke Testing on the JVM with Geb

CERN Multimedia

CERN. Geneva

2015-01-01

to prevent catastrophic failures from reaching the production environment. We will show how we have leveraged Geb -- a browser automation tool built on top of Selenium -- to develop a full suite of smoke tests for CERN's Electronic Document Handling (EDH) system -- a large web application with over 1 million lines of Java code, in production since 1998. Though the tool is aimed for use on the JVM, the concepts that will be presented can be applied in other languages that have wrappers for Selenium. In particular, patterns that can be used to better describe and structure functional/smoke tests, as well as how to integrate these tests with continuous integration systems, such as Atlassian Bamboo, using headless browsers (e.g. PhantomJS) or virtual frame buffers.

Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host.

Science.gov (United States)

Gilbert, Maarten J; Duim, Birgitta; Timmerman, Arjen J; Zomer, Aldert L; Wagenaar, Jaap A

2017-08-21

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.

O anseio da lí­ngua-mãe nas entrelinhas da tradução automática

Directory of Open Access Journals (Sweden)

Leila Cristina De Mello Darin

2008-11-01

Full Text Available No presente artigo, examinaremos a possí­vel interligação entre o mito da Lí­nguamãe - tomando-se como referência o mito bí­blico da Torre de Babel - e os programas de tradução automática. Ao longo de sua história, a humanidade (inconscientemente almeja alcançar uma lí­ngua universal, pré-babélica, registrando este anseio por meio de poemas, canções, mitos, relatos folclóricos, bem como de projetos de lí­nguas universais como o Esperanto. Acreditamos que subjacente às propostas de softwares de tradução automática, como Systran e Globalink Power Translator Pro, que prometem "remover" as barreiras lingüí­sticas impostas pela multiplicidade de idiomas através de um únicocomando, há o desejo de uma tal lí­ngua primeira e ancestral, cuja mera possibilidade de existência nega a necessidade da tradução.Abstract: In this paper we intend to examine the possible interwining of the myth of the Proto-language - particularly as expressed in the biblical myth of the Tower of Babel - with projects of computarized translation. Throughout history, humankind has (unconsciouslywished to achieve a universal, pre-Babelian language and has recorded this dream by means of poems, songs, mythical tales, folklore, as well as projects of universal languages like Esperanto. It is our contention that underlying the proposal of translation software packages like Systran or Globalink Power Translator Pro, whichpromise to "remove" the linguistic barriers imposed by the multiplicity of languages by means of a single command, there is a longing for such a primeval, ancestral language, the very possibility of existence of which negates the need for translation.

Translator from the symbol coding language for the BUTs-20 processor of the in-core reactor control system

International Nuclear Information System (INIS)

Vorob'ev, D.M.; Golovanov, M.N.; Levin, G.L.; Parfenova, T.K.; Filatov, V.P.

1978-01-01

A symbolic-language code translator is described; it has been developed for automation of making up programs for in-core control systems. The translator is written in the ASSEMBLER language which is included in the software of the M-6000 computer. Two scannings of the source program are required for making up the operating program in the internal language of the BUTs-2O processor. The flowsheet and listing of the interrogation program of an analog-to-digital converter are presented. It is emphasized that the translator proposed allows a time reduction for constructing programs for the in-core control systems by a factor of 10-15 and an improvement of their quality

World-wide distribution automation systems

International Nuclear Information System (INIS)

Devaney, T.M.

1994-01-01

A worldwide power distribution automation system is outlined. Distribution automation is defined and the status of utility automation is discussed. Other topics discussed include a distribution management system, substation feeder, and customer functions, potential benefits, automation costs, planning and engineering considerations, automation trends, databases, system operation, computer modeling of system, and distribution management systems

WIDAFELS flexible automation systems

International Nuclear Information System (INIS)

Shende, P.S.; Chander, K.P.; Ramadas, P.

1990-01-01

After discussing the various aspects of automation, some typical examples of various levels of automation are given. One of the examples is of automated production line for ceramic fuel pellets. (M.G.B.)

Mammals on the EDGE: conservation priorities based on threat and phylogeny.

Directory of Open Access Journals (Sweden)

Nick J B Isaac

2007-03-01

Full Text Available Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.

A semi-automated tool for treatment plan-quality evaluation and clinical trial quality assurance

Science.gov (United States)

Wang, Jiazhou; Chen, Wenzhou; Studenski, Matthew; Cui, Yunfeng; Lee, Andrew J.; Xiao, Ying

2013-07-01

The goal of this work is to develop a plan-quality evaluation program for clinical routine and multi-institutional clinical trials so that the overall evaluation efficiency is improved. In multi-institutional clinical trials evaluating the plan quality is a time-consuming and labor-intensive process. In this note, we present a semi-automated plan-quality evaluation program which combines MIMVista, Java/MATLAB, and extensible markup language (XML). More specifically, MIMVista is used for data visualization; Java and its powerful function library are implemented for calculating dosimetry parameters; and to improve the clarity of the index definitions, XML is applied. The accuracy and the efficiency of the program were evaluated by comparing the results of the program with the manually recorded results in two RTOG trials. A slight difference of about 0.2% in volume or 0.6 Gy in dose between the semi-automated program and manual recording was observed. According to the criteria of indices, there are minimal differences between the two methods. The evaluation time is reduced from 10-20 min to 2 min by applying the semi-automated plan-quality evaluation program.

