WorldWideScience

Sample records for regular expression development

  1. Regular Expression Pocket Reference

    CERN Document Server

    Stubblebine, Tony

    2007-01-01

    This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp

  2. Regular expressions cookbook

    CERN Document Server

    Goyvaerts, Jan

    2009-01-01

    This cookbook provides more than 100 recipes to help you crunch data and manipulate text with regular expressions. Every programmer can find uses for regular expressions, but their power doesn't come worry-free. Even seasoned users often suffer from poor performance, false positives, false negatives, or perplexing bugs. Regular Expressions Cookbook offers step-by-step instructions for some of the most common tasks involving this tool, with recipes for C#, Java, JavaScript, Perl, PHP, Python, Ruby, and VB.NET. With this book, you will: Understand the basics of regular expressions through a

  3. Regular expression containment

    DEFF Research Database (Denmark)

    Henglein, Fritz; Nielsen, Lasse

    2011-01-01

    We present a new sound and complete axiomatization of regular expression containment. It consists of the conventional axiomatiza- tion of concatenation, alternation, empty set and (the singleton set containing) the empty string as an idempotent semiring, the fixed- point rule E* = 1 + E × E......* for Kleene-star, and a general coin- duction rule as the only additional rule. Our axiomatization gives rise to a natural computational inter- pretation of regular expressions as simple types that represent parse trees, and of containment proofs as coercions. This gives the axiom- atization a Curry......-Howard-style constructive interpretation: Con- tainment proofs do not only certify a language-theoretic contain- ment, but, under our computational interpretation, constructively transform a membership proof of a string in one regular expres- sion into a membership proof of the same string in another regular expression. We...

  4. Automating InDesign with Regular Expressions

    CERN Document Server

    Kahrel, Peter

    2006-01-01

    If you need to make automated changes to InDesign documents beyond what basic search and replace can handle, you need regular expressions, and a bit of scripting to make them work. This Short Cut explains both how to write regular expressions, so you can find and replace the right things, and how to use them in InDesign specifically.

  5. Fast and compact regular expression matching

    DEFF Research Database (Denmark)

    Bille, Philip; Farach-Colton, Martin

    2008-01-01

    We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how...... to improve the space and/or remove a dependency on the alphabet size for each problem using either an improved tabulation technique of an existing algorithm or by combining known algorithms in a new way....

  6. Regular Expression Matching and Operational Semantics

    Directory of Open Access Journals (Sweden)

    Asiri Rathnayake

    2011-08-01

    Full Text Available Many programming languages and tools, ranging from grep to the Java String library, contain regular expression matchers. Rather than first translating a regular expression into a deterministic finite automaton, such implementations typically match the regular expression on the fly. Thus they can be seen as virtual machines interpreting the regular expression much as if it were a program with some non-deterministic constructs such as the Kleene star. We formalize this implementation technique for regular expression matching using operational semantics. Specifically, we derive a series of abstract machines, moving from the abstract definition of matching to increasingly realistic machines. First a continuation is added to the operational semantics to describe what remains to be matched after the current expression. Next, we represent the expression as a data structure using pointers, which enables redundant searches to be eliminated via testing for pointer equality. From there, we arrive both at Thompson's lockstep construction and a machine that performs some operations in parallel, suitable for implementation on a large number of cores, such as a GPU. We formalize the parallel machine using process algebra and report some preliminary experiments with an implementation on a graphics processor using CUDA.

  7. Deterministic automata for extended regular expressions

    Directory of Open Access Journals (Sweden)

    Syzdykov Mirzakhmet

    2017-12-01

    Full Text Available In this work we present the algorithms to produce deterministic finite automaton (DFA for extended operators in regular expressions like intersection, subtraction and complement. The method like “overriding” of the source NFA(NFA not defined with subset construction rules is used. The past work described only the algorithm for AND-operator (or intersection of regular languages; in this paper the construction for the MINUS-operator (and complement is shown.

  8. Bit-coded regular expression parsing

    DEFF Research Database (Denmark)

    Nielsen, Lasse; Henglein, Fritz

    2011-01-01

    the DFA-based parsing algorithm due to Dub ´e and Feeley to emit the bits of the bit representation without explicitly materializing the parse tree itself. We furthermore show that Frisch and Cardelli’s greedy regular expression parsing algorithm can be straightforwardly modified to produce bit codings...

  9. Regular expressions compiler and some applications

    International Nuclear Information System (INIS)

    Saldana A, H.

    1978-01-01

    We deal with high level programming language of a Regular Expressions Compiler (REC). The first chapter is an introduction in which the history of the REC development and the problems related to its numerous applicatons are described. The syntactic and sematic rules as well as the language features are discussed just after the introduction. Concerning the applicatons as examples, an adaptation is given in order to solve numerical problems and another for the data manipulation. The last chapter is an exposition of ideas and techniques about the compiler construction. Examples of the adaptation to numerical problems show the applications to education, vector analysis, quantum mechanics, physics, mathematics and other sciences. The rudiments of an operating system for a minicomputer are the examples of the adaptation to symbolic data manipulaton. REC is a programming language that could be applied to solve problems in almost any human activity. Handling of computer graphics, control equipment, research on languages, microprocessors and general research are some of the fields in which this programming language can be applied and developed. (author)

  10. Stream Processing Using Grammars and Regular Expressions

    DEFF Research Database (Denmark)

    Rasmussen, Ulrik Terp

    disambiguation. The first algorithm operates in two passes in a semi-streaming fashion, using a constant amount of working memory and an auxiliary tape storage which is written in the first pass and consumed by the second. The second algorithm is a single-pass and optimally streaming algorithm which outputs...... as much of the parse tree as is semantically possible based on the input prefix read so far, and resorts to buffering as many symbols as is required to resolve the next choice. Optimality is obtained by performing a PSPACE-complete pre-analysis on the regular expression. In the second part we present...... Kleenex, a language for expressing high-performance streaming string processing programs as regular grammars with embedded semantic actions, and its compilation to streaming string transducers with worst-case linear-time performance. Its underlying theory is based on transducer decomposition into oracle...

  11. Two-pass greedy regular expression parsing

    DEFF Research Database (Denmark)

    Grathwohl, Niels Bjørn Bugge; Henglein, Fritz; Nielsen, Lasse

    2013-01-01

    We present new algorithms for producing greedy parses for regular expressions (REs) in a semi-streaming fashion. Our lean-log algorithm executes in time O(mn) for REs of size m and input strings of size n and outputs a compact bit-coded parse tree representation. It improves on previous algorithms...... by: operating in only 2 passes; using only O(m) words of random-access memory (independent of n); requiring only kn bits of sequentially written and read log storage, where k ... and not requiring it to be stored at all. Previous RE parsing algorithms do not scale linearly with input size, or require substantially more log storage and employ 3 passes where the first consists of reversing the input, or do not or are not known to produce a greedy parse. The performance of our unoptimized C...

  12. International regularity development partnership (IRDP)

    Energy Technology Data Exchange (ETDEWEB)

    Melani, Ai; Chang, Soon Heung [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2010-10-15

    Nuclear Energy enters a renaissance era. Several countries consider nuclear as one of their energy resources. For example at the present Vietnam just sign an agreement with Russia for their first nuclear power plants, Malaysia expected that the first nuclear power plant will be operated and commercially available in around the year of 2021. Thailand, Singapore and Indonesia also consider having nuclear power plant in the time frame around 2025. Each country recently tries to prepare their regulatory infrastructure for their first nuclear power plant. The problems are each country doesn't have enough human resource and experience in preparing the nuclear power plant regulations infrastructure. The remains regulations resource is from IAEA which are too general to implement and USNRC which are too detail and difficult to implement for the lack of human resources. Therefore this International Regulatory Development Partnership (IRDP) could be the solutions for the demand of regulatory infrastructure preparations for those countries who's want to emerging nuclear power plant in their country

  13. Expressiveness modulo Bisimilarity of Regular Expressions with Parallel Composition (Extended Abstract

    Directory of Open Access Journals (Sweden)

    Jos C. M. Baeten

    2010-11-01

    Full Text Available The languages accepted by finite automata are precisely the languages denoted by regular expressions. In contrast, finite automata may exhibit behaviours that cannot be described by regular expressions up to bisimilarity. In this paper, we consider extensions of the theory of regular expressions with various forms of parallel composition and study the effect on expressiveness. First we prove that adding pure interleaving to the theory of regular expressions strictly increases its expressiveness up to bisimilarity. Then, we prove that replacing the operation for pure interleaving by ACP-style parallel composition gives a further increase in expressiveness. Finally, we prove that the theory of regular expressions with ACP-style parallel composition and encapsulation is expressive enough to express all finite automata up to bisimilarity. Our results extend the expressiveness results obtained by Bergstra, Bethke and Ponse for process algebras with (the binary variant of Kleene's star operation.

  14. Identification of cyclic nucleotide gated channels using regular expressions

    KAUST Repository

    Zelman, Alice K.

    2013-09-03

    Cyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one- pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin-binding domain. Despite their functional similarities, the plant CNGC family members appear to have different conserved amino acid motifs within corresponding functional domains than animal and bacterial CNGCs do. Here we describe the development and application of methods employing plant CNGC-specific sequence motifs as diagnostic tools to identify novel candidate channels in different plants. These methods are used to evaluate the validity of annotations of putative orthologs of CNGCs from plant genomes. The methods detail how to employ regular expressions of conserved amino acids in functional domains of annotated CNGCs and together with Web tools such as PHI-BLAST and ScanProsite to identify novel candidate CNGCs in species including Physcomitrella patens. © Springer Science+Business Media New York 2013.

  15. Processing SPARQL queries with regular expressions in RDF databases

    Science.gov (United States)

    2011-01-01

    Background As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users’ requests for extracting information from the RDF data as well as the lack of users’ knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns. PMID:21489225

  16. Processing SPARQL queries with regular expressions in RDF databases

    Directory of Open Access Journals (Sweden)

    Cho Hune

    2011-03-01

    Full Text Available Abstract Background As the Resource Description Framework (RDF data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf or Bio2RDF (bio2rdf.org, SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users’ requests for extracting information from the RDF data as well as the lack of users’ knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1 We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2 We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3 We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.

  17. Processing SPARQL queries with regular expressions in RDF databases.

    Science.gov (United States)

    Lee, Jinsoo; Pham, Minh-Duc; Lee, Jihwan; Han, Wook-Shin; Cho, Hune; Yu, Hwanjo; Lee, Jeong-Hoon

    2011-03-29

    As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.

  18. Iterated Process Analysis over Lattice-Valued Regular Expressions

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Nielson, Flemming; Nielson, Hanne Riis

    2016-01-01

    We present an iterated approach to statically analyze programs of two processes communicating by message passing. Our analysis operates over a domain of lattice-valued regular expressions, and computes increasingly better approximations of each process's communication behavior. Overall the work e...... extends traditional semantics-based program analysis techniques to automatically reason about message passing in a manner that can simultaneously analyze both values of variables as well as message order, message content, and their interdependencies.......We present an iterated approach to statically analyze programs of two processes communicating by message passing. Our analysis operates over a domain of lattice-valued regular expressions, and computes increasingly better approximations of each process's communication behavior. Overall the work...

  19. Cleaning OCR'd text with Regular Expressions

    Directory of Open Access Journals (Sweden)

    Laura Turner O'Hara

    2013-05-01

    Full Text Available Optical Character Recognition (OCR—the conversion of scanned images to machine-encoded text—has proven a godsend for historical research. This process allows texts to be searchable on one hand and more easily parsed and mined on the other. But we’ve all noticed that the OCR for historic texts is far from perfect. Old type faces and formats make for unique OCR. How might we improve poor quality OCR? The answer is Regular Expressions or “regex.”

  20. Cleaning OCR'd text with Regular Expressions

    OpenAIRE

    Laura Turner O'Hara

    2013-01-01

    Optical Character Recognition (OCR)—the conversion of scanned images to machine-encoded text—has proven a godsend for historical research. This process allows texts to be searchable on one hand and more easily parsed and mined on the other. But we’ve all noticed that the OCR for historic texts is far from perfect. Old type faces and formats make for unique OCR. How might we improve poor quality OCR? The answer is Regular Expressions or “regex.”

  1. Regularities development of entrepreneurial structures in regions

    Directory of Open Access Journals (Sweden)

    Julia Semenovna Pinkovetskaya

    2012-12-01

    Full Text Available Consider regularities and tendencies for the three types of entrepreneurial structures — small enterprises, medium enterprises and individual entrepreneurs. The aim of the research was to confirm the possibilities of describing indicators of aggregate entrepreneurial structures with the use of normal law distribution functions. Presented proposed by the author the methodological approach and results of construction of the functions of the density distribution for the main indicators for the various objects: the Russian Federation, regions, as well as aggregates ofentrepreneurial structures, specialized in certain forms ofeconomic activity. All the developed functions, as shown by the logical and statistical analysis, are of high quality and well-approximate the original data. In general, the proposed methodological approach is versatile and can be used in further studies of aggregates of entrepreneurial structures. The received results can be applied in solving a wide range of problems justify the need for personnel and financial resources at the federal, regional and municipal levels, as well as the formation of plans and forecasts of development entrepreneurship and improvement of this sector of the economy.

  2. FPGA-accelerated algorithm for the regular expression matching system

    Science.gov (United States)

    Russek, P.; Wiatr, K.

    2015-01-01

    This article describes an algorithm to support a regular expressions matching system. The goal was to achieve an attractive performance system with low energy consumption. The basic idea of the algorithm comes from a concept of the Bloom filter. It starts from the extraction of static sub-strings for strings of regular expressions. The algorithm is devised to gain from its decomposition into parts which are intended to be executed by custom hardware and the central processing unit (CPU). The pipelined custom processor architecture is proposed and a software algorithm explained accordingly. The software part of the algorithm was coded in C and runs on a processor from the ARM family. The hardware architecture was described in VHDL and implemented in field programmable gate array (FPGA). The performance results and required resources of the above experiments are given. An example of target application for the presented solution is computer and network security systems. The idea was tested on nearly 100,000 body-based viruses from the ClamAV virus database. The solution is intended for the emerging technology of clusters of low-energy computing nodes.

  3. Determine point-to-point networking interactions using regular expressions

    Directory of Open Access Journals (Sweden)

    Konstantin S. Deev

    2015-06-01

    Full Text Available As Internet growth and becoming more popular, the number of concurrent data flows start to increasing, which makes sense in bandwidth requested. Providers and corporate customers need ability to identify point-to-point interactions. The best is to use special software and hardware implementations that distribute the load in the internals of the complex, using the principles and approaches, in particular, described in this paper. This paper represent the principles of building system, which searches for a regular expression match using computing on graphics adapter in server station. A significant computing power and capability to parallel execution on modern graphic processor allows inspection of large amounts of data through sets of rules. Using the specified characteristics can lead to increased computing power in 30…40 times compared to the same setups on the central processing unit. The potential increase in bandwidth capacity could be used in systems that provide packet analysis, firewalls and network anomaly detectors.

  4. Hessian regularization based non-negative matrix factorization for gene expression data clustering.

    Science.gov (United States)

    Liu, Xiao; Shi, Jun; Wang, Congzhi

    2015-01-01

    Since a key step in the analysis of gene expression data is to detect groups of genes that have similar expression patterns, clustering technique is then commonly used to analyze gene expression data. Data representation plays an important role in clustering analysis. The non-negative matrix factorization (NMF) is a widely used data representation method with great success in machine learning. Although the traditional manifold regularization method, Laplacian regularization (LR), can improve the performance of NMF, LR still suffers from the problem of its weak extrapolating power. Hessian regularization (HR) is a newly developed manifold regularization method, whose natural properties make it more extrapolating, especially for small sample data. In this work, we propose the HR-based NMF (HR-NMF) algorithm, and then apply it to represent gene expression data for further clustering task. The clustering experiments are conducted on five commonly used gene datasets, and the results indicate that the proposed HR-NMF outperforms LR-based NMM and original NMF, which suggests the potential application of HR-NMF for gene expression data.

  5. Inclusion Professional Development Model and Regular Middle School Educators

    Science.gov (United States)

    Royster, Otelia; Reglin, Gary L.; Losike-Sedimo, Nonofo

    2014-01-01

    The purpose of this study was to determine the impact of a professional development model on regular education middle school teachers' knowledge of best practices for teaching inclusive classes and attitudes toward teaching these classes. There were 19 regular education teachers who taught the core subjects. Findings for Research Question 1…

  6. Regular website transformation to mobile friendly methodology development

    OpenAIRE

    Miščenkov, Ilja

    2017-01-01

    Nowadays, rate of technology improvement grows faster than ever which results in increased mobile device usage. Internet users often choose to browse their favorite websites via computers as well as mobile devices, however, not every website is suited to be displayed on both types of technology. As an example the website of Vilnius University’s Mathematics and Informatics faculty. Therefore the objective of this work is to develop a step-by-step procedure which is used to turn a regular websi...

  7. Adaptive L1/2 Shooting Regularization Method for Survival Analysis Using Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Xiao-Ying Liu

    2013-01-01

    Full Text Available A new adaptive L1/2 shooting regularization method for variable selection based on the Cox’s proportional hazards mode being proposed. This adaptive L1/2 shooting algorithm can be easily obtained by the optimization of a reweighed iterative series of L1 penalties and a shooting strategy of L1/2 penalty. Simulation results based on high dimensional artificial data show that the adaptive L1/2 shooting regularization method can be more accurate for variable selection than Lasso and adaptive Lasso methods. The results from real gene expression dataset (DLBCL also indicate that the L1/2 regularization method performs competitively.

  8. Express web application development

    CERN Document Server

    Yaapa, Hage

    2013-01-01

    Express Web Application Development is a practical introduction to learning about Express. Each chapter introduces you to a different area of Express, using screenshots and examples to get you up and running as quickly as possible.If you are looking to use Express to build your next web application, ""Express Web Application Development"" will help you get started and take you right through to Express' advanced features. You will need to have an intermediate knowledge of JavaScript to get the most out of this book.

  9. Hessian regularization based symmetric nonnegative matrix factorization for clustering gene expression and microbiome data.

    Science.gov (United States)

    Ma, Yuanyuan; Hu, Xiaohua; He, Tingting; Jiang, Xingpeng

    2016-12-01

    Nonnegative matrix factorization (NMF) has received considerable attention due to its interpretation of observed samples as combinations of different components, and has been successfully used as a clustering method. As an extension of NMF, Symmetric NMF (SNMF) inherits the advantages of NMF. Unlike NMF, however, SNMF takes a nonnegative similarity matrix as an input, and two lower rank nonnegative matrices (H, H T ) are computed as an output to approximate the original similarity matrix. Laplacian regularization has improved the clustering performance of NMF and SNMF. However, Laplacian regularization (LR), as a classic manifold regularization method, suffers some problems because of its weak extrapolating ability. In this paper, we propose a novel variant of SNMF, called Hessian regularization based symmetric nonnegative matrix factorization (HSNMF), for this purpose. In contrast to Laplacian regularization, Hessian regularization fits the data perfectly and extrapolates nicely to unseen data. We conduct extensive experiments on several datasets including text data, gene expression data and HMP (Human Microbiome Project) data. The results show that the proposed method outperforms other methods, which suggests the potential application of HSNMF in biological data clustering. Copyright © 2016. Published by Elsevier Inc.

  10. Learning SAS’s Perl Regular Expression Matching the Easy Way: By Doing

    Science.gov (United States)

    2015-01-12

    Doing 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Paul Genovesi 5d. PROJECT NUMBER 5e. TASK NUMBER 5f...regex_learning_tool allows both beginner and expert to efficiently practice PRX matching by selecting and processing only the match records that the user is interested...perl regular expression and/or source string. The regex_learning_tool allows both beginner and expert to efficiently practice PRX matching by

  11. Schnek: A C++ library for the development of parallel simulation codes on regular grids

    Science.gov (United States)

    Schmitz, Holger

    2018-05-01

    A large number of algorithms across the field of computational physics are formulated on grids with a regular topology. We present Schnek, a library that enables fast development of parallel simulations on regular grids. Schnek contains a number of easy-to-use modules that greatly reduce the amount of administrative code for large-scale simulation codes. The library provides an interface for reading simulation setup files with a hierarchical structure. The structure of the setup file is translated into a hierarchy of simulation modules that the developer can specify. The reader parses and evaluates mathematical expressions and initialises variables or grid data. This enables developers to write modular and flexible simulation codes with minimal effort. Regular grids of arbitrary dimension are defined as well as mechanisms for defining physical domain sizes, grid staggering, and ghost cells on these grids. Ghost cells can be exchanged between neighbouring processes using MPI with a simple interface. The grid data can easily be written into HDF5 files using serial or parallel I/O.

  12. Regularization strategies for hyperplane classifiers: application to cancer classification with gene expression data.

    Science.gov (United States)

    Andries, Erik; Hagstrom, Thomas; Atlas, Susan R; Willman, Cheryl

    2007-02-01

    Linear discrimination, from the point of view of numerical linear algebra, can be treated as solving an ill-posed system of linear equations. In order to generate a solution that is robust in the presence of noise, these problems require regularization. Here, we examine the ill-posedness involved in the linear discrimination of cancer gene expression data with respect to outcome and tumor subclasses. We show that a filter factor representation, based upon Singular Value Decomposition, yields insight into the numerical ill-posedness of the hyperplane-based separation when applied to gene expression data. We also show that this representation yields useful diagnostic tools for guiding the selection of classifier parameters, thus leading to improved performance.

  13. A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

    Science.gov (United States)

    Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

    2017-12-19

    Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

  14. Flowchart Programs, Regular Expressions, and Decidability of Polynomial Growth-Rate

    Directory of Open Access Journals (Sweden)

    Amir M. Ben-Amram

    2016-07-01

    Full Text Available We present a new method for inferring complexity properties for a class of programs in the form of flowcharts annotated with loop information. Specifically, our method can (soundly and completely decide if computed values are polynomially bounded as a function of the input; and similarly for the running time. Such complexity properties are undecidable for a Turing-complete programming language, and a common work-around in program analysis is to settle for sound but incomplete solutions. In contrast, we consider a class of programs that is Turing-incomplete, but strong enough to include several challenges for this kind of analysis. For a related language that has well-structured syntax, similar to Meyer and Ritchie's LOOP programs, the problem has been previously proved to be decidable. The analysis relied on the compositionality of programs, hence the challenge in obtaining similar results for flowchart programs with arbitrary control-flow graphs. Our answer to the challenge is twofold: first, we propose a class of loop-annotated flowcharts, which is more general than the class of flowcharts that directly represent structured programs; secondly, we present a technique to reuse the ideas from the work on tructured programs and apply them to such flowcharts. The technique is inspired by the classic translation of non-deterministic automata to regular expressions, but we obviate the exponential cost of constructing such an expression, obtaining a polynomial-time analysis. These ideas may well be applicable to other analysis problems.

  15. Quantitative regularities of development of endogenous infection in irradiated organism

    International Nuclear Information System (INIS)

    Mal'tsev, V.N.

    1979-01-01

    A statistical analysis of data from the literature and the author's own experimental results are reviewed to show the functional relationships between the radiation dose and the development of endogenous infection in irradiated organisms. A direct linear dependence was found between the dose of radiation and the severity of endogenous infection at doses causing death from the ''bone marrow'' syndrome in acute radiation sickness. In case of death from the ''intestinal'' syndrome, an inverse linear dependence can be observed between the radiation dose and the culture yield of microbes from internal organs. In this case, the pathological effect on the organism is due to bacterial endotoxins formed during the disintegration of microbial cells in the organism. Endogenous infection and endotoxinaemia essentially aggravate the progress of acute radiation disease. The importance of endogenous infection for the death of the organism is minimized in irradiation at doses causing death ''under the ray''. (author)

  16. DEVELOPMENT OF INNOVATION MANAGEMENT THEORY BASED ON SYSTEM-WIDE REGULARITIES

    Directory of Open Access Journals (Sweden)

    Violetta N. Volkova

    2013-01-01

    Full Text Available The problem of a comprehension of the innovation management theory and an ability of its development on basis of system theory is set up. The authors consider features of management of socio-economic systems as open, self-organising systems with active components and give a classification of the systems’ regularities illustrating these features. The need to take into account the regularities of emergent, hierarchical order, equifinality, Ashby’s law of requisite variety, historicity and self-organization is shown.

  17. Contribution to regularizing iterative method development for attenuation correction in gamma emission tomography

    International Nuclear Information System (INIS)

    Cao, A.

    1981-07-01

    This study is concerned with the transverse axial gamma emission tomography. The problem of self-attenuation of radiations in biologic tissues is raised. The regularizing iterative method is developed, as a reconstruction method of 3 dimensional images. The different steps from acquisition to results, necessary to its application, are described. Organigrams relative to each step are explained. Comparison notion between two reconstruction methods is introduced. Some methods used for the comparison or to bring about the characteristics of a reconstruction technique are defined. The studies realized to test the regularizing iterative method are presented and results are analyzed [fr

  18. Glaucoma screening during regular optician visits : can the population at risk of developing glaucoma be reached?

    NARCIS (Netherlands)

    Stoutenbeek, R.; Jansonius, N. M.

    2006-01-01

    Aim: To determine the percentage of the population at risk of developing glaucoma, which can potentially be reached by conducting glaucoma screening during regular optician visits. Methods: 1200 inhabitants aged > 40 years were randomly selected from Dutch community population databases. A

  19. Coordinate-invariant regularization

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1987-01-01

    A general phase-space framework for coordinate-invariant regularization is given. The development is geometric, with all regularization contained in regularized DeWitt Superstructures on field deformations. Parallel development of invariant coordinate-space regularization is obtained by regularized functional integration of the momenta. As representative examples of the general formulation, the regularized general non-linear sigma model and regularized quantum gravity are discussed. copyright 1987 Academic Press, Inc

  20. Advanced express web application development

    CERN Document Server

    Keig, Andrew

    2013-01-01

    A practical book, guiding the reader through the development of a single page application using a feature-driven approach.If you are an experienced JavaScript developer who wants to build highly scalable, real-world applications using Express, this book is ideal for you. This book is an advanced title and assumes that the reader has some experience with node, Javascript MVC web development frameworks, and has heard of Express before, or is familiar with it. You should also have a basic understanding of Redis and MongoDB. This book is not a tutorial on Node, but aims to explore some of the more

  1. Expression of RAGE and HMGB1 in thymic epithelial tumors, thymic hyperplasia and regular thymic morphology.

    Directory of Open Access Journals (Sweden)

    Bernhard Moser

    Full Text Available Recently, a role of the receptor for advanced glycation endproducts (RAGE in myasthenia gravis was described. RAGE and its ligand high mobility group box 1 (HMGB1 play key roles in autoimmunity and cancer. To test whether these molecules are involved in patients with thymic abnormalities we applied immunohistochemical analysis in 33 cases of thymic epithelial tumors, comprising 27 thymomas and 6 thymic carcinomas, and 21 nonneoplastic thymuses. Both molecules were detected in neoplastic epithelial cells: RAGE staining was most intense in WHO type B2 thymomas and thymic carcinomas (pB3>thymic carcinoma (p<0.001. Conversely, HMGB1 cytoplasmic staining intensities were as follows: A and AB (none, B1 (strong, B2 (moderate, B3 and thymic carcinoma (weak; (p<0.001. Fetal thymic tissue showed a distinct expression of RAGE and HMGB1 in subcapsular cortical epithelial cells which was found in 50% of myasthenic patients. Furthermore RAGE and HMGB1 were expressed in thymocytes, macrophages, Hassall's corpuscles, thymic medulla, and germinal center cells in myasthenic patients. Immunohistochemistry results were complemented by systemic measurements (immunosorbent assay: serum levels of soluble RAGE were significantly reduced in patients with epithelial tumors (p = 0.008; and in invasive tumors (p = 0.008. Whereas RAGE was equally reduced in thymic hyperplasia and epithelial tumors (p = 0.003, HMGB1 was only elevated in malignancies (p = 0.036. Results were most pronounced in thymic carcinomas. Thus, RAGE and HMGB1 are involved in the (patho-physiology of thymus, as evidenced by differentiated thymic and systemic expression patterns that may act as diagnostic or therapeutic targets in autoimmune disease and cancer.

  2. Expression of RAGE and HMGB1 in thymic epithelial tumors, thymic hyperplasia and regular thymic morphology.

    Science.gov (United States)

    Moser, Bernhard; Janik, Stefan; Schiefer, Ana-Iris; Müllauer, Leonhard; Bekos, Christine; Scharrer, Anke; Mildner, Michael; Rényi-Vámos, Ferenc; Klepetko, Walter; Ankersmit, Hendrik Jan

    2014-01-01

    Recently, a role of the receptor for advanced glycation endproducts (RAGE) in myasthenia gravis was described. RAGE and its ligand high mobility group box 1 (HMGB1) play key roles in autoimmunity and cancer. To test whether these molecules are involved in patients with thymic abnormalities we applied immunohistochemical analysis in 33 cases of thymic epithelial tumors, comprising 27 thymomas and 6 thymic carcinomas, and 21 nonneoplastic thymuses. Both molecules were detected in neoplastic epithelial cells: RAGE staining was most intense in WHO type B2 thymomas and thymic carcinomas (pB3>thymic carcinoma (pepithelial cells which was found in 50% of myasthenic patients. Furthermore RAGE and HMGB1 were expressed in thymocytes, macrophages, Hassall's corpuscles, thymic medulla, and germinal center cells in myasthenic patients. Immunohistochemistry results were complemented by systemic measurements (immunosorbent assay): serum levels of soluble RAGE were significantly reduced in patients with epithelial tumors (p = 0.008); and in invasive tumors (p = 0.008). Whereas RAGE was equally reduced in thymic hyperplasia and epithelial tumors (p = 0.003), HMGB1 was only elevated in malignancies (p = 0.036). Results were most pronounced in thymic carcinomas. Thus, RAGE and HMGB1 are involved in the (patho-)physiology of thymus, as evidenced by differentiated thymic and systemic expression patterns that may act as diagnostic or therapeutic targets in autoimmune disease and cancer.

  3. A geometric buckling expression for regular polygons: II. Analyses based on the multiple reciprocity boundary element method

    International Nuclear Information System (INIS)

    Itagaki, Masafumi; Miyoshi, Yoshinori; Hirose, Hideyuki

    1993-01-01

    A procedure is presented for the determination of geometric buckling for regular polygons. A new computation technique, the multiple reciprocity boundary element method (MRBEM), has been applied to solve the one-group neutron diffusion equation. The main difficulty in applying the ordinary boundary element method (BEM) to neutron diffusion problems has been the need to compute a domain integral, resulting from the fission source. The MRBEM has been developed for transforming this type of domain integral into an equivalent boundary integral. The basic idea of the MRBEM is to apply repeatedly the reciprocity theorem (Green's second formula) using a sequence of higher order fundamental solutions. The MRBEM requires discretization of the boundary only rather than of the domain. This advantage is useful for extensive survey analyses of buckling for complex geometries. The results of survey analyses have indicated that the general form of geometric buckling is B g 2 = (a n /R c ) 2 , where R c represents the radius of the circumscribed circle of the regular polygon under consideration. The geometric constant A n depends on the type of regular polygon and takes the value of π for a square and 2.405 for a circle, an extreme case that has an infinite number of sides. Values of a n for a triangle, pentagon, hexagon, and octagon have been calculated as 4.190, 2.281, 2.675, and 2.547, respectively

  4. Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

    Science.gov (United States)

    Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

    2005-01-01

    As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

  5. Construction of Egr1-mediated human truncated apoptosis inducing factor expression vector and its expression regularity induced by radiation in breast cancer MCF-7 cells

    International Nuclear Information System (INIS)

    Wang Jianfeng; Gong Shouliang; Wang Zhicheng; Fang Fang; Liu Yang; Wu Jiahui

    2012-01-01

    Objective: To clone human truncated apoptosis inducing factor (AIF) cDNA sequence, and to construct early growth response 1 (Egr1)-mediated recombinant expression vector pcDNA 3.1-Egr1-AIF Δ1-480 (pEgr1-AIFΔ 1-480 ), and to observe its regularity induced by radiation in human breast cancer MCF-7 cells. Methods: The total mRNA extracted from human leukemia Jurkat cells used as template, and the human AIFΔ 1-480 was acquired by RT-PCR, and it was linked to pMD18T vector for sequencing. Egr1 fragment was digested from pMD19T-Egr1 by restrictive enzyme, and the Egr1-mediated expression plasmid pEgr1-AIFΔ 1-480 was constructed by gene recombination. There were control group, pcDNA3.1 group, pAIFΔ 1-480 group and pEgr1-AIFΔ 1-480 group in the experiment. After the plasmids in various groups were transfected into human breast cancer MCF-7 cells, the AIF and AIFΔ 1-480 protein expression time-effect (0, 2, 4, 12, 24 and 48 h after 2.0 Gy irradiation) and dose-effect (24 h after 0, 0.2, 0.5, 1.0, 2.0 and 5.0 Gy irradiation) regularity were measured by Western blotting method. Results: The sequencing results showed that the AIFΔ 1-480 acquired by RT-PCR was consistent with the sequence expected, the pEgr-AIFΔ 1-480 was confirmed by PCR and restrictive enzyme digestion. After 0-48 h the MCF-7 cells were irradiated by 2.0 Gy, and the AIF protein expressed in the cells in each group, and it increased significantly from 4 h and the AIF expressions in 4, 12, 24 and 48 h groups were higher than that in 0 h group (P<0.05), and it reached to maximum value at 48 h. But the AIFΔ 1-480 protein expressed in the cells in pAIFΔ 1-480 and pEgr1-AIFΔ 1-480 groups from 2 h (P<0.05), and it reached to peak value at 24 h. The AIFΔ 1-480 expressions in pEgr1-AIFΔ 1-480 group were higher than those in pAIFΔ 1-480 group at and 48 h (P<0.05). After the MCF-7 cells were irradiated by 0-5 Gy for 24 h, the AIF protein expressed in the cells in each group, but the AIFΔ 1-480 protein

  6. Understanding Regular Expressions

    Directory of Open Access Journals (Sweden)

    Doug Knox

    2013-06-01

    Full Text Available In this exercise we will use advanced find-and-replace capabilities in a word processing application in order to make use of structure in a brief historical document that is essentially a table in the form of prose. Without using a general programming language, we will gain exposure to some aspects of computational thinking, especially pattern matching, that can be immediately helpful to working historians (and others using word processors, and can form the basis for subsequent learning with more general programming environments.

  7. Regularities of development of unspecific reaction of cells, and modification of chemical protection

    International Nuclear Information System (INIS)

    Veksler, A.M.; Korystov, Yu.N.; Kublik, L.N.; Ehjdus, L.Kh.

    1979-01-01

    Regularities of development of a unspecific reaction of cells under the effect of different substances belonging to weak electrolytes have been studied. It was demonstrated that the rate of the unspecific reaction development under the effect of cysteamine and caffeine-benzoate depends on the agent concentration, temperature and pH of a medium. It was established that the response of a cell is determined by the overall intracellular concentration of the agent rather than by its specific character. The total concentration of the substance inside the cell depends on its physico-chemical characteristics and, with a pH gradient between cell and medium, can markedly vary from that in the medium. With similar intracellular content, both substances proved to be virtually equally effective. This suggests that it is possible to assess the effectiveness of some other biologically active substances many of which are weak electrolytes

  8. Alteration of Neurokinin B Gene Expression and Hypothalamic-Pituitary- Gonadal Axis in Response to One-month Regular Moderate Physical Activity

    Directory of Open Access Journals (Sweden)

    Nazli Khajehnasiri

    2017-08-01

    Full Text Available Abstract Background: The advantageous effects of the regular moderate physical activity (Exercise on reproduction is widely accepted, but until now, the alterations of the expression of hypothalamic arcuate nuclei gene affecting on reproduction axis in response to this type of physical activity are not clear. Therefore, the goal of the present investigation was to study the effect of one –month regular moderate physical activity on neurokinin B gene expression and reproductive axis hormonal changes. Materials and Methods: In the experimental study, fourteen adult male Wistar rats were randomly divided into control and one- month regular moderate exercise groups. After one - month physical activity (20m/min, the arcuate nucleus was isolated from brain and stored in -80 refrigerators for neurokinin B gene expression assay by Real-time PCR method. In addition, serum samples were taken to assess the corticosterone, luteinizing hormone and testosterone levels by ELISA method. Data were analyzed by Independent t-test in SPSS. Results: Neurokinin-B gene expression level was lower in the group which received physical activity than the control group(p<0.05. Also, corticosterone serum concentration was decreased in the physical activity group(p<0.05. By contrast, the physical activity induced luteinizing hormone and Testosterone serum levels evaluation in exersice group compared with control group (p<0.05. Conclusion: Regular moderate physical activity may improve male reproductive performance by reducing the corticosterone hormone level and decreasing neurokinin B expression.

  9. Students with Down syndrome in primary education in the Netherlands: regular or special? : effects of school placement on the development and the social network of children with Down syndrome and conditions for inclusive education

    OpenAIRE

    de Graaf, Gerrit

    2014-01-01

    Since the 1980s in the Netherlands more and more children with Down syndrome are entering regular schools. Three research questions were explored. 1. What does the development of Down syndrome regular elementary school placement look like expressed in numbers? In chapter 2 and chapter 3, a demographic model for birth and population prevalence of Down syndrome was developed and validated. For the Netherlands, birth prevalence currently is estimated at 14 per 10,000 with around 275 total annual...

  10. 25 CFR 39.132 - Can a school integrate Language Development programs into its regular instructional program?

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Can a school integrate Language Development programs into... Language Development Programs § 39.132 Can a school integrate Language Development programs into its regular instructional program? A school may offer Language Development programs to students as part of its...

  11. Structural development of child's artistic expression

    OpenAIRE

    Sanja Filipović; Milica Vojvodić

    2017-01-01

    Abstract Structural development implies control and capability of the expression usage in terms of independent creative expression and making. Understanding of structural development of child's artistic expression as a phenomenon (which is suitable to child's age) has some implications on methodical acts considering artistic education of children and youngsters. Therefore, it is of unexceptional importance to know these laws as well as methodical acts which encourage the structural develop...

  12. Distance-regular graphs

    NARCIS (Netherlands)

    van Dam, Edwin R.; Koolen, Jack H.; Tanaka, Hajime

    2016-01-01

    This is a survey of distance-regular graphs. We present an introduction to distance-regular graphs for the reader who is unfamiliar with the subject, and then give an overview of some developments in the area of distance-regular graphs since the monograph 'BCN'[Brouwer, A.E., Cohen, A.M., Neumaier,

  13. To d, or not to d. Recent developments and comparisons of regularization schemes

    Energy Technology Data Exchange (ETDEWEB)

    Gnendiger, C.; Pruna, G.M. [Paul Scherrer Institut, Villigen (Switzerland); Signer, A.; Ulrich, Y.; Visconti, A. [Paul Scherrer Institut, Villigen (Switzerland); Universitaet Zuerich, Physik-Institut, Zuerich (Switzerland); Stoeckinger, D. [Institut fuer Kern- und Teilchenphysik, Dresden (Germany); Broggio, A. [Technische Universitaet Muenchen, Physik Department T31, Garching (Germany); Cherchiglia, A.L. [Centro de Ciencias Naturais e Humanas, UFABC, Santo Andre (Brazil); Driencourt-Mangin, F.; Rodrigo, G. [Universitat de Valencia, Insituto de Fisica Corpuscular, UVEG-CSIC, Paterna (Spain); Fazio, A.R. [Universidad Nacional de Colombia, Departamento de Fisica, Bogota D.C. (Colombia); Hiller, B. [University of Coimbra, CFisUC, Department of Physics, Coimbra (Portugal); Mastrolia, P. [Universita di Padova, Dipartimento di Fisica ed Astronomia, Padua (Italy); INFN, Sezione di Padova, Padua (Italy); Peraro, T. [The University of Edinburgh, Higgs Centre for Theoretical Physics, Edinburgh (United Kingdom); Pittau, R. [Universidad de Granada, Dept. de Fisica Teorica y del Cosmos yd CAFPE, Granada (Spain); Sampaio, M. [ICEX, UFMG, Departamento de Fisica, Belo Horizonte (Brazil); Sborlini, G. [Universitat de Valencia, Insituto de Fisica Corpuscular, UVEG-CSIC, Paterna (Spain); Universita di Milano, Dipartimento di Fisica, Milan (Italy); INFN, Sezione di Milano, Milan (Italy); Bobadilla, W.J.T. [Universitat de Valencia, Insituto de Fisica Corpuscular, UVEG-CSIC, Paterna (Spain); Universita di Padova, Dipartimento di Fisica ed Astronomia, Padua (Italy); INFN, Sezione di Padova, Padua (Italy); Tramontano, F. [Universita di Napoli, Dipartimento di Fisica, Naples (Italy); INFN, Sezione di Napoli, Naples (Italy)

    2017-07-15

    We give an introduction to several regularization schemes that deal with ultraviolet and infrared singularities appearing in higher-order computations in quantum field theories. Comparing the computation of simple quantities in the various schemes, we point out similarities and differences between them. (orig.)

  14. Regular Meals at School as a Factor of Physical Development of Children and Adolescents: Results of a Cohort Study

    OpenAIRE

    Igor J. Esaulenko; Tatiana L. Nastausheva; Olga A. Zhdanova; Olga V. Minakova; Iya I. Logvinova; Ludmila I. Ippolitova

    2016-01-01

    Background: In Russian schools, children are provided with meals, and certain categories of students get free meals. However, not all school students eat regularly.Objective: Our aim was to study the role of school meals in physical development of children and adolescents.Methods: The survey of schoolchildren aged 8–18 years (Voronezh) revealed two groups of students who eat at school regularly (Group 1) and on occasions (Group 2). We calculated Z scores of body length and body mass index (BM...

  15. The Effect of Regular Physical Education in the Transformation Motor Development of Children with Special Needs

    Directory of Open Access Journals (Sweden)

    Danilo Bojanić

    2016-02-01

    Full Text Available The aim of the research is to determine the level of quantitative changes of motor abilities of pupils with special needs under the influence of kinetic activity regular physical education teaching. The survey was conducted on students of the Centre for children and youth with special needs in Mostar, the city of Los Rosales in Mostar and day care facilities for children with special needs in Niksic. The sample was composed of boys of 46 subjects, who were involved in regular physical education for a period of one school year. The level of quantitative and qualitative changes in motor skills, written under the influence of kinesiology operators within regular school physical education classes, was estimated by applying appropriate tests of motor skills, selected in accordance with the degree of mental ability and biological age. Manifest variables applied in this experiment were processed using standard descriptive methods in order to determine their distribution function and basic function parameters. Comparisons of results of measures of central dispersion parameters initial and final measurement, it is evident that the applied program of physical education and sport contribute to changing the distribution of central and dispersion parameters, and that the same distribution of the final measurement closer to the normal distribution of results.

  16. Heat adaptation from regular hot water immersion decreases proinflammatory responses, HSP70 expression, and physical heat stress.

    Science.gov (United States)

    Yang, Fwu-Lin; Lee, Chia-Chi; Subeq, Yi-Maun; Lee, Chung-Jen; Ke, Chun-Yen; Lee, Ru-Ping

    2017-10-01

    Hot-water immersion (HWI) is a type of thermal therapy for treating various diseases. In our study, the physiological responses to occasional and regular HWI have been explored. The rats were divided into a control group, occasional group (1D), and regular group (7D). The 1D and 7D groups received 42°C during 15mins HWI for 1 and 7 days, respectively. The blood samples were collected for proinflammatory cytokines examinations, the heart, liver and kidney were excised for subsequent IHC analysis to measure the level of heat shock protein 70 (HSP70). The results revealed that the body temperature increased significantly during HWI on Day 3 and significantly declined on Days 6 and 7. For the 7D group, body weight, heart rate, hematocrit, platelet, osmolarity, and lactate level were lower than those in the 1D group. Furthermore, the levels of granulocyte counts, tumor necrosis factor-α, and interleukin-6 were lower in the 7D group than in the 1D group. The induction of HSP70 in the 1D group was higher than in the other groups. Physiological responses to occasional HWI are disadvantageous because of heat stress. However, adaptation to heat from regular HWI resulted in decreased proinflammatory responses and physical heat stress. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Report of third regular inspection of Tokai reprocessing facilities, Power Reactor and Nuclear Fuel Development Corp

    International Nuclear Information System (INIS)

    Anon.

    1987-01-01

    The reprocessing facilities passed the inspection before use on December 25, 1980, and started the full operation. Since then, this is the third regular inspection. It was begun on April 1, 1986, and finished on August 18, 1986, with the inspection of the rate of recovery of products. The reprocessing facilities which became the object of inspection were the facilities for accepting and storing spent fuel, the reprocessing facilities proper (the facilities of shearing, dissolution, separation, refining, denitration and recovery of acid and solvent), the facilities for storing products, measurement and control system, radioactive waste facilities, radiation control facilities and attached facilities (power, water, steam and testing). The main works carried out during the period of this regular inspection were the repair of an enriched uranium dissolution tank by welding, the renewal of a piping for a low activity waste liquid storing tank, and the removal of a washing tank. The total exposure dose in the first half of fiscal year 1986 was about 30.81 man-rem. (Kako, I.)

  18. Clustered Regularly Interspaced Short Palindromic Repeat-Dependent, Biofilm-Specific Death of Pseudomonas aeruginosa Mediated by Increased Expression of Phage-Related Genes.

    Science.gov (United States)

    Heussler, Gary E; Cady, Kyle C; Koeppen, Katja; Bhuju, Sabin; Stanton, Bruce A; O'Toole, George A

    2015-05-12

    The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (CRISPR/Cas) system is an adaptive immune system present in many archaea and bacteria. CRISPR/Cas systems are incredibly diverse, and there is increasing evidence of CRISPR/Cas systems playing a role in cellular functions distinct from phage immunity. Previously, our laboratory reported one such alternate function in which the type 1-F CRISPR/Cas system of the opportunistic pathogen Pseudomonas aeruginosa strain UCBPP-PA14 (abbreviated as P. aeruginosa PA14) inhibits both biofilm formation and swarming motility when the bacterium is lysogenized by the bacteriophage DMS3. In this study, we demonstrated that the presence of just the DMS3 protospacer and the protospacer-adjacent motif (PAM) on the P. aeruginosa genome is necessary and sufficient for this CRISPR-dependent loss of these group behaviors, with no requirement of additional DMS3 sequences. We also demonstrated that the interaction of the CRISPR system with the DMS3 protospacer induces expression of SOS-regulated phage-related genes, including the well-characterized pyocin operon, through the activity of the nuclease Cas3 and subsequent RecA activation. Furthermore, our data suggest that expression of the phage-related genes results in bacterial cell death on a surface due to the inability of the CRISPR-engaged strain to downregulate phage-related gene expression, while these phage-related genes have minimal impact on growth and viability under planktonic conditions. Deletion of the phage-related genes restores biofilm formation and swarming motility while still maintaining a functional CRISPR/Cas system, demonstrating that the loss of these group behaviors is an indirect effect of CRISPR self-targeting. The various CRISPR/Cas systems found in both archaea and bacteria are incredibly diverse, and advances in understanding the complex mechanisms of these varied systems has not only increased our knowledge of host

  19. Development of a Regularized Dynamic System Response Curve for Real-Time Flood Forecasting Correction

    Directory of Open Access Journals (Sweden)

    Yiqun Sun

    2018-04-01

    Full Text Available The dynamic system response curve (DSRC is commonly applied as a real-time flood forecasting error correction method to improve the accuracy of real-time flood forecasting. It has been widely recognized that the least squares (OLS/LS method, employed by DSRC, breaks down ill-posed problems, and therefore, the DSRC method may lead to deterioration in performance caused by meaningless solutions. To address this problem, a diagnostically theoretical analysis was conducted to investigate the relationship between the numerical solution of the Fredholm equation of the first kind and the DSRC method. The analysis clearly demonstrates the derivation of the problem and has implications for an improved approach. To overcome the unstable problem, a new method using regularization techniques (Tikhonov regularization and L-Curve criterion is proposed. Moreover, in this study, to improve the performance of hydrological models, the new method is used as an error correction method to correct a variable from a hydrological model. The proposed method incorporates the information from a hydrological model structure. Based on the analysis of the hydrological model, the free water storage of the Xinanjiang rainfall-runoff (XAJ model is corrected to improve the model’s performance. A numerical example and a real case study are presented to compare the two methods. Results from the numerical example indicate that the mean Nash–Sutcliffe efficiency value (NSE of the regularized DSRC method (RDSRC decreased from 0.99 to 0.55, while the mean NSE of DSRC decreased from 0.98 to −1.84 when the noise level was increased. The overall performance measured by four different criteria clearly demonstrates the robustness of the RDSRC method. Similar results were obtained for the real case study. The mean NSE of 35 flood events obtained by RDSRC method was 0.92, which is significantly higher than the mean NSE of DSRC (0.7. The results demonstrate that the RDSRC method is much

  20. Regularities in development of surface cracks in low-alloy steel under asymmetric cyclic bending

    International Nuclear Information System (INIS)

    Letunov, V.I.; Shul'ginov, B.S.; Plundrova, I.; Vajnshtok, V.A.; Kramarenko, I.V.

    1985-01-01

    Semielliptical cracks in low-alloy 09g2 and 12gn2mfayu steels are studied for regularities of their growth. It is shown that the growth rate of the semielliptical crack at the preset ΔK and R values is higher in the maximally depressed point of the front than in the point on the surface on the specimen under cyclic bending. A decrease of the 1/C parameter with growth of the semielliptical crack is experimentally established being attributed to the increase in difference of ΔK both in maximally depressed point of the crack front (phi=0) and in the point on the specimen surface (phi= π/2). Experiments have proved the correctness of the previously established formulas of stress-intensity factor calculation for semielliptical surface cracks under bending

  1. Expression of Sox genes in tooth development.

    Science.gov (United States)

    Kawasaki, Katsushige; Kawasaki, Maiko; Watanabe, Momoko; Idrus, Erik; Nagai, Takahiro; Oommen, Shelly; Maeda, Takeyasu; Hagiwara, Nobuko; Que, Jianwen; Sharpe, Paul T; Ohazama, Atsushi

    2015-01-01

    Members of the Sox gene family play roles in many biological processes including organogenesis. We carried out comparative in situ hybridization analysis of seventeen sox genes (Sox1-14, 17, 18, 21) during murine odontogenesis from the epithelial thickening to the cytodifferentiation stages. Localized expression of five Sox genes (Sox6, 9, 13, 14 and 21) was observed in tooth bud epithelium. Sox13 showed restricted expression in the primary enamel knots. At the early bell stage, three Sox genes (Sox8, 11, 17 and 21) were expressed in pre-ameloblasts, whereas two others (Sox5 and 18) showed expression in odontoblasts. Sox genes thus showed a dynamic spatio-temporal expression during tooth development.

  2. Regular Meals at School as a Factor of Physical Development of Children and Adolescents: Results of a Cohort Study

    Directory of Open Access Journals (Sweden)

    Igor J. Esaulenko

    2016-01-01

    Full Text Available Background: In Russian schools, children are provided with meals, and certain categories of students get free meals. However, not all school students eat regularly.Objective: Our aim was to study the role of school meals in physical development of children and adolescents.Methods: The survey of schoolchildren aged 8–18 years (Voronezh revealed two groups of students who eat at school regularly (Group 1 and on occasions (Group 2. We calculated Z scores of body length and body mass index (BMI using ANTHROPlus software. Nutritional status was determined based on the values of standard BMI deviations ( +2, +2 to +1, -1 to -2, -2. Health groups were formed according to the Children Health Comprehensive Assessment Instruction.Results: 484 schoolchildren (students of grades 3–11 were examined. 251 (52% school students had regular meals at school. Regular meal frequency decreased from 69% in the group of 8–10 year old students to 30% in the group of 15–18-year-olds. Z scores of body length in students of Groups 1 and 2 did not differ (0.44 ± 1.00 and 0.30 ± 1.00, respectively; p = 0.124. At the same time, children in Group 1 had higher Z scores of BMI (0.44 ± 1.30 and 0.12 ± 1.30, respectively; p = 0.007. In Group 1, the incidence of overweight and obesity decreased from 40% in group of 8–10 year old students to 15% in 15–18-year-olds, in Group 2 — from 35 to 18%, respectively; incidence of malnutrition increased from 9 to 24% in Group 1 and from 11 to 15% in Group 2. In Group 1, the number of students with health group III or IV was smaller (30% compared to 42% in the control group; p = 0.005.Conclusion: Regular meals at school are an important, but not critical factor in the physical development of children. The absence of regular meals at school may be a risk factor for chronic diseases in schoolchildren.

  3. Mastering web application development with Express

    CERN Document Server

    Vlăduțu, Alexandru

    2014-01-01

    If you are a Node.js developer who wants to take your Express skills to the next level and develop high performing, reliable web applications using best practices, this book is ideal for you. The only prerequisite is knowledge of Node.js.

  4. Adaptive regularization

    DEFF Research Database (Denmark)

    Hansen, Lars Kai; Rasmussen, Carl Edward; Svarer, C.

    1994-01-01

    Regularization, e.g., in the form of weight decay, is important for training and optimization of neural network architectures. In this work the authors provide a tool based on asymptotic sampling theory, for iterative estimation of weight decay parameters. The basic idea is to do a gradient desce...

  5. Structural development of child's artistic expression

    Directory of Open Access Journals (Sweden)

    Sanja Filipović

    2017-03-01

    Full Text Available Structural development implies control and capability of the expression usage in terms of independent creative expression and making. Understanding of structural development of child's artistic expression as a phenomenon (which is suitable to child's age has some implications on methodical acts considering the artistic education of children and youngsters. Therefore, it is of unexceptional importance to know these laws as well as methodical acts which encourage the structural development of artistic capabilities from an early age. Various experts dealt with this phenomenon, particularly Bogomil Karlavaris. In his methodical research, he has given an unexceptional part to this problem. It has been a starting point for analysis of certain methodical questions which are included in this work.

  6. Gene expression analysis of flax seed development

    Science.gov (United States)

    2011-01-01

    Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

  7. Gene expression analysis of flax seed development

    Directory of Open Access Journals (Sweden)

    Sharpe Andrew

    2011-04-01

    Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

  8. Inclusion in education: comparing pupils' development in special and regular education

    NARCIS (Netherlands)

    Peetsma, T.T.D.; Vergeer, M.M.; Roeleveld, J.; Karsten, S.

    2001-01-01

    Large-scale longitudinal data on differences in pupils' cognitive and psychosocial development in various types of special and mainstream schools are reported in this article. The study focuses on comparing the development of matched pairs of primary-aged pupils in mainstream and special education

  9. Developing logistic regression models using purchase attributes and demographics to predict the probability of purchases of regular and specialty eggs.

    Science.gov (United States)

    Bejaei, M; Wiseman, K; Cheng, K M

    2015-01-01

    Consumers' interest in specialty eggs appears to be growing in Europe and North America. The objective of this research was to develop logistic regression models that utilise purchaser attributes and demographics to predict the probability of a consumer purchasing a specific type of table egg including regular (white and brown), non-caged (free-run, free-range and organic) or nutrient-enhanced eggs. These purchase prediction models, together with the purchasers' attributes, can be used to assess market opportunities of different egg types specifically in British Columbia (BC). An online survey was used to gather data for the models. A total of 702 completed questionnaires were submitted by BC residents. Selected independent variables included in the logistic regression to develop models for different egg types to predict the probability of a consumer purchasing a specific type of table egg. The variables used in the model accounted for 54% and 49% of variances in the purchase of regular and non-caged eggs, respectively. Research results indicate that consumers of different egg types exhibit a set of unique and statistically significant characteristics and/or demographics. For example, consumers of regular eggs were less educated, older, price sensitive, major chain store buyers, and store flyer users, and had lower awareness about different types of eggs and less concern regarding animal welfare issues. However, most of the non-caged egg consumers were less concerned about price, had higher awareness about different types of table eggs, purchased their eggs from local/organic grocery stores, farm gates or farmers markets, and they were more concerned about care and feeding of hens compared to consumers of other eggs types.

  10. Keeping it regular: Development of thermoregulation in four tropical seabird species.

    Science.gov (United States)

    Hart, Lorinda A; Downs, Colleen T; Brown, Mark

    2017-02-01

    The thermoregulatory capacity of a species can determine which climatic niche it occupies. Its development in avian chicks is influenced by numerous factors. Furthermore, it is suggested that altricial chicks develop their thermoregulatory capacity post-hatching, while precocial chicks develop aspects of this in the egg. We investigated the development of thermoregulation of four co-occurring seabird species in the Seychelles; namely white, ground-nesting white-tailed tropicbirds (Phaethon lepturus) and tree-nesting fairy terns (Gygis alba); and dark plumaged, tree-nesting lesser noddies (Anous tenuirostris) and ground- and tree-nesting brown noddies (A. stolidus). White-tailed tropicbirds have semi-altricial chicks, while the remaining species have semi-precocial chicks. Cloacal temperatures (T b ) were measured at five day intervals from newly hatched chicks and compared over time, and with adult T b s. Initial T b s of all chicks, except fairy terns, were lower than those taken when chicks were older. Brooding cessation generally coincided with feather development, as did an increase in T b. Mean chick T b was significantly lower than mean adult T b for all species, but only white-tailed tropicbird and brown noddy chicks in tree nests differed significantly from mean adult T b when chick T b at five day intervals were considered. There was a significant interactive effect of nest site and age on brown noddy chick T b, but chick colour did not have a significant effect on T b . However, brown noddy chicks on dune crests maintained a constant T b sooner than chicks in tree nests. Our results demonstrate that tropical seabird species have a more delayed onset of thermoregulatory capabilities when compared with those in temperate environments, perhaps as nest sites are less thermally challenging. Nest microhabitats and behavioural thermoregulation, are likely more important during early chick development for these species. Copyright © 2016 Elsevier Ltd. All rights

  11. Using the regularities of high and critical technologies developing in innovative project management

    Directory of Open Access Journals (Sweden)

    S. G. Selivanov

    2014-01-01

    Full Text Available Problem-orientated to the innovative activity, computer-aided systems of production engineering (CASPE integrates design, manufacture, and organization activities using the interrelated innovation principles thus leaning the innovative activity towards the creation of innovative products and technological innovations of high science and technology level and efficiency. In this situation the innovative activity uses in practice not only the newest experience, but also the science laws and consequences, that is, in particular, “Science of Innovations”. The mentioned science laws explain wave dynamics of technical (technological systems development. In the course of innovation activities and/or innovation designing a modification of continuously acting technological system, usually, causes its developing and growing upwards by Sshaped curve. Changing a principle of action changes S-shaped curve development (Fig. 1. If such changes are within the certain “trace tube” we are entitled to state the steady system development.Analysis of changing target function of technological system within the “trace tube” of its steady development characterizes its growing wave dynamics (Fig. 1 using the S-shaped curves (sigmoid type relations. S-shaped innovative development relations of technological systems are, usually, explained by different mathematical models, each being in compliance with the certain process of science and technology. Singular innovative project management using the S-shaped curves can be explained by the following example (Fig.2.To use such management technique it is very important to know the mathematical models of S-curves for different types of innovation projects. That is why we consider given S-shaped relations in-detail for:- developing the high and critical technologies during R&D implementation using the cutting-edge CASSR (computer-aided systems of scientific research of high and critical technologies in innovation

  12. Formation and development of a breaker bar under regular waves. Part 2: Sediment transport and morphology

    DEFF Research Database (Denmark)

    Jacobsen, Niels Gjøl; Fredsøe, Jørgen

    2014-01-01

    In Part 2 of this work, the hydrodynamic model described in Part 1 is applied for the simulation of sediment transport and the associated morphological development of breaker bars. The sediment description is split into bed load and suspended load, and like the hydrodynamics the sediment transport...

  13. Regularization of finite temperature string theories

    International Nuclear Information System (INIS)

    Leblanc, Y.; Knecht, M.; Wallet, J.C.

    1990-01-01

    The tachyonic divergences occurring in the free energy of various string theories at finite temperature are eliminated through the use of regularization schemes and analytic continuations. For closed strings, we obtain finite expressions which, however, develop an imaginary part above the Hagedorn temperature, whereas open string theories are still plagued with dilatonic divergences. (orig.)