A semi-automated tool for treatment plan-quality evaluation and clinical trial quality assurance

International Nuclear Information System (INIS)

Wang, Jiazhou; Chen, Wenzhou; Studenski, Matthew; Cui, Yunfeng; Xiao, Ying; Lee, Andrew J

2013-01-01

The goal of this work is to develop a plan-quality evaluation program for clinical routine and multi-institutional clinical trials so that the overall evaluation efficiency is improved. In multi-institutional clinical trials evaluating the plan quality is a time-consuming and labor-intensive process. In this note, we present a semi-automated plan-quality evaluation program which combines MIMVista, Java/MATLAB, and extensible markup language (XML). More specifically, MIMVista is used for data visualization; Java and its powerful function library are implemented for calculating dosimetry parameters; and to improve the clarity of the index definitions, XML is applied. The accuracy and the efficiency of the program were evaluated by comparing the results of the program with the manually recorded results in two RTOG trials. A slight difference of about 0.2% in volume or 0.6 Gy in dose between the semi-automated program and manual recording was observed. According to the criteria of indices, there are minimal differences between the two methods. The evaluation time is reduced from 10–20 min to 2 min by applying the semi-automated plan-quality evaluation program. (note)

Automation in Clinical Microbiology

Science.gov (United States)

Ledeboer, Nathan A.

2013-01-01

Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

Virtual automation.

Science.gov (United States)

Casis, E; Garrido, A; Uranga, B; Vives, A; Zufiaurre, C

2001-01-01

Total laboratory automation (TLA) can be substituted in mid-size laboratories by a computer sample workflow control (virtual automation). Such a solution has been implemented in our laboratory using PSM, software developed in cooperation with Roche Diagnostics (Barcelona, Spain), to this purpose. This software is connected to the online analyzers and to the laboratory information system and is able to control and direct the samples working as an intermediate station. The only difference with TLA is the replacement of transport belts by personnel of the laboratory. The implementation of this virtual automation system has allowed us the achievement of the main advantages of TLA: workload increase (64%) with reduction in the cost per test (43%), significant reduction in the number of biochemistry primary tubes (from 8 to 2), less aliquoting (from 600 to 100 samples/day), automation of functional testing, drastic reduction of preanalytical errors (from 11.7 to 0.4% of the tubes) and better total response time for both inpatients (from up to 48 hours to up to 4 hours) and outpatients (from up to 10 days to up to 48 hours). As an additional advantage, virtual automation could be implemented without hardware investment and significant headcount reduction (15% in our lab).

The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis

Czech Academy of Sciences Publication Activity Database

Fiala, Ivan

2006-01-01

Roč. 36, č. 14 (2006), s. 1521-1534 ISSN 0020-7519 R&D Projects: GA MŠk LC522 Grant - others:Grantová agentura Jihočeské univerzity(CZ) 58/2002//P-BF Institutional research plan: CEZ:AV0Z60220518 Keywords : Myxosporea * SSU rDNA * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.337, year: 2006

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.

Science.gov (United States)

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters' approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

Automation of Test Cases for Web Applications : Automation of CRM Test Cases

OpenAIRE

Seyoum, Alazar

2012-01-01

The main theme of this project was to design a test automation framework for automating web related test cases. Automating test cases designed for testing a web interface provide a means of improving a software development process by shortening the testing phase in the software development life cycle. In this project an existing AutoTester framework and iMacros test automation tools were used. CRM Test Agent was developed to integrate AutoTester to iMacros and to enable the AutoTester,...

C language program analysis system (CLAS) part 1: graphical user interface (GUI)

International Nuclear Information System (INIS)

Bhattacharjee, A.K.; Seby, A.; Sen, Gopa; Dhodapkar, S.D.

1994-01-01

CLAS (C Language Program Analysis System) is a reverse engineering tool intended for use in the verification and validation (V and V) phase of software programs developed in the ANSI C language. From the source code, CLAS generates data pertaining to two conceptual models of software programs viz., Entity-Relationship (E-R) model and Control Flow Graphs (CFG) model. Browsing tools within CLAS, make use of this data, to provide different graphical views of the project. Static analysis tools have been developed earlier for analysing assembly language programs. CLAS is a continuation of this work to provide automated support in analysis of ANSI C language programs. CLAS provides an integrated Graphical User Interface (GUI) based environment under which programs can be analysed into the above mentioned models and the analysed data can be viewed using the browsing tools. The GUI of CLAS is implemented using an OPEN LOOK compliant tool kit XVIEW on Sun SPARC IPC workstation running Sun OS 4.1.1 rev. B. This report describes the GUI of CLAS. CLAS is also expected to be useful in other contexts which may involve understanding architecture/structure of already developed C language programs. Such requirements can arise while carrying out activities like code modification, parallelising etc. (author). 5 refs., 13 figs., 1 appendix

Using natural language processing techniques to inform research on nanotechnology

Directory of Open Access Journals (Sweden)

Nastassja A. Lewinski

2015-07-01

Full Text Available Literature in the field of nanotechnology is exponentially increasing with more and more engineered nanomaterials being created, characterized, and tested for performance and safety. With the deluge of published data, there is a need for natural language processing approaches to semi-automate the cataloguing of engineered nanomaterials and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine natural language processing (NLP-based tools were identified: NanoPort, NanoMapper, TechPerceptor, a Text Mining Framework, a Nanodevice Analyzer, a Clinical Trial Document Classifier, Nanotoxicity Searcher, NanoSifter, and NEIMiner. We conclude with recommendations for sharing NLP-related tools through online repositories to broaden participation in nanoinformatics.

Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola

Czech Academy of Sciences Publication Activity Database

Nováková, Eva; Hypša, Václav; Klein, J.; Foottit, R. G.; von Dohlen, C.D.; Moran, N. A.