  14. Effect of a postnatal high-fat diet exposure on puberty onset, estrous cycle regularity, and kisspeptin expression in female rats

    DEFF Research Database (Denmark)

    Lie, Maria Elena Klibo; Overgaard, Agnete; Mikkelsen, Jens D

    2013-01-01

    Kisspeptin, encoded by Kiss1, plays a key role in pubertal maturation and reproduction as a positive upstream regulator of the hypothalamic-pituitary-gonadal (HPG) axis. To examine the role of high-fat diet (HFD) on puberty onset, estrous cycle regularity, and kisspeptin expression, female rats...... were exposed to HFD in distinct postnatal periods. Three groups of rats were exposed to HFD containing 60% energy from fat during the pre-weaning period (postnatal day (PND) 1-16, HFD PND 1-16), post-weaning period (HFD PND 21-34), or during both periods (HFD PND 1-34). Puberty onset, evaluated...... that postnatal HFD exposure induced irregular estrous cycles, but had no effect on puberty onset or kisspeptin....

  15. Regular physical activity attenuates the blood pressure response to public speaking and delays the development of hypertension.

    Science.gov (United States)

    Palatini, Paolo; Bratti, Paolo; Palomba, Daniela; Saladini, Francesca; Zanatta, Nello; Maraglino, Giuseppe

    2010-06-01

    The objective of this study was to investigate the effect of regular physical activity on the haemodynamic response to public speaking and to evaluate the long-term effect of exercise on development of hypertension. We assessed 75 sedentary and 44 active participants screened for stage 1 hypertension with consistent activity habits and 63 normotensive individuals as control. The blood pressure (BP) response to public speaking was assessed with beat-to-beat noninvasive recording. Definition of incident hypertension was based either on clinic or 24-h BP measurement. The BP response to public speaking was greater in the hypertensive than the normotensive participants (P=0.018/0.009). Among the former, sedentary participants showed increased BP reactivity to the speech test (45.2+/-22.6/22.2+/-11.5mmHg, Ppublic speaking into the Cox model influenced the strength of the association only marginally [hazard ratio=0.55 (95% CI 0.30-0.97) and hazard ratio=0.59 (95% CI 0.36-0.99), respectively]. Regular physical activity attenuates the BP reaction to psychosocial stressors. However, this mechanism seems to be only partially responsible for the long-term effect of exercise on BP.

  16. Quantitative regularities of development of endogenous infection in irradiated organism. (Survey of literature)

    Energy Technology Data Exchange (ETDEWEB)

    Mal' tsev, V N [Institut Biofiziki, Moscow (USSR)

    1979-01-01

    A statistical analysis of data from the literature and the author's own experimental results are reviewed to show the functional relationships between the radiation dose and the development of endogenous infection in irradiated organisms. A direct linear dependence was found between the dose of radiation and the severity of endogenous infection at doses causing death from the ''bone marrow'' syndrome in acute radiation sickness. In case of death from the ''intestinal'' syndrome, an inverse linear dependence can be observed between the radiation dose and the culture yield of microbes from internal organs. In this case, the pathological effect on the organism is due to bacterial endotoxins formed during the disintegration of microbial cells in the organism. Endogenous infection and endotoxinaemia essentially aggravate the progress of acute radiation disease. The importance of endogenous infection for the death of the organism is minimized in irradiation at doses causing death ''under the ray''.

  17. The Recent Development of Croatia's Population – Regular and Irregular Population Trends

    Directory of Open Access Journals (Sweden)

    Ivan Lajić

    2004-09-01

    Full Text Available The recent development of Croatia’s population is burdened by many phenomena, due to which we can define it as irregular. Aggression against the newly-independent Croatian state, as well as the wars in its neighbourhood, brought about mechanical population movements that to a great degree enter into the category of forced migrations. The war death rate in the early 1990s and the strong refugee and expellee flows caused the strongest depopulation in recent times. Depopulation was present not only in war-effected areas – its further consequences were felt throughout Croatia. The mechanical, rather than the biological component determined this regressive development. The paper identifies the key modalities in migration flows in Croatia, which show that it is at the same time both an emigration and an immigration country. Wars in former Yugoslavia, which were to a high degree characterized by inter-ethnic conflicts, resulted in migration flows of people to their ethnic core areas. Thus, Croatia has received a strong immigration current made up of Croats from Bosnia and Herzegovina, Serbia and Montenegro, whereas emigration from Croatia to the latter countries mostly involved rural Serbs. Besides these migration trends, members of the ethnically Croatian (majority population and also other groups from Croatia, have migrated to Western Europe, which was a continuation of traditional migration trends. Among these migrants there is a large contingent which could be denoted as part of the “brain drain”. The census conducted in 2001 applied a different methodology than earlier censuses. The problem of different census methodologies is especially pertinent in a country which has a large number of refugees and economic migrants that cannot be classified into the category of emigrants. Thus the 2001 Census registered that Croatia has 4,437,460 inhabitants, or 7.25% less than in 1991.

  18. The Regularities of the Cyclical Development of the World Economy in the Current Phase

    Directory of Open Access Journals (Sweden)

    Revyakin Georgy V.

    2017-09-01

    Full Text Available The article is aimed at identifying and describing the key tendencies in the cyclical development of the world economy. In order to allocate the cyclical component in the dynamics of the world-wide GDP growth, a time series decomposition was performed using the Hodrick-Prescott filter and the relationship of economic cycles to the dynamics of different indicators of economic conditions was analyzed. The persistent relationship between inflation, unemployment and the current phase of the economic cycle have been identified and described. The truth of the Phillips curve has been empirically demonstrated: existence of an inverse relationship between the rate of inflation and the level of unemployment. A new classification of branches of economy has been provided according to their susceptibility to the current phase of the economic cycle. According to this criterion, all branches of economy have been divided into the cyclical and the non-cyclical sectors. A hypothesis that there is a direct relationship between the average annual growth rate of GDP and the structure of the national economy has been suggested.

  19. Some problems concerning the regularities in the development of the latitudinal distribution of solar magnetic fields

    International Nuclear Information System (INIS)

    Bumba, V.; Hejna, L.

    1988-01-01

    From the comparison of several modes of time development of the latitudinal distribution of solar magnetic fields, obtained by different authors using different basic observational material and different methods, the following results were obtained: At high solar latitudes (|φ|> or ∼ 40deg) all distributions agree irrespective of the method of construction. In zones of activity around the solar equator, there is a qualitatively good but quantitatively poor agreement of the integrated, directly observed fields (from Mt. Wilson Observatory) and of the highly integrated fields derived from Hα synoptic charts. The mode of field distribution at high latitudes, more uniform and unipolar, is probably different from the field distribution at low latitudes where the more concentrated leading polarity occupies practically the same area as the less concentrated following polarity fields, if they are highly integrated. The large difference between Makarov's distribution and other modes of distribution seems to be natural if we take the method of construction into account, and very probably represents its close relationship with the smaller magnetic field elements connected with newer activity, while the other types of distribution demonstrate larger-scale, redistributed, older fields. The areas covered by the positive and negative polarities on the whole Sun during the investigated one and a half solar cycles (No 20 and 21) are practically equal. (author). 5 figs., 10 refs

  20. Factors influencing the development of routes for regular oil transport from Dikson

    Energy Technology Data Exchange (ETDEWEB)

    Riska, K. [ILS Ltd., Helsinki (Finland); Breivik, K.; Eide, I.S.; Gudmestad, O.; Hilden, T. [Statoil ASA, Stavanger (Norway)

    2006-11-15

    Many oil and gas companies have increased their exploration efforts in the Arctic where a considerable part of the world's remaining oil and gas resources are located. Several large fields have been discovered in areas far from markets. This paper described the challenge of finding methods for efficient, reliable and economic transport to markets. Traditionally, shipping operations in Arctic waters has taken place by using icebreakers. However, large scale development of oil and gas fields in the Arctic will require large tankers that are designed for operation under severe Arctic conditions. For that reason, Statoil initiated a program in 2005 to study the operation of large tankers in ice infested waters and under Arctic conditions. The primary objective was to demonstrate that large vessels could operate in ice infested waters and to study the effect of using vessels with large beams. Factors influencing the design of the vessels used for reliable year-round oil transportation by ships from the north-western Russian Arctic areas were investigated with special attention to one icebreaker escorting tanker with wider beam than that of the icebreaker; passage through pressurized ice fields; and, passage through ridge fields. The design of the whole transport system was described in this paper along with an investigation of the physics of the above factors. An ice model tank at the Helsinki University of Technology was used to carry out the tests for oil transport from a possible terminal in the vicinity of the port of Dikson to Murmansk. Three types of winter/ice conditions were analyzed, notably mild, average and severe. For each of these conditions, the parameters of the ice cover were determined along the whole route. The average transport speed was determined based on the ice conditions and ship characteristics for the whole route from Dikson to Murmansk and return. 2 refs., 14 figs.

  1. The Discovery of the Regular Movements of Celestial Bodies and the Development of Monotheism in the Ancient Near East

    Science.gov (United States)

    Lanfranchi, G. B.

    2011-06-01

    For Ancient Mesopotamians, astronomical phenomena were signs signifying the gods' judgment on human behaviour. Mesopotamian scholars studied celestial phenomena for understanding the gods' will, and strongly developed astrology. From the 8th to the 6th century BC Assyrian and Babylonian astronomers achieved the ability to predict solar and lunar eclipses, and the planets' movements through mathematical calculations. Predictability of astral phenomena solicited the awareness that they are all regular, and that the universe is governed by an eternal, immutable order fixed at its very beginning. This finally favoured the idea that the cosmic order depended on the will of one god only, displacing polytheism in favour of monotheism; and astrology lost its religious importance as a mean to know the divine will.

  2. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yunji; Jing, Bing-Yi; Gao, Xin

    2015-01-01

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  3. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan

    2015-02-12

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  4. Regularization of divergent integrals

    OpenAIRE

    Felder, Giovanni; Kazhdan, David

    2016-01-01

    We study the Hadamard finite part of divergent integrals of differential forms with singularities on submanifolds. We give formulae for the dependence of the finite part on the choice of regularization and express them in terms of a suitable local residue map. The cases where the submanifold is a complex hypersurface in a complex manifold and where it is a boundary component of a manifold with boundary, arising in string perturbation theory, are treated in more detail.

  5. The Air Traffic Controller Work-Shift Scheduling Problem in Spain from a Multiobjective Perspective: A Metaheuristic and Regular Expression-Based Approach

    Directory of Open Access Journals (Sweden)

    Faustino Tello

    2018-01-01

    Full Text Available We address an air traffic control operator (ATCo work-shift scheduling problem. We consider a multiple objective perspective where the number of ATCos is fixed in advance and a set of ATCo labor conditions have to be satisfied. The objectives deal with the ATCo work and rest periods and positions, the structure of the solution, the number of control center changes, or the distribution of the ATCo workloads. We propose a three-phase problem-solving methodology. In the first phase, a heuristic is used to derive infeasible initial solutions on the basis of templates. Then, a multiple independent run of the simulated annealing metaheuristic is conducted aimed at reaching feasible solutions in the second phase. Finally, a multiple independent simulated annealing run is again conducted from the initial feasible solutions to optimize the objective functions. To do this, we transform the multiple to single optimization problem by using the rank-order centroid function. In the search processes in phases 2 and 3, we use regular expressions to check the ATCo labor conditions in the visited solutions. This provides high testing speed. The proposed approach is illustrated using a real example, and the optimal solution which is reached outperforms an existing template-based reference solution.

  6. UNFOLDED REGULAR AND SEMI-REGULAR POLYHEDRA

    Directory of Open Access Journals (Sweden)

    IONIŢĂ Elena

    2015-06-01

    Full Text Available This paper proposes a presentation unfolding regular and semi-regular polyhedra. Regular polyhedra are convex polyhedra whose faces are regular and equal polygons, with the same number of sides, and whose polyhedral angles are also regular and equal. Semi-regular polyhedra are convex polyhedra with regular polygon faces, several types and equal solid angles of the same type. A net of a polyhedron is a collection of edges in the plane which are the unfolded edges of the solid. Modeling and unfolding Platonic and Arhimediene polyhedra will be using 3dsMAX program. This paper is intended as an example of descriptive geometry applications.

  7. Combination of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 technique with the piggybac transposon system for mouse in utero electroporation to study cortical development.

    Science.gov (United States)

    Cheng, Man; Jin, Xubin; Mu, Lili; Wang, Fangyu; Li, Wei; Zhong, Xiaoling; Liu, Xuan; Shen, Wenchen; Liu, Ying; Zhou, Yan

    2016-09-01

    In utero electroporation (IUE) is commonly used to study cortical development of cerebrum by downregulating or overexpressing genes of interest in neural progenitor cells (NPCs) of small mammals. However, exogenous plasmids are lost or diluted over time. Furthermore, gene knockdown based on short-hairpin RNAs may exert nonspecific effects that lead to aberrant neuronal migration. Genomic engineering by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has great research and therapeutic potentials. Here we integrate the CRISPR/Cas9 components into the piggyBac (PB) transposon system (the CRISPR/Cas9-PB toolkit) for cortical IUEs. The mouse Sry-related HMG box-2 (Sox2) gene was selected as the target for its application. Most transduced cortical NPCs were depleted of SOX2 protein as early as 3 days post-IUE, whereas expressions of SOX1 and PAX6 remained intact. Furthermore, both the WT Cas9 and the D10A nickase mutant Cas9n showed comparable knockout efficiency. Transduced cortical cells were purified with fluorescence-activated cell sorting, and effective gene editing at the Sox2 loci was confirmed. Thus, application of the CRISPR/Cas9-PB toolkit in IUE is a promising strategy to study gene functions in cortical NPCs and their progeny. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  8. Selection of regularization parameter for l1-regularized damage detection

    Science.gov (United States)

    Hou, Rongrong; Xia, Yong; Bao, Yuequan; Zhou, Xiaoqing

    2018-06-01

    The l1 regularization technique has been developed for structural health monitoring and damage detection through employing the sparsity condition of structural damage. The regularization parameter, which controls the trade-off between data fidelity and solution size of the regularization problem, exerts a crucial effect on the solution. However, the l1 regularization problem has no closed-form solution, and the regularization parameter is usually selected by experience. This study proposes two strategies of selecting the regularization parameter for the l1-regularized damage detection problem. The first method utilizes the residual and solution norms of the optimization problem and ensures that they are both small. The other method is based on the discrepancy principle, which requires that the variance of the discrepancy between the calculated and measured responses is close to the variance of the measurement noise. The two methods are applied to a cantilever beam and a three-story frame. A range of the regularization parameter, rather than one single value, can be determined. When the regularization parameter in this range is selected, the damage can be accurately identified even for multiple damage scenarios. This range also indicates the sensitivity degree of the damage identification problem to the regularization parameter.

  9. Bond slip and crack development in FRC and regular concrete specimens longitudinally reinforced with FRP or steel under tension loading

    DEFF Research Database (Denmark)

    Lárusson, Lárus Helgi; Fischer, Gregor

    2012-01-01

    tensile loading using high definition image analysis in two unique test setups. Two different types of cementitious materials, conventional concrete and highly ductile Engineered Cementitious Composite (ECC), and two types of reinforcement bars, regular steel and Glass Fiber Reinforcement Polymer (GFRP......The governing mechanism in the structural response of reinforced concrete members in tension is the interaction between structural reinforcement and the surrounding concrete matrix. The composite response and the mechanical integrations of reinforced cementitious members were investigated during......), were tested. It was found that the ductile ECC in contrast to regular brittle concrete decreases crack widths significantly which effectively results in decreased bond slip between the reinforcement and surrounding matrix. Furthermore the use of elastic GFRP in comparison to elastic/plastic steel...

  10. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  11. Expressive Communication and Human Development in the New Broadband Environment

    Science.gov (United States)

    Carey, John

    2004-01-01

    An understanding of the structure and functions of expressive communication in face-to-face communication and audiovisual media can inform the development of new educational services for human development across cultures in the emerging broadband environment.

  12. Regular endurance training reduces the exercise induced HIF-1alpha and HIF-2alpha mRNA expression in human skeletal muscle in normoxic conditions

    DEFF Research Database (Denmark)

    Lundby, Carsten; Gassmann, Max; Pilegaard, Henriette

    2005-01-01

    and 2 (HIFs) are clearly related heterodimeric transcription factors that consist of an oxygen-depended alpha-subunit and a constitutive beta-subunit. With hypoxic exposure, HIF-1alpha and HIF-2alpha protein are stabilized. Upon heterodimerization, HIFs induce the transcription of a variety of genes......Regular exercise induces a variety of adaptive responses that enhance the oxidative and metabolic capacity of human skeletal muscle. Although the physiological adjustments of regular exercise have been known for decades, the underlying mechanisms are still unclear. The hypoxia inducible factors 1...... including erythropoietin (EPO), transferrin and its receptor, as well as vascular endothelial growth factor (VEGF) and its receptor. Considering that several of these genes are also induced with exercise, we tested the hypothesis that the mRNA level of HIF-1alpha and HIF-2alpha subunits increases...

  13. Globals of Completely Regular Monoids

    Institute of Scientific and Technical Information of China (English)

    Wu Qian-qian; Gan Ai-ping; Du Xian-kun

    2015-01-01

    An element of a semigroup S is called irreducible if it cannot be expressed as a product of two elements in S both distinct from itself. In this paper we show that the class C of all completely regular monoids with irreducible identity elements satisfies the strong isomorphism property and so it is globally determined.

  14. Bypassing the Limits of Ll Regularization: Convex Sparse Signal Processing Using Non-Convex Regularization

    Science.gov (United States)

    Parekh, Ankit

    Sparsity has become the basis of some important signal processing methods over the last ten years. Many signal processing problems (e.g., denoising, deconvolution, non-linear component analysis) can be expressed as inverse problems. Sparsity is invoked through the formulation of an inverse problem with suitably designed regularization terms. The regularization terms alone encode sparsity into the problem formulation. Often, the ℓ1 norm is used to induce sparsity, so much so that ℓ1 regularization is considered to be `modern least-squares'. The use of ℓ1 norm, as a sparsity-inducing regularizer, leads to a convex optimization problem, which has several benefits: the absence of extraneous local minima, well developed theory of globally convergent algorithms, even for large-scale problems. Convex regularization via the ℓ1 norm, however, tends to under-estimate the non-zero values of sparse signals. In order to estimate the non-zero values more accurately, non-convex regularization is often favored over convex regularization. However, non-convex regularization generally leads to non-convex optimization, which suffers from numerous issues: convergence may be guaranteed to only a stationary point, problem specific parameters may be difficult to set, and the solution is sensitive to the initialization of the algorithm. The first part of this thesis is aimed toward combining the benefits of non-convex regularization and convex optimization to estimate sparse signals more effectively. To this end, we propose to use parameterized non-convex regularizers with designated non-convexity and provide a range for the non-convex parameter so as to ensure that the objective function is strictly convex. By ensuring convexity of the objective function (sum of data-fidelity and non-convex regularizer), we can make use of a wide variety of convex optimization algorithms to obtain the unique global minimum reliably. The second part of this thesis proposes a non-linear signal

  15. Regular algebra and finite machines

    CERN Document Server

    Conway, John Horton

    2012-01-01

    World-famous mathematician John H. Conway based this classic text on a 1966 course he taught at Cambridge University. Geared toward graduate students of mathematics, it will also prove a valuable guide to researchers and professional mathematicians.His topics cover Moore's theory of experiments, Kleene's theory of regular events and expressions, Kleene algebras, the differential calculus of events, factors and the factor matrix, and the theory of operators. Additional subjects include event classes and operator classes, some regulator algebras, context-free languages, communicative regular alg

  16. LL-regular grammars

    NARCIS (Netherlands)

    Nijholt, Antinus

    1980-01-01

    Culik II and Cogen introduced the class of LR-regular grammars, an extension of the LR(k) grammars. In this paper we consider an analogous extension of the LL(k) grammars called the LL-regular grammars. The relation of this class of grammars to other classes of grammars will be shown. Any LL-regular

  17. Moonlight controls lunar-phase-dependency and regular oscillation of clock gene expressions in a lunar-synchronized spawner fish, Goldlined spinefoot.

    Science.gov (United States)

    Takeuchi, Yuki; Kabutomori, Ryo; Yamauchi, Chihiro; Miyagi, Hitomi; Takemura, Akihiro; Okano, Keiko; Okano, Toshiyuki

    2018-04-18

    Goldlined spinefoot, Siganus guttatus, inhabits tropical and subtropical waters and synchronizes its spawning around the first quarter moon likely using an hourglass-like lunar timer. In previous studies, we have found that clock genes (Cryptochrome3 and Period1) could play the role of state variable in the diencephalon when determining the lunar phase for spawning. Here, we identified three Cry, two Per, two Clock, and two Bmal genes in S. guttatus and investigated their expression patterns in the diencephalon and pituitary gland. We further evaluated the effect on their expression patterns by daily interruptions of moonlight stimuli for 1 lunar cycle beginning at the new moon. It significantly modified the expression patterns in many of the examined clock(-related) genes including Cry3 in the diencephalon and/or pituitary gland. Acute interruptions of moonlight around the waxing gibbous moon upregulated nocturnal expressions of Cry1b and Cry2 in the diencephalon and pituitary gland, respectively, but did not affect expression levels of the other clock genes. These results highlighted the importance of repetitive moonlight illumination for stable or lunar-phase-specific daily expression of clock genes in the next lunar cycle that may be important for the lunar-phase-synchronized spawning on the next first quarter moon.

  18. MicroRNA expression profiling of the porcine developing brain

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Busk, Peter Kamp

    2011-01-01

    MicroRNAs are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in the control of developmental and physiological processes. In particular, the developing brain contains an impressive diversity of microRNAs. Most micro...... and the growth curve when compared to humans. Considering these similarities, studies examining microRNA expression during porcine brain development could potentially be used to predict the expression profile and role of microRNAs in the human brain....

  19. [TSA improve transgenic porcine cloned embryo development and transgene expression].

    Science.gov (United States)

    Kong, Qing-Ran; Zhu, Jiang; Huang, Bo; Huan, Yan-Jun; Wang, Feng; Shi, Yong-Qian; Liu, Zhong-Feng; Wu, Mei-Ling; Liu, Zhong-Hua

    2011-07-01

    Uncompleted epigenetic reprogramming is attributed to the low efficiency of producing transgenic cloned animals. Histone modification associated with epigenetics can directly influence the embryo development and transgene expression. Trichostatin A (TSA), as an inhibitor of histone deacetylase, can change the status of histone acetylation, improve somatic cell reprogramming, and enhance cloning efficiency. TSA prevents the chromatin structure from being condensed, so that transcription factor could binds to DNA sequence easily and enhance transgene expression. Our study established the optimal TSA treatment on porcine donor cells and cloned embryos, 250 nmol/L, 24 h and 40 nmol/L, 24 h, respectively. Furthermore, we found that both the cloned embryo and the donor cell treated by TSA resulted in the highest development efficiency. Meanwhile, TSA can improve transgene expression in donor cell and cloned embryo. In summary, TSA can significantly improve porcine reconstructed embryo development and transgene expression.

  20. Gene expression profile data for mouse facial development

    Directory of Open Access Journals (Sweden)

    Sonia M. Leach

    2017-08-01

    Full Text Available This article contains data related to the research articles "Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences" (Feng et al., 2009 [1] and “Systems Biology of facial development: contributions of ectoderm and mesenchyme” (Hooper et al., 2017 In press [2]. Embryonic mammalian craniofacial development is a complex process involving the growth, morphogenesis, and fusion of distinct facial prominences into a functional whole. Aberrant gene regulation during this process can lead to severe craniofacial birth defects, including orofacial clefting. As a means to understand the genes involved in facial development, we had previously dissected the embryonic mouse face into distinct prominences: the mandibular, maxillary or nasal between E10.5 and E12.5. The prominences were then processed intact, or separated into ectoderm and mesenchyme layers, prior analysis of RNA expression using microarrays (Feng et al., 2009, Hooper et al., 2017 in press [1,2]. Here, individual gene expression profiles have been built from these datasets that illustrate the timing of gene expression in whole prominences or in the separated tissue layers. The data profiles are presented as an indexed and clickable list of the genes each linked to a graphical image of that gene׳s expression profile in the ectoderm, mesenchyme, or intact prominence. These data files will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence, and expression trajectory.

  1. Gene expression during testis development in Duroc boars

    DEFF Research Database (Denmark)

    Lervik, Siri; Kristoffersen, Anja Bråthen; Conley, Lene

    2015-01-01

    . Nine clusters of genes with significant differential expression over time and 49 functional charts were found in the analysed testis samples. Prominent pathways in the prepubertal testis were associated with tissue renewal, cell respiration and increased endocytocis. E-cadherines may be associated...... with the onset of pubertal development. With elevated steroidogenesis (weeks 16 to 27), there was an increase in the expression of genes in the MAPK pathway, STAR and its analogue STARD6. A pubertal shift in genes coding for cellular cholesterol transport was observed. Increased expression of meiotic pathways...

  2. Condition Number Regularized Covariance Estimation.

    Science.gov (United States)

    Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala

    2013-06-01

    Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the "large p small n " setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required.

  3. Condition Number Regularized Covariance Estimation*

    Science.gov (United States)

    Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala

    2012-01-01

    Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the “large p small n” setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required. PMID:23730197

  4. Mapping organism expression levels at cellular resolution in developing Drosophila

    Science.gov (United States)

    Knowles, David W.; Keranen, Soile; Biggin, Mark D.; Sudar, Damir

    2002-05-01

    The development of an animal embryo is orchestrated by a network of genetically determined, temporal and spatial gene expression patterns that determine the animals final form. To understand such networks, we are developing novel quantitative optical imaging techniques to map gene expression levels at cellular and sub-cellular resolution within pregastrula Drosophila. Embryos at different stages of development are labeled for total DNA and specific gene products using different fluorophors and imaged in 3D with confocal microscopy. Innovative steps have been made which allow the DNA-image to be automatically segmented to produce a morphological mask of the individual nuclear boundaries. For each stage of development an average morphology is chosen to which images from different embryo are compared. The morphological mask is then used to quantify gene-product on a per nuclei basis. What results is an atlas of the relative amount of the specific gene product expressed within the nucleus of every cell in the embryo at the various stages of development. We are creating a quantitative database of transcription factor and target gene expression patterns in wild-type and factor mutant embryos with single cell resolution. Our goal is to uncover the rules determining how patterns of gene expression are generated.

  5. [Efficacy of regular or intermittent inhalation of corticosteroids in treatment of asthma and its effects on growth and development in children].

    Science.gov (United States)

    Li, Lin-Wei; Huang, Ying; Luo, Rong; Yan, Li; Li, Qu-Bei; Peng, Dong-Hong; Shu, Chang

    2015-03-01

    To observe the efficacy of regular or intermittent inhalation of salmeterol/fluticasone propionate (SM/FP) in the treatment of bronchial asthma and its effects on growth and development in children. A total of 112 children diagnosed with bronchial asthma between September 2012 and October 2013 were assigned to standardized treatment (standard group, n=56) and non-standardized treatment (intermittent group, n=56). Comparisons of clinical symptom scores and main pulmonary function indicators between the two groups were carried out before treatment and at 6 and 12 months after treatment. The growth velocity and changes in body mass index (BMI) were observed in the two groups. At 6 and 12 months after the treatment, the standard group had significantly reduced clinical symptom scores and significantly increased pulmonary function indicators (percentage of predicted peak expiratory flow, PEF%; percentage of forced expiratory volume in 1 second, FEV1%) (P0.05). Compared with intermittent inhalation, long-term regular inhalation of SM/FP performs better in controlling clinical symptoms and enhancing pulmonary function in children with asthma. Inhalation of SM/FP for one year reveals no apparent effect on the growth and development of these children.

  6. Regularization by External Variables

    DEFF Research Database (Denmark)

    Bossolini, Elena; Edwards, R.; Glendinning, P. A.

    2016-01-01

    Regularization was a big topic at the 2016 CRM Intensive Research Program on Advances in Nonsmooth Dynamics. There are many open questions concerning well known kinds of regularization (e.g., by smoothing or hysteresis). Here, we propose a framework for an alternative and important kind of regula......Regularization was a big topic at the 2016 CRM Intensive Research Program on Advances in Nonsmooth Dynamics. There are many open questions concerning well known kinds of regularization (e.g., by smoothing or hysteresis). Here, we propose a framework for an alternative and important kind...

  7. CITED1 Expression in Liver Development and Hepatoblastoma

    Directory of Open Access Journals (Sweden)

    Andrew J. Murphy

    2012-12-01

    Full Text Available Hepatoblastoma, the most common pediatric liver cancer, consists of epithelial mixed embryonal/fetal (EMEF and pure fetal histologic subtypes, with the latter exhibiting a more favorable prognosis. Few embryonal histology markers that yield insight into the biologic basis for this prognostic discrepancy exist. CBP/P-300 interacting transactivator 1 (CITED1, a transcriptional co-activator, is expressed in the self-renewing nephron progenitor population of the developing kidney and broadly in its malignant analog, Wilms tumor (WT. In this current study, CITED1 expression is detected in mouse embryonic liver initially on post-coitum day 10.5 (e10.5, begins to taper by e14.5, and is undetectable in e18.5 and adult livers. CITED1 expression is detected in regenerating murine hepatocytes following liver injury by partial hepatectomy and 3,5-diethoxycarbonyl-1,4-dihydrocollidine. Importantly, while CITED1 is undetectable in normal human adult livers, 36 of 41 (87.8% hepatoblastoma specimens express CITED1, where it is enriched in EMEF specimens compared to specimens of pure fetal histology. CITED1 overexpression in Hep293TT human hepatoblastoma cells induces cellular proliferation and upregulates the Wnt inhibitors Kringle containing transmembrane protein 1 (KREMEN1 and CXXC finger protein 4 (CXXC4. CITED1 mRNA expression correlates with expression of CXXC4 and KREMEN1 in clinical hepatoblastoma specimens. These data show that CITED1 is expressed during a defined time course of liver development and is no longer expressed in the adult liver but is upregulated in regenerating hepatocytes following liver injury. Moreover, as in WT, this embryonic marker is reexpressed in hepatoblastoma and correlates with embryonal histology. These findings identify CITED1 as a novel marker of hepatic progenitor cells that is re-expressed following liver injury and in embryonic liver tumors.

  8. Expression and function of scleraxis in the developing auditory system.

    Directory of Open Access Journals (Sweden)

    Zoe F Mann

    Full Text Available A study of genes expressed in the developing inner ear identified the bHLH transcription factor Scleraxis (Scx in the developing cochlea. Previous work has demonstrated an essential role for Scx in the differentiation and development of tendons, ligaments and cells of chondrogenic lineage. Expression in the cochlea has been shown previously, however the functional role for Scx in the cochlea is unknown. Using a Scx-GFP reporter mouse line we examined the spatial and temporal patterns of Scx expression in the developing cochlea between embryonic day 13.5 and postnatal day 25. Embryonically, Scx is expressed broadly throughout the cochlear duct and surrounding mesenchyme and at postnatal ages becomes restricted to the inner hair cells and the interdental cells of the spiral limbus. Deletion of Scx results in hearing impairment indicated by elevated auditory brainstem response (ABR thresholds and diminished distortion product otoacoustic emission (DPOAE amplitudes, across a range of frequencies. No changes in either gross cochlear morphology or expression of the Scx target genes Col2A, Bmp4 or Sox9 were observed in Scx(-/- mutants, suggesting that the auditory defects observed in these animals may be a result of unidentified Scx-dependent processes within the cochlea.

  9. Intermediate filament protein nestin is expressed in developing meninges.

    Science.gov (United States)

    Yay, A; Ozdamar, S; Canoz, O; Baran, M; Tucer, B; Sonmez, M F

    2014-01-01

    Nestin is a type VI intermediate filament protein known as a marker for progenitor cells that can be mostly found in tissues during the embryonic and fetal periods. In our study, we aimed to determine the expression of nestin in meninges covering the brain tissue at different developmental stages and in the new born. In this study 10 human fetuses in different development stages between developmental weeks 9-34 and a newborn brain tissue were used. Fetuses in paraffin section were stained with H+E and nestin immunohistochemical staining protocol was performed. In this study, in the human meninges intense nestin expression was detected as early as in the 9th week of development. Intensity of this expression gradually decreased in later stages of development and nestin expression still persisted in a small population of newborn meningeal cells. In the present study, nestin positive cells gradually diminished in the developing and maturing meninges during the fetal period. This probably depends on initiation of a decrease in nestin expression and replacement with other tissue-specific intermediate filaments while the differentiation process continues. These differences can make significant contributions to the investigation and diagnosis of various pathological disorders (Tab. 1, Fig. 3, Ref. 36).

  10. Expression of Gla proteins during fish skeletal development

    OpenAIRE

    Gavaia, Paulo J.

    2006-01-01

    Senegal sole skeletal development; Skeletal malformations; Skeletal malformation in mediterranean species; Senegal sole skeletal deformities; Zebra fish as model system: skeletal development; Identification of bone cells / skeletal development; Spatial - temporal pattern of bgp expression; Single cell resolution: localization of bgp mRNA; Single cell resolution: Immunolocalization of Bgp; Single cell resolution: localization of mgp mRNA; Single cell resolution: Immunolocalization of Mgp; An i...

  11. Regularities of Multifractal Measures

    Indian Academy of Sciences (India)

    First, we prove the decomposition theorem for the regularities of multifractal Hausdorff measure and packing measure in R R d . This decomposition theorem enables us to split a set into regular and irregular parts, so that we can analyze each separately, and recombine them without affecting density properties. Next, we ...

  12. Stochastic analytic regularization

    International Nuclear Information System (INIS)

    Alfaro, J.

    1984-07-01

    Stochastic regularization is reexamined, pointing out a restriction on its use due to a new type of divergence which is not present in the unregulated theory. Furthermore, we introduce a new form of stochastic regularization which permits the use of a minimal subtraction scheme to define the renormalized Green functions. (author)

  13. Comprehension of idiomatic expressions by Russian speaking typically developing children

    Directory of Open Access Journals (Sweden)

    Eliseeva N.N.

    2017-12-01

    Full Text Available Background. The ability to understand idiomatic expressions begins to develop at an early age. However, such skill is not achieved within the same age and at the same pace in children speaking di erent languages. Objective. This study assesses comprehension of idiomatic expressions by Russian-speaking monolingual children aged 4 to 12 and monitoring the age dynamics of gurative language understanding. Design. 80 children were split in 4 age groups balanced for gender and level of formal education. e participants were asked to identify the correct non-literal meaning of 10 idioms. For each idiomatic expression, children heard three potential interpretations (one correct, and two incorrect ones of which one was literal while the other was overtly wrong. Results. Age-related di erences were analysed by performing a series of univariate ANOVAs. ese analyses showed that already at preschool age children begin to understand some kinds of idiomatic expressions and that such ability slowly develops throughout childhood. Interestingly, until the age of 6 children predominantly interpreted idioms literally. By the age of 7 their ability to correctly understand the non-literal meanings of idiomatic expressions enhanced signi cantly until it reached a plateau around the age of 12. Conclusion. The results of the study are in line with those found for children speaking other languages. The findings are interpreted in light of recent theories of language and cognitive development. Potential limitations of the study are also discussed.

  14. Gesture and Signing in Support of Expressive Language Development

    Science.gov (United States)

    Baker-Ramos, Leslie K.

    2017-01-01

    The purpose of this teacher inquiry is to explore the effects of signing and gesturing on the expressive language development of non-verbal children. The first phase of my inquiry begins with the observations of several non-verbal students with various etiologies in three different educational settings. The focus of these observations is to…

  15. Empirical laws, regularity and necessity

    NARCIS (Netherlands)

    Koningsveld, H.

    1973-01-01

    In this book I have tried to develop an analysis of the concept of an empirical law, an analysis that differs in many ways from the alternative analyse's found in contemporary literature dealing with the subject.

    1 am referring especially to two well-known views, viz. the regularity and

  16. Metric regularity and subdifferential calculus

    International Nuclear Information System (INIS)

    Ioffe, A D

    2000-01-01

    The theory of metric regularity is an extension of two classical results: the Lyusternik tangent space theorem and the Graves surjection theorem. Developments in non-smooth analysis in the 1980s and 1990s paved the way for a number of far-reaching extensions of these results. It was also well understood that the phenomena behind the results are of metric origin, not connected with any linear structure. At the same time it became clear that some basic hypotheses of the subdifferential calculus are closely connected with the metric regularity of certain set-valued maps. The survey is devoted to the metric theory of metric regularity and its connection with subdifferential calculus in Banach spaces

  17. Identification and expression analysis of zebrafish glypicans during embryonic development.

    Directory of Open Access Journals (Sweden)

    Mansi Gupta

    Full Text Available Heparan sulfate Proteoglycans (HSPG are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG's, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish glypicans like Gpc1a, Gpc3, Gpc4, Gpc6a and Gpc6b show conserved synteny with their mammalian cognate genes. Many glypicans are expressed during the gastrulation stage, but their expression becomes more tissue specific and defined during somitogenesis stages, particularly in the developing central nervous system. Existence of multiple glypican orthologs in fish with diverse expression pattern suggests highly specialized and/or redundant function of these genes during embryonic development.

  18. Sparse structure regularized ranking

    KAUST Repository

    Wang, Jim Jing-Yan; Sun, Yijun; Gao, Xin

    2014-01-01

    Learning ranking scores is critical for the multimedia database retrieval problem. In this paper, we propose a novel ranking score learning algorithm by exploring the sparse structure and using it to regularize ranking scores. To explore the sparse

  19. Supersymmetric dimensional regularization

    International Nuclear Information System (INIS)

    Siegel, W.; Townsend, P.K.; van Nieuwenhuizen, P.

    1980-01-01

    There is a simple modification of dimension regularization which preserves supersymmetry: dimensional reduction to real D < 4, followed by analytic continuation to complex D. In terms of component fields, this means fixing the ranges of all indices on the fields (and therefore the numbers of Fermi and Bose components). For superfields, it means continuing in the dimensionality of x-space while fixing the dimensionality of theta-space. This regularization procedure allows the simple manipulation of spinor derivatives in supergraph calculations. The resulting rules are: (1) First do all algebra exactly as in D = 4; (2) Then do the momentum integrals as in ordinary dimensional regularization. This regularization procedure needs extra rules before one can say that it is consistent. Such extra rules needed for superconformal anomalies are discussed. Problems associated with renormalizability and higher order loops are also discussed

  20. Ensemble manifold regularization.

    Science.gov (United States)

    Geng, Bo; Tao, Dacheng; Xu, Chao; Yang, Linjun; Hua, Xian-Sheng

    2012-06-01

    We propose an automatic approximation of the intrinsic manifold for general semi-supervised learning (SSL) problems. Unfortunately, it is not trivial to define an optimization function to obtain optimal hyperparameters. Usually, cross validation is applied, but it does not necessarily scale up. Other problems derive from the suboptimality incurred by discrete grid search and the overfitting. Therefore, we develop an ensemble manifold regularization (EMR) framework to approximate the intrinsic manifold by combining several initial guesses. Algorithmically, we designed EMR carefully so it 1) learns both the composite manifold and the semi-supervised learner jointly, 2) is fully automatic for learning the intrinsic manifold hyperparameters implicitly, 3) is conditionally optimal for intrinsic manifold approximation under a mild and reasonable assumption, and 4) is scalable for a large number of candidate manifold hyperparameters, from both time and space perspectives. Furthermore, we prove the convergence property of EMR to the deterministic matrix at rate root-n. Extensive experiments over both synthetic and real data sets demonstrate the effectiveness of the proposed framework.

  1. Regularities in the +H14C assimilate supply of peach fruits at their last development stage within the range of a fruit-bearing branchlet

    International Nuclear Information System (INIS)

    Petrov, A.; Manolov, P.

    1977-01-01

    Studies have been accomplished by means of 14 C and autoradiography on the transport link between individual shoots and Redhaven fruits in their advanced development (about a week before maturity) which have formed within the range of a fruit-bearing branchlet. This confirms the conception of directing the photosynthetic prod%cts mainly to the ripening fruits. The basic regularities of the photoassimilate transport prove to be the same as at an early phase of fruit development. Nevertheless, there are also some new traits of morphological and physiological essence such as relatively a large phloem fibre scope of the fruit-bearing branchlet, creating better possibilities of taking over the transport products of the photosynthesis and enhanced attraction opwer of fruits, conditioning a strengthened linear and additional transversal transport, thus contributing to the rapid growth of fruits in their last development phase. Under the influence of these factors, the independence of individual shoots and fruits along and around a fruit-bearing branchlet is substantially less than at an early development phase. (author)

  2. Regular and context-free nominal traces

    DEFF Research Database (Denmark)

    Degano, Pierpaolo; Ferrari, Gian-Luigi; Mezzetti, Gianluca

    2017-01-01

    Two kinds of automata are presented, for recognising new classes of regular and context-free nominal languages. We compare their expressive power with analogous proposals in the literature, showing that they express novel classes of languages. Although many properties of classical languages hold ...

  3. Development of Gene Expression Signatures for Practical Radiation Biodosimetry

    International Nuclear Information System (INIS)

    Paul, Sunirmal; Amundson, Sally A.

    2008-01-01

    Purpose: In a large-scale radiologic emergency, estimates of exposure doses and radiation injury would be required for individuals without physical dosimeters. Current methods are inadequate for the task, so we are developing gene expression profiles for radiation biodosimetry. This approach could provide both an estimate of physical radiation dose and an indication of the extent of individual injury or future risk. Methods and Materials: We used whole genome microarray expression profiling as a discovery platform to identify genes with the potential to predict radiation dose across an exposure range relevant for medical decision making in a radiologic emergency. Human peripheral blood from 10 healthy donors was irradiated ex vivo, and global gene expression was measured both 6 and 24 h after exposure. Results: A 74-gene signature was identified that distinguishes between four radiation doses (0.5, 2, 5, and 8 Gy) and controls. More than one third of these genes are regulated by TP53. A nearest centroid classifier using these same 74 genes correctly predicted 98% of samples taken either 6 h or 24 h after treatment as unexposed, exposed to 0.5, 2, or ≥5 Gy. Expression patterns of five genes (CDKN1A, FDXR, SESN1, BBC3, and PHPT1) from this signature were also confirmed by real-time polymerase chain reaction. Conclusion: The ability of a single gene set to predict radiation dose throughout a window of time without need for individual pre-exposure controls represents an important advance in the development of gene expression for biodosimetry

  4. Expressive vocabulary of children with normal and deviant phonological development.

    Science.gov (United States)

    Athayde, Marcia de Lima; Mota, Helena Bolli; Mezzomo, Carolina Lisbôa

    2010-01-01

    expressive vocabulary of children with normal and deviant phonological development. to determine whether alterations presented by children with phonological disorders occur only at the phonological level or if there are any impacts on lexical acquisition; to compare the vocabulary performance of children with phonological disorders to reference values presented by the used test. participants of the study were 36 children of both genders, 14 with phonological disorders (Study group) and 22 with typical language development (Control Group). The ABFW - Vocabulary Test (Befi-Lopes, 2000) was used for assessing the expressive vocabulary of children and later to compare the performance of both groups. the performance of children with phonological disorder in the expressive vocabulary test is similar to that of children with normal phonological development. Most of the children of both groups reached the benchmarks proposed by the test for the different semantic fields. The semantic field Places demonstrated to be the most complex for both groups. the alterations presented by children with phonological disorder area limited to the phonological level, having no impact on the lexical aspect of language.

  5. MAEWEST expression in flower development of two petunia species.

    Science.gov (United States)

    Segatto, Ana Lúcia A; Turchetto-Zolet, Andreia Carina; Aizza, Lilian Cristina B; Monte-Bello, Carolina C; Dornelas, Marcelo C; Margis, Rogerio; Freitas, Loreta B

    2013-07-03

    Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae), adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST (MAW) homologs in different Petunia species may be associated with adaptive changes in floral morphology. The Petunia × hybrida MAW gene belongs to the WOX (WUSCHEL-related homeobox) transcription factor family and has been identified as a controller of petal fusion during corolla formation. We analyzed the expression patterns of P. inflata and P. axillaris MAW orthologs (PiMAW and PaMAW, respectively) by reverse transcriptase polymerase chain reaction (RT-PCR), reverse transcription-quantitative PCR (qRT-PCR) and in situ hybridization in different tissues and different developmental stages of flowers in both species. The spatial expression patterns of PiMAW and PaMAW were similar in P. inflata and P. axillaris. Nevertheless, PaMAW expression level in P. axillaris was higher during the late bud development stage as compared to PiMAW in P. inflata. This work represents an expansion of petunia developmental research to wild accessions.

  6. MAEWEST Expression in Flower Development of Two Petunia Species

    Directory of Open Access Journals (Sweden)

    Ana Lúcia A. Segatto

    2013-07-01

    Full Text Available Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae, adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST (MAW homologs in different Petunia species may be associated with adaptive changes in floral morphology. The Petunia × hybrida MAW gene belongs to the WOX (WUSCHEL-related homeobox transcription factor family and has been identified as a controller of petal fusion during corolla formation. We analyzed the expression patterns of P. inflata and P. axillaris MAW orthologs (PiMAW and PaMAW, respectively by reverse transcriptase polymerase chain reaction (RT-PCR, reverse transcription–quantitative PCR (qRT-PCR and in situ hybridization in different tissues and different developmental stages of flowers in both species. The spatial expression patterns of PiMAW and PaMAW were similar in P. inflata and P. axillaris. Nevertheless, PaMAW expression level in P. axillaris was higher during the late bud development stage as compared to PiMAW in P. inflata. This work represents an expansion of petunia developmental research to wild accessions.

  7. Regularities of intermediate adsorption complex relaxation

    International Nuclear Information System (INIS)

    Manukova, L.A.

    1982-01-01

    The experimental data, characterizing the regularities of intermediate adsorption complex relaxation in the polycrystalline Mo-N 2 system at 77 K are given. The method of molecular beam has been used in the investigation. The analytical expressions of change regularity in the relaxation process of full and specific rates - of transition from intermediate state into ''non-reversible'', of desorption into the gas phase and accumUlation of the particles in the intermediate state are obtained

  8. Manifold Regularized Reinforcement Learning.

    Science.gov (United States)

    Li, Hongliang; Liu, Derong; Wang, Ding

    2018-04-01

    This paper introduces a novel manifold regularized reinforcement learning scheme for continuous Markov decision processes. Smooth feature representations for value function approximation can be automatically learned using the unsupervised manifold regularization method. The learned features are data-driven, and can be adapted to the geometry of the state space. Furthermore, the scheme provides a direct basis representation extension for novel samples during policy learning and control. The performance of the proposed scheme is evaluated on two benchmark control tasks, i.e., the inverted pendulum and the energy storage problem. Simulation results illustrate the concepts of the proposed scheme and show that it can obtain excellent performance.

  9. Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress.

    Science.gov (United States)

    Jiang, Qian-Tao; Liu, Tao; Ma, Jian; Wei, Yu-Ming; Lu, Zhen-Xiang; Lan, Xiu-Jin; Dai, Shou-Fen; Zheng, You-Liang

    2011-10-01

    The pre-mRNA processing (Prp1) gene encodes a spliceosomal protein. It was firstly identified in fission yeast and plays a regular role during spliceosome activation and cell cycle. Plant Prp1 genes have only been identified from rice, Sorghum and Arabidopsis thaliana. In this study, we reported the identification and isolation of a novel Prp1 gene from barley, and further explored its expressional pattern by using real-time quantitative RTPCR, promoter prediction and analysis of microarray data. The putative barley Prp1 protein has a similar primary structure features to those of other known Prp1 protein in this family. The results of amino acid comparison indicated that Prp1 protein of barley and other plant species has a highly conserved 30 termnal region while their 50 sequences greatly varied. The results of expressional analysis revealed that the expression level of barley Prp1 gene is always stable in different vegetative tissues, except it is up-regulated at the mid- and late stages of seed development or under the condition of cold stress. This kind of expressional pattern for barley Prp1 is also supported by our results of comparison of microarray data from barley, rice and Arabidopsis. For the molecular mechanism of its expressional pattern, we conclude that the expression of Prp1 gene may be up-regulated by the increase of pre-mRNAs and not be constitutive or ubiquitous.

  10. During development intense Sox2 expression marks not only Prox1-expressing taste bud cell but also perigemmal cell lineages.

    Science.gov (United States)

    Nakayama, Ayumi; Miura, Hirohito; Ooki, Makoto; Harada, Shuitsu

    2015-03-01

    Sox2 is proposed to regulate the differentiation of bipotential progenitor cells into taste bud cells. However, detailed expression of Sox2 remains unclear. In this report, Sox2 expression during taste bud development in the fungiform (FF), circumvallate (CV) and soft palate (SP) areas is examined together with Prox1. First, we immunohistochemically checked Prox1 expression in adults and found that almost all taste bud cells are Prox1-positive. During FF development, intense Sox2 expression was restricted to taste bud primordia expressing Prox1 at E12.5. However, at E14.5, Sox2 was intensely expressed outside the developing taste buds resolving to perigemmal Sox2 expression in adults. In the SP, at E14.5, taste bud primordia emerged as Prox1-expressing cell clusters. However, intense Sox2 expression was not restricted to taste bud primordia but was detected widely in the epithelium. During development, Sox2 expression outside developing taste buds was generally down-regulated but was retained in the perigemmal region similarly to that in the FF. In the CV, the initial stage of taste bud development remained unclear because of the lack of taste bud primordia comparable to that in the FF and SP. Here, we show that Prox1-expressing cells appear in the apical epithelium at E12.5, in the inner trench wall at E17.5 and in the outer trench wall at E18.5. Sox2 was again not restricted to developing taste bud cells expressing Prox1 during CV development. The expression patterns support that Sox2 does not serve as a cell fate selector between taste bud cells and surrounding keratinocytes but rather may contribute to them both.

  11. Diverse Regular Employees and Non-regular Employment (Japanese)

    OpenAIRE

    MORISHIMA Motohiro

    2011-01-01

    Currently there are high expectations for the introduction of policies related to diverse regular employees. These policies are a response to the problem of disparities between regular and non-regular employees (part-time, temporary, contract and other non-regular employees) and will make it more likely that workers can balance work and their private lives while companies benefit from the advantages of regular employment. In this paper, I look at two issues that underlie this discussion. The ...

  12. Sparse structure regularized ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-04-17

    Learning ranking scores is critical for the multimedia database retrieval problem. In this paper, we propose a novel ranking score learning algorithm by exploring the sparse structure and using it to regularize ranking scores. To explore the sparse structure, we assume that each multimedia object could be represented as a sparse linear combination of all other objects, and combination coefficients are regarded as a similarity measure between objects and used to regularize their ranking scores. Moreover, we propose to learn the sparse combination coefficients and the ranking scores simultaneously. A unified objective function is constructed with regard to both the combination coefficients and the ranking scores, and is optimized by an iterative algorithm. Experiments on two multimedia database retrieval data sets demonstrate the significant improvements of the propose algorithm over state-of-the-art ranking score learning algorithms.

  13. Differentially expressed regulatory genes in honey bee caste development

    Science.gov (United States)

    Hepperle, C.; Hartfelder, K.

    2001-03-01

    In the honey bee, an eminently fertile queen with up to 200 ovarioles per ovary monopolizes colony level reproduction. In contrast, worker bees have only few ovarioles and are essentially sterile. This phenotype divergence is a result of caste-specifically modulated juvenile hormone and ecdysteroid titers in larval development. In this study we employed a differential-display reverse transcription (DDRT)-PCR protocol to detect ecdysteroid-regulated gene expression during a critical phase of caste development. We identified a Ftz-F1 homolog and a Cut-like transcript. Ftz-F1 could be a putative element of the metamorphic ecdysone response cascade of bees, whereas Cut-like proteins are described as transcription factors involved in maintaining cellular differentiation states. The downregulation of both factors can be interpreted as steps in the metamorphic degradation of ovarioles in worker-bee ovaries.

  14. 'Regular' and 'emergency' repair

    International Nuclear Information System (INIS)

    Luchnik, N.V.

    1975-01-01

    Experiments on the combined action of radiation and a DNA inhibitor using Crepis roots and on split-dose irradiation of human lymphocytes lead to the conclusion that there are two types of repair. The 'regular' repair takes place twice in each mitotic cycle and ensures the maintenance of genetic stability. The 'emergency' repair is induced at all stages of the mitotic cycle by high levels of injury. (author)

  15. Regularizing portfolio optimization

    International Nuclear Information System (INIS)

    Still, Susanne; Kondor, Imre

    2010-01-01

    The optimization of large portfolios displays an inherent instability due to estimation error. This poses a fundamental problem, because solutions that are not stable under sample fluctuations may look optimal for a given sample, but are, in effect, very far from optimal with respect to the average risk. In this paper, we approach the problem from the point of view of statistical learning theory. The occurrence of the instability is intimately related to over-fitting, which can be avoided using known regularization methods. We show how regularized portfolio optimization with the expected shortfall as a risk measure is related to support vector regression. The budget constraint dictates a modification. We present the resulting optimization problem and discuss the solution. The L2 norm of the weight vector is used as a regularizer, which corresponds to a diversification 'pressure'. This means that diversification, besides counteracting downward fluctuations in some assets by upward fluctuations in others, is also crucial because it improves the stability of the solution. The approach we provide here allows for the simultaneous treatment of optimization and diversification in one framework that enables the investor to trade off between the two, depending on the size of the available dataset.

  16. Regularizing portfolio optimization

    Science.gov (United States)

    Still, Susanne; Kondor, Imre

    2010-07-01

    The optimization of large portfolios displays an inherent instability due to estimation error. This poses a fundamental problem, because solutions that are not stable under sample fluctuations may look optimal for a given sample, but are, in effect, very far from optimal with respect to the average risk. In this paper, we approach the problem from the point of view of statistical learning theory. The occurrence of the instability is intimately related to over-fitting, which can be avoided using known regularization methods. We show how regularized portfolio optimization with the expected shortfall as a risk measure is related to support vector regression. The budget constraint dictates a modification. We present the resulting optimization problem and discuss the solution. The L2 norm of the weight vector is used as a regularizer, which corresponds to a diversification 'pressure'. This means that diversification, besides counteracting downward fluctuations in some assets by upward fluctuations in others, is also crucial because it improves the stability of the solution. The approach we provide here allows for the simultaneous treatment of optimization and diversification in one framework that enables the investor to trade off between the two, depending on the size of the available dataset.

  17. The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells.

    Science.gov (United States)

    Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A; Zhang, Feng; Lei, Hetian

    2016-07-29

    The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. EXPRESS

    International Nuclear Information System (INIS)

    Ancelin, C.; Le, P.; DeSaint-Quentin, S.; Villatte, N.

    1987-01-01

    This paper presents EXPRESS, an expert system developed for the automation of reliability studies. The first part consists in the description of the method for static thermohydraulic systems. In this step, the authors define the knowledge representation based on the two inference engines - ALOUETTE and LCR developed by EDF. They explain all the process to construct a fault tree from a topological and functional description of the system. Numerous examples are exhibited in illustration of the method. This is followed by the lessons derived from the studies performed on some safety systems of the PALUEL nuclear plant. The development of the same approach for electric power systems is described, insisting on the difference resulting from the sequential nature of these systems. Finally, they show the main advantages identified during the studies

  19. Regular Single Valued Neutrosophic Hypergraphs

    Directory of Open Access Journals (Sweden)

    Muhammad Aslam Malik

    2016-12-01

    Full Text Available In this paper, we define the regular and totally regular single valued neutrosophic hypergraphs, and discuss the order and size along with properties of regular and totally regular single valued neutrosophic hypergraphs. We also extend work on completeness of single valued neutrosophic hypergraphs.

  20. The geometry of continuum regularization

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1987-03-01

    This lecture is primarily an introduction to coordinate-invariant regularization, a recent advance in the continuum regularization program. In this context, the program is seen as fundamentally geometric, with all regularization contained in regularized DeWitt superstructures on field deformations

  1. Global regularization method for planar restricted three-body problem

    Directory of Open Access Journals (Sweden)

    Sharaf M.A.

    2015-01-01

    Full Text Available In this paper, global regularization method for planar restricted three-body problem is purposed by using the transformation z = x+iy = ν cos n(u+iv, where i = √−1, 0 < ν ≤ 1 and n is a positive integer. The method is developed analytically and computationally. For the analytical developments, analytical solutions in power series of the pseudotime τ are obtained for positions and velocities (u, v, u', v' and (x, y, x˙, y˙ in both regularized and physical planes respectively, the physical time t is also obtained as power series in τ. Moreover, relations between the coefficients of the power series are obtained for two consequent values of n. Also, we developed analytical solutions in power series form for the inverse problem of finding τ in terms of t. As typical examples, three symbolic expressions for the coefficients of the power series were developed in terms of initial values. As to the computational developments, the global regularized equations of motion are developed together with their initial values in forms suitable for digital computations using any differential equations solver. On the other hand, for numerical evolutions of power series, an efficient method depending on the continued fraction theory is provided.

  2. Development of double-pair double difference location algorithm and its application to the regular earthquakes and non-volcanic tremors

    Science.gov (United States)

    Guo, H.; Zhang, H.

    2016-12-01

    Relocating high-precision earthquakes is a central task for monitoring earthquakes and studying the structure of earth's interior. The most popular location method is the event-pair double-difference (DD) relative location method, which uses the catalog and/or more accurate waveform cross-correlation (WCC) differential times from event pairs with small inter-event separations to the common stations to reduce the effect of the velocity uncertainties outside the source region. Similarly, Zhang et al. [2010] developed a station-pair DD location method which uses the differential times from common events to pairs of stations to reduce the effect of the velocity uncertainties near the source region, to relocate the non-volcanic tremors (NVT) beneath the San Andreas Fault (SAF). To utilize advantages of both DD location methods, we have proposed and developed a new double-pair DD location method to use the differential times from pairs of events to pairs of stations. The new method can remove the event origin time and station correction terms from the inversion system and cancel out the effects of the velocity uncertainties near and outside the source region simultaneously. We tested and applied the new method on the northern California regular earthquakes to validate its performance. In comparison, among three DD location methods, the new double-pair DD method can determine more accurate relative locations and the station-pair DD method can better improve the absolute locations. Thus, we further proposed a new location strategy combining station-pair and double-pair differential times to determine accurate absolute and relative locations at the same time. For NVTs, it is difficult to pick the first arrivals and derive the WCC event-pair differential times, thus the general practice is to measure station-pair envelope WCC differential times. However, station-pair tremor locations are scattered due to the low-precision relative locations. The ability that double-pair data

  3. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... and metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  4. Regularity of Minimal Surfaces

    CERN Document Server

    Dierkes, Ulrich; Tromba, Anthony J; Kuster, Albrecht

    2010-01-01

    "Regularity of Minimal Surfaces" begins with a survey of minimal surfaces with free boundaries. Following this, the basic results concerning the boundary behaviour of minimal surfaces and H-surfaces with fixed or free boundaries are studied. In particular, the asymptotic expansions at interior and boundary branch points are derived, leading to general Gauss-Bonnet formulas. Furthermore, gradient estimates and asymptotic expansions for minimal surfaces with only piecewise smooth boundaries are obtained. One of the main features of free boundary value problems for minimal surfaces is t

  5. Regularities of radiation heredity

    International Nuclear Information System (INIS)

    Skakov, M.K.; Melikhov, V.D.

    2001-01-01

    One analyzed regularities of radiation heredity in metals and alloys. One made conclusion about thermodynamically irreversible changes in structure of materials under irradiation. One offers possible ways of heredity transmittance of radiation effects at high-temperature transformations in the materials. Phenomenon of radiation heredity may be turned to practical use to control structure of liquid metal and, respectively, structure of ingot via preliminary radiation treatment of charge. Concentration microheterogeneities in material defect structure induced by preliminary irradiation represent the genetic factor of radiation heredity [ru

  6. Phenotypic expression in the developing murine enteric nervous system

    International Nuclear Information System (INIS)

    Rothman, T.P.; Gershon, M.D.