2013-01-01

Roč. 68, č. 1 (2013), s. 42-54 ISSN 1055-7903 R&D Projects: GA ČR GD206/09/H026 Institutional support: RVO:60077344 Keywords : Aphid * Evolution * Buchnera * Phylogeny * Informative markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.018, year: 2013

Molecular phylogeny of Duvenhage virus

Directory of Open Access Journals (Sweden)

Louis H. Nel

2011-11-01

Full Text Available The Duvenhage virus (DUVV constitutes one of the 11 species in the Lyssavirus genus and causes fatal rabies encephalitis. The virus is associated with insectivorous bat species and three human cases have been reported, all of which were linked to contact with bats. Few of these isolates have been studied and thus little is known about the phylogeny and epidemiology of this lyssavirus. Until 2007, when an isolate was made from the East African country of Kenya, all isolations of this virus had been from southern Africa. This discovery led to many questions regarding the spread and diversity of this lyssavirus. Phylogenetic analysis indicated that the DUVV isolates constitute two different lineages, in which the southern African isolates group together to form one lineage and the more recent isolate from Kenya constitutes a new, second lineage. We found that the new isolate has a genetic variation that has not yet been seen for DUVV. Not only is our lack of knowledge regarding the geographical distribution of this uniquely African virus emphasised, but we have also demonstrated the potential diversity within this genotype.

An Automation Planning Primer.

Science.gov (United States)

Paynter, Marion

1988-01-01

This brief planning guide for library automation incorporates needs assessment and evaluation of options to meet those needs. A bibliography of materials on automation planning and software reviews, library software directories, and library automation journals is included. (CLB)

Automation in Immunohematology

Directory of Open Access Journals (Sweden)

Meenu Bajpai

2012-01-01

Full Text Available There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process.

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

Czech Academy of Sciences Publication Activity Database

Musilová, Zuzana; Říčan, Oldřich; Janko, Karel; Novák, J.

2008-01-01

Roč. 46, - (2008), s. 659-672 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Grant - others:GA UK(CZ) 182/2004/B-BIO; GA UK(CZ) 139407 Institutional research plan: CEZ:AV0Z50450515 Keywords : molecular phylogeny * Cichlids * south America Subject RIV: EG - Zoology Impact factor: 3.871, year: 2008

Process understanding and cooperative design. Keys to high quality automation

International Nuclear Information System (INIS)

Tommila, T.; Heinonen, R.

1995-01-01

A systematic approach to the specification of process control systems, and four practical methods supporting user participation and interdisciplinary co-operation are described. The main steps of the design approach are: (1) hierarchical decomposition of the plant to process items of different types; (2) analysis and definition of requirements and control strategies associated with each process item; (3) definition of automation degree; and (4) functional specification of the control system and its user interface. The specification language used for this step is a combination of principles found in object oriented design, structured analysis as well as new language standards for programmable controllers and open information systems. The design review methods presented include structured control strategy meetings, safety analysis of sequential controls, review of graphic displays, and a usability questionnaire for existing plants. These methods can be used to elicit users' needs and operational experience, to gain a common understanding of the process functionality, or to detect errors in design specifications or in existing systems. (8 refs., 9 figs.)

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

Science.gov (United States)

Reck-Kortmann, Maikel; Silva-Arias, Gustavo Adolfo; Segatto, Ana Lúcia Anversa; Mäder, Geraldo; Bonatto, Sandro Luis; de Freitas, Loreta Brandão

2014-12-01

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China.

Directory of Open Access Journals (Sweden)

Xin Zhao

Full Text Available The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens. Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.

DNA variation within Juncaceae: Comparison of impact of organelle regions on phylogeny

Czech Academy of Sciences Publication Activity Database

Záveská Drábková, Lenka; Vlček, Čestmír

2009-01-01

Roč. 278, č. 3 (2009), s. 169-186 ISSN 0378-2697 R&D Projects: GA ČR GP206/07/P147; GA MŠk(CZ) 1M0520 Grant - others:EU(XE) SYNTHESYS DK-TAF 1295; EU(XE) SYNTHESYS GB-TAF 2052 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50520514 Keywords : molecular phylogeny * Juncaceae * mtDNA Subject RIV: EF - Botanics Impact factor: 1.410, year: 2009

Automated Budget System -

Data.gov (United States)

Department of Transportation — The Automated Budget System (ABS) automates management and planning of the Mike Monroney Aeronautical Center (MMAC) budget by providing enhanced capability to plan,...

Bioprocessing automation in cell therapy manufacturing: Outcomes of special interest group automation workshop.

Science.gov (United States)

Ball, Oliver; Robinson, Sarah; Bure, Kim; Brindley, David A; Mccall, David

2018-04-01

Phacilitate held a Special Interest Group workshop event in Edinburgh, UK, in May 2017. The event brought together leading stakeholders in the cell therapy bioprocessing field to identify present and future challenges and propose potential solutions to automation in cell therapy bioprocessing. Here, we review and summarize discussions from the event. Deep biological understanding of a product, its mechanism of action and indication pathogenesis underpin many factors relating to bioprocessing and automation. To fully exploit the opportunities of bioprocess automation, therapeutics developers must closely consider whether an automation strategy is applicable, how to design an 'automatable' bioprocess and how to implement process modifications with minimal disruption. Major decisions around bioprocess automation strategy should involve all relevant stakeholders; communication between technical and business strategy decision-makers is of particular importance. Developers should leverage automation to implement in-process testing, in turn applicable to process optimization, quality assurance (QA)/ quality control (QC), batch failure control, adaptive manufacturing and regulatory demands, but a lack of precedent and technical opportunities can complicate such efforts. Sparse standardization across product characterization, hardware components and software platforms is perceived to complicate efforts to implement automation. The use of advanced algorithmic approaches such as machine learning may have application to bioprocess and supply chain optimization. Automation can substantially de-risk the wider supply chain, including tracking and traceability, cryopreservation and thawing and logistics. The regulatory implications of automation are currently unclear because few hardware options exist and novel solutions require case-by-case validation, but automation can present attractive regulatory incentives. Copyright © 2018 International Society for Cellular Therapy

Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data

Czech Academy of Sciences Publication Activity Database

Ogden, T. H.; Gattolliat, J. L.; Sartori, M.; Staniczek, A. H.; Soldán, Tomáš; Whiting, M. F.