    1982-01-01

    The development of the enteric nervous system was examined in fetal mice. Synthesis of [3H] acetylcholine ([3H]ACh) from [3H]choline and acetylcholinesterase histochemistry were used as phenotypic markers for cholinergic neurons, while the radioautographic detection of the specific uptake of [3H]serotonin (5-[3H]HT) and immunocytochemical staining with antiserum to 5-HT marked serotonergic neurons. The gut also was examined by light and electron microscopy. Development of the gut was studied in situ and in explants grown in organotypic tissue culture. Neurons were first detected morphologically in the foregut on embryonic day 12 (E12). Synthesis of [3H]ACh was detectable on days E10 to E12 but increased markedly between days E13 and E14. Uptake and radioautographic labeling by 5-[3H]HT was seen first in the foregut on day E12, in the colon on day E13, and in the terminal colon on day E14. Gut explanted from both distal and proximal bowel prior to the time when neurons could be detected (days E9 to E11) nevertheless formed neurons in culture. These cultures of early explants displayed markers for both cholinergic and serotonergic neurons. Enhances development of both cholinergic and serotonergic neurons was found in cultures explanted at day E11 over that found in cultures explanted on days E9 or E10. The evidence presented indicates (1) that enteric neurons develop from nonrecognizable precursors, (2) that the proximodistal gradient in neuronal phenotypic expression probably is not related to a proximodistal migration of precursor cells down the gut, (3) that the colonization of the bowel by neuronal precursors may be a prolonged process continuing from day E9 at least through day E11, (4) that the first pool of neuronal primordia to colonize the developing bowel can produce both cholinergic and serotonergic neurons

  7. On the regularized fermionic projector of the vacuum

    Science.gov (United States)

    Finster, Felix

    2008-03-01

    We construct families of fermionic projectors with spherically symmetric regularization, which satisfy the condition of a distributional MP-product. The method is to analyze regularization tails with a power law or logarithmic scaling in composite expressions in the fermionic projector. The resulting regularizations break the Lorentz symmetry and give rise to a multilayer structure of the fermionic projector near the light cone. Furthermore, we construct regularizations which go beyond the distributional MP-product in that they yield additional distributional contributions supported at the origin. The remaining freedom for the regularization parameters and the consequences for the normalization of the fermionic states are discussed.

  8. On the regularized fermionic projector of the vacuum

    International Nuclear Information System (INIS)

    Finster, Felix

    2008-01-01

    We construct families of fermionic projectors with spherically symmetric regularization, which satisfy the condition of a distributional MP-product. The method is to analyze regularization tails with a power law or logarithmic scaling in composite expressions in the fermionic projector. The resulting regularizations break the Lorentz symmetry and give rise to a multilayer structure of the fermionic projector near the light cone. Furthermore, we construct regularizations which go beyond the distributional MP-product in that they yield additional distributional contributions supported at the origin. The remaining freedom for the regularization parameters and the consequences for the normalization of the fermionic states are discussed

  9. Regularized Statistical Analysis of Anatomy

    DEFF Research Database (Denmark)

    Sjöstrand, Karl

    2007-01-01

    This thesis presents the application and development of regularized methods for the statistical analysis of anatomical structures. Focus is on structure-function relationships in the human brain, such as the connection between early onset of Alzheimer’s disease and shape changes of the corpus...... and mind. Statistics represents a quintessential part of such investigations as they are preluded by a clinical hypothesis that must be verified based on observed data. The massive amounts of image data produced in each examination pose an important and interesting statistical challenge...... efficient algorithms which make the analysis of large data sets feasible, and gives examples of applications....

  10. Manifold regularization for sparse unmixing of hyperspectral images.

    Science.gov (United States)

    Liu, Junmin; Zhang, Chunxia; Zhang, Jiangshe; Li, Huirong; Gao, Yuelin

    2016-01-01

    Recently, sparse unmixing has been successfully applied to spectral mixture analysis of remotely sensed hyperspectral images. Based on the assumption that the observed image signatures can be expressed in the form of linear combinations of a number of pure spectral signatures known in advance, unmixing of each mixed pixel in the scene is to find an optimal subset of signatures in a very large spectral library, which is cast into the framework of sparse regression. However, traditional sparse regression models, such as collaborative sparse regression , ignore the intrinsic geometric structure in the hyperspectral data. In this paper, we propose a novel model, called manifold regularized collaborative sparse regression , by introducing a manifold regularization to the collaborative sparse regression model. The manifold regularization utilizes a graph Laplacian to incorporate the locally geometrical structure of the hyperspectral data. An algorithm based on alternating direction method of multipliers has been developed for the manifold regularized collaborative sparse regression model. Experimental results on both the simulated and real hyperspectral data sets have demonstrated the effectiveness of our proposed model.

  11. Isomyosin expression in developing chicken atria: a marker for the development of conductive tissue?

    NARCIS (Netherlands)

    de Groot, I. J.; Sanders, E.; Visser, S. D.; Lamers, W. H.; de Jong, F.; Los, J. A.; Moorman, A. F.

    1987-01-01

    Isomyosin expression patterns in embryonic chicken atria during the first two weeks of development were analyzed immunohistochemically. In the 3-days embryonic chicken heart (HH19-20), strong coexpression of both isomyosins can be found as band-like zones at the lateral sides of the sinoatrial

  12. Diagrammatic methods in phase-space regularization

    International Nuclear Information System (INIS)

    Bern, Z.; Halpern, M.B.; California Univ., Berkeley

    1987-11-01

    Using the scalar prototype and gauge theory as the simplest possible examples, diagrammatic methods are developed for the recently proposed phase-space form of continuum regularization. A number of one-loop and all-order applications are given, including general diagrammatic discussions of the nogrowth theorem and the uniqueness of the phase-space stochastic calculus. The approach also generates an alternate derivation of the equivalence of the large-β phase-space regularization to the more conventional coordinate-space regularization. (orig.)

  13. Effective field theory dimensional regularization

    International Nuclear Information System (INIS)

    Lehmann, Dirk; Prezeau, Gary

    2002-01-01

    A Lorentz-covariant regularization scheme for effective field theories with an arbitrary number of propagating heavy and light particles is given. This regularization scheme leaves the low-energy analytic structure of Greens functions intact and preserves all the symmetries of the underlying Lagrangian. The power divergences of regularized loop integrals are controlled by the low-energy kinematic variables. Simple diagrammatic rules are derived for the regularization of arbitrary one-loop graphs and the generalization to higher loops is discussed

  14. Effective field theory dimensional regularization

    Science.gov (United States)

    Lehmann, Dirk; Prézeau, Gary

    2002-01-01

    A Lorentz-covariant regularization scheme for effective field theories with an arbitrary number of propagating heavy and light particles is given. This regularization scheme leaves the low-energy analytic structure of Greens functions intact and preserves all the symmetries of the underlying Lagrangian. The power divergences of regularized loop integrals are controlled by the low-energy kinematic variables. Simple diagrammatic rules are derived for the regularization of arbitrary one-loop graphs and the generalization to higher loops is discussed.

  15. 75 FR 76006 - Regular Meeting

    Science.gov (United States)

    2010-12-07

    ... FARM CREDIT SYSTEM INSURANCE CORPORATION Regular Meeting AGENCY: Farm Credit System Insurance Corporation Board. ACTION: Regular meeting. SUMMARY: Notice is hereby given of the regular meeting of the Farm Credit System Insurance Corporation Board (Board). Date and Time: The meeting of the Board will be held...

  16. Secondary school as a context for expressing and developing creativity

    Directory of Open Access Journals (Sweden)

    Maksić Slavica

    2015-01-01

    Full Text Available The paper presents the results of a research on the views of teachers about expressing and developing creativity of students at the secondary educational level. The analysis of the discussion with ten grammar school teachers allocated as the most important the teachers' views of the nature of creativity, the capacity of the school to stimulate creativity in students and the conditions for stimulating creativity in school. The majority of teachers saw creativity as a complex phenomenon for whose understanding a multi-perspective approach is needed. Although only few teachers believe in distributivity of creativity, the majority agreed that school should stimulate students' creativity, but that it does not do it sufficiently. Among the factors which support creativity they singled out the teacher's engagement, specificities of certain school subjects, the application of certain teaching techniques and the image of the school. Among the factors that obstruct creativity they stated curricular requirements, selection of students, characteristics of young generations and current social values.

  17. CELLULAR LOCALIZATION AND EXPRESSION OF pygo DURING DROSOPHILA DEVELOPMENT

    Institute of Scientific and Technical Information of China (English)

    LINXin-da; LINXin-hua; CHENGJia-an

    2003-01-01

    Wg/Wnt signaling is a key signaling pathway in Drosophila. Many genes involved in Wingless(wg) signal transduction pathway downstream of Wg, or it'' s vertebrate Wg homologue Wnt, have been identified.Transduction of the Wg signal downstream of Wg is mediated by nuclear TCF/LEF-1, through association with Ar-madillo (Arm)/β-catenin. Pygopus (pygo) is a new identified component in this pathway . Cellular localization experiment showed that pygo was expressed specifically in the nucleus. The expression profile of pygo in embryos was examined using in situ hybridization. Although pygo expressed ubiquitously in the embryos, it expressed at relatively high level in pre-blastoderm embryos which indicate a high degree of maternally provided message, fol-lowed by a low level of ubiquitous zygotic expression. This continues into larval tissues (including wing disc, eye disc and leg disc), where pygo appears to be expressed at low level. Comparison of pygo expression levels, in the wing disc, eye disc and leg disc, showed pygo expression level in the wing disc pouch and leg disc were rela-tive higher.

  18. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-11-19

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  19. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-01-01

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  20. Multiple graph regularized protein domain ranking.

    Science.gov (United States)

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-11-19

    Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  1. Multiple graph regularized protein domain ranking

    Directory of Open Access Journals (Sweden)

    Wang Jim

    2012-11-01

    Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  2. RES: Regularized Stochastic BFGS Algorithm

    Science.gov (United States)

    Mokhtari, Aryan; Ribeiro, Alejandro

    2014-12-01

    RES, a regularized stochastic version of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) quasi-Newton method is proposed to solve convex optimization problems with stochastic objectives. The use of stochastic gradient descent algorithms is widespread, but the number of iterations required to approximate optimal arguments can be prohibitive in high dimensional problems. Application of second order methods, on the other hand, is impracticable because computation of objective function Hessian inverses incurs excessive computational cost. BFGS modifies gradient descent by introducing a Hessian approximation matrix computed from finite gradient differences. RES utilizes stochastic gradients in lieu of deterministic gradients for both, the determination of descent directions and the approximation of the objective function's curvature. Since stochastic gradients can be computed at manageable computational cost RES is realizable and retains the convergence rate advantages of its deterministic counterparts. Convergence results show that lower and upper bounds on the Hessian egeinvalues of the sample functions are sufficient to guarantee convergence to optimal arguments. Numerical experiments showcase reductions in convergence time relative to stochastic gradient descent algorithms and non-regularized stochastic versions of BFGS. An application of RES to the implementation of support vector machines is developed.

  3. Call for Expressions of Interest: Capacity development of Myanmar's ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    ... support, but usually for one-off projects, which the donor agency often designs and leads. ... Expressions of interest will detail how the institution's strategy for ... consultants, equipment, international travel, research expenses, evaluation, ...

  4. Expression of FGFs during early mouse tongue development

    Czech Academy of Sciences Publication Activity Database

    Du, W.; Procházka, Jan; Procházková, Michaela; Klein, O.D.

    2016-01-01

    Roč. 20, č. 2 (2016), s. 81-87 ISSN 1567-133X Institutional support: RVO:68378050 Keywords : Tongue * FGF * Expression * Papilla Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.158, year: 2016

  5. Development of Gene Expression Fingerprints for Identification of Environmental Contaminants Using cDNA Arrays

    National Research Council Canada - National Science Library

    Inouye, L

    2004-01-01

    ...) to develop cDNA array-based assays that map gene expression from contaminant exposures. Results substantiate that distinct gene expression profiles exist for major contaminant classes such as PARs, PCBs, and PCDD/Fs...

  6. Adaptive Regularization of Neural Classifiers

    DEFF Research Database (Denmark)

    Andersen, Lars Nonboe; Larsen, Jan; Hansen, Lars Kai

    1997-01-01

    We present a regularization scheme which iteratively adapts the regularization parameters by minimizing the validation error. It is suggested to use the adaptive regularization scheme in conjunction with optimal brain damage pruning to optimize the architecture and to avoid overfitting. Furthermo......, we propose an improved neural classification architecture eliminating an inherent redundancy in the widely used SoftMax classification network. Numerical results demonstrate the viability of the method...

  7. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  8. Ibie'ka (Ideographs): Developing Visual Signs for Expressing ...

    African Journals Online (AJOL)

    Visual signs (ideographs) are artistic codified expressions that promote social and cultural integration. They are normally based on popular conventions which over a period of time become generally accepted. In pre-western literate Africa, apart from oral communication, visual codes were employed within social groups.

  9. The regulation of APAF1 expression during development and tumourigenesis

    DEFF Research Database (Denmark)

    Hickman, E S; Helin, K

    2002-01-01

    Apoptosis Protease-Activating Factor 1, APAF1, was originally isolated four years ago and shown to be the mammalian homologue of the C. elegans pro-apoptotic ced4 gene. Since then, the expression of APAF1 has been demonstrated to be involved in several cell death pathways, including the induction...

  10. Mozambique - Urban Land Regularization

    Data.gov (United States)

    Millennium Challenge Corporation — This baseline survey was developed for the impact evaluation of activities related to 'improving land access in urban hotspot areas.' The site-specific interventions...

  11. The use of expressive methods for developing empathic skills.

    Science.gov (United States)

    Ozcan, Neslihan Keser; Bilgin, Hülya; Eracar, Nevin

    2011-01-01

    Empathy is one of the fundamental concepts in nursing, and it is an ability that can be learned. Various education models have been tested for improving empathic skills. Research has focused on using oral presentations, videos, modeling, practiced negotiation based on experiences, and psychodrama methods, such as role playing, as ways to improve empathy in participants. This study looked at the use of expressive arts to improve empathic skills of nursing students. The study was conducted with 48 students who were separated into five different groups. All groups lasted for two hours, and met for 12 weeks. Expressive art and psychodrama methods were used in the group studies. The Scale of Empathic Skill was administered to participants before and after the group studies. Before the group study took place, the average score for empathic skill was 127.97 (SD = 21.26). After the group study, it increased to 138.87 (SD = 20.40). The average score for empathic skill increased after the group (t = 3.996, p = .000). Results show that expressive methods are easier, more effective, and enjoyable processes in nursing training.

  12. Novel leukocyte protein, Trojan, differentially expressed during thymocyte development.

    Science.gov (United States)

    Petrov, Petar; Motobu, Maki; Salmi, Jussi; Uchida, Tatsuya; Vainio, Olli

    2010-04-01

    "Trojan" is a novel cell surface protein, discovered from chicken embryonic thymocytes on the purpose to identify molecules involved in T cell differentiation. The molecule is predicted as a type I transmembrane protein having a Sushi and two fibronectin type III domains and a pair of intracellular phosphorylation sites. Its transcript expression is specific for lymphoid tissues and the presence of the protein on the surface of recirculating lymphocytes and macrophages was confirmed by immunofluorescence analysis. In thymus, about half of the double negative (CD4(-) CD8(-)) and CD8 single positive and the majority of CD4 single positive cells express Trojan with a relatively high intensity. However, only a minority of the double positive (CD4(+) CD8(+)) cells are positive for Trojan. This expression pattern, similar to that of some proteins with anti-apoptotic and function, like IL-7Ralpha, makes Trojan an attractive candidate of having an anti-apoptotic role. Copyright 2010 Elsevier Ltd. All rights reserved.

  13. Methodological developments in qualitative longitudinal research: the advantages and challenges of regular telephone contact with participants in a qualitative longitudinal interview study.

    Science.gov (United States)

    Carduff, Emma; Murray, Scott A; Kendall, Marilyn

    2015-04-11

    Qualitative longitudinal research is an evolving methodology, particularly within health care research. It facilitates a nuanced understanding of how phenomena change over time and is ripe for innovative approaches. However, methodological reflections which are tailored to health care research are scarce. This article provides a synthesised and practical account of the advantages and challenges of maintaining regular telephone contact between interviews with participants in a qualitative longitudinal study. Participants with metastatic colorectal cancer were interviewed at 3 time points over the course of a year. Half the group also received monthly telephone calls to explore the added value and the feasibility of capturing change as close to when it was occurring as possible. The data gathered from the telephone calls added context to the participants' overall narrative and informed subsequent interviews. The telephone calls meant we were able to capture change close to when it happened and there was a more evolved, and involved, relationship between the researcher and the participants who were called on a monthly basis. However, ethical challenges were amplified, boundaries of the participant/researcher relationship questioned, and there was the added analytical burden. The telephone calls facilitated a more nuanced understanding of the illness experience to emerge, when compared with the interview only group. The findings suggest that intensive telephone contact may be justified if retention is an issue, when the phenomena being studied is unpredictable and when participants feel disempowered or lack control. These are potential issues for research involving participants with long-term illness.

  14. 75 FR 53966 - Regular Meeting

    Science.gov (United States)

    2010-09-02

    ... FARM CREDIT SYSTEM INSURANCE CORPORATION Regular Meeting AGENCY: Farm Credit System Insurance Corporation Board. SUMMARY: Notice is hereby given of the regular meeting of the Farm Credit System Insurance Corporation Board (Board). DATE AND TIME: The meeting of the Board will be held at the offices of the Farm...

  15. Online co-regularized algorithms

    NARCIS (Netherlands)

    Ruijter, T. de; Tsivtsivadze, E.; Heskes, T.

    2012-01-01

    We propose an online co-regularized learning algorithm for classification and regression tasks. We demonstrate that by sequentially co-regularizing prediction functions on unlabeled data points, our algorithm provides improved performance in comparison to supervised methods on several UCI benchmarks

  16. MRI reconstruction with joint global regularization and transform learning.

    Science.gov (United States)

    Tanc, A Korhan; Eksioglu, Ender M

    2016-10-01

    Sparsity based regularization has been a popular approach to remedy the measurement scarcity in image reconstruction. Recently, sparsifying transforms learned from image patches have been utilized as an effective regularizer for the Magnetic Resonance Imaging (MRI) reconstruction. Here, we infuse additional global regularization terms to the patch-based transform learning. We develop an algorithm to solve the resulting novel cost function, which includes both patchwise and global regularization terms. Extensive simulation results indicate that the introduced mixed approach has improved MRI reconstruction performance, when compared to the algorithms which use either of the patchwise transform learning or global regularization terms alone. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Expression of SPIG1 reveals development of a retinal ganglion cell subtype projecting to the medial terminal nucleus in the mouse.

    Directory of Open Access Journals (Sweden)

    Keisuke Yonehara

    Full Text Available Visual information is transmitted to the brain by roughly a dozen distinct types of retinal ganglion cells (RGCs defined by a characteristic morphology, physiology, and central projections. However, our understanding about how these parallel pathways develop is still in its infancy, because few molecular markers corresponding to individual RGC types are available. Previously, we reported a secretory protein, SPIG1 (clone name; D/Bsp120I #1, preferentially expressed in the dorsal region in the developing chick retina. Here, we generated knock-in mice to visualize SPIG1-expressing cells with green fluorescent protein. We found that the mouse retina is subdivided into two distinct domains for SPIG1 expression and SPIG1 effectively marks a unique subtype of the retinal ganglion cells during the neonatal period. SPIG1-positive RGCs in the dorsotemporal domain project to the dorsal lateral geniculate nucleus (dLGN, superior colliculus, and accessory optic system (AOS. In contrast, in the remaining region, here named the pan-ventronasal domain, SPIG1-positive cells form a regular mosaic and project exclusively to the medial terminal nucleus (MTN of the AOS that mediates the optokinetic nystagmus as early as P1. Their dendrites costratify with ON cholinergic amacrine strata in the inner plexiform layer as early as P3. These findings suggest that these SPIG1-positive cells are the ON direction selective ganglion cells (DSGCs. Moreover, the MTN-projecting cells in the pan-ventronasal domain are apparently composed of two distinct but interdependent regular mosaics depending on the presence or absence of SPIG1, indicating that they comprise two functionally distinct subtypes of the ON DSGCs. The formation of the regular mosaic appears to be commenced at the end of the prenatal stage and completed through the peak period of the cell death at P6. SPIG1 will thus serve as a useful molecular marker for future studies on the development and function of ON DSGCs.

  18. Development of a radiation-responsive gene expression system

    International Nuclear Information System (INIS)

    Ogawa, Ryohei; Morii, Akihiro; Watanabe, Akihiko

    2013-01-01

    We have obtained a promoter enhancing expression of a gene of our interest connected downstream after activation in response to radiation stimulation and it could be used in radiogenetic therapy, a combination between radiotherapy and gene therapy. The promoter has been chosen out of a library of DNA fragments constructed by connecting the TATA box to randomly combined binding sequences of transcription factors that are activated in response to radiation. Although it was shown that the promoter activation was cell type specific, it turned out that radiation responsive promoters could be obtained for a different type of cells by using another set of transcription factor binding sequences, suggesting that the method would be feasible to obtain promoters functioning in any type of cells. Radiation reactivity of obtained promoters could be improved by techniques such as random introduction of point mutations. The improved promoters significantly enhanced expression of the luciferase gene connected downstream in response to radiation even in vivo, in addition, a gene cassette composed of one such promoter and the fcy::fur gene was confirmed useful for suicide gene therapy as shown in vitro simulation experiment, suggesting possible clinical application. (author)

  19. Immunohistochemical Examination for the Distribution of Podoplanin-Expressing Cells in Developing Mouse Molar Tooth Germs

    Science.gov (United States)

    Imaizumi, Yuri; Amano, Ikuko; Tsuruga, Eichi; Kojima, Hiroshi; Sawa, Yoshihiko

    2010-01-01

    We recently reported the expression of podoplanin in the apical bud of adult mouse incisal tooth. This study was aimed to investigate the distribution of podoplanin-expressing cells in mouse tooth germs at several developing stages. At the bud stage podoplanin was expressed in oral mucous epithelia and in a tooth bud. At the cap stage podoplanin was expressed on inner and outer enamel epithelia but not in mesenchymal cells expressing the neural crest stem cell marker nestin. At the early bell stage nestin and podoplanin were expressed in cervical loop and odontoblasts. At the root formation stage both nestin and podoplanin were weakly expressed in odontoblasts generating radicular dentin. Podoplanin expression was also found in the Hertwig epithelial sheath. These results suggest that epithelial cells of developing tooth germ acquire the ability to express nestin, and that tooth germ epithelial cells maintain the ability to express podoplanin in oral mucous epithelia. The expression of podoplanin in odontoblasts was induced as tooth germ development advanced, but was suppressed with the completion of the primary dentin, suggesting that podoplanin may be involved in the cell growth of odontoblasts. Nestin may function as an intermediate filament that binds podoplanin in odontoblasts. PMID:21060740

  20. Regularities, Natural Patterns and Laws of Nature

    Directory of Open Access Journals (Sweden)

    Stathis Psillos

    2014-02-01

    Full Text Available  The goal of this paper is to sketch an empiricist metaphysics of laws of nature. The key idea is that there are regularities without regularity-enforcers. Differently put, there are natural laws without law-makers of a distinct metaphysical kind. This sketch will rely on the concept of a natural pattern and more significantly on the existence of a network of natural patterns in nature. The relation between a regularity and a pattern will be analysed in terms of mereology.  Here is the road map. In section 2, I will briefly discuss the relation between empiricism and metaphysics, aiming to show that an empiricist metaphysics is possible. In section 3, I will offer arguments against stronger metaphysical views of laws. Then, in section 4 I will motivate nomic objectivism. In section 5, I will address the question ‘what is a regularity?’ and will develop a novel answer to it, based on the notion of a natural pattern. In section 6, I will raise the question: ‘what is a law of nature?’, the answer to which will be: a law of nature is a regularity that is characterised by the unity of a natural pattern.

  1. Call for Expressions of Interest Capacity development of Myanmar's ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Fabiola Dieudonne

    Gender considerations: Strong understanding of how to apply a gender lens to organizational development ... Clear gender focus in organizational activities including research, outreach, human resource ... infrastructure and communications.

  2. Continuum-regularized quantum gravity

    International Nuclear Information System (INIS)

    Chan Huesum; Halpern, M.B.

    1987-01-01

    The recent continuum regularization of d-dimensional Euclidean gravity is generalized to arbitrary power-law measure and studied in some detail as a representative example of coordinate-invariant regularization. The weak-coupling expansion of the theory illustrates a generic geometrization of regularized Schwinger-Dyson rules, generalizing previous rules in flat space and flat superspace. The rules are applied in a non-trivial explicit check of Einstein invariance at one loop: the cosmological counterterm is computed and its contribution is included in a verification that the graviton mass is zero. (orig.)

  3. GENE EXPRESSION PROFILES IN THE DEVELOPING RAT CEREBELLUM AND HIPPOCAMPUS

    Science.gov (United States)

    Development of the nervous system is a complex program, involving coordinated growth of axons and their targets. In rodents, rapid brain growth occurs during early postnatal development. At this time, several fundamental processes, such as dendritic and axonal outgrowth and the e...

  4. New regular black hole solutions

    International Nuclear Information System (INIS)

    Lemos, Jose P. S.; Zanchin, Vilson T.

    2011-01-01

    In the present work we consider general relativity coupled to Maxwell's electromagnetism and charged matter. Under the assumption of spherical symmetry, there is a particular class of solutions that correspond to regular charged black holes whose interior region is de Sitter, the exterior region is Reissner-Nordstroem and there is a charged thin-layer in-between the two. The main physical and geometrical properties of such charged regular black holes are analyzed.

  5. Regular variation on measure chains

    Czech Academy of Sciences Publication Activity Database

    Řehák, Pavel; Vitovec, J.

    2010-01-01

    Roč. 72, č. 1 (2010), s. 439-448 ISSN 0362-546X R&D Projects: GA AV ČR KJB100190701 Institutional research plan: CEZ:AV0Z10190503 Keywords : regularly varying function * regularly varying sequence * measure chain * time scale * embedding theorem * representation theorem * second order dynamic equation * asymptotic properties Subject RIV: BA - General Mathematics Impact factor: 1.279, year: 2010 http://www.sciencedirect.com/science/article/pii/S0362546X09008475

  6. Manifold Regularized Correlation Object Tracking

    OpenAIRE

    Hu, Hongwei; Ma, Bo; Shen, Jianbing; Shao, Ling

    2017-01-01

    In this paper, we propose a manifold regularized correlation tracking method with augmented samples. To make better use of the unlabeled data and the manifold structure of the sample space, a manifold regularization-based correlation filter is introduced, which aims to assign similar labels to neighbor samples. Meanwhile, the regression model is learned by exploiting the block-circulant structure of matrices resulting from the augmented translated samples over multiple base samples cropped fr...

  7. On geodesics in low regularity

    Science.gov (United States)

    Sämann, Clemens; Steinbauer, Roland

    2018-02-01

    We consider geodesics in both Riemannian and Lorentzian manifolds with metrics of low regularity. We discuss existence of extremal curves for continuous metrics and present several old and new examples that highlight their subtle interrelation with solutions of the geodesic equations. Then we turn to the initial value problem for geodesics for locally Lipschitz continuous metrics and generalize recent results on existence, regularity and uniqueness of solutions in the sense of Filippov.

  8. Alteration of rice growth and development via antisense expression ...

    African Journals Online (AJOL)

    user

    OsGA20ox2 in regulating plant growth and development, we used reverse genomic approach to ... pathways. Similarly, Carmen et al. (2007) suggested that. Carrizo citrange plants have produced antisense ... universal SP6 and T7 primers to conform their reality (Sangon, ..... Optimising the tissue culture conditions for.

  9. Nodulin gene expression during soybean (Glycine max) nodule development.

    NARCIS (Netherlands)

    Gloudemans, T.; Vries, de S.; Bussink, H.J.; Malik, N.S.A.; Franssen, H.; Louwerse, J.; Bisseling, T.

    1987-01-01

    In vitro translation products of total RNA isolated from soybean nodules at successive stages of nodule development were analyzed by two-dimensional gel electrophoresis. In that way the occurrence of over 20 mRNAs specifically transcribed from nodulin genes was detected. The nodulin genes could be

  10. Call for Expressions of Interest for capacity development of ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2017-07-25

    Jul 25, 2017 ... Think tanks, POLICY RESEARCH, ECONOMIC DEVELOPMENT ... This call is open to independent policy research institutions (“think tanks”), based in Myanmar whose ... Health, SDGs, and public policy—the role of policy research institutions ... Ideas from the global climate change hotspot research.

  11. Gender Expression and Homophobia: A Motor Development and Learning Perspective

    Science.gov (United States)

    Garcia, Clersida

    2011-01-01

    Homosexuality and homophobia are rarely discussed in schools, yet they are relevant in motor-development and motor-learning settings because people hold gender-stereotyped beliefs about movement and about lesbian, gay, bisexual, or transgendered individuals. This article addresses homophobia and related stereotypes in physical education settings…

  12. Development of a fully automated, web-based, tailored intervention promoting regular physical activity among insufficiently active adults with type 2 diabetes: integrating the I-change model, self-determination theory, and motivational interviewing components.

    Science.gov (United States)

    Moreau, Michel; Gagnon, Marie-Pierre; Boudreau, François

    2015-02-17

    Type 2 diabetes is a major challenge for Canadian public health authorities, and regular physical activity is a key factor in the management of this disease. Given that fewer than half of people with type 2 diabetes in Canada are sufficiently active to meet the recommendations, effective programs targeting the adoption of regular physical activity (PA) are in demand for this population. Many researchers argue that Web-based, tailored interventions targeting PA are a promising and effective avenue for sedentary populations like Canadians with type 2 diabetes, but few have described the detailed development of this kind of intervention. This paper aims to describe the systematic development of the Web-based, tailored intervention, Diabète en Forme, promoting regular aerobic PA among adult Canadian francophones with type 2 diabetes. This paper can be used as a reference for health professionals interested in developing similar interventions. We also explored the integration of theoretical components derived from the I-Change Model, Self-Determination Theory, and Motivational Interviewing, which is a potential path for enhancing the effectiveness of tailored interventions on PA adoption and maintenance. The intervention development was based on the program-planning model for tailored interventions of Kreuter et al. An additional step was added to the model to evaluate the intervention's usability prior to the implementation phase. An 8-week intervention was developed. The key components of the intervention include a self-monitoring tool for PA behavior, a weekly action planning tool, and eight tailored motivational sessions based on attitude, self-efficacy, intention, type of motivation, PA behavior, and other constructs and techniques. Usability evaluation, a step added to the program-planning model, helped to make several improvements to the intervention prior to the implementation phase. The intervention development cost was about CDN $59,700 and took approximately

  13. Continuum regularized Yang-Mills theory

    International Nuclear Information System (INIS)

    Sadun, L.A.

    1987-01-01

    Using the machinery of stochastic quantization, Z. Bern, M. B. Halpern, C. Taubes and I recently proposed a continuum regularization technique for quantum field theory. This regularization may be implemented by applying a regulator to either the (d + 1)-dimensional Parisi-Wu Langevin equation or, equivalently, to the d-dimensional second order Schwinger-Dyson (SD) equations. This technique is non-perturbative, respects all gauge and Lorentz symmetries, and is consistent with a ghost-free gauge fixing (Zwanziger's). This thesis is a detailed study of this regulator, and of regularized Yang-Mills theory, using both perturbative and non-perturbative techniques. The perturbative analysis comes first. The mechanism of stochastic quantization is reviewed, and a perturbative expansion based on second-order SD equations is developed. A diagrammatic method (SD diagrams) for evaluating terms of this expansion is developed. We apply the continuum regulator to a scalar field theory. Using SD diagrams, we show that all Green functions can be rendered finite to all orders in perturbation theory. Even non-renormalizable theories can be regularized. The continuum regulator is then applied to Yang-Mills theory, in conjunction with Zwanziger's gauge fixing. A perturbative expansion of the regulator is incorporated into the diagrammatic method. It is hoped that the techniques discussed in this thesis will contribute to the construction of a renormalized Yang-Mills theory is 3 and 4 dimensions

  14. Expression and thermotolerance of calreticulin during pollen development in tobacco

    Czech Academy of Sciences Publication Activity Database

    Hrubá, Petra; Honys, David; Tupý, Jaroslav

    2005-01-01

    Roč. 18, č. 3 (2005), s. 143-148 ISSN 0934-0882 R&D Projects: GA ČR GP522/02/D075; GA MŠk LZ1K03018; GA AV ČR KJB6038409 Institutional research plan: CEZ:AV0Z50380511 Keywords : tobacco * pollen development * thermotolerance Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.278, year: 2005

  15. Geometric continuum regularization of quantum field theory

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1989-01-01

    An overview of the continuum regularization program is given. The program is traced from its roots in stochastic quantization, with emphasis on the examples of regularized gauge theory, the regularized general nonlinear sigma model and regularized quantum gravity. In its coordinate-invariant form, the regularization is seen as entirely geometric: only the supermetric on field deformations is regularized, and the prescription provides universal nonperturbative invariant continuum regularization across all quantum field theory. 54 refs

  16. Serving human needs: Nuclear technology for sustainable development. Scientific forum during the 45th regular session of the IAEA General Conference. Programme and extended abstracts

    International Nuclear Information System (INIS)

    2001-01-01

    The objective of this year's Scientific Forum is to increase Member States' awareness that technical co-operation in non-power applications can produce cost-effective solutions to high-priority problems of sustainable development. The major themes covered include nuclear applications in food production and preservation, human and animal health, pest control and eradication

  17. Serving human needs: Nuclear technology for sustainable development. Scientific forum during the 45th regular session of the IAEA General Conference. Programme and extended abstracts

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    The objective of this year's Scientific Forum is to increase Member States' awareness that technical co-operation in non-power applications can produce cost-effective solutions to high-priority problems of sustainable development. The major themes covered include nuclear applications in food production and preservation, human and animal health, pest control and eradication.

  18. The Development and Initial Validation of a Questionnaire of Inclusive Teachers' Competency for Meeting Special Educational Needs in Regular Classrooms in China

    Science.gov (United States)

    Deng, Meng; Wang, Sisi; Guan, Wenjun; Wang, Yan

    2017-01-01

    The aim of this study was to develop and validate an instrument of inclusive teachers' competencies for teaching students with special educational needs in China. Data were obtained from a preliminary and large-scale investigation in Beijing. The primary analyses included exploratory factor analysis and confirmatory factor analysis. The findings…

  19. Expression of Msx genes in regenerating and developing limbs of axolotl.

    Science.gov (United States)

    Koshiba, K; Kuroiwa, A; Yamamoto, H; Tamura, K; Ide, H

    1998-12-15

    Msx genes, homeobox-containing genes, have been isolated as homologues of the Drosophila msh gene and are thought to play important roles in the development of chick or mouse limb buds. We isolated two Msx genes, Msx1 and Msx2, from regenerating blastemas of axolotl limbs and examined their expression patterns using Northern blot and whole mount in situ hybridization during regeneration and development. Northern blot analysis revealed that the expression level of both Msx genes increased during limb regeneration. The Msx2 expression level increased in the blastema at the early bud stage, and Msx1 expression level increased at the late bud stage. Whole mount in situ hybridization revealed that Msx2 was expressed in the distal mesenchyme and Msx1 in the entire mesenchyme of the blastema at the late bud stage. In the developing limb bud, Msx1 was expressed in the entire mesenchyme, while Msx2 was expressed in the distal and peripheral mesenchyme. The expression patterns of Msx genes in the blastemas and limb buds of the axolotl were different from those reported for chick or mouse limb buds. These expression patterns of axolotl Msx genes are discussed in relation to the blastema or limb bud morphology and their possible roles in limb patterning.

  20. Expression Studies of Gibberellin Oxidases in Developing Pumpkin Seeds1

    Science.gov (United States)

    Frisse, Andrea; Pimenta, Maria João; Lange, Theo

    2003-01-01

    Two cDNA clones, 3-ox and 2-ox, have been isolated from developing pumpkin (Cucurbita maxima) embryos that show significant amino acid homology to gibberellin (GA) 3-oxidases and 2-oxidases, respectively. Recombinant fusion protein of clone 3-ox converted GA12-aldehyde, GA12, GA15, GA24, GA25, and GA9 to GA14-aldehyde, GA14, GA37, GA36, GA13, and GA4, respectively. Recombinant 2-ox protein oxidized GA9, GA4, and GA1 to GA51, GA34, and GA8, respectively. Previously cloned GA 7-oxidase revealed additional 3β-hydroxylation activity of GA12. Transcripts of this gene were identified in endosperm and embryo of the developing seed by quantitative reverse transcriptase-polymerase chain reaction and localized in protoderm, root apical meristem, and quiescent center by in situ hybridization. mRNA of the previously cloned GA 20-oxidase from pumpkin seeds was localized in endosperm and in tissues of protoderm, ground meristem, and cotyledons of the embryo. However, transcripts of the recently cloned GA 20-oxidase from pumpkin seedlings were found all over the embryo, and in tissues of the inner seed coat at the micropylar end. Previously cloned GA 2β,3β-hydroxylase mRNA molecules were specifically identified in endosperm tissue. Finally, mRNA molecules of the 3-ox and 2-ox genes were found in the embryo only. 3-ox transcripts were localized in tissues of cotyledons, protoderm, and inner cell layers of the root apical meristem, and 2-ox transcripts were found in all tissues of the embryo except the root tips. These results indicate tissue-specific GA-biosynthetic pathways operating within the developing seed. PMID:12644672

  1. Expression of Msx-2 during development, regeneration, and wound healing in axolotl limbs.

    Science.gov (United States)

    Carlson, M R; Bryant, S V; Gardiner, D M

    1998-12-15

    Msx genes are transcription factors that are expressed during embryogenesis of developing appendages in regions of epithelial-mesenchymal interactions. Various lines of evidence indicate that these genes function to maintain embryonic tissues in an undifferentiated, proliferative state. We have identified the axolotl homolog of Msx-2, and investigated its expression during limb development, limb regeneration, and wound healing. As in limb buds of higher vertebrates, axolotl Msx-2 is expressed in the apical epidermis and mesenchyme; however, its expression domain is more extensive, reflecting the broader region of the apical epidermal cap in amphibians. Msx-2 expression is downregulated at late stages of limb development, but is reexpressed within one hour after limb amputation. Msx-2 is also reexpressed during wound healing, and may be essential in the early stages of initiation of the limb regeneration cascade.

  2. Recognition of Emotion from Facial Expressions with Direct or Averted Eye Gaze and Varying Expression Intensities in Children with Autism Disorder and Typically Developing Children

    Directory of Open Access Journals (Sweden)

    Dina Tell

    2014-01-01

    Full Text Available Eye gaze direction and expression intensity effects on emotion recognition in children with autism disorder and typically developing children were investigated. Children with autism disorder and typically developing children identified happy and angry expressions equally well. Children with autism disorder, however, were less accurate in identifying fear expressions across intensities and eye gaze directions. Children with autism disorder rated expressions with direct eyes, and 50% expressions, as more intense than typically developing children. A trend was also found for sad expressions, as children with autism disorder were less accurate in recognizing sadness at 100% intensity with direct eyes than typically developing children. Although the present research showed that children with autism disorder are sensitive to eye gaze direction, impairments in the recognition of fear, and possibly sadness, exist. Furthermore, children with autism disorder and typically developing children perceive the intensity of emotional expressions differently.

  3. Multimedia Content Development as a Facial Expression Datasets for Recognition of Human Emotions

    Science.gov (United States)

    Mamonto, N. E.; Maulana, H.; Liliana, D. Y.; Basaruddin, T.

    2018-02-01

    Datasets that have been developed before contain facial expression from foreign people. The development of multimedia content aims to answer the problems experienced by the research team and other researchers who will conduct similar research. The method used in the development of multimedia content as facial expression datasets for human emotion recognition is the Villamil-Molina version of the multimedia development method. Multimedia content developed with 10 subjects or talents with each talent performing 3 shots with each capturing talent having to demonstrate 19 facial expressions. After the process of editing and rendering, tests are carried out with the conclusion that the multimedia content can be used as a facial expression dataset for recognition of human emotions.

  4. Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling

    Directory of Open Access Journals (Sweden)

    Wobus Ulrich

    2009-01-01

    Full Text Available Abstract Background Barley (Hordeum vulgare L. seed development is a highly regulated process with fine-tuned interaction of various tissues controlling distinct physiological events during prestorage, storage and dessication phase. As potential regulators involved within this process we studied 172 transcription factors and 204 kinases for their expression behaviour and anchored a subset of them to the barley linkage map to promote marker-assisted studies on barley grains. Results By a hierachical clustering of the expression profiles of 376 potential regulatory genes expressed in 37 different tissues, we found 50 regulators preferentially expressed in one of the three grain tissue fractions pericarp, endosperm and embryo during seed development. In addition, 27 regulators found to be expressed during both seed development and germination and 32 additional regulators are characteristically expressed in multiple tissues undergoing cell differentiation events during barley plant ontogeny. Another 96 regulators were, beside in the developing seed, ubiquitously expressed among all tissues of germinating seedlings as well as in reproductive tissues. SNP-marker development for those regulators resulted in anchoring 61 markers on the genetic linkage map of barley and the chromosomal assignment of another 12 loci by using wheat-barley addition lines. The SNP frequency ranged from 0.5 to 1.0 SNP/kb in the parents of the various mapping populations and was 2.3 SNP/kb over all eight lines tested. Exploration of macrosynteny to rice revealed that the chromosomal orders of the mapped putative regulatory factors were predominantly conserved during evolution. Conclusion We identified expression patterns of major transcription factors and signaling related genes expressed during barley ontogeny and further assigned possible functions based on likely orthologs functionally well characterized in model plant species. The combined linkage map and reference

  5. Analytic regularization of the Yukawa model at finite temperature

    International Nuclear Information System (INIS)

    Malbouisson, A.P.C.; Svaiter, N.F.; Svaiter, B.F.

    1996-07-01

    It is analysed the one-loop fermionic contribution for the scalar effective potential in the temperature dependent Yukawa model. Ir order to regularize the model a mix between dimensional and analytic regularization procedures is used. It is found a general expression for the fermionic contribution in arbitrary spacetime dimension. It is also found that in D = 3 this contribution is finite. (author). 19 refs

  6. Podoplanin expression in the development and progression of laryngeal squamous cell carcinomas

    Science.gov (United States)

    2010-01-01

    Background Podoplanin expression is attracting interest as a marker for cancer diagnosis and prognosis. We therefore investigated the expression pattern and clinical significance of podoplanin during the development and progression of laryngeal carcinomas. Results Podoplanin expression was determined by immunohistochemistry in paraffin-embedded tissue specimens from 84 patients with laryngeal premalignancies and 53 patients with laryngeal squamous cell carcinomas. We found podoplanin expression extending from the basal to the suprabasal layer of the epithelium in 37 (44%) of 84 dysplastic lesions, whereas normal epithelium showed negligible expression. Patients carrying podoplanin-positive lesions had a higher laryngeal cancer incidence than those with negative expression reaching borderline statistical significance (51% versus 30%, P = 0.071). Podoplanin expression in laryngeal carcinomas exhibited two distinct patterns. 20 (38%) cases showed diffuse expression in most tumour cells and 33 (62%) focal expression at the proliferating periphery of tumour nests. High podoplanin expression was inversely correlated with T classification (P = 0.033), disease stage (P = 0.006), and pathological grade (P = 0.04). There was a trend, although not significant, towards reduced disease-specific survival for patients with low podoplanin levels (P = 0.31) and diffuse expression pattern (P = 0.08). Conclusions Podoplanin expression increases in the early stages of laryngeal tumourigenesis and it seems to be associated with a higher laryngeal cancer risk. Podoplanin expression in laryngeal squamous cell carcinomas, however, diminishes during tumour progression. Taken together, these data support a role for podoplanin expression in the initiation but not in the progression of laryngeal cancers. PMID:20196862

  7. Podoplanin expression in the development and progression of laryngeal squamous cell carcinomas

    Directory of Open Access Journals (Sweden)

    Fresno Manuel F

    2010-03-01

    Full Text Available Abstract Background Podoplanin expression is attracting interest as a marker for cancer diagnosis and prognosis. We therefore investigated the expression pattern and clinical significance of podoplanin during the development and progression of laryngeal carcinomas. Results Podoplanin expression was determined by immunohistochemistry in paraffin-embedded tissue specimens from 84 patients with laryngeal premalignancies and 53 patients with laryngeal squamous cell carcinomas. We found podoplanin expression extending from the basal to the suprabasal layer of the epithelium in 37 (44% of 84 dysplastic lesions, whereas normal epithelium showed negligible expression. Patients carrying podoplanin-positive lesions had a higher laryngeal cancer incidence than those with negative expression reaching borderline statistical significance (51% versus 30%, P = 0.071. Podoplanin expression in laryngeal carcinomas exhibited two distinct patterns. 20 (38% cases showed diffuse expression in most tumour cells and 33 (62% focal expression at the proliferating periphery of tumour nests. High podoplanin expression was inversely correlated with T classification (P = 0.033, disease stage (P = 0.006, and pathological grade (P = 0.04. There was a trend, although not significant, towards reduced disease-specific survival for patients with low podoplanin levels (P = 0.31 and diffuse expression pattern (P = 0.08. Conclusions Podoplanin expression increases in the early stages of laryngeal tumourigenesis and it seems to be associated with a higher laryngeal cancer risk. Podoplanin expression in laryngeal squamous cell carcinomas, however, diminishes during tumour progression. Taken together, these data support a role for podoplanin expression in the initiation but not in the progression of laryngeal cancers.

  8. Construction and development of an auto-regulatory gene expression system in Bacillus subtilis.

    Science.gov (United States)

    Guan, Chengran; Cui, Wenjing; Cheng, Jintao; Zhou, Li; Guo, Junling; Hu, Xu; Xiao, Guoping; Zhou, Zhemin

    2015-09-21

    Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression

  9. Fluctuations of quantum fields via zeta function regularization

    International Nuclear Information System (INIS)

    Cognola, Guido; Zerbini, Sergio; Elizalde, Emilio

    2002-01-01

    Explicit expressions for the expectation values and the variances of some observables, which are bilinear quantities in the quantum fields on a D-dimensional manifold, are derived making use of zeta function regularization. It is found that the variance, related to the second functional variation of the effective action, requires a further regularization and that the relative regularized variance turns out to be 2/N, where N is the number of the fields, thus being independent of the dimension D. Some illustrating examples are worked through. The issue of the stress tensor is also briefly addressed

  10. Manifold Regularized Correlation Object Tracking.

    Science.gov (United States)

    Hu, Hongwei; Ma, Bo; Shen, Jianbing; Shao, Ling

    2018-05-01

    In this paper, we propose a manifold regularized correlation tracking method with augmented samples. To make better use of the unlabeled data and the manifold structure of the sample space, a manifold regularization-based correlation filter is introduced, which aims to assign similar labels to neighbor samples. Meanwhile, the regression model is learned by exploiting the block-circulant structure of matrices resulting from the augmented translated samples over multiple base samples cropped from both target and nontarget regions. Thus, the final classifier in our method is trained with positive, negative, and unlabeled base samples, which is a semisupervised learning framework. A block optimization strategy is further introduced to learn a manifold regularization-based correlation filter for efficient online tracking. Experiments on two public tracking data sets demonstrate the superior performance of our tracker compared with the state-of-the-art tracking approaches.

  11. Developing Culture-Adaptive Competency Through Experiences with Expressive Avatars

    Science.gov (United States)

    Silverglate, Daniel S.; Sims, Edward M.; Glover, Gerald; Friedman, Harris

    2012-01-01

    Modern Warfighters often find themselves in a variety of non-combat roles such as negotiator, peacekeeper, reconstruction, and disaster relief. They are expected to perform these roles within a culture alien to their own. Each individual they encounter brings their own set of values to the interaction that must be understood and reconciled. To navigate the human terrain of these complex interactions, the Warfighter must not only consider the specifics of the target culture, but also identify the stakeholders, recognize the influencing cultural dimensions, and adapt to the situation to achieve the best possible outcome. Vcom3D is using game-based scenarios to develop culturally adaptive competency. The avatars that represent the stakeholders must be able to portray culturally accurate behavior, display complex emotion, and communicate through verbal and non-verbal cues. This paper will discuss the use of emerging game technologies to better simulate human behavior in cross-cultural dilemmas. Nomenclature: culture, adaptive, values, cultural values dimensions, dilemmas, virtual humans, non-verbal communications

  12. Unique Temporal Expression of Triplicated Long-Wavelength Opsins in Developing Butterfly Eyes

    Directory of Open Access Journals (Sweden)

    Kentaro Arikawa

    2017-11-01

    Full Text Available Following gene duplication events, the expression patterns of the resulting gene copies can often diverge both spatially and temporally. Here we report on gene duplicates that are expressed in distinct but overlapping patterns, and which exhibit temporally divergent expression. Butterflies have sophisticated color vision and spectrally complex eyes, typically with three types of heterogeneous ommatidia. The eyes of the butterfly Papilio xuthus express two green- and one red-absorbing visual pigment, which came about via gene duplication events, in addition to one ultraviolet (UV- and one blue-absorbing visual pigment. We localized mRNAs encoding opsins of these visual pigments in developing eye disks throughout the pupal stage. The mRNAs of the UV and blue opsin are expressed early in pupal development (pd, specifying the type of the ommatidium in which they appear. Red sensitive photoreceptors first express a green opsin mRNA, which is replaced later by the red opsin mRNA. Broadband photoreceptors (that coexpress the green and red opsins first express the green opsin mRNA, later change to red opsin mRNA and finally re-express the green opsin mRNA in addition to the red mRNA. Such a unique temporal and spatial expression pattern of opsin mRNAs may reflect the evolution of visual pigments and provide clues toward understanding how the spectrally complex eyes of butterflies evolved.

  13. Construction of heterologous gene expression cassettes for the development of recombinant Clostridium beijerinckii.

    Science.gov (United States)

    Oh, Young Hoon; Eom, Gyeong Tae; Kang, Kyoung Hee; Joo, Jeong Chan; Jang, Young-Ah; Choi, Jae Woo; Song, Bong Keun; Lee, Seung Hwan; Park, Si Jae

    2016-04-01

    Gene-expression cassettes for the construction of recombinant Clostridium beijerinckii were developed as potential tools for metabolic engineering of C. beijerinckii. Gene expression cassettes containing ColE1 origin and pAMB origin along with the erythromycin resistance gene were constructed, in which promoters from Escherichia coli, Lactococcus lactis, Ralstonia eutropha, C. acetobutylicum, and C. beijerinckii are examined as potential promoters in C. beijerinckii. Zymogram analysis of the cell extracts and comparison of lipase activities of the recombinant C. beijerinckii strains expressing Pseudomonas fluorescens tliA gene suggested that the tliA gene was functionally expressed by all the examined promoters with different expression level. Also, recombinant C. beijerinckii expressing C. beijerinckii secondary alcohol dehydrogenase by the constructed expression cassettes successfully produced 2-propanol from glucose. The best promoter for TliA expression was the R. eutropha phaP promoter while that for 2-propanol production was the putative C. beijerinckii pta promoter. Gene expression cassettes developed in this study may be useful tools for the construction of recombinant C. beijerinckii strains as host strains for the valuable chemicals and fuels from renewable resources.

  14. Differential maturation of rhythmic clock gene expression during early development in medaka (Oryzias latipes).

    Science.gov (United States)

    Cuesta, Ines H; Lahiri, Kajori; Lopez-Olmeda, Jose Fernando; Loosli, Felix; Foulkes, Nicholas S; Vallone, Daniela

    2014-05-01

    One key challenge for the field of chronobiology is to identify how circadian clock function emerges during early embryonic development. Teleosts such as the zebrafish are ideal models for studying circadian clock ontogeny since the entire process of development occurs ex utero in an optically transparent chorion. Medaka (Oryzias latipes) represents another powerful fish model for exploring early clock function with, like the zebrafish, many tools available for detailed genetic analysis. However, to date there have been no reports documenting circadian clock gene expression during medaka development. Here we have characterized the expression of key clock genes in various developmental stages and in adult tissues of medaka. As previously reported for other fish, light dark cycles are required for the emergence of clock gene expression rhythms in this species. While rhythmic expression of per and cry genes is detected very early during development and seems to be light driven, rhythmic clock and bmal expression appears much later around hatching time. Furthermore, the maturation of clock function seems to correlate with the appearance of rhythmic expression of these positive elements of the clock feedback loop. By accelerating development through elevated temperatures or by artificially removing the chorion, we show an earlier onset of rhythmicity in clock and bmal expression. Thus, differential maturation of key elements of the medaka clock mechanism depends on the developmental stage and the presence of the chorion.

  15. Dimensional regularization in configuration space

    International Nuclear Information System (INIS)

    Bollini, C.G.; Giambiagi, J.J.

    1995-09-01

    Dimensional regularization is introduced in configuration space by Fourier transforming in D-dimensions the perturbative momentum space Green functions. For this transformation, Bochner theorem is used, no extra parameters, such as those of Feynman or Bogoliubov-Shirkov are needed for convolutions. The regularized causal functions in x-space have ν-dependent moderated singularities at the origin. They can be multiplied together and Fourier transformed (Bochner) without divergence problems. The usual ultraviolet divergences appear as poles of the resultant functions of ν. Several example are discussed. (author). 9 refs

  16. Matrix regularization of 4-manifolds

    OpenAIRE

    Trzetrzelewski, M.

    2012-01-01

    We consider products of two 2-manifolds such as S^2 x S^2, embedded in Euclidean space and show that the corresponding 4-volume preserving diffeomorphism algebra can be approximated by a tensor product SU(N)xSU(N) i.e. functions on a manifold are approximated by the Kronecker product of two SU(N) matrices. A regularization of the 4-sphere is also performed by constructing N^2 x N^2 matrix representations of the 4-algebra (and as a byproduct of the 3-algebra which makes the regularization of S...

  17. Chimeric mitochondrial peptides from contiguous regular and swinger RNA.

    Science.gov (United States)

    Seligmann, Hervé

    2016-01-01

    Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

  18. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development

    DEFF Research Database (Denmark)

    Venø, Morten T; Hansen, Thomas B; Venø, Susanne T

    2015-01-01

    BACKGROUND: Recently, thousands of circular RNAs (circRNAs) have been discovered in various tissues and cell types from human, mouse, fruit fly and nematodes. However, expression of circRNAs across mammalian brain development has never been examined. RESULTS: Here we profile the expression of circ......RNA in five brain tissues at up to six time-points during fetal porcine development, constituting the first report of circRNA in the brain development of a large animal. An unbiased analysis reveals a highly complex regulation pattern of thousands of circular RNAs, with a distinct spatio-temporal expression...... are functionally conserved between mouse and human. Furthermore, we observe that "hot-spot" genes produce multiple circRNA isoforms, which are often differentially expressed across porcine brain development. A global comparison of porcine circRNAs reveals that introns flanking circularized exons are longer than...

  19. Expression of receptor-type protein tyrosine phosphatase in developing and adult renal vasculature.

    Directory of Open Access Journals (Sweden)

    Keiko Takahashi

    Full Text Available Renal vascular development is a coordinated process that requires ordered endothelial cell proliferation, migration, intercellular adhesion, and morphogenesis. In recent decades, studies have defined the pivotal role of endothelial receptor tyrosine kinases (RPTKs in the development and maintenance of renal vasculature. However, the expression and the role of receptor tyrosine phosphatases (RPTPs in renal endothelium are poorly understood, though coupled and counterbalancing roles of RPTKs and RPTPs are well defined in other systems. In this study, we evaluated the promoter activity and immunolocalization of two endothelial RPTPs, VE-PTP and PTPμ, in developing and adult renal vasculature using the heterozygous LacZ knock-in mice and specific antibodies. In adult kidneys, both VE-PTP and PTPμ were expressed in the endothelium of arterial, glomerular, and medullary vessels, while their expression was highly limited in peritubular capillaries and venous endothelium. VE-PTP and PTPμ promoter activity was also observed in medullary tubular segments in adult kidneys. In embryonic (E12.5, E13.5, E15.5, E17.5 and postnatal (P0, P3, P7 kidneys, these RPTPs were expressed in ingrowing renal arteries, developing glomerular microvasculature (as early as the S-shaped stage, and medullary vessels. Their expression became more evident as the vasculatures matured. Peritubular capillary expression of VE-PTP was also noted in embryonic and postnatal kidneys. Compared to VE-PTP, PTPμ immunoreactivity was relatively limited in embryonic and neonatal renal vasculature and evident immunoreactivity was observed from the P3 stage. These findings indicate 1 VE-PTP and PTPμ are expressed in endothelium of arterial, glomerular, and medullary renal vasculature, 2 their expression increases as renal vascular development proceeds, suggesting that these RPTPs play a role in maturation and maintenance of these vasculatures, and 3 peritubular capillary VE-PTP expression

  20. The Development of Expressive Drawing Abilities during Childhood and into Adolescence

    OpenAIRE

    Picard, Delphine; Gauthier, Christophe

    2012-01-01

    The way children portray emotions in their drawings of human and nonhuman topics is assumed to reflect their artistic, emotional, and cognitive development. This study was designed to investigate the development of expressive drawings during childhood and into adolescence, using a large age range (5–15 years) and sample size (N=480), so as to provide a precise and comprehensive view of age-related changes in children’s ability to produce expressive drawings. More specifically, we focused on c...

  1. Characterisation of microRNA expression in post-natal mouse mammary gland development

    Directory of Open Access Journals (Sweden)

    Karagavriilidou Konstantina

    2009-11-01

    Full Text Available Abstract Background The differential expression pattern of microRNAs (miRNAs during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results One third (n = 102 of all murine miRNAs analysed were detected during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show changes, we observed inverse patterns of miRNA and target expression. The data sets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusion MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.

  2. Gene expression patterns during the larval development of European sea bass (dicentrarchus labrax) by microarray analysis.

    Science.gov (United States)

    Darias, M J; Zambonino-Infante, J L; Hugot, K; Cahu, C L; Mazurais, D

    2008-01-01

    During the larval period, marine teleosts undergo very fast growth and dramatic changes in morphology, metabolism, and behavior to accomplish their metamorphosis into juvenile fish. Regulation of gene expression is widely thought to be a key mechanism underlying the management of the biological processes required for harmonious development over this phase of life. To provide an overall analysis of gene expression in the whole body during sea bass larval development, we monitored the expression of 6,626 distinct genes at 10 different points in time between 7 and 43 days post-hatching (dph) by using heterologous hybridization of a rainbow trout cDNA microarray. The differentially expressed genes (n = 485) could be grouped into two categories: genes that were generally up-expressed early, between 7 and 23 dph, and genes up-expressed between 25 and 43 dph. Interestingly, among the genes regulated during the larval period, those related to organogenesis, energy pathways, biosynthesis, and digestion were over-represented compared with total set of analyzed genes. We discuss the quantitative regulation of whole-body contents of these specific transcripts with regard to the ontogenesis and maturation of essential functions that take place over larval development. Our study is the first utilization of a transcriptomic approach in sea bass and reveals dynamic changes in gene expression patterns in relation to marine finfish larval development.

  3. Regularization of Nonmonotone Variational Inequalities

    International Nuclear Information System (INIS)

    Konnov, Igor V.; Ali, M.S.S.; Mazurkevich, E.O.

    2006-01-01

    In this paper we extend the Tikhonov-Browder regularization scheme from monotone to rather a general class of nonmonotone multivalued variational inequalities. We show that their convergence conditions hold for some classes of perfectly and nonperfectly competitive economic equilibrium problems

  4. Lattice regularized chiral perturbation theory

    International Nuclear Information System (INIS)

    Borasoy, Bugra; Lewis, Randy; Ouimet, Pierre-Philippe A.

    2004-01-01

    Chiral perturbation theory can be defined and regularized on a spacetime lattice. A few motivations are discussed here, and an explicit lattice Lagrangian is reviewed. A particular aspect of the connection between lattice chiral perturbation theory and lattice QCD is explored through a study of the Wess-Zumino-Witten term

  5. 76 FR 3629 - Regular Meeting

    Science.gov (United States)

    2011-01-20

    ... Meeting SUMMARY: Notice is hereby given of the regular meeting of the Farm Credit System Insurance Corporation Board (Board). Date and Time: The meeting of the Board will be held at the offices of the Farm... meeting of the Board will be open to the [[Page 3630

  6. Forcing absoluteness and regularity properties

    NARCIS (Netherlands)

    Ikegami, D.

    2010-01-01

    For a large natural class of forcing notions, we prove general equivalence theorems between forcing absoluteness statements, regularity properties, and transcendence properties over L and the core model K. We use our results to answer open questions from set theory of the reals.