2009-01-01

Roč. 34, č. 4 (2009), s. 616-634 ISSN 0307-6970 R&D Projects: GA AV ČR 1QS500070505 Institutional research plan: CEZ:AV0Z50070508 Keywords : Ephemeroptera * phylogeny * morfological a molecular data Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.467, year: 2009

Nuclear and original DNA application in Oryza taxonomy and phylogeny

International Nuclear Information System (INIS)

Romero, Gabriel O.

1998-01-01

Conventional taxonomy and phylogeny of germplasm are based on the tedious characterization of morphological variation. The ability to assay DNA variation that underlies morphological variation offers great promise as a convenient alternative for the genetic characterization of germplasm. Restriction fragment length polymorphism (RFLP) was used to survey DNA variation in 22 species of the genus Oryza. At the ribosomal DNA (rDNA) multigene family, 15 rDNA spacer length (sl) variants were identified using restriction enzyme Sst1 and wheatrDNA unit as probe. Particular sl variants predominated in certain isozyme groups of O. sativa, indicating a potential of sl ploymorphism in varietal classification. The distribution of sl variants supports the origin of O. sativa and O. nivara from O. rufipogon, and that O. spontanea arose from introgressions among O. sativa, O. nivara, and O. rufipogon. The distribution also suggests that the CCgenome, of all the genomes in the Officinalis complex, may be closest to the Sativa complex genomes, and it affirms the genetic position of the Officinalis complex intermediate between the Sativa and Ridleyi complexes. Variation at the Oryza organelle genomes was probed with a maize mitochondrial gene, atpA, a wheat chloroplast inverted repeat segment, p6. Results indicated that the complexes can be differentiated by their mitochondrial genome, but not their chloroplast genome when digested by Sst1 or BamH1. Therefore, the natural DNA variation in the nuclear and mitochondrial genomes has demonstrated great potential in complementing the conventional basis of taxa classification and phylogeny in the genus Oryza. (Author)

Software for an automated processing system for radioisotope information from multichannel radiodiagnostic instruments

International Nuclear Information System (INIS)

Zelenin, P.E.; Meier, V.P.

1985-01-01

The SAORI-01 system for the automated processing of radioisotope information is designed for the collection, processing, and representation of information coming from gamma chambers and multichannel radiodiagnostic instruments (MRI) and is basically oriented toward the radiodiagnostic laboratories of major multidisciplinary hospitals and scientific-research institutes. The functional characteristics of the basic software are discussed, and permits performance of the following functions: collection of information regarding MRI; processing and representation of recorded information; storage of patient files on magnetic carriers; and writing of special processing programs in the FORTRAN and BASIC high-level language

NASA Goddard Space Flight Center Robotic Processing System Program Automation Systems, volume 2

Science.gov (United States)

Dobbs, M. E.

1991-01-01

Topics related to robot operated materials processing in space (RoMPS) are presented in view graph form. Some of the areas covered include: (1) mission requirements; (2) automation management system; (3) Space Transportation System (STS) Hitchhicker Payload; (4) Spacecraft Command Language (SCL) scripts; (5) SCL software components; (6) RoMPS EasyLab Command & Variable summary for rack stations and annealer module; (7) support electronics assembly; (8) SCL uplink packet definition; (9) SC-4 EasyLab System Memory Map; (10) Servo Axis Control Logic Suppliers; and (11) annealing oven control subsystem.

Open-Source Assisted Laboratory Automation through Graphical User Interfaces and 3D Printers: Application to Equipment Hyphenation for Higher-Order Data Generation.

Science.gov (United States)

Siano, Gabriel G; Montemurro, Milagros; Alcaráz, Mirta R; Goicoechea, Héctor C

2017-10-17

Higher-order data generation implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation are the key to obtaining higher-order data, the required simultaneous control of them demands funds for new hardware, software, and licenses, in addition to very skilled operators. In this work, we present Design of Inputs-Outputs with Sikuli (DIOS), a free and open-source code program that provides a general framework for the design of automated experimental procedures without prior knowledge of programming or electronics. Basically, instruments and devices are considered as nodes in a network, and every node is associated both with physical and virtual inputs and outputs. Virtual components, such as graphical user interfaces (GUIs) of equipment, are handled by means of image recognition tools provided by Sikuli scripting language, while handling of their physical counterparts is achieved using an adapted open-source three-dimensional (3D) printer. Two previously reported experiments of our research group, related to fluorescence matrices derived from kinetics and high-performance liquid chromatography, were adapted to be carried out in a more automated fashion. Satisfactory results, in terms of analytical performance, were obtained. Similarly, advantages derived from open-source tools assistance could be appreciated, mainly in terms of lesser intervention of operators and cost savings.

A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats

KAUST Repository

Hundt, Peter J.

2014-01-01

The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100. bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies. © 2013 Elsevier Inc.

Phylogeny and morphological variability of trypanosomes from African pelomedusid turtles with redescription of Trypanosoma mocambicum Pienaar, 1962

Czech Academy of Sciences Publication Activity Database

Dvořáková, N.; Čepička, I.; Qablan, M. A.; Gibson, W.; Blažek, Radim; Široký, P.

2015-01-01

Roč. 166, č. 6 (2015), s. 599-608 ISSN 1434-4610 Institutional support: RVO:68081766 Keywords : Trypanosoma * turtle * Pelusios * polymorphism * phylogeny * SSU rRNA gene Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers

Science.gov (United States)

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters’ approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers. PMID:26508826

Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters

Science.gov (United States)

Tarasov, Sergei; Génier, François

2015-01-01

Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a

Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels

Czech Academy of Sciences Publication Activity Database

Liu, H.-Z.; Zhu, Y.-R.; Smith, C.; Reichard, Martin

2006-01-01

Roč. 45, č. 3 (2006), s. 428-434 ISSN 1021-5506 Grant - others:NSFC(CN) 30470237; NSFC(CN) 40432003; Innovation Program of the Chinese Academy of Sciences(CN) KZCX3-SW-126 Institutional research plan: CEZ:AV0Z60930519 Keywords : bitterling * host specificity * coevolution * phylogeny Subject RIV: EG - Zoology Impact factor: 0.943, year: 2006 http://zoolstud.sinica.edu.tw/Journals/45.3/428.pdf

Revisiting the phylogeny of Ocellularieae, the second largest tribe within Graphidaceae (lichenized Ascomycota: Ostropales)

Science.gov (United States)

Ekaphan Kraichak; Sittiporn Parnmen; Robert Lücking; Eimy Rivas Plata; Andre Aptroot; Marcela E.S. Caceres; Damien Ertz; Armin Mangold; Joel A. Mercado-Diaz; Khwanruan Papong; Dries Van der Broeck; Gothamie Weerakoon; H. Thorsten. Lumbsch; NO-VALUE

2014-01-01

We present an updated 3-locus molecular phylogeny of tribe Ocellularieae, the second largest tribe within subfamily Graphidoideae in the Graphidaceae. Adding 165 newly generated sequences from the mitochondrial small subunit rDNA (mtSSU), the nuclear large subunit rDNA (nuLSU), and the second largest subunit of the DNA-directed RNA polymerase II (RPB2), we currently...

The effect of written text on comprehension of spoken English as a foreign language.

Science.gov (United States)

Diao, Yali; Chandler, Paul; Sweller, John

2007-01-01

Based on cognitive load theory, this study investigated the effect of simultaneous written presentations on comprehension of spoken English as a foreign language. Learners' language comprehension was compared while they used 3 instructional formats: listening with auditory materials only, listening with a full, written script, and listening with simultaneous subtitled text. Listening with the presence of a script and subtitles led to better understanding of the scripted and subtitled passage but poorer performance on a subsequent auditory passage than listening with the auditory materials only. These findings indicated that where the intention was learning to listen, the use of a full script or subtitles had detrimental effects on the construction and automation of listening comprehension schemas.

Molecular phylogeny of Anopheles hyrcanus group (Diptera: Culicidae) based on mtDNA COI.

Science.gov (United States)

Fang, Yuan; Shi, Wen-Qi; Zhang, Yi

2017-05-08

The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy. Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range. The results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions. In summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay

Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata: phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

Directory of Open Access Journals (Sweden)

Jang Kuem

2009-04-01

Full Text Available Abstract Background The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny. Results The complete mitochondrial genome (15,433 bp of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata, one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of F. hispida (Bryozoa, Gymnolaemata, Ctenostomata, which has only 36 components with loss of tRNAser(ucn genes. The B. neritina mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida and a chiton Katharina tunicate than to that of F. hispida. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (B. neritina and F. hispida was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta. Conclusion This study presents the complete mitochondrial genome of a

Coloration mechanisms and phylogeny of Morpho butterflies.

Science.gov (United States)

Giraldo, M A; Yoshioka, S; Liu, C; Stavenga, D G

2016-12-15

Morpho butterflies are universally admired for their iridescent blue coloration, which is due to nanostructured wing scales. We performed a comparative study on the coloration of 16 Morpho species, investigating the morphological, spectral and spatial scattering properties of the differently organized wing scales. In numerous previous studies, the bright blue Morpho coloration has been fully attributed to the multi-layered ridges of the cover scales' upper laminae, but we found that the lower laminae of the cover and ground scales play an important additional role, by acting as optical thin film reflectors. We conclude that Morpho coloration is a subtle combination of overlapping pigmented and/or unpigmented scales, multilayer systems, optical thin films and sometimes undulated scale surfaces. Based on the scales' architecture and their organization, five main groups can be distinguished within the genus Morpho, largely agreeing with the accepted phylogeny. © 2016. Published by The Company of Biologists Ltd.

Molecular phylogeny of Acerentomidae (Protura), with description of Acerentuloides bernardi sp. nov. from North America

Czech Academy of Sciences Publication Activity Database

Shrubovych, J.; Starý, Josef; D'Haese, C.A.

2017-01-01

Roč. 100, č. 2 (2017), s. 433-443 ISSN 0015-4040 R&D Projects: GA MŠk ME08019 Institutional support: RVO:60077344 Keywords : Acerentulus * DNA barcoding * Indiana * phylogeny * Podolinella * USA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 0.964, year: 2016

Language variety, language hierarchy, and language choice in the international university

DEFF Research Database (Denmark)

Haberland, Hartmut; Mortensen, Janus

2012-01-01

Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university......Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university...

Phylogeny of Gobioidei and the origin of European gobies

Directory of Open Access Journals (Sweden)

Ainhoa Agorreta

2015-11-01

Full Text Available The percomorph order Gobioidei comprises over 2200 species worldwide distributed that occupy most freshwater, brackish and marine environments, and show a spectacular variety in morphology, ecology, and behaviour. However, phylogenetic relationships among many gobioid groups still remain poorly understood. Such is the case of Gobiidae, a rapidly radiating lineage that encompass an unusually high diversity of species (nearly 2000, including the largely endemic European species whose origin and ancestry remain uncertain. The resolution and accuracy of previous molecular phylogenetic studies has been limited due to the use of only a few (generally mitochondrial molecular markers and/or the absence of representatives of several key lineages. Our study (built on Agorreta et al. 2013 is the first to include multiple nuclear and mitochondrial genes for nearly 300 terminal taxa representing the vast diversity of gobioid lineages. We have used this information to reconstruct a robust phylogeny of Gobioidei, and we are now investigating the historical biogeography and diversification times of European gobies with a time-calibrated molecular phylogeny. Robustness of the inferred phylogenetic trees is significantly higher than that of previous studies, hence providing the most compelling molecular phylogenetic hypotheses for Gobioidei thus far. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade followed by the Butidae as the sister-group of the Gobiidae. Several monophyletic groups are identified within the two major Gobiidae subclades, the gobionelline-like and the gobiine-like gobiids. The European gobies cluster in three distinct lineages (Pomatoschistus-, Aphia-, and Gobius-lineages, each with different affinities with gobiids from the Indo-Pacific and perhaps the New World. Our ongoing more-detailed study on European gobies will reveal whether their origin is related to vicariant events linked to the

78 FR 66039 - Modification of National Customs Automation Program Test Concerning Automated Commercial...

Science.gov (United States)

2013-11-04

... Customs Automation Program Test Concerning Automated Commercial Environment (ACE) Cargo Release (Formerly...) plan to both rename and modify the National Customs Automation Program (NCAP) test concerning the... data elements required to obtain release for cargo transported by air. The test will now be known as...