  7. Fluid queues and regular variation

    NARCIS (Netherlands)

    Boxma, O.J.

    1996-01-01

    This paper considers a fluid queueing system, fed by N independent sources that alternate between silence and activity periods. We assume that the distribution of the activity periods of one or more sources is a regularly varying function of index ¿. We show that its fat tail gives rise to an even

  8. Fluid queues and regular variation

    NARCIS (Netherlands)

    O.J. Boxma (Onno)

    1996-01-01

    textabstractThis paper considers a fluid queueing system, fed by $N$ independent sources that alternate between silence and activity periods. We assume that the distribution of the activity periods of one or more sources is a regularly varying function of index $zeta$. We show that its fat tail

  9. Interval matrices: Regularity generates singularity

    Czech Academy of Sciences Publication Activity Database

    Rohn, Jiří; Shary, S.P.

    2018-01-01

    Roč. 540, 1 March (2018), s. 149-159 ISSN 0024-3795 Institutional support: RVO:67985807 Keywords : interval matrix * regularity * singularity * P-matrix * absolute value equation * diagonally singilarizable matrix Subject RIV: BA - General Mathematics Impact factor: 0.973, year: 2016

  10. Regularization in Matrix Relevance Learning

    NARCIS (Netherlands)

    Schneider, Petra; Bunte, Kerstin; Stiekema, Han; Hammer, Barbara; Villmann, Thomas; Biehl, Michael

    A In this paper, we present a regularization technique to extend recently proposed matrix learning schemes in learning vector quantization (LVQ). These learning algorithms extend the concept of adaptive distance measures in LVQ to the use of relevance matrices. In general, metric learning can

  11. A Priori Regularity of Parabolic Partial Differential Equations

    KAUST Repository

    Berkemeier, Francisco

    2018-05-13

    In this thesis, we consider parabolic partial differential equations such as the heat equation, the Fokker-Planck equation, and the porous media equation. Our aim is to develop methods that provide a priori estimates for solutions with singular initial data. These estimates are obtained by understanding the time decay of norms of solutions. First, we derive regularity results for the heat equation by estimating the decay of Lebesgue norms. Then, we apply similar methods to the Fokker-Planck equation with suitable assumptions on the advection and diffusion. Finally, we conclude by extending our techniques to the porous media equation. The sharpness of our results is confirmed by examining known solutions of these equations. The main contribution of this thesis is the use of functional inequalities to express decay of norms as differential inequalities. These are then combined with ODE methods to deduce estimates for the norms of solutions and their derivatives.

  12. Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

    Directory of Open Access Journals (Sweden)

    McArtney Steve

    2008-02-01

    Full Text Available Abstract Background Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45–55 bases designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple. Results Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes. Conclusion Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.

  13. Expression patterns and role of PTEN in rat peripheral nerve development and injury.

    Science.gov (United States)

    Chen, Hui; Xiang, Jianping; Wu, Junxia; He, Bo; Lin, Tao; Zhu, Qingtang; Liu, Xiaolin; Zheng, Canbin

    2018-05-29

    Studies have suggested that phosphatase and tensin homolog (PTEN) plays an important role in neuroprotection and neuronal regeneration. To better understand the potential role of PTEN with respect to peripheral nerve development and injury, we investigated the expression pattern of PTEN at different stages of rat peripheral nerve development and injury and subsequently assessed the effect of pharmacological inhibition of PTEN using bpV(pic) on axonal regeneration in a rat sciatic nerve crush injury model. During the early stages of development, PTEN exhibits low expression in neuronal cell bodies and axons. From embryonic day (E) 18.5 and postnatal day (P)5 to adult, PTEN protein becomes more detectable, with high expression in the dorsal root ganglia (DRG) and axons. PTEN expression is inhibited in peripheral nerves, preceding myelination during neuronal development and remyelination after acute nerve injury. Low PTEN expression after nerve injury promotes Akt/mammalian target of rapamycin (mTOR) signaling pathway activity. In vivo pharmacological inhibition of PTEN using bpV(pic) promoted axonal regrowth, increased the number of myelinated nerve fibers, improved locomotive recovery and enhanced the amplitude response and nerve conduction velocity following stimulation in a rat sciatic nerve crush injury model. Thus, we suggest that PTEN may play potential roles in peripheral nerve development and regeneration and that inhibition of PTEN expression is beneficial for nerve regeneration and functional recovery after peripheral nerve injury. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Expression of the metastasis-associated mts1 gene during mouse development

    DEFF Research Database (Denmark)

    Klingelhöfer, Jörg; Ambartsumian, N S; Lukanidin, E M

    1997-01-01

    motility. In order to understand the function of this gene, we studied the expression of the mts1 mRNA and protein in vivo during mouse development. Both mRNA and protein were present in high concentrations from 12.5 to 18.5 days post coitum (dpc) in a variety of developing embryonic tissue of mesodermal....... In developing bone, Mts1 was expressed in invasive mesenchymal cells and in osteoclasts. The results presented here suggest that Mtsl plays an important role in mouse development during differentiation and function of macrophages and might be involved in different processes associated with mesenchymal...

  15. Regularized Biot-Savart Laws for Modeling Magnetic Flux Ropes

    Science.gov (United States)

    Titov, Viacheslav; Downs, Cooper; Mikic, Zoran; Torok, Tibor; Linker, Jon A.

    2017-08-01

    Many existing models assume that magnetic flux ropes play a key role in solar flares and coronal mass ejections (CMEs). It is therefore important to develop efficient methods for constructing flux-rope configurations constrained by observed magnetic data and the initial morphology of CMEs. As our new step in this direction, we have derived and implemented a compact analytical form that represents the magnetic field of a thin flux rope with an axis of arbitrary shape and a circular cross-section. This form implies that the flux rope carries axial current I and axial flux F, so that the respective magnetic field is a curl of the sum of toroidal and poloidal vector potentials proportional to I and F, respectively. The vector potentials are expressed in terms of Biot-Savart laws whose kernels are regularized at the rope axis. We regularized them in such a way that for a straight-line axis the form provides a cylindrical force-free flux rope with a parabolic profile of the axial current density. So far, we set the shape of the rope axis by tracking the polarity inversion lines of observed magnetograms and estimating its height and other parameters of the rope from a calculated potential field above these lines. In spite of this heuristic approach, we were able to successfully construct pre-eruption configurations for the 2009 February13 and 2011 October 1 CME events. These applications demonstrate that our regularized Biot-Savart laws are indeed a very flexible and efficient method for energizing initial configurations in MHD simulations of CMEs. We discuss possible ways of optimizing the axis paths and other extensions of the method in order to make it more useful and robust.Research supported by NSF, NASA's HSR and LWS Programs, and AFOSR.

  16. Gene expression in the lignin biosynthesis pathway during soybean seed development.

    Science.gov (United States)

    Baldoni, A; Von Pinho, E V R; Fernandes, J S; Abreu, V M; Carvalho, M L M

    2013-02-28

    The study of gene expression in plants is fundamental, and understanding the molecular mechanisms involved in important biological processes, such as biochemical pathways or signaling that are used or manipulated in improvement programs, are key for the production of high-quality soybean seeds. Reports related to gene expression of lignin in seeds are scarce in the literature. We studied the expression of the phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase, 4-hydroxycinnamate 3-hydroxylase, and cinnamyl alcohol dehydrogenase genes involved in lignin biosynthesis during the development of soybean (Glycine max L. Merrill) seeds. As the endogenous control, the eukaryotic elongation factor 1-beta gene was used in two biological replicates performed in triplicate. Relative quantitative expression of these genes during the R4, R5, R6, and R7 development stages was analyzed. Real-time polymerase chain reaction was used for the gene expression study. The analyses were carried out in an ABI PRISM 7500 thermocycler using the comparative Ct method and SYBR Green to detect amplification. The seed samples at the R4 stage were chosen as calibrators. Increased expression of the cinnamate-4-hydroxylase and PAL genes occurred in soybean seeds at the R5 and R6 development stages. The cinnamyl alcohol dehydrogenase gene was expressed during the final development phases of soybean seeds. In low-lignin soybean cultivars, the higher expression of the PAL gene occurs at development stages R6 and R7. Activation of the genes involved in the lignin biosynthesis pathway occurs at the beginning of soybean seed development.

  17. Synchronized Progression of Prestin Expression and Auditory Brainstem Response during Postnatal Development in Rats

    Directory of Open Access Journals (Sweden)

    Jianfeng Hang

    2016-01-01

    Full Text Available Prestin is the motor protein expressed in the cochlear outer hair cells (OHCs of mammalian inner ear. The electromotility of OHCs driven by prestin is responsible for the cochlear amplification which is required for normal hearing in adult animals. Postnatal expression of prestin and activity of OHCs may contribute to the maturation of hearing in rodents. However, the temporal and spatial expression of prestin in cochlea during the development is not well characterized. In the present study, we examined the expression and function of prestin from the OHCs in apical, middle, and basal turns of the cochleae of postnatal rats. Prestin first appeared at postnatal day 6 (P6 for basal turn, P7 in middle turn, and P9 for apical turn of cochlea. The expression level increased progressively over the next few days and by P14 reached the mature level for all three segments. By comparison with the time course of the development of auditory brainstem response for different frequencies, our data reveal that prestin expression synchronized with the hearing development. The present study suggests that the onset time of hearing may require the expression of prestin and is determined by the mature function of OHCs.

  18. Abnormal expression of ephrin-A5 affects brain development of congenital hypothyroidism rats.

    Science.gov (United States)

    Suo, Guihai; Shen, Feifei; Sun, Baolan; Song, Honghua; Xu, Meiyu; Wu, Youjia

    2018-05-14

    EphA5 and its ligand ephrin-A5 interaction can trigger synaptogenesis during early hippocampus development. We have previously reported that abnormal EphA5 expression can result in synaptogenesis disorder in congenital hypothyroidism (CH) rats. To better understand its precise molecular mechanism, we further analyzed the characteristics of ephrin-A5 expression in the hippocampus of CH rats. Our study revealed that ephrin-A5 expression was downregulated by thyroid hormone deficiency in the developing hippocampus and hippocampal neurons in rats. Thyroxine treatment for hypothyroid hippocampus and triiodothyronine treatment for hypothyroid hippocampal neurons significantly improved ephrin-A5 expression but could not restore its expression to control levels. Hypothyroid hippocampal neurons in-vitro showed synaptogenesis disorder characterized by a reduction in the number and length of neurites. Furthermore, the synaptogenesis-associated molecular expressions of NMDAR-1 (NR1), PSD95 and CaMKII were all downregulated correspondingly. These results suggest that ephrin-A5 expression may be decreased in CH, and abnormal activation of ephrin-A5/EphA5 signaling affects synaptogenesis during brain development. Such findings provide an important basis for exploring the pathogenesis of CH genetically.

  19. Environmental history impacts gene expression during diapause development in the alfalfa leafcutting bee, Megachile rotundata.

    Science.gov (United States)

    Yocum, George D; Childers, Anna K; Rinehart, Joseph P; Rajamohan, Arun; Pitts-Singer, Theresa L; Greenlee, Kendra J; Bowsher, Julia H

    2018-05-10

    Our understanding of the mechanisms controlling insect diapause has increased dramatically with the introduction of global gene expression techniques, such as RNA-seq. However, little attention has been given to how ecologically relevant field conditions may affect gene expression during diapause development because previous studies have focused on laboratory reared and maintained insects. To determine whether gene expression differs between laboratory and field conditions, prepupae of the alfalfa leafcutting bee, Megachile rotundata , entering diapause early or late in the growing season were collected. These two groups were further subdivided in early autumn into laboratory and field maintained groups, resulting in four experimental treatments of diapausing prepupae: early and late field, and early and late laboratory. RNA-seq and differential expression analyses were performed on bees from the four treatment groups in November, January, March and May. The number of treatment-specific differentially expressed genes (97 to 1249) outnumbered the number of differentially regulated genes common to all four treatments (14 to 229), indicating that exposure to laboratory or field conditions had a major impact on gene expression during diapause development. Principle component analysis and hierarchical cluster analysis yielded similar grouping of treatments, confirming that the treatments form distinct clusters. Our results support the conclusion that gene expression during the course of diapause development is not a simple ordered sequence, but rather a highly plastic response determined primarily by the environmental history of the individual insect. © 2018. Published by The Company of Biologists Ltd.

  20. Chronological changes in microRNA expression in the developing human brain.

    Directory of Open Access Journals (Sweden)

    Michael P Moreau

    Full Text Available MicroRNAs (miRNAs are endogenously expressed noncoding RNA molecules that are believed to regulate multiple neurobiological processes. Expression studies have revealed distinct temporal expression patterns in the developing rodent and porcine brain, but comprehensive profiling in the developing human brain has not been previously reported.We performed microarray and TaqMan-based expression analysis of all annotated mature miRNAs (miRBase 10.0 as well as 373 novel, predicted miRNAs. Expression levels were measured in 48 post-mortem brain tissue samples, representing gestational ages 14-24 weeks, as well as early postnatal and adult time points.Expression levels of 312 miRNAs changed significantly between at least two of the broad age categories, defined as fetal, young, and adult.We have constructed a miRNA expression atlas of the developing human brain, and we propose a classification scheme to guide future studies of neurobiological function.

  1. Regular and conformal regular cores for static and rotating solutions

    Energy Technology Data Exchange (ETDEWEB)

    Azreg-Aïnou, Mustapha

    2014-03-07

    Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

  2. Regular and conformal regular cores for static and rotating solutions

    International Nuclear Information System (INIS)

    Azreg-Aïnou, Mustapha

    2014-01-01

    Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

  3. Higher order total variation regularization for EIT reconstruction.

    Science.gov (United States)

    Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Zhang, Fan; Mueller-Lisse, Ullrich; Moeller, Knut

    2018-01-08

    Electrical impedance tomography (EIT) attempts to reveal the conductivity distribution of a domain based on the electrical boundary condition. This is an ill-posed inverse problem; its solution is very unstable. Total variation (TV) regularization is one of the techniques commonly employed to stabilize reconstructions. However, it is well known that TV regularization induces staircase effects, which are not realistic in clinical applications. To reduce such artifacts, modified TV regularization terms considering a higher order differential operator were developed in several previous studies. One of them is called total generalized variation (TGV) regularization. TGV regularization has been successively applied in image processing in a regular grid context. In this study, we adapted TGV regularization to the finite element model (FEM) framework for EIT reconstruction. Reconstructions using simulation and clinical data were performed. First results indicate that, in comparison to TV regularization, TGV regularization promotes more realistic images. Graphical abstract Reconstructed conductivity changes located on selected vertical lines. For each of the reconstructed images as well as the ground truth image, conductivity changes located along the selected left and right vertical lines are plotted. In these plots, the notation GT in the legend stands for ground truth, TV stands for total variation method, and TGV stands for total generalized variation method. Reconstructed conductivity distributions from the GREIT algorithm are also demonstrated.

  4. Long non-coding RNA expression profiling of mouse testis during postnatal development.

    Directory of Open Access Journals (Sweden)

    Jin Sun

    Full Text Available Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (>200 nt non-coding RNAs (lncRNAs are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old and adult (8-week-old mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to protein-coding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis.

  5. Cross-Language Associations in the Development of Preschoolers' Receptive and Expressive Vocabulary.

    Science.gov (United States)

    Maier, Michelle F; Bohlmann, Natalie L; Palacios, Natalia A

    The increasing population of dual language learners (DLLs) entering preschool classrooms highlights a continued need for research on the development of dual language acquisition, and specifically vocabulary skills, in this age group. This study describes young DLL children's ( N = 177) vocabulary development in both English and Spanish simultaneously, and how vocabulary skills in each language relate to one another, during a contextual shift that places greater emphasis on the acquisition of academic English language skills. Findings demonstrated that DLL preschoolers made gains in vocabulary in both languages with more change evidenced in receptive, in comparison to expressive, vocabulary as well as in English in comparison to Spanish. When examining whether children's vocabulary scores in one language at the beginning of preschool interact with their vocabulary scores in the other language to predict vocabulary growth, no significant associations were found for receptive vocabulary. In contrast, the interaction between initial English and Spanish expressive vocabulary scores was negatively related to growth in English expressive vocabulary. This cross-language association suggests that children who have low expressive vocabulary skills in both languages tend to grow faster in their English expressive vocabulary. The study extends previous work on dual language development by examining growth in expressive and receptive vocabulary in both English and Spanish. It also provides suggestions for future work to inform a more comprehensive understanding of DLL children's development in both languages.

  6. Cross-Language Associations in the Development of Preschoolers’ Receptive and Expressive Vocabulary

    Science.gov (United States)

    Maier, Michelle F.; Bohlmann, Natalie L.; Palacios, Natalia A.

    2016-01-01

    The increasing population of dual language learners (DLLs) entering preschool classrooms highlights a continued need for research on the development of dual language acquisition, and specifically vocabulary skills, in this age group. This study describes young DLL children's (N = 177) vocabulary development in both English and Spanish simultaneously, and how vocabulary skills in each language relate to one another, during a contextual shift that places greater emphasis on the acquisition of academic English language skills. Findings demonstrated that DLL preschoolers made gains in vocabulary in both languages with more change evidenced in receptive, in comparison to expressive, vocabulary as well as in English in comparison to Spanish. When examining whether children's vocabulary scores in one language at the beginning of preschool interact with their vocabulary scores in the other language to predict vocabulary growth, no significant associations were found for receptive vocabulary. In contrast, the interaction between initial English and Spanish expressive vocabulary scores was negatively related to growth in English expressive vocabulary. This cross-language association suggests that children who have low expressive vocabulary skills in both languages tend to grow faster in their English expressive vocabulary. The study extends previous work on dual language development by examining growth in expressive and receptive vocabulary in both English and Spanish. It also provides suggestions for future work to inform a more comprehensive understanding of DLL children's development in both languages. PMID:26807002

  7. Low dose trichloroethylene alters cytochrome P450 - 2C subfamily expression in the developing chick heart

    Science.gov (United States)

    Makwana, Om; Ahles, Lauren; Lencinas, Alejandro; Selmin, Ornella I.; Runyan, Raymond B.

    2013-01-01

    Trichloroethylene (TCE) is an organic solvent and common environmental contaminant. TCE exposure is associated with heart defects in humans and animal models. Primary metabolism of TCE in adult rodent models is by specific hepatic cytochrome P450 enzymes (Lash et al., 2000). As association of TCE exposure with cardiac defects is in exposed embryos prior to normal liver development, we investigated metabolism of TCE in the early embryo. Developing chick embryos were dosed in ovo with environmentally relevant doses of TCE (8 ppb and 800 ppb) and RNA was extracted from cardiac and extra-cardiac tissue (whole embryo without heart). Real time PCR showed upregulation of CYP2H1 transcripts in response to TCE exposure in the heart. No detectable cytochrome expression was found in extra-cardiac tissue. As seen previously, the dose response was non-monotonic and 8ppb elicited stronger upregulation than 800 ppb. Immunostaining for CYP2C subfamily expression confirmed protein expression and showed localization in both myocardium and endothelium. TCE exposure increased protein expression in both tissues. These data demonstrate that the earliest embryonic expression of phase I detoxification enzymes is in the developing heart. Expression of these CYPs is likely to be relevant to the susceptibility of the developing heart to environmental teratogens. PMID:22855351

  8. Spatiotemporal expression of chondroitin sulfate sulfotransferases in the postnatal developing mouse cerebellum.

    Science.gov (United States)

    Ishii, Maki; Maeda, Nobuaki

    2008-08-01

    Chondroitin sulfate (CS) proteoglycans are major components of the cell surface and the extracellular matrix in the developing brain and bind to various proteins via CS chains in a CS structure-dependent manner. This study demonstrated the expression pattern of three CS sulfotransferase genes, dermatan 4-O-sulfotransferase (D4ST), uronyl 2-O-sulfotransferase (UST), and N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase (GalNAc4S-6ST), in the mouse postnatal cerebellum. These sulfotransferases are responsible for the biosynthesis of oversulfated structures in CS chains such as B, D, and E units, which constitute the binding sites for various heparin-binding proteins. Real-time reverse transcription-polymerase chain reaction analysis indicated that the expression of UST increased remarkably during cerebellar development. The amounts of B and D units, which are generated by UST activity, in the cerebellar CS chains also increased during development. In contrast, the expression of GalNAc4S-6ST and its biosynthetic product, E unit, decreased during postnatal development. In situ hybridization experiments revealed the levels of UST and GalNAc4S-6ST mRNAs to correlate inversely in many cells including Purkinje cells, granule cells in the external granular layer, and inhibitory interneurons. In these neurons, the expression of UST increased and that of GalNAc4S-6ST decreased during development and/or maturation. D4ST was also expressed by many neurons, but its expression was not simply correlated with development, which might contribute to the diversification of CS structures expressed by distinct neurons. These results suggest that the CS structures of various cerebellar neurons change during development and such changes of CS are involved in the regulation of various signaling pathways.

  9. Development of expression vectors for Escherichia coli based on the pCR2 replicon

    Directory of Open Access Journals (Sweden)

    Deb J K

    2007-05-01

    Full Text Available Abstract Background Recent developments in metabolic engineering and the need for expanded compatibility required for co-expression studies, underscore the importance of developing new plasmid vectors with properties such as stability and compatibility. Results We utilized the pCR2 replicon of Corynebacterium renale, which harbours multiple plasmids, for constructing a range of expression vectors. Different antibiotic-resistance markers were introduced and the vectors were found to be 100% stable over a large number of generations in the absence of selection pressure. Compatibility of this plasmid was studied with different Escherichia coli plasmid replicons viz. pMB1 and p15A. It was observed that pCR2 was able to coexist with these E.coli plasmids for 60 generations in the absence of selection pressure. Soluble intracellular production was checked by expressing GFP under the lac promoter in an expression plasmid pCR2GFP. Also high level production of human IFNγ was obtained by cloning the h-IFNγ under a T7 promoter in the expression plasmid pCR2-IFNγ and using a dual plasmid heat shock system for expression. Repeated sub-culturing in the absence of selection pressure for six days did not lead to any fall in the production levels post induction, for both GFP and h-IFNγ, demonstrating that pCR2 is a useful plasmid in terms of stability and compatibility. Conclusion We have constructed a series of expression vectors based on the pCR2 replicon and demonstrated its high stability and sustained expression capacity, in the absence of selection pressure which will make it an efficient tool for metabolic engineering and co-expression studies, as well as for scale up of expression.

  10. Sex-biased gene expression during head development in a sexually dimorphic stalk-eyed fly.

    Directory of Open Access Journals (Sweden)

    Gerald S Wilkinson

    Full Text Available Stalk-eyed flies (family Diopsidae are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in many species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To identify candidate genes required for development of dimorphic eyestalks and investigate how sex-biased expression arose on the novel X, we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue or adult heads in the dimorphic diopsid, Teleopsis dalmanni. Microarray analysis revealed sex-biased expression for 26% of 3,748 genes expressed in eye-antennal imaginal discs and concordant sex-biased expression for 86 genes in adult heads. Overall, 415 female-biased and 482 male-biased genes were associated with dimorphic eyestalk development but not differential expression in the adult head. Functional analysis revealed that male-biased genes are disproportionately associated with growth and mitochondrial function while female-biased genes are associated with cell differentiation and patterning or are novel transcripts. With regard to chromosomal effects, dosage compensation occurs by elevated expression of X-linked genes in males. Genes with female-biased expression were more common on the X and less common on autosomes than expected, while male-biased genes exhibited no chromosomal pattern. Rates of protein evolution were lower for female-biased genes but higher for genes that moved on or off the novel X chromosome. These findings cannot be due to meiotic sex chromosome inactivation or by constraints associated with dosage compensation. Instead, they could be consistent with sexual conflict in which female-biased genes on the novel X act primarily to reduce eyespan in females while other genes increase eyespan in both sexes. Additional information on sex-biased gene expression in other tissues and

  11. Differential expression of homeobox-containing genes Msx-1 and Msx-2 and homeoprotein Msx-2 expression during chick craniofacial development.

    Science.gov (United States)

    Nishikawa, K; Nakanishi, T; Aoki, C; Hattori, T; Takahashi, K; Taniguchi, S

    1994-03-01

    The expression pattern of chick Msx-1 and Msx-2 homeobox genes in craniofacial primordia was examined by in situ hybridization using cRNA probes. Both genes were expressed in the distal region of the facial primordia, where the distribution of Msx-2 expression was restricted distally within the Msx-1 expression domain. On the contrary, Msx-2 expression in the lateral choroid plexus and cranial skull was broader and more intensive than Msx-1 expression. Our findings suggest that these two genes cooperate to play differential roles in craniofacial development. Msx-2 protein was detected immunohistochemically, and its localization essentially corresponded to the mRNA expression pattern, substantiating the involvement of Msx-2 protein as a transcriptional regulator in developing limb and face.

  12. Extreme values, regular variation and point processes

    CERN Document Server

    Resnick, Sidney I

    1987-01-01

    Extremes Values, Regular Variation and Point Processes is a readable and efficient account of the fundamental mathematical and stochastic process techniques needed to study the behavior of extreme values of phenomena based on independent and identically distributed random variables and vectors It presents a coherent treatment of the distributional and sample path fundamental properties of extremes and records It emphasizes the core primacy of three topics necessary for understanding extremes the analytical theory of regularly varying functions; the probabilistic theory of point processes and random measures; and the link to asymptotic distribution approximations provided by the theory of weak convergence of probability measures in metric spaces The book is self-contained and requires an introductory measure-theoretic course in probability as a prerequisite Almost all sections have an extensive list of exercises which extend developments in the text, offer alternate approaches, test mastery and provide for enj...

  13. Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

    Energy Technology Data Exchange (ETDEWEB)

    Hermsen, Sanne A.B., E-mail: Sanne.Hermsen@rivm.nl [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands); Pronk, Tessa E. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Brandhof, Evert-Jan van den [Centre for Environmental Quality, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Ven, Leo T.M. van der [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Piersma, Aldert H. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands)

    2013-10-01

    The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.

  14. Development of multigene expression signature maps at the protein level from digitized immunohistochemistry slides.

    Directory of Open Access Journals (Sweden)

    Gregory J Metzger

    Full Text Available Molecular classification of diseases based on multigene expression signatures is increasingly used for diagnosis, prognosis, and prediction of response to therapy. Immunohistochemistry (IHC is an optimal method for validating expression signatures obtained using high-throughput genomics techniques since IHC allows a pathologist to examine gene expression at the protein level within the context of histologically interpretable tissue sections. Additionally, validated IHC assays may be readily implemented as clinical tests since IHC is performed on routinely processed clinical tissue samples. However, methods have not been available for automated n-gene expression profiling at the protein level using IHC data. We have developed methods to compute expression level maps (signature maps of multiple genes from IHC data digitized on a commercial whole slide imaging system. Areas of cancer for these expression level maps are defined by a pathologist on adjacent, co-registered H&E slides, allowing assessment of IHC statistics and heterogeneity within the diseased tissue. This novel way of representing multiple IHC assays as signature maps will allow the development of n-gene expression profiling databases in three dimensions throughout virtual whole organ reconstructions.

  15. Energy functions for regularization algorithms

    Science.gov (United States)

    Delingette, H.; Hebert, M.; Ikeuchi, K.

    1991-01-01

    Regularization techniques are widely used for inverse problem solving in computer vision such as surface reconstruction, edge detection, or optical flow estimation. Energy functions used for regularization algorithms measure how smooth a curve or surface is, and to render acceptable solutions these energies must verify certain properties such as invariance with Euclidean transformations or invariance with parameterization. The notion of smoothness energy is extended here to the notion of a differential stabilizer, and it is shown that to void the systematic underestimation of undercurvature for planar curve fitting, it is necessary that circles be the curves of maximum smoothness. A set of stabilizers is proposed that meet this condition as well as invariance with rotation and parameterization.

  16. Physical model of dimensional regularization

    Energy Technology Data Exchange (ETDEWEB)

    Schonfeld, Jonathan F.

    2016-12-15

    We explicitly construct fractals of dimension 4-ε on which dimensional regularization approximates scalar-field-only quantum-field theory amplitudes. The construction does not require fractals to be Lorentz-invariant in any sense, and we argue that there probably is no Lorentz-invariant fractal of dimension greater than 2. We derive dimensional regularization's power-law screening first for fractals obtained by removing voids from 3-dimensional Euclidean space. The derivation applies techniques from elementary dielectric theory. Surprisingly, fractal geometry by itself does not guarantee the appropriate power-law behavior; boundary conditions at fractal voids also play an important role. We then extend the derivation to 4-dimensional Minkowski space. We comment on generalization to non-scalar fields, and speculate about implications for quantum gravity. (orig.)

  17. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-07

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  18. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yi; Zhao, Shiguang; Gao, Xin

    2014-01-01

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  19. Sparse regularization for force identification using dictionaries

    Science.gov (United States)

    Qiao, Baijie; Zhang, Xingwu; Wang, Chenxi; Zhang, Hang; Chen, Xuefeng

    2016-04-01

    The classical function expansion method based on minimizing l2-norm of the response residual employs various basis functions to represent the unknown force. Its difficulty lies in determining the optimum number of basis functions. Considering the sparsity of force in the time domain or in other basis space, we develop a general sparse regularization method based on minimizing l1-norm of the coefficient vector of basis functions. The number of basis functions is adaptively determined by minimizing the number of nonzero components in the coefficient vector during the sparse regularization process. First, according to the profile of the unknown force, the dictionary composed of basis functions is determined. Second, a sparsity convex optimization model for force identification is constructed. Third, given the transfer function and the operational response, Sparse reconstruction by separable approximation (SpaRSA) is developed to solve the sparse regularization problem of force identification. Finally, experiments including identification of impact and harmonic forces are conducted on a cantilever thin plate structure to illustrate the effectiveness and applicability of SpaRSA. Besides the Dirac dictionary, other three sparse dictionaries including Db6 wavelets, Sym4 wavelets and cubic B-spline functions can also accurately identify both the single and double impact forces from highly noisy responses in a sparse representation frame. The discrete cosine functions can also successfully reconstruct the harmonic forces including the sinusoidal, square and triangular forces. Conversely, the traditional Tikhonov regularization method with the L-curve criterion fails to identify both the impact and harmonic forces in these cases.

  20. PASSIOMA: Exploring Expressed Sequence Tags during Flower Development in Passiflora spp.

    Directory of Open Access Journals (Sweden)

    Lucas Cutri

    2012-01-01

    Full Text Available The genus Passiflora provides a remarkable example of floral complexity and diversity. The extreme variation of Passiflora flower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs as an approach for the characterization of genes expressed during Passiflora reproductive development. Analyzing the Passiflora floral EST database (named PASSIOMA, we found sequences showing significant sequence similarity to genes known to be involved in reproductive development such as MADS-box genes. Some of these sequences were studied using RT-PCR and in situ hybridization confirming their expression during Passiflora flower development. The detection of these novel sequences can contribute to the development of EST-based markers for important agronomic traits as well as to the establishment of genomic tools to study the naturally occurring floral diversity among Passiflora species.

  1. Regularized strings with extrinsic curvature

    International Nuclear Information System (INIS)

    Ambjoern, J.; Durhuus, B.

    1987-07-01

    We analyze models of discretized string theories, where the path integral over world sheet variables is regularized by summing over triangulated surfaces. The inclusion of curvature in the action is a necessity for the scaling of the string tension. We discuss the physical properties of models with extrinsic curvature terms in the action and show that the string tension vanishes at the critical point where the bare extrinsic curvature coupling tends to infinity. Similar results are derived for models with intrinsic curvature. (orig.)

  2. Circuit complexity of regular languages

    Czech Academy of Sciences Publication Activity Database

    Koucký, Michal

    2009-01-01

    Roč. 45, č. 4 (2009), s. 865-879 ISSN 1432-4350 R&D Projects: GA ČR GP201/07/P276; GA MŠk(CZ) 1M0545 Institutional research plan: CEZ:AV0Z10190503 Keywords : regular languages * circuit complexity * upper and lower bounds Subject RIV: BA - General Mathematics Impact factor: 0.726, year: 2009

  3. P-OTX: a PIT-1-interacting homeodomain factor expressed during anterior pituitary gland development.

    OpenAIRE

    Szeto, D P; Ryan, A K; O'Connell, S M; Rosenfeld, M G

    1996-01-01

    A novel OTX-related homeodomain transcription factor has been identified on the basis of its ability to interact with the transactivation domain of the pituitary-specific POU domain protein, Pit-1. This factor, referred to as P-OTX (pituitary OTX-related factor), is expressed in primordial Rathke's pouch, oral epithelium, first bronchial arch, duodenum, and hindlimb. In the developing anterior pituitary, it is expressed in all regions from which cells with distinct phenotypes will emerge in t...

  4. Temporal and spatial expression of Drosophila DLGS97 during neural development.

    Science.gov (United States)

    Albornoz, Valeria; Mendoza-Topaz, Carolina; Oliva, Carlos; Tello, Judith; Olguín, Patricio; Sierralta, Jimena

    2008-07-01

    The products of the Drosophila discs-large (dlg) gene are members of the MAGUK family of proteins, a group of proteins involved in localization, transport and recycling of receptors and channels in cell junctions, including the synapse. In vertebrates, four genes with multiple splice variants homologous to dlg are described. dlg originates two main proteins, DLGA, similar to the vertebrate neuronal protein PSD95, and DLGS97, similar to the vertebrate neuronal and epithelial protein SAP97. DLGA is expressed in epithelia, neural tissue and muscle. DLGS97 is expressed in neural tissue and muscle but not in epithelia. The distinctive difference between them is the presence in DLGS97 of an L27 domain. The differential expression between these variants makes the study of DLGS97 of key relevance to understand the in vivo role of synaptic MAGUKs in neurons. Here we present the temporal and spatial expression pattern of DLGS97 during embryonic and larval nervous system development, during eye development and in adult brain. Our results show that DLGS97 is expressed zygotically, in neurons in the embryo, larvae and adult, and is absent at all stages in glial cells. During eye development DLGS97 starts to be expressed in photoreceptor cells at early stages of differentiation and localizes basal to the basolateral junctions. In the brain, DLGS97 is expressed in the mushroom bodies and optic lobes at larval and adult stages; and in the antennal lobe in the adult stage. In addition we show that both, dlgS97 and dlgA transcripts, express during development multiple splice variants with differences in the use of exons in two sites.

  5. Does Facial Expression Recognition Provide a Toehold for the Development of Emotion Understanding?

    Science.gov (United States)

    Strand, Paul S.; Downs, Andrew; Barbosa-Leiker, Celestina

    2016-01-01

    The authors explored predictions from basic emotion theory (BET) that facial emotion expression recognition skills are insular with respect to their own development, and yet foundational to the development of emotional perspective-taking skills. Participants included 417 preschool children for whom estimates of these 2 emotion understanding…

  6. Expression analysis of asthma candidate genes during human and murine lung development.

    Science.gov (United States)

    Melén, Erik; Kho, Alvin T; Sharma, Sunita; Gaedigk, Roger; Leeder, J Steven; Mariani, Thomas J; Carey, Vincent J; Weiss, Scott T; Tantisira, Kelan G

    2011-06-23

    Little is known about the role of most asthma susceptibility genes during human lung development. Genetic determinants for normal lung development are not only important early in life, but also for later lung function. To investigate the role of expression patterns of well-defined asthma susceptibility genes during human and murine lung development. We hypothesized that genes influencing normal airways development would be over-represented by genes associated with asthma. Asthma genes were first identified via comprehensive search of the current literature. Next, we analyzed their expression patterns in the developing human lung during the pseudoglandular (gestational age, 7-16 weeks) and canalicular (17-26 weeks) stages of development, and in the complete developing lung time series of 3 mouse strains: A/J, SW, C57BL6. In total, 96 genes with association to asthma in at least two human populations were identified in the literature. Overall, there was no significant over-representation of the asthma genes among genes differentially expressed during lung development, although trends were seen in the human (Odds ratio, OR 1.22, confidence interval, CI 0.90-1.62) and C57BL6 mouse (OR 1.41, CI 0.92-2.11) data. However, differential expression of some asthma genes was consistent in both developing human and murine lung, e.g. NOD1, EDN1, CCL5, RORA and HLA-G. Among the asthma genes identified in genome wide association studies, ROBO1, RORA, HLA-DQB1, IL2RB and PDE10A were differentially expressed during human lung development. Our data provide insight about the role of asthma susceptibility genes during lung development and suggest common mechanisms underlying lung morphogenesis and pathogenesis of respiratory diseases.

  7. Spatiotemporal expression of caveolin-1 and EMMPRIN during mouse tooth development.

    Science.gov (United States)

    Shi, Lu; Li, Lingyun; Wang, Ding; Li, Shu; Chen, Zhi; An, Zhengwen

    2016-06-01

    Caveolin-1 is a scaffolding protein involved in the formation of cholesterol-rich caveolae lipid rafts within the plasma membrane and is capable of collecting signaling molecules into the caveolae and regulating their activity, including extracellular matrix metalloproteinase inducer (EMMPRIN). However, detailed expression patterns of caveolin-1 and EMMPRIN in the developing dental germ are largely unknown. The present study investigated the expression patterns of caveolin-1 and EMMPRIN in the developing mouse tooth germ by immunohistochemistry and real-time polymerase chain reaction. At the bud stage, caveolin-1 expression was initiated in the epithelium bud and mesenchymal cells, while EMMPRIN was weakly expressed at this stage. At the cap stage, caveolin-1 protein was located in the lingual part of the tooth germ; however, EMMPRIN protein was located in the labial part. From the bell stage to 2 days postnatal, caveolin-1 expression was detected in the ameloblasts and cervical loop area; with EMMPRIN expression in the ameloblasts and odontoblasts. Real-time polymerase chain reaction results showed that both caveolin-1 and EMMPRIN mRNA levels increased gradually with progression of developmental stages, and peaked at day two postnatal. The current finding suggests that both caveolin-1 and EMMPRIN take part in mouse tooth development, especially in the differentiation and organization of odontogenic tissues.

  8. Caspase activity and expression of cell death genes during development of human preimplantation embryos.

    Science.gov (United States)

    Spanos, S; Rice, S; Karagiannis, P; Taylor, D; Becker, D L; Winston, R M L; Hardy, K

    2002-09-01

    It has been observed that apoptosis occurs in human blastocysts. In other types of cell, the characteristic morphological changes seen in apoptotic cells are executed by caspases, which are regulated by the BCL-2 family of proteins. This study investigated whether these components of the apoptotic cascade are present throughout human preimplantation development. Developing and arrested two pronucleate embryos at all stages were incubated with a fluorescently tagged caspase inhibitor that binds only to active caspases, fixed, counterstained with 4,6-diamidino-2-phenylindole (DAPI) to assess nuclear morphology and examined using confocal microscopy. Active caspases were detected only after compaction, at the morula and blastocyst stages, and were frequently associated with apoptotic nuclei. Occasional labelling was seen in arrested embryos. Expression of proapoptotic BAX and BAD and anti-apoptotic BCL-2 was examined in single embryos using RT-PCR and immunohistochemistry. BAX and BCL-2 mRNAs were expressed throughout development, whereas BAD mRNA was expressed mainly after compaction. Simultaneous expression of BAX and BCL-2 proteins within individual embryos was confirmed using immunohistochemistry. The onset of caspase activity and BAD expression after compaction correlates with the previously reported appearance of apoptotic nuclei. As in other types of cell, human embryos express common molecular components of the apoptotic cascade, although apoptosis appears to be suppressed before compaction and differentiation.

  9. Expression of the Norrie disease gene (Ndp) in developing and adult mouse eye, ear, and brain.

    Science.gov (United States)

    Ye, Xin; Smallwood, Philip; Nathans, Jeremy

    2011-01-01

    The Norrie disease gene (Ndp) codes for a secreted protein, Norrin, that activates canonical Wnt signaling by binding to its receptor, Frizzled-4. This signaling system is required for normal vascular development in the retina and for vascular survival in the cochlea. In mammals, the pattern of Ndp expression beyond the retina is poorly defined due to the low abundance of Norrin mRNA and protein. Here, we characterize Ndp expression during mouse development by studying a knock-in mouse that carries the coding sequence of human placental alkaline phosphatase (AP) inserted at the Ndp locus (Ndp(AP)). In the CNS, Ndp(AP) expression is apparent by E10.5 and is dynamic and complex. The anatomically delimited regions of Ndp(AP) expression observed prenatally in the CNS are replaced postnatally by widespread expression in astrocytes in the forebrain and midbrain, Bergman glia in the cerebellum, and Müller glia in the retina. In the developing and adult cochlea, Ndp(AP) expression is closely associated with two densely vascularized regions, the stria vascularis and a capillary plexus between the organ of Corti and the spiral ganglion. These observations suggest the possibility that Norrin may have developmental and/or homeostatic functions beyond the retina and cochlea. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. The Development of Expressive Drawing Abilities during Childhood and into Adolescence

    Directory of Open Access Journals (Sweden)

    Delphine Picard

    2012-01-01

    Full Text Available The way children portray emotions in their drawings of human and nonhuman topics is assumed to reflect their artistic, emotional, and cognitive development. This study was designed to investigate the development of expressive drawings during childhood and into adolescence, using a large age range (5–15 years and sample size (N=480, so as to provide a precise and comprehensive view of age-related changes in children’s ability to produce expressive drawings. More specifically, we focused on children’s developing ability to use the techniques of literal and metaphorical expression, either alone or in combination. We also examined the effects of sex, topics (house, tree, or person, and the depicted emotion (happiness or sadness on the use of each expressive technique. The main findings were that there is a developmental shift between childhood (5–10 years and adolescence (11–15 years in the use of expressive techniques, from simple (literal to more complex forms of expression (metaphorical.

  11. Global analysis of gene expression profiles in developing physic nut (Jatropha curcas L.) seeds.

    Science.gov (United States)

    Jiang, Huawu; Wu, Pingzhi; Zhang, Sheng; Song, Chi; Chen, Yaping; Li, Meiru; Jia, Yongxia; Fang, Xiaohua; Chen, Fan; Wu, Guojiang

    2012-01-01

    Physic nut (Jatropha curcas L.) is an oilseed plant species with high potential utility as a biofuel. Furthermore, following recent sequencing of its genome and the availability of expressed sequence tag (EST) libraries, it is a valuable model plant for studying carbon assimilation in endosperms of oilseed plants. There have been several transcriptomic analyses of developing physic nut seeds using ESTs, but they have provided limited information on the accumulation of stored resources in the seeds. We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of developing physic nut seeds 14, 19, 25, 29, 35, 41, and 45 days after pollination (DAP). The acquired profiles reveal the key genes, and their expression timeframes, involved in major metabolic processes including: carbon flow, starch metabolism, and synthesis of storage lipids and proteins in the developing seeds. The main period of storage reserves synthesis in the seeds appears to be 29-41 DAP, and the fatty acid composition of the developing seeds is consistent with relative expression levels of different isoforms of acyl-ACP thioesterase and fatty acid desaturase genes. Several transcription factor genes whose expression coincides with storage reserve deposition correspond to those known to regulate the process in Arabidopsis. The results will facilitate searches for genes that influence de novo lipid synthesis, accumulation and their regulatory networks in developing physic nut seeds, and other oil seeds. Thus, they will be helpful in attempts to modify these plants for efficient biofuel production.

  12. General inverse problems for regular variation

    DEFF Research Database (Denmark)

    Damek, Ewa; Mikosch, Thomas Valentin; Rosinski, Jan

    2014-01-01

    Regular variation of distributional tails is known to be preserved by various linear transformations of some random structures. An inverse problem for regular variation aims at understanding whether the regular variation of a transformed random object is caused by regular variation of components ...

  13. Cloning of zebrafish Mustn1 orthologs and their expression during early development.

    Science.gov (United States)

    Camarata, Troy; Vasilyev, Aleksandr; Hadjiargyrou, Michael

    2016-11-15

    Mustn1 is a small nuclear protein that is involved in the development and regeneration of the musculoskeletal system. Previous work established a role for Mustn1 in myogenic and chondrogenic differentiation. In addition, recent evidence suggests a potential role for Mustn1 in cilia function in zebrafish. A detailed study of Mustn1 expression has yet to be conducted in zebrafish. As such, we report herein the cloning of the zebrafish Mustn1 orthologs, mustn1a and mustn1b, and their expression during zebrafish embryonic and larval development. Results indicate a 44% nucleotide identity between the two paralogs. Phylogenetic analysis further confirmed that the Mustn1a and 1b predicted proteins were highly related to other vertebrate members of the Mustn1 protein family. Whole mount in situ hybridization revealed expression of both mustn1a and 1b at the 7-somite stage through 72hpf in structures such as Kupffer's vesicle, segmental mesoderm, head structures, and otic vesicle. Additionally, in 5day old larva, mustn1a and 1b expression is detected in the neurocranium, otic capsule, and the gut. Although both were expressed in the neurocranium, mustn1a was localized in the hypophyseal fenestra whereas mustn1b was found near the posterior basicapsular commissure. mustn1b also displayed expression in the ceratohyal and ceratobranchial elements of the pharyngeal skeleton. These expression patterns were verified temporally by q-PCR analysis. Taken together, we conclude that Mustn1 expression is conserved in vertebrates and that the variations in expression of the two zebrafish paralogs suggest different modes of molecular regulation. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

    Directory of Open Access Journals (Sweden)

    Siegmund Kimberly D

    2009-03-01

    Full Text Available Abstract Background Cross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed probes. Based on the most recent human and chimpanzee genome assemblies, we developed updated and accessible probe masking methods that allow human Affymetrix oligonucleotide microarrays to be used for robust genome-wide expression analyses in both species. In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis. Results To characterize the utility of this resource, we applied our mask protocols to existing expression data from brains, livers, hearts, testes, and kidneys derived from both species and determined the effects probe numbers have on expression scores of specific transcripts. In all five tissues, probe sets with decreasing numbers of probes showed non-linear trends towards increased variation in expression scores. The relationships between expression variation and probe number in brain data closely matched those observed in simulated expression data sets subjected to random probe masking. However, there is evidence that additional factors affect the observed relationships between gene expression scores and probe number in tissues such as liver and kidney. In parallel, we observed that decreasing the number of probes within probe sets lead to linear increases in both gained and lost inferences of differential cross-species expression in all five tissues, which will affect the interpretation of expression data subject to masking. Conclusion We introduce a readily implemented and updated resource for human and chimpanzee transcriptome analysis through a commonly used microarray platform. Based on empirical observations derived from the analysis of five distinct data sets, we provide novel guidelines

  15. Convergence and fluctuations of Regularized Tyler estimators

    KAUST Repository

    Kammoun, Abla; Couillet, Romain; Pascal, Frederic; Alouini, Mohamed-Slim

    2015-01-01

    This article studies the behavior of regularized Tyler estimators (RTEs) of scatter matrices. The key advantages of these estimators are twofold. First, they guarantee by construction a good conditioning of the estimate and second, being a derivative of robust Tyler estimators, they inherit their robustness properties, notably their resilience to the presence of outliers. Nevertheless, one major problem that poses the use of RTEs in practice is represented by the question of setting the regularization parameter p. While a high value of p is likely to push all the eigenvalues away from zero, it comes at the cost of a larger bias with respect to the population covariance matrix. A deep understanding of the statistics of RTEs is essential to come up with appropriate choices for the regularization parameter. This is not an easy task and might be out of reach, unless one considers asymptotic regimes wherein the number of observations n and/or their size N increase together. First asymptotic results have recently been obtained under the assumption that N and n are large and commensurable. Interestingly, no results concerning the regime of n going to infinity with N fixed exist, even though the investigation of this assumption has usually predated the analysis of the most difficult N and n large case. This motivates our work. In particular, we prove in the present paper that the RTEs converge to a deterministic matrix when n → ∞ with N fixed, which is expressed as a function of the theoretical covariance matrix. We also derive the fluctuations of the RTEs around this deterministic matrix and establish that these fluctuations converge in distribution to a multivariate Gaussian distribution with zero mean and a covariance depending on the population covariance and the parameter.

  16. Convergence and fluctuations of Regularized Tyler estimators

    KAUST Repository

    Kammoun, Abla

    2015-10-26

    This article studies the behavior of regularized Tyler estimators (RTEs) of scatter matrices. The key advantages of these estimators are twofold. First, they guarantee by construction a good conditioning of the estimate and second, being a derivative of robust Tyler estimators, they inherit their robustness properties, notably their resilience to the presence of outliers. Nevertheless, one major problem that poses the use of RTEs in practice is represented by the question of setting the regularization parameter p. While a high value of p is likely to push all the eigenvalues away from zero, it comes at the cost of a larger bias with respect to the population covariance matrix. A deep understanding of the statistics of RTEs is essential to come up with appropriate choices for the regularization parameter. This is not an easy task and might be out of reach, unless one considers asymptotic regimes wherein the number of observations n and/or their size N increase together. First asymptotic results have recently been obtained under the assumption that N and n are large and commensurable. Interestingly, no results concerning the regime of n going to infinity with N fixed exist, even though the investigation of this assumption has usually predated the analysis of the most difficult N and n large case. This motivates our work. In particular, we prove in the present paper that the RTEs converge to a deterministic matrix when n → ∞ with N fixed, which is expressed as a function of the theoretical covariance matrix. We also derive the fluctuations of the RTEs around this deterministic matrix and establish that these fluctuations converge in distribution to a multivariate Gaussian distribution with zero mean and a covariance depending on the population covariance and the parameter.

  17. A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

    Science.gov (United States)

    Guardia, Gabriela D A; Pires, Luís Ferreira; Vêncio, Ricardo Z N; Malmegrim, Kelen C R; de Farias, Cléver R G

    2015-01-01

    Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

  18. A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

    Directory of Open Access Journals (Sweden)

    Gabriela D A Guardia

    Full Text Available Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

  19. Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds

    Directory of Open Access Journals (Sweden)

    Byrne Keren A

    2007-08-01

    Full Text Available Abstract Background The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60, secondary myogenesis (d 135, as well as beginning (d 195 and final stages (birth of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24 were from Hereford dams and crossed with either Wagyu (high intramuscular fat or Piedmontese (GDF8 mutant sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. Results We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5 RNA at birth. The developing longissimus muscle of

  20. Expression and regulation of glucocorticoid-induced leucine zipper in the developing anterior pituitary gland.

    Science.gov (United States)

    Ellestad, Laura E; Malkiewicz, Stefanie A; Guthrie, H David; Welch, Glenn R; Porter, Tom E

    2009-02-01

    The expression profile of glucocorticoid-induced leucine zipper (GILZ) in the anterior pituitary during the second half of embryonic development in the chick is consistent with in vivo regulation by circulating corticosteroids. However, nothing else has been reported about the presence of GILZ in the neuroendocrine system. We sought to characterize expression and regulation of GILZ in the chicken embryonic pituitary gland and determine the effect of GILZ overexpression on anterior pituitary hormone levels. Pituitary GILZ mRNA levels increased during embryogenesis to a maximum on the day of hatch, and decreased through the first week after hatch. GILZ expression was rapidly upregulated by corticosterone in embryonic pituitary cells. To determine whether GILZ regulates hormone gene expression in the developing anterior pituitary, we overexpressed GILZ in embryonic pituitary cells and measured mRNA for the major pituitary hormones. Exogenous GILZ increased prolactin mRNA above basal levels, but not as high as that in corticosterone-treated cells, indicating that GILZ may play a small role in lactotroph differentiation. The largest effect we observed was a twofold increase in FSH beta subunit in cells transfected with GILZ but not treated with corticosterone, suggesting that GILZ may positively regulate gonadotroph development in a manner not involving glucocorticoids. In conclusion, this is the first report to characterize avian GILZ and examine its regulation in the developing neuroendocrine system. We have shown that GILZ is upregulated by glucocorticoids in the embryonic pituitary gland and may regulate expression of several pituitary hormones.

  1. Expression of Pannexin 1 and Pannexin 3 during skeletal muscle development, regeneration, and Duchenne muscular dystrophy.

    Science.gov (United States)

    Pham, Tammy L; St-Pierre, Marie-Eve; Ravel-Chapuis, Aymeric; Parks, Tara E C; Langlois, Stéphanie; Penuela, Silvia; Jasmin, Bernard J; Cowan, Kyle N

    2018-05-10

    Pannexin 1 (Panx1) and Pannexin 3 (Panx3) are single membrane channels recently implicated in myogenic commitment, as well as myoblast proliferation and differentiation in vitro. However, their expression patterns during skeletal muscle development and regeneration had yet to be investigated. Here, we show that Panx1 levels increase during skeletal muscle development becoming highly expressed together with Panx3 in adult skeletal muscle. In adult mice, Panx1 and Panx3 were differentially expressed in fast- and slow-twitch muscles. We also report that Panx1/PANX1 and Panx3/PANX3 are co-expressed in mouse and human satellite cells, which play crucial roles in skeletal muscle regeneration. Interestingly, Panx1 and Panx3 levels were modulated in muscle degeneration/regeneration, similar to the pattern seen during skeletal muscle development. As Duchenne muscular dystrophy is characterized by skeletal muscle degeneration and impaired regeneration, we next used mild and severe mouse models of this disease and found a significant dysregulation of Panx1 and Panx3 levels in dystrophic skeletal muscles. Together, our results are the first demonstration that Panx1 and Panx3 are differentially expressed amongst skeletal muscle types with their levels being highly modulated during skeletal muscle development, regeneration, and dystrophy. These findings suggest that Panx1 and Panx3 channels may play important and distinct roles in healthy and diseased skeletal muscles. © 2018 Wiley Periodicals, Inc.

  2. Expression profile of Lgi1 gene in mouse brain during development.

    Science.gov (United States)

    Ribeiro, Patrícia A O; Sbragia, Lourenço; Gilioli, Rovilson; Langone, Francesco; Conte, Fábio F; Lopes-Cendes, Iscia

    2008-07-01

    Mutations in LGI1 were described in patients with autosomal dominant partial epilepsy with auditory features (ADPEAF), and recent clinical findings have implicated LGI1 in human brain development. However, the precise role of LGI1 in epileptogenesis remains largely unknown. The objective of this study was to determine the expression pattern of Lgi1 in mice brain during development and in adult animals. Real-time polymerase chain reaction (PCR) quantification and Western blot experiments showed a relative low expression during intrauterine stages, increasing until adulthood. In addition, we did not find significant differences between left and right hemispheres. The hippocampus presented higher levels of Lgi1 expression when compared to the neocortex and the cerebellum of adult animals; however, these results did not reach statistical significance. This study was the first to determine a specific profile of Lgi1 gene expression during central nervous system development, which suggests a possible inhibitory function in latter stages of development. In addition, we did not find differences in hemispheric expression that could explain the predominance of left-sided abnormalities in patients with ADPEAF.

  3. Germ cell development in the Honeybee (Apis mellifera; Vasa and Nanos expression

    Directory of Open Access Journals (Sweden)

    Dearden Peter K

    2006-02-01

    Full Text Available Abstract Background Studies of specification of germ-cells in insect embryos has indicated that in many taxa the germ cells form early in development, and their formation is associated with pole plasm, germ plasm or an organelle called the oosome. None of these morphological features associated with germ cell formation have been identified in the Honeybee Apis mellifera. In this study I report the cloning and expression analysis of Honeybee homologues of vasa and nanos, germ cell markers in insects and other animals. Results Apis vasa and nanos RNAs are present in early honeybee embryos, but the RNAs clear rapidly, without any cells expressing these germ cell markers past stage 2. These genes are then only expressed in a line of cells in the abdomen from stage 9 onwards. These cells are the developing germ cells that are moved dorsally by dorsal closure and are placed in the genital ridge. Conclusion This study of the expression of germ cell markers in the honeybee implies that in this species either germ cells are formed by an inductive event, late in embryogenesis, or they are formed early in development in the absence of vasa and nanos expression. This contrasts with germ cell development in other members of the Hymenoptera, Diptera and Lepidoptera.

  4. Changes in gravitational force affect gene expression in developing organ systems at different developmental times

    Directory of Open Access Journals (Sweden)

    Moorman Stephen J

    2005-05-01

    Full Text Available Abstract Background Little is known about the affect of microgravity on gene expression, particularly in vivo during embryonic development. Using transgenic zebrafish that express the gfp gene under the influence of a β-actin promoter, we examined the affect of simulated-microgravity on GFP expression in the heart, notochord, eye, somites, and rohon beard neurons. We exposed transgenic zebrafish to simulated-microgravity for different durations at a variety of developmental times in an attempt to determine periods of susceptibility for the different developing organ systems. Results The developing heart had a period of maximum susceptibility between 32 and 56 hours after fertilization when there was an approximately 30% increase in gene expression. The notochord, eye, somites, and rohon beard neurons all showed periods of susceptibility occurring between 24 and 72 hours after fertilization. In addition, the notochord showed a second period of susceptibility between 8 and 32 hours after fertilization. Interestingly, all organs appeared to be recovering by 80 hours after fertilization despite continued exposure to simulated-microgravity. Conclusion These results support the idea that exposure to microgravity can cause changes in gene expression in a variety of developing organ systems in live embryos and that there are periods of maximum susceptibility to the effects.

  5. Alcohol exposure decreases CREB binding protein expression and histone acetylation in the developing cerebellum.

    Directory of Open Access Journals (Sweden)

    Weixiang Guo

    Full Text Available Fetal alcohol exposure affects 1 in 100 children making it the leading cause of mental retardation in the US. It has long been known that alcohol affects cerebellum development and function. However, the underlying molecular mechanism is unclear.We demonstrate that CREB binding protein (CBP is widely expressed in granule and Purkinje neurons of the developing cerebellar cortex of naïve rats. We also show that exposure to ethanol during the 3(rd trimester-equivalent of human pregnancy reduces CBP levels. CBP is a histone acetyltransferase, a component of the epigenetic mechanism controlling neuronal gene expression. We further demonstrate that the acetylation of both histone H3 and H4 is reduced in the cerebellum of ethanol-treated rats.These findings indicate that ethanol exposure decreases the expression and function of CBP in the developing cerebellum. This effect of ethanol may be responsible for the motor coordination deficits that characterize fetal alcohol spectrum disorders.

  6. Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

    Directory of Open Access Journals (Sweden)

    Belmamoune Mounia

    2008-06-01

    Full Text Available The Gene Expression Management System (GEMS is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ. In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval . The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.

  7. Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development

    KAUST Repository

    Xu, Wei

    2014-06-01

    Postnatal cerebral development is a complicated biological process precisely controlled by multiple genes. To understand the molecular mechanism of cerebral development, we compared dynamics of mouse cerebrum transcriptome through three developmental stages using high-throughput RNA-seq technique. Three libraries were generated from the mouse cerebrum at infancy, adolescence and adulthood, respectively. Consequently, 44,557,729 (infancy), 59,257,530 (adolescence) and 72,729,636 (adulthood) reads were produced, which were assembled into 15,344, 16,048 and 15,775 genes, respectively. We found that the overall gene expression level increased from infancy to adolescence and decreased later on upon reaching adulthood. The adolescence cerebrum has the most active gene expression, with expression of a large number of regulatory genes up-regulated and some crucial pathways activated. Transcription factor (TF) analysis suggested the similar dynamics as expression profiling, especially those TFs functioning in neurogenesis differentiation, oligodendrocyte lineage determination and circadian rhythm regulation. Moreover, our data revealed a drastic increase in myelin basic protein (MBP)-coding gene expression in adolescence and adulthood, suggesting that the brain myelin may be generated since mouse adolescence. In addition, differential gene expression analysis indicated the activation of rhythmic pathway, suggesting the function of rhythmic movement since adolescence; Furthermore, during infancy and adolescence periods, gene expression related to axon. repulsion and attraction showed the opposite trends, indicating that axon repulsion was activated after birth, while axon attraction might be activated at the embryonic stage and declined during the postnatal development. Our results from the present study may shed light on the molecular mechanism underlying the postnatal development of the mammalian cerebrum. © 2014 .

  8. High-resolution temporal and regional mapping of MAPT expression and splicing in human brain development.

    Science.gov (United States)

    Hefti, Marco M; Farrell, Kurt; Kim, SoongHo; Bowles, Kathryn R; Fowkes, Mary E; Raj, Towfique; Crary, John F

    2018-01-01

    The microtubule associated protein tau plays a critical role in the pathogenesis of neurodegenerative disease. Recent studies suggest that tau also plays a role in disorders of neuronal connectivity, including epilepsy and post-traumatic stress disorder. Animal studies have shown that the MAPT gene, which codes for the tau protein, undergoes complex pre-mRNA alternative splicing to produce multiple isoforms during brain development. Human data, particularly on temporal and regional variation in tau splicing during development are however lacking. In this study, we present the first detailed examination of the temporal and regional sequence of MAPT alternative splicing in the developing human brain. We used a novel computational analysis of large transcriptomic datasets (total n = 502 patients), quantitative polymerase chain reaction (qPCR) and western blotting to examine tau expression and splicing in post-mortem human fetal, pediatric and adult brains. We found that MAPT exons 2 and 10 undergo abrupt shifts in expression during the perinatal period that are unique in the canonical human microtubule-associated protein family, while exon 3 showed small but significant temporal variation. Tau isoform expression may be a marker of neuronal maturation, temporally correlated with the onset of axonal growth. Immature brain regions such as the ganglionic eminence and rhombic lip had very low tau expression, but within more mature regions, there was little variation in tau expression or splicing. We thus demonstrate an abrupt, evolutionarily conserved shift in tau isoform expression during the human perinatal period that may be due to tau expression in maturing neurons. Alternative splicing of the MAPT pre-mRNA may play a vital role in normal brain development across multiple species and provides a basis for future investigations into the developmental and pathological functions of the tau protein.

  9. Sex difference in mecp2 expression during a critical period of rat brain development.

    Science.gov (United States)

    Kurian, Joseph R; Forbes-Lorman, Robin M; Auger, Anthony P

    2007-09-01

    Pervasive developmental disorder is a classification covering five related conditions including the neurodevelopmental disorder Rett syndrome (RTT) and autism. Of these five conditions, only RTT has a known genetic cause with mutations in Methyl-CpG-binding protein 2 (MeCP2), a global repressor of gene expression, responsible for the majority of RTT cases. However, recent evidence indicates that reduced MeCP2 expression or activity is also found in autism and other disorders with overlapping phenotypes. Considering the sex difference in autism diagnosis, with males diagnosed four times more often than females, we questioned if a sex difference existed in the expression of MeCP2, in particular within the amygdala, a region that develops atypically in autism. We found that male rats express significantly less mecp2 mRNA and protein than females within the amygdala, as well as the ventromedial hypothalamus (VMH), but not within the preoptic area (POA) on post-natal day 1 (PN1). At PN10 these differences were gone; however, on this day males had more mecp2 mRNA than females within the POA. The transient sex difference of mecp2 expression during the steroid-sensitive period of brain development suggests that mecp2 may participate in normal sexual differentiation of the rat brain. Considering the strong link between MeCP2 and neurodevelopmental disorders, the lower levels of mecp2 expression in males may also underlie a biological risk for mecp2-related neural disorders.

  10. Cell-type-specific expression of NFIX in the developing and adult cerebellum.

    Science.gov (United States)

    Fraser, James; Essebier, Alexandra; Gronostajski, Richard M; Boden, Mikael; Wainwright, Brandon J; Harvey, Tracey J; Piper, Michael

    2017-07-01

    Transcription factors from the nuclear factor one (NFI) family have been shown to play a central role in regulating neural progenitor cell differentiation within the embryonic and post-natal brain. NFIA and NFIB, for instance, promote the differentiation and functional maturation of granule neurons within the cerebellum. Mice lacking Nfix exhibit delays in the development of neuronal and glial lineages within the cerebellum, but the cell-type-specific expression of this transcription factor remains undefined. Here, we examined the expression of NFIX, together with various cell-type-specific markers, within the developing and adult cerebellum using both chromogenic immunohistochemistry and co-immunofluorescence labelling and confocal microscopy. In embryos, NFIX was expressed by progenitor cells within the rhombic lip and ventricular zone. After birth, progenitor cells within the external granule layer, as well as migrating and mature granule neurons, expressed NFIX. Within the adult cerebellum, NFIX displayed a broad expression profile, and was evident within granule cells, Bergmann glia, and interneurons, but not within Purkinje neurons. Furthermore, transcriptomic profiling of cerebellar granule neuron progenitor cells showed that multiple splice variants of Nfix are expressed within this germinal zone of the post-natal brain. Collectively, these data suggest that NFIX plays a role in regulating progenitor cell biology within the embryonic and post-natal cerebellum, as well as an ongoing role within multiple neuronal and glial populations within the adult cerebellum.

  11. Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE).

    Science.gov (United States)

    Taft, A S; Vermeire, J J; Bernier, J; Birkeland, S R; Cipriano, M J; Papa, A R; McArthur, A G; Yoshino, T P

    2009-04-01

    Infection of the snail, Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke, Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of the S. mansoni miracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia and in vitro cultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of the B. glabrata embryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to the S. mansoni gene predictions (v4.0e) either by estimating theoretical 3' UTR lengths or using existing 3' EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

  12. Statistical Considerations for Immunohistochemistry Panel Development after Gene Expression Profiling of Human Cancers

    Science.gov (United States)

    Betensky, Rebecca A.; Nutt, Catherine L.; Batchelor, Tracy T.; Louis, David N.

    2005-01-01

    In recent years there have been a number of microarray expression studies in which different types of tumors were classified by identifying a panel of differentially expressed genes. Immunohistochemistry is a practical and robust method for extending gene expression data to common pathological specimens with the advantage of being applicable to paraffin-embedded tissues. However, the number of assays required for successful immunohistochemical classification remains unclear. We propose a simulation-based method for assessing sample size for an immunohistochemistry investigation after a promising gene expression study of human tumors. The goals of such an immunohistochemistry study would be to develop and validate a marker panel that yields improved prognostic classification of cancer patients. We demonstrate how the preliminary gene expression data, coupled with certain realistic assumptions, can be used to estimate the number of immunohistochemical assays required for development. These assumptions are more tenable than alternative assumptions that would be required for crude analytic sample size calculations and that may yield underpowered and inefficient studies. We applied our methods to the design of an immunohistochemistry study for glioma classification and estimated the number of assays required to ensure satisfactory technical and prognostic validation. Simulation approaches for computing power and sample size that are based on existing gene expression data provide a powerful tool for efficient design of follow-up genomic studies. PMID:15858152

  13. Expression and location of α-fetoprotein during rat colon development

    Science.gov (United States)

    Liu, Xiao-Yan; Dong, Dan; Sun, Peng; Du, Jun; Gu, Luo; Ge, Ying-Bin

    2009-01-01

    AIM: To investigate the expression of α-fetoprotein (AFP), a cancer-associated fetal glycoprotein, and its involvement during rat colon development. METHODS: Colons from Sprague-Dawley rat fetuses, young and adult (8 wk old) animals were used in this study. Expression levels of AFP in colons of different development stage were detected by reverse-transcriptase PCR (RT-PCR) and Western blotting. To identify the cell location of AFP in the developing rat colons, double-immunofluorescent staining was performed using antibodies to specific cell markers and AFP, respectively. RESULTS: The highest levels of AFP mRNA were detected in colons of rats at embryonic day 18.5 (e18.5). Compared to e18.5 d, the AFP expression was significantly decreased during rat development [85% for e20.5, P colon from the embryo to the weaning stage by immunofluorescence and presents 72-kDa isoform in the developing rat colons by Western blotting. The dynamic expression of AFP in the various developmental stages of the colon indicates that AFP might be involved in many aspects of colon development. PMID:19360917

  14. Vector Development for the Expression of Foreign Proteins in the Vaccine Strain Brucella abortus S19

    Science.gov (United States)

    Comerci, Diego J.; Pollevick, Guido D.; Vigliocco, Ana M.; Frasch, Alberto C. C.; Ugalde, Rodolfo A.

    1998-01-01

    A vector for the expression of foreign antigens in the vaccine strain Brucella abortus S19 was developed by using a DNA fragment containing the regulatory sequences and the signal peptide of the Brucella bcsp31 gene. This fragment was cloned in broad-host-range plasmid pBBR4MCS, resulting in plasmid pBEV. As a reporter protein, a repetitive antigen of Trypanosoma cruzi was used. The recombinant fusion protein is stably expressed and secreted into the Brucella periplasmic space, inducing a good antibody response against the T. cruzi antigen. The expression of the repetitive antigen in Brucella neither altered its growth pattern nor generated a toxic or lethal effect during experimental infection. The application of this strategy for the generation of live recombinant vaccines and the tagging of B. abortus S19 vaccine is discussed. This is the first time that a recombinant protein has been expressed in the periplasm of brucellae. PMID:9673273

  15. Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene

    Directory of Open Access Journals (Sweden)

    Rathjen Tina

    2011-01-01

    Full Text Available Abstract Background Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~ 2.5 Mb did not reveal any other miRNAs and no novel miRNAs were predicted. Conclusions Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in

  16. Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene.

    Science.gov (United States)

    Surridge, Alison K; Lopez-Gomollon, Sara; Moxon, Simon; Maroja, Luana S; Rathjen, Tina; Nadeau, Nicola J; Dalmay, Tamas; Jiggins, Chris D

    2011-01-26

    Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~2.5 Mb) did not reveal any other miRNAs and no novel miRNAs were predicted. Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in butterfly wing development. Two miRNAs were located in the Hm

  17. Regularized plane-wave least-squares Kirchhoff migration

    KAUST Repository

    Wang, Xin; Dai, Wei; Schuster, Gerard T.

    2013-01-01

    A Kirchhoff least-squares migration (LSM) is developed in the prestack plane-wave domain to increase the quality of migration images. A regularization term is included that accounts for mispositioning of reflectors due to errors in the velocity

  18. Expression of hLAMP-1-Positive Particles During Early Heart Development in the Chick.

    Science.gov (United States)

    Abd-Elhamid, T H; Conway, M L; Sinning, A R

    2017-10-01

    Heart development requires coordinated activity of various factors, the disturbance of which can lead to congenital heart defects. Heart lectin-associated matrix protein-1 (hLAMP-1) is a matrix protein expressed within Hensen's node at Hamburger-Hamilton (HH) stage 4, in the lateral mesoderm by HH stages 5-6 and enhanced within the left pre-cardiac field at HH stage 7. At HH stages 15-16, hLAMP-1 expression is observed in the atrioventricular canal and the outflow tract. Also, the role of hLAMP-1 in induction of mesenchyme formation in chick heart has been well documented. To further elucidate the role of this molecule in heart development, we examined its expression patterns during HH stages 8-14 in the chick. In this regard, we immunostained sections of the heart during HH stages 8-14 with antibodies specific to hLAMP-1. Our results showed prominent expression of hLAMP-1-positive particles in the extracellular matrix associated with the pre-cardiac mesoderm, the endoderm, ectoderm as well as neuroectoderm at HH stages 8-9. After formation of the linear heart tube at HH stage 10, the expression of hLAMP-1-stained particles disappears in those regions of original contact between the endoderm and heart forming fields due to rupture of the dorsal mesocardium while their expression becomes confined to the arterial and venous poles of the heart tube. This expression pattern is maintained until HH stage 14. This expression pattern suggests that hLAMP-1 may be involved in the formation of the endocardial tube. © 2017 Blackwell Verlag GmbH.

  19. Regularization methods in Banach spaces

    CERN Document Server

    Schuster, Thomas; Hofmann, Bernd; Kazimierski, Kamil S

    2012-01-01

    Regularization methods aimed at finding stable approximate solutions are a necessary tool to tackle inverse and ill-posed problems. Usually the mathematical model of an inverse problem consists of an operator equation of the first kind and often the associated forward operator acts between Hilbert spaces. However, for numerous problems the reasons for using a Hilbert space setting seem to be based rather on conventions than on an approprimate and realistic model choice, so often a Banach space setting would be closer to reality. Furthermore, sparsity constraints using general Lp-norms or the B

  20. Academic Training Lecture - Regular Programme

    CERN Multimedia

    PH Department

    2011-01-01

    Regular Lecture Programme 9 May 2011 ACT Lectures on Detectors - Inner Tracking Detectors by Pippa Wells (CERN) 10 May 2011 ACT Lectures on Detectors - Calorimeters (2/5) by Philippe Bloch (CERN) 11 May 2011 ACT Lectures on Detectors - Muon systems (3/5) by Kerstin Hoepfner (RWTH Aachen) 12 May 2011 ACT Lectures on Detectors - Particle Identification and Forward Detectors by Peter Krizan (University of Ljubljana and J. Stefan Institute, Ljubljana, Slovenia) 13 May 2011 ACT Lectures on Detectors - Trigger and Data Acquisition (5/5) by Dr. Brian Petersen (CERN) from 11:00 to 12:00 at CERN ( Bldg. 222-R-001 - Filtration Plant )

  1. DEVELOPING VISUAL NOVEL GAME WITH SPEECH-RECOGNITION INTERACTIVITY TO ENHANCE STUDENTS’ MASTERY ON ENGLISH EXPRESSIONS

    Directory of Open Access Journals (Sweden)

    Elizabeth Anggraeni Amalo

    2017-11-01

    Full Text Available The teaching of English-expressions has always been done through conversation samples in form of written texts, audio recordings, and videos. In the meantime, the development of computer-aided learning technology has made autonomous language learning possible. Game, as one of computer-aided learning technology products, can serve as a medium to provide educational contents like that of language teaching and learning. Visual Novel is considered as a conversational game that is suitable to be combined with English-expressions material. Unlike the other click-based interaction Visual Novel Games, the visual novel game in this research implements speech recognition as the interaction trigger. Hence, this paper aims at elaborating how visual novel games are utilized to deliver English-expressions with speech recognition command for the interaction. This research used Research and Development (R&D method with Experimental design through control and experimental groups to measure its effectiveness in enhancing students’ English-expressions mastery. ANOVA was utilized to prove the significant differences between the control and experimental groups. It is expected that the result of this development and experiment can devote benefits to the English teaching and learning, especially on English-expressions.

  2. F-spondin/spon1b expression patterns in developing and adult zebrafish.

    Directory of Open Access Journals (Sweden)

    Veronica Akle

    Full Text Available F-spondin, an extracellular matrix protein, is an important player in embryonic morphogenesis and CNS development, but its presence and role later in life remains largely unknown. We generated a transgenic zebrafish in which GFP is expressed under the control of the F-spondin (spon1b promoter, and used it in combination with complementary techniques to undertake a detailed characterization of the expression patterns of F-spondin in developing and adult brain and periphery. We found that F-spondin is often associated with structures forming long neuronal tracts, including retinal ganglion cells, the olfactory bulb, the habenula, and the nucleus of the medial longitudinal fasciculus (nMLF. F-spondin expression coincides with zones of adult neurogenesis and is abundant in CSF-contacting secretory neurons, especially those in the hypothalamus. Use of this new transgenic model also revealed F-spondin expression patterns in the peripheral CNS, notably in enteric neurons, and in peripheral tissues involved in active patterning or proliferation in adults, including the endoskeleton of zebrafish fins and the continuously regenerating pharyngeal teeth. Moreover, patterning of the regenerating caudal fin following fin amputation in adult zebrafish was associated with F-spondin expression in the blastema, a proliferative region critical for tissue reconstitution. Together, these findings suggest major roles for F-spondin in the CNS and periphery of the developing and adult vertebrate.

  3. Parallel expression of synaptophysin and evoked neurotransmitter release during development of cultured neurons

    DEFF Research Database (Denmark)

    Ehrhart-Bornstein, M; Treiman, M; Hansen, Gert Helge

    1991-01-01

    Primary cultures of GABAergic cerebral cortex neurons and glutamatergic cerebellar granule cells were used to study the expression of synaptophysin, a synaptic vesicle marker protein, along with the ability of each cell type to release neurotransmitter upon stimulation. The synaptophysin expression...... by quantitative immunoblotting and light microscope immunocytochemistry, respectively. In both cell types, a close parallelism was found between the temporal pattern of development in synaptophysin expression and neurotransmitter release. This temporal pattern differed between the two types of neurons....... The cerebral cortex neurons showed a biphasic time course of increase in synaptophysin content, paralleled by a biphasic pattern of development in their ability to release [3H]GABA in response to depolarization by glutamate or elevated K+ concentrations. In contrast, a monophasic, approximately linear increase...

  4. Differentially displayed expressed sequence tags in Melipona scutellaris (Hymenoptera, Apidae, Meliponini) development.

    Science.gov (United States)

    Santana, Flávia A; Nunes, Francis M F; Vieira, Carlos U; Machado, Maria Alice M S; Kerr, Warwick E; Silva, Wilson A; Bonetti, Ana Maria

    2006-03-01

    We have compared gene expression, using the Differential Display Reverse Transcriptase-Polymerase Chain Reaction (DDRT-PCR) technique, by means of mRNA profile in Melipona scutellaris during ontogenetic postembryonic development, in adult worker, and in both Natural and Juvenile Hormone III-induced adult queen. Six, out of the nine ESTs described here, presented differentially expressed in the phases L1 or L2, or even in both of them, suggesting that key mechanisms to the development of Melipona scutellaris are regulated in these stages. The combination HT11G-AP05 revealed in L1 and L2 a product which matches to thioredoxin reductase protein domain in the Clostridium sporogenes, an important protein during cellular oxidoreduction processes. This study represents the first molecular evidence of differential gene expression profiles toward a description of the genetic developmental traits in the genus Melipona.

  5. Differentially displayed expressed sequence tags in Melipona scutellaris (Hymenoptera, Apidae, Meliponini development

    Directory of Open Access Journals (Sweden)

    Santana Flávia A.

    2006-01-01

    Full Text Available We have compared gene expression, using the Differential Display Reverse Transcriptase - Polymerase Chain Reaction (DDRT-PCR technique, by means of mRNA profile in Melipona scutellaris during ontogenetic postembryonic development, in adult worker, and in both Natural and Juvenile Hormone III-induced adult queen. Six, out of the nine ESTs described here, presented differentially expressed in the phases L1 or L2, or even in both of them, suggesting that key mechanisms to the development of Melipona scutellaris are regulated in these stages. The combination HT11G-AP05 revealed in L1 and L2 a product which matches to thioredoxin reductase protein domain in the Clostridium sporogenes, an important protein during cellular oxidoreduction processes. This study represents the first molecular evidence of differential gene expression profiles toward a description of the genetic developmental traits in the genus Melipona.

  6. Gene expression during blow fly development: improving the precision of age estimates in forensic entomology.

    Science.gov (United States)

    Tarone, Aaron M; Foran, David R

    2011-01-01

    Forensic entomologists use size and developmental stage to estimate blow fly age, and from those, a postmortem interval. Since such estimates are generally accurate but often lack precision, particularly in the older developmental stages, alternative aging methods would be advantageous. Presented here is a means of incorporating developmentally regulated gene expression levels into traditional stage and size data, with a goal of more precisely estimating developmental age of immature Lucilia sericata. Generalized additive models of development showed improved statistical support compared to models that did not include gene expression data, resulting in an increase in estimate precision, especially for postfeeding third instars and pupae. The models were then used to make blind estimates of development for 86 immature L. sericata raised on rat carcasses. Overall, inclusion of gene expression data resulted in increased precision in aging blow flies. © 2010 American Academy of Forensic Sciences.

  7. Defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development

    DEFF Research Database (Denmark)

    D'Antuono, Alejandra L; Ott, Thomas; Krusell, Lene

    2008-01-01

    cDNA array technology was used to compare transcriptome profiles of Lotus japonicus roots inoculated with a Mesorhizobium loti wild-type and two mutant strains affected in cyclic beta(1-2) glucan synthesis (cgs) and in lipopolysaccharide synthesis (lpsbeta2). Expression of genes associated...... with the development of a fully functional nodule was significantly affected in plants inoculated with the cgs mutant. Array results also revealed that induction of marker genes for nodule development was delayed when plants were inoculated with the lpsbeta2 mutant. Quantitative real-time reverse......-transcriptase polymerase chain reaction was used to quantify gene expression of a subset of genes involved in plant defense response, redox metabolism, or genes that encode for nodulins. The majority of the genes analyzed in this study were more highly expressed in roots inoculated with the wild type compared with those...

  8. Regularized Label Relaxation Linear Regression.

    Science.gov (United States)

    Fang, Xiaozhao; Xu, Yong; Li, Xuelong; Lai, Zhihui; Wong, Wai Keung; Fang, Bingwu

    2018-04-01

    Linear regression (LR) and some of its variants have been widely used for classification problems. Most of these methods assume that during the learning phase, the training samples can be exactly transformed into a strict binary label matrix, which has too little freedom to fit the labels adequately. To address this problem, in this paper, we propose a novel regularized label relaxation LR method, which has the following notable characteristics. First, the proposed method relaxes the strict binary label matrix into a slack variable matrix by introducing a nonnegative label relaxation matrix into LR, which provides more freedom to fit the labels and simultaneously enlarges the margins between different classes as much as possible. Second, the proposed method constructs the class compactness graph based on manifold learning and uses it as the regularization item to avoid the problem of overfitting. The class compactness graph is used to ensure that the samples sharing the same labels can be kept close after they are transformed. Two different algorithms, which are, respectively, based on -norm and -norm loss functions are devised. These two algorithms have compact closed-form solutions in each iteration so that they are easily implemented. Extensive experiments show that these two algorithms outperform the state-of-the-art algorithms in terms of the classification accuracy and running time.

  9. Sparsity regularization for parameter identification problems

    International Nuclear Information System (INIS)

    Jin, Bangti; Maass, Peter

    2012-01-01

    The investigation of regularization schemes with sparsity promoting penalty terms has been one of the dominant topics in the field of inverse problems over the last years, and Tikhonov functionals with ℓ p -penalty terms for 1 ⩽ p ⩽ 2 have been studied extensively. The first investigations focused on regularization properties of the minimizers of such functionals with linear operators and on iteration schemes for approximating the minimizers. These results were quickly transferred to nonlinear operator equations, including nonsmooth operators and more general function space settings. The latest results on regularization properties additionally assume a sparse representation of the true solution as well as generalized source conditions, which yield some surprising and optimal convergence rates. The regularization theory with ℓ p sparsity constraints is relatively complete in this setting; see the first part of this review. In contrast, the development of efficient numerical schemes for approximating minimizers of Tikhonov functionals with sparsity constraints for nonlinear operators is still ongoing. The basic iterated soft shrinkage approach has been extended in several directions and semi-smooth Newton methods are becoming applicable in this field. In particular, the extension to more general non-convex, non-differentiable functionals by variational principles leads to a variety of generalized iteration schemes. We focus on such iteration schemes in the second part of this review. A major part of this survey is devoted to applying sparsity constrained regularization techniques to parameter identification problems for partial differential equations, which we regard as the prototypical setting for nonlinear inverse problems. Parameter identification problems exhibit different levels of complexity and we aim at characterizing a hierarchy of such problems. The operator defining these inverse problems is the parameter-to-state mapping. We first summarize some

  10. The murine homeobox gene Msx-3 shows highly restricted expression in the developing neural tube.

    Science.gov (United States)

    Shimeld, S M; McKay, I J; Sharpe, P T

    1996-04-01

    The mouse homeobox-genes Msx-1 and Msx-2 are expressed in several areas of the developing embryo, including the neural tube, neural crest, facial processes and limb buds. Here we report the characterisation of a third mouse Msx gene, which we designate Msx-3. The embryonic expression of Msx-3 was found to differ from that of Msx-1 and -2 in that it was confined to the dorsal neural tube. In embryos with 5-8 somites a segmental pattern of expression was observed in the hindbrain, with rhombomeres 3 and 5 lacking Msx-3 while other rhombomeres expressed Msx-3. This pattern was transient, however, such that in embryos with 18 or more somites expression was continuous throughout the dorsal hindbrain and anterior dorsal spinal cord. Differentiation of dorsal cell types in the neural tube can be induced by addition of members of the Tgf-beta family. Additionally, Msx-1 and -2 have been shown to be activated by addition of the Tgf-beta family member Bmp-4. To determine if Bmp-4 could activate Msx-3, we incubated embryonic hindbrain explants with exogenous Bmp-4. The dorsal expression of Msx-3 was seen to expand into more ventral regions of the neurectoderm in Bmp-4-treated cultures, implying that Bmp-4 may be able to mimic an in vivo signal that induces Msx-3.

  11. Bayesian regularization of diffusion tensor images

    DEFF Research Database (Denmark)

    Frandsen, Jesper; Hobolth, Asger; Østergaard, Leif

    2007-01-01

    Diffusion tensor imaging (DTI) is a powerful tool in the study of the course of nerve fibre bundles in the human brain. Using DTI, the local fibre orientation in each image voxel can be described by a diffusion tensor which is constructed from local measurements of diffusion coefficients along...... several directions. The measured diffusion coefficients and thereby the diffusion tensors are subject to noise, leading to possibly flawed representations of the three dimensional fibre bundles. In this paper we develop a Bayesian procedure for regularizing the diffusion tensor field, fully utilizing...

  12. Development and Use of English Evaluative Expressions in Narratives of Chinese-English Bilinguals

    Science.gov (United States)

    Chen, Liang; Yan, Ruixia

    2011-01-01

    This study compares the development and use of evaluative expressions in the English narratives elicited from 80 Chinese-English bilinguals and 80 American monolingual peers at four ages--five, eight, ten, and young adults--using the wordless picture book "Frog, where are you?" (Mayer, 1969). Results revealed both similarities and differences…

  13. Development of a rapid yeast estrogen bioassay, based on the expression of green fluorescent protein

    NARCIS (Netherlands)

    Bovee, T.F.H.; Helsdingen, R.J.R.; Koks, P.D.; Kuiper, H.A.; Hoogenboom, L.A.P.; Keijer, J.

    2004-01-01

    The aim of this study was to develop an estrogen transcription activation assay that is sensitive, fast and easy to use in the routine screening of estrogen activity in complex matrices such as agricultural products. Recombinant yeast cells were constructed that express the human estrogen receptor ¿

  14. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis

    DEFF Research Database (Denmark)

    Müller, H; Bracken, A P; Vernell, R

    2001-01-01

    The retinoblastoma protein (pRB) and its two relatives, p107 and p130, regulate development and cell proliferation in part by inhibiting the activity of E2F-regulated promoters. We have used high-density oligonucleotide arrays to identify genes in which expression changed in response to activation...

  15. Sex-specific gonadal and gene expression changes throughout development in fathead minnow

    Science.gov (United States)

    Although fathead minnows (Pimephales promelas) are commonly used as a model fish in endocrine disruption studies, none have characterized sex-specific baseline expression of genes involved in sex differentiation during development in this species. Using a sex-linked DNA marker t...

  16. Myosin heavy chain expression in rabbit masseter muscle during postnatal development

    NARCIS (Netherlands)

    Bredman, J. J.; Weijs, W. A.; Korfage, H. A.; Brugman, P.; Moorman, A. F.

    1992-01-01

    The expression of isoforms of myosin heavy chain (MHC) during postnatal development was studied in the masseter muscle of the rabbit. Evidence is presented that in addition to adult fast and slow myosin, the rabbit masseter contains neonatal and 'cardiac' alpha-MHC. During postnatal growth myosin

  17. Understanding Emotions from Standardized Facial Expressions in Autism and Normal Development

    Science.gov (United States)

    Castelli, Fulvia

    2005-01-01

    The study investigated the recognition of standardized facial expressions of emotion (anger, fear, disgust, happiness, sadness, surprise) at a perceptual level (experiment 1) and at a semantic level (experiments 2 and 3) in children with autism (N= 20) and normally developing children (N= 20). Results revealed that children with autism were as…

  18. An RNA gene expressed during cortical development evolved rapidly in humans

    DEFF Research Database (Denmark)

    Pollard, Katherine S; Salama, Sofie R; Lambert, Nelle

    2006-01-01

    in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other...

  19. Developing a General Outcome Measure of Growth in the Expressive Communication of Infants and Toddlers.

    Science.gov (United States)

    Luze, Gayle J.; Linebarger, Deborah L.; Greenwood, Charles R.; Carta, Judith J.; Walker, Dale; Leitschuh, Carol; Atwater, Jane B.

    2001-01-01

    Describes the development of an experimental measure for assessing growth in expressive communication in children from birth to 3 years of age Results from a sample of 50 infants and toddlers assessed monthly for 9 months in indicated that the measure displayed adequate psychometric properties of reliability and validity and was sensitive to…

  20. Expression of truncated PITX3 in the developing lens leads to microphthalmia and aphakia in mice.

    Directory of Open Access Journals (Sweden)

    Kenta Wada

    Full Text Available Microphthalmia is a severe ocular disorder, and this condition is typically caused by mutations in transcription factors that are involved in eye development. Mice carrying mutations in these transcription factors would be useful tools for defining the mechanisms underlying developmental eye disorders. We discovered a new spontaneous recessive microphthalmos mouse mutant in the Japanese wild-derived inbred strain KOR1/Stm. The homozygous mutant mice were histologically characterized as microphthalmic by the absence of crystallin in the lens, a condition referred to as aphakia. By positional cloning, we identified the nonsense mutation c.444C>A outside the genomic region that encodes the homeodomain of the paired-like homeodomain transcription factor 3 gene (Pitx3 as the mutation responsible for the microphthalmia and aphakia. We examined Pitx3 mRNA expression of mutant mice during embryonic stages using RT-PCR and found that the expression levels are higher than in wild-type mice. Pitx3 over-expression in the lens during developmental stages was also confirmed at the protein level in the microphthalmos mutants via immunohistochemical analyses. Although lens fiber differentiation was not observed in the mutants, strong PITX3 protein signals were observed in the lens vesicles of the mutant lens. Thus, we speculated that abnormal PITX3, which lacks the C-terminus (including the OAR domain as a result of the nonsense mutation, is expressed in mutant lenses. We showed that the expression of the downstream genes Foxe3, Prox1, and Mip was altered because of the Pitx3 mutation, with large reductions in the lens vesicles in the mutants. Similar profiles were observed by immunohistochemical analysis of these proteins. The expression profiles of crystallins were also altered in the mutants. Therefore, we speculated that the microphthalmos/aphakia in this mutant is caused by the expression of truncated PITX3, resulting in the abnormal expression of

  1. Dynamic expression of Lgr6 in the developing and mature mouse cochlea

    Science.gov (United States)

    Zhang, Yanping; Chen, Yan; Ni, Wenli; Guo, Luo; Lu, Xiaoling; Liu, Liman; Li, Wen; Sun, Shan; Wang, Lei; Li, Huawei

    2015-01-01

    The Wnt/β-catenin signaling pathway plays important roles in mammalian inner ear development. Lgr5, one of the downstream target genes of the Wnt/β-catenin signaling pathway, has been reported to be a marker for inner ear hair cell progenitors. Lgr6 shares approximately 50% sequence homology with Lgr5 and has been identified as a stem cell marker in several organs. However, the detailed expression profiles of Lgr6 have not yet been investigated in the mouse inner ear. Here, we first used Lgr6-EGFP-Ires-CreERT2 mice to examine the spatiotemporal expression of Lgr6 protein in the cochlear duct during embryonic and postnatal development. Lgr6-EGFP was first observed in one row of prosensory cells in the middle and basal turn at embryonic day 15.5 (E15.5). From E18.5 to postnatal day 3 (P3), the expression of Lgr6-EGFP was restricted to the inner pillar cells (IPCs). From P7 to P15, the Lgr6-EGFP expression level gradually decreased in the IPCs and gradually increased in the inner border cells (IBCs). At P20, Lgr6-EGFP was only expressed in the IBCs, and by P30 Lgr6-EGFP expression had completely disappeared. Next, we demonstrated that Wnt/β-catenin signaling is required to maintain the Lgr6-EGFP expression in vitro. Finally, we demonstrated that the Lgr6-EGFP-positive cells isolated by flow cytometry could differentiate into myosin 7a-positive hair cells after 10 days in-culture, and this suggests that the Lgr6-positive cells might serve as the hair cell progenitor cells in the cochlea. PMID:26029045

  2. Expression of XPG protein in the development, progression and prognosis of gastric cancer.

    Directory of Open Access Journals (Sweden)

    Na Deng

    Full Text Available BACKGROUND: Xeroderma pigmentosum group G (XPG plays a critical role in preventing cells from oxidative DNA damage. This study aimed to investigate XPG protein expression in different gastric tissues and in patients with diverse prognoses, thus providing insights into its role in the development, progression and prognosis of gastric cancer (GC. METHODS: A total of 176 GC, 131 adjacent non-tumour tissues, 53 atrophic gastritis (AG and 49 superficial gastritis (SG samples were included. Immunohistochemical staining was used to detect XPG protein expression. RESULTS: XPG expression was significantly higher in GC tissues compared with adjacent non-tumour tissues. In the progressive disease sequence SG→AG→GC, XPG expression was significantly higher in AG and GC compared with SG. Analysis of clinicopathological parameters and survival in GC patients demonstrated a significant association between XPG expression level and depth of tumour invasion, macroscopic type, Lauren's classification, smoking, Helicobacter pylori infection and family history. Cox multivariate survival analysis indicated that patients with positive XPG expression had significantly longer overall survival (P = 0.020, HR = 0.394, 95%CI 0.179-0.866, especially in aged younger than 60 years (P = 0.027, HR = 0.361, 95%CI 0.147-0.888 and male patients (P = 0.002, HR = 0.209, 95%CI 0.077-0.571. CONCLUSIONS: This study demonstrated that XPG protein expression was related to the development, progression and prognosis of GC, and might thus serve as a potential biomarker for its diagnosis and prognosis.

  3. Dynamic Expression of Lgr6 in the Developing and Mature Mouse Cochlea

    Directory of Open Access Journals (Sweden)

    Yanping eZhang

    2015-05-01

    Full Text Available The Wnt/β-catenin signaling pathway plays important roles in mammalian inner ear development. Lgr5, one of the downstream target genes of the Wnt/β-catenin signaling pathway, has been reported to be a marker for inner ear hair cell progenitors. Lgr6 shares approximately 50% sequence homology with Lgr5 and has been identified as a stem cell marker in several organs. However, the detailed expression profiles of Lgr6 have not yet been investigated in the mouse inner ear. Here, we first used Lgr6-EGFP-Ires-CreERT2 mice to examine the spatiotemporal expression of Lgr6 protein in the cochlear duct during embryonic and postnatal development. Lgr6-EGFP was first observed in one row of prosensory cells in the middle and basal turn at embryonic day 15.5 (E15.5. From E18.5 to postnatal day 3 (P3, the expression of Lgr6-EGFP was restricted to the inner pillar cells (IPCs. From P7 to P15, the Lgr6-EGFP expression level gradually decreased in the IPCs and gradually increased in the inner border cells (IBCs. At P20, Lgr6-EGFP was only expressed in the IBCs, and by P30 Lgr6-EGFP expression had completely disappeared. Next, we demonstrated that Wnt/β-catenin signaling is required to maintain the Lgr6-EGFP expression in vitro. Finally, we demonstrated that the Lgr6-EGFP-positive cells isolated by flow cytometry could differentiate into myosin 7a-positive hair cells after 10 days in-culture, and this suggests that the Lgr6-positive cells might serve as the hair cell progenitor cells in the cochlea.

  4. Expression profile and distribution of Efhc1 gene transcript during rodent brain development.

    Science.gov (United States)

    Conte, Fábio F; Ribeiro, Patrícia A O; Marchesini, Rafael B; Pascoal, Vinícius D B; Silva, Joelcimar M; Oliveira, Amanda R; Gilioli, Rovílson; Sbragia, Lourenço; Bittencourt, Jackson C; Lopes-Cendes, Iscia

    2009-09-01

    One of the putative causative genes for juvenile myoclonic epilepsy (JME) is EFHC1. We report here the expression profile and distribution of Efhc1 messenger RNA (mRNA) during mouse and rat brain development. Real-time polymerase chain reaction revealed that there is no difference in the expression of Efhc1 mRNA between right and left hemispheres in both species. In addition, the highest levels of Efhc1 mRNA were found at intra-uterine stages in mouse and in adulthood in rat. In common, there was a progressive decrease in Efhc1 expression from 1-day-old neonates to 14-day-old animals in both species. In situ hybridization studies showed that rat and mouse Efhc1 mRNAs are expressed in ependymal cells of ventricle walls. Our findings suggest that Efhc1 expression is more important during initial phases of brain development and that at this stage it could be involved in key developmental mechanisms underlying JME.

  5. Expression pattern of the homeotic gene Bapx1 during early chick gastrointestinal tract development.

    Science.gov (United States)

    Faure, Sandrine; Georges, Maxime; McKey, Jennifer; Sagnol, Sébastien; de Santa Barbara, Pascal

    2013-12-01

    Regulation of the Bone Morphogenetic Protein (BMP) signaling pathway is essential for the normal development of vertebrate gastrointestinal (GI) tract, but also for the differentiation of the digestive mesenchymal layer into smooth muscles and submucosal layer. Different studies demonstrated that Bapx1 (for bagpipe homeobox homolog 1) negatively regulates the BMP pathway, but its precise expression pattern during the development and the differentiation of the GI tract mesenchyme actually remains to be examined. Here, we present the spatio-temporal expression profile of Bapx1 in the chick GI tract. We show that Bapx1 is first expressed in the undifferentiated mesenchyme of the gizzard and the colon. After the differentiation of the digestive mesenchyme, we found Bapx1 strongly expressed in the gizzard smooth muscle and in the submucosa layer of the colon. This expression pattern provides new insights into the roles of Bapx1 during the regionalization of the GI tract and the differentiation of the digestive mesenchyme of the colon and the stomach. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Sox9-dependent expression of Gstm6 in Sertoli cells during testis development in mice.

    Science.gov (United States)

    Beverdam, Annemiek; Svingen, Terje; Bagheri-Fam, Stefan; Bernard, Pascal; McClive, Peter; Robson, Mathew; Khojasteh, Mahdi Banan; Salehi, Mahboubeh; Sinclair, Andrew H; Harley, Vincent R; Koopman, Peter

    2009-03-01

    Glutathione S-transferases (GSTs) are an important family of multifunctional enzymes that play a role in the protection of tissues by the detoxification of hazardous and carcinogenic compounds. We found previously that Gstm6 is upregulated in the somatic cells of male mouse fetal gonads relative to female gonads. In this study, we describe the spatial and temporal expression pattern of Gstm6 during mouse development. We show that Gstm6 is predominantly expressed in the reproductive system, at significantly higher levels in XY gonads compared with XX gonads from 11.5 dpc onwards, and remains expressed in the testes in adult mice. Its expression is associated with the Sertoli cell lineage, and is dependent on the expression of the male sex-determining gene Sox9. Our data suggest that Gstm6 plays a male-specific role in gonad development or function, possibly by modulating the exposure of somatic tissue and/or germ cells to endogenous or exogenous toxicants.

  7. NorWood: a gene expression resource for evo-devo studies of conifer wood development.

    Science.gov (United States)

    Jokipii-Lukkari, Soile; Sundell, David; Nilsson, Ove; Hvidsten, Torgeir R; Street, Nathaniel R; Tuominen, Hannele

    2017-10-01

    The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  8. 'Fluorescent Cell Chip' for immunotoxicity testing: Development of the c-fos expression reporter cell lines

    International Nuclear Information System (INIS)

    Trzaska, Dominika; Zembek, Patrycja; Olszewski, Maciej; Adamczewska, Violetta; Ulleras, Erik; Dastych, JarosIaw

    2005-01-01

    The Fluorescent Cell Chip for in vitro immunotoxicity testing employs cell lines derived from lymphocytes, mast cells, and monocytes-macrophages transfected with various EGFP cytokine reporter gene constructs. While cytokine expression is a valid endpoint for in vitro immunotoxicity screening, additional marker for the immediate-early response gene expression level could be of interest for further development and refinement of the Fluorescent Cell Chip. We have used BW.5147.3 murine thymoma transfected with c-fos reporter constructs to obtain reporter cell lines expressing ECFP under the control of murine c-fos promoter. These cells upon serum withdrawal and readdition and incubation with heavy metal compounds showed paralleled induction of c-Fos expression as evidenced by Real-Time PCR and ECFP fluorescence as evidenced by computer-supported fluorescence microscopy. In conclusion, we developed fluorescent reporter cell lines that could be employed in a simple and time-efficient screening assay for possible action of chemicals on c-Fos expression in lymphocytes. The evaluation of usefulness of these cells for the Fluorescent Cell Chip-based detection of immunotoxicity will require additional testing with a larger number of chemicals

  9. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication.

    Science.gov (United States)

    Rapp, Ryan A; Haigler, Candace H; Flagel, Lex; Hovav, Ran H; Udall, Joshua A; Wendel, Jonathan F

    2010-11-15

    Understanding the evolutionary genetics of modern crop phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern upland cotton (Gossypium hirsutum L.) was developed following thousands of years of artificial selection from a wild form, G. hirsutum var. yucatanense, which bears a shorter, sparser, layer of single-celled, ovular trichomes ('fibre'). In order to gain an insight into the nature of the developmental genetic transformations that accompanied domestication and crop improvement, we studied the transcriptomes of cotton fibres from wild and domesticated accessions over a developmental time course. Fibre cells were harvested between 2 and 25 days post-anthesis and encompassed the primary and secondary wall synthesis stages. Using amplified messenger RNA and a custom microarray platform designed to interrogate expression for 40,430 genes, we determined global patterns of expression during fibre development. The fibre transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over twice as many genes being differentially expressed during development (12,626 versus 5273). Remarkably, a total of 9465 genes were diagnosed as differentially expressed between wild and domesticated fibres when summed across five key developmental time points. Human selection during the initial domestication and subsequent crop improvement has resulted in a biased upregulation of components of the transcriptional network that are important for agronomically advanced fibre, especially in the early stages of development. About 15% of the differentially expressed genes in wild versus domesticated cotton fibre have no homology to the genes in databases. We show that artificial selection during crop domestication can radically alter the transcriptional developmental network of even a single-celled structure, affecting nearly a quarter of the genes in the genome. Gene expression during fibre development within accessions and expression

  10. Evidence of a bigenomic regulation of mitochondrial gene expression by thyroid hormone during rat brain development

    International Nuclear Information System (INIS)

    Sinha, Rohit Anthony; Pathak, Amrita; Mohan, Vishwa; Babu, Satish; Pal, Amit; Khare, Drirh; Godbole, Madan M.

    2010-01-01

    Hypothyroidism during early mammalian brain development is associated with decreased expression of various mitochondrial encoded genes along with evidence for mitochondrial dysfunction. However, in-spite of the similarities between neurological disorders caused by perinatal hypothyroidism and those caused by various genetic mitochondrial defects we still do not know as to how thyroid hormone (TH) regulates mitochondrial transcription during development and whether this regulation by TH is nuclear mediated or through mitochondrial TH receptors? We here in rat cerebellum show that hypothyroidism causes reduction in expression of nuclear encoded genes controlling mitochondrial biogenesis like PGC-1α, NRF-1α and Tfam. Also, we for the first time demonstrate a mitochondrial localization of thyroid hormone receptor (mTR) isoform in developing brain capable of binding a TH response element (DR2) present in D-loop region of mitochondrial DNA. These results thus indicate an integrated nuclear-mitochondrial cross talk in regulation of mitochondrial transcription by TH during brain development.

  11. Evidence of a bigenomic regulation of mitochondrial gene expression by thyroid hormone during rat brain development

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, Rohit Anthony; Pathak, Amrita; Mohan, Vishwa; Babu, Satish; Pal, Amit; Khare, Drirh [Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014 (India); Godbole, Madan M., E-mail: madangodbole@yahoo.co.in [Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014 (India)

    2010-07-02

    Hypothyroidism during early mammalian brain development is associated with decreased expression of various mitochondrial encoded genes along with evidence for mitochondrial dysfunction. However, in-spite of the similarities between neurological disorders caused by perinatal hypothyroidism and those caused by various genetic mitochondrial defects we still do not know as to how thyroid hormone (TH) regulates mitochondrial transcription during development and whether this regulation by TH is nuclear mediated or through mitochondrial TH receptors? We here in rat cerebellum show that hypothyroidism causes reduction in expression of nuclear encoded genes controlling mitochondrial biogenesis like PGC-1{alpha}, NRF-1{alpha} and Tfam. Also, we for the first time demonstrate a mitochondrial localization of thyroid hormone receptor (mTR) isoform in developing brain capable of binding a TH response element (DR2) present in D-loop region of mitochondrial DNA. These results thus indicate an integrated nuclear-mitochondrial cross talk in regulation of mitochondrial transcription by TH during brain development.

  12. MeCP2 Expression and Promoter Methylation of Cyclin D1 Gene Are Associated with Cyclin D1 Expression in Developing Rat Epididymal Duct

    International Nuclear Information System (INIS)

    Darwanto, Agus; Kitazawa, Riko; Mori, Kiyoshi; Kondo, Takeshi; Kitazawa, Sohei

    2008-01-01

    Hypermethylation-dependent silencing of the gene is achieved by recruiting methyl-CpG binding proteins (MeCPs). Among the MeCPs, MeCP2 is the most abundantly and ubiquitously expressed in various types of cells. We first screened the distribution and expression pattern of MeCP2 in adult and developing rat tissues and found strong MeCP2 expression, albeit rather ubiquitously among normal tissues, in ganglion cells and intestinal epithelium in the small intestine, in Purkinje cells and neurons in the brain, in spermatogonia and in epithelial cells in the epididymal duct of the testis. We then assessed the expression and the methylation pattern of the promoter region of cyclin D1 by immunohistochemistry and sodium bisulfite mapping, and found that cyclin D1 expression in the epididymal duct decreased rapidly during rat development: strong in newborn rats and very weak or almost negative in 7-day-old rats. Mirroring the decrease of cyclin D1 expression, methylated cytosine at both CpG and non-CpG loci in the cyclin D1 promoter was frequently observed in the epididymal duct of 7-day-old rats but not in that of newborn rats. Interestingly, MeCP2 expression also increased concomitant with the increase of methylation. Cyclin D1 expression in the epididymal duct may be efficiently regulated by the epigenetic mechanism of the cooperative increase of MeCP2 expression and promoter methylation

  13. Nipbl and mediator cooperatively regulate gene expression to control limb development.

    Directory of Open Access Journals (Sweden)

    Akihiko Muto

    2014-09-01

    Full Text Available Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS, the most common "cohesinopathy". It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb, knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions.

  14. Experimental and Modeling Approaches for Understanding the Effect of Gene Expression Noise in Biological Development

    Directory of Open Access Journals (Sweden)

    David M. Holloway

    2018-04-01

    Full Text Available Biological development involves numerous chemical and physical processes which must act in concert to reliably produce a cell, a tissue, or a body. To be successful, the developing organism must be robust to variability at many levels, such as the environment (e.g., temperature, moisture, upstream information (such as long-range positional information gradients, or intrinsic noise due to the stochastic nature of low concentration chemical kinetics. The latter is especially relevant to the regulation of gene expression in cell differentiation. The temporal stochasticity of gene expression has been studied in single celled organisms for nearly two decades, but only recently have techniques become available to gather temporally-resolved data across spatially-distributed gene expression patterns in developing multicellular organisms. These demonstrate temporal noisy “bursting” in the number of gene transcripts per cell, raising the question of how the transcript number defining a particular cell type is produced, such that one cell type can reliably be distinguished from a neighboring cell of different type along a tissue boundary. Stochastic spatio-temporal modeling of tissue-wide expression patterns can identify signatures for specific types of gene regulation, which can be used to extract regulatory mechanism information from experimental time series. This Perspective focuses on using this type of approach to study gene expression noise during the anterior-posterior segmentation of the fruit fly embryo. Advances in experimental and theoretical techniques will lead to an increasing quantification of expression noise that can be used to understand how regulatory mechanisms contribute to embryonic robustness across a range of developmental processes.

  15. Global analysis of gene expression profiles in developing physic nut (Jatropha curcas L. seeds.

    Directory of Open Access Journals (Sweden)

    Huawu Jiang

    Full Text Available BACKGROUND: Physic nut (Jatropha curcas L. is an oilseed plant species with high potential utility as a biofuel. Furthermore, following recent sequencing of its genome and the availability of expressed sequence tag (EST libraries, it is a valuable model plant for studying carbon assimilation in endosperms of oilseed plants. There have been several transcriptomic analyses of developing physic nut seeds using ESTs, but they have provided limited information on the accumulation of stored resources in the seeds. METHODOLOGY/PRINCIPAL FINDINGS: We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of developing physic nut seeds 14, 19, 25, 29, 35, 41, and 45 days after pollination (DAP. The acquired profiles reveal the key genes, and their expression timeframes, involved in major metabolic processes including: carbon flow, starch metabolism, and synthesis of storage lipids and proteins in the developing seeds. The main period of storage reserves synthesis in the seeds appears to be 29-41 DAP, and the fatty acid composition of the developing seeds is consistent with relative expression levels of different isoforms of acyl-ACP thioesterase and fatty acid desaturase genes. Several transcription factor genes whose expression coincides with storage reserve deposition correspond to those known to regulate the process in Arabidopsis. CONCLUSIONS/SIGNIFICANCE: The results will facilitate searches for genes that influence de novo lipid synthesis, accumulation and their regulatory networks in developing physic nut seeds, and other oil seeds. Thus, they will be helpful in attempts to modify these plants for efficient biofuel production.

  16. DNA methylation mediated control of gene expression is critical for development of crown gall tumors.

    Directory of Open Access Journals (Sweden)

    Jochen Gohlke

    Full Text Available Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA-mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes

  17. The development of emotion expression during the first two years of life.

    Science.gov (United States)

    Malatesta, C Z; Culver, C; Tesman, J R; Shepard, B

    1989-01-01

    This study examines the course of emotion expression development over the first 2 years of life in a sample of full-term and preterm children. 58 mother/infant pairs were videotaped at infant ages of 2 1/2, 5, 7 1/2, and 22 months, recording face-to-face interaction involving play and separation/reunion sessions. The tapes were coded on a second-to-second basis using Izard's facial affect coding system. Data analysis focused on (1) differences in expressive behavior at 22 months as a function of risk status, gender, attachment status, and patterns of earlier maternal contingency behavior; (2) stability of specific emotional expressive patterns across assessment periods; and (3) the relation of expressive behavior and security of attachment at 2 years to qualities of earlier affective interchange. Mother's contingency behavior (both general level and specific contingency patterns) appeared to have a material effect on the course of emotional development, as did birth status and gender. Prematurity was associated with differential socioemotional development well into the second year, much in contrast to the "catch-up effect" observed in linguistic and cognitive functioning. Discrete emotions analysis of attachment groups yielded differentiation along a broad negative/positive dimension, but it also showed that insecurely attached children can be characterized as showing inhibited anger expression. The results of this study are discussed within the framework of organizational models of infant affective development; attachment theory and discrete emotions approaches were found to yield different yet equally informative data on the course of socioemotional development.

  18. Development of the Korean Facial Emotion Stimuli: Korea University Facial Expression Collection 2nd Edition

    Directory of Open Access Journals (Sweden)

    Sun-Min Kim

    2017-05-01

    Full Text Available Background: Developing valid emotional facial stimuli for specific ethnicities creates ample opportunities to investigate both the nature of emotional facial information processing in general and clinical populations as well as the underlying mechanisms of facial emotion processing within and across cultures. Given that most entries in emotional facial stimuli databases were developed with western samples, and given that very few of the eastern emotional facial stimuli sets were based strictly on the Ekman’s Facial Action Coding System, developing valid emotional facial stimuli of eastern samples remains a high priority.Aims: To develop and examine the psychometric properties of six basic emotional facial stimuli recruiting professional Korean actors and actresses based on the Ekman’s Facial Action Coding System for the Korea University Facial Expression Collection-Second Edition (KUFEC-II.Materials And Methods: Stimulus selection was done in two phases. First, researchers evaluated the clarity and intensity of each stimulus developed based on the Facial Action Coding System. Second, researchers selected a total of 399 stimuli from a total of 57 actors and actresses, which were then rated on accuracy, intensity, valence, and arousal by 75 independent raters.Conclusion: The hit rates between the targeted and rated expressions of the KUFEC-II were all above 80%, except for fear (50% and disgust (63%. The KUFEC-II appears to be a valid emotional facial stimuli database, providing the largest set of emotional facial stimuli. The mean intensity score was 5.63 (out of 7, suggesting that the stimuli delivered the targeted emotions with great intensity. All positive expressions were rated as having a high positive valence, whereas all negative expressions were rated as having a high negative valence. The KUFEC II is expected to be widely used in various psychological studies on emotional facial expression. KUFEC-II stimuli can be obtained through

  19. Gene expression during Drosophila melanogaster egg development before and after reproductive diapause

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    Baker Dean A

    2009-05-01

    Full Text Available Abstract Background Despite the importance of egg development to the female life cycle in Drosophila, global patterns of gene expression have not been examined in detail, primarily due to the difficulty in isolating synchronised developmental stages in sufficient quantities for gene expression profiling. Entry into vitellogenesis is a key stage of oogenesis and by forcing females into reproductive diapause we are able to arrest oogenesis at the pre-vitellogenic stages. Releasing females from diapause allows collection of relatively synchronous developing egg populations and an investigation of some of the transcriptional dynamics apparent before and after reproductive diapause. Results Focusing on gender-biased transcription, we identified mechanisms of egg development suppressed during reproductive dormancy as well as other molecular changes unique to the diapausing female. A microarray based analysis generated a set of 3565 transcripts with at least 2-fold greater expression in females as compared to control males, 1392 such changes were biased during reproductive dormancy. In addition, we also detect 1922 up-regulated transcriptional changes after entry into vitellogenesis, which were classified into discrete blocks of co-expression. We discuss some of the regulatory aspects apparent after re-initiation of egg development, exploring the underlying functions, maternal contribution and evolutionary conservation of co-expression patterns involved in egg production. Conclusion Although much of the work we present is descriptive, fundamental aspects of egg development and gender-biased transcription can be derived from our time-series experiment. We believe that our dataset will facilitate further exploration of the developmental and evolutionary characteristics of oogenesis as well as the nature of reproductive arrest in Drosophila.

  20. The essential role of endogenous ghrelin in growth hormone expression during zebrafish adenohypophysis development.

    Science.gov (United States)

    Li, Xi; He, Jiangyan; Hu, Wei; Yin, Zhan

    2009-06-01

    Ghrelin, a multifunctional hormone, including potent GH stimulation activity, has been suggested to be important during embryonic development. Expression of ghrelin has been confirmed in the zebrafish pancreas during embryonic stages. Interfering with ghrelin function using two specific antisense morpholino oligonucleotides causes defects during zebrafish embryonic development. In ghrelin morphants the expression of GH was abolished in zebrafish somatotropes, whereas the expression patterns of the other key molecules involved in hypothalamic-pituitary development and distinct pituitary hormones genes remain largely intact at the appropriate time during zebrafish adenohypophysis development. Effective rescue of the ghrelin morphants with exogenous ghrelin mRNA showed that the correct gene had been targeted. Moreover, by analyzing the efficiencies of the ghrelin morphants rescue experiments with various forms of exogenous mutant ghrelin mRNAs, we also demonstrated the essentiality of the form acyl-ghrelin on GH stimulation during zebrafish adenohypophysis development. Our in vivo experiments, for the first time, also provided evidence of the existence of functional obestatin in the C-terminal part of zebrafish proghrelin peptides. Our research here has demonstrated that zebrafish is a unique model for functional studies of endogenous ghrelin, especially during embryonic development.

  1. Regularization theory for ill-posed problems selected topics

    CERN Document Server

    Lu, Shuai

    2013-01-01

    Thismonograph is a valuable contribution to thehighly topical and extremly productive field ofregularisationmethods for inverse and ill-posed problems. The author is an internationally outstanding and acceptedmathematicianin this field. In his book he offers a well-balanced mixtureof basic and innovative aspects.He demonstrates new,differentiatedviewpoints, and important examples for applications. The bookdemontrates thecurrent developments inthe field of regularization theory,such as multiparameter regularization and regularization in learning theory. The book is written for graduate and PhDs

  2. Hypoxia-Inducible Factor-1α Expression in Macrophages Promotes Development of Atherosclerosis

    DEFF Research Database (Denmark)

    Pedersen, Annemarie Aarup; Pedersen, Tanja X; Junker, Nanna

    2016-01-01

    transplanted with bone marrow from mice with HIF-1α deficiency in the myeloid cells or control bone marrow. The HIF-1α deficiency in myeloid cells reduced atherosclerosis in aorta of the Ldlr(-/-) recipient mice by ≈72% (P=0.006).In vitro, HIF-1α-deficient macrophages displayed decreased differentiation...... to proinflammatory M1 macrophages and reduced expression of inflammatory genes. HIF-1α deficiency also affected glucose uptake, apoptosis, and migratory abilities of the macrophages. CONCLUSIONS: HIF-1α expression in macrophages affects their intrinsic inflammatory profile and promotes development of atherosclerosis....

  3. Glial and neuronal connexin expression patterns in the rat spinal cord during development and following injury

    DEFF Research Database (Denmark)

    Lee, I. Hui; Lindqvist, Eva; Kiehn, Ole

    2005-01-01

    Spinal cord injury induces a complex cascade of degenerative and remodeling events evolving over time. The possible roles of changed intercellular communication via gap junctions after spinal cord injury (SCI) have remained relatively unexplored. We investigated the temporospatial expression...... patterns of gap junctional genes and proteins, connexin 43 (Cx43), Cx36, and Cx32, by in situ hybridization and immunohistochemistry in the rat neonatal, adult normal, and adult injured spinal cord. Cx36 was strongly expressed in immature neurons, and levels declined markedly during development, whereas Cx...

  4. From inactive to regular jogger

    DEFF Research Database (Denmark)

    Lund-Cramer, Pernille; Brinkmann Løite, Vibeke; Bredahl, Thomas Viskum Gjelstrup

    study was conducted using individual semi-structured interviews on how a successful long-term behavior change had been achieved. Ten informants were purposely selected from participants in the DANO-RUN research project (7 men, 3 women, average age 41.5). Interviews were performed on the basis of Theory...... of Planned Behavior (TPB) and The Transtheoretical Model (TTM). Coding and analysis of interviews were performed using NVivo 10 software. Results TPB: During the behavior change process, the intention to jogging shifted from a focus on weight loss and improved fitness to both physical health, psychological......Title From inactive to regular jogger - a qualitative study of achieved behavioral change among recreational joggers Authors Pernille Lund-Cramer & Vibeke Brinkmann Løite Purpose Despite extensive knowledge of barriers to physical activity, most interventions promoting physical activity have proven...

  5. Facial Affect Recognition Using Regularized Discriminant Analysis-Based Algorithms

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Shih

    2010-01-01

    Full Text Available This paper presents a novel and effective method for facial expression recognition including happiness, disgust, fear, anger, sadness, surprise, and neutral state. The proposed method utilizes a regularized discriminant analysis-based boosting algorithm (RDAB with effective Gabor features to recognize the facial expressions. Entropy criterion is applied to select the effective Gabor feature which is a subset of informative and nonredundant Gabor features. The proposed RDAB algorithm uses RDA as a learner in the boosting algorithm. The RDA combines strengths of linear discriminant analysis (LDA and quadratic discriminant analysis (QDA. It solves the small sample size and ill-posed problems suffered from QDA and LDA through a regularization technique. Additionally, this study uses the particle swarm optimization (PSO algorithm to estimate optimal parameters in RDA. Experiment results demonstrate that our approach can accurately and robustly recognize facial expressions.

  6. cDNA cloning and expression of carotenogenic genes during flower development in Gentiana lutea.

    Science.gov (United States)

    Zhu, Changfu; Yamamura, Saburo; Koiwa, Hiroyuki; Nishihara, Masashiro; Sandmann, Gerhard

    2002-02-01

    All cDNAs involved in carotenoid biosynthesis leading to lycopene in yellow petals of Gentiana lutea have been cloned from a cDNA library. They encode a geranylgeranyl pyrophosphate synthase, a phytoene synthase, a phytoene desaturase and a zeta-carotene desaturase. The indicated function of all cDNAs was established by heterologous complementation in Escherichia coli. The amino acid sequences deduced from the cDNAs were between 47.5% and 78.9% identical to those reported for the corresponding enzymes from other higher plants. Southern analysis suggested that the genes for each enzyme probably represent a small multi-gene family. Tissue-specific expression of the genes and expression during flower development was investigated. The expression of the phytoene synthase gene, psy, was enhanced in flowers but transcripts were not detected in stems and leaves by northern blotting. Transcripts of the genes for geranylgeranyl pyrophosphate (ggpps), phytoene desaturase (pds) and zeta-carotene desaturase (zds) were detected in flowers and leaves but not in stems. Analysis of the expression of psy and zds in petals revealed that levels of the transcripts were lowest in young buds and highest in fully open flowers, in parallel with the formation of carotenoids. Obviously, the transcription of these genes control the accumulation of carotenoids during flower development in G. lutea. For pds only a very slight increase of mRNA was found whereas the transcripts of ggpps decreased during flower development.

  7. Global gene expression profiling of individual human oocytes and embryos demonstrates heterogeneity in early development.

    Directory of Open Access Journals (Sweden)

    Lisa Shaw

    Full Text Available Early development in humans is characterised by low and variable embryonic viability, reflected in low fecundity and high rates of miscarriage, relative to other mammals. Data from assisted reproduction programmes provides additional evidence that this is largely mediated at the level of embryonic competence and is highly heterogeneous among embryos. Understanding the basis of this heterogeneity has important implications in a number of areas including: the regulation of early human development, disorders of pregnancy, assisted reproduction programmes, the long term health of children which may be programmed in early development, and the molecular basis of pluripotency in human stem cell populations. We have therefore investigated global gene expression profiles using polyAPCR amplification and microarray technology applied to individual human oocytes and 4-cell and blastocyst stage embryos. In order to explore the basis of any variability in detail, each developmental stage is replicated in triplicate. Our data show that although transcript profiles are highly stage-specific, within each stage they are relatively variable. We describe expression of a number of gene families and pathways including apoptosis, cell cycle and amino acid metabolism, which are variably expressed and may be reflective of embryonic developmental competence. Overall, our data suggest that heterogeneity in human embryo developmental competence is reflected in global transcript profiles, and that the vast majority of existing human embryo gene expression data based on pooled oocytes and embryos need to be reinterpreted.

  8. Differential Expression of Growth-, Angiogenesis- and Invasion-Related Factors in The Development of Placenta Accreta

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    Jenn-Jhy Tseng

    2006-06-01

    Full Text Available Placenta accreta is the major cause of maternal death complicated by massive peripartum hemorrhage. Its development is traditionally considered to be related to a decidual defect caused by previous cesarean deliveries or uterine curettages. Usually, placental villi firmly adhere to the superficial myometrium and deeply invade, or even penetrate, the uterine wall. Abnormal uteroplacental neovascularization is another characteristic. Therefore, we hypothesized that placenta accreta develops as a result of abnormal expressions of growth-, angiogenesis- and invasion-related factors in trophoblast populations. We have found, in pregnancies complicated by placenta accreta: upregulated epidermal growth factor receptor and downregulated c-erbB-2 oncoprotein in syncytiotrophoblasts; downregulated vasculoendothelial growth factor receptor-2 expression in syncytiotrophoblasts and increased vasculoendothelial growth factor in placental lysates; and downregulated Tie-2 expression in syncytiotrophoblasts and enhanced angiopoietin-2 level in placental lysates. However, matrix metalloproteinase expression was not upregulated, so the association of these invasion-related molecules with placenta accreta is less likely. Taken together, these findings imply that complex factors, either alone or in combination, might be responsible for the development of placenta accreta. Further studies are needed to understand the signaling pathways and possible genetic events.

  9. Spatiotemporal expression profile of the Pumilio gene in the embryonic development of silkworm.

    Science.gov (United States)

    Chen, Liang; You, Zaizhi; Xia, Hengchuan; Tang, Qi; Zhou, Yang; Yao, Qin; Chen, Keping

    2014-01-01

    We previously identified a pumilio gene in silkworm (Bombyx mori L.), designated BmPUM, which was specifically expressed in the ovary and testis. To further characterize this gene's involvement in silkworm development, we have determined the spatiotemporal expression pattern of BmPUM during all embryonic stages. Real-time polymerase chain reaction (RT-PCR) analysis revealed that BmPUM was expressed in all stages of silkworm embryos and that its transcript levels displayed two distinct peaks. The first was observed at the germ-band formation stage (1 d after oviposition) and dropped to a low level at the gonad formation stage (5 d after oviposition). The second was detected at the stage of bristle follicle occurrence (6 d after oviposition), which was confirmed by Western blot analysis and immunohistochemistry. Nanos (Nos), functioning together with Pum in abdomen formation of Drosophila embryos, was also highly expressed at the beginning (0 h to 1 d after oviposition) of embryogenesis, but its transcript levels were very low after the stage of germ-band formation. These results suggest that BmPUM functions with Bombyx mori nanos (Bm-nanos) at the early stages of silkworm embryonic development, and may then play a role in gonad formation and the occurrence of bristle follicles. Our data thus provide a foundation to uncover the role of BmPUM during silkworm development.

  10. The Expression of Embryonic Liver Development Genes in Hepatitis C Induced Cirrhosis and Hepatocellular Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Behnke, Martha, E-mail: mbehnke@mcvh-vcu.edu [Transplant Program Administration, Virginia Commonwealth University Health System, 1200 E. Broad St., Richmond, VA 23298 (United States); Reimers, Mark [Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, 800 E Leigh St., Richmond, VA 23298 (United States); Fisher, Robert [Department of Surgery, Virginia Commonwealth University, 1200 E. Broad St., Richmond, VA 23298 (United States)

    2012-09-18

    Hepatocellular carcinoma (HCC) remains a difficult disease to study even after a decade of genomic analysis. Patient and disease heterogeneity, differences in statistical methods and multiple testing issues have resulted in a fragmented understanding of the molecular basis of tumor biology. Some researchers have suggested that HCC appears to share pathways with embryonic development. Therefore we generated targeted hypotheses regarding changes in developmental genes specific to the liver in HCV-cirrhosis and HCV-HCC. We obtained microarray studies from 30 patients with HCV-cirrhosis and 49 patients with HCV-HCC and compared to 12 normal livers. Genes specific to non-liver development have known associations with other cancer types but none were expressed in either adult liver or tumor tissue, while 98 of 179 (55%) genes specific to liver development had differential expression between normal and cirrhotic or HCC samples. We found genes from each developmental stage dysregulated in tumors compared to normal and cirrhotic samples. Although there was no single tumor marker, we identified a set of genes (Bone Morphogenetic Protein inhibitors GPC3, GREM1, FSTL3, and FST) in which at least one gene was over-expressed in 100% of the tumor samples. Only five genes were differentially expressed exclusively in late-stage tumors, indicating that while developmental genes appear to play a profound role in cirrhosis and malignant transformation, they play a limited role in late-stage HCC.

  11. Tessellating the Sphere with Regular Polygons

    Science.gov (United States)

    Soto-Johnson, Hortensia; Bechthold, Dawn

    2004-01-01

    Tessellations in the Euclidean plane and regular polygons that tessellate the sphere are reviewed. The regular polygons that can possibly tesellate the sphere are spherical triangles, squares and pentagons.

  12. On the equivalence of different regularization methods

    International Nuclear Information System (INIS)

    Brzezowski, S.

    1985-01-01

    The R-circunflex-operation preceded by the regularization procedure is discussed. Some arguments are given, according to which the results may depend on the method of regularization, introduced in order to avoid divergences in perturbation calculations. 10 refs. (author)

  13. The uniqueness of the regularization procedure

    International Nuclear Information System (INIS)

    Brzezowski, S.

    1981-01-01

    On the grounds of the BPHZ procedure, the criteria of correct regularization in perturbation calculations of QFT are given, together with the prescription for dividing the regularized formulas into the finite and infinite parts. (author)

  14. Development of a transient expression assay for detecting environmental oestrogens in zebrafish and medaka embryos

    Directory of Open Access Journals (Sweden)

    Lee Okhyun

    2012-06-01

    Full Text Available Abstract Background Oestrogenic contaminants are widespread in the aquatic environment and have been shown to induce adverse effects in both wildlife (most notably in fish and humans, raising international concern. Available detecting and testing systems are limited in their capacity to elucidate oestrogen signalling pathways and physiological impacts. Here we developed a transient expression assay to investigate the effects of oestrogenic chemicals in fish early life stages and to identify target organs for oestrogenic effects. To enhance the response sensitivity to oestrogen, we adopted the use of multiple tandem oestrogen responsive elements (EREc38 in a Tol2 transposon mediated Gal4ff-UAS system. The plasmid constructed (pTol2_ERE-TATA-Gal4ff, contains three copies of oestrogen response elements (3ERE that on exposure to oestrogen induces expression of Gal4ff which this in turn binds Gal4-responsive Upstream Activated Sequence (UAS elements, driving the expression of a second reporter gene, EGFP (Enhanced Green Fluorescent Protein. Results The response of our construct to oestrogen exposure in zebrafish embryos was examined using a transient expression assay. The two plasmids were injected into 1–2 cell staged zebrafish embryos, and the embryos were exposed to various oestrogens including the natural steroid oestrogen 17ß-oestradiol (E2, the synthetic oestrogen 17α- ethinyloestradiol (EE2, and the relatively weak environmental oestrogen nonylphenol (NP, and GFP expression was examined in the subsequent embryos using fluorescent microscopy. There was no GFP expression detected in unexposed embryos, but specific and mosaic expression of GFP was detected in the liver, heart, somite muscle and some other tissue cells for exposures to steroid oestrogen treatments (EE2; 10 ng/L, E2; 100 ng/L, after 72 h exposures. For the NP exposures, GFP expression was observed at 10 μg NP/L after 72 h (100 μg NP/L was toxic to the fish. We

  15. Expression of transmembrane carbonic anhydrases, CAIX and CAXII, in human development

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    Lerman Michael I

    2009-03-01

    Full Text Available Abstract Background Transmembrane CAIX and CAXII are members of the alpha carbonic anhydrase (CA family. They play a crucial role in differentiation, proliferation, and pH regulation. Expression of CAIX and CAXII proteins in tumor tissues is primarily induced by hypoxia and this is particularly true for CAIX, which is regulated by the transcription factor, hypoxia inducible factor-1 (HIF-1. Their distributions in normal adult human tissues are restricted to highly specialized cells that are not always hypoxic. The human fetus exists in a relatively hypoxic environment. We examined expression of CAIX, CAXII and HIF-1α in the developing human fetus and postnatal tissues to determine whether expression of CAIX and CAXII is exclusively regulated by HIF-1. Results The co-localization of CAIX and HIF-1α was limited to certain cell types in embryonic and early fetal tissues. Those cells comprised the primitive mesenchyma or involved chondrogenesis and skin development. Transient CAIX expression was limited to immature tissues of mesodermal origin and the skin and ependymal cells. The only tissues that persistently expressed CAIX protein were coelomic epithelium (mesothelium and its remnants, the epithelium of the stomach and biliary tree, glands and crypt cells of duodenum and small intestine, and the cells located at those sites previously identified as harboring adult stem cells in, for example, the skin and large intestine. In many instances co-localization of CAIX and HIF-1α was not evident. CAXII expression is restricted to cells involved in secretion and water absorption such as parietal cells of the stomach, acinar cells of the salivary glands and pancreas, epithelium of the large intestine, and renal tubules. Co-localization of CAXII with CAIX or HIF-1α was not observed. Conclusion The study has showed that: 1 HIF-1α and CAIX expression co- localized in many, but not all, of the embryonic and early fetal tissues; 2 There is no evidence of

  16. Application of a scalable plant transient gene expression platform for malaria vaccine development

    Directory of Open Access Journals (Sweden)

    Holger eSpiegel

    2015-12-01

    Full Text Available Despite decades of intensive research efforts there is currently no vaccine that provides sustained sterile immunity against malaria. In this context, a large number of targets from the different stages of the Plasmodium falciparum life cycle have been evaluated as vaccine candidates. None of these candidates has fulfilled expectations, and as long as we lack a single target that induces strain-transcending protective immune responses, combining key antigens from different life cycle stages seems to be the most promising route towards the development of efficacious malaria vaccines. After the identification of potential targets using approaches such as omics-based technology and reverse immunology, the rapid expression, purification and characterization of these proteins, as well as the generation and analysis of fusion constructs combining different promising antigens or antigen domains before committing to expensive and time consuming clinical development, represents one of the bottlenecks in the vaccine development pipeline. The production of recombinant proteins by transient gene expression in plants is a robust and versatile alternative to cell-based microbial and eukaryotic production platforms. The transfection of plant tissues and/or whole plants using Agrobacterium tumefaciens offers a low technical entry barrier, low costs and a high degree of flexibility embedded within a rapid and scalable workflow. Recombinant proteins can easily be targeted to different subcellular compartments according to their physicochemical requirements, including post-translational modifications, to ensure optimal yields of high quality product, and to support simple and economical downstream processing. Here we demonstrate the use of a plant transient expression platform based on transfection with A. tumefaciens as essential component of a malaria vaccine development workflow involving screens for expression, solubility and stability using fluorescent fusion

  17. Proteomic identification of differentially expressed proteins during alfalfa (Medicago sativa L. flower development

    Directory of Open Access Journals (Sweden)

    Lingling Chen

    2016-10-01

    Full Text Available Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa (Medicago sativa L. seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1, pollination (S2, and the post-pollination senescence period (S3. Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD. Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs, carbonic anhydrase (CA, and NADPH: quinone oxidoreductase-like protein (NQOLs. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower

  18. Proteomic Identification of Differentially Expressed Proteins during Alfalfa (Medicago sativa L.) Flower Development.

    Science.gov (United States)

    Chen, Lingling; Chen, Quanzhu; Zhu, Yanqiao; Hou, Longyu; Mao, Peisheng

    2016-01-01

    Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa ( Medicago sativa L.) seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1), pollination (S2), and the post-pollination senescence period (S3). Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD). Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs), carbonic anhydrase, and NADPH: quinone oxidoreductase-like protein. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower development and

  19. Bovine ovarian follicular growth and development correlate with lysophosphatidic acid expression.

    Science.gov (United States)

    Sinderewicz, Emilia; Grycmacher, Katarzyna; Boruszewska, Dorota; Kowalczyk-Zięba, Ilona; Staszkiewicz, Joanna; Ślężak, Tomasz; Woclawek-Potocka, Izabela

    2018-01-15

    The basis of successful reproduction is proper ovarian follicular growth and development. In addition to prostaglandins and vascular endothelial growth factor, a number of novel factors are suggested as important regulators of follicular growth and development: PGES, TFG, CD36, RABGAP1, DBI and BTC. This study focuses on examining the expression of these factors in granulosa and thecal cells that originate from different ovarian follicle types and their link with the expression of lysophosphatidic acid (LPA), known local regulator of reproductive functions in the cow. Ovarian follicles were divided into healthy, transitional, and atretic categories. The mRNA expression levels for PGES, TFG, CD36, RABGAP1, DBI and BTC in granulosa and thecal cells in different follicle types were measured by real-time PCR. The correlations among expression of enzymes synthesizing LPA (autotaxin, phospholipase A2), receptors for LPA and examined factors were measured. Immunolocalization of PGES, TFG, CD36, RABGAP1, DBI and BTC was examined by immunohistochemistry. We investigated follicle-type dependent mRNA expression of factors potentially involved in ovarian follicular growth and development, both in granulosa and thecal cells of bovine ovarian follicles. Strong correlations among receptors for LPA, enzymes synthesizing LPA, and the examined factors in healthy and transitional follicles were observed, with its strongest interconnection with TFG, DBI and RABGAP1 in granulosa cells, and TFG in thecal cells; whereas no correlations in atretic follicles were detected. A greater number of correlations were found in thecal cells than in granulosa cells as well as in healthy follicles than in transitional follicles. These data indicate the role of LPA in the growth, development and physiology of the bovine ovarian follicle. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Roles of the sister chromatid cohesion apparatus in gene expression, development, and human syndromes

    Science.gov (United States)

    Dorsett, Dale

    2006-01-01

    The sister chromatid cohesion apparatus mediates physical pairing of duplicated chromosomes. This pairing is essential for appropriate distribution of chromosomes into the daughter cells upon cell division. Recent evidence shows that the cohesion apparatus, which is a significant structural component of chromosomes during interphase, also affects gene expression and development. The Cornelia de Lange (CdLS) and Roberts/SC phocomelia (RBS/SC) genetic syndromes in humans are caused by mutations affecting components of the cohesion apparatus. Studies in Drosophila suggest that effects on gene expression are most likely responsible for developmental alterations in CdLS. Effects on chromatid cohesion are apparent in RBS/SC syndrome, but data from yeast and Drosophila point to the likelihood that changes in expression of genes located in heterochromatin could contribute to the developmental deficits. PMID:16819604

  1. Development and validation of an Argentine set of facial expressions of emotion.

    Science.gov (United States)

    Vaiman, Marcelo; Wagner, Mónica Anna; Caicedo, Estefanía; Pereno, Germán Leandro

    2017-02-01

    Pictures of facial expressions of emotion are used in a wide range of experiments. The last decade has seen an increase in the number of studies presenting local sets of emotion stimuli. However, only a few existing sets contain pictures of Latin Americans, despite the growing attention emotion research is receiving in this region. Here we present the development and validation of the Universidad Nacional de Cordoba, Expresiones de Emociones Faciales (UNCEEF), a Facial Action Coding System (FACS)-verified set of pictures of Argentineans expressing the six basic emotions, plus neutral expressions. FACS scores, recognition rates, Hu scores, and discrimination indices are reported. Evidence of convergent validity was obtained using the Pictures of Facial Affect in an Argentine sample. However, recognition accuracy was greater for UNCEEF. The importance of local sets of emotion pictures is discussed.

  2. Expression patterns of the aquaporin gene family during renal development: influence of genetic variability.

    Science.gov (United States)

    Parreira, Kleber S; Debaix, Huguette; Cnops, Yvette; Geffers, Lars; Devuyst, Olivier

    2009-08-01

    High-throughput analyses have shown that aquaporins (AQPs) belong to a cluster of genes that are differentially expressed during kidney organogenesis. However, the spatiotemporal expression patterns of the AQP gene family during tubular maturation and the potential influence of genetic variation on these patterns and on water handling remain unknown. We investigated the expression patterns of all AQP isoforms in fetal (E13.5 to E18.5), postnatal (P1 to P28), and adult (9 weeks) kidneys of inbred (C57BL/6J) and outbred (CD-1) mice. Using quantitative polymerase chain reaction (PCR), we evidenced two mRNA patterns during tubular maturation in C57 mice. The AQPs 1-7-11 showed an early (from E14.5) and progressive increase to adult levels, similar to the mRNA pattern observed for proximal tubule markers (Megalin, NaPi-IIa, OAT1) and reflecting the continuous increase in renal cortical structures during development. By contrast, AQPs 2-3-4 showed a later (E15.5) and more abrupt increase, with transient postnatal overexpression. Most AQP genes were expressed earlier and/or stronger in maturing CD-1 kidneys. Furthermore, adult CD-1 kidneys expressed more AQP2 in the collecting ducts, which was reflected by a significant delay in excreting a water load. The expression patterns of proximal vs. distal AQPs and the earlier expression in the CD-1 strain were confirmed by immunoblotting and immunostaining. These data (1) substantiate the clustering of important genes during tubular maturation and (2) demonstrate that genetic variability influences the regulation of the AQP gene family during tubular maturation and water handling by the mature kidney.

  3. Sex-Specificity of Mineralocorticoid Target Gene Expression during Renal Development, and Long-Term Consequences

    Science.gov (United States)

    Dumeige, Laurence; Storey, Caroline; Decourtye, Lyvianne; Nehlich, Melanie; Lhadj, Christophe; Viengchareun, Say; Kappeler, Laurent; Lombès, Marc; Martinerie, Laetitia

    2017-01-01

    Sex differences have been identified in various biological processes, including hypertension. The mineralocorticoid signaling pathway is an important contributor to early arterial hypertension, however its sex-specific expression has been scarcely studied, particularly with respect to the kidney. Basal systolic blood pressure (SBP) and heart rate (HR) were measured in adult male and female mice. Renal gene expression studies of major players of mineralocorticoid signaling were performed at different developmental stages in male and female mice using reverse transcription quantitative PCR (RT-qPCR), and were compared to those of the same genes in the lung, another mineralocorticoid epithelial target tissue that regulates ion exchange and electrolyte balance. The role of sex hormones in the regulation of these genes was also investigated in differentiated KC3AC1 renal cells. Additionally, renal expression of the 11 β-hydroxysteroid dehydrogenase type 2 (11βHSD2) protein, a regulator of mineralocorticoid specificity, was measured by immunoblotting and its activity was indirectly assessed in the plasma using liquid-chromatography coupled to mass spectrometry in tandem (LC-MSMS) method. SBP and HR were found to be significantly lower in females compared to males. This was accompanied by a sex- and tissue-specific expression profile throughout renal development of the mineralocorticoid target genes serum and glucocorticoid-regulated kinase 1 (Sgk1) and glucocorticoid-induced leucine zipper protein (Gilz), together with Hsd11b2, Finally, the implication of sex hormones in this sex-specific expression profile was demonstrated in vitro, most notably for Gilz mRNA expression. We demonstrate a tissue-specific, sex-dependent and developmentally-regulated pattern of expression of the mineralocorticoid pathway that could have important implications in physiology and pathology. PMID:28230786

  4. Expression of 14-3-3 protein isoforms in mouse oocytes, eggs and ovarian follicular development

    Directory of Open Access Journals (Sweden)

    De Santanu

    2012-01-01

    Full Text Available Abstract Background The 14-3-3 (YWHA proteins are a highly conserved, ubiquitously expressed family of proteins. Seven mammalian isoforms of 14-3-3 are known (β, γ, ε, ζ, η, τ and, σ. These proteins associate with many intracellular proteins involved in a variety of cellular processes including regulation of the cell cycle, metabolism and protein trafficking. We are particularly interested in the role of 14-3-3 in meiosis in mammalian eggs and the role 14-3-3 proteins may play in ovarian function. Therefore, we examined the expression of 14-3-3 proteins in mouse oocyte and egg extracts by Western blotting after polyacrylamide gel electrophoresis, viewed fixed cells by indirect immunofluorescence, and examined mouse ovarian cells by immunohistochemical staining to study the expression of the different 14-3-3 isoforms. Results We have determined that all of the mammalian 14-3-3 isoforms are expressed in mouse eggs and ovarian follicular cells including oocytes. Immunofluorescence confocal microscopy of isolated oocytes and eggs confirmed the presence of all of the isoforms with characteristic differences in some of their intracellular localizations. For example, some isoforms (β, ε, γ, and ζ are expressed more prominently in peripheral cytoplasm compared to the germinal vesicles in oocytes, but are uniformly dispersed within eggs. On the other hand, 14-3-3η is diffusely dispersed in the oocyte, but attains a uniform punctate distribution in the egg with marked accumulation in the region of the meiotic spindle apparatus. Immunohistochemical staining detected all isoforms within ovarian follicles, with some similarities as well as notable differences in relative amounts, localizations and patterns of expression in multiple cell types at various stages of follicular development. Conclusions We found that mouse oocytes, eggs and follicular cells within the ovary express all seven isoforms of the 14-3-3 protein. Examination of the

  5. Multiview Hessian regularization for image annotation.

    Science.gov (United States)

    Liu, Weifeng; Tao, Dacheng

    2013-07-01

    The rapid development of computer hardware and Internet technology makes large scale data dependent models computationally tractable, and opens a bright avenue for annotating images through innovative machine learning algorithms. Semisupervised learning (SSL) therefore received intensive attention in recent years and was successfully deployed in image annotation. One representative work in SSL is Laplacian regularization (LR), which smoothes the conditional distribution for classification along the manifold encoded in the graph Laplacian, however, it is observed that LR biases the classification function toward a constant function that possibly results in poor generalization. In addition, LR is developed to handle uniformly distributed data (or single-view data), although instances or objects, such as images and videos, are usually represented by multiview features, such as color, shape, and texture. In this paper, we present multiview Hessian regularization (mHR) to address the above two problems in LR-based image annotation. In particular, mHR optimally combines multiple HR, each of which is obtained from a particular view of instances, and steers the classification function that varies linearly along the data manifold. We apply mHR to kernel least squares and support vector machines as two examples for image annotation. Extensive experiments on the PASCAL VOC'07 dataset validate the effectiveness of mHR by comparing it with baseline algorithms, including LR and HR.

  6. EIT image reconstruction with four dimensional regularization.

    Science.gov (United States)

    Dai, Tao; Soleimani, Manuchehr; Adler, Andy

    2008-09-01

    Electrical impedance tomography (EIT) reconstructs internal impedance images of the body from electrical measurements on body surface. The temporal resolution of EIT data can be very high, although the spatial resolution of the images is relatively low. Most EIT reconstruction algorithms calculate images from data frames independently, although data are actually highly correlated especially in high speed EIT systems. This paper proposes a 4-D EIT image reconstruction for functional EIT. The new approach is developed to directly use prior models of the temporal correlations among images and 3-D spatial correlations among image elements. A fast algorithm is also developed to reconstruct the regularized images. Image reconstruction is posed in terms of an augmented image and measurement vector which are concatenated from a specific number of previous and future frames. The reconstruction is then based on an augmented regularization matrix which reflects the a priori constraints on temporal and 3-D spatial correlations of image elements. A temporal factor reflecting the relative strength of the image correlation is objectively calculated from measurement data. Results show that image reconstruction models which account for inter-element correlations, in both space and time, show improved resolution and noise performance, in comparison to simpler image models.

  7. Expression of proteinase inhibitor II proteins during floral development in Solanum americanum.

    Science.gov (United States)

    Sin, Suk-Fong; Chye, Mee-Len

    2004-10-01

    The heterologous expression of serine proteinase inhibitor II (PIN2) proteins confers insect resistance in transgenic plants, but little is known of their endogenous roles. We have cloned two cDNAs encoding Solanum americanum PIN2 proteins, SaPIN2a and SaPIN2b. SaPIN2a is highly expressed in stem, particularly in the phloem, suggesting it could possibly regulate proteolysis in the sieve elements. When SaPIN2a was expressed in transgenic lettuce, we observed an inhibition of endogenous trypsin- and chymotrypsin-like activities. Here, we demonstrate that both SaPIN2a and SaPIN2b are expressed in floral tissues that are destined to undergo developmental programmed cell death (PCD), suggesting possible endogenous roles in inhibiting trypsin- and chymotrypsin-like activities during flower development. Northern and western blot analyses revealed that SaPIN2a and SaPIN2b mRNAs and proteins show highest expression early in floral development. In situ hybridization analysis and immunolocalization on floral sections, localized SaPIN2a and SaPIN2b mRNAs and their proteins to tissues that would apparently undergo PCD: the ovules, the stylar transmitting tissue, the stigma and the vascular bundles. Detection of PCD in floral sections was achieved using terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL) analysis. Examination of the mid-style before, and 1 day after, pollination revealed that high expression of SaPIN2a and SaPIN2b in the style was inversely correlated with PCD.

  8. Trichloroethylene perturbs HNF4a expression and activity in the developing chick heart.

    Science.gov (United States)

    Harris, Alondra P; Ismail, Kareem A; Nunez, Martha; Martopullo, Ira; Lencinas, Alejandro; Selmin, Ornella I; Runyan, Raymond B

    2018-03-15

    Exposure to trichloroethylene (TCE) is linked to formation of congenital heart defects in humans and animals. Prior interactome analysis identified the transcription factor, Hepatocyte Nuclear Factor 4 alpha (HNF4a), as a potential target of TCE exposure. As a role for HNF4a is unknown in the heart, we examined developing avian hearts for HNF4a expression and for sensitivity to TCE and the HNF4a agonist, Benfluorex. In vitro analysis using a HNF4a reporter construct showed both TCE and HFN4a to be antagonists of HNF4a-mediated transcription at the concentrations tested. HNF4a mRNA is expressed transiently in the embryonic heart during valve formation and cardiac development. Embryos were examined for altered gene expression in the presence of TCE or Benfluorex. TCE altered expression of selected mRNAs including HNF4a, TRAF6 and CYP2C45. There was a transition between inhibition and induction of marker gene expression in embryos as TCE concentration increased. Benfluorex was largely inhibitory to selected markers. Echocardiography of exposed embryos showed reduced cardiac function with both TCE and Benfluorex. Cardiac contraction was reduced by 29% and 23%, respectively at 10 ppb. The effects of TCE and Benfluorex on autocrine regulation of HNF4a, selected markers and cardiac function argue for a functional interaction of TCE and HNF4a. Further, the dose-sensitive shift between inhibition and induction of marker expression may explain the nonmonotonic-like dose response observed with TCE exposure in the heart. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Application of Turchin's method of statistical regularization

    Science.gov (United States)

    Zelenyi, Mikhail; Poliakova, Mariia; Nozik, Alexander; Khudyakov, Alexey

    2018-04-01

    During analysis of experimental data, one usually needs to restore a signal after it has been convoluted with some kind of apparatus function. According to Hadamard's definition this problem is ill-posed and requires regularization to provide sensible results. In this article we describe an implementation of the Turchin's method of statistical regularization based on the Bayesian approach to the regularization strategy.

  10. Regular extensions of some classes of grammars

    NARCIS (Netherlands)

    Nijholt, Antinus

    Culik and Cohen introduced the class of LR-regular grammars, an extension of the LR(k) grammars. In this report we consider the analogous extension of the LL(k) grammers, called the LL-regular grammars. The relations of this class of grammars to other classes of grammars are shown. Every LL-regular

  11. Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

    Directory of Open Access Journals (Sweden)

    Qiusheng Kong

    Full Text Available Gene expression analysis in watermelon (Citrullus lanatus fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC, β-actin (ClACT, and alpha tubulin 5 (ClTUA5 as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1, a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

  12. Disease Development and Symptom Expression of Xanthomonas axonopodis pv. citri in Various Citrus Plant Tissues.

    Science.gov (United States)

    Vernière, C J; Gottwald, T R; Pruvost, O

    2003-07-01

    ABSTRACT Experimental inoculations of Xanthomonas axonopodis pv. citri in different tissues of Tahiti lime and Pineapple sweet orange were conducted monthly under natural conditions on Réunion Island. The interactions between a set of environmental and epidemic variables associated with disease expression and 184 different factor combinations were investigated to determine the parameters needed to explain Asiatic citrus canker (ACC) disease expression. Area under the disease progress curve (AUDPC), inoculation date (Id), fruit and leaf age ratings (FAR and LAR), and number of days during the first 2 weeks postinoculation for which the temperature was less than 14 degrees C (T(min)) or more than 28 degrees C (T(max)) were retained by principal component analysis and canonical correlation analysis as the most meaningful epidemic and environmental variables, respectively. AUDPC as the strongest dependent variable and combinations of the environmental variables as independent variables were used in multiple regression analyses. Tissue age rating at the time of infection was a good predictor for disease resulting from spray inoculation on fruits and leaves and also on fruits following a wound inoculation. Temperature, as expressed by T(min) or T(max), was also a significant factor in determining disease development described by AUDPC. Mature green stems were highly susceptible after wounding, similarly to leaves, but buds and leaf scars expressed the lowest susceptibility. These variations in disease expression according to the tissues will have different impacts on ACC epidemiology.

  13. Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

    Science.gov (United States)

    Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Liqiang; Cheng, Fei; Huang, Yuan; Bie, Zhilong

    2015-01-01

    Gene expression analysis in watermelon (Citrullus lanatus) fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR) is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC), β-actin (ClACT), and alpha tubulin 5 (ClTUA5) as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND) was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1), a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

  14. Region-specific expression of mitochondrial complex I genes during murine brain development.

    Directory of Open Access Journals (Sweden)

    Stefanie Wirtz

    Full Text Available Mutations in the nuclear encoded subunits of mitochondrial complex I (NADH:ubiquinone oxidoreductase may cause circumscribed cerebral lesions ranging from degeneration of the striatal and brainstem gray matter (Leigh syndrome to leukodystrophy. We hypothesized that such pattern of regional pathology might be due to local differences in the dependence on complex I function. Using in situ hybridization we investigated the relative expression of 33 nuclear encoded complex I subunits in different brain regions of the mouse at E11.5, E17.5, P1, P11, P28 and adult (12 weeks. With respect to timing and relative intensity of complex I gene expression we found a highly variant pattern in different regions during development. High average expression levels were detected in periods of intense neurogenesis. In cerebellar Purkinje and in hippocampal CA1/CA3 pyramidal neurons we found a second even higher peak during the period of synaptogenesis and maturation. The extraordinary dependence of these structures on complex I gene expression during synaptogenesis is in accord with our recent findings that gamma oscillations--known to be associated with higher cognitive functions of the mammalian brain--strongly depend on the complex I activity. However, with the exception of the mesencephalon, we detected only average complex I expression levels in the striatum and basal ganglia, which does not explain the exquisite vulnerability of these structures in mitochondrial disorders.

  15. Development of inducer-free expression plasmids based on IPTG-inducible promoters for Bacillus subtilis.

    Science.gov (United States)

    Tran, Dinh Thi Minh; Phan, Trang Thi Phuong; Huynh, Thanh Kieu; Dang, Ngan Thi Kim; Huynh, Phuong Thi Kim; Nguyen, Tri Minh; Truong, Tuom Thi Tinh; Tran, Thuoc Linh; Schumann, Wolfgang; Nguyen, Hoang Duc

    2017-07-25

    Besides Escherichia coli, Bacillus subtilis is an important bacterial species for the production of recombinant proteins. Recombinant genes are inserted into shuttle expression vectors which replicate in both E. coli and in B. subtilis. The ligation products are first transformed into E. coli cells, analyzed for correct insertions, and the correct recombinant plasmids are then transformed into B. subtilis. A major problem using E. coli cells can be the strong basal level of expression of the recombinant protein which may interfere with the stability of the cells. To minimize this problem, we developed strong expression vectors being repressed in E. coli and inducer-free in B. subtilis. In general, induction of IPTG-inducible expression vectors is determined by the regulatory lacI gene encoding the LacI repressor in combination with the lacO operator on the promoter. To investigate the inducer-free properties of the vectors, we constructed inducer-free expression plasmids by removing the lacI gene and characterized their properties. First, we examined the ability to repress a reporter gene in E. coli, which is a prominent property facilitating the construction of the expression vectors carrying a target gene. The β-galactosidase (bgaB gene) basal levels expressed from Pgrac01-bgaB could be repressed at least twice in the E. coli cloning strain. Second, the inducer-free production of BgaB from four different plasmids with the Pgrac01 promoter in B. subtilis was investigated. As expected, BgaB expression levels of inducer-free constructs are at least 37 times higher than that of the inducible constructs in the absence of IPTG, and comparable to those in the presence of the inducer. Third, using efficient IPTG-inducible expression vectors containing the strong promoter Pgrac100, we could convert them into inducer-free expression plasmids. The BgaB production levels from the inducer-free plasmid in the absence of the inducer were at least 4.5 times higher than that of

  16. Learning regularization parameters for general-form Tikhonov

    International Nuclear Information System (INIS)

    Chung, Julianne; Español, Malena I

    2017-01-01

    Computing regularization parameters for general-form Tikhonov regularization can be an expensive and difficult task, especially if multiple parameters or many solutions need to be computed in real time. In this work, we assume training data is available and describe an efficient learning approach for computing regularization parameters that can be used for a large set of problems. We consider an empirical Bayes risk minimization framework for finding regularization parameters that minimize average errors for the training data. We first extend methods from Chung et al (2011 SIAM J. Sci. Comput. 33 3132–52) to the general-form Tikhonov problem. Then we develop a learning approach for multi-parameter Tikhonov problems, for the case where all involved matrices are simultaneously diagonalizable. For problems where this is not the case, we describe an approach to compute near-optimal regularization parameters by using operator approximations for the original problem. Finally, we propose a new class of regularizing filters, where solutions correspond to multi-parameter Tikhonov solutions, that requires less data than previously proposed optimal error filters, avoids the generalized SVD, and allows flexibility and novelty in the choice of regularization matrices. Numerical results for 1D and 2D examples using different norms on the errors show the effectiveness of our methods. (paper)

  17. The Development of Dynamic Facial Expression Recognition at Different Intensities in 4- to 18-Year-Olds

    Science.gov (United States)

    Montirosso, Rosario; Peverelli, Milena; Frigerio, Elisa; Crespi, Monica; Borgatti, Renato

    2010-01-01

    The primary purpose of this study was to examine the effect of the intensity of emotion expression on children's developing ability to label emotion during a dynamic presentation of five facial expressions (anger, disgust, fear, happiness, and sadness). A computerized task (AFFECT--animated full facial expression comprehension test) was used to…

  18. Anther-preferential expressing gene PMR is essential for the mitosis of pollen development in rice.

    Science.gov (United States)

    Liu, Yaqin; Xu, Ya; Ling, Sheng; Liu, Shasha; Yao, Jialing

    2017-06-01

    Phenotype identification, expression examination, and function prediction declared that the anther-preferential expressing gene PMR may participate in regulation of male gametophyte development in rice. Male germline development in flowering plants produces the pair of sperm cells for double fertilization and the pollen mitosis is a key process of it. Although the structural features of male gametophyte have been defined, the molecular mechanisms regulating the mitotic cell cycle are not well elucidated in rice. Here, we reported an anther-preferential expressing gene in rice, PMR (Pollen Mitosis Relative), playing an essential role in male gametogenesis. When PMR gene was suppressed via RNAi, the mitosis of microspore was severely damaged, and the plants formed unmatured pollens containing only one or two nucleuses at the anthesis, ultimately leading to serious reduction of pollen fertility and seed-setting. The CRISPR mutants, pmr-1 and pmr-2, both showed the similar defects as the PMR-RNAi lines. Further analysis revealed that PMR together with its co-expressing genes were liable to participate in the regulation of DNA metabolism in the nucleus, and affected the activities of some enzymes related to the cell cycle. We finally discussed that unknown protein PMR contained the PHD, SWIB and Plus-3 domains and they might have coordinating functions in regulation pathway of the pollen mitosis in rice.

  19. Role of Myofibril-Inducing RNA in cardiac TnT expression in developing Mexican axolotl

    Science.gov (United States)

    Sferrazza, Gian-Franco; Zhang, Chi; Jia, Pingping; Lemanski, Sharon L.; Athauda, Gagani; Stassi, Alyssa; Halager, Kristine; Maier, Jennifer A.; Rueda-de-Leon, Elena; Gupta, Amit; Dube, Syamalima; Huang, Xupei; Prentice, Howard M.; Dube, Dipak K.; Lemanski, Larry F.

    2007-01-01

    The Mexican axolotl, Ambystoma mexicanum, has been a useful animal model to study heart development and cardiac myofibrillogenesis. A naturally-occurring recessive mutant, gene “c”, for cardiac non-function in the Mexican axolotl causes a failure of myofibrillogenesis due to a lack of tropomyosin expression in homozygous mutant (c/c) embryonic hearts.. Myofibril-Inducing RNA (MIR) rescues mutant hearts in vitro by promoting tropomyosin expression and myofibril formation thereafter. We have studied the effect of MIR on the expression of various isoforms of cardiac Troponin-T (cTnT), a component of the thin filament that binds with tropomyosin. Four alternatively spliced cTnT isoforms have been characterized from developing axolotl heart. The expression of various cTnT isoforms in normal, mutant, and mutant hearts corrected with MIR, is evaluated by real-time RT-PCR using isoform specific primer pairs; MIR affects the total transcription as well as the splicing of the cTnT in axolotl heart PMID:17408593

  20. Spatial and temporal expression of the Grainyhead-like transcription factor family during murine development.

    Science.gov (United States)

    Auden, Alana; Caddy, Jacinta; Wilanowski, Tomasz; Ting, Stephen B; Cunningham, John M; Jane, Stephen M

    2006-10-01

    The Drosophila transcription factor Grainyhead (grh) is expressed in ectoderm-derived tissues where it regulates several key developmental events including cuticle formation, tracheal elongation and dorsal closure. Our laboratory has recently identified three novel mammalian homologues of the grh gene, Grainyhead-like 1, -2 and -3 (Grhl1-3) that rewrite the phylogeny of this family. Using gene targeting in mice, we have shown that Grhl3 is essential for neural tube closure, skin barrier formation and wound healing. Despite their extensive sequence homology, Grhl1 and Grhl2 are unable to compensate for loss of Grhl3 in these developmental processes. To explore this lack of redundancy, and to gain further insights into the functions of this gene family in mammalian development we have performed an extensive in situ hybridisation analysis. We demonstrate that, although all three Grhl genes are highly expressed in the developing epidermis, they display subtle differences in the timing and level of expression. Surprisingly, we also demonstrate differential expression patterns in non-ectoderm-derived tissues, including the heart, the lung, and the metanephric kidney. These findings expand our understanding of the unique role of Grhl3 in neurulation and epidermal morphogenesis, and provide a focus for further functional analysis of the Grhl genes during mouse embryogenesis.

  1. Postnatal development of cerebellar zones revealed by neurofilament heavy chain protein expression

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    Joshua J White

    2013-05-01

    Full Text Available The cerebellum is organized into parasagittal zones that control sensory-motor behavior. Although the architecture of adult zones is well understood, very little is known about how zones emerge during development. Understanding the process of zone formation is an essential step towards unraveling how circuits are constructed to support specific behaviors. Therefore, we focused this study on postnatal development to determine the spatial and temporal changes that establish zonal patterns during circuit formation. We used a combination of wholemount and tissue section immunohistochemistry in mice to show that the cytoskeletal protein neurofilament heavy chain (NFH is a robust marker for postnatal cerebellar zonal patterning. The patterned expression of NFH is initiated shortly after birth, and compared to the domains of several known zonal markers such as zebrin II, HSP25, neurogranin, and phospholipase Cβ4 (PLCβ4, NFH does not exhibit transient expression patterns that are typically remodeled between stages, and the adult zones do not emerge after a period of uniform expression in all lobules. Instead, we found that throughout postnatal development NFH gradually reveals distinct zones in each cerebellar lobule. The boundaries of individual NFH zones sharpen over time, as zones are refined during the second and third weeks after birth. Double labeling with neurogranin and PLCβ4 further revealed that although the postnatal expression of NFH is spatially and temporally unique, its pattern of zones respects a fundamental and well-known molecular topography in the cerebellum. The dynamics of NFH expression support the hypothesis that adult circuits are derived from an embryonic map that is refined into zones during the first three-weeks of life.

  2. VEGF receptor expression decreases during lung development in congenital diaphragmatic hernia induced by nitrofen

    Directory of Open Access Journals (Sweden)

    L. Sbragia

    2014-02-01

    Full Text Available Changes in vascular endothelial growth factor (VEGF in pulmonary vessels have been described in congenital diaphragmatic hernia (CDH and may contribute to the development of pulmonary hypoplasia and hypertension; however, how the expression of VEGF receptors changes during fetal lung development in CDH is not understood. The aim of this study was to compare morphological evolution with expression of VEGF receptors, VEGFR1 (Flt-1 and VEGFR2 (Flk-1, in pseudoglandular, canalicular, and saccular stages of lung development in normal rat fetuses and in fetuses with CDH. Pregnant rats were divided into four groups (n=20 fetuses each of four different gestational days (GD 18.5, 19.5, 20.5, 21.5: external control (EC, exposed to olive oil (OO, exposed to 100 mg nitrofen, by gavage, without CDH (N-, and exposed to nitrofen with CDH (CDH on GD 9.5 (term=22 days. The morphological variables studied were: body weight (BW, total lung weight (TLW, left lung weight, TLW/BW ratio, total lung volume, and left lung volume. The histometric variables studied were: left lung parenchymal area density and left lung parenchymal volume. VEGFR1 and VEGFR2 expression were determined by Western blotting. The data were analyzed using analysis of variance with the Tukey-Kramer post hoc test. CDH frequency was 37% (80/216. All the morphological and histometric variables were reduced in the N- and CDH groups compared with the controls, and reductions were more pronounced in the CDH group (P<0.05 and more evident on GD 20.5 and GD 21.5. Similar results were observed for VEGFR1 and VEGFR2 expression. We conclude that N- and CDH fetuses showed primary pulmonary hypoplasia, with a decrease in VEGFR1 and VEGFR2 expression.

  3. VEGF receptor expression decreases during lung development in congenital diaphragmatic hernia induced by nitrofen

    Energy Technology Data Exchange (ETDEWEB)

    Sbragia, L. [Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil, Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP (Brazil); Nassr, A.C.C. [Departamento de Hidrobiologia do Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brasil, Departamento de Hidrobiologia do Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP (Brazil); Gonçalves, F.L.L. [Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil, Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP (Brazil); Schmidt, A.F. [Pediatrics House Office, Cincinnati Children' s Hospital Medical Center, Cincinnati, OH, USA, Pediatrics House Office, Cincinnati Children' s Hospital Medical Center, Cincinnati, OH (United States); Zuliani, C.C. [Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP (Brazil); Garcia, P.V. [Departamento de Histologia e Embriologia, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, SP, Brasil, Departamento de Histologia e Embriologia, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, SP (Brazil); Gallindo, R.M. [Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil, Divisão de Cirurgia Pediátrica, Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP (Brazil); Pereira, L.A.V. [Departamento de Histologia e Embriologia, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, SP, Brasil, Departamento de Histologia e Embriologia, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, SP (Brazil)

    2014-02-17

    Changes in vascular endothelial growth factor (VEGF) in pulmonary vessels have been described in congenital diaphragmatic hernia (CDH) and may contribute to the development of pulmonary hypoplasia and hypertension; however, how the expression of VEGF receptors changes during fetal lung development in CDH is not understood. The aim of this study was to compare morphological evolution with expression of VEGF receptors, VEGFR1 (Flt-1) and VEGFR2 (Flk-1), in pseudoglandular, canalicular, and saccular stages of lung development in normal rat fetuses and in fetuses with CDH. Pregnant rats were divided into four groups (n=20 fetuses each) of four different gestational days (GD) 18.5, 19.5, 20.5, 21.5: external control (EC), exposed to olive oil (OO), exposed to 100 mg nitrofen, by gavage, without CDH (N-), and exposed to nitrofen with CDH (CDH) on GD 9.5 (term=22 days). The morphological variables studied were: body weight (BW), total lung weight (TLW), left lung weight, TLW/BW ratio, total lung volume, and left lung volume. The histometric variables studied were: left lung parenchymal area density and left lung parenchymal volume. VEGFR1 and VEGFR2 expression were determined by Western blotting. The data were analyzed using analysis of variance with the Tukey-Kramer post hoc test. CDH frequency was 37% (80/216). All the morphological and histometric variables were reduced in the N- and CDH groups compared with the controls, and reductions were more pronounced in the CDH group (P<0.05) and more evident on GD 20.5 and GD 21.5. Similar results were observed for VEGFR1 and VEGFR2 expression. We conclude that N- and CDH fetuses showed primary pulmonary hypoplasia, with a decrease in VEGFR1 and VEGFR2 expression.

  4. Ciliary and non-ciliary expression and function of PACRG during vertebrate development

    Directory of Open Access Journals (Sweden)

    Thumberger Thomas

    2012-08-01

    Full Text Available Abstract Background Park2-co-regulated gene (PACRG is evolutionarily highly conserved from green algae to mammals. In Chlamydomonas and trypanosomes, the PACRG protein associates with flagella. Loss of PACRG results in shortened or absent flagella. In mouse the PACRG protein is required for spermatogenesis. The purpose of the present study was to analyze (1 the expression patterns of PACRG during vertebrate embryogenesis, and (2 whether the PACRG protein was required for left-right (LR axis specification through cilia-driven leftward flow in Xenopus laevis. Methods PACRG cDNAs were cloned and expression was analyzed during early embryonic development of Xenopus, mouse, rabbit and zebrafish. Antisense morpholino oligonucleotide (MO mediated gene knockdown was applied in Xenopus to investigate LR development at the level of tissue morphology, leftward flow and asymmetric marker gene expression, using timelapse videography, scanning electron microscopy (SEM and whole-mount in situ hybridization. Results were statistically evaluated using Wilcoxon paired and χ2 tests. Results PACRG mRNA expression was found in cells and tissues harboring cilia throughout the vertebrates. Highly localized expression was also detected in the brain. During early development, PACRG was specifically localized to epithelia where leftward flow arises, that is, the gastrocoel roof plate (GRP in Xenopus, the posterior notochord (PNC in mammals and Kupffer’s vesicle (KV in zebrafish. Besides its association with ciliary axonemes, subcellular localization of PACRG protein was found around the nucleus and in a spotty pattern in the cytoplasm. A green fluorescent protein (GFP fusion construct preferentially labeled cilia, rendering PACRG a versatile marker for live imaging. Loss-of-function in the frog resulted dose dependently in LR, neural tube closure and gastrulation defects, representing ciliary and non-ciliary functions of PACRG. Conclusions The PACRG protein is a novel

  5. VEGF receptor expression decreases during lung development in congenital diaphragmatic hernia induced by nitrofen

    International Nuclear Information System (INIS)

    Sbragia, L.; Nassr, A.C.C.; Gonçalves, F.L.L.; Schmidt, A.F.; Zuliani, C.C.; Garcia, P.V.; Gallindo, R.M.; Pereira, L.A.V.

    2014-01-01

    Changes in vascular endothelial growth factor (VEGF) in pulmonary vessels have been described in congenital diaphragmatic hernia (CDH) and may contribute to the development of pulmonary hypoplasia and hypertension; however, how the expression of VEGF receptors changes during fetal lung development in CDH is not understood. The aim of this study was to compare morphological evolution with expression of VEGF receptors, VEGFR1 (Flt-1) and VEGFR2 (Flk-1), in pseudoglandular, canalicular, and saccular stages of lung development in normal rat fetuses and in fetuses with CDH. Pregnant rats were divided into four groups (n=20 fetuses each) of four different gestational days (GD) 18.5, 19.5, 20.5, 21.5: external control (EC), exposed to olive oil (OO), exposed to 100 mg nitrofen, by gavage, without CDH (N-), and exposed to nitrofen with CDH (CDH) on GD 9.5 (term=22 days). The morphological variables studied were: body weight (BW), total lung weight (TLW), left lung weight, TLW/BW ratio, total lung volume, and left lung volume. The histometric variables studied were: left lung parenchymal area density and left lung parenchymal volume. VEGFR1 and VEGFR2 expression were determined by Western blotting. The data were analyzed using analysis of variance with the Tukey-Kramer post hoc test. CDH frequency was 37% (80/216). All the morphological and histometric variables were reduced in the N- and CDH groups compared with the controls, and reductions were more pronounced in the CDH group (P<0.05) and more evident on GD 20.5 and GD 21.5. Similar results were observed for VEGFR1 and VEGFR2 expression. We conclude that N- and CDH fetuses showed primary pulmonary hypoplasia, with a decrease in VEGFR1 and VEGFR2 expression

  6. Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Fan; Manisseri, Chithra; Fagerström, Alexandra; Peck, Matthew L.; Vega-Sánchez, Miguel E.; Williams, Brian; Chiniquy, Dawn M.; Saha, Prasenjit; Pattathil, Sivakumar; Conlin, Brian; Zhu, Lan; Hahn, Michael G.; Willats, William G. T.; Scheller, Henrik V.; Ronald, Pamela C.; Bartley, Laura E.

    2016-08-01

    Cell walls of grasses, including cereal crops and biofuel grasses, comprise the majority of plant biomass and intimately influence plant growth, development and physiology. However, the functions of many cell wall synthesis genes, and the relationships among and the functions of cell wall components remain obscure. To better understand the patterns of cell wall accumulation and identify genes that act in grass cell wall biosynthesis, we characterized 30 samples from aerial organs of rice (Oryza sativa cv. Kitaake) at 10 developmental time points, 3-100 d post-germination. Within these samples, we measured 15 cell wall chemical components, enzymatic digestibility and 18 cell wall polysaccharide epitopes/ligands. We also used quantitative reverse transcription-PCR to measure expression of 50 glycosyltransferases, 15 acyltransferases and eight phenylpropanoid genes, many of which had previously been identified as being highly expressed in rice. Most cell wall components vary significantly during development, and correlations among them support current understanding of cell walls. We identified 92 significant correlations between cell wall components and gene expression and establish nine strong hypotheses for genes that synthesize xylans, mixed linkage glucan and pectin components. This work provides an extensive analysis of cell wall composition throughout rice development, identifies genes likely to synthesize grass cell walls, and provides a framework for development of genetically improved grasses for use in lignocellulosic biofuel production and agriculture.

  7. Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development

    KAUST Repository

    Xin, Chengqi; Liu, Wanfei; Lin, Qiang; Zhang, Xiaowei; Cui, Peng; Li, Fusen; Zhang, Guangyu; Pan, Linlin; Al-Amer, Ali; Mei, Hailiang; Al-Mssallem, Ibrahim S.; Hu, Songnian; Al-Johi, Hasan Awad; Yu, Jun

    2015-01-01

    MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.

  8. A chronological expression profile of gene activity during embryonic mouse brain development.

    Science.gov (United States)

    Goggolidou, P; Soneji, S; Powles-Glover, N; Williams, D; Sethi, S; Baban, D; Simon, M M; Ragoussis, I; Norris, D P

    2013-12-01

    The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

  9. Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development

    KAUST Repository

    Xin, Chengqi

    2015-01-29

    MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.

  10. Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Barker Gary LA

    2009-07-01

    Full Text Available Abstract Background The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is natural variation among C. elegans lines in the sensitivity of this decision to environmental conditions; that is, there is variation in the phenotypic plasticity of dauer larva development. We hypothesised that these differences may be transcriptionally controlled in early stage larvae. We investigated this by microarray analysis of different C. elegans lines under different environmental conditions, specifically the presence and absence of dauer larva-inducing pheromone. Results There were substantial transcriptional differences between four C. elegans lines under the same environmental conditions. The expression of approximately 2,000 genes differed between genetically different lines, with each line showing a largely line-specific transcriptional profile. The expression of genes that are markers of larval moulting suggested that the lines may be developing at different rates. The expression of a total of 89 genes was putatively affected by dauer larva or non-dauer larva-inducing conditions. Among the upstream regions of these genes there was an over-representation of DAF-16-binding motifs. Conclusion Under the same environmental conditions genetically different lines of C. elegans had substantial transcriptional differences. This variation may be due to differences in the developmental rates of the lines. Different environmental conditions had a rather smaller effect on transcription. The preponderance of DAF-16-binding motifs upstream of these genes was consistent with these genes playing a key role in the decision between development into dauer or into non-dauer larvae. There was little overlap between the genes whose expression was affected by environmental conditions and previously identified loci involved in

  11. Transgenic APP expression during postnatal development causes persistent locomotor hyperactivity in the adult.

    Science.gov (United States)

    Rodgers, Shaefali P; Born, Heather A; Das, Pritam; Jankowsky, Joanna L

    2012-06-18

    Transgenic mice expressing disease-associated proteins have become standard tools for studying human neurological disorders. Transgenes are often expressed using promoters chosen to drive continuous high-level expression throughout life rather than temporal and spatial fidelity to the endogenous gene. This approach has allowed us to recapitulate diseases of aging within the two-year lifespan of the laboratory mouse, but has the potential for creating aberrant phenotypes by mechanisms unrelated to the human disorder. We show that overexpression of the Alzheimer's-related amyloid precursor protein (APP) during early postnatal development leads to severe locomotor hyperactivity that can be significantly attenuated by delaying transgene onset until adulthood. Our data suggest that exposure to transgenic APP during maturation influences the development of neuronal circuits controlling motor activity. Both when matched for total duration of APP overexpression and when matched for cortical amyloid burden, animals exposed to transgenic APP as juveniles are more active in locomotor assays than animals in which APP overexpression was delayed until adulthood. In contrast to motor activity, the age of APP onset had no effect on thigmotaxis in the open field as a rough measure of anxiety, suggesting that the interaction between APP overexpression and brain development is not unilateral. Our findings indicate that locomotor hyperactivity displayed by the tet-off APP transgenic mice and several other transgenic models of Alzheimer's disease may result from overexpression of mutant APP during postnatal brain development. Our results serve as a reminder of the potential for unexpected interactions between foreign transgenes and brain development to cause long-lasting effects on neuronal function in the adult. The tet-off APP model provides an easy means of avoiding developmental confounds by allowing transgene expression to be delayed until the mice reach adulthood.

  12. Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle

    Directory of Open Access Journals (Sweden)

    Velleman Sandra G

    2011-03-01

    Full Text Available Abstract Background Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia, 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy, and 16wk (market age from two genetic lines: a randombred control line (RBC2 maintained without selection pressure, and a line (F selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage. Results A total of 3474 genes were differentially expressed (false discovery rate; FDR Conclusions The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of

  13. Expression profiles of aquaporin homologues and petal movement during petal development in Tulipa gesneriana.

    Science.gov (United States)

    Azad, Abul Kalam; Hanawa, Ryosuke; Ishikawa, Takahiro; Sawa, Yoshihiro; Shibata, Hitoshi

    2013-07-01

    Previously, we have characterized two tonoplast intrinsic proteins (TIPs) and four plasma membrane intrinsic proteins (PIPs) from the 2-day-old petals of tulip (Tulipa gesneriana). In this study, we analyzed the development of tulip petals and stems, temperature-dependent petal movement, the amount of ³H₂O transported into petals and stems during petal movement, and the transcript levels of two TIP (TgTIP1;1 and TgTIP1;2) and four TgPIP genes in petals and stems, from the first day of petal opening to day 12. The development of the petals and stems was completed by days 6 and 9, respectively, after the first day of petal opening. Temperature-dependent petal movement and the amount of ³H₂O that was transported into petals could be detected at significant levels up to day 6 with petal movement reaching a peak at day 3. Real-time reverse transcription-polymerase chain reaction analysis revealed that TgTIP1;1 and TgTIP1;2 were expressed ubiquitously in petals, stems, leaves, bulbs and roots. However, the expression level of TgTIP1;2 was very low in bulbs. The expression of both TgTIP1 genes was upregulated in close association with the development of petals but not with that of the stem. The four TgPIP genes were expressed at almost the same level during the development of the petals and the stem. However, the levels of the TgTIP1 and TgPIP transcripts in petals decreased during the course of petal wilting from day 9 onwards. These results suggest that TgTIP1;1 and TgTIP1;2 may contribute to petal development. Copyright © Physiologia Plantarum 2012.

  14. Maternal Diabetes Alters Expression of MicroRNAs that Regulate Genes Critical for Neural Tube Development

    Directory of Open Access Journals (Sweden)

    Seshadri Ramya

    2017-07-01

    Full Text Available Maternal diabetes is known to cause neural tube defects (NTDs in embryos and neuropsychological deficits in infants. Several metabolic pathways and a plethora of genes have been identified to be deregulated in developing brain of embryos by maternal diabetes, although the exact mechanism remains unknown. Recently, miRNAs have been shown to regulate genes involved in brain development and maturation. Therefore, we hypothesized that maternal diabetes alters the expression of miRNAs that regulate genes involved in biological pathways critical for neural tube development and closure during embryogenesis. To address this, high throughput miRNA expression profiling in neural stem cells (NSCs isolated from the forebrain of embryos from normal or streptozotocin-induced diabetic pregnancy was carried out. It is known that maternal diabetes results in fetal hypoglycemia/hyperglycemia or hypoxia. Hence, NSCs from embryos of control pregnant mice were exposed to low or high glucose or hypoxia in vitro. miRNA pathway analysis revealed distinct deregulation of several biological pathways, including axon guidance pathway, which are critical for brain development in NSCs exposed to different treatments. Among the differentially expressed miRNAs, the miRNA-30 family members which are predicted to target genes involved in brain development was upregulated in NSCs from embryos of diabetic pregnancy when compared to control. miRNA-30b was found to be upregulated while its target gene Sirtuin 1 (Sirt1, as revealed by luciferase assay, was down regulated in NSCs from embryos of diabetic pregnancy. Further, overexpression of miRNA-30b in NSCs, resulted in decreased expression of Sirt1 protein, and altered the neuron/glia ratio. On the other hand, siRNA mediated knockdown of Sirt1 in NSCs promoted astrogenesis, indicating that miRNA-30b alters lineage specification via Sirt1. Overall, these results suggest that maternal diabetes alters the genes involved in neural tube

  15. Global analysis of gene expression in the developing brain of Gtf2ird1 knockout mice.

    Directory of Open Access Journals (Sweden)

    Jennifer O'Leary

    Full Text Available Williams-Beuren Syndrome (WBS is a neurodevelopmental disorder caused by a hemizygous deletion of a 1.5 Mb region on chromosome 7q11.23 encompassing 26 genes. One of these genes, GTF2IRD1, codes for a putative transcription factor that is expressed throughout the brain during development. Genotype-phenotype studies in patients with atypical deletions of 7q11.23 implicate this gene in the neurological features of WBS, and Gtf2ird1 knockout mice show reduced innate fear and increased sociability, consistent with features of WBS. Multiple studies have identified in vitro target genes of GTF2IRD1, but we sought to identify in vivo targets in the mouse brain.We performed the first in vivo microarray screen for transcriptional targets of Gtf2ird1 in brain tissue from Gtf2ird1 knockout and wildtype mice at embryonic day 15.5 and at birth. Changes in gene expression in the mutant mice were moderate (0.5 to 2.5 fold and of candidate genes with altered expression verified using real-time PCR, most were located on chromosome 5, within 10 Mb of Gtf2ird1. siRNA knock-down of Gtf2ird1 in two mouse neuronal cell lines failed to identify changes in expression of any of the genes identified from the microarray and subsequent analysis showed that differences in expression of genes on chromosome 5 were the result of retention of that chromosome region from the targeted embryonic stem cell line, and so were dependent upon strain rather than Gtf2ird1 genotype. In addition, specific analysis of genes previously identified as direct in vitro targets of GTF2IRD1 failed to show altered expression.We have been unable to identify any in vivo neuronal targets of GTF2IRD1 through genome-wide expression analysis, despite widespread and robust expression of this protein in the developing rodent brain.

  16. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles.

    Science.gov (United States)

    Guo, Shaogui; Liu, Jingan; Zheng, Yi; Huang, Mingyun; Zhang, Haiying; Gong, Guoyi; He, Hongju; Ren, Yi; Zhong, Silin; Fei, Zhangjun; Xu, Yong

    2011-09-21

    Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues. We performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression

  17. Identification of differentially expressed genes between developing seeds of different soybean cultivars

    Directory of Open Access Journals (Sweden)

    Rongshuang Lin

    2015-12-01

    Full Text Available Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits

  18. The FOUR LIPS and MYB88 transcription factor genes are widely expressed in Arabidopsis thaliana during development.

    Science.gov (United States)

    Lei, Qin; Lee, EunKyoung; Keerthisinghe, Sandra; Lai, Lien; Li, Meng; Lucas, Jessica R; Wen, Xiaohong; Ren, Xiaolin; Sack, Fred D

    2015-09-01

    The FOUR LIPS (FLP) and MYB88 transcription factors, which are closely related in structure and function, control the development of stomata, as well as entry into megasporogenesis in Arabidopsis thaliana. However, other locations where these transcription factors are expressed are poorly described. Documenting additional locations where these genes are expressed might define new functions for these genes. Expression patterns were examined throughout vegetative and reproductive development. The expression from two transcriptional-reporter fusions were visualized with either β-glucuronidase (GUS) or green fluorescence protein (GFP). Both flp and myb88 genes were expressed in many, previously unreported locations, consistent with the possibility of additional functions for FLP and MYB88. Moreover, expression domains especially of FLP display sharp cutoffs or boundaries. In addition to stomatal and reproductive development, FLP and MYB88, which are R2R3 MYB transcription factor genes, are expressed in many locations in cells, tissues, and organs. © 2015 Botanical Society of America.

  19. ADOLESCENT DEVELOPMENT IN THE 21ST CENTURY: DEVELOPING CRITICAL THINKING SKILLS THROUGH EXPRESSIVE DRAWING TECHNIQUES

    OpenAIRE

    Marfu’i, Lucky Nindi Riandika

    2017-01-01

    Adolescent is a formal operational stage of cognitivedevelopment. The development of an educational program prioritizes four skillsto support success in meeting the challenges of the 21st century. One of thepriority skills of the four skills is critical thinking skill. Criticalthinking skill is a skill which shows the performance of individual cognitionin interpreting, analyzing, and doing self-regulation regarding problems andinformation received. Critical thinking skill is closely related t...

  20. Class of regular bouncing cosmologies

    Science.gov (United States)

    Vasilić, Milovan

    2017-06-01

    In this paper, I construct a class of everywhere regular geometric sigma models that possess bouncing solutions. Precisely, I show that every bouncing metric can be made a solution of such a model. My previous attempt to do so by employing one scalar field has failed due to the appearance of harmful singularities near the bounce. In this work, I use four scalar fields to construct a class of geometric sigma models which are free of singularities. The models within the class are parametrized by their background geometries. I prove that, whatever background is chosen, the dynamics of its small perturbations is classically stable on the whole time axis. Contrary to what one expects from the structure of the initial Lagrangian, the physics of background fluctuations is found to carry two tensor, two vector, and two scalar degrees of freedom. The graviton mass, which naturally appears in these models, is shown to be several orders of magnitude smaller than its experimental bound. I provide three simple examples to demonstrate how this is done in practice. In particular, I show that graviton mass can be made arbitrarily small.

  1. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development.

    Science.gov (United States)

    Alba, Rob; Fei, Zhangjun; Payton, Paxton; Liu, Yang; Moore, Shanna L; Debbie, Paul; Cohn, Jonathan; D'Ascenzo, Mark; Gordon, Jeffrey S; Rose, Jocelyn K C; Martin, Gregory; Tanksley, Steven D; Bouzayen, Mondher; Jahn, Molly M; Giovannoni, Jim

    2004-09-01

    Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.

  2. Emotion regulation deficits in regular marijuana users.

    Science.gov (United States)

    Zimmermann, Kaeli; Walz, Christina; Derckx, Raissa T; Kendrick, Keith M; Weber, Bernd; Dore, Bruce; Ochsner, Kevin N; Hurlemann, René; Becker, Benjamin

    2017-08-01

    Effective regulation of negative affective states has been associated with mental health. Impaired regulation of negative affect represents a risk factor for dysfunctional coping mechanisms such as drug use and thus could contribute to the initiation and development of problematic substance use. This study investigated behavioral and neural indices of emotion regulation in regular marijuana users (n = 23) and demographically matched nonusing controls (n = 20) by means of an fMRI cognitive emotion regulation (reappraisal) paradigm. Relative to nonusing controls, marijuana users demonstrated increased neural activity in a bilateral frontal network comprising precentral, middle cingulate, and supplementary motor regions during reappraisal of negative affect (P marijuana users relative to controls. Together, the present findings could reflect an unsuccessful attempt of compensatory recruitment of additional neural resources in the context of disrupted amygdala-prefrontal interaction during volitional emotion regulation in marijuana users. As such, impaired volitional regulation of negative affect might represent a consequence of, or risk factor for, regular marijuana use. Hum Brain Mapp 38:4270-4279, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. Efficient multidimensional regularization for Volterra series estimation

    Science.gov (United States)

    Birpoutsoukis, Georgios; Csurcsia, Péter Zoltán; Schoukens, Johan

    2018-05-01

    This paper presents an efficient nonparametric time domain nonlinear system identification method. It is shown how truncated Volterra series models can be efficiently estimated without the need of long, transient-free measurements. The method is a novel extension of the regularization methods that have been developed for impulse response estimates of linear time invariant systems. To avoid the excessive memory needs in case of long measurements or large number of estimated parameters, a practical gradient-based estimation method is also provided, leading to the same numerical results as the proposed Volterra estimation method. Moreover, the transient effects in the simulated output are removed by a special regularization method based on the novel ideas of transient removal for Linear Time-Varying (LTV) systems. Combining the proposed methodologies, the nonparametric Volterra models of the cascaded water tanks benchmark are presented in this paper. The results for different scenarios varying from a simple Finite Impulse Response (FIR) model to a 3rd degree Volterra series with and without transient removal are compared and studied. It is clear that the obtained models capture the system dynamics when tested on a validation dataset, and their performance is comparable with the white-box (physical) models.

  4. Protein expression of MEF2C during the critical period for visual development in vervet monkeys

    OpenAIRE

    Bernad, Daniel M; Lachance, Pascal E; Chaudhuri, Avijit

    2008-01-01

    During the early development of the visual cortex, there is a critical period when neuronal connections are highly sensitive to changes in visual input. Deprivation of visual stimuli during the critical period elicits robust anatomical and physiological rearrangements in the monkey visual cortex and serves as an excellent model for activity-dependent neuroplasticity. DNA microarray experiments were previously performed in our lab to analyze gene expression patterns in area V1 of vervet monkey...

  5. Bone Signaling in Middle Ear Development: A Genome‐Wide Differential Expression Analysis

    DEFF Research Database (Denmark)

    Nielsen, Michelle Christine; Bertelsen, Tomas Martin; Friis, Morten

    2014-01-01

    Common middle ear diseases may affect bone behavior in the middle ear air cell system. To understand this pathologic pneumatization, the normal development of bone in the middle ear should be investigated. The objective of this study was to analyze gene expression of bone‐related signaling factor...... of the bulla wall. Anat Rec, 297:2349–2355, 2014. © 2014 Wiley Periodicals, Inc....

  6. Development of a flagellin surface display expression system in a moderate thermophile, Bacillus halodurans Alk36

    CSIR Research Space (South Africa)

    Crampton, Michael C

    2007-06-01

    Full Text Available BIOTECHNOLOGY The development of a flagellin surface display expression system in a moderate thermophile, Bacillus halodurans Alk36 Michael Crampton & Eldie Berger & Sharon Reid & Maureen Louw Received: 3 October 2006 /Revised: 29 January 2007 /Accepted... techniques Plasmid DNA was isolated using a Plasmid Midi Kit (Qiagen). Restriction enzymes were used as specified by the manufacturer (Fermentas and Roche Diagnostics). All mini-preps were done using Perfectprep Plasmid Mini Kit (Eppendorf). All DNA...

  7. DEVELOPING VISUAL NOVEL GAME WITH SPEECH-RECOGNITION INTERACTIVITY TO ENHANCE STUDENTS’ MASTERY ON ENGLISH EXPRESSIONS

    OpenAIRE

    Elizabeth Anggraeni Amalo; Imam Dui Agusalim; Citra Devi Murdaningtyas

    2017-01-01

    The teaching of English-expressions has always been done through conversation samples in form of written texts, audio recordings, and videos. In the meantime, the development of computer-aided learning technology has made autonomous language learning possible. Game, as one of computer-aided learning technology products, can serve as a medium to provide educational contents like that of language teaching and learning. Visual Novel is considered as a conversational game that is suitable to be c...

  8. Hox gene expression leads to differential hind leg development between honeybee castes.

    Science.gov (United States)

    Bomtorin, Ana Durvalina; Barchuk, Angel Roberto; Moda, Livia Maria; Simoes, Zila Luz Paulino

    2012-01-01

    Beyond the physiological and behavioural, differences in appendage morphology between the workers and queens of Apis mellifera are pre-eminent. The hind legs of workers, which are highly specialized pollinators, deserve special attention. The hind tibia of worker has an expanded bristle-free region used for carrying pollen and propolis, the corbicula. In queens this structure is absent. Although the morphological differences are well characterized, the genetic inputs driving the development of this alternative morphology remain unknown. Leg phenotype determination takes place between the fourth and fifth larval instar and herein we show that the morphogenesis is completed at brown-eyed pupa. Using results from the hybridization of whole genome-based oligonucleotide arrays with RNA samples from hind leg imaginal discs of pre-pupal honeybees of both castes we present a list of 200 differentially expressed genes. Notably, there are castes preferentially expressed cuticular protein genes and members of the P450 family. We also provide results of qPCR analyses determining the developmental transcription profiles of eight selected genes, including abdominal-A, distal-less and ultrabithorax (Ubx), whose roles in leg development have been previously demonstrated in other insect models. Ubx expression in workers hind leg is approximately 25 times higher than in queens. Finally, immunohistochemistry assays show that Ubx localization during hind leg development resembles the bristles localization in the tibia/basitarsus of the adult legs in both castes. Our data strongly indicate that the development of the hind legs diphenism characteristic of this corbiculate species is driven by a set of caste-preferentially expressed genes, such as those encoding cuticular protein genes, P450 and Hox proteins, in response to the naturally different diets offered to honeybees during the larval period.

  9. Identification of cyclic nucleotide gated channels using regular expressions

    KAUST Repository

    Zelman, Alice K.; Dawe, Adam Sean; Berkowitz, Gerald A.

    2013-01-01

    Cyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one- pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin

  10. Parsing with Regular Expressions & Extensions to Kleene Algebra

    DEFF Research Database (Denmark)

    Grathwohl, Niels Bjørn Bugge

    . In the second part of this thesis, we study two extensions to Kleene algebra. Chomsky algebra is an algebra with a structure similar to Kleene algebra, but with a generalized mu-operator for recursion instead of the Kleene star. We show that the axioms of idempotent semirings along with continuity of the mu......-operator completely axiomatize the equational theory of the context-free languages. KAT+B! is an extension to Kleene algebra with tests (KAT) that adds mutable state. We describe a test algebra B! for mutable tests and give a commutative coproduct between KATs. Combining the axioms of B! with those of KAT and some...

  11. Cheetah interspecific SCNT followed by embryo aggregation improves in vitro development but not pluripotent gene expression.

    Science.gov (United States)

    Moro, L N; Hiriart, M I; Buemo, C; Jarazo, J; Sestelo, A; Veraguas, D; Rodriguez-Alvarez, L; Salamone, D F

    2015-07-01

    The aim of this study was to evaluate the capacity of domestic cat (Dc, Felis silvestris) oocytes to reprogram the nucleus of cheetah (Ch, Acinonyx jubatus) cells by interspecies SCNT (iSCNT), by using embryo aggregation. Dc oocytes were in vitro matured and subjected to zona pellucida free (ZP-free) SCNT or iSCNT, depending on whether the nucleus donor cell was of Dc or Ch respectively. ZP-free reconstructed embryos were then cultured in microwells individually (Dc1X and Ch1X groups) or in couples (Dc2X and Ch2X groups). Embryo aggregation improved in vitro development obtaining 27.4, 47.7, 16.7 and 28.3% of blastocyst rates in the Dc1X, Dc2X, Ch1X and Ch2X groups, respectively (P<0.05). Moreover, aggregation improved the morphological quality of blastocysts from the Dc2X over the Dc1X group. Gene expression analysis revealed that Ch1X and Ch2X blastocysts had significantly lower relative expression of OCT4, CDX2 and NANOG than the Dc1X, Dc2X and IVF control groups. The OCT4, NANOG, SOX2 and CDX2 genes were overexpressed in Dc1X blastocysts, but the relative expression of these four genes decreased in the Dc2X, reaching similar relative levels to those of Dc IVF blastocysts. In conclusion, Ch blastocysts were produced using Dc oocytes, but with lower relative expression of pluripotent and trophoblastic genes, indicating that nuclear reprogramming could be still incomplete. Despite this, embryo aggregation improved the development of Ch and Dc embryos, and normalized Dc gene expression, which suggests that this strategy could improve full-term developmental efficiency of cat and feline iSCNT embryos. © 2015 Society for Reproduction and Fertility.

  12. Development of Verbal Expressive Skills Management Programme (VESMP for Patients with Brocas Aphasia

    Directory of Open Access Journals (Sweden)

    Humaira Shamim

    2017-06-01

    Full Text Available Introduction: Disorders of communication, including aphasia (mainly post stroke caused by the left hemisphere brain damage, is a major community health issue. The prevalence of aphasia after stroke is 25% in Pakistan in which Broca’s aphasia is predominant in stroke patients who have anterior lesion in the frontal lobe of the left hemispheres. The verbal expressive skills management programme (VESMP is the software which developed augmented management for patients to enhance verbal expressive skills for patients with severe Broca’s aphasia from different geographic areas. Moreover, the software increases the independencies which are not observed in other traditional techniques. This study is the pathway for maintaining and improving the functional life of patients. Objectives: The main objective was to develop the verbal expressive skills management programme (VESMP to enhance verbal expressive skills of patients with severe Broca’s aphasia. Methodology: Initially a pilot study with eight cases is carried out. The nonprobability purposive sampling technique was used to recruit the patients with severe aphasia who received therapy through VESMP programme on their smart phones. It contains seven domains: spontaneous speech, comprehension, naming, reading, writing, imitation, and automated speech. The programme was developed in Urdu language and its content was selected from grade three Urdu Punjab text books. The program was then updated with the help of guidance and feedback received from five experts of the relevant field. The patients scoring is recorded for each domain on basis of correct responses. The study was conducted in YUSRA general hospital and Pakistan Railway Hospital, Rawalpindi. The study includes patients that are 40+ years old, and have three months of post stroke with diagnosis of chronic Broca’s Aphasias, patients with severe cognitive impairment were excluded from the study. The pre-and post score was recorded for each

  13. Cardiac-specific activation of Cre expression at late fetal development

    International Nuclear Information System (INIS)

    Opherk, Jan P.; Yampolsky, Peter; Hardt, Stefan E.; Schoels, Wolfgang; Katus, Hugo A.; Koenen, Michael; Zehelein, Joerg

    2007-01-01

    In a first step towards dissecting molecular mechanisms that contribute to the development of cardiac diseases, we have generated transgenic mice that express a Cre-GFP fusion protein under the transcriptional control of a 4.3 kb murine cardiac Troponin I gene (cTnI) promoter. Cre-GFP expression, similar in three transgenic lines, is described in one line. In mouse embryos, transgenic for the Cre-GFP and ROSA lacZ reporter allele, first Cre-mediated recombination appeared at 16.5 dpc selectively at the heart. Like the endogenous cTnI gene, transgenic Cre expression showed a slow rise through fetal development that increased neonatally. Bitransgenic hearts, stained at 30 days of age, showed intense signals in ventricular and atrial myocytes while no recombination occurred in other tissues. The delayed onset of Cre activity in cTnI-Cre mice could provide a useful genetic tool to evaluate the function of loxP targeted cardiac genes without interference of recombination during early heart development

  14. Examining continuity of early expressive vocabulary development: the generation R study.

    Science.gov (United States)

    Henrichs, Jens; Rescorla, Leslie; Schenk, Jacqueline J; Schmidt, Henk G; Jaddoe, Vincent W V; Hofman, Albert; Raat, Hein; Verhulst, Frank C; Tiemeier, Henning

    2011-06-01

    The authors investigated continuity and discontinuity of vocabulary skills in a population-based cohort in the Netherlands. Mothers of 3,759 children completed the Dutch version of the MacArthur Short Form Vocabulary Checklist (Zink & Lejaegere, 2003) at 18 months and a Dutch translation of the Language Development Survey (Rescorla, 1989) at 30 months. At both ages, expressive vocabulary delay was defined as vocabulary scores vocabulary development at both ages, 6.2% were "late bloomers," 6.0% had late onset expressive vocabulary delay, and 2.6% had persistent expressive vocabulary delay. Word production and comprehension at 18 months explained 11.5% of the variance in 30-month vocabulary scores, with low birth weight, child age, gender and ethnicity, maternal age and education, and parenting stress explaining an additional 6.2%. Multinomial logistic regression was used to identify biological, demographic, and psychological factors associated with each of the vocabulary delay outcome groups relative to the typically developing group. Although multiple perinatal, demographic, and maternal psychosocial factors significantly predicted vocabulary skills at 30 months, positive predictive value and sensitivity were low. Future studies should address to what extent additional factors, such as brain maturation and genetic influences, can improve the prediction and understanding of continuity and discontinuity of language delay.

  15. GLUT3 gene expression is critical for embryonic growth, brain development and survival.

    Science.gov (United States)

    Carayannopoulos, Mary O; Xiong, Fuxia; Jensen, Penny; Rios-Galdamez, Yesenia; Huang, Haigen; Lin, Shuo; Devaskar, Sherin U

    2014-04-01

    Glucose is the primary energy source for eukaryotic cells and the predominant substrate for the brain. GLUT3 is essential for trans-placental glucose transport and highly expressed in the mammalian brain. To further elucidate the role of GLUT3 in embryonic development, we utilized the vertebrate whole animal model system of Danio rerio as a tractable system for defining the cellular and molecular mechanisms altered by impaired glucose transport and metabolism related to perturbed expression of GLUT3. The comparable orthologue of human GLUT3 was identified and the expression of this gene abrogated during early embryonic development. In a dose-dependent manner embryonic brain development was disrupted resulting in a phenotype of aberrant brain organogenesis, associated with embryonic growth restriction and increased cellular apoptosis. Rescue of the morphant phenotype was achieved by providing exogenous GLUT3 mRNA. We conclude that GLUT3 is critically important for brain organogenesis and embryonic growth. Disruption of GLUT3 is responsible for the phenotypic spectrum of embryonic growth restriction to demise and neural apoptosis with microcephaly. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Identification of microRNAs differentially expressed involved in male flower development.

    Science.gov (United States)

    Wang, Zhengjia; Huang, Jianqin; Sun, Zhichao; Zheng, Bingsong

    2015-03-01

    Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

  17. Two human homeobox genes, c1 and c8: structure analysis and expression in embryonic development

    International Nuclear Information System (INIS)

    Simeone, A.; Mavilio, F.; Acampora, D.

    1987-01-01

    Two human cDNA clones (HHO.c1.95 and HHO.c8.5111) containing a homeobox region have been characterized, and the respective genomic regions have been partially analyzed. Expression of the corresponding genes, termed c1 and c8, was evaluated in different organs and body parts during human embryonic/fetal development. HHO.c1.95 apparently encodes a 217-amino acid protein containing a class I homeodomain that shares 60 out of 61 amino acid residues with the Antennapedia homeodomain of Drosophila melanogaster. HHO.c8.5111 encodes a 153-amino acid protein containing a homeodomains identical to that of the frog AC1 gene. Clones HHO.c1 and HHO.c8 detect by blot-hybridization one and two specific polyadenylylated transcripts, respectively. These are differentially expressed in spinal cord, backbone rudiments, limb buds (or limbs), heart, and skin of human embryos and early fetuses in the 5- to 9-week postfertilization period, thus suggesting that the c1 and c8 genes play a key role in a variety of developmental processes. Together, the results of the embryonic/fetal expression of c1 and c8 and those of two previously analyzed genes (c10 and c13) indicate a coherent pattern of expression of these genes in early human ontogeny

  18. The Development and Activity-Dependent Expression of Aggrecan in the Cat Visual Cortex

    Science.gov (United States)

    Sengpiel, F.; Beaver, C. J.; Crocker-Buque, A.; Kelly, G. M.; Matthews, R. T.; Mitchell, D. E.

    2013-01-01

    The Cat-301 monoclonal antibody identifies aggrecan, a chondroitin sulfate proteoglycan in the cat visual cortex and dorsal lateral geniculate nucleus (dLGN). During development, aggrecan expression increases in the dLGN with a time course that matches the decline in plasticity. Moreover, examination of tissue from selectively visually deprived cats shows that expression is activity dependent, suggesting a role for aggrecan in the termination of the sensitive period. Here, we demonstrate for the first time that the onset of aggrecan expression in area 17 also correlates with the decline in experience-dependent plasticity in visual cortex and that this expression is experience dependent. Dark rearing until 15 weeks of age dramatically reduced the density of aggrecan-positive neurons in the extragranular layers, but not in layer IV. This effect was reversible as dark-reared animals that were subsequently exposed to light showed normal numbers of Cat-301-positive cells. The reduction in aggrecan following certain early deprivation regimens is the first biochemical correlate of the functional changes to the γ-aminobutyric acidergic system that have been reported following early deprivation in cats. PMID:22368089

  19. Two human homeobox genes, c1 and c8: structure analysis and expression in embryonic development.

    Science.gov (United States)

    Simeone, A; Mavilio, F; Acampora, D; Giampaolo, A; Faiella, A; Zappavigna, V; D'Esposito, M; Pannese, M; Russo, G; Boncinelli, E

    1987-07-01

    Two human cDNA clones (HHO.c1.95 and HHO.c8.5111) containing a homeobox region have been characterized, and the respective genomic regions have been partially analyzed. Expression of the corresponding genes, termed c1 and c8, was evaluated in different organs and body parts during human embryonic/fetal development. HHO.c1.95 apparently encodes a 217-amino acid protein containing a class I homeodomain that shares 60 out of 61 amino acid residues with the Antennapedia homeodomain of Drosophila melanogaster. HHO.c8.5111 encodes a 153-amino acid protein containing a homeodomain identical to that of the frog AC1 gene. Clones HHO.c1 and HHO.c8 detect by blot-hydridization one and two specific polyadenylylated transcripts, respectively. These are differentially expressed in spinal cord, backbone rudiments, limb buds (or limbs), heart, and skin of human embryos and early fetuses in the 5- to 9-week postfertilization period, thus suggesting that the c1 and c8 genes play a key role in a variety of developmental processes. Together, the results of the embryonic/fetal expression of c1 and c8 and those of two previously analyzed genes (c10 and c13) indicate a coherent pattern of expression of these genes in early human ontogeny.

  20. Ryanodine receptors, a family of intracellular calcium ion channels, are expressed throughout early vertebrate development

    Directory of Open Access Journals (Sweden)

    Wu Houdini HT

    2011-12-01

    Full Text Available Abstract Background Calcium signals ([Ca2+]i direct many aspects of embryo development but their regulation is not well characterised. Ryanodine receptors (RyRs are a family of intracellular Ca2+ release channels that control the flux of Ca2+ from internal stores into the cytosol. RyRs are primarily known for their role in excitation-contraction coupling in adult striated muscle and ryr gene mutations are implicated in several human diseases. Current evidence suggests that RyRs do not have a major role to play prior to organogenesis but regulate tissue differentiation. Findings The sequences of the five zebrafish ryr genes were confirmed, their evolutionary relationship established and the primary sequences compared to other vertebrates, including humans. RyRs are differentially expressed in slow (ryr1a, fast (ryr3 and both types (ryr1b of developing skeletal muscle. There are two ryr2 genes (ryr2a and ryr2b which are expressed exclusively in developing CNS and cardiac tissue, respectively. In addition, ryr3 and ryr2a mRNA is detectable in the initial stages of development, prior to embryonic axis formation. Conclusions Our work reveals that zebrafish ryr genes are differentially expressed throughout the developing embryo from cleavage onwards. The data suggests that RyR-regulated Ca2+ signals are associated with several aspects of embryonic development, from organogenesis through to the differentiation of the musculoskeletal, cardiovascular and nervous system. These studies will facilitate further work to explore the developmental function of RyRs in each of these tissue types.

  1. Expression patterns of Wnt genes during development of an anterior part of the chicken eye

    OpenAIRE

    Fokina, Valentina M.; Frolova, Elena I.

    2006-01-01

    To address the roles of Wnts in the development of the anterior eye, we used a chicken model to perform comprehensive expression analysis of all Wnt genes during anterior eye development. In analyzing the available genomic sequences, we found that the chicken genome encodes 18 Wnt proteins that are homologous to corresponding human and mouse proteins. The mRNA sequences for 12 chicken Wnt genes are available in GenBank, and mRNAs for six other Wnt genes (Wnt2, Wnt5b, Wnt7b, Wnt8b, Wnt9b and W...

  2. Redeployment of germ layers related TFs shows regionalized expression during two non-embryonic developments.

    Science.gov (United States)

    Ricci, Lorenzo; Cabrera, Fabien; Lotito, Sonia; Tiozzo, Stefano

    2016-08-01

    In all non-vertebrate metazoan phyla, species that evolved non-embryonic developmental pathways as means of propagation or regeneration can be found. In this context, new bodies arise through asexual reproduction processes (such as budding) or whole body regeneration, that lack the familiar temporal and spatial cues classically associated with embryogenesis, like maternal determinants, or gastrulation. The molecular mechanisms underlying those non-embryonic developments (i.e., regeneration and asexual reproduction), and their relationship to those deployed during embryogenesis are poorly understood. We have addressed this question in the colonial ascidian Botryllus schlosseri, which undergoes an asexual reproductive process via palleal budding (PB), as well as a whole body regeneration by vascular budding (VB). We identified early regenerative structures during VB and then followed the fate of differentiating tissues during both non-embryonic developments (PB and VB) by monitoring the expression of genes known to play key functions in germ layer specification with well conserved expression patterns in solitary ascidian embryogenesis. The expression patterns of FoxA1, GATAa, GATAb, Otx, Bra, Gsc and Tbx2/3 were analysed during both PB and VB. We found that the majority of these transcription factors were expressed during both non-embryonic developmental processes, revealing a regionalization of the palleal and vascular buds. Knockdown of GATAa by siRNA in palleal buds confirmed that preventing the correct development of one of these regions blocks further tissue specification. Our results indicate that during both normal and injury-induced budding, a similar alternative developmental program operates via early commitment of epithelial regions. Copyright © 2016. Published by Elsevier Inc.

  3. Coordinated Expression of Phosphoinositide Metabolic Genes during Development and Aging of Human Dorsolateral Prefrontal Cortex.

    Directory of Open Access Journals (Sweden)

    Stanley I Rapoport

    Full Text Available Phosphoinositides, lipid-signaling molecules, participate in diverse brain processes within a wide metabolic cascade.Gene transcriptional networks coordinately regulate the phosphoinositide cascade during human brain Development and Aging.We used the public BrainCloud database for human dorsolateral prefrontal cortex to examine age-related expression levels of 49 phosphoinositide metabolic genes during Development (0 to 20+ years and Aging (21+ years.We identified three groups of partially overlapping genes in each of the two intervals, with similar intergroup correlations despite marked phenotypic differences between Aging and Development. In each interval, ITPKB, PLCD1, PIK3R3, ISYNA1, IMPA2, INPPL1, PI4KB, and AKT1 are in Group 1, PIK3CB, PTEN, PIK3CA, and IMPA1 in Group 2, and SACM1L, PI3KR4, INPP5A, SYNJ1, and PLCB1 in Group 3. Ten of the genes change expression nonlinearly during Development, suggesting involvement in rapidly changing neuronal, glial and myelination events. Correlated transcription for some gene pairs likely is facilitated by colocalization on the same chromosome band.Stable coordinated gene transcriptional networks regulate brain phosphoinositide metabolic pathways during human Development and Aging.

  4. Znrg, a novel gene expressed mainly in the developing notochord of zebrafish.

    Science.gov (United States)

    Zhou, Yaping; Xu, Yan; Li, Jianzhen; Liu, Yao; Zhang, Zhe; Deng, Fengjiao

    2010-06-01

    The notochord, a defining characteristic of the chordate embryo is a critical midline structure required for axial skeletal formation in vertebrates, and acts as a signaling center throughout embryonic development. We utilized the digital differential display program of the National Center for Biotechnology Information, and identified a contig of expressed sequence tags (no. Dr. 83747) from the zebrafish ovary library in Genbank. Full-length cDNA of the identified gene was cloned by 5'- and 3'- RACE, and the resulting sequence was confirmed by polymerase chain reaction and sequencing. The cDNA clone contains 2,505 base pairs and encodes a novel protein of 707 amino acids that shares no significant homology with any known proteins. This gene was expressed in mature oocytes and at the one-cell stage, and persisted until the 5th day of development, as determined by RT-PCR. Transcripts were detected by whole-mount RNA in situ hybridization from the two-cell stage to 72 h of embryonic development. This gene was uniformly distributed from the cleavage stage up to the blastula stage. During early gastrulation, it was present in the dorsal region, and became restricted to the notochord and pectoral fin at 48 and 72 h of embryonic development. Based on its abundance in the notochord, we hypothesized that the novel gene may play an important role in notochord development in zebrafish; we named this gene, zebrafish notochord-related gene, or znrg.

  5. Expression Analysis of the Hippo Cascade Indicates a Role in Pituitary Stem Cell Development

    Directory of Open Access Journals (Sweden)

    Emily J Lodge

    2016-03-01

    Full Text Available The pituitary gland is a primary endocrine organ that controls major physiological processes. Abnormal development or homeostatic disruptions can lead to human disorders such as hypopituitarism or tumours. Multiple signalling pathways, including WNT, BMP, FGF and SHH regulate pituitary development but the role of the Hippo-YAP1/TAZ cascade is currently unknown. In multiple tissues, the Hippo kinase cascade underlies neoplasias; it influences organ size through the regulation of proliferation and apoptosis, and has roles in determining stem cell potential. We have used a sensitive mRNA in situ hybridisation method (RNAscope to determine the expression patterns of the Hippo pathway components during mouse pituitary development. We have also carried out immunolocalisation studies to determine when YAP1 and TAZ, the transcriptional effectors of the Hippo pathway, are active. We find that YAP1/TAZ are active in the stem/progenitor cell population throughout development and at postnatal stages, consistent with their role in promoting the stem cell state. Our results demonstrate for the first time the collective expression of major components of the Hippo pathway during normal embryonic and postnatal development of the pituitary gland.

  6. Shift of galectin-3 expression in the human kidney during development

    Directory of Open Access Journals (Sweden)

    Clara Gerosa

    2013-06-01

    Full Text Available Galectin-3 (Gal-3 is a member of the lectin family, including 14 mammalian galectins, and has been shown to be involved in the many biological processes. In fact it has been reported to be expressed during human nephrogenesis, in the ureteric bud tips and in the medullary regions. In 11 developing human kidney the immunoexpression of Gal-3 was studied. Previously observations on Gal-3 expression in collecting ducts were confirmed and a wild variable reactivity was detected among the range from 20 to 36 weeks of gestational age considered. Between the early and late phases of gestation two phases have been identified: the first, from 20 up to 26 weeks of gestation, with a strong reactivity and the second, from 30 to 36 weeks, with a decrease in Gal-3 expression. This finding clearly indicates a major role for Gal-3 in early human nephrogenesis ending around the 30th week of gestation. In conclusion, Gal-3 apparently plays a role in kidney development at different check points, participating both to ureteric bud proliferation and to differentiation of structures originating from the metanephric mesenchyme. Proceedings of the 9th International Workshop on Neonatology · Cagliari (Italy · October 23rd-26th, 2013 · Learned lessons, changing practice and cutting-edge research

  7. Heterogeneity of astrocytes: from development to injury - single cell gene expression.

    Directory of Open Access Journals (Sweden)

    Vendula Rusnakova

    Full Text Available Astrocytes perform control and regulatory functions in the central nervous system; heterogeneity among them is still a matter of debate due to limited knowledge of their gene expression profiles and functional diversity. To unravel astrocyte heterogeneity during postnatal development and after focal cerebral ischemia, we employed single-cell gene expression profiling in acutely isolated cortical GFAP/EGFP-positive cells. Using a microfluidic qPCR platform, we profiled 47 genes encoding glial markers and ion channels/transporters/receptors participating in maintaining K(+ and glutamate homeostasis per cell. Self-organizing maps and principal component analyses revealed three subpopulations within 10-50 days of postnatal development (P10-P50. The first subpopulation, mainly immature glia from P10, was characterized by high transcriptional activity of all studied genes, including polydendrocytic markers. The second subpopulation (mostly from P20 was characterized by low gene transcript levels, while the third subpopulation encompassed mature astrocytes (mainly from P30, P50. Within 14 days after ischemia (D3, D7, D14, additional astrocytic subpopulations were identified: resting glia (mostly from P50 and D3, transcriptionally active early reactive glia (mainly from D7 and permanent reactive glia (solely from D14. Following focal cerebral ischemia, reactive astrocytes underwent pronounced changes in the expression of aquaporins, nonspecific cationic and potassium channels, glutamate receptors and reactive astrocyte markers.

  8. Distinct spatiotemporal expression of ISM1 during mouse and chick development.

    Science.gov (United States)

    Osório, Liliana; Wu, Xuewei; Zhou, Zhongjun

    2014-01-01

    Isthmin 1 (ISM1) constitutes the founder of a new family of secreted proteins characterized by the presence of 2 functional domains: thrombospondin type 1 repeat (TSR1) and adhesion-associated domain in MUC4 and other proteins (AMOP). ISM1 was identified in the frog embryo as a member of the FGF8 synexpression group due to its expression in the brain midbrain-hindbrain boundary (MHB) or isthmus. In zebrafish, ISM1 was described as a WNT- and NODAL-regulated gene. The function of ISM1 remains largely elusive. So far, ISM1 has been described as an angiogenesis inhibitor that has a dual function in endothelial cell survival and cell death. For a better understanding of ISM1 function, we examined its spatiotemporal distribution in mouse and chick using RT-PCR, ISH, and IHC analyses. In the mouse, ISM1 transcripts are found in tissues such as the anterior mesendoderm, paraxial and lateral plate mesoderm, MHB and trunk neural tube, as well as in the somites and dermomyotome. In the newborn and adult, ISM1 is prominently expressed in the lung and brain. In addition to its putative role during embryonic and postnatal development, ISM1 may also be important for organ homeostasis in the adult. In the chick embryo, ISM1 transcripts are strongly detected in the ear, eye, and spinal cord primordia. Remarkable differences in ISM1 spatiotemporal expression were found during mouse and chick development, despite the high homology of ISM1 orthologs in these species.

  9. A comparison of anterior-posterior development in the porcine versus the chicken embryo, using goosecoid expression as a marker

    NARCIS (Netherlands)

    Pavert, van de S.A.; Schipper, H.; Wit, de A.A.C.; Soede, N.M.; Hurk, van den R.; Taverne, M.A.M.; Boerjan, M.L.; Stroband, H.W.J.

    2001-01-01

    During early embryonic development, pig and chicken embryos share striking morphological similarities. In the present study, the timing and location of expression of mRNA for goosecoid (gsc), a gene classically expressed in the nodal region of developing embryos, was examined and compared in

  10. Expression of Oct-4 is significantly associated with the development and prognosis of colorectal cancer

    Science.gov (United States)

    ZHOU, HUAN; HU, YU; WANG, WEIPENG; MAO, YONG; ZHU, JINGJIE; ZHOU, BIN; SUN, JING; ZHANG, XUEGUANG

    2015-01-01

    Octamer-binding transcription factor 4 (Oct-4), is an essential transcription factor, which is required for pluripotency and self-renewal in embryonic stem cells and germ cells. It is also involved in maintaining cancer stem-like properties in certain types of tumor, and is an important biomarker for cancer stem cells. The present study investigated whether Oct-4 expression was associated with colorectal cancer (CRC). In order to achieve this, primary CRC tissues, matched non-tumor tissues and benign polyp tissues, representing different stages of carcinogenesis, were obtained, and Oct-4 expression was analyzed using reverse transcription-quantitative polymerase chain reaction, flow cytometry analysis and immunohistochemistry. Furthermore, the medical records of patients with CRC were reviewed, and clinicopathological analysis was performed in order to assess the association between Oct-4 expression and certain clinicopathological parameters. It was shown that the transcription and translation of Oct-4 increased in a stepwise manner, from non-tumor to benign polyp tissues, and from benign polyps to CRC tissues. Oct-4 expression in CRC was significantly correlated with histological grade (P=0.007), lymph node metastasis (P=0.027), distant metastasis (P=0.017) and TNM stage (P=0.041). Kaplan-Meier survival curve analysis demonstrated that Oct-4+ cases had a shorter median survival time (37.0 months) compared with Oct-4− cases (76.0 months; P=0.001). These results indicated that aberrant expression of Oct-4 may be involved in the development of CRC. Thus, Oct-4 may be a biomarker for the prediction, diagnosis or assessment of prognosis in CRC, in addition to a potential target for the treatment of this disease. PMID:26622555

  11. Pancreas developing markers expressed on human mononucleated umbilical cord blood cells

    International Nuclear Information System (INIS)

    Pessina, A.; Eletti, B.; Croera, C.; Savalli, N.; Diodovich, C.; Gribaldo, L.

    2004-01-01

    Haematopoietic system represents the main source of haematopoietic stem cells and probably of multipotential adult progenitor cells and mesenchimal stem cells at first described as colony forming unit-fibroblast. Whereas there are many studies on the gene expression profile of the different precursors along their haematopoietic differentiation, few data (sometimes conflicting) have been reported about the phenotype of the cells (present in bone marrow and possibly in cord blood) able to differentiate into non-haematopoietic cells. As both postnatal bone marrow and umbilical cord blood contain nestin positive cells able to proliferate and differentiate into the main neural phenotype (neuron, astroglia and oligodendroglia) many authors considered nestin a neuroepithelial precursor marker that seems to be essential also in multipotential progenitor cells of pancreas present both in rat and in human pancreatic islets (called nestin positive islet derived progenitors). Although the importance of nestin in these cells appears to be evident, it remains yet to clarify the number and the sequential expression of the genes coding all the transcription factors essential for beta cells differentiation and therefore the conditions able to induce the expression of many important transcription factors genes such as isl-1, pax-4, pdx-1 and ngn-3. Among them pdx-1 is a gene essential for pancreas development which is able to control ngn-3 in activating the expression of other differentiation factors for endocrine cells. Here, we describe for the first time in human umbilical cord blood cells (UCB) the pattern of expression of a panel of markers (nestin, CK-8, CK-18) and transcription factors (Isl-1, Pdx-1, Pax-4, Ngn-3) considered important for beta cells differentiation. Our data demonstrate that UCB contains a cell population having a phenotype very similar to endocrine cell precursors in transition to beta cells

  12. Leukemia inhibitory factor in rat fetal lung development: expression and functional studies.

    Directory of Open Access Journals (Sweden)

    Cristina Nogueira-Silva

    Full Text Available BACKGROUND: Leukemia inhibitory factor (LIF and interleukin-6 (IL-6 are members of the family of the glycoprotein 130 (gp130-type cytokines. These cytokines share gp130 as a common signal transducer, which explains why they show some functional redundancy. Recently, it was demonstrated that IL-6 promotes fetal lung branching. Additionally, LIF has been implicated in developmental processes of some branching organs. Thus, in this study LIF expression pattern and its effects on fetal rat lung morphogenesis were assessed. METHODOLOGY/PRINCIPAL FINDINGS: LIF and its subunit receptor LIFRα expression levels were evaluated by immunohistochemistry and western blot in fetal rat lungs of different gestational ages, ranging from 13.5 to 21.5 days post-conception. Throughout all gestational ages studied, LIF was constitutively expressed in pulmonary epithelium, whereas LIFRα was first mainly expressed in the mesenchyme, but after pseudoglandular stage it was also observed in epithelial cells. These results point to a LIF epithelium-mesenchyme cross-talk, which is known to be important for lung branching process. Regarding functional studies, fetal lung explants were cultured with increasing doses of LIF or LIF neutralizing antibodies during 4 days. MAPK, AKT, and STAT3 phosphorylation in the treated lung explants was analyzed. LIF supplementation significantly inhibited lung growth in spite of an increase in p44/42 phosphorylation. On the other hand, LIF inhibition significantly stimulated lung growth via p38 and Akt pathways. CONCLUSIONS/SIGNIFICANCE: The present study describes that LIF and its subunit receptor LIFRα are constitutively expressed during fetal lung development and that they have an inhibitory physiological role on fetal lung branching.

  13. High Temperature-Induced Expression of Rice α-Amylases in Developing Endosperm Produces Chalky Grains

    Directory of Open Access Journals (Sweden)

    Masaru Nakata

    2017-12-01

    Full Text Available Global warming impairs grain filling in rice and reduces starch accumulation in the endosperm, leading to chalky-appearing grains, which damages their market value. We found previously that high temperature-induced expression of starch-lytic α-amylases during ripening is crucial for grain chalkiness. Because the rice genome carries at least eight functional α-amylase genes, identification of the α-amylase(s that contribute most strongly to the production of chalky grains could accelerate efficient breeding. To identify α-amylase genes responsible for the production of chalky grains, we characterized the histological expression pattern of eight α-amylase genes and the influences of their overexpression on grain appearance and carbohydrate components through a series of experiments with transgenic rice plants. The promoter activity of most α-amylase genes was elevated to various extents at high temperature. Among them, the expression of Amy1A and Amy3C was induced in the internal, especially basal to dorsal, region of developing endosperm, whereas that of Amy3D was confined near the ventral aleurone. These regions coincided with the site of occurrence of chalkiness, which was in clear contrast to conventionally known expression patterns of the enzyme in the scutellum and aleurone during seed germination. Furthermore, overexpression of α-amylase genes, except for Amy3E, in developing endosperm produced various degrees of chalky grains without heat exposure, whereas that of Amy3E yielded normal translucent grains, as was the case in the vector control, even though Amy3E-overexpressing grains contained enhanced α-amylase activities. The weight of the chalky grains was decreased due to reduced amounts of starch, and microscopic observation of the chalky part of these grains revealed that their endosperm consisted of loosely packed round starch granules that had numerous pits on their surface, confirming the hydrolysis of the starch reserve by

  14. Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos.

    Directory of Open Access Journals (Sweden)

    Amber L Famiglietti

    Full Text Available Mucin-type O-glycosylation is a ubiquitous posttranslational modification in which N-Acetylgalactosamine (GalNAc is added to the hydroxyl group of select serine or threonine residues of a protein by the family of UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferases (GalNAc-Ts; EC 2.4.1.41. Previous studies demonstrate that O-glycosylation plays essential roles in protein function, cell-cell interactions, cell polarity and differentiation in developing mouse and Drosophila embryos. Although this type of protein modification is highly conserved among higher eukaryotes, little is known about this family of enzymes in echinoderms, basal deuterostome relatives of the chordates. To investigate the potential role of GalNAc-Ts in echinoderms, we have begun the characterization of this enzyme family in the purple sea urchin, S. purpuratus. We have fully or partially cloned a total of 13 genes (SpGalnts encoding putative sea urchin SpGalNAc-Ts, and have confirmed enzymatic activity of five recombinant proteins. Amino acid alignments revealed high sequence similarity among sea urchin and mammalian glycosyltransferases, suggesting the presence of putative orthologues. Structural models underscored these similarities and helped reconcile some of the substrate preferences observed. Temporal and spatial expression of SpGalnt transcripts, was studied by whole-mount in situ hybridization. We found that many of these genes are transcribed early in developing embryos, often with restricted expression to the endomesodermal region. Multicolor fluorescent in situ hybridization (FISH demonstrated that transcripts encoding SpGalnt7-2 co-localized with both Endo16 (a gene expressed in the endoderm, and Gcm (a gene expressed in secondary mesenchyme cells at the early blastula stage, 20 hours post fertilization (hpf. At late blastula stage (28 hpf, SpGalnt7-2 message co-expresses with Gcm, suggesting that it may play a role in secondary mesenchyme development. We

  15. Flowering in Xanthium strumarium: INITIATION AND DEVELOPMENT OF FEMALE INFLORESCENCE AND SEX EXPRESSION.

    Science.gov (United States)

    Leonard, M; Kinet, J M; Bodson, M; Havelange, A; Jacqmard, A; Bernier, G

    1981-06-01

    Vegetative plants of Xanthium strumarium L. grown in long days were induced to flower by exposure to one or several 16-hour dark periods. The distribution of male and female inflorescences on the flowering shoot was described, and a scoring system was designed to assess the development of the female inflorescences. The time of movement of the floral stimulus out of the induced leaf and the timing of action of high temperature were shown to be similar for both the apical male and lateral female inflorescences.Strong photoperiodic induction of the plants favored female sex expression, while maleness was enhanced by exogenous gibberellic acid. The problem of the control of sex expression in Xanthium is discussed in relation to the distribution pattern of male and female inflorescences on the flowering shoot and to the state of the meristem at the time of the arrival of the floral stimulus.

  16. Development of new USER-based cloning vectors for multiple genes expression in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Kildegaard, Kanchana Rueksomtawin; Jensen, Niels Bjerg; Maury, Jerome

    2013-01-01

    auxotrophic and dominant markers for convenience of use. Our vector set also contains both integrating and multicopy vectors for stability of protein expression and high expression level. We will make the new vector system available to the yeast community and provide a comprehensive protocol for cloning...... the production strain with the proper phenotype and product yield. However, the sequential number of metabolic engineering is time-consuming. Furthermore, the number of available selectable markers is also limiting the number of genetic modifications. To overcome these limitations, we have developed a new set...... of shuttle vectors for convenience of use for high-throughput cloning and selectable marker recycling. The new USER-based cloning vectors consist of a unique USER site and a CRE-loxP-mediated marker recycling system. The USER site allows insertion of genes of interest along with a bidirectional promoter...

  17. Working memory mediates the effects of gestational age at birth on expressive language development in children.

    Science.gov (United States)

    Riva, Valentina; Cantiani, Chiara; Dionne, Ginette; Marini, Andrea; Mascheretti, Sara; Molteni, Massimo; Marino, Cecilia

    2017-07-01

    This study tested the role of temporary memory, measured by phonological short-term memory (pSTM) and verbal working memory (vWM), as a mediator of the effect of 3 putative risk factors (i.e., socioeconomic status, home literacy environment, birth gestational age) upon expressive and receptive language. A community-based sample of 646 Italian children aged 6-11 years was assessed with a comprehensive battery of language and cognitive tests. A mediation analysis was used to examine whether memory mediates environmental/biological effects on language. The results demonstrated a developmental cascade of effects, whereby the duration of pregnancy drives vWM functioning that, in turn, may affect expressive linguistic outcome Conclusion: Treatments focused on vWM, specifically to preterm children, may improve their language development, with enduring consequences on educational and psychosocial outcomes. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  18. Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival.

    Directory of Open Access Journals (Sweden)

    Maria Teresa Landi

    2008-02-01

    Full Text Available Tobacco smoking is responsible for over 90% of lung cancer cases, and yet the precise molecular alterations induced by smoking in lung that develop into cancer and impact survival have remained obscure.We performed gene expression analysis using HG-U133A Affymetrix chips on 135 fresh frozen tissue samples of adenocarcinoma and paired noninvolved lung tissue from current, former and never smokers, with biochemically validated smoking information. ANOVA analysis adjusted for potential confounders, multiple testing procedure, Gene Set Enrichment Analysis, and GO-functional classification were conducted for gene selection. Results were confirmed in independent adenocarcinoma and non-tumor tissues from two studies. We identified a gene expression signature characteristic of smoking that includes cell cycle genes, particularly those involved in the mitotic spindle formation (e.g., NEK2, TTK, PRC1. Expression of these genes strongly differentiated both smokers from non-smokers in lung tumors and early stage tumor tissue from non-tumor tissue (p1.5, for each comparison, consistent with an important role for this pathway in lung carcinogenesis induced by smoking. These changes persisted many years after smoking cessation. NEK2 (p<0.001 and TTK (p = 0.002 expression in the noninvolved lung tissue was also associated with a 3-fold increased risk of mortality from lung adenocarcinoma in smokers.Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers.

  19. Development and evaluation of the Expressions of Moral Injury Scale-Military Version.

    Science.gov (United States)

    Currier, Joseph M; Farnsworth, Jacob K; Drescher, Kent D; McDermott, Ryon C; Sims, Brook M; Albright, David L

    2018-05-01

    There is consensus that military personnel can encounter a far more diverse set of challenges than researchers and clinicians have historically appreciated. Moral injury (MI) represents an emerging construct to capture behavioural, social, and spiritual suffering that may transcend and overlap with mental health diagnoses (e.g., post-traumatic stress disorder and major depressive disorder). The Expressions of Moral Injury Scale-Military Version (EMIS-M) was developed to provide a reliable and valid means for assessing the warning signs of a MI in military populations. Drawing on independent samples of veterans who had served in a war-zone environment, factor analytic results revealed 2 distinct factors related to MI expressions directed at both self (9 items) and others (8 items). These subscales generated excellent internal consistency and temporal stability over a 6-month period. When compared to measures of post-traumatic stress disorder, major depressive disorder, and other theoretically relevant constructs (e.g., forgiveness, social support, moral emotions, and combat exposure), EMIS-M scores demonstrated strong convergent, divergent, and incremental validity. In addition, although structural equation modelling findings supported a possible general MI factor in Study 2, the patterns of associations for self- and other-directed expressions yielded evidence for differential validity with varying forms of forgiveness and combat exposure. As such, the EMIS-M provides a face valid, psychometrically validated tool for assessing expressions of apparent MI subtypes in research and clinical settings. Looking ahead, the EMIS-M will hopefully advance the scientific understanding of MI while supporting innovation for clinicians to tailor evidence-based treatments and/or develop novel approaches for addressing MI in their work. Copyright © 2017 John Wiley & Sons, Ltd.

  20. The bactericidal agent triclosan modulates thyroid hormone-associated gene expression and disrupts postembryonic anuran development

    International Nuclear Information System (INIS)

    Veldhoen, Nik; Skirrow, Rachel C.; Osachoff, Heather; Wigmore, Heidi; Clapson, David J.; Gunderson, Mark P.; Van Aggelen, Graham; Helbing, Caren C.

    2006-01-01

    We investigated whether exposure to environmentally relevant concentrations of the bactericidal agent, triclosan, induces changes in the thyroid hormone-mediated process of metamorphosis of the North American bullfrog, Rana catesbeiana and alters the expression profile of thyroid hormone receptor (TR) α and β, basic transcription element binding protein (BTEB) and proliferating nuclear cell antigen (PCNA) gene transcripts. Premetamorphic tadpoles were immersed in environmentally relevant concentrations of triclosan and injected with 1 x 10 -11 mol/g body weight 3,5,3'-triiodothyronine (T 3 ) or vehicle control. Morphometric measurements and steady-state mRNA levels obtained by quantitative polymerase chain reaction were determined. mRNA abundance was also examined in Xenopus laevis XTC-2 cells treated with triclosan and/or 10 nM T 3 . Tadpoles pretreated with triclosan concentrations as low as 0.15 ± 0.03 μg/L for 4 days showed increased hindlimb development and a decrease in total body weight following T 3 administration. Triclosan exposure also resulted in decreased T 3 -mediated TRβ mRNA expression in the tadpole tail fin and increased levels of PCNA transcript in the brain within 48 h of T 3 treatment whereas TRα and BTEB were unaffected. Triclosan alone altered thyroid hormone receptor α transcript levels in the brain of premetamorphic tadpoles and induced a transient weight loss. In XTC-2 cells, exposure to T 3 plus nominal concentrations of triclosan as low as 0.03 μg/L for 24 h resulted in altered thyroid hormone receptor mRNA expression. Exposure to low levels of triclosan disrupts thyroid hormone-associated gene expression and can alter the rate of thyroid hormone-mediated postembryonic anuran development

  1. The bactericidal agent triclosan modulates thyroid hormone-associated gene expression and disrupts postembryonic anuran development

    Energy Technology Data Exchange (ETDEWEB)

    Veldhoen, Nik [Department of Biochemistry and Microbiology, P.O. Box 3055, Stn. CSC, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada); Skirrow, Rachel C. [Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2 (Canada); Osachoff, Heather [Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2 (Canada); Wigmore, Heidi [Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2 (Canada); Clapson, David J. [Department of Biochemistry and Microbiology, P.O. Box 3055, Stn. CSC, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada); Gunderson, Mark P. [Department of Biochemistry and Microbiology, P.O. Box 3055, Stn. CSC, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada); Van Aggelen, Graham [Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2 (Canada); Helbing, Caren C. [Department of Biochemistry and Microbiology, P.O. Box 3055, Stn. CSC, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada)]. E-mail: chelbing@uvic.ca

    2006-12-01

    We investigated whether exposure to environmentally relevant concentrations of the bactericidal agent, triclosan, induces changes in the thyroid hormone-mediated process of metamorphosis of the North American bullfrog, Rana catesbeiana and alters the expression profile of thyroid hormone receptor (TR) {alpha} and {beta}, basic transcription element binding protein (BTEB) and proliferating nuclear cell antigen (PCNA) gene transcripts. Premetamorphic tadpoles were immersed in environmentally relevant concentrations of triclosan and injected with 1 x 10{sup -11} mol/g body weight 3,5,3'-triiodothyronine (T{sub 3}) or vehicle control. Morphometric measurements and steady-state mRNA levels obtained by quantitative polymerase chain reaction were determined. mRNA abundance was also examined in Xenopus laevis XTC-2 cells treated with triclosan and/or 10 nM T{sub 3}. Tadpoles pretreated with triclosan concentrations as low as 0.15 {+-} 0.03 {mu}g/L for 4 days showed increased hindlimb development and a decrease in total body weight following T{sub 3} administration. Triclosan exposure also resulted in decreased T{sub 3}-mediated TR{beta} mRNA expression in the tadpole tail fin and increased levels of PCNA transcript in the brain within 48 h of T{sub 3} treatment whereas TR{alpha} and BTEB were unaffected. Triclosan alone altered thyroid hormone receptor {alpha} transcript levels in the brain of premetamorphic tadpoles and induced a transient weight loss. In XTC-2 cells, exposure to T{sub 3} plus nominal concentrations of triclosan as low as 0.03 {mu}g/L for 24 h resulted in altered thyroid hormone receptor mRNA expression. Exposure to low levels of triclosan disrupts thyroid hormone-associated gene expression and can alter the rate of thyroid hormone-mediated postembryonic anuran development.

  2. Identification and expression profiling analysis of TCP family genes involved in growth and development in maize.

    Science.gov (United States)

    Chai, Wenbo; Jiang, Pengfei; Huang, Guoyu; Jiang, Haiyang; Li, Xiaoyu

    2017-10-01

    The TCP family is a group of plant-specific transcription factors. TCP genes encode proteins harboring bHLH structure, which is implicated in DNA binding and protein-protein interactions and known as the TCP domain. TCP genes play important roles in plant development and have been evolutionarily and functionally elaborated in various plants, however, no overall phylogenetic analysis or expression profiling of TCP genes in Zea mays has been reported. In the present study, a systematic analysis of molecular evolution and functional prediction of TCP family genes in maize ( Z . mays L.) has been conducted. We performed a genome-wide survey of TCP genes in maize, revealing the gene structure, chromosomal location and phylogenetic relationship of family members. Microsynteny between grass species and tissue-specific expression profiles were also investigated. In total, 29 TCP genes were identified in the maize genome, unevenly distributed on the 10 maize chromosomes. Additionally, ZmTCP genes were categorized into nine classes based on phylogeny and purifying selection may largely be responsible for maintaining the functions of maize TCP genes. What's more, microsynteny analysis suggested that TCP genes have been conserved during evolution. Finally, expression analysis revealed that most TCP genes are expressed in the stem and ear, which suggests that ZmTCP genes influence stem and ear growth. This result is consistent with the previous finding that maize TCP genes represses the growth of axillary organs and enables the formation of female inflorescences. Altogether, this study presents a thorough overview of TCP family in maize and provides a new perspective on the evolution of this gene family. The results also indicate that TCP family genes may be involved in development stage in plant growing conditions. Additionally, our results will be useful for further functional analysis of the TCP gene family in maize.

  3. The relationship between lifestyle regularity and subjective sleep quality

    Science.gov (United States)

    Monk, Timothy H.; Reynolds, Charles F 3rd; Buysse, Daniel J.; DeGrazia, Jean M.; Kupfer, David J.

    2003-01-01

    In previous work we have developed a diary instrument-the Social Rhythm Metric (SRM), which allows the assessment of lifestyle regularity-and a questionnaire instrument--the Pittsburgh Sleep Quality Index (PSQI), which allows the assessment of subjective sleep quality. The aim of the present study was to explore the relationship between lifestyle regularity and subjective sleep quality. Lifestyle regularity was assessed by both standard (SRM-17) and shortened (SRM-5) metrics; subjective sleep quality was assessed by the PSQI. We hypothesized that high lifestyle regularity would be conducive to better sleep. Both instruments were given to a sample of 100 healthy subjects who were studied as part of a variety of different experiments spanning a 9-yr time frame. Ages ranged from 19 to 49 yr (mean age: 31.2 yr, s.d.: 7.8 yr); there were 48 women and 52 men. SRM scores were derived from a two-week diary. The hypothesis was confirmed. There was a significant (rho = -0.4, p subjects with higher levels of lifestyle regularity reported fewer sleep problems. This relationship was also supported by a categorical analysis, where the proportion of "poor sleepers" was doubled in the "irregular types" group as compared with the "non-irregular types" group. Thus, there appears to be an association between lifestyle regularity and good sleep, though the direction of causality remains to be tested.

  4. Bounded Perturbation Regularization for Linear Least Squares Estimation

    KAUST Repository

    Ballal, Tarig

    2017-10-18

    This paper addresses the problem of selecting the regularization parameter for linear least-squares estimation. We propose a new technique called bounded perturbation regularization (BPR). In the proposed BPR method, a perturbation with a bounded norm is allowed into the linear transformation matrix to improve the singular-value structure. Following this, the problem is formulated as a min-max optimization problem. Next, the min-max problem is converted to an equivalent minimization problem to estimate the unknown vector quantity. The solution of the minimization problem is shown to converge to that of the ℓ2 -regularized least squares problem, with the unknown regularizer related to the norm bound of the introduced perturbation through a nonlinear constraint. A procedure is proposed that combines the constraint equation with the mean squared error (MSE) criterion to develop an approximately optimal regularization parameter selection algorithm. Both direct and indirect applications of the proposed method are considered. Comparisons with different Tikhonov regularization parameter selection methods, as well as with other relevant methods, are carried out. Numerical results demonstrate that the proposed method provides significant improvement over state-of-the-art methods.

  5. Patterns of MADS-box gene expression mark flower-type development in Gerbera hybrida (Asteraceae

    Directory of Open Access Journals (Sweden)

    Teeri Teemu H

    2006-06-01

    Full Text Available Abstract Background The inflorescence of the cut-flower crop Gerbera hybrida (Asteraceae consists of two principal flower types, ray and disc, which form a tightly packed head, or capitulum. Despite great interest in plant morphological evolution and the tractability of the gerbera system, very little is known regarding genetic mechanisms involved in flower type specification. Here, we provide comparative staging of ray and disc flower development and microarray screening for differentially expressed genes, accomplished via microdissection of hundreds of coordinately developing flower primordia. Results Using a 9K gerbera cDNA microarray we identified a number of genes with putative specificity to individual flower types. Intrestingly, several of these encode homologs of MADS-box transcription factors otherwise known to regulate flower organ development. From these and previously obtained data, we hypothesize the functions and protein-protein interactions of several gerbera MADS-box factors. Conclusion Our RNA expression results suggest that flower-type specific MADS protein complexes may play a central role in differential development of ray and disc flowers across the gerbera capitulum, and that some commonality is shared with known protein functions in floral organ determination. These findings support the intriguing conjecture that the gerbera flowering head is more than a mere floral analog at the level of gene regulation.

  6. Involvement of ethylene in sex expression and female flower development in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Manzano, Susana; Martínez, Cecilia; García, Juan Manuel; Megías, Zoraida; Jamilena, Manuel

    2014-12-01

    Although it is known that ethylene has a masculinizing effect on watermelon, the specific role of this hormone in sex expression and flower development has not been analyzed in depth. By using different approaches the present work demonstrates that ethylene regulates differentially two sex-related developmental processes: sexual expression, i.e. the earliness and the number of female flowers per plant, and the development of individual floral buds. Ethylene production in the shoot apex as well as in male, female and bisexual flowers demonstrated that the female flower requires much more ethylene than the male one to develop, and that bisexual flowers result from a decrease in ethylene production in the female floral bud. The occurrence of bisexual flowers was found to be associated with elevated temperatures in the greenhouse, concomitantly with a reduction of ethylene production in the shoot apex. External treatments with ethephon and AVG, and the use of Cucurbita rootstocks with different ethylene production and sensitivity, confirmed that, as occurs in other cucurbit species, ethylene is required to arrest the development of stamens in the female flower. Nevertheless, in watermelon ethylene inhibits the transition from male to female flowering and reduces the number of pistillate flowers per plant, which runs contrary to findings in other cucurbit species. The use of Cucurbita rootstocks with elevated ethylene production delayed the production of female flowers but reduced the number of bisexual flowers, which is associated with a reduced fruit set and altered fruit shape.

  7. Adaptive regularization of noisy linear inverse problems

    DEFF Research Database (Denmark)

    Hansen, Lars Kai; Madsen, Kristoffer Hougaard; Lehn-Schiøler, Tue

    2006-01-01

    In the Bayesian modeling framework there is a close relation between regularization and the prior distribution over parameters. For prior distributions in the exponential family, we show that the optimal hyper-parameter, i.e., the optimal strength of regularization, satisfies a simple relation: T......: The expectation of the regularization function, i.e., takes the same value in the posterior and prior distribution. We present three examples: two simulations, and application in fMRI neuroimaging....

  8. Higher derivative regularization and chiral anomaly

    International Nuclear Information System (INIS)

    Nagahama, Yoshinori.

    1985-02-01

    A higher derivative regularization which automatically leads to the consistent chiral anomaly is analyzed in detail. It explicitly breaks all the local gauge symmetry but preserves global chiral symmetry and leads to the chirally symmetric consistent anomaly. This regularization thus clarifies the physics content contained in the consistent anomaly. We also briefly comment on the application of this higher derivative regularization to massless QED. (author)

  9. Regularity effect in prospective memory during aging

    Directory of Open Access Journals (Sweden)

    Geoffrey Blondelle

    2016-10-01

    Full Text Available Background: Regularity effect can affect performance in prospective memory (PM, but little is known on the cognitive processes linked to this effect. Moreover, its impacts with regard to aging remain unknown. To our knowledge, this study is the first to examine regularity effect in PM in a lifespan perspective, with a sample of young, intermediate, and older adults. Objective and design: Our study examined the regularity effect in PM in three groups of participants: 28 young adults (18–30, 16 intermediate adults (40–55, and 25 older adults (65–80. The task, adapted from the Virtual Week, was designed to manipulate the regularity of the various activities of daily life that were to be recalled (regular repeated activities vs. irregular non-repeated activities. We examine the role of several cognitive functions including certain dimensions of executive functions (planning, inhibition, shifting, and binding, short-term memory, and retrospective episodic memory to identify those involved in PM, according to regularity and age. Results: A mixed-design ANOVA showed a main effect of task regularity and an interaction between age and regularity: an age-related difference in PM performances was found for irregular activities (older < young, but not for regular activities. All participants recalled more regular activities than irregular ones with no age effect. It appeared that recalling of regular activities only involved planning for both intermediate and older adults, while recalling of irregular ones were linked to planning, inhibition, short-term memory, binding, and retrospective episodic memory. Conclusion: Taken together, our data suggest that planning capacities seem to play a major role in remembering to perform intended actions with advancing age. Furthermore, the age-PM-paradox may be attenuated when the experimental design is adapted by implementing a familiar context through the use of activities of daily living. The clinical

  10. Regularity effect in prospective memory during aging

    OpenAIRE

    Blondelle, Geoffrey; Hainselin, Mathieu; Gounden, Yannick; Heurley, Laurent; Voisin, Hélène; Megalakaki, Olga; Bressous, Estelle; Quaglino, Véronique

    2016-01-01

    Background: Regularity effect can affect performance in prospective memory (PM), but little is known on the cognitive processes linked to this effect. Moreover, its impacts with regard to aging remain unknown. To our knowledge, this study is the first to examine regularity effect in PM in a lifespan perspective, with a sample of young, intermediate, and older adults.Objective and design: Our study examined the regularity effect in PM in three groups of participants: 28 young adults (18–30), 1...

  11. Regularization and error assignment to unfolded distributions

    CERN Document Server

    Zech, Gunter

    2011-01-01

    The commonly used approach to present unfolded data only in graphical formwith the diagonal error depending on the regularization strength is unsatisfac-tory. It does not permit the adjustment of parameters of theories, the exclusionof theories that are admitted by the observed data and does not allow the com-bination of data from different experiments. We propose fixing the regulariza-tion strength by a p-value criterion, indicating the experimental uncertaintiesindependent of the regularization and publishing the unfolded data in additionwithout regularization. These considerations are illustrated with three differentunfolding and smoothing approaches applied to a toy example.

  12. Iterative Regularization with Minimum-Residual Methods

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Hansen, Per Christian

    2007-01-01

    subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES their success......We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... as regularization methods is highly problem dependent....

  13. Iterative regularization with minimum-residual methods

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Hansen, Per Christian

    2006-01-01

    subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES - their success......We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... as regularization methods is highly problem dependent....

  14. Development of phytase-expressing chlamydomonas reinhardtii for monogastric animal nutrition.

    Science.gov (United States)

    Erpel, Fernanda; Restovic, Franko; Arce-Johnson, Patricio

    2016-03-12

    In plant-derived animal feedstuffs, nearly 80 % of the total phosphorus content is stored as phytate. However, phytate is poorly digested by monogastric animals such as poultry, swine and fish, as they lack the hydrolytic enzyme phytase; hence it is regarded as a nutritionally inactive compound from a phosphate bioavailability point of view. In addition, it also chelates important dietary minerals and essential amino acids. Therefore, dietary supplementation with bioavailable phosphate and exogenous phytases are required to achieve optimal animal growth. In order to simplify the obtaining and application processes, we developed a phytase expressing cell-wall deficient Chlamydomonas reinhardtii strain. In this work, we developed a transgenic microalgae expressing a fungal phytase to be used as a food supplement for monogastric animals. A codon optimized Aspergillus niger PhyA E228K phytase (mE228K) with improved performance at pH 3.5 was transformed into the plastid genome of Chlamydomonas reinhardtii in order to achieve optimal expression. We engineered a plastid-specific construction harboring the mE228K gene, which allowed us to obtain high expression level lines with measurable in vitro phytase activity. Both wild-type and cell-wall deficient strains were selected, as the latter is a suitable model for animal digestion. The enzymatic activity of the mE228K expressing lines were approximately 5 phytase units per gram of dry biomass at pH 3.5 and 37 °C, similar to physiological conditions and economically competitive for use in commercial activities. A reference basis for the future biotechnological application of microalgae is provided in this work. A cell-wall deficient transgenic microalgae with phytase activity at gastrointestinal pH and temperature and suitable for pellet formation was developed. Moreover, the associated microalgae biomass costs of this strain would be between US$5 and US$60 per ton of feedstuff, similar to the US$2 per ton of feedstuffs

  15. Regularization of Localized Degradation Processes

    National Research Council Canada - National Science Library

    William, Kaspar

    1996-01-01

    .... In this project explicit analytical and geometrical Mohr-type envelope methods were developed to determine discontinuous failure modes in elastoplastic softening and elastic damaging materials...

  16. Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection

    Directory of Open Access Journals (Sweden)

    Liang Xuanqiang

    2008-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is an important crop economically and nutritionally, and is one of the most susceptible host crops to colonization of Aspergillus parasiticus and subsequent aflatoxin contamination. Knowledge from molecular genetic studies could help to devise strategies in alleviating this problem; however, few peanut DNA sequences are available in the public database. In order to understand the molecular basis of host resistance to aflatoxin contamination, a large-scale project was conducted to generate expressed sequence tags (ESTs from developing seeds to identify resistance-related genes involved in defense response against Aspergillus infection and subsequent aflatoxin contamination. Results We constructed six different cDNA libraries derived from developing peanut seeds at three reproduction stages (R5, R6 and R7 from a resistant and a susceptible cultivated peanut genotypes, 'Tifrunner' (susceptible to Aspergillus infection with higher aflatoxin contamination and resistant to TSWV and 'GT-C20' (resistant to Aspergillus with reduced aflatoxin contamination and susceptible to TSWV. The developing peanut seed tissues were challenged by A. parasiticus and drought stress in the field. A total of 24,192 randomly selected cDNA clones from six libraries were sequenced. After removing vector sequences and quality trimming, 21,777 high-quality EST sequences were generated. Sequence clustering and assembling resulted in 8,689 unique EST sequences with 1,741 tentative consensus EST sequences (TCs and 6,948 singleton ESTs. Functional classification was performed according to MIPS functional catalogue criteria. The unique EST sequences were divided into twenty-two categories. A similarity search against the non-redundant protein database available from NCBI indicated that 84.78% of total ESTs showed significant similarity to known proteins, of which 165 genes had been previously reported in peanuts. There were

  17. Development of library preparation method able to correct gene expression levels in rice anther and isolate a trace expression gene mediated in cold-resistance

    International Nuclear Information System (INIS)

    Yamaguchi, Tomoya; Koike, Setsuo

    2000-01-01

    When cDNA library is prepared by a previously developed method, genes of which expression level is high are apt to be cloned at a high frequency, whereas genes of which expression level are low, are difficult to be cloned. A low-expression gene has been cloned at very low frequency. Therefore, the gene encoding the key enzyme that is involved in growth disturbance of rice pollen has not been identified. In this study, development of a library preparing method able to correct the expression level was attempted using highly sensitive detection method with radioisotope and some genes related to cold-resistance of rice were isolated. Double strand DNAs were synthesized using mRNA extract from rice anthers and annealed following heat-denaturation. It has been known that single strand DNA molecules abundantly existing in DNA solution can easily aggregate to form double strand DNA, but single stranded DNA molecules poor in the solution are apt to still remain as single strand after annealing. Thus, the amount of single strand DNA would be balanced in the solution between abundant DNA and poor DNA species. The authors succeeded to prepare a gene library including low and high expression genes at similar proportions. Moreover, spin trap method that allows RI labeling of DNA bound to latex particle, was developed to detect with high sensitivity, especially for genes that are expressed at low level. The present method could be used for recovery, detection and quantitative analysis of radiolabeled single strand DNA. Thus, it was demonstrated that the stage from tetrad sperm to small sperm might be easily affected by cold stress. The present results suggest that the expressions of β-1 and β-3 glucanase, which are involved in the release of small sperms following meiosis in the pollen formation, might be easily affected by cold stress. (M.N.)

  18. Development of library preparation method able to correct gene expression levels in rice anther and isolate a trace expression gene mediated in cold-resistance

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Tomoya; Koike, Setsuo [Tohoku National Agricultural Experiment Station, Morioka (Japan)

    2000-02-01

    When cDNA library is prepared by a previously developed method, genes of which expression level is high are apt to be cloned at a high frequency, whereas genes of which expression level are low, are difficult to be cloned. A low-expression gene has been cloned at very low frequency. Therefore, the gene encoding the key enzyme that is involved in growth disturbance of rice pollen has not been identified. In this study, development of a library preparing method able to correct the expression level was attempted using highly sensitive detection method with radioisotope and some genes related to cold-resistance of rice were isolated. Double strand DNAs were synthesized using mRNA extract from rice anthers and annealed following heat-denaturation. It has been known that single strand DNA molecules abundantly existing in DNA solution can easily aggregate to form double strand DNA, but single stranded DNA molecules poor in the solution are apt to still remain as single strand after annealing. Thus, the amount of single strand DNA would be balanced in the solution between abundant DNA and poor DNA species. The authors succeeded to prepare a gene library including low and high expression genes at similar proportions. Moreover, spin trap method that allows RI labeling of DNA bound to latex particle, was developed to detect with high sensitivity, especially for genes that are expressed at low level. The present method could be used for recovery, detection and quantitative analysis of radiolabeled single strand DNA. Thus, it was demonstrated that the stage from tetrad sperm to small sperm might be easily affected by cold stress. The present results suggest that the expressions of {beta}-1 and {beta}-3 glucanase, which are involved in the release of small sperms following meiosis in the pollen formation, might be easily affected by cold stress. (M.N.)

  19. Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development

    KAUST Repository

    Xu, Wei; Xin, Chengqi; Lin, Qiang; Ding, Feng; Gong, Wei; Zhou, Yuanyuan; Yu, Jun; Cui, Peng; Hu, Songnian

    2014-01-01

    has the most active gene expression, with expression of a large number of regulatory genes up-regulated and some crucial pathways activated. Transcription factor (TF) analysis suggested the similar dynamics as expression profiling, especially those TFs

  20. Transcriptome profiling reveals novel expression markers that predispose patients to develop post- photorefractive keratectomy corneal haze

    Directory of Open Access Journals (Sweden)

    Nimisha Nimisha

    2017-10-01

    Full Text Available Photorefractive keratectomy is an excimer laser [1] based ablation surgery of corneal surface used for correcting refractive errors. Corneal haze is the result of an aggressive wound healing response with an incidence rate [2] of 1.44% post PRK, making it an important health burden. Studies thus far have only focused on molecular alterations post haze development. Since the corneal epithelium is an important mediator of the stromal haze response, we studies its role in predisposing subjects to develop aberrant wound healing response. Corneal epithelium samples collected intra-operatively from clinically healthy patients during PRK. This epithelium from 6 eyes that developed haze postoperatively and 10 eyes of age matched controls without haze were compared. Gene expression microarrays were performed for the mRNA samples followed by ontological analysis of underlying molecular pathways. The identified targets were validated in an independent set of post haze epithelial samples from 3 subjects with PRK induced haze. In vitro studies were done on HCE cells for differential dose of TGFβ for inflammatory markers, corneal structure & fibrosis associated genes and regulators of signal transduction. In addition, loss and gain of function studies was performed using PREX1 as a novel, prototype target. Mean age of groups was 25-28 years. A total of 1100 up and 1700 down regulated genes were revealed by microarray. Alterations in Oxidative stress, ECM-Receptor interactions, Wnt signaling pathway and CXC motif containing chemokines contributes to cellular proliferation and wound healing, which is observed in in vitro model. In cornea novel target PREX1, an oxidative stress gene, when over expressed exhibits faster wound closure in HCE cells with and without TGFβ. Loss of function using PREX1 shRNA shows reduced wound closure. Our study shows that novel genes are involved in pathogenesis of post PRK haze. PREX1 over expression results in faster wound

  1. Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis.

    Science.gov (United States)

    Zhao, Lihua; He, Jiangman; Cai, Hanyang; Lin, Haiyan; Li, Yanqiang; Liu, Renyi; Yang, Zhenbiao; Qin, Yuan

    2014-11-01

    Megasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high-throughput tag-sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild-type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence-assisted cell sorting followed by RNA-seq analysis of DMC1:GFP-labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  2. Process development and economic evaluation of recombinant human lactoferrin expressed in rice grain.

    Science.gov (United States)

    Nandi, Somen; Yalda, Dorice; Lu, Stephen; Nikolov, Zivko; Misaki, Ryo; Fujiyama, Kazuhito; Huang, Ning

    2005-06-01

    In this paper, we show that recombinant human lactoferrin (rhLF) has been stably expressed at 0.5% brown rice flour weight for nine generations. Process development indicates that rhLF can be efficiently extracted from rice flour in 20 mM phosphate buffer (pH 7.0) containing up to 0.5 M NaCl and at a ratio of 1 kg flour to 10 L buffer. After solid/liquid separation, the extract can then be loaded directly onto an ion-exchange column and rhLF can be eluted using 0.8 M NaCl. The resulting rhLF is about 95% pure. A range of biochemical and biophysical analyses were carried out and results indicated that the purified rhLF was identical to its native human counterpart other than its glycosylation. Economic analysis shows that at 600 kg/year scale, the cash cost to produce 1 g of rhLF of pharmaceutical grade is US$ 5.90. Analysis also indicates that the expression level has profound impact on costs related to planting, milling, extraction and purification, thus high level expression of recombinant protein in plants is one of the key parameters for the success of plant made pharmaceuticals.

  3. EBF factors drive expression of multiple classes of target genes governing neuronal development.

    Science.gov (United States)

    Green, Yangsook S; Vetter, Monica L

    2011-04-30

    Early B cell factor (EBF) family members are transcription factors known to have important roles in several aspects of vertebrate neurogenesis, including commitment, migration and differentiation. Knowledge of how EBF family members contribute to neurogenesis is limited by a lack of detailed understanding of genes that are transcriptionally regulated by these factors. We performed a microarray screen in Xenopus animal caps to search for targets of EBF transcriptional activity, and identified candidate targets with multiple roles, including transcription factors of several classes. We determined that, among the most upregulated candidate genes with expected neuronal functions, most require EBF activity for some or all of their expression, and most have overlapping expression with ebf genes. We also found that the candidate target genes that had the most strongly overlapping expression patterns with ebf genes were predicted to be direct transcriptional targets of EBF transcriptional activity. The identification of candidate targets that are transcription factor genes, including nscl-1, emx1 and aml1, improves our understanding of how EBF proteins participate in the hierarchy of transcription control during neuronal development, and suggests novel mechanisms by which EBF activity promotes migration and differentiation. Other candidate targets, including pcdh8 and kcnk5, expand our knowledge of the types of terminal differentiated neuronal functions that EBF proteins regulate.

  4. EBF factors drive expression of multiple classes of target genes governing neuronal development

    Directory of Open Access Journals (Sweden)

    Vetter Monica L

    2011-04-01

    Full Text Available Abstract Background Early B cell factor (EBF family members are transcription factors known to have important roles in several aspects of vertebrate neurogenesis, including commitment, migration and differentiation. Knowledge of how EBF family members contribute to neurogenesis is limited by a lack of detailed understanding of genes that are transcriptionally regulated by these factors. Results We performed a microarray screen in Xenopus animal caps to search for targets of EBF transcriptional activity, and identified candidate targets with multiple roles, including transcription factors of several classes. We determined that, among the most upregulated candidate genes with expected neuronal functions, most require EBF activity for some or all of their expression, and most have overlapping expression with ebf genes. We also found that the candidate target genes that had the most strongly overlapping expression patterns with ebf genes were predicted to be direct transcriptional targets of EBF transcriptional activity. Conclusions The identification of candidate targets that are transcription factor genes, including nscl-1, emx1 and aml1, improves our understanding of how EBF proteins participate in the hierarchy of transcription control during neuronal development, and suggests novel mechanisms by which EBF activity promotes migration and differentiation. Other candidate targets, including pcdh8 and kcnk5, expand our knowledge of the types of terminal differentiated neuronal functions that EBF proteins regulate.

  5. Biological Roles of Aberrantly Expressed Glycosphingolipids and Related Enzymes in Human Cancer Development and Progression

    Directory of Open Access Journals (Sweden)

    Dinghao Zhuo

    2018-05-01

    Full Text Available Glycosphingolipids (GSLs, which consist of a hydrophobic ceramide backbone and a hydrophilic carbohydrate residue, are an important type of glycolipid expressed in surface membranes of all animal cells. GSLs play essential roles in maintenance of plasma membrane stability, in regulation of numerous cellular processes (including adhesion, proliferation, apoptosis, and recognition, and in modulation of signal transduction pathways. GSLs have traditionally been classified as ganglio-series, lacto-series, or globo-series on the basis of their diverse types of oligosaccharide chains. Structures and functions of specific GSLs are also determined by their oligosaccharide chains. Different cells and tissues show differential expression of GSLs, and changes in structures of GSL glycan moieties occur during development of numerous types of human cancer. Association of GSLs and/or related enzymes with initiation and progression of cancer has been documented in 100s of studies, and many such GSLs are useful markers or targets for cancer diagnosis or therapy. In this review, we summarize (i recent studies on aberrant expression and distribution of GSLs in common human cancers (breast, lung, colorectal, melanoma, prostate, ovarian, leukemia, renal, bladder, gastric; (ii biological functions of specific GSLs in these cancers.

  6. Coordination of gene expression of arachidonic and docosahexaenoic acid cascade enzymes during human brain development and aging.

    Science.gov (United States)

    Ryan, Veronica H; Primiani, Christopher T; Rao, Jagadeesh S; Ahn, Kwangmi; Rapoport, Stanley I; Blanchard, Helene

    2014-01-01

    The polyunsaturated arachidonic and docosahexaenoic acids (AA and DHA) participate in cell membrane synthesis during neurodevelopment, neuroplasticity, and neurotransmission throughout life. Each is metabolized via coupled enzymatic reactions within separate but interacting metabolic cascades. AA and DHA pathway genes are coordinately expressed and underlie cascade interactions during human brain development and aging. The BrainCloud database for human non-pathological prefrontal cortex gene expression was used to quantify postnatal age changes in mRNA expression of 34 genes involved in AA and DHA metabolism. Expression patterns were split into Development (0 to 20 years) and Aging (21 to 78 years) intervals. Expression of genes for cytosolic phospholipases A2 (cPLA2), cyclooxygenases (COX)-1 and -2, and other AA cascade enzymes, correlated closely with age during Development, less so during Aging. Expression of DHA cascade enzymes was less inter-correlated in each period, but often changed in the opposite direction to expression of AA cascade genes. Except for the PLA2G4A (cPLA2 IVA) and PTGS2 (COX-2) genes at 1q25, highly inter-correlated genes were at distant chromosomal loci. Coordinated age-related gene expression during the brain Development and Aging intervals likely underlies coupled changes in enzymes of the AA and DHA cascades and largely occur through distant transcriptional regulation. Healthy brain aging does not show upregulation of PLA2G4 or PTGS2 expression, which was found in Alzheimer's disease.

  7. Coordination of gene expression of arachidonic and docosahexaenoic acid cascade enzymes during human brain development and aging.

    Directory of Open Access Journals (Sweden)

    Veronica H Ryan

    Full Text Available The polyunsaturated arachidonic and docosahexaenoic acids (AA and DHA participate in cell membrane synthesis during neurodevelopment, neuroplasticity, and neurotransmission throughout life. Each is metabolized via coupled enzymatic reactions within separate but interacting metabolic cascades.AA and DHA pathway genes are coordinately expressed and underlie cascade interactions during human brain development and aging.The BrainCloud database for human non-pathological prefrontal cortex gene expression was used to quantify postnatal age changes in mRNA expression of 34 genes involved in AA and DHA metabolism.Expression patterns were split into Development (0 to 20 years and Aging (21 to 78 years intervals. Expression of genes for cytosolic phospholipases A2 (cPLA2, cyclooxygenases (COX-1 and -2, and other AA cascade enzymes, correlated closely with age during Development, less so during Aging. Expression of DHA cascade enzymes was less inter-correlated in each period, but often changed in the opposite direction to expression of AA cascade genes. Except for the PLA2G4A (cPLA2 IVA and PTGS2 (COX-2 genes at 1q25, highly inter-correlated genes were at distant chromosomal loci.Coordinated age-related gene expression during the brain Development and Aging intervals likely underlies coupled changes in enzymes of the AA and DHA cascades and largely occur through distant transcriptional regulation. Healthy brain aging does not show upregulation of PLA2G4 or PTGS2 expression, which was found in Alzheimer's disease.

  8. Differential gene expression patterns during embryonic development of sea urchin exposed to triclosan.

    Science.gov (United States)

    Hwang, Jinik; Suh, Sung-Suk; Park, Mirye; Park, So Yun; Lee, Sukchan; Lee, Taek-Kyun

    2017-02-01

    Triclosan (TCS; 2,4,4'-trichloro-2'-hydroxydiphenyl ether) is a broad-spectrum antibacterial agent used in common industrial, personal care and household products which are eventually rinsed down the drain and discharged with wastewater effluent. It is therefore commonly found in the aquatic environment, leading to the continual exposure of aquatic organisms to TCS and the accumulation of the antimicrobial and its harmful degradation products in their bodies. Toxic effects of TCS on reproductive and developmental progression of some aquatic organisms have been suggested but the underlying molecular mechanisms have not been defined. We investigated the expression patterns of genes involved in the early development of TCS-treated sea urchin Strongylocentrotus nudus using cDNA microarrays. We observed that the predominant consequence of TCS treatment in this model system was the widespread repression of TCS-modulated genes. In particular, empty spiracles homeobox 1 (EMX-1), bone morphogenic protein, and chromosomal binding protein genes showed a significant decrease in expression in response to TCS. These results suggest that TCS can induce abnormal development of sea urchin embryos through the concomitant suppression of a number of genes that are necessary for embryonic differentiation in the blastula stage. Our data provide new insight into the crucial role of genes associated with embryonic development in response to TCS. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 426-433, 2017. © 2016 Wiley Periodicals, Inc.

  9. Gene expression analysis after low dose ionising radiation exposure of the developing organism

    International Nuclear Information System (INIS)

    Abderrafi Benotmane, M.

    2007-01-01

    Measuring gene expression using microarrays is relevant to many areas of biology and medicine, such as follow up of developmental stages and diseases onset, and treatment study. Since there can be tens of thousands of distinct probes on an array, each micro array experiment can accomplish the equivalent number of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations. For example, microarrays can be used to identify stress response genes by comparing gene expression in challenged versus normal cells. In the Molecular and Cellular Biology lab (MCB), the micro array experiments are performed within the Genomic Platform, fully equipped to analyse either the behaviour of bacteria during long space flight, the effect of low dose ionising radiation on the developing organism in mice, or the human individual radiation sensitivity. For the low dose effect, two main stages of development are of interest; 1) the gastrula stage at which ionizing radiation can induce several malformations. 2) the organogenesis. During brain development, epidemiological studies of the atomic bomb survivors of Hiroshima/Nagasaki showed increased risk of mental retardation in children of women exposed between weeks 8-15 of pregnancy or at a lower extend between weeks 15 to 25

  10. Spatio-temporal expression patterns of Wnt signaling pathway during the development of temporomandibular condylar cartilage.

    Science.gov (United States)

    Chen, Kan; Quan, Huixin; Chen, Gang; Xiao, Di

    2017-11-01

    There is a growing body of evidence supporting the involvement of the Wnt signaling pathway in various aspects of skeletal and joint development; however, it is unclear whether it is involved in the process of temporomandibular joint development. In order to clarify this issue, we examined the spatio-temporal distribution of mRNAs and proteins of the Wnt family during the formation of the mandibular condylar cartilage at the prenatal and postnatal stages. An in situ hybridization test revealed no mRNAs of β-catenin and Axin2 during early mesenchymal condensation; the ligands surveyed in this study (including Wnt-4, 5a, and 9a) were clearly detected at various ranges of expression, mainly in the condylar blastema and later distinct cartilaginous layers. Apart from β-catenin and Axin2, the Wnt family members surveyed in this study, including Lef-1, were found to be immunopositive during early chondrogenesis in the condylar cartilage at E14.5. After distinct chondrocyte layers were identified within the cartilage at E16.5, the expression of the Wnt signaling members was different and mainly restricted to proliferating cells and mineralized hypertrophic chondrocytes. In the adult mandibular condylar cartilage, the Wnt-4 mRNA, as well as the Wnt-4 and Wnt-9a proteins, was not observed. Our findings demonstrated that the Wnt signaling pathway was associated with the development of mandibular condylar cartilage. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Protein Expression Landscape of Mouse Embryos during Pre-implantation Development

    Directory of Open Access Journals (Sweden)

    Yawei Gao

    2017-12-01

    Full Text Available Pre-implantation embryo development is an intricate and precisely regulated process orchestrated by maternally inherited proteins and newly synthesized proteins following zygotic genome activation. Although genomic and transcriptomic studies have enriched our understanding of the genetic programs underlying this process, the protein expression landscape remains unexplored. Using quantitative mass spectrometry, we identified nearly 5,000 proteins from 8,000 mouse embryos of each stage (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst. We found that protein expression in zygotes, morulas, and blastocysts is distinct from 2- to 8-cell embryos. Analysis of protein phosphorylation identified critical kinases and signal transduction pathways. We highlight key factors and their important roles in embryo development. Combined analysis of transcriptomic and proteomic data reveals coordinated control of RNA degradation, transcription, and translation and identifies previously undefined exon-junction-derived peptides. Our study provides an invaluable resource for further mechanistic studies and suggests core factors regulating pre-implantation embryo development.

  12. Stage-specific gene expression during sexual development in Phytophthora infestans

    DEFF Research Database (Denmark)

    Fabritius, Anna-Liisa; Cvitanich, Cristina; Judelson, Howard S.

    2002-01-01

    Eight genes that are upregulated during sexual development in the heterothallic oomycete, Phytophthora infestans, were identified by suppression subtractive hybridization. Two genes showed very low but detectable expression in vegetative hyphae and became induced about 40- to >100-fold early...... revealed that the predicted products of three of the genes had similarity to proteins that influence RNA stability, namely a ribonuclease activator, the pumilio family of RNA-binding proteins and RNase H. The products of two other mating-induced genes resembled two types of Phytophthora proteins previously...

  13. Dimensional regularization in position space and a forest formula for regularized Epstein-Glaser renormalization

    International Nuclear Information System (INIS)

    Keller, Kai Johannes

    2010-04-01

    The present work contains a consistent formulation of the methods of dimensional regularization (DimReg) and minimal subtraction (MS) in Minkowski position space. The methods are implemented into the framework of perturbative Algebraic Quantum Field Theory (pAQFT). The developed methods are used to solve the Epstein-Glaser recursion for the construction of time-ordered products in all orders of causal perturbation theory. A solution is given in terms of a forest formula in the sense of Zimmermann. A relation to the alternative approach to renormalization theory using Hopf algebras is established. (orig.)

  14. Dimensional regularization in position space and a forest formula for regularized Epstein-Glaser renormalization

    Energy Technology Data Exchange (ETDEWEB)

    Keller, Kai Johannes

    2010-04-15

    The present work contains a consistent formulation of the methods of dimensional regularization (DimReg) and minimal subtraction (MS) in Minkowski position space. The methods are implemented into the framework of perturbative Algebraic Quantum Field Theory (pAQFT). The developed methods are used to solve the Epstein-Glaser recursion for the construction of time-ordered products in all orders of causal perturbation theory. A solution is given in terms of a forest formula in the sense of Zimmermann. A relation to the alternative approach to renormalization theory using Hopf algebras is established. (orig.)

  15. Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene.

    Directory of Open Access Journals (Sweden)

    Shivani Nayyar

    Full Text Available Sugarcane (Saccharum spp. is a commercially important crop, vulnerable to fungal disease red rot caused by Colletotrichum falcatum Went. The pathogen attacks sucrose accumulating parenchyma cells of cane stalk leading to severe losses in cane yield and sugar recovery. We report development of red rot resistant transgenic sugarcane through expression of β-1,3-glucanase gene from Trichoderma spp. The transgene integration and its expression were confirmed by quantitative reverse transcription-PCR in first clonal generation raised from T0 plants revealing up to 4.4-fold higher expression, in comparison to non-transgenic sugarcane. Bioassay of transgenic plants with two virulent C. falcatum pathotypes, Cf 08 and Cf 09 causing red rot disease demonstrated that some plants were resistant to Cf 08 and moderately resistant to Cf 09. The electron micrographs of sucrose storing stalk parenchyma cells from these plants displayed characteristic sucrose-filled cells inhibiting Cf 08 hyphae and lysis of Cf 09 hyphae; in contrast, the cells of susceptible plants were sucrose depleted and prone to both the pathotypes. The transgene expression was up-regulated (up to 2.0-fold in leaves and 5.0-fold in roots after infection, as compared to before infection in resistant plants. The transgene was successfully transmitted to second clonal generation raised from resistant transgenic plants. β-1,3-glucanase protein structural model revealed that active sites Glutamate 628 and Aspartate 569 of the catalytic domain acted as proton donor and nucleophile having role in cleaving β-1,3-glycosidic bonds and pathogen hyphal lysis.

  16. Distinct GAGE and MAGE-A expression during early human development indicate specific roles in lineage differentiation

    DEFF Research Database (Denmark)

    Gjerstorff, Morten; Harkness, Linda; Kassem, Moustapha

    2008-01-01

    BACKGROUND: Expression of cancer/testis-associated proteins (CTAs) has traditionally been considered to be restricted to germ cells in normal tissues and to different types of malignancies. We have evaluated the potential role of CTAs in early human development. METHODS: Using immunohistochemistry...... and RT-PCR, we investigated the expression of CTAs in differentiated human embryonic stem cells (hESC) and in late embryos and early fetuses. RESULTS: We found that melanoma antigen A (MAGE-A) family members were expressed during differentiation of hESC to embryoid bodies and in teratomas, and overlapped...... with expression of the neuroectodermal markers beta-tubulin 3, Pax6 and nestin. A widespread expression of MAGE-A was also observed in neurons of the early developing central nervous system and peripheral nerves. G antigen (GAGE) expression was present in the early ectoderm of embryos, including cells...

  17. Discriminative Elastic-Net Regularized Linear Regression.

    Science.gov (United States)

    Zhang, Zheng; Lai, Zhihui; Xu, Yong; Shao, Ling; Wu, Jian; Xie, Guo-Sen

    2017-03-01

    In this paper, we aim at learning compact and discriminative linear regression models. Linear regression has been widely used in different problems. However, most of the existing linear regression methods exploit the conventional zero-one matrix as the regression targets, which greatly narrows the flexibility of the regression model. Another major limitation of these methods is that the learned projection matrix fails to precisely project the image features to the target space due to their weak discriminative capability. To this end, we present an elastic-net regularized linear regression (ENLR) framework, and develop two robust linear regression models which possess the following special characteristics. First, our methods exploit two particular strategies to enlarge the margins of different classes by relaxing the strict binary targets into a more feasible variable matrix. Second, a robust elastic-net regularization of singular values is introduced to enhance the compactness and effectiveness of the learned projection matrix. Third, the resulting optimization problem of ENLR has a closed-form solution in each iteration, which can be solved efficiently. Finally, rather than directly exploiting the projection matrix for recognition, our methods employ the transformed features as the new discriminate representations to make final image classification. Compared with the traditional linear regression model and some of its variants, our method is much more accurate in image classification. Extensive experiments conducted on publicly available data sets well demonstrate that the proposed framework can outperform the state-of-the-art methods. The MATLAB codes of our methods can be available at http://www.yongxu.org/lunwen.html.

  18. Novel Harmonic Regularization Approach for Variable Selection in Cox’s Proportional Hazards Model

    Directory of Open Access Journals (Sweden)

    Ge-Jin Chu

    2014-01-01

    Full Text Available Variable selection is an important issue in regression and a number of variable selection methods have been proposed involving nonconvex penalty functions. In this paper, we investigate a novel harmonic regularization method, which can approximate nonconvex Lq  (1/2regularizations, to select key risk factors in the Cox’s proportional hazards model using microarray gene expression data. The harmonic regularization method can be efficiently solved using our proposed direct path seeking approach, which can produce solutions that closely approximate those for the convex loss function and the nonconvex regularization. Simulation results based on the artificial datasets and four real microarray gene expression datasets, such as real diffuse large B-cell lymphoma (DCBCL, the lung cancer, and the AML datasets, show that the harmonic regularization method can be more accurate for variable selection than existing Lasso series methods.

  19. Regularized lattice Boltzmann model for immiscible two-phase flows with power-law rheology

    Science.gov (United States)

    Ba, Yan; Wang, Ningning; Liu, Haihu; Li, Qiang; He, Guoqiang

    2018-03-01

    In this work, a regularized lattice Boltzmann color-gradient model is developed for the simulation of immiscible two-phase flows with power-law rheology. This model is as simple as the Bhatnagar-Gross-Krook (BGK) color-gradient model except that an additional regularization step is introduced prior to the collision step. In the regularization step, the pseudo-inverse method is adopted as an alternative solution for the nonequilibrium part of the total distribution function, and it can be easily extended to other discrete velocity models no matter whether a forcing term is considered or not. The obtained expressions for the nonequilibrium part are merely related to macroscopic variables and velocity gradients that can be evaluated locally. Several numerical examples, including the single-phase and two-phase layered power-law fluid flows between two parallel plates, and the droplet deformation and breakup in a simple shear flow, are conducted to test the capability and accuracy of the proposed color-gradient model. Results show that the present model is more stable and accurate than the BGK color-gradient model for power-law fluids with a wide range of power-law indices. Compared to its multiple-relaxation-time counterpart, the present model can increase the computing efficiency by around 15%, while keeping the same accuracy and stability. Also, the present model is found to be capable of reasonably predicting the critical capillary number of droplet breakup.

  20. Material parameters characterization for arbitrary N-sided regular polygonal invisible cloak

    International Nuclear Information System (INIS)

    Wu Qun; Zhang Kuang; Meng Fanyi; Li Lewei

    2009-01-01

    Arbitrary N-sided regular polygonal cylindrical cloaks are proposed and designed based on the coordinate transformation theory. First, the general expressions of constitutive tensors of the N-sided regular polygonal cylindrical cloaks are derived, then there are some full-wave simulations of the cloaks that are composed of inhomogeneous and anisotropic metamaterials, which will bend incoming electromagnetic waves and guide them to propagate around the inner region; such electromagnetic waves will return to their original propagation directions without distorting the waves outside the polygonal cloak. The results of full-wave simulations validate the general expressions of constitutive tensors of the N-sided regular polygonal cylindrical cloaks we derived.

  1. Dynamics of coherent states in regular and chaotic regimes of the non-integrable Dicke model

    Science.gov (United States)

    Lerma-Hernández, S.; Chávez-Carlos, J.; Bastarrachea-Magnani, M. A.; López-del-Carpio, B.; Hirsch, J. G.

    2018-04-01

    The quantum dynamics of initial coherent states is studied in the Dicke model and correlated with the dynamics, regular or chaotic, of their classical limit. Analytical expressions for the survival probability, i.e. the probability of finding the system in its initial state at time t, are provided in the regular regions of the model. The results for regular regimes are compared with those of the chaotic ones. It is found that initial coherent states in regular regions have a much longer equilibration time than those located in chaotic regions. The properties of the distributions for the initial coherent states in the Hamiltonian eigenbasis are also studied. It is found that for regular states the components with no negligible contribution are organized in sequences of energy levels distributed according to Gaussian functions. In the case of chaotic coherent states, the energy components do not have a simple structure and the number of participating energy levels is larger than in the regular cases.

  2. Nutritionally driven differential gene expression leads to heterochronic brain development in honeybee castes.

    Directory of Open Access Journals (Sweden)

    Lívia Maria Moda

    Full Text Available The differential feeding regimes experienced by the queen and worker larvae of the honeybee Apis mellifera shape a complex endocrine response cascade that ultimately gives rise to differences in brain morphologies. Brain development analyzed at the morphological level from the third (L3 through fifth (L5 larval instars revealed an asynchrony between queens and workers. In the feeding phase of the last larval instar (L5F, two well-formed structures, pedunculi and calyces, are identifiable in the mushroom bodies of queens, both of which are not present in workers until a later phase (spinning phase, L5S. Genome-wide expression analyses and normalized transcript expression experiments monitoring specific genes revealed that this differential brain development starts earlier, during L3. Analyzing brains from L3 through L5S1 larvae, we identified 21 genes with caste-specific transcription patterns (e.g., APC-4, GlcAT-P, fax, kr-h1 and shot, which encode proteins that are potentially involved in the development of brain tissues through controlling the cell proliferation rate (APC4, kr-h1 and fasciculation (GlcAT-P, fax, and shot. Shot, whose expression is known to be required for axon extension and cell proliferation, was found to be transcribed at significantly higher levels in L4 queens compared with worker larvae. Moreover, the protein encoded by this gene was immunolocalized to the cytoplasm of cells near the antennal lobe neuropiles and proximal to the Kenyon cells in the brains of L4 queens. In conclusion, during the larval period, the brains of queens are larger and develop more rapidly than workers' brains, which represents a developmental heterochrony reflecting the effect of the differential feeding regime of the two castes on nervous system development. Furthermore, this differential development is characterized by caste-specific transcriptional profiles of a set of genes, thus pointing to a link between differential nutrition and

  3. Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn.

    Directory of Open Access Journals (Sweden)

    Huifeng Zhang

    2016-10-01

    Full Text Available Tropical evergreen perennials undergo recurrent flush growth, and their terminal buds alternate between growth and dormancy. In sharp contrast to intensive studies on bud development in temperate deciduous trees, there is little information about bud development regulation in tropical trees. In this study, litchi (Litchi chinensis Sonn. was used as a model tropical perennial for morphological characterization and transcriptomic analysis of bud development. Litchi buds are naked with apical meristem embraced by rudimentary leaves, which are brown at dormant stage (Stage I. They swell and turn greenish as buds break (Stage II, and as growth accelerates, the rudimentary leaves elongate and open exposing the inner leaf primodia. With the outgrowth of the needle-like leaflets, bud growth reaches a maximum (Stage III. When leaflets expand, bud growth cease with the abortion of the rudimentary leaves at upper positions (Stage IV. Then buds turn brown and reenter dormant status. Budbreak occurs again when new leaves become hard green. Buds at four stages (Stage I to IV were collected for respiration measurements and in-depth RNA sequencing. Respiration rate was lowest at Stage I and highest at Stage II, decreasing towards growth cessation. RNA sequencing obtained over 5 Gb data from each of the bud samples and de novo assembly generated a total of 59999 unigenes, 40119 of which were annotated. Pair-wise comparison of gene expression between stages, gene profiling across stages, GO/KEGG enrichment analysis, and the expression patterns of 17 major genes highlighted by principal component (PC analysis displayed significant changes in stress resistance, hormone signal pathways, circadian rhythm, photosynthesis, cell division, carbohydrate metabolism, programmed cell death during bud development, which might be under epigenetic control involving chromatin methylation. The qPCR results of 8 selected unigenes with high PC scores agreed with the RPKM values

  4. Nutritionally driven differential gene expression leads to heterochronic brain development in honeybee castes.

    Science.gov (United States)

    Moda, Lívia Maria; Vieira, Joseana; Guimarães Freire, Anna Cláudia; Bonatti, Vanessa; Bomtorin, Ana Durvalina; Barchuk, Angel Roberto; Simões, Zilá Luz Paulino

    2013-01-01

    The differential feeding regimes experienced by the queen and worker larvae of the honeybee Apis mellifera shape a complex endocrine response cascade that ultimately gives rise to differences in brain morphologies. Brain development analyzed at the morphological level from the third (L3) through fifth (L5) larval instars revealed an asynchrony between queens and workers. In the feeding phase of the last larval instar (L5F), two well-formed structures, pedunculi and calyces, are identifiable in the mushroom bodies of queens, both of which are not present in workers until a later phase (spinning phase, L5S). Genome-wide expression analyses and normalized transcript expression experiments monitoring specific genes revealed that this differential brain development starts earlier, during L3. Analyzing brains from L3 through L5S1 larvae, we identified 21 genes with caste-specific transcription patterns (e.g., APC-4, GlcAT-P, fax, kr-h1 and shot), which encode proteins that are potentially involved in the development of brain tissues through controlling the cell proliferation rate (APC4, kr-h1) and fasciculation (GlcAT-P, fax, and shot). Shot, whose expression is known to be required for axon extension and cell proliferation, was found to be transcribed at significantly higher levels in L4 queens compared with worker larvae. Moreover, the protein encoded by this gene was immunolocalized to the cytoplasm of cells near the antennal lobe neuropiles and proximal to the Kenyon cells in the brains of L4 queens. In conclusion, during the larval period, the brains of queens are larger and develop more rapidly than workers' brains, which represents a developmental heterochrony reflecting the effect of the differential feeding regime of the two castes on nervous system development. Furthermore, this differential development is characterized by caste-specific transcriptional profiles of a set of genes, thus pointing to a link between differential nutrition and differential

  5. A regularized stationary mean-field game

    KAUST Repository

    Yang, Xianjin

    2016-01-01

    In the thesis, we discuss the existence and numerical approximations of solutions of a regularized mean-field game with a low-order regularization. In the first part, we prove a priori estimates and use the continuation method to obtain the existence of a solution with a positive density. Finally, we introduce the monotone flow method and solve the system numerically.

  6. A regularized stationary mean-field game

    KAUST Repository

    Yang, Xianjin

    2016-04-19

    In the thesis, we discuss the existence and numerical approximations of solutions of a regularized mean-field game with a low-order regularization. In the first part, we prove a priori estimates and use the continuation method to obtain the existence of a solution with a positive density. Finally, we introduce the monotone flow method and solve the system numerically.

  7. On infinite regular and chiral maps

    OpenAIRE

    Arredondo, John A.; Valdez, Camilo Ramírez y Ferrán

    2015-01-01

    We prove that infinite regular and chiral maps take place on surfaces with at most one end. Moreover, we prove that an infinite regular or chiral map on an orientable surface with genus can only be realized on the Loch Ness monster, that is, the topological surface of infinite genus with one end.

  8. From recreational to regular drug use

    DEFF Research Database (Denmark)

    Järvinen, Margaretha; Ravn, Signe

    2011-01-01

    This article analyses the process of going from recreational use to regular and problematic use of illegal drugs. We present a model containing six career contingencies relevant for young people’s progress from recreational to regular drug use: the closing of social networks, changes in forms...

  9. Regularization modeling for large-eddy simulation

    NARCIS (Netherlands)

    Geurts, Bernardus J.; Holm, D.D.

    2003-01-01

    A new modeling approach for large-eddy simulation (LES) is obtained by combining a "regularization principle" with an explicit filter and its inversion. This regularization approach allows a systematic derivation of the implied subgrid model, which resolves the closure problem. The central role of

  10. 29 CFR 779.18 - Regular rate.

    Science.gov (United States)

    2010-07-01

    ... employee under subsection (a) or in excess of the employee's normal working hours or regular working hours... Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR STATEMENTS OF GENERAL POLICY OR... not less than one and one-half times their regular rates of pay. Section 7(e) of the Act defines...

  11. Breast ultrasound tomography with total-variation regularization

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Lianjie [Los Alamos National Laboratory; Li, Cuiping [KARMANOS CANCER INSTIT.; Duric, Neb [KARMANOS CANCER INSTIT

    2009-01-01

    Breast ultrasound tomography is a rapidly developing imaging modality that has the potential to impact breast cancer screening and diagnosis. A new ultrasound breast imaging device (CURE) with a ring array of transducers has been designed and built at Karmanos Cancer Institute, which acquires both reflection and transmission ultrasound signals. To extract the sound-speed information from the breast data acquired by CURE, we have developed an iterative sound-speed image reconstruction algorithm for breast ultrasound transmission tomography based on total-variation (TV) minimization. We investigate applicability of the TV tomography algorithm using in vivo ultrasound breast data from 61 patients, and compare the results with those obtained using the Tikhonov regularization method. We demonstrate that, compared to the Tikhonov regularization scheme, the TV regularization method significantly improves image quality, resulting in sound-speed tomography images with sharp (preserved) edges of abnormalities and few artifacts.

  12. Plant expression systems, a budding way to confront chikungunya and Zika in developing countries? [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Jaime A. Cardona-Ospina

    2016-08-01

    Full Text Available Plant expression systems could be used as biofactories of heterologous proteins that have the potential to be used with biopharmaceutical aims and vaccine design. This technology is scalable, safe and cost-effective and it has been previously proposed as an option for vaccine and protein pharmaceutical development in developing countries. Here we present a proposal of how plant expression systems could be used to address Zika and chikungunya outbreaks through development of vaccines and rapid diagnostic kits.

  13. Development of heart failure is independent of K+ channel-interacting protein 2 expression

    Science.gov (United States)

    Speerschneider, Tobias; Grubb, Søren; Metoska, Artina; Olesen, Søren-Peter; Calloe, Kirstine; Thomsen, Morten B

    2013-01-01

    Abnormal ventricular repolarization in ion channelopathies and heart disease is a major cause of ventricular arrhythmias and sudden cardiac death. K+ channel-interacting protein 2 (KChIP2) expression is significantly reduced in human heart failure (HF), contributing to a loss of the transient outward K+ current (Ito). We aim to investigate the possible significance of a changed KChIP2 expression on the development of HF and proarrhythmia. Transverse aortic constrictions (TAC) and sham operations were performed in wild-type (WT) and KChIP2−/− mice. Echocardiography was performed before and every 2 weeks after the operation. Ten weeks post-surgery, surface ECG was recorded and we paced the heart in vivo to induce arrhythmias. Afterwards, tissue from the left ventricle was used for immunoblotting. Time courses of HF development were comparable in TAC-operated WT and KChIP2−/− mice. Ventricular protein expression of KChIP2 was reduced by 70% after 10 weeks TAC in WT mice. The amplitudes of the J and T waves were enlarged in KChIP2−/− control mice. Ventricular effective refractory period, RR, QRS and QT intervals were longer in mice with HF compared to sham-operated mice of either genotype. Pacing-induced ventricular tachycardia (VT) was observed in 5/10 sham-operated WT mice compared with 2/10 HF WT mice with HF. Interestingly, and contrary to previously published data, sham-operated KChIP2−/− mice were resistant to pacing-induced VT resulting in only 1/10 inducible mice. KChIP2−/− with HF mice had similar low vulnerability to inducible VT (1/9). Our results suggest that although KChIP2 is downregulated in HF, it is not orchestrating the development of HF. Moreover, KChIP2 affects ventricular repolarization and lowers arrhythmia susceptibility. Hence, downregulation of KChIP2 expression in HF may be antiarrhythmic in mice via reduction of the fast transient outward K+ current. PMID:24099801

  14. Pod-1/Capsulin shows a sex- and stage-dependent expression pattern in the mouse gonad development and represses expression of Ad4BP/SF-1.

    Science.gov (United States)

    Tamura, M; Kanno, Y; Chuma, S; Saito, T; Nakatsuji, N

    2001-04-01

    Mammalian sex-determination and differentiation are controlled by several genes, such as Sry, Sox-9, Dax-1 and Mullerian inhibiting substance (MIS), but their upstream and downstream genes are largely unknown. Ad4BP/SF-1, encoding a zinc finger transcription factor, plays important roles in gonadogenesis. Disruption of this gene caused disappearance of the urogenital system including the gonad. Ad4BP/SF-1, however, is also involved in the sex differentiation of the gonad at later stages, such as the regulation of steroid hormones and MIS. Pod-1/Capsulin, a member of basic helix-loop-helix transcription factors, is expressed in a pattern closely related but mostly complimentary to that of the Ad4BP/SF-1 expression in the developing gonad. In the co-transfection experiment using cultured cells, overexpression of Pod-1/Capsulin repressed expression of a reporter gene that carried the upstream regulatory region of the Ad4BP/SF-1 gene. Furthermore, forced expression of Pod-1/Capsulin repressed expression of Ad4BP/SF-1 in the Leydig cell-derived I-10 cells. These results suggest that Pod-1/Capsulin may play important roles in the development and sex differentiation of the mammalian gonad via transcriptional regulation of Ad4BP/SF-1.

  15. Detailed analysis of the δ-crystallin mRNA-expressing region in early development of the chick pituitary gland.

    Science.gov (United States)

    Inoue, Makiko; Shiina, Tomoya; Aizawa, Sayaka; Sakata, Ichiro; Takagi, Hiroyasu; Sakai, Takafumi

    2012-06-01

    Although δ-crystallin (δ-crys), also known as lens protein, is transiently expressed in Rathke's pouch (RP) of the chick embryo, detailed temporal and spatial expression patterns have been obscure. In this study, to understand the relationship between the δ-crys mRNA-expressing region and RP formation, we examined the embryonic expression pattern of δ-crys mRNA in the primordium of the adenohypophysis. δ-crys mRNA expression was initially found at stage 15 anterior to the foregut and posterior to the invaginated oral ectoderm. After RP formation, the δ-crys mRNA was expressed in the post-ventral region of RP and the anterior region of RP. δ-crys mRNA expression was then restricted to the cephalic lobe of the pituitary gland. From stage 20, the δ-crys and alpha-glycoprotein subunit (αGSU) mRNA-expressing regions were almost completely overlapping. The αGSU mRNA-expressing region is thought to be the primordium of the pars tuberalis, and these regions were overlapped with the Lhx3 mRNA-expressing region. The intensity of δ-crys mRNA expression gradually decreased with development and completely disappeared by stage 34. These results suggest that the embryonic chick pituitary gland consists of two different regions labeled with δ-crys and Lhx3.

  16. Angiotensin-converting enzyme in Spodoptera littoralis: molecular characterization, expression and activity profile during development.

    Science.gov (United States)

    Lemeire, Els; Vanholme, Bartel; Van Leeuwen, Thomas; Van Camp, John; Smagghe, Guy

    2008-02-01

    The characterization of the full-length angiotensin-converting enzyme (ACE) cDNA sequence of the lepidopteran Spodoptera littoralis is reported in this study. The predicted open reading frame encodes a 647 amino acids long protein (SlACE) and shows 63.6% identity with the Bombyx mori ACE sequence. A 3D-model, consisting of 26 alpha-helices and three beta-sheets, was predicted for the sequence. SlACE expression was studied in the embryonic, larval and pupal stages of S. littoralis and in different tissues of the last larval stage by reverse-transcribed PCR. This revealed that the gene is expressed throughout the life cycle and especially in brain, gut and fat body tissue of the last stage. These results are in agreement with a role of ACE in the metabolism of neuropeptides and gut hormones. In addition, ACE activity has been studied in more detail during development, making use of a fluorescent assay. High ACE peptidase activity coincides with every transition state, from embryo to larva, from larva to larva and from larva to pupa. A peak value in activity occurs during the early pupal stage. These results indicate the importance of SlACE during metamorphosis and reveal the high correlation of ACE activity with the insect's development, which is regulated by growth and developmental hormones.

  17. BER analysis of regularized least squares for BPSK recovery

    KAUST Repository

    Ben Atitallah, Ismail; Thrampoulidis, Christos; Kammoun, Abla; Al-Naffouri, Tareq Y.; Hassibi, Babak; Alouini, Mohamed-Slim

    2017-01-01

    This paper investigates the problem of recovering an n-dimensional BPSK signal x0 ∈ {−1, 1}n from m-dimensional measurement vector y = Ax+z, where A and z are assumed to be Gaussian with iid entries. We consider two variants of decoders based on the regularized least squares followed by hard-thresholding: the case where the convex relaxation is from {−1, 1}n to ℝn and the box constrained case where the relaxation is to [−1, 1]n. For both cases, we derive an exact expression of the bit error probability when n and m grow simultaneously large at a fixed ratio. For the box constrained case, we show that there exists a critical value of the SNR, above which the optimal regularizer is zero. On the other side, the regularization can further improve the performance of the box relaxation at low to moderate SNR regimes. We also prove that the optimal regularizer in the bit error rate sense for the unboxed case is nothing but the MMSE detector.

  18. BER analysis of regularized least squares for BPSK recovery

    KAUST Repository

    Ben Atitallah, Ismail

    2017-06-20

    This paper investigates the problem of recovering an n-dimensional BPSK signal x0 ∈ {−1, 1}n from m-dimensional measurement vector y = Ax+z, where A and z are assumed to be Gaussian with iid entries. We consider two variants of decoders based on the regularized least squares followed by hard-thresholding: the case where the convex relaxation is from {−1, 1}n to ℝn and the box constrained case where the relaxation is to [−1, 1]n. For both cases, we derive an exact expression of the bit error probability when n and m grow simultaneously large at a fixed ratio. For the box constrained case, we show that there exists a critical value of the SNR, above which the optimal regularizer is zero. On the other side, the regularization can further improve the performance of the box relaxation at low to moderate SNR regimes. We also prove that the optimal regularizer in the bit error rate sense for the unboxed case is nothing but the MMSE detector.

  19. [Expression of vimentin and GFAP and development of the retina in the trout].

    Science.gov (United States)

    De Guevara, R; Pairault, C; Pinganaud, G

    1994-08-01

    The glial cell development was studied during the edification of the retina and the optic tract, in a teleost, the rainbow trout. The intermediate filament proteins, vimentin and glial fibrillary acidic protein (GFAP) were visualized by an indirect immunohistochemical method. Results show that both vimentin and GFAP are early expressed in the developing retina and, particularly in the Müller cells, a coexpression of vimentin and GFAP is observed from embryonic to adult stages. The ganglion cell layer and the optic fiber layer both exhibit GFAP-positive structures. The deep staining for GFAP is also seen in the optic nerve and induces us to credit astrocyte-like cells with a leading role in the pattern formation of this tract.

  20. Several synthetic progestins disrupt the glial cell specific-brain aromatase expression in developing zebra fish

    International Nuclear Information System (INIS)

    Cano-Nicolau, Joel; Garoche, Clémentine; Hinfray, Nathalie; Pellegrini, Elisabeth; Boujrad, Noureddine; Pakdel, Farzad; Kah, Olivier; Brion, François

    2016-01-01

    The effects of some progestins on fish reproduction have been recently reported revealing the hazard of this class of steroidal pharmaceuticals. However, their effects at the central nervous system level have been poorly studied until now. Notwithstanding, progesterone, although still widely considered primarily a sex hormone, is an important agent affecting many central nervous system functions. Herein, we investigated the effects of a large set of synthetic ligands of the nuclear progesterone receptor on the glial-specific expression of the zebrafish brain aromatase (cyp19a1b) using zebrafish mechanism-based assays. Progesterone and 24 progestins were first screened on transgenic cyp19a1b-GFP zebrafish embryos. We showed that progesterone, dydrogesterone, drospirenone and all the progesterone-derived progestins had no effect on GFP expression. Conversely, all progestins derived from 19-nortesterone induced GFP in a concentration-dependent manner with EC 50 ranging from the low nM range to hundreds nM. The 19-nortestosterone derived progestins levonorgestrel (LNG) and norethindrone (NET) were further tested in a radial glial cell context using U251-MG cells co-transfected with zebrafish ER subtypes (zfERα, zfERβ1 or zfERβ2) and cyp19a1b promoter linked to luciferase. Progesterone had no effect on luciferase activity while NET and LNG induced luciferase activity that was blocked by ICI 182,780. Zebrafish-ERs competition assays showed that NET and LNG were unable to bind to ERs, suggesting that the effects of these compounds on cyp19a1b require metabolic activation prior to elicit estrogenic activity. Overall, we demonstrate that 19-nortestosterone derived progestins elicit estrogenic activity by inducing cyp19a1b expression in radial glial cells. Given the crucial role of radial glial cells and neuro-estrogens in early development of brain, the consequences of exposure of fish to these compounds require further investigation. - Highlights: • P4 + 24 progestins