Novel intron markers to study the phylogeny of closely related mammalian species

Directory of Open Access Journals (Sweden)

Castresana Jose

2010-11-01

Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence.

Science.gov (United States)

Zhang, Liang; Zhang, Li-Bing

2018-01-01

The brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major clades identified earlier are recovered here and we further identified a new major clade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

Knowledge modelling and reliability processing: presentation of the Figaro language and associated tools

International Nuclear Information System (INIS)

Bouissou, M.; Villatte, N.; Bouhadana, H.; Bannelier, M.

1991-12-01

EDF has been developing for several years an integrated set of knowledge-based and algorithmic tools for automation of reliability assessment of complex (especially sequential) systems. In this environment, the reliability expert has at his disposal all the powerful software tools for qualitative and quantitative processing, besides he gets various means to generate automatically the inputs for these tools, through the acquisition of graphical data. The development of these tools has been based on FIGARO, a specific language, which was built to get an homogeneous system modelling. Various compilers and interpreters get a FIGARO model into conventional models, such as fault-trees, Markov chains, Petri Networks. In this report, we introduce the main basics of FIGARO language, illustrating them with examples

Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae)

Czech Academy of Sciences Publication Activity Database

Fehrer, Judith; Gemeinholzer, B.; Chrtek, Jindřich; Bräutigam, S.

2007-01-01

Roč. 42, - (2007), s. 347-361 ISSN 1055-7903 R&D Projects: GA MŽP SE/610/3/00 Institutional research plan: CEZ:AV0Z60050516 Keywords : molecular phylogeny * Hieracium * chloroplast capture Subject RIV: EF - Botanics Impact factor: 3.994, year: 2007

Automation-aided Task Loads Index based on the Automation Rate Reflecting the Effects on Human Operators in NPPs

International Nuclear Information System (INIS)

Lee, Seungmin; Seong, Poonghyun; Kim, Jonghyun

2013-01-01

Many researchers have found that a high automation rate does not guarantee high performance. Therefore, to reflect the effects of automation on human performance, a new estimation method of the automation rate that considers the effects of automation on human operators in nuclear power plants (NPPs) was suggested. These suggested measures express how much automation support human operators but it cannot express the change of human operators' workload, whether the human operators' workload is increased or decreased. Before considering automation rates, whether the adopted automation is good or bad might be estimated in advance. In this study, to estimate the appropriateness of automation according to the change of the human operators' task loads, automation-aided task loads index is suggested based on the concept of the suggested automation rate. To insure plant safety and efficiency on behalf of human operators, various automation systems have been installed in NPPs, and many works which were previously conducted by human operators can now be supported by computer-based operator aids. According to the characteristics of the automation types, the estimation method of the system automation and the cognitive automation rate were suggested. The proposed estimation method concentrates on the effects of introducing automation, so it directly express how much the automated system support human operators. Based on the suggested automation rates, the way to estimate how much the automated system can affect the human operators' cognitive task load is suggested in this study. When there is no automation, the calculated index is 1, and it means there is no change of human operators' task load

Asleep at the automated wheel-Sleepiness and fatigue during highly automated driving.

Science.gov (United States)

Vogelpohl, Tobias; Kühn, Matthias; Hummel, Thomas; Vollrath, Mark

2018-03-20

Due to the lack of active involvement in the driving situation and due to monotonous driving environments drivers with automation may be prone to become fatigued faster than manual drivers (e.g. Schömig et al., 2015). However, little is known about the progression of fatigue during automated driving and its effects on the ability to take back manual control after a take-over request. In this driving simulator study with Nö=ö60 drivers we used a three factorial 2ö×ö2ö×ö12 mixed design to analyze the progression (12ö×ö5ömin; within subjects) of driver fatigue in drivers with automation compared to manual drivers (between subjects). Driver fatigue was induced as either mainly sleep related or mainly task related fatigue (between subjects). Additionally, we investigated the drivers' reactions to a take-over request in a critical driving scenario to gain insights into the ability of fatigued drivers to regain manual control and situation awareness after automated driving. Drivers in the automated driving condition exhibited facial indicators of fatigue after 15 to 35ömin of driving. Manual drivers only showed similar indicators of fatigue if they suffered from a lack of sleep and then only after a longer period of driving (approx. 40ömin). Several drivers in the automated condition closed their eyes for extended periods of time. In the driving with automation condition mean automation deactivation times after a take-over request were slower for a certain percentage (about 30%) of the drivers with a lack of sleep (Mö=ö3.2; SDö=ö2.1ös) compared to the reaction times after a long drive (Mö=ö2.4; SDö=ö0.9ös). Drivers with automation also took longer than manual drivers to first glance at the speed display after a take-over request and were more likely to stay behind a braking lead vehicle instead of overtaking it. Drivers are unable to stay alert during extended periods of automated driving without non-driving related tasks. Fatigued drivers could

Slowdowns in diversification rates from real phylogenies may not be real.

Science.gov (United States)

Cusimano, Natalie; Renner, Susanne S

2010-07-01

Studies of diversification patterns often find a slowing in lineage accumulation toward the present. This seemingly pervasive pattern of rate downturns has been taken as evidence for adaptive radiations, density-dependent regulation, and metacommunity species interactions. The significance of rate downturns is evaluated with statistical tests (the gamma statistic and Monte Carlo constant rates (MCCR) test; birth-death likelihood models and Akaike Information Criterion [AIC] scores) that rely on null distributions, which assume that the included species are a random sample of the entire clade. Sampling in real phylogenies, however, often is nonrandom because systematists try to include early-diverging species or representatives of previous intrataxon classifications. We studied the effects of biased sampling, structured sampling, and random sampling by experimentally pruning simulated trees (60 and 150 species) as well as a completely sampled empirical tree (58 species) and then applying the gamma statistic/MCCR test and birth-death likelihood models/AIC scores to assess rate changes. For trees with random species sampling, the true model (i.e., the one fitting the complete phylogenies) could be inferred in most cases. Oversampling deep nodes, however, strongly biases inferences toward downturns, with simulations of structured and biased sampling suggesting that this occurs when sampling percentages drop below 80%. The magnitude of the effect and the sensitivity of diversification rate models is such that a useful rule of thumb may be not to infer rate downturns from real trees unless they have >80% species sampling.

Procedure automation: the effect of automated procedure execution on situation awareness and human performance

International Nuclear Information System (INIS)

Andresen, Gisle; Svengren, Haakan; Heimdal, Jan O.; Nilsen, Svein; Hulsund, John-Einar; Bisio, Rossella; Debroise, Xavier

2004-04-01

As advised by the procedure workshop convened in Halden in 2000, the Halden Project conducted an experiment on the effect of automation of Computerised Procedure Systems (CPS) on situation awareness and human performance. The expected outcome of the study was to provide input for guidance on CPS design, and to support the Halden Project's ongoing research on human reliability analysis. The experiment was performed in HAMMLAB using the HAMBO BWR simulator and the COPMA-III CPS. Eight crews of operators from Forsmark 3 and Oskarshamn 3 participated. Three research questions were investigated: 1) Does procedure automation create Out-Of-The-Loop (OOTL) performance problems? 2) Does procedure automation affect situation awareness? 3) Does procedure automation affect crew performance? The independent variable, 'procedure configuration', had four levels: paper procedures, manual CPS, automation with breaks, and full automation. The results showed that the operators experienced OOTL problems in full automation, but that situation awareness and crew performance (response time) were not affected. One possible explanation for this is that the operators monitored the automated procedure execution conscientiously, something which may have prevented the OOTL problems from having negative effects on situation awareness and crew performance. In a debriefing session, the operators clearly expressed their dislike for the full automation condition, but that automation with breaks could be suitable for some tasks. The main reason why the operators did not like the full automation was that they did not feel being in control. A qualitative analysis addressing factors contributing to response time delays revealed that OOTL problems did not seem to cause delays, but that some delays could be explained by the operators having problems with the freeze function of the CPS. Also other factors such as teamwork and operator tendencies were of importance. Several design implications were drawn

Generación automática del diagrama entidad-relación y su representación en SQL desde un lenguaje controlado (UN-LENCEP Automatic generation of entity-relationship diagram and its representation in SQL from a controlled language (UN-LENCEP

Directory of Open Access Journals (Sweden)

Carlos Mario Zapata Jaramillo

2011-01-01

Full Text Available Entidad-relación es uno de los diagramas que se utilizan en el desarrollo de modelos para representar la información de un dominio. Con el fin de agilizar y mejorar el proceso de desarrollo de software, diferentes propuestas surgieron para contribuir en la obtención automática o semiautomática del diagrama entidad-relación. Varias de estas propuestas utilizan como punto de partida lenguaje natural o lenguaje controlado, mientras otras propuestas utilizan representaciones intermedias. Los interesados en el desarrollo de una aplicación de software no suelen comprender varias de las representaciones utilizadas sin tener previa capacitación, lo cual restringe la participación activa del interesado en todas las etapas del desarrollo. Con el fin de solucionar estos problemas, en este artículo se propone un conjunto de reglas heurísticas para la obtención automática del diagrama entidad-relación y su representación en SQL. Se toma como punto de partida el lenguaje controlado UN-Lencep, que ya se emplea para la generación de otros artefactos en el desarrollo de aplicaciones de software.Entity-relationship diagram (ERD is one of the used in modelling the domain information. Several proposals have emerged for speeding up and improving the software development process by either automatically or semi-automatically obtain the ERD. Natural language, controlled languages, and intermediate representations have been used in such a task. The stakeholders (people with some concern in application development, when untrained, are incapable to understand several of such representations. As a consequence, stakeholder active participation in software development is highly restricted. Trying to solve these problems, a set of heuristic rules for automatically obtaining ERD and its SQL-based equivalence is proposed in this paper. The starting point is UN-Lencep, a controlled language already used for generating other artefacts belonging to software

Automated Reporting of DXA Studies Using a Custom-Built Computer Program.

Science.gov (United States)

England, Joseph R; Colletti, Patrick M

2018-06-01

Dual-energy x-ray absorptiometry (DXA) scans are a critical population health tool and relatively simple to interpret but can be time consuming to report, often requiring manual transfer of bone mineral density and associated statistics into commercially available dictation systems. We describe here a custom-built computer program for automated reporting of DXA scans using Pydicom, an open-source package built in the Python computer language, and regular expressions to mine DICOM tags for patient information and bone mineral density statistics. This program, easy to emulate by any novice computer programmer, has doubled our efficiency at reporting DXA scans and has eliminated dictation errors.

Models and automation technologies for the curriculum development

Directory of Open Access Journals (Sweden)

V. N. Volkova

2016-01-01

Full Text Available The aim of the research was to determine the sequence of the curriculum development stages on the basis of the system analysis, as well as to create models and information technologies for the implementation of thesestages.The methods and the models of the systems’ theory and the system analysis, including methods and automated procedures for structuring organizational aims, models and automated procedures for organizing complex expertise.On the basis of the analysis of existing studies in the field of curriculum modeling, using formal mathematical language, including optimization models, that help to make distribution of disciplines by years and semesters in accordance with the relevant restrictions, it is shown, that the complexity and dimension of these tasks require the development of special software; the problem of defining the input data and restrictions requires a large time investment, that seems to be difficult to provide in real conditions of plans’ developing, thus it is almost impossible to verify the objectivity of the input data and the restrictions in such models. For a complete analysis of the process of curriculum development it is proposed to use the system definition, based on the system-targeted approach. On the basis of this definition the reasonable sequence of the integrated stages for the development of the curriculum was justified: 1 definition (specification of the requirements for the educational content; 2 determining the number of subjects, included in the curriculum; 3 definition of the sequence of the subjects; 4 distribution of subjects by semesters. The models and technologies for the implementation of these stages of curriculum development were given in the article: 1 models, based on the information approach of A.Denisov and the modified degree of compliance with objectives based on Denisov’s evaluation index (in the article the idea of evaluating the degree of the impact of disciplines for realization

Comparison Between Manual Auditing and a Natural Language Process With Machine Learning Algorithm to Evaluate Faculty Use of Standardized Reports in Radiology.

Science.gov (United States)

Guimaraes, Carolina V; Grzeszczuk, Robert; Bisset, George S; Donnelly, Lane F

2018-03-01

When implementing or monitoring department-sanctioned standardized radiology reports, feedback about individual faculty performance has been shown to be a useful driver of faculty compliance. Most commonly, these data are derived from manual audit, which can be both time-consuming and subject to sampling error. The purpose of this study was to evaluate whether a software program using natural language processing and machine learning could accurately audit radiologist compliance with the use of standardized reports compared with performed manual audits. Radiology reports from a 1-month period were loaded into such a software program, and faculty compliance with use of standardized reports was calculated. For that same period, manual audits were performed (25 reports audited for each of 42 faculty members). The mean compliance rates calculated by automated auditing were then compared with the confidence interval of the mean rate by manual audit. The mean compliance rate for use of standardized reports as determined by manual audit was 91.2% with a confidence interval between 89.3% and 92.8%. The mean compliance rate calculated by automated auditing was 92.0%, within that confidence interval. This study shows that by use of natural language processing and machine learning algorithms, an automated analysis can accurately define whether reports are compliant with use of standardized report templates and language, compared with manual audits. This may avoid significant labor costs related to conducting the manual auditing process. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa

Czech Academy of Sciences Publication Activity Database

Bryja, J.; Mikula, Ondřej; Šumbera, R.; Meheretu, Y.; Aghová, T.; Lavrenchenko, L. A.; Mazoch, V.; Oguge, N.; Mbau, J. S.; Welegerima, K.; Amundala, N.; Colyn, M.; Leirs, H.; Verheyen, E.

2014-01-01

Roč. 14, č. 256 (2014) ISSN 1471-2148 R&D Projects: GA ČR GAP506/10/0983 Institutional support: RVO:67985904 Keywords : biogeography * tropical Africa * molecular phylogeny Subject RIV: EG - Zoology Impact factor: 3.368, year: 2014

Automation-aided Task Loads Index based on the Automation Rate Reflecting the Effects on Human Operators in NPPs

Energy Technology Data Exchange (ETDEWEB)

Lee, Seungmin; Seong, Poonghyun [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of); Kim, Jonghyun [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

2013-05-15

Many researchers have found that a high automation rate does not guarantee high performance. Therefore, to reflect the effects of automation on human performance, a new estimation method of the automation rate that considers the effects of automation on human operators in nuclear power plants (NPPs) was suggested. These suggested measures express how much automation support human operators but it cannot express the change of human operators' workload, whether the human operators' workload is increased or decreased. Before considering automation rates, whether the adopted automation is good or bad might be estimated in advance. In this study, to estimate the appropriateness of automation according to the change of the human operators' task loads, automation-aided task loads index is suggested based on the concept of the suggested automation rate. To insure plant safety and efficiency on behalf of human operators, various automation systems have been installed in NPPs, and many works which were previously conducted by human operators can now be supported by computer-based operator aids. According to the characteristics of the automation types, the estimation method of the system automation and the cognitive automation rate were suggested. The proposed estimation method concentrates on the effects of introducing automation, so it directly express how much the automated system support human operators. Based on the suggested automation rates, the way to estimate how much the automated system can affect the human operators' cognitive task load is suggested in this study. When there is no automation, the calculated index is 1, and it means there is no change of human operators' task load.

Automated Planning Enables Complex Protocols on Liquid-Handling Robots.

Science.gov (United States)

Whitehead, Ellis; Rudolf, Fabian; Kaltenbach, Hans-Michael; Stelling, Jörg

2018-03-16

Robotic automation in synthetic biology is especially relevant for liquid handling to facilitate complex experiments. However, research tasks that are not highly standardized are still rarely automated in practice. Two main reasons for this are the substantial investments required to translate molecular biological protocols into robot programs, and the fact that the resulting programs are often too specific to be easily reused and shared. Recent developments of standardized protocols and dedicated programming languages for liquid-handling operations addressed some aspects of ease-of-use and portability of protocols. However, either they focus on simplicity, at the expense of enabling complex protocols, or they entail detailed programming, with corresponding skills and efforts required from the users. To reconcile these trade-offs, we developed Roboliq, a software system that uses artificial intelligence (AI) methods to integrate (i) generic formal, yet intuitive, protocol descriptions, (ii) complete, but usually hidden, programming capabilities, and (iii) user-system interactions to automatically generate executable, optimized robot programs. Roboliq also enables high-level specifications of complex tasks with conditional execution. To demonstrate the system's benefits for experiments that are difficult to perform manually because of their complexity, duration, or time-critical nature, we present three proof-of-principle applications for the reproducible, quantitative characterization of GFP variants.

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

Science.gov (United States)

Graham Reynolds, R; Niemiller, Matthew L; Revell, Liam J

2014-02-01

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers