Zheng, Fangyang
2002-01-01
The theory of complex manifolds overlaps with several branches of mathematics, including differential geometry, algebraic geometry, several complex variables, global analysis, topology, algebraic number theory, and mathematical physics. Complex manifolds provide a rich class of geometric objects, for example the (common) zero locus of any generic set of complex polynomials is always a complex manifold. Yet complex manifolds behave differently than generic smooth manifolds; they are more coherent and fragile. The rich yet restrictive character of complex manifolds makes them a special and interesting object of study. This book is a self-contained graduate textbook that discusses the differential geometric aspects of complex manifolds. The first part contains standard materials from general topology, differentiable manifolds, and basic Riemannian geometry. The second part discusses complex manifolds and analytic varieties, sheaves and holomorphic vector bundles, and gives a brief account of the surface classifi...
Residues of Logarithmic Differential Forms in Complex Analysis and Geometry
Institute of Scientific and Technical Information of China (English)
A.G.Aleksandrov
2014-01-01
In the article, we discuss basic concepts of the residue theory of logarithmic and multi-logarithmic differential forms, and describe some aspects of the theory, de-veloped by the author in the past few years. In particular, we introduce the notion of logarithmic differential forms with the use of the classical de Rham lemma and give an explicit description of regular meromorphic differential forms in terms of residues of logarithmic or multi-logarithmic differential forms with respect to hypersurfaces, com-plete intersections or pure-dimensional Cohen-Macaulay spaces. Among other things, several useful applications are considered, which are related with the theory of holo-nomic D-modules, the theory of Hodge structures, the theory of residual currents and others.
Directory of Open Access Journals (Sweden)
Erica Chimara
2004-11-01
Full Text Available Mycobacterium tuberculosis complex (MTBC members are causative agents of human and animal tuberculosis. Differentiation of MTBC members is required for appropriate treatment of individual patients and for epidemiological purposes. Strains from six MTBC species - M. tuberculosis, M. bovis subsp. bovis, M. bovis BCG, M. africanum, M. pinnipedii, and "M. canetti" - were studied using gyrB-restriction fragment length polymorphism (gyrB-RFLP analysis. A table was elaborated, based on observed restriction patterns and published gyrB sequences. To evaluate applicability of gyrB-RFLP at Instituto Adolfo Lutz, São Paulo, Mycobacterial Reference Laboratory, 311 MTBC clinical isolates, previously identified using traditional methods as M. tuberculosis (306, M. bovis (3, and M. bovis BCG (2, were analyzed by gyrB-RFLP. All isolates were correctly identified by the molecular method, but no distinction between M. bovis and M. bovis BCG was obtained. Differentiation of M. tuberculosis and M. bovis is of utmost importance, because they require different treatment schedules. In conclusion, gyrB-RFLP is accurate and easy-to-perform, with potential to reduce time needed for conventional differentiation methods. However, application for epidemiological studies remains limited, because it cannot differentiate M. tuberculosis from M. africanum subtype II, and "M. canetti", M. africanum subtype I from M. pinnipedii, and. M. bovis from M. bovis BCG.
Freitag, Eberhard
2005-01-01
The guiding principle of this presentation of ``Classical Complex Analysis'' is to proceed as quickly as possible to the central results while using a small number of notions and concepts from other fields. Thus the prerequisites for understanding this book are minimal; only elementary facts of calculus and algebra are required. The first four chapters cover the essential core of complex analysis: - differentiation in C (including elementary facts about conformal mappings) - integration in C (including complex line integrals, Cauchy's Integral Theorem, and the Integral Formulas) - sequences and series of analytic functions, (isolated) singularities, Laurent series, calculus of residues - construction of analytic functions: the gamma function, Weierstrass' Factorization Theorem, Mittag-Leffler Partial Fraction Decomposition, and -as a particular highlight- the Riemann Mapping Theorem, which characterizes the simply connected domains in C. Further topics included are: - the theory of elliptic functions based on...
2015-01-01
The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ−δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652
Directory of Open Access Journals (Sweden)
Parkin Isobel AP
2008-09-01
Full Text Available Abstract Background Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses. The wide range of physiological, biochemical and molecular changes that occur in plants exposed to low temperature require a robust global approach to studying the response. We have employed Serial Analysis of Gene Expression (SAGE to uncover changes in the transcriptome of Arabidopsis thaliana over a time course of low temperature stress. Results Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C. Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Interpretation of these data was facilitated by representing the SAGE data by gene identifier, allowing more robust statistical analysis, cross-platform comparisons and the identification of genes sharing common expression profiles. Simultaneous statistical calculations across all five libraries identified 920 low temperature responsive genes, only 24% of which overlapped with previous global expression analysis performed using microarrays, although similar functional categories were affected. Clustering of the differentially regulated genes facilitated the identification of novel loci correlated with the development of freezing tolerance. Analysis of their promoter sequences revealed subsets of genes that were independent of CBF and ABA regulation and could provide a mechanism for elucidating complementary signalling pathways. The SAGE data emphasised the complexity of the plant response, with alternate pre-mRNA processing events increasing at low temperatures
Shinar, J.; Siegel, A.W.
1988-01-01
The investigation is motivated by the dynamic conflict in an air-to-air combat between two aggressive aircraft, both equipped with medium-range guided missiles. It is a two-target differential game with two independent pursuit-evasion games. A description is given of the analysis of the conflict by
Shinar, J.; Siegel, A.W.
1988-01-01
The investigation is motivated by the dynamic conflict in an air-to-air combat between two aggressive aircraft, both equipped with medium-range guided missiles. It is a two-target differential game with two independent pursuit-evasion games. A description is given of the analysis of the conflict by
Introduction to complex theory of differential equations
Savin, Anton
2017-01-01
This book discusses the complex theory of differential equations or more precisely, the theory of differential equations on complex-analytic manifolds. Although the theory of differential equations on real manifolds is well known – it is described in thousands of papers and its usefulness requires no comments or explanations – to date specialists on differential equations have not focused on the complex theory of partial differential equations. However, as well as being remarkably beautiful, this theory can be used to solve a number of problems in real theory, for instance, the Poincaré balayage problem and the mother body problem in geophysics. The monograph does not require readers to be familiar with advanced notions in complex analysis, differential equations, or topology. With its numerous examples and exercises, it appeals to advanced undergraduate and graduate students, and also to researchers wanting to familiarize themselves with the subject.
On Complex Singularity Analysis for Some Linear Partial Differential Equations in
Directory of Open Access Journals (Sweden)
A. Lastra
2013-01-01
Full Text Available We investigate the existence of local holomorphic solutions Y of linear partial differential equations in three complex variables whose coefficients are holomorphic on some polydisc in outside some singular set . The coefficients are written as linear combinations of powers of a solution X of some first-order nonlinear partial differential equation following an idea, we have initiated in a previous work (Malek and Stenger 2011. The solutions Y are shown to develop singularities along with estimates of exponential type depending on the growth's rate of X near the singular set. We construct these solutions with the help of series of functions with infinitely many variables which involve derivatives of all orders of X in one variable. Convergence and bounds estimates of these series are studied using a majorant series method which leads to an auxiliary functional equation that contains differential operators in infinitely many variables. Using a fixed point argument, we show that these functional equations actually have solutions in some Banach spaces of formal power series.
Identification and comparative analysis of the epidermal differentiation complex in snakes
Brigit Holthaus, Karin; Mlitz, Veronika; Strasser, Bettina; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold
2017-01-01
The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes. PMID:28345630
Identification and comparative analysis of the epidermal differentiation complex in snakes.
Brigit Holthaus, Karin; Mlitz, Veronika; Strasser, Bettina; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold
2017-03-27
The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes.
Gianolio, D.; Borfecchia, E.; Garino, C.; Ruiu, T.; Lamberti, C.; Salassa, L.
2013-04-01
X-ray Absorption Spectroscopy (XAS) is a sensitive and powerful technique in revealing the structure of a material, providing as well high accuracy on interatomic distances. Nevertheless, when dealing with systems that differ only by small structural features, a standard data analysis might be unable of discriminating between such differences. A differential approach was proposed by Bressler, Chergui, and co-workers [2003, Phys. Rev. Lett. 90, 047403][2006, J. Phys. Chem B, 110, 14035][2009 Angew. Chem., Int. Ed. 48 2711] to solve this problem and differentiate between excited and unexcited state structures during pump-and-probe transient XAS experiments. In this contribution, we apply the differential data analysis procedure to the study of two closely-related molecular complexes, namely cis-[Ru(bpy)2(py)2]2+ and cis-[Ru(bpy)2(py)(H2O)]2+, characterized under static conditions. It is herein demonstrated that the method, based on a direct fit of differential curves, is able to reveal the small differences present between the two structures which, conversely, could not be resolved by standard EXAFS fitting of full spectra.
Fractional complex transform for fractional differential equations
National Research Council Canada - National Science Library
Lİ, Zheng Biao; HE, Ji Huan
2010-01-01
Fractional complex transform is proposed to convert fractional differential equations into ordinary differential equations, so that all analytical methods devoted to advanced calculus can be easily...
Pawlowski, Roger P; Salinger, Andrew G; Owen, Steven J; Siefert, Christopher M; Staten, Matthew L
2012-01-01
A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.
Fractional complex transforms for fractional differential equations
National Research Council Canada - National Science Library
Ibrahim, Rabha W
2012-01-01
The fractional complex transform is employed to convert fractional differential equations analytically in the sense of the Srivastava-Owa fractional operator and its generalization in the unit disk...
Directory of Open Access Journals (Sweden)
Roger P. Pawlowski
2012-01-01
Full Text Available A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012, 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs. We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.
Yu, XiaoChun; Bai, YuGuang; Cui, Miao; Gao, XiaoWei
2013-05-01
This paper presents a new inverse analysis approach to sensitivity analysis and material property identification in transient non-homogeneous and non-linear heat conduction Boundary Element Method (BEM) analysis based on Complex Variable Differentiation Method (CVDM). In this approach, the material properties are taken as the optimization variables, and the sensitivity coefficients are computed by CVDM. The advantages of using CVDM are that the computation of partial derivatives of an implicit function is reduced to function calculation in a complex domain, and the parameter sensitivity coefficients can be determined in a more accurate way than the traditional Finite Difference Method (FDM). Based on BEM and CVDM in evaluation of the sensitivity matrix of heat flux, the parameter such as thermal conductivity can be accurately identified. Six numerical examples are given to demonstrate the potential of the proposed approach. The results indicate that the presented method is efficient for identifying the thermal conductivity with single or multiple parameters.
On a complex differential Riccati equation
Energy Technology Data Exchange (ETDEWEB)
Khmelnytskaya, Kira V; Kravchenko, Vladislav V [Department of Mathematics, CINVESTAV del IPN, Unidad Queretaro, Libramiento Norponiente No. 2000, Fracc. Real de Juriquilla, Queretaro, Qro. C.P. 76230 Mexico (Mexico)], E-mail: vkravchenko@qro.cinvestav.mx
2008-02-29
We consider a nonlinear partial differential equation for complex-valued functions which is related to the two-dimensional stationary Schroedinger equation and enjoys many properties similar to those of the ordinary differential Riccati equation such as the famous Euler theorems, the Picard theorem and others. Besides these generalizations of the classical 'one-dimensional' results, we discuss new features of the considered equation including an analogue of the Cauchy integral theorem.
DEFF Research Database (Denmark)
Manteca, Angel; Jung, Hye R; Schwämmle, Veit
2010-01-01
Streptomyces species produce many clinically important secondary metabolites and present a complex developmental cycle that includes programmed cell death (PCD) phenomena and sporulation. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains...... of the different developmental stages in liquid and solid S. coelicolor cultures, in order to give new insights in Streptomyces biology, and improve industrial fermentations. Using iTRAQ labeling and LC-MS/MS analysis of peptides, we demonstrate that differentiation in S. coelicolor liquid cultures is comparable...
Directory of Open Access Journals (Sweden)
Jörg Servos
Full Text Available The regulation of cellular copper homeostasis is crucial in biology. Impairments lead to severe dysfunctions and are known to affect aging and development. Previously, a loss-of-function mutation in the gene encoding the copper-sensing and copper-regulated transcription factor GRISEA of the filamentous fungus Podospora anserina was reported to lead to cellular copper depletion and a pleiotropic phenotype with hypopigmentation of the mycelium and the ascospores, affected fertility and increased lifespan by approximately 60% when compared to the wild type. This phenotype is linked to a switch from a copper-dependent standard to an alternative respiration leading to both a reduced generation of reactive oxygen species (ROS and of adenosine triphosphate (ATP. We performed a genome-wide comparative transcriptome analysis of a wild-type strain and the copper-depleted grisea mutant. We unambiguously assigned 9,700 sequences of the transcriptome in both strains to the more than 10,600 predicted and annotated open reading frames of the P. anserina genome indicating 90% coverage of the transcriptome. 4,752 of the transcripts differed significantly in abundance with 1,156 transcripts differing at least 3-fold. Selected genes were investigated by qRT-PCR analyses. Apart from this general characterization we analyzed the data with special emphasis on molecular pathways related to the grisea mutation taking advantage of the available complete genomic sequence of P. anserina. This analysis verified but also corrected conclusions from earlier data obtained by single gene analysis, identified new candidates of factors as part of the cellular copper homeostasis system including target genes of transcription factor GRISEA, and provides a rich reference source of quantitative data for further in detail investigations. Overall, the present study demonstrates the importance of systems biology approaches also in cases were mutations in single genes are analyzed to
Mathematical analysis differentiation and integration
Aramanovich, IG; Lyusternik, LA; Sneddon, I N
1965-01-01
Mathematical Analysis: Differentiation and Integration is devoted to two basic operations of mathematical analysis, differentiation and integration. The problems directly connected with the operations of differentiation and integration of functions of one or several variables are discussed, together with elementary generalizations of these operations. This volume is comprised of seven chapters and begins by considering the differentiation of functions of one variable and of n variables, paying particular attention to derivatives and differentials as well as their properties. The next chapter d
Liu, Jian; Bi, Shuping; Yang, Li; Gu, Xiaodong; Ma, Pengju; Gan, Ning; Wang, Xianlong; Long, Xiufeng; Zhang, Fuping
2002-12-01
The biological effects of aluminium have received much attention in recent years. Speciation of Al is of basic relevance as it concerns its reactivity and bioavailability. A differential pulse voltammetry (DPV) procedure is proposed for speciation analysis of Al(III) in natural waters and biological fluids using six catechols (L-dopa, dopamine, epinephrine, norepinephrine, caffeic acid and o-benzenediol) as electroactive ligands. The decrease of the DPV anodic peak current for each catechol ligand is linear with the increase of Al concentration. This speciation analysis idea is based on the measurement of the complexation capacity, namely, different affinities of Al(III) for catechols and organic ligands under two pH conditions. The labile monomeric Al fraction (mainly inorganic aluminium) is determined at pH 4.6, while the total monomeric Al fraction is determined at pH 8.5. The principle for Al(III) speciation analysis by an electrochemical method is discussed. This sensitive and simple fractionation method is successfully applied to the speciation analysis of Al in natural waters and the results agree well with those of Driscoll's method. The speciation analysis of Al in biological fluids is also explored and the results are compared with those obtained by ultrafiltration and dialysis. Compared with other speciation protocols the electrochemical method possesses some remarkable advantages: rapidity, high sensitivity, cheap instrumentation and a simple operation procedure.
Integrator complex plays an essential role in adipose differentiation
Energy Technology Data Exchange (ETDEWEB)
Otani, Yuichiro; Nakatsu, Yusuke [Department of Medical Chemistry, Division of Molecular Medical Science, Graduate School of Biomedical Sciences, Hiroshima University (Japan); Sakoda, Hideyuki [Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Tokyo (Japan); Fukushima, Toshiaki [Department of Medical Chemistry, Division of Molecular Medical Science, Graduate School of Biomedical Sciences, Hiroshima University (Japan); Fujishiro, Midori [Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Tokyo (Japan); Kushiyama, Akifumi [Department of Internal Medicine, The Institute for Adult Diseases, Asahi Life Foundation, Tokyo (Japan); Okubo, Hirofumi; Tsuchiya, Yoshihiro; Ohno, Haruya [Department of Medical Chemistry, Division of Molecular Medical Science, Graduate School of Biomedical Sciences, Hiroshima University (Japan); Takahashi, Shin-Ichiro [Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo (Japan); Nishimura, Fusanori [Department of Dental Science for Health Promotion, Division of Cervico-Gnathostomatology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima (Japan); Kamata, Hideaki [Department of Medical Chemistry, Division of Molecular Medical Science, Graduate School of Biomedical Sciences, Hiroshima University (Japan); Katagiri, Hideki [Division of Molecular Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai (Japan); Asano, Tomoichiro, E-mail: tasano@hiroshima-u.ac.jp [Department of Medical Chemistry, Division of Molecular Medical Science, Graduate School of Biomedical Sciences, Hiroshima University (Japan)
2013-05-03
Highlights: •IntS6 and IntS11 are subunits of the Integrator complex. •Expression levels of IntS6 and IntS11 were very low in 3T3-L1 fibroblast. •IntS6 and IntS11 were upregulated during adipose differentiation. •Suppression of IntS6 or IntS11 expression inhibited adipose differentiation. -- Abstract: The dynamic process of adipose differentiation involves stepwise expressions of transcription factors and proteins specific to the mature fat cell phenotype. In this study, it was revealed that expression levels of IntS6 and IntS11, subunits of the Integrator complex, were increased in 3T3-L1 cells in the period when the cells reached confluence and differentiated into adipocytes, while being reduced to basal levels after the completion of differentiation. Suppression of IntS6 or IntS11 expression using siRNAs in 3T3-L1 preadipocytes markedly inhibited differentiation into mature adipocytes, based on morphological findings as well as mRNA analysis of adipocyte-specific genes such as Glut4, perilipin and Fabp4. Although Pparγ2 protein expression was suppressed in IntS6 or IntS11-siRNA treated cells, adenoviral forced expression of Pparγ2 failed to restore the capacity for differentiation into mature adipocytes. Taken together, these findings demonstrate that increased expression of Integrator complex subunits is an indispensable event in adipose differentiation. Although further study is necessary to elucidate the underlying mechanism, the processing of U1, U2 small nuclear RNAs may be involved in cell differentiation steps.
Differential geometry of complex vector bundles
Kobayashi, Shoshichi
2014-01-01
Holomorphic vector bundles have become objects of interest not only to algebraic and differential geometers and complex analysts but also to low dimensional topologists and mathematical physicists working on gauge theory. This book, which grew out of the author's lectures and seminars in Berkeley and Japan, is written for researchers and graduate students in these various fields of mathematics. Originally published in 1987. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeto
Energy Technology Data Exchange (ETDEWEB)
Berezowski, Marek [Faculty of Mathematics and Physics, Institute of Mathematics, Silesian University of Technology, 44-100 Gliwice, ul. Kaszubska 23 (Poland)]. E-mail: Marek.Berezowski@polsl.pl
2005-06-01
The paper deals with the mathematical-numerical analysis of the logistic Mandelbrot equation extended by the dynamic continuous term. The possibilities of generation of fractal patterns with the mathematical form, defined in such a manner, were investigated. The decay of fractal structure with time was demonstrated.
A differential model of the complex cell.
Hansard, Miles; Horaud, Radu
2011-09-01
The receptive fields of simple cells in the visual cortex can be understood as linear filters. These filters can be modeled by Gabor functions or gaussian derivatives. Gabor functions can also be combined in an energy model of the complex cell response. This letter proposes an alternative model of the complex cell, based on gaussian derivatives. It is most important to account for the insensitivity of the complex response to small shifts of the image. The new model uses a linear combination of the first few derivative filters, at a single position, to approximate the first derivative filter, at a series of adjacent positions. The maximum response, over all positions, gives a signal that is insensitive to small shifts of the image. This model, unlike previous approaches, is based on the scale space theory of visual processing. In particular, the complex cell is built from filters that respond to the 2D differential structure of the image. The computational aspects of the new model are studied in one and two dimensions, using the steerability of the gaussian derivatives. The response of the model to basic images, such as edges and gratings, is derived formally. The response to natural images is also evaluated, using statistical measures of shift insensitivity. The neural implementation and predictions of the model are discussed.
DEFF Research Database (Denmark)
Nord, Martin
2004-01-01
This paper presents a simulation study of a low-complexity optical packet switching quality of service differentiation scheme, aiming at minimising the penalty of offering packet loss rate isolation in an optical packet switch with a wavelength converter pool. Special emphasis is given to potential...
Silverman, Richard A
1984-01-01
A shorter version of A. I. Markushevich's masterly three-volume Theory of Functions of a Complex Variable, this edition is appropriate for advanced undergraduate and graduate courses in complex analysis. Numerous worked-out examples and more than 300 problems, some with hints and answers, make it suitable for independent study. 1967 edition.
Partial differential equations in several complex variables
Chen, So-Chin
2001-01-01
This book is intended both as an introductory text and as a reference book for those interested in studying several complex variables in the context of partial differential equations. In the last few decades, significant progress has been made in the fields of Cauchy-Riemann and tangential Cauchy-Riemann operators. This book gives an up-to-date account of the theories for these equations and their applications. The background material in several complex variables is developed in the first three chapters, leading to the Levi problem. The next three chapters are devoted to the solvability and regularity of the Cauchy-Riemann equations using Hilbert space techniques. The authors provide a systematic study of the Cauchy-Riemann equations and the \\bar\\partial-Neumann problem, including L^2 existence theorems on pseudoconvex domains, \\frac 12-subelliptic estimates for the \\bar\\partial-Neumann problems on strongly pseudoconvex domains, global regularity of \\bar\\partial on more general pseudoconvex domains, boundary ...
Differential transendothelial transport of adiponectin complexes
2014-01-01
Background Adiponectin’s effects on systemic physiology and cell-specific responses are well-defined, but little is known about how this insulin-sensitizing and anti-inflammatory adipokine reaches its target cells. All molecules face active and passive transport limitations, but adiponectin is particularly noteworthy due to the diverse size range and high molecular weights of its oligomers. Additionally, its metabolic target organs possess a range of endothelial permeability. Methods Full-length recombinant murine adiponectin was produced and oligomer fractions isolated by gel filtration. Adiponectin complex sizes were measured by dynamic light scattering to determine Stokes radii. Transendothelial transport of purified oligomers was quantitatively assessed under a number of different conditions in vitro using murine endothelial cells and in vivo using several mouse models of altered endothelial function. Results Adiponectin oligomers exhibit large transport radii that limit transendothelial transport. Oligomerization is a significant determinant of flux across endothelial monolayers in vitro; low molecular weight adiponectin is preferentially transported. In vivo sampled sera from the heart, liver, and tail vein demonstrated significantly different complex distribution of lower molecular weight oligomers. Pharmacological interventions, such as PPARγ agonist treatment, differentially affect adiponectin plasma clearance and tissue uptake. Exercise induces enhanced adiponectin uptake to oxidative skeletal muscles, wherein adiponectin potently lowers ceramide levels. In total, endothelial barriers control adiponectin transport in a cell- and tissue-specific manner. Conclusions Adiponectin oligomer efficacy in a given tissue may therefore be endothelial transport mediated. Targeting endothelial dysfunction in the metabolic syndrome through exercise and pharmaceuticals may afford an effective approach to increasing adiponectin’s beneficial effects. PMID:24552349
Introduction to complex analysis
Priestley, H A
2003-01-01
Complex analysis is a classic and central area of mathematics, which is studied and exploited in a range of important fields, from number theory to engineering. Introduction to Complex Analysis was first published in 1985, and for this much awaited second edition the text has been considerably expanded, while retaining the style of the original. More detailed presentation is given of elementary topics, to reflect the knowledge base of current students. Exercise sets have beensubstantially revised and enlarged, with carefully graded exercises at the end of each chapter.This is the latest additi
Complexity analysis of angiogenesis vasculature
Mahadevan, Vijay; Tyrell, James A.; Tong, Ricky T.; Brown, Edward B.; Jain, Rakesh K.; Roysam, Badrinath
2005-04-01
Tumor vasculature has a high degree of irregularity as compared to normal vasculature. The quantification of the morphometric complexity in tumor images can be useful in diagnosis. Also, it is desirable in several other medical applications to have an automated complexity analysis to aid in diagnosis and prognosis under treatment. e.g. in diabetic retinopathy and in arteriosclerosis. In addition, prior efforts at segmentation of the tumor vasculature using matched filtering, template matching and splines have been hampered by the irregularity of these vessels. We try to solve both problems by introducing a novel technique for vessel detection, followed by a tracing-independent complexity analysis based on a combination of ideas. First, the vessel cross-sectional profile is modeled using a continuous and everywhere differentiable family of super-Gaussian curves. This family generates rectangular profiles that can accurately localize the vessel boundaries in microvasculature images. Second, a robust non-linear regression algorithm based on M-estimators is used to estimate the parameters that optimally characterize the vessel"s shape. A framework for the quantitative analysis of the complexity of the vasculature based on the vessel detection is presented. A set of measures that quantify the complexity are proposed viz. Squared Error, Entropy-based and Minimum Description Length-based Shape Complexities. They are completely automatic and can deal with complexities of the entire vessel unlike existing tortuousity measures which deal only with vessel centerlines. The results are validated using carefully constructed phantom and real image data with ground truth information from an expert observer.
A complex Noether approach for variational partial differential equations
Naz, R.; Mahomed, F. M.
2015-10-01
Scalar complex partial differential equations which admit variational formulations are studied. Such a complex partial differential equation, via a complex dependent variable, splits into a system of two real partial differential equations. The decomposition of the Lagrangian of the complex partial differential equation in the real domain is shown to yield two real Lagrangians for the split system. The complex Maxwellian distribution, transonic gas flow, Maxwellian tails, dissipative wave and Klein-Gordon equations are considered. The Noether symmetries and gauge terms of the split system that correspond to both the Lagrangians are constructed by the Noether approach. In the case of coupled split systems, the same Noether symmetries are obtained. The Noether symmetries for the uncoupled split systems are different. The conserved vectors of the split system which correspond to both the Lagrangians are compared to the split conserved vectors of the complex partial differential equation for the examples. The split conserved vectors of the complex partial differential equation are the same as the conserved vectors of the split system of real partial differential equations in the case of coupled systems. Moreover a Noether-like theorem for the split system is proved which provides the Noether-like conserved quantities of the split system from knowledge of the Noether-like operators. An interesting result on the split characteristics and the conservation laws is shown as well. The Noether symmetries and gauge terms of the Lagrangian of the split system with the split Noether-like operators and gauge terms of the Lagrangian of the given complex partial differential equation are compared. Folklore suggests that the split Noether-like operators of a Lagrangian of a complex Euler-Lagrange partial differential equation are symmetries of the Lagrangian of the split system of real partial differential equations. This is not the case. They are proved to be the same if the
Complex Transforms for Systems of Fractional Differential Equations
Directory of Open Access Journals (Sweden)
Rabha W. Ibrahim
2012-01-01
Full Text Available We provide a complex transform that maps the complex fractional differential equation into a system of fractional differential equations. The homogeneous and nonhomogeneous cases for equivalence equations are discussed and also nonequivalence equations are studied. Moreover, the existence and uniqueness of solutions are established and applications are illustrated.
Yagüe, Paula; Rodríguez-García, Antonio; López-García, María Teresa; Rioseras, Beatriz; Martín, Juan Francisco; Sánchez, Jesús; Manteca, Angel
2014-01-01
Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4) and undecylprodigiosin (redF); activation of secondary metabolism (absR1, ndsA); genes regulating hydrophobic cover formation (aerial mycelium) (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS); and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ). The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters) were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr) were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures.
Directory of Open Access Journals (Sweden)
Paula Yagüe
Full Text Available Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4 and undecylprodigiosin (redF; activation of secondary metabolism (absR1, ndsA; genes regulating hydrophobic cover formation (aerial mycelium (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS; and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ. The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures.
New Fractional Complex Transform for Conformable Fractional Partial Differential Equations
Directory of Open Access Journals (Sweden)
Çenesiz Y.
2016-12-01
Full Text Available Conformable fractional complex transform is introduced in this paper for converting fractional partial differential equations to ordinary differential equations. Hence analytical methods in advanced calculus can be used to solve these equations. Conformable fractional complex transform is implemented to fractional partial differential equations such as space fractional advection diffusion equation and space fractional telegraph equation to obtain the exact solutions of these equations.
Group analysis of differential equations
Ovsiannikov, L V
1982-01-01
Group Analysis of Differential Equations provides a systematic exposition of the theory of Lie groups and Lie algebras and its application to creating algorithms for solving the problems of the group analysis of differential equations.This text is organized into eight chapters. Chapters I to III describe the one-parameter group with its tangential field of vectors. The nonstandard treatment of the Banach Lie groups is reviewed in Chapter IV, including a discussion of the complete theory of Lie group transformations. Chapters V and VI cover the construction of partial solution classes for the g
Advanced complex trait analysis.
Gray, A; Stewart, I; Tenesa, A
2012-12-01
The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min. The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. a.gray@ed.ac.uk Supplementary data are available at Bioinformatics online.
Differential and complex geometry origins, abstractions and embeddings
Wells, Jr , Raymond O
2017-01-01
Differential and complex geometry are two central areas of mathematics with a long and intertwined history. This book, the first to provide a unified historical perspective of both subjects, explores their origins and developments from the sixteenth to the twentieth century. Providing a detailed examination of the seminal contributions to differential and complex geometry up to the twentieth century embedding theorems, this monograph includes valuable excerpts from the original documents, including works of Descartes, Fermat, Newton, Euler, Huygens, Gauss, Riemann, Abel, and Nash. Suitable for beginning graduate students interested in differential, algebraic or complex geometry, this book will also appeal to more experienced readers.
Invariant distances and metrics in complex analysis
Jarnicki, Marek
2013-01-01
As in the field of ""Invariant Distances and Metrics in Complex Analysis"" there was and is a continuous progress this is the second extended edition of the corresponding monograph. This comprehensive book is about the study of invariant pseudodistances (non-negative functions on pairs of points) and pseudometrics (non-negative functions on the tangent bundle) in several complex variables. It is an overview over a highly active research area at the borderline between complex analysis, functional analysis and differential geometry. New chapters are covering the Wu, Bergman and several other met
Operator calculus - the exterior differential complex
Harrison, Jenny
2011-01-01
This paper and its sequels lay the groundwork for an operator calculus based on a spectral pair ('B,O) where 'B is a complete locally convex topological vector space of "differential chains" and O is an algebra of continuous operators acting on 'B. The topological dual of 'B is isomorphic to the classical Fr\\'echet space B of differential forms with uniform bounds on each of its directional derivatives. In a sequel H. Pugh and the author show that 'B is not generally reflexive. Since basic operators sufficient for a full calculus described in this paper, and important products are closed in 'B, there is little need for the larger double dual space B'. The covariant, constructive viewpoint of chains takes precedence over the contravariant, abstract viewpoint of cochains. In other words, chains come first. Applications include the first proof of a solution to Plateau's problem for soap films, solving a two hundred year old problem.
Invitation to complex analysis
Boas, Ralph P
2010-01-01
Ideal for a first course in complex analysis, this book can be used either as a classroom text or for independent study. Written at a level accessible to advanced undergraduates and beginning graduate students, the book is suitable for readers acquainted with advanced calculus or introductory real analysis. The treatment goes beyond the standard material of power series, Cauchy's theorem, residues, conformal mapping, and harmonic functions by including accessible discussions of intriguing topics that are uncommon in a book at this level. The flexibility afforded by the supplementary topics and applications makes the book adaptable either to a short, one-term course or to a comprehensive, full-year course. Detailed solutions of the exercises both serve as models for students and facilitate independent study. Supplementary exercises, not solved in the book, provide an additional teaching tool. This second edition has been painstakingly revised by the author's son, himself an award-winning mathematical expositor...
Analysis Approach and Differential Diagnosis of Wide QRS Complex Tachycardia%宽QRS波心动过速的分析思路及鉴别诊断要点
Institute of Scientific and Technical Information of China (English)
吴愧; 张英力; 刘仁光
2014-01-01
宽QRS波心动过速( Wide QRS complex tachycardia, WCT)是临床急症心电图,可见于室性心动过速( Ventric-ular Tachycardia, VT)和室上性心动过速( Supraventricular Tachycardia, SVT)。对它们的鉴别诊断是临床心电图分析的难点。本文结合文献,对WCT的分析思路和鉴别诊断要点做一简述。%Wide QRS complex tachycardia ( WCT) is a common and emergent clinical arrhythmia. Both Ventricular Tachycardia ( VT) and Supraventricular Tachycardia ( SVT) can present an electrocardiogram of WCT. The differential diagnosis of them is a chal-lenge. This paper is to summarize the analysis approach and key points of differential diagnosis of WCT.
Optimal control of complex networks based on matrix differentiation
Li, Guoqi; Ding, Jie; Wen, Changyun; Pei, Jing
2016-09-01
Finding the key node set to be connected to external control sources so as to minimize the energy for controlling a complex network, known as the minimum-energy control problem, is of critical importance but remains open. We address this critical problem where matrix differentiation is involved. To this end, the differentiation of energy/cost function with respect to the input matrix is obtained based on tensor analysis, and the Hessian matrix is compressed from a fourth-order tensor. Normalized projected gradient method (NPGM) normalized projected trust-region method (NPTM) are proposed with established convergence property. We show that NPGM is more computationally efficient than NPTM. Simulation results demonstrate satisfactory performance of the algorithms, and reveal important insights as well. Two interesting phenomena are observed. One is that the key node set tends to divide elementary paths equally. The other is that the low-degree nodes may be more important than hubs from a control point of view, indicating that controlling hub nodes does not help to lower the control energy. These results suggest a way of achieving optimal control of complex networks, and provide meaningful insights for future researches.
Complex networks analysis of language complexity
Amancio, Diego R; Oliveira, Osvaldo N; Costa, Luciano da F; 10.1209/0295-5075/100/58002
2013-01-01
Methods from statistical physics, such as those involving complex networks, have been increasingly used in quantitative analysis of linguistic phenomena. In this paper, we represented pieces of text with different levels of simplification in co-occurrence networks and found that topological regularity correlated negatively with textual complexity. Furthermore, in less complex texts the distance between concepts, represented as nodes, tended to decrease. The complex networks metrics were treated with multivariate pattern recognition techniques, which allowed us to distinguish between original texts and their simplified versions. For each original text, two simplified versions were generated manually with increasing number of simplification operations. As expected, distinction was easier for the strongly simplified versions, where the most relevant metrics were node strength, shortest paths and diversity. Also, the discrimination of complex texts was improved with higher hierarchical network metrics, thus point...
Some Penrose transforms in complex differential geometry
Institute of Scientific and Technical Information of China (English)
ANCO; Stephen; BLAND; John; EASTWOOD; Michael
2006-01-01
In this article, we review a construction in the complex geometry often known as the Penrose transform. We then present two new applications of this transform. One concerns the construction of symmetries of the massless field equations from mathematical physics. The otherconcerns obstructions to the embedding of CR structures on the three-sphere.
Differential network analysis in human cancer research.
Gill, Ryan; Datta, Somnath; Datta, Susmita
2014-01-01
A complex disease like cancer is hardly caused by one gene or one protein singly. It is usually caused by the perturbation of the network formed by several genes or proteins. In the last decade several research teams have attempted to construct interaction maps of genes and proteins either experimentally or reverse engineer interaction maps using computational techniques. These networks were usually created under a certain condition such as an environmental condition, a particular disease, or a specific tissue type. Lately, however, there has been greater emphasis on finding the differential structure of the existing network topology under a novel condition or disease status to elucidate the perturbation in a biological system. In this review/tutorial article we briefly mention some of the research done in this area; we mainly illustrate the computational/statistical methods developed by our team in recent years for differential network analysis using publicly available gene expression data collected from a well known cancer study. This data includes a group of patients with acute lymphoblastic leukemia and a group with acute myeloid leukemia. In particular, we describe the statistical tests to detect the change in the network topology based on connectivity scores which measure the association or interaction between pairs of genes. The tests under various scores are applied to this data set to perform a differential network analysis on gene expression for human leukemia. We believe that, in the future, differential network analysis will be a standard way to view the changes in gene expression and protein expression data globally and these types of tests could be useful in analyzing the complex differential signatures.
Multidimensional real analysis I differentiation
Duistermaat, J J; van Braam Houckgeest, J P
2004-01-01
Part one of the authors' comprehensive and innovative work on multidimensional real analysis. This book is based on extensive teaching experience at Utrecht University and gives a thorough account of differential analysis in multidimensional Euclidean space. It is an ideal preparation for students who wish to go on to more advanced study. The notation is carefully organized and all proofs are clean, complete and rigorous. The authors have taken care to pay proper attention to all aspects of the theory. In many respects this book presents an original treatment of the subject and it contains man
Applied analysis and differential equations
Cârj, Ovidiu
2007-01-01
This volume contains refereed research articles written by experts in the field of applied analysis, differential equations and related topics. Well-known leading mathematicians worldwide and prominent young scientists cover a diverse range of topics, including the most exciting recent developments. A broad range of topics of recent interest are treated: existence, uniqueness, viability, asymptotic stability, viscosity solutions, controllability and numerical analysis for ODE, PDE and stochastic equations. The scope of the book is wide, ranging from pure mathematics to various applied fields such as classical mechanics, biomedicine, and population dynamics.
An experimental-differential investigation of cognitive complexity
Directory of Open Access Journals (Sweden)
2009-12-01
Full Text Available Cognitive complexity as defined by differential and experimental traditions was explored to investigate the theoretical advantage and utility of relational complexity (RC theory as a common framework for studying fluid cognitive functions. RC theory provides a domain general account of processing demand as a function of task complexity. In total, 142 participants completed two tasks in which RC was manipulated, and two tasks entailing manipulations of complexity derived from the differential psychology literature. A series of analyses indicated that, as expected, task manipulations influenced item difficulty. However, comparable changes in a psychometric index of complexity were not consistently observed. Active maintenance of information across multiple steps of the problem solving process, which entails strategic coordination of storage and processing that cannot be modelled under the RC framework was found to be an important component of cognitive complexity.
Indian Academy of Sciences (India)
R Naz; F M Mahomed
2014-07-01
The Lie and Noether point symmetry analyses of a th-order system of complex ordinary differential equations (ODEs) with dependent variables are performed. The decomposition of complex symmetries of the given system of complex ODEs yields Lie- and Noether-like operators. The system of complex ODEs can be split into 2 coupled real partial differential equations (PDEs) and 2 Cauchy–Riemann (CR) equations. The classical approach is invoked to compute the symmetries of the 4 real PDEs and these are compared with the decomposed Lie- and Noetherlike operators of the system of complex ODEs. It is shown that, in general, the Lie- and Noether-like operators of the system of complex ODEs and the symmetries of the decomposed system of real PDEs are not the same. A similar analysis is carried out for restricted systems of complex ODEs that split into 2 coupled real ODEs. We summarize our findings on restricted complex ODEs in two propositions.
DEFF Research Database (Denmark)
Rosendahl, Mads
1989-01-01
One way to analyse programs is to to derive expressions for their computational behaviour. A time bound function (or worst-case complexity) gives an upper bound for the computation time as a function of the size of input. We describe a system to derive such time bounds automatically using abstrac...
DEFF Research Database (Denmark)
Rosendahl, Mads
1989-01-01
One way to analyse programs is to to derive expressions for their computational behaviour. A time bound function (or worst-case complexity) gives an upper bound for the computation time as a function of the size of input. We describe a system to derive such time bounds automatically using abstrac...... interpretation. The semantics-based setting makes it possible to prove the correctness of the time bound function. The system can analyse programs in a first-order subset of Lisp and we show how the system also can be used to analyse programs in other languages....
Directory of Open Access Journals (Sweden)
Catherine Creppe
2014-12-01
Full Text Available Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Our project aimed to identify Cbx8 binding sites in differentiating mouse embryonic stem cells. Therefore, we used a genome-wide chromatin immunoprecipitation of endogenous Cbx8 coupled to direct massive parallel sequencing (ChIP-Seq. Our analysis identified 171 high confidence peaks. By crossing our data with previously published microarray analysis, we show that several differentiation genes transiently recruit Cbx8 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. Both interaction analysis, as well as chromatin immunoprecipitation experiments support the idea that activating Cbx8 acts in the context of an intact PRC1 complex. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3 and H2A ubiquitination. The composition of PRC1 is highly modular and changes when embryonic stem cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together, our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs.
Selected papers on analysis and differential equations
Society, American Mathematical
2010-01-01
This volume contains translations of papers that originally appeared in the Japanese journal Sūgaku. These papers range over a variety of topics in ordinary and partial differential equations, and in analysis. Many of them are survey papers presenting new results obtained in the last few years. This volume is suitable for graduate students and research mathematicians interested in analysis and differential equations.
Differential analysis of matrix convex functions II
DEFF Research Database (Denmark)
Hansen, Frank; Tomiyama, Jun
2009-01-01
We continue the analysis in [F. Hansen, and J. Tomiyama, Differential analysis of matrix convex functions. Linear Algebra Appl., 420:102--116, 2007] of matrix convex functions of a fixed order defined in a real interval by differential methods as opposed to the characterization in terms of divide...
Differentiation, ageing, and terminal differentiation: a semantic analysis.
Reiner, J M
1983-12-21
The largely unsolved problems in the theoretical analysis of differentiation and ageing involve a substantial component of linguistic (semantic) difficulties. Some of these are simple traps of ambiguity, resulting from metaphorical or analogical employment of established terms--for example, "terminal differentiation" (loss of division potential in vitro) as a borrowing from "differentiation" as used by developmental biologists, or "commitment" by analogy with "determination". Some difficulties represent a failure to adopt (at least provisionally) an operational (empirical) view--for example, failure to ask what is the nature of the evidence for the view that a fertilized ovum is totipotential, or to scrutinize the evidence for the view that cells "terminally differentiated" in vitro in a conventional medium are in fact moribund under all conditions, or to examine more closely the view that the differentiated state and the cycling state are mutually exclusive. With respect to the problem of ageing, we review some of the critical experiments on "terminal differentiation" or "clonal senescence". We then proceed to consider some of the models that have been proposed, including a molecular model proposed by the author which appears to overcome some of the objections to other models. Some of the models exemplify the results of what are ultimately semantic vices. The problems with which these remarks began should indeed yield to the immense and novel resources of molecular biology. But the development of complete analyses demands not only good luck and delicate technique but also critical semantic clarity and severity. Given the best tools, we shall solve major theoretical problems only if we understand quite fully what problem it is that we are trying to solve--and the history of science illustrates that this is not as elementary a matter as it sounds.(ABSTRACT TRUNCATED AT 250 WORDS)
Double symbolic joint entropy in nonlinear dynamic complexity analysis
Yao, Wenpo; Wang, Jun
2017-07-01
Symbolizations, the base of symbolic dynamic analysis, are classified as global static and local dynamic approaches which are combined by joint entropy in our works for nonlinear dynamic complexity analysis. Two global static methods, symbolic transformations of Wessel N. symbolic entropy and base-scale entropy, and two local ones, namely symbolizations of permutation and differential entropy, constitute four double symbolic joint entropies that have accurate complexity detections in chaotic models, logistic and Henon map series. In nonlinear dynamical analysis of different kinds of heart rate variability, heartbeats of healthy young have higher complexity than those of the healthy elderly, and congestive heart failure (CHF) patients are lowest in heartbeats' joint entropy values. Each individual symbolic entropy is improved by double symbolic joint entropy among which the combination of base-scale and differential symbolizations have best complexity analysis. Test results prove that double symbolic joint entropy is feasible in nonlinear dynamic complexity analysis.
Numerical Analysis of Partial Differential Equations
Lui, S H
2011-01-01
A balanced guide to the essential techniques for solving elliptic partial differential equations Numerical Analysis of Partial Differential Equations provides a comprehensive, self-contained treatment of the quantitative methods used to solve elliptic partial differential equations (PDEs), with a focus on the efficiency as well as the error of the presented methods. The author utilizes coverage of theoretical PDEs, along with the nu merical solution of linear systems and various examples and exercises, to supply readers with an introduction to the essential concepts in the numerical analysis
Sanjuan-Jimenez, Rocio; Colmenero, Juan D; Bermúdez, Pilar; Alonso, Antonio; Morata, Pilar
2013-01-01
Some sites of extrapulmonary tuberculosis and focal complications of brucellosis are very difficult to differentiate clinically, radiologically, and even histopathologically. Conventional microbiological methods for the diagnosis of extrapulmonary tuberculosis and complicated brucellosis not only lack adequate sensitivity, they are also time consuming, which could lead to an unfavourable prognosis. The aim of this work was to develop a multiplex real-time PCR assay based on SYBR Green I to simultaneously detect Brucella spp and Mycobacterium tuberculosis complex and evaluate the efficacy of the technique with different candidate genes. The IS711, bcsp31 and omp2a genes were used for the identification of Brucella spp and the IS6110, senX3-regX3 and cfp31 genes were targeted for the detection of the M. tuberculosis complex. As a result of the different combinations of primers, nine different reactions were evaluated. A test was defined as positive only when the gene combinations were capable of co-amplifying both pathogens in a single reaction tube and showed distinguishable melting temperatures for each microorganism. According to the melting analysis, only three combinations of amplicons (senX3-regX3+bcsp31, senX3-regX3+IS711 and IS6110+IS711) were visible. Detection limits of senX3-regX3+bcsp31 and senX3-regX3+IS711 were of 2 and 3 genome equivalents for M. tuberculosis complex and Brucella while for IS6110+IS711 they were of 200 and 300 genome equivalents, respectively. The three assays correctly identified all the samples, showing negative results for the control patients. The presence of multicopy elements and GC content were the components most influencing the efficiency of the test; this should be taken into account when designing a multiplex-based SYBR Green I assay. In conclusion, multiplex real time PCR assays based on the targets senX3-regX3+bcsp31 and senX3-regX3+IS711 using SYBR Green I are highly sensitive and reproducible. This may therefore be a
Directory of Open Access Journals (Sweden)
Rocio Sanjuan-Jimenez
Full Text Available Some sites of extrapulmonary tuberculosis and focal complications of brucellosis are very difficult to differentiate clinically, radiologically, and even histopathologically. Conventional microbiological methods for the diagnosis of extrapulmonary tuberculosis and complicated brucellosis not only lack adequate sensitivity, they are also time consuming, which could lead to an unfavourable prognosis. The aim of this work was to develop a multiplex real-time PCR assay based on SYBR Green I to simultaneously detect Brucella spp and Mycobacterium tuberculosis complex and evaluate the efficacy of the technique with different candidate genes. The IS711, bcsp31 and omp2a genes were used for the identification of Brucella spp and the IS6110, senX3-regX3 and cfp31 genes were targeted for the detection of the M. tuberculosis complex. As a result of the different combinations of primers, nine different reactions were evaluated. A test was defined as positive only when the gene combinations were capable of co-amplifying both pathogens in a single reaction tube and showed distinguishable melting temperatures for each microorganism. According to the melting analysis, only three combinations of amplicons (senX3-regX3+bcsp31, senX3-regX3+IS711 and IS6110+IS711 were visible. Detection limits of senX3-regX3+bcsp31 and senX3-regX3+IS711 were of 2 and 3 genome equivalents for M. tuberculosis complex and Brucella while for IS6110+IS711 they were of 200 and 300 genome equivalents, respectively. The three assays correctly identified all the samples, showing negative results for the control patients. The presence of multicopy elements and GC content were the components most influencing the efficiency of the test; this should be taken into account when designing a multiplex-based SYBR Green I assay. In conclusion, multiplex real time PCR assays based on the targets senX3-regX3+bcsp31 and senX3-regX3+IS711 using SYBR Green I are highly sensitive and reproducible. This may
Analysis of Anther Cell Differentiation
Energy Technology Data Exchange (ETDEWEB)
Ma, Hong [Pennsylvania State Univ., University Park, PA (United States)
2015-01-19
This grant supports research on genes that regulate Arabidopsis anther development. The proposed research largely concerns that functions of two key regulatory genes: SPL and DYT1, which encode two putative transcription factors, as well as genes that interact with these genes. Last year, we reported progress in preparation for ChIP analysis with SPL and DYT1, in dyt1 and ams microarray experiments and initial data analysis, in functional analysis of one of the DYT1 target gene, MYB35.
Directory of Open Access Journals (Sweden)
Shengcai Liu
Full Text Available Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis--based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS, adult seedling (ASS, flower bud (FBS, and flowering (FS stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39% were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the
Workshop on Recent Trends in Complex Methods for Partial Differential Equations
Celebi, A; Tutschke, Wolfgang
1999-01-01
This volume is a collection of manscripts mainly originating from talks and lectures given at the Workshop on Recent Trends in Complex Methods for Par tial Differential Equations held from July 6 to 10, 1998 at the Middle East Technical University in Ankara, Turkey, sponsored by The Scientific and Tech nical Research Council of Turkey and the Middle East Technical University. This workshop is a continuation oftwo workshops from 1988 and 1993 at the In ternational Centre for Theoretical Physics in Trieste, Italy entitled Functional analytic Methods in Complex Analysis and Applications to Partial Differential Equations. Since classical complex analysis of one and several variables has a long tra dition it is of high level. But most of its basic problems are solved nowadays so that within the last few decades it has lost more and more attention. The area of complex and functional analytic methods in partial differential equations, however, is still a growing and flourishing field, in particular as these ...
Painlevé differential equations in the complex plane
Gromak, Valerii I; Shimomura, Shun
2002-01-01
This book is the first comprehensive treatment of Painlevé differential equations in the complex plane. Starting with a rigorous presentation for the meromorphic nature of their solutions, the Nevanlinna theory will be applied to offer a detailed exposition of growth aspects and value distribution of Painlevé transcendents. The subsequent main part of the book is devoted to topics of classical background such as representations and expansions of solutions, solutions of special type like rational and special transcendental solutions, Bäcklund transformations and higher order analogues, treated separately for each of these six equations. The final chapter offers a short overview of applications of Painlevé equations, including an introduction to their discrete counterparts. Due to the present important role of Painlevé equations in physical applications, this monograph should be of interest to researchers in both mathematics and physics and to graduate students interested in mathematical physics and the th...
Efficient Analysis of Complex Structures
Kapania, Rakesh K.
2000-01-01
Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).
Music analysis and Kolmogorov complexity
DEFF Research Database (Denmark)
Meredith, David
that the program represents. If such an effective measure of analysis quality can be found, it could be used in a system that automatically finds the optimal analysis for any passage of music. Measuring program length in terms of number of source-code characters is shown to be problematic and an expression......The goal of music analysis is to find the most satisfying explanations for musical works. It is proposed that this can best be achieved by attempting to write computer programs that are as short as possible and that generate representations that are as detailed as possible of the music...... is proposed that overcomes some but not all of these problems. It is suggested that the solutions to the remaining problems may lie either in the field of concrete Kolmogorov complexity or in the design of languages specialized for expressing musical structure....
Elementary real and complex analysis
Shilov, Georgi E
1996-01-01
In this book the renowned Russian mathematician Georgi E. Shilov brings his unique perspective to real and complex analysis, an area of perennial interest in mathematics. Although there are many books available on the topic, the present work is specially designed for undergraduates in mathematics, science and engineering. A high level of mathematical sophistication is not required.The book begins with a systematic study of real numbers, understood to be a set of objects satisfying certain definite axioms. The concepts of a mathematical structure and an isomorphism are introduced in Chapter 2,
Structural Analysis of Complex Networks
Dehmer, Matthias
2011-01-01
Filling a gap in literature, this self-contained book presents theoretical and application-oriented results that allow for a structural exploration of complex networks. The work focuses not only on classical graph-theoretic methods, but also demonstrates the usefulness of structural graph theory as a tool for solving interdisciplinary problems. Applications to biology, chemistry, linguistics, and data analysis are emphasized. The book is suitable for a broad, interdisciplinary readership of researchers, practitioners, and graduate students in discrete mathematics, statistics, computer science,
On automatic differentiation of codes with COMPLEX arithmetic with respect to real variables
Energy Technology Data Exchange (ETDEWEB)
Pusch, G.D.; Bischof, C. [Argonne National Lab., IL (United States); Carle, A. [Rice Univ., St. Houston, TX (United States)
1995-06-01
We explore what it means to apply automatic differentiation with respect to a set of real variables to codes containing complex arithmetic. That is, both dependent and independent variables with respect to differentiation are real variables, but in order to exploit features of complex mathematics, part of the code is expressed by employing complex arithmetic. We investigate how one can apply automatic differentiation to complex variables if one exploits the homomorphism of the complex numbers C onto R{sup 2}. It turns out that, by and large, the usual rules of differentiation apply, but subtle differences in special cases arise for sqrt (), abs (), and the power operator.
Khuansuwan, Sataree; Gamse, Joshua T
2014-11-01
We describe a method for isolating RNA suitable for high-throughput RNA sequencing (RNA-seq) from small numbers of fluorescently labeled cells isolated from live zebrafish (Danio rerio) embryos without using costly, commercially available columns. This method ensures high cell viability after dissociation and suspension of cells and gives a very high yield of intact RNA. We demonstrate the utility of our new protocol by isolating RNA from fluorescence activated cell sorted (FAC sorted) pineal complex neurons in wild-type and tbx2b knockdown embryos at 24 hours post-fertilization. Tbx2b is a transcription factor required for pineal complex formation. We describe a bioinformatics pipeline used to analyze differential expression following high-throughput sequencing and demonstrate the validity of our results using in situ hybridization of differentially expressed transcripts. This protocol brings modern transcriptome analysis to the study of small cell populations in zebrafish.
Complex analysis conformal inequalities and the Bieberbach conjecture
Kythe, Prem K
2015-01-01
Complex Analysis: Conformal Inequalities and the Bieberbach Conjecture discusses the mathematical analysis created around the Bieberbach conjecture, which is responsible for the development of many beautiful aspects of complex analysis, especially in the geometric-function theory of univalent functions. Assuming basic knowledge of complex analysis and differential equations, the book is suitable for graduate students engaged in analytical research on the topics and researchers working on related areas of complex analysis in one or more complex variables. The author first reviews the theory of analytic functions, univalent functions, and conformal mapping before covering various theorems related to the area principle and discussing Löwner theory. He then presents Schiffer’s variation method, the bounds for the fourth and higher-order coefficients, various subclasses of univalent functions, generalized convexity and the class of a-convex functions, and numerical estimates of the coefficient problem. The boo...
A note on the Dirichlet problem for model complex partial differential equations
Ashyralyev, Allaberen; Karaca, Bahriye
2016-08-01
Complex model partial differential equations of arbitrary order are considered. The uniqueness of the Dirichlet problem is studied. It is proved that the Dirichlet problem for higher order of complex partial differential equations with one complex variable has infinitely many solutions.
Multifractal analysis of complex networks
Institute of Scientific and Technical Information of China (English)
Wang Dan-Ling; Yu Zu-Guo; Anh V
2012-01-01
Complex networks have recently attracted much attention in diverse areas of science and technology.Many networks such as the WWW and biological networks are known to display spatial heterogeneity which can be characterized by their fractal dimensions.Multifractal analysis is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns.In this paper,we introduce a new box-covering algorithm for muttifractal analysis of complex networks.This algorithm is used to calculate the generalized fractal dimensions Dq of some theoretical networks,namely scale-free networks,small world networks,and random networks,and one kind of real network,namely protein-protein interaction networks of different species.Our numerical results indicate the existence of multifractality in scale-free networks and protein-protein interaction networks,while the multifractal behavior is not clear-cut for small world networks and random networks.The possible variation of Dq due to changes in the parameters of the theoretical network models is also discussed.
Indian Academy of Sciences (India)
Ting-Bin Cao; Hong-Yan Xu; Chuan-Xi Zhu
2010-09-01
In this paper, we investigate the complex oscillation of differential polynomials generated by meromorphic solutions of differential equations $$f^{(k)}+A(z)f=0,\\quad k≥ 2,$$ where the coefficient is meromorphic in the unit disc $\\mathbb{D}=\\{z:|z| < 1\\}$.
DGCA: A comprehensive R package for Differential Gene Correlation Analysis.
McKenzie, Andrew T; Katsyv, Igor; Song, Won-Min; Wang, Minghui; Zhang, Bin
2016-11-15
Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions. To minimize parametric assumptions, DGCA computes empirical p-values via permutation testing. To understand differential correlations at a systems level, DGCA performs higher-order analyses such as measuring the average difference in correlation and multiscale clustering analysis of differential correlation networks. Through a simulation study, we show that the straightforward z-score based method that DGCA employs significantly outperforms the existing alternative methods for calculating differential correlation. Application of DGCA to the TCGA RNA-seq data in breast cancer not only identifies key changes in the regulatory relationships between TP53 and PTEN and their target genes in the presence of inactivating mutations, but also reveals an immune-related differential correlation module that is specific to triple negative breast cancer (TNBC). DGCA is an R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. This user-friendly, effective, and comprehensive software tool will greatly facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signaling pathways, biomarkers, and targets in complex biological systems and diseases.
DNA microarray analysis of genes differentially expressed in adipocyte differentiation
Indian Academy of Sciences (India)
Chunyan Yin; Yanfeng Xiao; Wei Zhang; Erdi Xu; Weihua Liu; Xiaoqing Yi; Ming Chang
2014-06-01
In the present study, the human liposarcoma cell line SW872 was used to identify global changes in gene expression profiles occurring during adipogenesis. We further explored some of the genes expressed during the late phase of adipocyte differentiation. These genes may play a major role in promoting excessive proliferation and accumulation of lipid droplets, which contribute to the development of obesity. By using microarray-based technology, we examined differential gene expression in early differentiated adipocytes and late differentiated adipocytes. Validated genes exhibited a ≥ 10-fold increase in the late phase of adipocyte differentiation by polymerase chain reaction (RT-PCR). Compared with undifferentiated preadipocytes, we found that 763 genes were increased in early differentiated adipocytes, and 667 genes were increased in later differentiated adipocytes. Furthermore, 21 genes were found being expressed 10-fold higher in the late phase of adipocyte differentiation. The results were in accordance with the RT-PCR test, which validated 11 genes, namely, CIDEC, PID1, LYRM1, ADD1, PPAR2, ANGPTL4, ADIPOQ, ACOX1, FIP1L1, MAP3K2 and PEX14. Most of these genes were found being expressed in the later phase of adipocyte differentiation involved in obesity-related diseases. The findings may help to better understand the mechanism of obesity and related diseases.
DNA microarray analysis of genes differentially expressed in adipocyte differentiation.
Yin, Chunyan; Xiao, Yanfeng; Zhang, Wei; Xu, Erdi; Liu, Weihua; Yi, Xiaoqing; Chang, Ming
2014-06-01
In the present study, the human liposarcoma cell line SW872 was used to identify global changes in gene expression profiles occurring during adipogenesis. We further explored some of the genes expressed during the late phase of adipocyte differentiation. These genes may play a major role in promoting excessive proliferation and accumulation of lipid droplets, which contribute to the development of obesity. By using microarray-based technology, we examined differential gene expression in early differentiated adipocytes and late differentiated adipocytes. Validated genes exhibited a greater than or equal to 10-fold increase in the late phase of adipocyte differentiation by polymerase chain reaction (RT-PCR). Compared with undifferentiated preadipocytes, we found that 763 genes were increased in early differentiated adipocytes, and 667 genes were increased in later differentiated adipocytes. Furthermore, 21 genes were found being expressed 10-fold higher in the late phase of adipocyte differentiation. The results were in accordance with the RTPCR test, which validated 11 genes, namely, CIDEC, PID1, LYRM1, ADD1, PPAR?2, ANGPTL4, ADIPOQ, ACOX1, FIP1L1, MAP3K2 and PEX14. Most of these genes were found being expressed in the later phase of adipocyte differentiation involved in obesity-related diseases. The findings may help to better understand the mechanism of obesity and related diseases.
Hierarchical Parallelization of Gene Differential Association Analysis
Directory of Open Access Journals (Sweden)
Dwarkadas Sandhya
2011-09-01
Full Text Available Abstract Background Microarray gene differential expression analysis is a widely used technique that deals with high dimensional data and is computationally intensive for permutation-based procedures. Microarray gene differential association analysis is even more computationally demanding and must take advantage of multicore computing technology, which is the driving force behind increasing compute power in recent years. In this paper, we present a two-layer hierarchical parallel implementation of gene differential association analysis. It takes advantage of both fine- and coarse-grain (with granularity defined by the frequency of communication parallelism in order to effectively leverage the non-uniform nature of parallel processing available in the cutting-edge systems of today. Results Our results show that this hierarchical strategy matches data sharing behavior to the properties of the underlying hardware, thereby reducing the memory and bandwidth needs of the application. The resulting improved efficiency reduces computation time and allows the gene differential association analysis code to scale its execution with the number of processors. The code and biological data used in this study are downloadable from http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm. Conclusions The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels.
Energy Technology Data Exchange (ETDEWEB)
Zhang Huiqun [College of Mathematical Science, Qingdao University, Qingdao, Shandong 266071 (China)], E-mail: hellozhq@yahoo.com.cn
2009-02-15
By using some exact solutions of an auxiliary ordinary differential equation, a direct algebraic method is described to construct the exact complex solutions for nonlinear partial differential equations. The method is implemented for the NLS equation, a new Hamiltonian amplitude equation, the coupled Schrodinger-KdV equations and the Hirota-Maccari equations. New exact complex solutions are obtained.
Algebroid Solutions of Second Order Complex Differential Equations
Directory of Open Access Journals (Sweden)
Lingyun Gao
2014-01-01
Full Text Available Using value distribution theory and maximum modulus principle, the problem of the algebroid solutions of second order algebraic differential equation is investigated. Examples show that our results are sharp.
Electrochemical analysis of metal complexes.
Jong, de H.G.
1987-01-01
The present study is concerned with the electroanalytical chemistry of complexes of metals with large ligands. The main purpose was to develop quantitative descriptions of the voltammetric current-potential relation of metal complex systems with different diffusion coefficients of the species involv
Directory of Open Access Journals (Sweden)
Abigail J Moore
Full Text Available Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae. We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.
Moore, Abigail J; Moore, William L; Baldwin, Bruce G
2014-01-01
Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.
Software Performs Complex Design Analysis
2008-01-01
Designers use computational fluid dynamics (CFD) to gain greater understanding of the fluid flow phenomena involved in components being designed. They also use finite element analysis (FEA) as a tool to help gain greater understanding of the structural response of components to loads, stresses and strains, and the prediction of failure modes. Automated CFD and FEA engineering design has centered on shape optimization, which has been hindered by two major problems: 1) inadequate shape parameterization algorithms, and 2) inadequate algorithms for CFD and FEA grid modification. Working with software engineers at Stennis Space Center, a NASA commercial partner, Optimal Solutions Software LLC, was able to utilize its revolutionary, one-of-a-kind arbitrary shape deformation (ASD) capability-a major advancement in solving these two aforementioned problems-to optimize the shapes of complex pipe components that transport highly sensitive fluids. The ASD technology solves the problem of inadequate shape parameterization algorithms by allowing the CFD designers to freely create their own shape parameters, therefore eliminating the restriction of only being able to use the computer-aided design (CAD) parameters. The problem of inadequate algorithms for CFD grid modification is solved by the fact that the new software performs a smooth volumetric deformation. This eliminates the extremely costly process of having to remesh the grid for every shape change desired. The program can perform a design change in a markedly reduced amount of time, a process that would traditionally involve the designer returning to the CAD model to reshape and then remesh the shapes, something that has been known to take hours, days-even weeks or months-depending upon the size of the model.
Analysis of linear partial differential operators
Hörmander , Lars
2005-01-01
This volume is an expanded version of Chapters III, IV, V and VII of my 1963 book "Linear partial differential operators". In addition there is an entirely new chapter on convolution equations, one on scattering theory, and one on methods from the theory of analytic functions of several complex variables. The latter is somewhat limited in scope though since it seems superfluous to duplicate the monographs by Ehrenpreis and by Palamodov on this subject. The reader is assumed to be familiar with distribution theory as presented in Volume I. Most topics discussed here have in fact been encountered in Volume I in special cases, which should provide the necessary motivation and background for a more systematic and precise exposition. The main technical tool in this volume is the Fourier- Laplace transformation. More powerful methods for the study of operators with variable coefficients will be developed in Volume III. However, constant coefficient theory has given the guidance for all that work. Although the field...
Differential thermal analysis microsystem for explosive detection
DEFF Research Database (Denmark)
Olsen, Jesper Kenneth; Greve, Anders; Senesac, L.
2011-01-01
A micro differential thermal analysis (DTA) system is used for detection of trace explosive particles. The DTA system consists of two silicon micro chips with integrated heaters and temperature sensors. One chip is used for reference and one for the measurement sample. The sensor is constructed...... as a small silicon nitride membrane incorporating heater elements and a temperature measurement resistor. In this manuscript the DTA system is described and tested by measuring calorimetric response of 3 different kinds of explosives (TNT, RDX and PETN). This project is carried out under the framework...
An introduction to complex analysis and geometry
D'Angelo, John P
2010-01-01
An Introduction to Complex Analysis and Geometry provides the reader with a deep appreciation of complex analysis and how this subject fits into mathematics. The book developed from courses given in the Campus Honors Program at the University of Illinois Urbana-Champaign. These courses aimed to share with students the way many mathematics and physics problems magically simplify when viewed from the perspective of complex analysis. The book begins at an elementary level but also contains advanced material. The first four chapters provide an introduction to complex analysis with many elementary
Weng, Yi; He, Xuan; Pan, Zhongqi
2016-02-01
Mode-division multiplexing (MDM) transmission systems utilizing few-mode fibers (FMF) have been intensively explored to sustain continuous traffic growth. The key challenges of MDM systems are inter-modal crosstalk due to random mode coupling (RMC), and largely-accumulated differential mode group delay (DMGD), whilst hinders mode-demultiplexer implementation. The adaptive multi-input multi-output (MIMO) frequency-domain equalization (FDE) can dynamically compensate DMGD using digital signal processing (DSP) algorithms. The frequency-domain least-mean squares (FD-LMS) algorithm has been universally adopted for high-speed MDM communications, mainly for its relatively low computational complexity. However, longer training sequence is appended for FD-LMS to achieve faster convergence, which incurs prohibitively higher system overhead and reduces overall throughput. In this paper, we propose a fast-convergent single-stage adaptive frequency-domain recursive least-squares (FD-RLS) algorithm with reduced complexity for DMGD compensation at MDM coherent receivers. The performance and complexity comparison of FD-RLS, with signal-PSD-dependent FD-LMS method and conventional FD-LMS approach, are performed in a 3000 km six-mode transmission system with 65 ps/km DMGD. We explore the convergence speed of three adaptive algorithms, including the normalized mean-square-error (NMSE) per fast Fourier transform (FFT) block at 14-30 dB OSNR. The fast convergence of FD-RLS is exploited at the expense of slightly-increased necessary tap numbers for MIMO equalizers, and it can partially save the overhead of training sequence. Furthermore, we demonstrate adaptive FD-RLS can also be used for chromatic dispersion (CD) compensation without increasing the filter tap length, thus prominently reducing the DSP implementation complexity for MDM systems.
Statistics for proteomics: experimental design and 2-DE differential analysis.
Chich, Jean-François; David, Olivier; Villers, Fanny; Schaeffer, Brigitte; Lutomski, Didier; Huet, Sylvie
2007-04-15
Proteomics relies on the separation of complex protein mixtures using bidimensional electrophoresis. This approach is largely used to detect the expression variations of proteins prepared from two or more samples. Recently, attention was drawn on the reliability of the results published in literature. Among the critical points identified were experimental design, differential analysis and the problem of missing data, all problems where statistics can be of help. Using examples and terms understandable by biologists, we describe how a collaboration between biologists and statisticians can improve reliability of results and confidence in conclusions.
A note on the Lie symmetries of complex partial differential equations and their split real systems
Indian Academy of Sciences (India)
F M Mahomed; Rehana Naz
2011-09-01
Folklore suggests that the split Lie-like operators of a complex partial differential equation are symmetries of the split system of real partial differential equations. However, this is not the case generally. We illustrate this by using the complex heat equation, wave equation with dissipation, the nonlinear Burgers equation and nonlinear KdV equations. We split the Lie symmetries of a complex partial differential equation in the real domain and obtain real Lie-like operators. Further, the complex partial differential equation is split into two coupled or uncoupled real partial differential equations which constitute a system of two equations for two real functions of two real variables. The Lie symmetries of this system are constructed by the classical Lie approach. We compare these Lie symmetries with the split Lie-like operators of the given complex partial differential equation for the examples considered. We conclude that the split Lie-like operators of complex partial differential equations are not in general symmetries of the split system of real partial differential equations. We prove a proposition that gives the criteria when the Lie-like operators are symmetries of the split system.
Delay differential analysis of time series.
Lainscsek, Claudia; Sejnowski, Terrence J
2015-03-01
Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time
Delay Differential Analysis of Time Series
Lainscsek, Claudia; Sejnowski, Terrence J.
2015-01-01
Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time
On the Complexity of Numerical Analysis
DEFF Research Database (Denmark)
Miltersen, Peter Bro; Kjeldgaard-Pedersen, Johan; Burgisser, Peter;
2006-01-01
We study two quite different approaches to understanding the complexity of fundamental problems in numerical analysis. We show that both hinge on the question of understanding the complexity of the following problem, which we call PosSLP: Given a division-free straight-line program producing...... of classical complexity classes) being PSPACE....
Harmonic and complex analysis in several variables
Krantz, Steven G
2017-01-01
Authored by a ranking authority in harmonic analysis of several complex variables, this book embodies a state-of-the-art entrée at the intersection of two important fields of research: complex analysis and harmonic analysis. Written with the graduate student in mind, it is assumed that the reader has familiarity with the basics of complex analysis of one and several complex variables as well as with real and functional analysis. The monograph is largely self-contained and develops the harmonic analysis of several complex variables from the first principles. The text includes copious examples, explanations, an exhaustive bibliography for further reading, and figures that illustrate the geometric nature of the subject. Each chapter ends with an exercise set. Additionally, each chapter begins with a prologue, introducing the reader to the subject matter that follows; capsules presented in each section give perspective and a spirited launch to the segment; preludes help put ideas into context. Mathematicians and...
Differential network analysis with multiply imputed lipidomic data.
Directory of Open Access Journals (Sweden)
Maiju Kujala
Full Text Available The importance of lipids for cell function and health has been widely recognized, e.g., a disorder in the lipid composition of cells has been related to atherosclerosis caused cardiovascular disease (CVD. Lipidomics analyses are characterized by large yet not a huge number of mutually correlated variables measured and their associations to outcomes are potentially of a complex nature. Differential network analysis provides a formal statistical method capable of inferential analysis to examine differences in network structures of the lipids under two biological conditions. It also guides us to identify potential relationships requiring further biological investigation. We provide a recipe to conduct permutation test on association scores resulted from partial least square regression with multiple imputed lipidomic data from the LUdwigshafen RIsk and Cardiovascular Health (LURIC study, particularly paying attention to the left-censored missing values typical for a wide range of data sets in life sciences. Left-censored missing values are low-level concentrations that are known to exist somewhere between zero and a lower limit of quantification. To make full use of the LURIC data with the missing values, we utilize state of the art multiple imputation techniques and propose solutions to the challenges that incomplete data sets bring to differential network analysis. The customized network analysis helps us to understand the complexities of the underlying biological processes by identifying lipids and lipid classes that interact with each other, and by recognizing the most important differentially expressed lipids between two subgroups of coronary artery disease (CAD patients, the patients that had a fatal CVD event and the ones who remained stable during two year follow-up.
Complex Wavelet Based Modulation Analysis
DEFF Research Database (Denmark)
Luneau, Jean-Marc; Lebrun, Jérôme; Jensen, Søren Holdt
2008-01-01
because only the magnitudes are taken into account and the phase data is often neglected. We remedy this problem with the use of a complex wavelet transform as a more appropriate envelope and phase processing tool. Complex wavelets carry both magnitude and phase explicitly with great sparsity and preserve well...... polynomial trends. Moreover an analytic Hilbert-like transform is possible with complex wavelets implemented as an orthogonal filter bank. By working in an alternative transform domain coined as “Modulation Subbands”, this transform shows very promising denoising capabilities and suggests new approaches for joint...
Static Complexity Analysis of Higher Order Programs
DEFF Research Database (Denmark)
Avery, James Emil; Kristiansen, Lars; Moyen, Jean-Yves
2009-01-01
The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs.......The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs....
Morphological evolution and genetic differentiation in Daphnia species complexes
Gießer, S.; Mader, E.; Schwenk, K.
1999-01-01
Despite many ecological and evolutionary studies, the history of several species complexes within the freshwater crustacean genus Daphnia (Branchiopoda, Anomopoda) is poorly understood. In particular, the Daphnia longispina group, comprising several large-lake species, is characterized by pronounced
Ten papers on complex analysis
Arakelyan, N U; Krushkal', S L; Gutlyanskii, V Ya; Kudyavin, V S
1984-01-01
The papers in this volume cover both one-variable and several-variable problems. An example of the former is a fifty-year-old classic on conformal mapping by M. A. Lavrent€´ev, while the latter is represented by a paper on the tangent complex of an analytic space by V. P. Palamodov.
Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations
Energy Technology Data Exchange (ETDEWEB)
Petzold, L; Cao, Y; Li, S; Serban, R
2005-08-09
Sensitivity analysis generates essential information for model development, design optimization, parameter estimation, optimal control, model reduction and experimental design. In this paper we describe the forward and adjoint methods for sensitivity analysis, and outline some of our recent work on theory, algorithms and software for sensitivity analysis of differential-algebraic equation (DAE) and time-dependent partial differential equation (PDE) systems.
Stochastic Computational Approach for Complex Nonlinear Ordinary Differential Equations
Institute of Scientific and Technical Information of China (English)
Junaid Ali Khan; Muhammad Asif Zahoor Raja; Ijaz Mansoor Qureshi
2011-01-01
@@ We present an evolutionary computational approach for the solution of nonlinear ordinary differential equations (NLODEs).The mathematical modeling is performed by a feed-forward artificial neural network that defines an unsupervised error.The training of these networks is achieved by a hybrid intelligent algorithm, a combination of global search with genetic algorithm and local search by pattern search technique.The applicability of this approach ranges from single order NLODEs, to systems of coupled differential equations.We illustrate the method by solving a variety of model problems and present comparisons with solutions obtained by exact methods and classical numerical methods.The solution is provided on a continuous finite time interval unlike the other numerical techniques with comparable accuracy.With the advent of neuroprocessors and digital signal processors the method becomes particularly interesting due to the expected essential gains in the execution speed.%We present an evolutionary computational approach for the solution of nonlinear ordinary differential equations (NLODEs). The mathematical modeling is performed by a feed-forward artificial neural network that defines an unsupervised error. The training of these networks is achieved by a hybrid intelligent algorithm, a combination of global search with genetic algorithm and local search by pattern search technique. The applicability of this approach ranges from single order NLODEs, to systems of coupled differential equations. We illustrate the method by solving a variety of model problems and present comparisons with solutions obtained by exact methods and classical numerical methods. The solution is provided on a continuous finite time interval unlike the other numerical techniques with comparable accuracy. With the advent of neuroprocessors and digital signal processors the method becomes particularly interesting due to the expected essential gains in the execution speed.
Numerical analysis of systems of ordinary and stochastic differential equations
Artemiev, S S
1997-01-01
This text deals with numerical analysis of systems of both ordinary and stochastic differential equations. It covers numerical solution problems of the Cauchy problem for stiff ordinary differential equations (ODE) systems by Rosenbrock-type methods (RTMs).
Zhao, Yanchuan; Swager, Timothy M
2013-12-18
Fluorinated tungsten calix[4]arene imido complexes were synthesized and used as receptors to detect and differentiate neutral organic compounds. It was found that the binding of specific neutral organic molecules to the tungsten centers induces an upfield shift of the fluorine atom appended on the arylimido group, the extent of which is highly dependent on electronic and steric properties. We demonstrate that the specific bonding and size-selectivity of calix[4]arene tungsten-imido complex combined with (19)F NMR spectroscopy is a powerful new method for the analysis of complex mixtures.
Directory of Open Access Journals (Sweden)
Lin Chih-Li
2010-02-01
Full Text Available Abstract Background Functional cooperation between FACT and the MCM helicase complex constitutes an integral step during DNA replication initiation. However, mode of regulation that underlies the proper functional interaction of FACT and MCM is poorly understood. Methods & Results Here we present evidence indicating that such interaction is coordinated with cell cycle progression and differential complex formation. We first demonstrate the existence of two distinct FACT-MCM subassemblies, FACT-MCM2/4/6/7 and FACT-MCM2/3/4/5. Both complexes possess DNA unwinding activity and are subject to cell cycle-dependent enzymatic regulation. Interestingly, analysis of functional attributes further suggests that they act at distinct, and possibly sequential, steps during origin establishment and replication initiation. Moreover, we show that the phosphorylation profile of the FACT-associated MCM4 undergoes a cell cycle-dependent change, which is directly correlated with the catalytic activity of the FACT-MCM helicase complexes. Finally, at the quaternary structure level, physical interaction between FACT and MCM complexes is generally dependent on persistent cell cycle and further stabilized upon S phase entry. Cessation of mitotic cycle destabilizes the complex formation and likely leads to compromised coordination and activities. Conclusions Together, our results correlate FACT-MCM functionally and temporally with S phase and DNA replication. They further demonstrate that enzymatic activities intrinsically important for DNA replication are tightly controlled at various levels, thereby ensuring proper progression of, as well as exit from, the cell cycle and ultimately euploid gene balance.
Fourier analysis in several complex variables
Ehrenpreis, Leon
2006-01-01
Suitable for advanced undergraduates and graduate students, this text develops comparison theorems to establish the fundamentals of Fourier analysis and to illustrate their applications to partial differential equations.The three-part treatment begins by establishing the quotient structure theorem or fundamental principle of Fourier analysis. Topics include the geometric structure of ideals and modules, quantitative estimates, and examples in which the theory can be applied. The second part focuses on applications to partial differential equations and covers the solution of homogeneous and inh
Differentiating morphology, form, and meaning: neural correlates of morphological complexity.
Bozic, Mirjana; Marslen-Wilson, William D; Stamatakis, Emmanuel A; Davis, Matthew H; Tyler, Lorraine K
2007-09-01
The role of morphological structure in word recognition raises issues about the nature and structure of the language system. One major issue is whether morphological factors provide an independent principle for lexical organization and processing, or whether morphological effects can be reduced to the joint contribution of form and meaning. The independence of form, meaning, and morphological structure can be directly investigated using derivationally complex words, because derived words can share form but need not share meaning (e.g., archer-arch). We used an event-related functional magnetic resonance imaging paradigm to investigate priming between pairs of words that potentially shared a stem, where this link was either semantically transparent (e.g., bravely-brave) or opaque (e.g., archer-arch). These morphologically related pairs were contrasted with identity priming (e.g., mist-mist) and priming for pairs of words that shared only form (e.g., scandal-scan) or meaning (e.g., accuse-blame). Morphologically related words produced significantly reduced activation in left frontal regions, whether the pairs were semantically transparent or opaque. The effect was not found for any of the control conditions (identity, form, or meaning). Morphological effects were observed separately from processing form and meaning and we propose that they reflect segmentation of complex derived words, a process triggered by surface morphological structure of complex words.
Analysis of Variance: Variably Complex
Drummond, Gordon B.; Vowler, Sarah L.
2012-01-01
These authors have previously described how to use the "t" test to compare two groups. In this article, they describe the use of a different test, analysis of variance (ANOVA) to compare more than two groups. ANOVA is a test of group differences: do at least two of the means differ from each other? ANOVA assumes (1) normal distribution of…
Institute of Scientific and Technical Information of China (English)
Seonmin Lee; Eunyoung Tak; Jisun Lee; MA Rashid; Michael P Murphy; Joohun Ha; Sung Soo Kim
2011-01-01
Mitochondrial reactive oxygen species(mROS)have been considered detrimental to cells. However, their physiological roles as signaling mediators have not been thoroughly explored. Here, we investigated whether mROS generated from mitochondrial electron transport chain(mETC)complex I stimulated muscle differentiation. Our results showed that the quantity of mROS was increased and that manganese superoxide dismutase(MnSOD)was induced via NF-KB activation during muscle differentiation. Mitochondria-targeted antioxidants(MitoQ and MitoTEMPOL)and mitochondria-targeted catalase decreased mROS quantity and suppressed muscle differentiation without affecting the amount of ATP Mitochondrial alterations, including the induction of mitochondrial transcription factor A and an increase in the number and size of mitochondria, and functional activations were observed during muscle differentiation. In particular, increased expression levels of mETC complex I subunits and a higher activity of complex I than other complexes were observed. Rotenone, an inhibitor of mETC complex I, decreased the mitochondrial NADH/NAD+ ratio and mROS levels during muscle differentiation. The inhibition of complex I using small interfering RNAs and rotenone reduced mROS levels, suppressed muscle differentiation, and depleted ATP levels with a concomitant increase in glycolysis. From these results, we conclude that complex I-derived O2, produced through reverse electron transport due to enhanced metabolism and a high activity of complex I, was dismutated into H2O2 by MnSOD induced via NF-KB activation and that the dismutated mH202 stimulated muscle differentiation as a signaling messenger.
Linear and complex analysis problem
Nikolski, Nikolai
1994-01-01
The 2-volume book is an updated, reorganized and considerably enlarged version of the previous edition of the Research Problem Book in Analysis (LNM 1043), a collection familiar to many analysts, that has sparked off much research. This new edition, created in a joint effort by a large team of analysts, is, like its predecessor, a collection of unsolved problems of modern analysis designed as informally written mini-articles, each containing not only a statement of a problem but also historical and methodological comments, motivation, conjectures and discussion of possible connections, of plausible approaches as well as a list of references. There are now 342 of these mini- articles, almost twice as many as in the previous edition, despite the fact that a good deal of them have been solved!
Linear and complex analysis problem
Nikolski, Nikolai
1994-01-01
The 2-volume-book is an updated, reorganized and considerably enlarged version of the previous edition of the Research Problem Book in Analysis (LNM 1043), a collection familiar to many analysts, that has sparked off much research. This new edition, created in a joint effort by a large team of analysts, is, like its predecessor, a collection of unsolved problems of modern analysis designed as informally written mini-articles, each containing not only a statement of a problem but also historical and metho- dological comments, motivation, conjectures and discussion of possible connections, of plausible approaches as well as a list of references. There are now 342 of these mini- articles, almost twice as many as in the previous edition, despite the fact that a good deal of them have been solved!
Safety analysis for complex systems
Onesty, J. P.; Peercy, R. L., Jr.
1981-01-01
Operational risk assessment considers hardware, environment, and human factors. Technique starts with division of postulated mission into segments which are further subdivided into separate operational steps. Consequences of steps, nonoccurrence, premature operation, out-of-sequence operation, and inadvertent execution are examined at subevent, event, and phase levels. Hazards are identified and treated individually. Analysis is well suited to application in energy and transportation fields.
The Effects of Differential Goal Weights on the Performance of a Complex Financial Task.
Edmister, Robert O.; Locke, Edwin A.
1987-01-01
Determined whether people could obtain outcomes on a complex task that would be in line with differential goal weights corresponding to different aspects of the task. Bank lending officers were run through lender-simulation exercises. Five performance goals were weighted. Demonstrated effectiveness of goal setting with complex tasks, using group…
A first course in partial differential equations with complex variables and transform methods
Weinberger, H F
1995-01-01
Suitable for advanced undergraduate and graduate students, this text presents the general properties of partial differential equations, including the elementary theory of complex variables. Topics include one-dimensional wave equation, properties of elliptic and parabolic equations, separation of variables and Fourier series, nonhomogeneous problems, and analytic functions of a complex variable. Solutions. 1965 edition.
Shape Morphing of Complex Geometries Using Partial Differential Equations
Directory of Open Access Journals (Sweden)
Gabriela González Castro
2007-11-01
Full Text Available An alternative technique for shape morphing using a surface generating method using partial differential equations is outlined throughout this work. The boundaryvalue nature that is inherent to this surface generation technique together with its mathematical properties are hereby exploited for creating intermediate shapes between an initial shape and a final one. Four alternative shape morphing techniques are proposed here. The first one is based on the use of a linear combination of the boundary conditions associated with the initial and final surfaces, the second one consists of varying the Fourier mode for which the PDE is solved whilst the third results from a combination of the first two. The fourth of these alternatives is based on the manipulation of the spine of the surfaces, which is computed as a by-product of the solution. Results of morphing sequences between two topologically nonequivalent surfaces are presented. Thus, it is shown that the PDE based approach for morphing is capable of obtaining smooth intermediate surfaces automatically in most of the methodologies presented in this work and the spine has been revealed as a powerful tool for morphing surfaces arising from the method proposed here.
Automated analysis of complex data
Saintamant, Robert; Cohen, Paul R.
1994-01-01
We have examined some of the issues involved in automating exploratory data analysis, in particular the tradeoff between control and opportunism. We have proposed an opportunistic planning solution for this tradeoff, and we have implemented a prototype, Igor, to test the approach. Our experience in developing Igor was surprisingly smooth. In contrast to earlier versions that relied on rule representation, it was straightforward to increment Igor's knowledge base without causing the search space to explode. The planning representation appears to be both general and powerful, with high level strategic knowledge provided by goals and plans, and the hooks for domain-specific knowledge are provided by monitors and focusing heuristics.
A complex analysis problem book
Alpay, Daniel
2016-01-01
This second edition presents a collection of exercises on the theory of analytic functions, including completed and detailed solutions. It introduces students to various applications and aspects of the theory of analytic functions not always touched on in a first course, while also addressing topics of interest to electrical engineering students (e.g., the realization of rational functions and its connections to the theory of linear systems and state space representations of such systems). It provides examples of important Hilbert spaces of analytic functions (in particular the Hardy space and the Fock space), and also includes a section reviewing essential aspects of topology, functional analysis and Lebesgue integration. Benefits of the 2nd edition Rational functions are now covered in a separate chapter. Further, the section on conformal mappings has been expanded.
DNA microsatellite analysis for tomato genetic differentiation
Directory of Open Access Journals (Sweden)
Miskoska-Milevska Elizabeta
2015-01-01
Full Text Available Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11 in genetic differentiation of six morphologically different tomato varieties (var. grandifolium from subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme and var. pyriforme from subsp. subspontaneum; and var. racemigerum from subsp. spontaneum. The fragment analyses was performed using Applied Biosystems DNA analyzer (ABI 3130 and GeneMapper® Software program. The data were analysed using the specific program Power Marker Software. The average number of detected alleles was 3,625. Also, the average PIC value for all 8 DNA microsatellites loci was 0,3571. The genetic differentiation test in the researched tomato subspecies showed minor differentiation for locus LELEUZIP (- 0,0009, modest differentiation for locus LECH13 (0,0896, locus LEMDDNa (0,0896 and locus LE21085 (0,0551 and major differentiation for locus LE2A11 (0,7633, locus LEEF1Aa (0,6167, locus TMS9 (0.4967 and locus LE20592 (0,4263. On the other hand, in the estimated tomato varieties, locus LE21085 (0,0297, locus LECH13 (0,0256 and locus LELEUZIP (0,0005 showed minor differentiation, locus LEMDDNa (0,1333 showed modest differentiation, while locus TMS9 (0,5929, locus LEEF1Aa (0,5006, locus LE2A11 (0,4013 and locus LE20592 (0,2606 showed major differentiation. The eight DNA microsatellite loci can be applicable solution for tomato genetic differentiation. The overall results suggest that these microsatellite loci could be used in further population genetic studies of tomatoes.
Separation and Analysis of Complex Samples
Institute of Scientific and Technical Information of China (English)
2011-01-01
@@ Founded on the basis of the CAS Key Lab of Separation Sciences for Analytical Chemistry, this group has been conducting research into separation and analysis of complex samples for five years.Thanks to their hard work, a number of achievements were scored in the following fields: highly selective and highly efficient separation and analysis of complex samples, high through-put analysis and highly sensitive detection.Besides, the group also made many efforts on the development and application of new technologies and as a result, a total of 13 innovative patents were or are being commercialized.Now, facing great demands for separation and analysis of complex samples in other areas such as lite sciences and environmental sciences, this group will further extend their research directions.
Stability analysis of impulsive functional differential equations
Stamova, Ivanka
2009-01-01
This book is devoted to impulsive functional differential equations which are a natural generalization of impulsive ordinary differential equations (without delay) and of functional differential equations (without impulses). At the present time the qualitative theory of such equationsis under rapid development. After a presentation of the fundamental theory of existence, uniqueness and continuability of solutions, a systematic development of stability theory for that class of problems is given which makes the book unique. It addresses to a wide audience such as mathematicians, applied research
Structure analysis of growing network based on partial differential equations
Directory of Open Access Journals (Sweden)
Junbo JIA
2016-04-01
Full Text Available The topological structure is one of the most important contents in the complex network research. Therein the node degree and the degree distribution are the most basic characteristic quantities to describe topological structure. In order to calculate the degree distribution, first of all, the node degree is considered as a continuous variable. Then, according to the Markov Property of growing network, the cumulative distribution function's evolution equation with time can be obtained. Finally, the partial differential equation (PDE model can be established through distortion processing. Taking the growing network with preferential and random attachment mechanism as an example, the PDE model is obtained. The analytic expression of degree distribution is obtained when this model is solved. Besides, the degree function over time is the same as the characteristic line of PDE. At last, the model is simulated. This PDE method of changing the degree distribution calculation into problem of solving PDE makes the structure analysis more accurate.
Hoffjan, S; Stemmler, S
2007-09-01
Undisturbed epidermal differentiation is crucial for an intact skin barrier function. The epidermal differentiation complex (EDC) is a cluster of genes on chromosome 1q21 encoding proteins that fulfil important functions in terminal differentiation in the human epidermis, including filaggrin, loricrin, S100 proteins and others. Recently, evidence emerged that variation within EDC genes plays an important role in the pathogenesis of three common skin disorders, ichthyosis vulgaris, atopic dermatitis (AD) and psoriasis. Two loss-of-function mutations in the filaggrin (FLG) gene, R501X and 2282del4, were identified as causative for ichthyosis vulgaris in 15 affected European families, and the mode of inheritance was found to be semidominant. As ichthyosis vulgaris and AD often occur concomitantly in affected individuals, these two mutations were subsequently investigated in AD patients and found to be strongly associated with the disease. Following this first report, seven replication studies have been performed that all confirm an association of these two mutations with AD (or AD subtypes) in several European cohorts. Additionally, two unique loss-of-function mutations in the FLG gene were identified in Japanese ichthyosis vulgaris families and found to be associated with AD in a Japanese cohort. Thus, the FLG mutations are among the most consistently replicated associations for AD. Additionally, linkage analysis has suggested that variation within the EDC might also predispose for psoriasis but the exact susceptibility variation(s) have not yet been elucidated. Taken together, these findings convincingly demonstrate the important role of barrier dysfunction in various common skin disorders.
Selected papers on analysis and differential equations
Nomizu, Katsumi
2003-01-01
This volume contains translations of papers that originally appeared in the Japanese journal, Sugaku. The papers range over a variety of topics, including nonlinear partial differential equations, C^*-algebras, and Schrödinger operators.
Multiplex-PCR for differentiation of Mycobacterium bovis from Mycobacterium tuberculosis complex.
Spositto, F L E; Campanerut, P A Z; Ghiraldi, L D; Leite, C Q F; Hirata, M H; Hirata, R D C; Siqueira, V L D; Cardoso, R Fressatti
2014-01-01
We evaluated a multiplex-PCR to differentiate Mycobacterium bovis from M. tuberculosis Complex (MTC) by one step amplification based on simultaneous detection of pncA 169 C > G change in M. bovis and the IS6110 present in MTC species. Our findings showed the proposed multiplex-PCR is a very useful tool for complementation in differentiating M. bovis from other cultured MTC species.
Numerical simulation of seismic wave propagation in complex media by convolutional differentiator
Institute of Scientific and Technical Information of China (English)
LI Xin-fu; LI Xiao-fan
2008-01-01
We apply the forward modeling algorithm constituted by the convolutional Forsyte polynomial differentiator pro- posed by former worker to seismic wave simulation of complex heterogeneous media and compare the efficiency and accuracy between this method and other seismic simulation methods such as finite difference and pseudospec- tral method. Numerical experiments demonstrate that the algorithm constituted by convolutional Forsyte polyno- mial differentiator has high efficiency and accuracy and needs less computational resources, so it is a numerical modeling method with much potential.
A second course in complex analysis
Veech, William A
2008-01-01
A clear, self-contained treatment of important areas in complex analysis, this text is geared toward upper-level undergraduates and graduate students. The material is largely classical, with particular emphasis on the geometry of complex mappings.Author William A. Veech, the Edgar Odell Lovett Professor of Mathematics at Rice University, presents the Riemann mapping theorem as a special case of an existence theorem for universal covering surfaces. His focus on the geometry of complex mappings makes frequent use of Schwarz's lemma. He constructs the universal covering surface of an arbitrary pl
Institute of Scientific and Technical Information of China (English)
WU; Jianhua; WANG; Zhaohui
2009-01-01
Digital libraries are complex systems and this brings difficulties for their evaluation.This paper proposes a hierarchical model to solve this problem,and puts the entangled matters into a clear-layered structure.Firstly,digital libraries(DLs thereafter)are classified into 5 groups in ascending gradations,i.e.mini DLs,small DLs,medium DLs,large DLs,and huge DLs by their scope of operation.Then,according to the characteristics of DLs at different operational scope and level of sophistication,they are further grouped into unitary DLs,union DLs and hybrid DLs accordingly.Based on this simulated structure,a hierarchical model for digital library evaluation is introduced,which evaluates DLs differentiatingly within a hierarchical scheme by using varying criteria based on their specific level of operational complexity such as at the micro-level,medium-level,and/or at the macro-level.Based on our careful examination and analysis of the current literature about DL evaluation system,an experiment is conducted by using the DL evaluation model along with its criteria for unitary DLs at micro-level.The main contents resulting from this evaluation experimentation and also those evaluation indicators and relevant issues of major concerns for DLs at medium-level and macro-level are also to be presented at some length.
Goodisman, Michael A D; Hahn, Daniel A
2005-10-01
All social insects live in highly organized societies. However, different social insect species display striking variation in social structure. This variation can significantly affect the genetic structure within populations and, consequently, the divergence between species. The purpose of this study was to determine if variation in social structure was associated with species diversification in the Camponotus festinatus desert carpenter ant species complex. We used polymorphic DNA microsatellite markers to dissect the breeding system of these ants and to determine if distinct C. festinatus forms hybridized in their natural range. Our analysis of single-queen colonies established in the laboratory revealed that queens typically mated with only a single male. The genotypes of workers sampled from a field population suggested that multiple, related queens occasionally reproduced within colonies and that colonies inhabited multiple nests. Camponotus festinatus workers derived from colonies of the same form originating at different locales were strongly differentiated, suggesting that gene flow was geographically restricted. Overall, our data indicate that C. festinatus populations are highly structured. Distinct C. festinatus forms possess similar social systems but are genetically isolated. Consequently, our data suggest that diversification in the C. festinatus species complex is not necessarily associated with a shift in social structure.
Visualization and Analysis of Complex Covert Networks
DEFF Research Database (Denmark)
Memon, Bisharat
systems that are covert and hence inherently complex. My Ph.D. is positioned within the wider framework of CrimeFighter project. The framework envisions a number of key knowledge management processes that are involved in the workflow, and the toolbox provides supporting tools to assist human end......This report discusses and summarize the results of my work so far in relation to my Ph.D. project entitled "Visualization and Analysis of Complex Covert Networks". The focus of my research is primarily on development of methods and supporting tools for visualization and analysis of networked......-users (intelligence analysts) in harvesting, filtering, storing, managing, structuring, mining, analyzing, interpreting, and visualizing data about offensive networks. The methods and tools proposed and discussed in this work can also be applied to analysis of more generic complex networks....
Differential maturation of brain signal complexity in the human auditory and visual system
Directory of Open Access Journals (Sweden)
Sarah Lippe
2009-11-01
Full Text Available Brain development carries with it a large number of structural changes at the local level which impact on the functional interactions of distributed neuronal networks for perceptual processing. Such changes enhance information processing capacity, which can be indexed by estimation of neural signal complexity. Here, we show that during development, EEG signal complexity increases from one month to 5 years of age in response to auditory and visual stimulation. However, the rates of change in complexity were not equivalent for the two responses. Infants’ signal complexity for the visual condition was greater than auditory signal complexity, whereas adults showed the same level of complexity to both types of stimuli. The differential rates of complexity change may reflect a combination of innate and experiential factors on the structure and function of the two sensory systems.
Mathematical Analysis of Evolution, Information, and Complexity
Arendt, Wolfgang
2009-01-01
Mathematical Analysis of Evolution, Information, and Complexity deals with the analysis of evolution, information and complexity. The time evolution of systems or processes is a central question in science, this text covers a broad range of problems including diffusion processes, neuronal networks, quantum theory and cosmology. Bringing together a wide collection of research in mathematics, information theory, physics and other scientific and technical areas, this new title offers elementary and thus easily accessible introductions to the various fields of research addressed in the book.
Continuous nowhere differentiable functions the monsters of analysis
Jarnicki, Marek
2015-01-01
This book covers the construction, analysis, and theory of continuous nowhere differentiable functions, comprehensively and accessibly. After illuminating the significance of the subject through an overview of its history, the reader is introduced to the sophisticated toolkit of ideas and tricks used to study the explicit continuous nowhere differentiable functions of Weierstrass, Takagi–van der Waerden, Bolzano, and others. Modern tools of functional analysis, measure theory, and Fourier analysis are applied to examine the generic nature of continuous nowhere differentiable functions, as well as linear structures within the (nonlinear) space of continuous nowhere differentiable functions. To round out the presentation, advanced techniques from several areas of mathematics are brought together to give a state-of-the-art analysis of Riemann’s continuous, and purportedly nowhere differentiable, function. For the reader’s benefit, claims requiring elaboration, and open problems, are clearly indicated. An a...
The nuclear pore complex acts as a master switch for nuclear and cell differentiation
Iwamoto, Masaaki; Hiraoka, Yasushi; Haraguchi, Tokuko
2015-01-01
Cell differentiation is associated with the functional differentiation of the nucleus, in which alteration of the expression profiles of transcription factors occurs to destine cell fate. Nuclear transport machineries, such as importin-α, have also been reported as critical factors that induce cell differentiation. Using various fluorescence live cell imaging methods, including time-lapse imaging, FRAP analysis and live-cell imaging associated correlative light and electron microscopy (Live CLEM) of Tetrahymena, a unicellular ciliated protozoan, we have recently discovered that type switching of the NPC is the earliest detectable event of nuclear differentiation. Our studies suggest that this type switching of the NPC directs the fate of the nucleus to differentiate into either a macronucleus or a micronucleus. Our findings in this organism may provide new insights into the role of the NPC in controlling nuclear functions in general in eukaryotes, including controlling cell fate leading to cell differentiation in multicellular metazoa. PMID:26479399
Tensor analysis and elementary differential geometry for physicists and engineers
Nguyen-Schäfer, Hung
2017-01-01
This book comprehensively presents topics, such as Dirac notation, tensor analysis, elementary differential geometry of moving surfaces, and k-differential forms. Additionally, two new chapters of Cartan differential forms and Dirac and tensor notations in quantum mechanics are added to this second edition. The reader is provided with hands-on calculations and worked-out examples at which he will learn how to handle the bra-ket notation, tensors, differential geometry, and differential forms; and to apply them to the physical and engineering world. Many methods and applications are given in CFD, continuum mechanics, electrodynamics in special relativity, cosmology in the Minkowski four-dimensional spacetime, and relativistic and non-relativistic quantum mechanics. Tensors, differential geometry, differential forms, and Dirac notation are very useful advanced mathematical tools in many fields of modern physics and computational engineering. They are involved in special and general relativity physics, quantum m...
Asymptotic analysis for functional stochastic differential equations
Bao, Jianhai; Yuan, Chenggui
2016-01-01
This brief treats dynamical systems that involve delays and random disturbances. The study is motivated by a wide variety of systems in real life in which random noise has to be taken into consideration and the effect of delays cannot be ignored. Concentrating on such systems that are described by functional stochastic differential equations, this work focuses on the study of large time behavior, in particular, ergodicity. This brief is written for probabilists, applied mathematicians, engineers, and scientists who need to use delay systems and functional stochastic differential equations in their work. Selected topics from the brief can also be used in a graduate level topics course in probability and stochastic processes.
Complex J-Symplectic Geometry With Application to Ordinary Differential Operators
Institute of Scientific and Technical Information of China (English)
王万义
2001-01-01
@@In this paper, we deal with complex J-symplectic geometry with application to ordinary differential operators. We define complex J-symplectic spaces and their J-Lagrangian subspaces and complete J-Lagrangian subspaces, and then we discuss their basic algebraic properties. Then we apply them to the theory of J-selfadjoint operators and give J-symplectic geometry complete characterizations of J-selfadjoint extensions of J-symmetric operators.
Differential analysis of matrix convex functions
DEFF Research Database (Denmark)
Hansen, Frank; Tomiyama, Jun
2007-01-01
We analyze matrix convex functions of a fixed order defined in a real interval by differential methods as opposed to the characterization in terms of divided differences given by Kraus [F. Kraus, Über konvekse Matrixfunktionen, Math. Z. 41 (1936) 18-42]. We obtain for each order conditions for ma...
Complex network analysis of time series
Gao, Zhong-Ke; Small, Michael; Kurths, Jürgen
2016-12-01
Revealing complicated behaviors from time series constitutes a fundamental problem of continuing interest and it has attracted a great deal of attention from a wide variety of fields on account of its significant importance. The past decade has witnessed a rapid development of complex network studies, which allow to characterize many types of systems in nature and technology that contain a large number of components interacting with each other in a complicated manner. Recently, the complex network theory has been incorporated into the analysis of time series and fruitful achievements have been obtained. Complex network analysis of time series opens up new venues to address interdisciplinary challenges in climate dynamics, multiphase flow, brain functions, ECG dynamics, economics and traffic systems.
Multivariate analysis: greater insights into complex systems
Many agronomic researchers measure and collect multiple response variables in an effort to understand the more complex nature of the system being studied. Multivariate (MV) statistical methods encompass the simultaneous analysis of all random variables (RV) measured on each experimental or sampling ...
The Impact of Mitochondrial Complex Inhibition on mESC Differentiation
The Impact of Mitochondrial Complex Inhibition on mESC Differentiation JE Royland, SH Warren, S Jeffay, MR Hoopes, HP Nichols, ES Hunter U.S. Environmental Protection Agency, Integrated Systems Toxicology Division, Research Triangle Park, NC The importance of mitochondrial funct...
Nonlinear eigenvalue approach to differential Riccati equations for contraction analysis
Kawano, Yu; Ohtsuka, Toshiyuki
2017-01-01
In this paper, we extend the eigenvalue method of the algebraic Riccati equation to the differential Riccati equation (DRE) in contraction analysis. One of the main results is showing that solutions to the DRE can be expressed as functions of nonlinear eigenvectors of the differential Hamiltonian ma
Engineering complex tissue-like microgel arrays for evaluating stem cell differentiation
DEFF Research Database (Denmark)
Guermani, Enrico; Shaki, Hossein; Mohanty, Soumyaranjan
2016-01-01
spreading and osteogenic differentiation of human mesenchymal stem cells (hMSCs) into complex tissue-like structures. In summary, we have developed a tissue-like microgel array for evaluating stem cell differentiation within complex and heterogeneous cell microenvironments. We anticipate that the developed......Development of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequisite for stem cell mediated generation of off-the-shelf-tissues. So far, the field of tissue engineering has not full-filled its grand potential of engineering such combinatorial scaffolds...... for engineering functional tissues. This is primarily due to the many challenges associated with finding the right microarchitectures and ECM compositions for optimal tissue regeneration. Here, we have developed a new microgel array to address this grand challenge through robotic printing of complex stem cell...
Differential Regulatory Analysis Based on Coexpression Network in Cancer Research
Directory of Open Access Journals (Sweden)
Junyi Li
2016-01-01
Full Text Available With rapid development of high-throughput techniques and accumulation of big transcriptomic data, plenty of computational methods and algorithms such as differential analysis and network analysis have been proposed to explore genome-wide gene expression characteristics. These efforts are aiming to transform underlying genomic information into valuable knowledges in biological and medical research fields. Recently, tremendous integrative research methods are dedicated to interpret the development and progress of neoplastic diseases, whereas differential regulatory analysis (DRA based on gene coexpression network (GCN increasingly plays a robust complement to regular differential expression analysis in revealing regulatory functions of cancer related genes such as evading growth suppressors and resisting cell death. Differential regulatory analysis based on GCN is prospective and shows its essential role in discovering the system properties of carcinogenesis features. Here we briefly review the paradigm of differential regulatory analysis based on GCN. We also focus on the applications of differential regulatory analysis based on GCN in cancer research and point out that DRA is necessary and extraordinary to reveal underlying molecular mechanism in large-scale carcinogenesis studies.
Schiesser, William E
2014-01-01
Features a solid foundation of mathematical and computational tools to formulate and solve real-world PDE problems across various fields With a step-by-step approach to solving partial differential equations (PDEs), Differential Equation Analysis in Biomedical Science and Engineering: Partial Differential Equation Applications with R successfully applies computational techniques for solving real-world PDE problems that are found in a variety of fields, including chemistry, physics, biology, and physiology. The book provides readers with the necessary knowledge to reproduce and extend the com
Schiesser, William E
2014-01-01
Features a solid foundation of mathematical and computational tools to formulate and solve real-world ODE problems across various fields With a step-by-step approach to solving ordinary differential equations (ODEs), Differential Equation Analysis in Biomedical Science and Engineering: Ordinary Differential Equation Applications with R successfully applies computational techniques for solving real-worldODE problems that are found in a variety of fields, including chemistry, physics, biology,and physiology. The book provides readers with the necessary knowledge to reproduce andextend the comp
Lie symmetry analysis of some time fractional partial differential equations
El Kinani, E. H.; Ouhadan, A.
2015-04-01
This paper uses Lie symmetry analysis to reduce the number of independent variables of time fractional partial differential equations. Then symmetry properties have been employed to construct some exact solutions.
Optimization Issues with Complex Rotorcraft Comprehensive Analysis
Walsh, Joanne L.; Young, Katherine C.; Tarzanin, Frank J.; Hirsh, Joel E.; Young, Darrell K.
1998-01-01
This paper investigates the use of the general purpose automatic differentiation (AD) tool called Automatic Differentiation of FORTRAN (ADIFOR) as a means of generating sensitivity derivatives for use in Boeing Helicopter's proprietary comprehensive rotor analysis code (VII). ADIFOR transforms an existing computer program into a new program that performs a sensitivity analysis in addition to the original analysis. In this study both the pros (exact derivatives, no step-size problems) and cons (more CPU, more memory) of ADIFOR are discussed. The size (based on the number of lines) of the VII code after ADIFOR processing increased by 70 percent and resulted in substantial computer memory requirements at execution. The ADIFOR derivatives took about 75 percent longer to compute than the finite-difference derivatives. However, the ADIFOR derivatives are exact and are not functions of step-size. The VII sensitivity derivatives generated by ADIFOR are compared with finite-difference derivatives. The ADIFOR and finite-difference derivatives are used in three optimization schemes to solve a low vibration rotor design problem.
Analysis of complex networks using aggressive abstraction.
Energy Technology Data Exchange (ETDEWEB)
Colbaugh, Richard; Glass, Kristin.; Willard, Gerald
2008-10-01
This paper presents a new methodology for analyzing complex networks in which the network of interest is first abstracted to a much simpler (but equivalent) representation, the required analysis is performed using the abstraction, and analytic conclusions are then mapped back to the original network and interpreted there. We begin by identifying a broad and important class of complex networks which admit abstractions that are simultaneously dramatically simplifying and property preserving we call these aggressive abstractions -- and which can therefore be analyzed using the proposed approach. We then introduce and develop two forms of aggressive abstraction: 1.) finite state abstraction, in which dynamical networks with uncountable state spaces are modeled using finite state systems, and 2.) onedimensional abstraction, whereby high dimensional network dynamics are captured in a meaningful way using a single scalar variable. In each case, the property preserving nature of the abstraction process is rigorously established and efficient algorithms are presented for computing the abstraction. The considerable potential of the proposed approach to complex networks analysis is illustrated through case studies involving vulnerability analysis of technological networks and predictive analysis for social processes.
Intentional risk management through complex networks analysis
Chapela, Victor; Moral, Santiago; Romance, Miguel
2015-01-01
This book combines game theory and complex networks to examine intentional technological risk through modeling. As information security risks are in constant evolution, the methodologies and tools to manage them must evolve to an ever-changing environment. A formal global methodology is explained in this book, which is able to analyze risks in cyber security based on complex network models and ideas extracted from the Nash equilibrium. A risk management methodology for IT critical infrastructures is introduced which provides guidance and analysis on decision making models and real situations. This model manages the risk of succumbing to a digital attack and assesses an attack from the following three variables: income obtained, expense needed to carry out an attack, and the potential consequences for an attack. Graduate students and researchers interested in cyber security, complex network applications and intentional risk will find this book useful as it is filled with a number of models, methodologies a...
Micro-macro analysis of complex networks.
Marchiori, Massimo; Possamai, Lino
2015-01-01
Complex systems have attracted considerable interest because of their wide range of applications, and are often studied via a "classic" approach: study a specific system, find a complex network behind it, and analyze the corresponding properties. This simple methodology has produced a great deal of interesting results, but relies on an often implicit underlying assumption: the level of detail on which the system is observed. However, in many situations, physical or abstract, the level of detail can be one out of many, and might also depend on intrinsic limitations in viewing the data with a different level of abstraction or precision. So, a fundamental question arises: do properties of a network depend on its level of observability, or are they invariant? If there is a dependence, then an apparently correct network modeling could in fact just be a bad approximation of the true behavior of a complex system. In order to answer this question, we propose a novel micro-macro analysis of complex systems that quantitatively describes how the structure of complex networks varies as a function of the detail level. To this extent, we have developed a new telescopic algorithm that abstracts from the local properties of a system and reconstructs the original structure according to a fuzziness level. This way we can study what happens when passing from a fine level of detail ("micro") to a different scale level ("macro"), and analyze the corresponding behavior in this transition, obtaining a deeper spectrum analysis. The obtained results show that many important properties are not universally invariant with respect to the level of detail, but instead strongly depend on the specific level on which a network is observed. Therefore, caution should be taken in every situation where a complex network is considered, if its context allows for different levels of observability.
Differentiation of clinical Mycobacterium tuberculosis complex isolates by their GyrB polymorphism
Directory of Open Access Journals (Sweden)
Abass N
2010-01-01
Full Text Available Purpose: To evaluate the reliability of the gyrB PCR-RFLP technique in differentiating clinical Mycobacterium tuberculosis complex isolates. Materials and Methods: A primer pair MTUB-f and MTUB-r for M. tuberculosis complex (MTBC was used to differentiate 79 mycobacterial isolates by specific amplification of the 1,020-bp fragment of the gyrB gene (gyrB-PCR1. The MTBC isolates were further differentiated using a set of specific primers MTUB-756-Gf and MTUB-1450-Cr that allowed selective amplification of the gyrB fragment specific for M. tuberculosis (gyrB-PCR2. The DNA polymorphisms in the 1,020-bp gyrB fragment for 7 M. tuberculosis strains confirmed by PCR as well as 2 reference strains; M. tuberculosis H37Rv and M. bovis BCG were analyzed with the restriction enzyme Rsa1. Results: Seventy-seven (97.5% isolates were positive for gyrB-PCR1 and thus identified as members of M. tuberculosis complex (MTBC and two (2.6% isolates were negative and identified as Mycobacteria other than tuberculosis (MOTT. All the M. tuberculosis isolates showed the typical M. tuberculosis specific Rsa1 RFLP patterns (100, 360, 560-bp while 360 and 480-bp fragments were generated from M. bovis BCG. Conclusion: The gyrB PCR-RFLP using the endonuclease Rsa1 can be used to differentiate M. tuberculosis from M. bovis in clinical isolates.
Empirical Bayes Model Comparisons for Differential Methylation Analysis
Directory of Open Access Journals (Sweden)
Mingxiang Teng
2012-01-01
Full Text Available A number of empirical Bayes models (each with different statistical distribution assumptions have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e.g., enrichment of transcription factor-binding sites (TFBSs, the sensitivity of such analyses, using various empirical Bayes models, remains unclear. In this paper, five empirical Bayes models were constructed, based on either a gamma distribution or a log-normal distribution, for the identification of differential methylated loci and their cell division—(1, 3, and 5 and drug-treatment-(cisplatin dependent methylation patterns. While differential methylation patterns generated by log-normal models were enriched with numerous TFBSs, we observed almost no TFBS-enriched sequences using gamma assumption models. Statistical and biological results suggest log-normal, rather than gamma, empirical Bayes model distribution to be a highly accurate and precise method for differential methylation microarray analysis. In addition, we presented one of the log-normal models for differential methylation analysis and tested its reproducibility by simulation study. We believe this research to be the first extensive comparison of statistical modeling for the analysis of differential DNA methylation, an important biological phenomenon that precisely regulates gene transcription.
Measures of complexity in signal analysis
Energy Technology Data Exchange (ETDEWEB)
Kurths, J.; Schwarz, U.; Witt, A. [Arbeitsgruppe Nichtlineare Dynamik der Max-Planck-Gesellschaft an der Universitaet Potsdam, Am Neuen Palais, D-14415 Potsdam, PSF 601553 (Germany); Krampe, R.T. [Institut fuer Psychologie, Universitaet Potsdam, Am Neuen Palais, D-14415 Potsdam, PSF 601553 (Germany); Abel, M. [Arbeitsgruppe Nichtlineare Dynamik der Max-Planck-Gessellschaft an der Universitaet Potsdam, Am Neuen Palais, D-14415 Potsdam, PSF 601553 (Germany)
1996-06-01
Observational data of natural systems, as measured in astrophysical, geophysical or physiological experiments are typically quite different from those obtained in laboratories. Due to the peculiarities with these data, well-known characteristics processes, such as periodicities or fractal dimension, often do not provide a suitable description. To study such data, we present here the use of measures of complexity, which are mainly basing on symbolic dynamics. We distinguish two types of such quantities: traditional measures (e.g. algorithmic complexity) which are measures of randomness and alternative measures (e.g. {epsilon}-complexity) which relate highest complexity to some critical points. It is important to note that there is no optimum measure of complexity. Its choice should depend on the context. Mostly, a combination of some such quantities is appropriate. Applying this concept to three examples in astrophysics, cardiology and cognitive psychology, we show that it can be helpful also in cases where other tools of data analysis fail. {copyright} {ital 1996 American Institute of Physics.}
Discrete complex analysis on isoradial graphs
Chelkak, Dmitry; Smirnov, Stanislav
2008-01-01
We study discrete complex analysis and potential theory on a large family of planar graphs, the so-called isoradial ones. Along with discrete analogues of several classical results, we prove uniform convergence of discrete harmonic measures, Green's functions and Poisson kernels to their continuous counterparts. Among other applications, the results can be used to establish universality of the critical Ising and other lattice models.
Dynamic data analysis modeling data with differential equations
Ramsay, James
2017-01-01
This text focuses on the use of smoothing methods for developing and estimating differential equations following recent developments in functional data analysis and building on techniques described in Ramsay and Silverman (2005) Functional Data Analysis. The central concept of a dynamical system as a buffer that translates sudden changes in input into smooth controlled output responses has led to applications of previously analyzed data, opening up entirely new opportunities for dynamical systems. The technical level has been kept low so that those with little or no exposure to differential equations as modeling objects can be brought into this data analysis landscape. There are already many texts on the mathematical properties of ordinary differential equations, or dynamic models, and there is a large literature distributed over many fields on models for real world processes consisting of differential equations. However, a researcher interested in fitting such a model to data, or a statistician interested in...
Greenlee, M H; Roosevelt, C B; Sakaguchi, D S
2001-02-12
SNARE complex proteins have critical functions during regulated vesicular release of neurotransmitter. In addition, they play critical roles during neurite outgrowth and synaptogenesis. Although it is clear that the function of any one SNARE complex protein during release of neurotransmitter is dependent on its association with other members of the complex, it is less certain whether their function during development and differentiation is dependent on interaction with one another. Previously, we have observed transient high levels of SNARE complex protein SNAP-25 in developing cholinergic amacrine cells (West Greenlee et al. [1998] J Comp Neurol 394:374-385). In addition, we detected, high levels of SNAP-25 in developing and mature photoreceptors. To better understand the functional significance of these high levels of SNAP-25 expression, we used immunocytochemistry to examine the developmental expression of the three members of the SNARE complex, SNAP-25, Syntaxin, and vesicle associated membrane protein (VAMP/also Synaptobrevin). Our results demonstrate that the high levels of SNAP-25 in cholinergic amacrine cells and photoreceptors are not accompanied by the same relatively high levels of other SNARE complex proteins. These results suggest that high levels of SNAP-25 in specific cell types may function independently of association with Syntaxin and VAMP. In this analysis, we characterized the changing patterns of immunoreactivity for the three SNARE complex proteins during the development and differentiation of the mammalian retina. We have compared the pattern of expression of the core SNARE complex proteins in the Brazilian opossum, Monodelphis domestica, and in the rat and found common patterns of expression between these diverse mammalian species. We observed temporal differences in the onset of immunoreactivity between these three proteins, and differences in their localization within synaptic layers in the developing and mature mammalian retina. This
Directory of Open Access Journals (Sweden)
Elsayed M.E. Zayed
2016-02-01
Full Text Available In this article, the modified extended tanh-function method is employed to solve fractional partial differential equations in the sense of the modified Riemann–Liouville derivative. Based on a nonlinear fractional complex transformation, certain fractional partial differential equations can be turned into nonlinear ordinary differential equations of integer orders. For illustrating the validity of this method, we apply it to four nonlinear equations namely, the space–time fractional generalized nonlinear Hirota–Satsuma coupled KdV equations, the space–time fractional nonlinear Whitham–Broer–Kaup equations, the space–time fractional nonlinear coupled Burgers equations and the space–time fractional nonlinear coupled mKdV equations.
Directory of Open Access Journals (Sweden)
Bengt Hansson
Full Text Available Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene
Complex surveys analysis of categorical data
Mukhopadhyay, Parimal
2016-01-01
The primary objective of this book is to study some of the research topics in the area of analysis of complex surveys which have not been covered in any book yet. It discusses the analysis of categorical data using three models: a full model, a log-linear model and a logistic regression model. It is a valuable resource for survey statisticians and practitioners in the field of sociology, biology, economics, psychology and other areas who have to use these procedures in their day-to-day work. It is also useful for courses on sampling and complex surveys at the upper-undergraduate and graduate levels. The importance of sample surveys today cannot be overstated. From voters’ behaviour to fields such as industry, agriculture, economics, sociology, psychology, investigators generally resort to survey sampling to obtain an assessment of the behaviour of the population they are interested in. Many large-scale sample surveys collect data using complex survey designs like multistage stratified cluster designs. The o...
Ravens, Sarina; Fournier, Marjorie; Ye, Tao; Stierle, Matthieu; Dembele, Doulaye; Chavant, Virginie; Tora, Làszlò
2014-01-01
The histone acetyltransferase (HAT) Mof is essential for mouse embryonic stem cell (mESC) pluripotency and early development. Mof is the enzymatic subunit of two different HAT complexes, MSL and NSL. The individual contribution of MSL and NSL to transcription regulation in mESCs is not well understood. Our genome-wide analysis show that i) MSL and NSL bind to specific and common sets of expressed genes, ii) NSL binds exclusively at promoters, iii) while MSL binds in gene bodies. Nsl1 regulates proliferation and cellular homeostasis of mESCs. MSL is the main HAT acetylating H4K16 in mESCs, is enriched at many mESC-specific and bivalent genes. MSL is important to keep a subset of bivalent genes silent in mESCs, while developmental genes require MSL for expression during differentiation. Thus, NSL and MSL HAT complexes differentially regulate specific sets of expressed genes in mESCs and during differentiation. DOI: http://dx.doi.org/10.7554/eLife.02104.001 PMID:24898753
Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex
Institute of Scientific and Technical Information of China (English)
CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun
2007-01-01
Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.
Dubois-Violette, Michel
2010-01-01
These are notes of lectures given at the Third School of Theoretical Physics in Jijel (Algeria, September 2009). The subject of these notes is differential geometry, complex and quaternionic structures with applications to theoretical physics. Concerning the physical applications, they contain several aspects of Penrose transformation in the Riemannian context (Euclidean signature) and various formulations of the Yang-Mills and Einstein equations among which several are unusual ones.
Differential PIXE analysis of Mesoamerican jewelry items
Demortier, G.; Ruvalcaba-Sil, J. L.
1996-09-01
Gold jewelry items of Mesoamerican origin (from Peru, Colombia, Mexico, etc,…) are usually cast in Tumbaga: a man-made gold-copper-silver alloy containing a large proportion of copper. In order to give the objects a colour close to that of pure gold, ancient Mesoamerican goldsmiths experimented with a procedure to eliminate less noble metals (like copper and silver) from the surface. RBS may be used to identify a possible enrichment in gold in the most external layer of the items but due to the low capability of this technique to separate scattered particles on gold and silver and due to the low Rutherford cross section for α-particles on copper by comparison with those on gold, the determination of the exact depth depletion of copper cannot be easily reached. Differential PIXE is an appropriate method to achieve this goal. It takes the relative X-ray intensities of Cu and Au lines into account. By varying the incident proton energy, this ratio is modified in a completely different way if the sample is homogeneous or exhibits a layered or depth profile structure.
Mathematical analysis of complex cellular activity
Bertram, Richard; Teka, Wondimu; Vo, Theodore; Wechselberger, Martin; Kirk, Vivien; Sneyd, James
2015-01-01
This book contains two review articles on mathematical physiology that deal with closely related topics but were written and can be read independently. The first article reviews the basic theory of calcium oscillations (common to almost all cell types), including spatio-temporal behaviors such as waves. The second article uses, and expands on, much of this basic theory to show how the interaction of cytosolic calcium oscillators with membrane ion channels can result in highly complex patterns of electrical spiking. Through these examples one can see clearly how multiple oscillatory processes interact within a cell, and how mathematical methods can be used to understand such interactions better. The two reviews provide excellent examples of how mathematics and physiology can learn from each other, and work jointly towards a better understanding of complex cellular processes. Review 1: Richard Bertram, Joel Tabak, Wondimu Teka, Theodore Vo, Martin Wechselberger: Geometric Singular Perturbation Analysis of Burst...
Aspects of Complexity in Sleep Analysis
Leitão, José M. N.; Da Rosa, Agostinho C.
The paper presents a selection of sleep analysis problems where some aspects and concepts of complexity come about. Emphasis is given to the electroencephalogram (EEG) as the most important sleep related variable. The conception of the EEG as a message to be deciphered stresses the importance of the communication and information theories in this field. An optimal detector of K complexes and vertex sharp waves based on a stochastic model of sleep EEG is considered. Besides detecting, the algorithm is also able to follow the evolution of the basic ongoing activity. It is shown that both the ostructure and microstructure of sleep can be described in terms of symbols and interpreted as sentences of a language. Syntactic models and Markov chain representations play in this context an important role.
Integrative Genomic Analysis of Complex traits
DEFF Research Database (Denmark)
Ehsani, Ali Reza
In the last decade rapid development in biotechnologies has made it possible to extract extensive information about practically all levels of biological organization. An ever-increasing number of studies are reporting miltilayered datasets on the entire DNA sequence, transceroption, protein...... expression, and metabolite abundance of more and more populations in a multitude of invironments. However, a solid model for including all of this complex information in one analysis, to disentangle genetic variation and the underlying genetic architecture of complex traits and diseases, has not yet been...... proposed. This thesis introduced a novel way to integrate such huge data sets in an efficient and informative procedure to dissect the comæexity of obesity related traits (e.g. body wight, body fat, feed intake, etc) and map the flow from DNA through RNA ending with individual phenotypes....
Structured analysis and modeling of complex systems
Strome, David R.; Dalrymple, Mathieu A.
1992-01-01
The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.
Comparative Analysis of VNSA Complex Engineering Efforts
Directory of Open Access Journals (Sweden)
Gary Ackerman
2016-03-01
Full Text Available The case studies undertaken in this special issue demonstrate unequivocally that, despite being forced to operate clandestinely and facing the pressures of security forces seeking to hunt them down and neutralize them, at least a subset of violent non-state actors (VNSAs are capable of some genuinely impressive feats of engineering. At the same time, success in such endeavours is not guaranteed and VNSAs will undoubtedly face a number of obstacles along the way. A comparative analysis of the cases also reveals new insights about the factors influencing the decision to pursue complex engineering efforts, the implementation of such decisions and the determinants of the ultimate outcome. These result in a set of hypotheses and indicators that, if confirmed by future research, can contribute to both operational and strategic intelligence assessments. Overall, the current study enriches our understanding of how and why VNSAs might engage in complex engineering efforts.
Solving Generalised Riccati Differential Equations by Homotopy Analysis Method
Directory of Open Access Journals (Sweden)
J. Vahidi
2013-07-01
Full Text Available In this paper, the quadratic Riccati differential equation is solved by means of an analytic technique, namely the homotopy analysis method (HAM. Comparisons are made between Adomian’s decomposition method (ADM and the exact solution and the homotopy analysis method. The results reveal that the proposed method is very effective and simple.
Epidermal Differentiation Complex: A Review on Its Epigenetic Regulation and Potential Drug Targets
Directory of Open Access Journals (Sweden)
Sinha Abhishek
2016-04-01
Full Text Available The primary feature of the mammalian skin includes the hair follicle, inter-follicular epidermis and the sebaceous glands, all of which form pilo-sebaceous units. The epidermal protective layer undergoes an ordered/programmed process of proliferation and differentiation, ultimately culminating in the formation of a cornified envelope consisting of enucleated corneocytes. These terminally differentiated cells slough off in a cyclic manner and this process is regulated via induction or repression of epidermal differentiation complex (EDC genes. These genes, spanning 2 Mb region of human chromosome 1q21, play a crucial role in epidermal development, through various mechanisms. Each of these mechanisms employs a unique chromatin re-modelling factor or an epigenetic modifier. These factors act to regulate epidermal differentiation singly and/or in combination. Diseases like psoriasis and cancer exhibit aberrations in proliferation and differentiation through, in part, dysregulation in these epigenetic mechanisms. Knowledge of the existing mechanisms in the physiological and the aforesaid pathological contexts may not only facilitate drug development, it also can make refinements to the existing drug delivery systems.
Epidermal Differentiation Complex: A Review on Its Epigenetic Regulation and Potential Drug Targets.
Abhishek, Sinha; Palamadai Krishnan, Suresh
2016-01-01
The primary feature of the mammalian skin includes the hair follicle, inter-follicular epidermis and the sebaceous glands, all of which form pilo-sebaceous units. The epidermal protective layer undergoes an ordered/programmed process of proliferation and differentiation, ultimately culminating in the formation of a cornified envelope consisting of enucleated corneocytes. These terminally differentiated cells slough off in a cyclic manner and this process is regulated via induction or repression of epidermal differentiation complex (EDC) genes. These genes, spanning 2 Mb region of human chromosome 1q21, play a crucial role in epidermal development, through various mechanisms. Each of these mechanisms employs a unique chromatin re-modelling factor or an epigenetic modifier. These factors act to regulate epidermal differentiation singly and/or in combination. Diseases like psoriasis and cancer exhibit aberrations in proliferation and differentiation through, in part, dysregulation in these epigenetic mechanisms. Knowledge of the existing mechanisms in the physiological and the aforesaid pathological contexts may not only facilitate drug development, it also can make refinements to the existing drug delivery systems.
[Analysis of complexity in Chinese meteria medica industrial chain].
Liu, Ying; Li, Qi; Wang, Xiao-Fan
2014-08-01
Chinese meteria medica (CMM) chain is a long-span chain covering agriculture which mainly depends on the forces of nature as well as high-tech CMM industry, CMM expertise industry and fast developing CMM circulation industry. Imbalance among the development of these industries produces bottlenecks and hinders the operation of the entire production chain. After analyzing the structure of Chinese meteria medica industrial chain from the perspective of national economy industry, three industry classifications and differentiation of factor intensity, we conclude that the complex structure of CMM industry chain is attributable to these three aspects. And the complexity is mainly shown at complex industry, varied product types, different coordination of various industrial sections and different technical growth speed of varied industry. We propose that structural complexity is the natural property of the chain, which is the main reason of industry sector development imbalance and bottleneck. Results of this research could provide theoretical analysis for future research on the coordination of industrial chain and the efficiency of resource allocation.
Analysis of Complex Valve and Feed Systems
Ahuja, Vineet; Hosangadi, Ashvin; Shipman, Jeremy; Cavallo, Peter; Dash, Sanford
2007-01-01
A numerical framework for analysis of complex valve systems supports testing of propulsive systems by simulating key valve and control system components in the test loop. In particular, it is designed to enhance the analysis capability in terms of identifying system transients and quantifying the valve response to these transients. This system has analysis capability for simulating valve motion in complex systems operating in diverse flow regimes ranging from compressible gases to cryogenic liquids. A key feature is the hybrid, unstructured framework with sub-models for grid movement and phase change including cryogenic cavitations. The multi-element unstructured framework offers improved predictions of valve performance characteristics under steady conditions for structurally complex valves such as pressure regulator valve. Unsteady simulations of valve motion using this computational approach have been carried out for various valves in operation at Stennis Space Center such as the split-body valve and the 10-in. (approx.25.4-cm) LOX (liquid oxygen) valve and the 4-in. (approx.10 cm) Y-pattern valve (liquid nitrogen). Such simulations make use of variable grid topologies, thereby permitting solution accuracy and resolving important flow physics in the seat region of the moving valve. An advantage to this software includes possible reduction in testing costs incurred due to disruptions relating to unexpected flow transients or functioning of valve/flow control systems. Prediction of the flow anomalies leading to system vibrations, flow resonance, and valve stall can help in valve scheduling and significantly reduce the need for activation tests. This framework has been evaluated for its ability to predict performance metrics like flow coefficient for cavitating venturis and valve coefficient curves, and could be a valuable tool in predicting and understanding anomalous behavior of system components at rocket propulsion testing and design sites.
Universality in complex networks: random matrix analysis.
Bandyopadhyay, Jayendra N; Jalan, Sarika
2007-08-01
We apply random matrix theory to complex networks. We show that nearest neighbor spacing distribution of the eigenvalues of the adjacency matrices of various model networks, namely scale-free, small-world, and random networks follow universal Gaussian orthogonal ensemble statistics of random matrix theory. Second, we show an analogy between the onset of small-world behavior, quantified by the structural properties of networks, and the transition from Poisson to Gaussian orthogonal ensemble statistics, quantified by Brody parameter characterizing a spectral property. We also present our analysis for a protein-protein interaction network in budding yeast.
Central Waste Complex (CWC) Waste Analysis Plan
Energy Technology Data Exchange (ETDEWEB)
ELLEFSON, M.D.
1999-12-01
The purpose of this waste analysis plan (WAP) is to document the waste acceptance process, sampling methodologies, analytical techniques, and overall processes that are undertaken for waste accepted for storage at the Central Waste Complex (CWC), which is located in the 200 West Area of the Hanford Facility, Richland, Washington. Because dangerous waste does not include the source, special nuclear, and by-product material components of mixed waste, radionuclides are not within the scope of this documentation. The information on radionuclides is provided only for general knowledge.
Tandem mass spectrometry: analysis of complex mixtures
Energy Technology Data Exchange (ETDEWEB)
Singleton, K.E.
1985-01-01
Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction products of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated.
Analysis of global sumoylation changes occurring during keratinocyte differentiation.
Directory of Open Access Journals (Sweden)
Phillip R Heaton
Full Text Available Sumoylation is a highly dynamic process that plays a role in a multitude of processes ranging from cell cycle progression to mRNA processing and cancer. A previous study from our lab demonstrated that SUMO plays an important role in keratinocyte differentiation. Here we present a new method of tracking the sumoylation state of proteins by creating a stably transfected HaCaT keratinocyte cell line expressing an inducible SNAP-SUMO3 protein. The SNAP-tag allows covalent fluorescent labeling that is denaturation resistant. When combined with two-dimensional gel electrophoresis, the SNAP-tag technology provides direct visualization of sumoylated targets and can be used to follow temporal changes in the global cohort of sumoylated proteins during dynamic processes such as differentiation. HaCaT keratinocyte cells expressing SNAP-SUMO3 displayed normal morphological and biochemical features that are consistent with typical keratinocyte differentiation. SNAP-SUMO3 also localized normally in these cells with a predominantly nuclear signal and some minor cytoplasmic staining, consistent with previous reports for untagged SUMO2/3. During keratinocyte differentiation the total number of proteins modified by SNAP-SUMO3 was highest in basal cells, decreased abruptly after induction of differentiation, and slowly rebounded beginning between 48 and 72 hours as differentiation progressed. However, within this overall trend the pattern of change for individual sumoylated proteins was highly variable with both increases and decreases in amount over time. From these results we conclude that sumoylation of proteins during keratinocyte differentiation is a complex process which likely reflects and contributes to the biochemical changes that drive differentiation.
Complex configuration analysis at transonic speeds
Boppe, C. W.; Aidala, P. V.
1980-01-01
Advanced performance requirements of new combat and transport aircraft together with design time constraints intensify the development and application of three dimensional computational analyses. A computational method which was developed for the specific purpose of providing an engineering analysis of complex aircraft configurations at transonic speeds. Particular attention is given to the recently incorporated wing viscous interaction and canard capabilities. The treatment of fuselage fairings, nacelles, and pylons is reviewed. The means for keeping computing resources at reasonable levels are identified. Three configurations were selected for correlations with experimental data. Taken together, the comparisons illustrate the full extent of current analysis capabilities. The configurations include: (1) a wing fuselage canard fighter; (2) a transport with fuselage fairings, four nacelles, four pylons; and (3) a space vehicle which includes an external fuel tank and rocket boosters (transonic launch configuration).
A Complexity Analysis of Functional Interpretations
DEFF Research Database (Denmark)
Hernest, Mircea-Dan; Kohlenbach, Ulrich
2003-01-01
We give a quantitative analysis of G ̈odel’s functional interpretation and its monotone variant. The two have been used for the extraction of programs and numerical bounds as well as for conservation results. They apply both to (semi-)intuitionistic as well as (combined with negative translation......) classical proofs. The proofs may be formalized in systems ranging from weak base systems to arithmetic and analysis (and numerous fragments of these). We give upper bounds in basic proof data on the depth, size, maximal type degree and maximal type arity of the extracted terms as well as on the depth...... of the verifying proof. In all cases terms of size linear in the size of the proof at input can be extracted and the corresponding extraction algorithms have cubic worst-time complexity. The verifying proofs have depth linear in the depth of the proof at input and the maximal size of a formula of this proof....
Central Waste Complex (CWC) Waste Analysis Plan
Energy Technology Data Exchange (ETDEWEB)
ELLEFSON, M.D.
2000-01-06
The purpose of this waste analysis plan (WAP) is to document the waste acceptance process, sampling methodologies, analytical techniques, and overall processes that are undertaken for waste accepted for storage at the Central Waste Complex (CWC), which is located in the 200 West Area of the Hanford Facility, Richland, Washington. Because dangerous waste does not include the source special nuclear and by-product material components of mixed waste, radionuclides are not within the scope of this document. The information on radionuclides is provided only for general knowledge. This document has been revised to meet the interim status waste analysis plan requirements of Washington Administrative Code (WAC) 173 303-300(5). When the final status permit is issued, permit conditions will be incorporated and this document will be revised accordingly.
Directory of Open Access Journals (Sweden)
Yi Gan
2014-01-01
Full Text Available Aim: The objective of this study is to characterize differential proteomic expression among well-differentiation and poor-differentiation colorectal carcinoma tissues and normal mucous epithelium. Materials and Methods: The study is based on quantitative 2-dimensional gel electrophoresis and analyzed by PDquest. Results: Excluding redundancies due to proteolysis and posttranslational modified isoforms of over 600 protein spots, 11 proteins were revealed as regulated with statistical variance being within the 95 th confidence level and were identified by peptide mass fingerprinting in matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Progression-associated proteins belong to the functional complexes of tumorigenesis, proliferation, differentiation, metabolism, and the regulation of major histocompatibility complex processing and other functions. Partial but significant overlap was revealed with previous proteomics and transcriptomics studies in CRC. Among various differentiation stage of CRC tissues, we identified calreticulin precursor, MHC class I antigen (human leukocyte antigen A , glutathione S-transferase pi1, keratin 8, heat shock protein 27, tubulin beta chain, triosephosphate, fatty acid-binding protein, hemoglobin (deoxy mutant with val b 1 replaced by met (HBB, and zinc finger protein 312 (FEZF2. Conclusions: Their functional networks were analyzed by Ingenuity systems Ingenuity Pathways Analysis and revealed the potential roles as novel biomarkers for progression in various differentiation stages of CRC.
Ferroelectric Field-Effect Transistor Differential Amplifier Circuit Analysis
Phillips, Thomas A.; MacLeod, Todd C.; Ho, Fat D.
2008-01-01
There has been considerable research investigating the Ferroelectric Field-Effect Transistor (FeFET) in memory circuits. However, very little research has been performed in applying the FeFET to analog circuits. This paper investigates the use of FeFETs in a common analog circuit, the differential amplifier. The two input Metal-Oxide-Semiconductor (MOS) transistors in a general MOS differential amplifier circuit are replaced with FeFETs. Resistors are used in place of the other three MOS transistors. The FeFET model used in the analysis has been previously reported and was based on experimental device data. Because of the FeFET hysteresis, the FeFET differential amplifier has four different operating modes depending on whether the FeFETs are positively or negatively polarized. The FeFET differential amplifier operation in the different modes was analyzed by calculating the amplifier voltage transfer and gain characteristics shown in figures 2 through 5. Comparisons were made between the FeFET differential amplifier and the standard MOS differential amplifier. Possible applications and benefits of the FeFET differential amplifier are discussed.
Suwanichkul, Adisak; Wenderfer, Scott E
2013-12-01
The precise mechanisms by which circulating immune complexes accumulate in the kidney to form deposits in glomerulonephritis are not well understood. In particular, the role of resident cells within glomeruli of the kidney has been widely debated. Immune complexes have been shown to bind one glomerular cell type (mesangial cells) leading to functional responses such as pro-inflammatory cytokine production. To further assess the presence of functional immunoreceptors on resident glomerular cells, cultured mouse renal epithelial, endothelial, and mesangial cells were treated with heat-aggregated mouse IgG or preformed murine immune complexes. Mesangial and renal endothelial cells were found to bind IgG complexes, whereas glomerular epithelial cell binding was minimal. A blocking antibody for Fc-gamma receptors reduced binding to mesangial cells but not renal endothelial cells, suggesting differential immunoreceptor utilization. RT-PCR and immunostaining based screening of cultured renal endothelial cells showed limited low-level expression of known Fc-receptors and Ig binding proteins. The interaction between mesangial cells and renal endothelial cells and immune complexes resulted in distinct, cell-specific patterns of chemokine and cytokine production. This novel pathway involving renal endothelial cells likely contributes to the predilection of circulating immune complex accumulation within the kidney and to the inflammatory responses that drive kidney injury.
Tensor and vector analysis with applications to differential geometry
Springer, C E
2012-01-01
Concise and user-friendly, this college-level text assumes only a knowledge of basic calculus in its elementary and gradual development of tensor theory. The introductory approach bridges the gap between mere manipulation and a genuine understanding of an important aspect of both pure and applied mathematics.Beginning with a consideration of coordinate transformations and mappings, the treatment examines loci in three-space, transformation of coordinates in space and differentiation, tensor algebra and analysis, and vector analysis and algebra. Additional topics include differentiation of vect
Asymptotical stability analysis of linear fractional differential systems
Institute of Scientific and Technical Information of China (English)
LI Chang-pin; ZHAO Zhen-gang
2009-01-01
It has been recently found that many models were established with the aid of fractional derivatives, such as viscoelastic systems, colored noise, electrode-electrolyte polarization, dielectric polarization, boundary layer effects in ducts,electromagnetic waves, quantitative finance, quantum evolution of complex systems, and fractional kinetics. In this paper, the asymptotical stability of higher-dimensional linear fractional differential systems with the Riemann-Liouville fractional order and Caputo fractional order were studied. The asymptotical stability theorems were also derived.
TDP-43 regulates the microprocessor complex activity during in vitro neuronal differentiation.
Di Carlo, Valerio; Grossi, Elena; Laneve, Pietro; Morlando, Mariangela; Dini Modigliani, Stefano; Ballarino, Monica; Bozzoni, Irene; Caffarelli, Elisa
2013-12-01
TDP-43 (TAR DNA-binding protein 43) is an RNA-binding protein implicated in RNA metabolism at several levels. Even if ubiquitously expressed, it is considered as a neuronal activity-responsive factor and a major signature for neurological pathologies, making the comprehension of its activity in the nervous system a very challenging issue. TDP-43 has also been described as an accessory component of the Drosha-DGCR8 (DiGeorge syndrome critical region gene 8) microprocessor complex, which is crucially involved in basal and tissue-specific RNA processing events. In the present study, we exploited in vitro neuronal differentiation systems to investigate the TDP-43 demand for the microprocessor function, focusing on both its canonical microRNA biosynthetic activity and its alternative role as a post-transcriptional regulator of gene expression. Our findings reveal a novel role for TDP-43 as an essential factor that controls the stability of Drosha protein during neuronal differentiation, thus globally affecting the production of microRNAs. We also demonstrate that TDP-43 is required for the Drosha-mediated regulation of Neurogenin 2, a master gene orchestrating neurogenesis, whereas post-transcriptional control of Dgcr8, another Drosha target, resulted to be TDP-43-independent. These results implicate a previously uncovered contribution of TDP-43 in regulating the abundance and the substrate specificity of the microprocessor complex and provide new insights into TDP-43 as a key player in neuronal differentiation.
Exergy Analysis of Complex Ship Energy Systems
Directory of Open Access Journals (Sweden)
Pierre Marty
2016-04-01
Full Text Available With multiple primary and secondary energy converters (diesel engines, steam turbines, waste heat recovery (WHR and oil-fired boilers, etc. and extensive energy networks (steam, cooling water, exhaust gases, etc., ships may be considered as complex energy systems. Understanding and optimizing such systems requires advanced holistic energy modeling. This modeling can be done in two ways: The simpler approach focuses on energy flows, and has already been tested, approved and presented; a new, more complicated approach, focusing on energy quality, i.e., exergy, is presented in this paper. Exergy analysis has rarely been applied to ships, and, as a general rule, the shipping industry is not familiar with this tool. This paper tries to fill this gap. We start by giving a short reminder of what exergy is and describe the principles of exergy modeling to explain what kind of results should be expected from such an analysis. We then apply these principles to the analysis of a large two-stroke diesel engine with its cooling and exhaust systems. Simulation results are then presented along with the exergy analysis. Finally, we propose solutions for energy and exergy saving which could be applied to marine engines and ships in general.
Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis.
Cao, Mu-Shui; Liu, Bing-Ya; Dai, Wen-Tao; Zhou, Wei-Xin; Li, Yi-Xue; Li, Yuan-Yuan
2015-01-01
Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differential coexpression analysis (DCEA), and two novel quantitative methods for differential regulation analysis. We first applied DCEA to a gene expression dataset of gastric normal mucosa, adenoma and carcinoma samples to identify gene interconnection changes during cancer progression, based on which we inferred normal, adenoma, and carcinoma-specific gene regulation networks by using linear regression model. It was observed that cancer genes and drug targets were enriched in each network. To investigate the dynamic changes of gene regulation during carcinogenesis, we then designed two quantitative methods to prioritize differentially regulated genes (DRGs) and gene pairs or links (DRLs) between adjacent stages. It was found that known cancer genes and drug targets are significantly higher ranked. The top 4% normal vs. adenoma DRGs (36 genes) and top 6% adenoma vs. carcinoma DRGs (56 genes) proved to be worthy of further investigation to explore their association with gastric cancer. Out of the 16 DRGs involved in two top-10 DRG lists of normal vs. adenoma and adenoma vs. carcinoma comparisons, 15 have been reported to be gastric cancer or cancer related. Based on our inferred differential networking information and known signaling pathways, we generated testable hypotheses on the roles of GATA6, ESRRG and their signaling pathways in gastric carcinogenesis. Compared with established approaches which build genome-scale GRNs, or sub-networks around differentially expressed genes, the present one proved to be better at enriching cancer genes and drug targets, and prioritizing
Natural Time Analysis and Complex Networks
Sarlis, Nicholas; Skordas, Efthimios; Lazaridou, Mary; Varotsos, Panayiotis
2013-04-01
Here, we review the analysis of complex time series in a new time domain, termed natural time, introduced by our group [1,2]. This analysis conforms to the desire to reduce uncertainty and extract signal information as much as possible [3]. It enables [4] the distinction between the two origins of self-similarity when analyzing data from complex systems, i.e., whether self-similarity solely results from long-range temporal correlations (the process's memory only) or solely from the process's increments infinite variance (heavy tails in their distribution). Natural time analysis captures the dynamical evolution of a complex system and identifies [5] when the system enters a critical stage. Hence, this analysis plays a key role in predicting forthcoming catastrophic events in general. Relevant examples, compiled in a recent monograph [6], have been presented in diverse fields, including Solid State Physics [7], Statistical Physics (for example systems exhibiting self-organized criticality [8]), Cardiology [9,10], Earth Sciences [11] (Geophysics, Seismology), Environmental Sciences (e.g. see Ref. [12]), etc. Other groups have proposed and developed a network approach to earthquake events with encouraging results. A recent study [13] reveals that this approach is strengthened if we combine it with natural time analysis. In particular, we find [13,14] that the study of the spatial distribution of the variability [15] of the order parameter fluctuations, defined in natural time, provides important information on the dynamical evolution of the system. 1. P. Varotsos, N. Sarlis, and E. Skordas, Practica of Athens Academy, 76, 294-321, 2001. 2. P.A. Varotsos, N.V. Sarlis, and E.S. Skordas, Phys. Rev. E, 66, 011902 , 2002. 3. S. Abe, N.V. Sarlis, E.S. Skordas, H.K. Tanaka and P.A. Varotsos, Phys. Rev. Lett. 94, 170601, 2005. 4. P.A. Varotsos, N.V. Sarlis, E.S. Skordas, H.K. Tanaka and M.S. Lazaridou, Phys. Rev. E, 74, 021123, 2006. 5. P.Varotsos, N. V. Sarlis, E. S. Skordas
Differentiated complexes of physical rehabilitation of young people with disorders of the spine
Directory of Open Access Journals (Sweden)
Vladimir Kotelevskiy
2014-12-01
Full Text Available Purpose: identification and analysis of differentiated approaches to physical rehabilitation of students with spine pathology with different types of behavioral responses to stress – coping strategies. Material and Methods: a theoretical analysis, synthesis and special scientific-methodical literature, the analysis of experimental studies on animals and the results of physical rehabilitation students ‘ strategies in 76 students 19–20 years with neurological manifestations of vertebral osteochondrosis of 1 degree. Results: identified and analyzed the main features of rehabilitation measures among youth with spinal pathology (correction, massage therapy, kinesiotherapy with different types of coping strategies. Conclusions: the proven effectiveness of differentiated application of physical rehabilitation on the basis of the definition of coping strategies among students with spine pathology.
Large-scale differential display analysis of T helper cell differentiation.
Ojala, Pekka; Virtanen, Eveliina; Chen, Zhi
2007-03-01
We have developed a novel large-scale multicapillary fluorescent differential display (FDD) platform amenable to further automation. The power of the method is demonstrated by the analysis of T helper cell differentiation. Eight RNA samples from wild type, Stat4 knockout and Stat6 knockout mice were analyzed with 16 anchoring primers and 24 arbitrary primers, resulting in 285 294 sample peaks. Visually selected patterns of differential expression suggest two major regulatory mechanisms: activation and Stat4 genotype. A subset of the findings is reproduced in the confirmatory differential display (DD) that included technical and biological replicates. In a small fragment identification pilot study, we identify Ifi27 and Cct8 to be up-regulated by T cell activation. We present a method for the analysis of electropherogram similarity across large datasets, based on correlation of low-resolution representations of electrophoretic data. We show how it can be applied to analyze experimental and technical variables. Using this method, we demonstrate the effect of activation and genotype. In addition, agreement of our real experimental data to the theoretical basis of DD, as well as issues in anchoring primer selectivity, are studied.
Directory of Open Access Journals (Sweden)
Syed Tauseef Mohyud-Din
2015-01-01
Full Text Available This paper witnesses the coupling of an analytical series expansion method which is called reduced differential transform with fractional complex transform. The proposed technique is applied on three mathematical models, namely, fractional Kaup-Kupershmidt equation, generalized fractional Drinfeld-Sokolov equations, and system of coupled fractional Sine-Gordon equations subject to the appropriate initial conditions which arise frequently in mathematical physics. The derivatives are defined in Jumarie’s sense. The accuracy, efficiency, and convergence of the proposed technique are demonstrated through the numerical examples. It is observed that the presented coupling is an alternative approach to overcome the demerit of complex calculation of fractional differential equations. The proposed technique is independent of complexities arising in the calculation of Lagrange multipliers, Adomian’s polynomials, linearization, discretization, perturbation, and unrealistic assumptions and hence gives the solution in the form of convergent power series with elegantly computed components. All the examples show that the proposed combination is a powerful mathematical tool to solve other nonlinear equations also.
Sun, Hyun Jin; Bahk, Young Yil; Choi, Yon Rak; Shim, Jung Hye; Han, Seung Hwan; Lee, Jin Woo
2006-11-01
Although previous studies have reported the effects of extensive subculturing on proliferation rates and osteogenic potential of human mesenchymal stem cells (hMSCs), the results remain controversial. The aim of our study was to characterize the proliferation and osteogenic potential of hMSCs during serial subculture, and also to identify proteins that are differentially regulated in hMSCs during serial subculture and osteogenic differentiation using proteome analysis. Here we show that the proliferation and osteogenic capacity of hMSCs decrease during serial subculturing. Several proteins were shown to be differentially regulated during serial subculture; among these the expression of T-complex protein 1 alpha subunit (TCP-1alpha), a protein known to be associated with cell proliferation, cell cycle, morphological changes, and apoptosis, gradually decreased during serial subculture. Among proteins that were differentially regulated during osteogenic differentiation, chloride intracellular channel 1 (CLIC1) was downregulated only during the early passages eukaryotic translation elongation factor, and acidic ribosomal phosphoprotein P0 was downregulated during the middle passages, while annexin V, LIM, and SH3 domain protein 1 (LASP-1), and 14-3-3 protein gamma (YWHAG) were upregulated during the later passage. These studies suggest that differentially regulated passage-specific proteins may play a role in the decrease of osteogenic differentiation potential under serial subculturing.
Partial differential equations modeling, analysis and numerical approximation
Le Dret, Hervé
2016-01-01
This book is devoted to the study of partial differential equation problems both from the theoretical and numerical points of view. After presenting modeling aspects, it develops the theoretical analysis of partial differential equation problems for the three main classes of partial differential equations: elliptic, parabolic and hyperbolic. Several numerical approximation methods adapted to each of these examples are analyzed: finite difference, finite element and finite volumes methods, and they are illustrated using numerical simulation results. Although parts of the book are accessible to Bachelor students in mathematics or engineering, it is primarily aimed at Masters students in applied mathematics or computational engineering. The emphasis is on mathematical detail and rigor for the analysis of both continuous and discrete problems. .
Particle production and complex path analysis
Srinivasan, K
1999-01-01
This paper discusses particle production in Schwarzchild-like spacetimes and in an uniform electric field. Both problems are approached using the method of complex path analysis. Particle production in Schwarzchild-like spacetimes with a horizon is obtained here by a new and simple semi-classical method based on the method of complex paths. Hawking radiation is obtained in the (t,r) co-ordinate system of the standard Schwarzchild metric {\\it without} requiring the Kruskal extension. The co-ordinate singularity present at the horizon manifests itself as a singularity in the expression for the semi-classical propagator for a scalar field. We give a prescription whereby this singularity is regularised with Hawking's result being recovered. In the case of the electric field, standard quantum field theoretic methods can be used to obtain particle production in a purely time-dependent gauge. In a purely space-dependent gauge, however, the tunnelling interpretation has to be resorted to. We attempt, in this paper, t...
Covariance analysis of differential drag-based satellite cluster flight
Ben-Yaacov, Ohad; Ivantsov, Anatoly; Gurfil, Pini
2016-06-01
One possibility for satellite cluster flight is to control relative distances using differential drag. The idea is to increase or decrease the drag acceleration on each satellite by changing its attitude, and use the resulting small differential acceleration as a controller. The most significant advantage of the differential drag concept is that it enables cluster flight without consuming fuel. However, any drag-based control algorithm must cope with significant aerodynamical and mechanical uncertainties. The goal of the current paper is to develop a method for examination of the differential drag-based cluster flight performance in the presence of noise and uncertainties. In particular, the differential drag control law is examined under measurement noise, drag uncertainties, and initial condition-related uncertainties. The method used for uncertainty quantification is the Linear Covariance Analysis, which enables us to propagate the augmented state and filter covariance without propagating the state itself. Validation using a Monte-Carlo simulation is provided. The results show that all uncertainties have relatively small effect on the inter-satellite distance, even in the long term, which validates the robustness of the used differential drag controller.
Function spaces and partial differential equations volume 2 : contemporary analysis
Taheri, Ali
2015-01-01
This is a book written primarily for graduate students and early researchers in the fields of Analysis and Partial Differential Equations (PDEs). Coverage of the material is essentially self-contained, extensive and novel with great attention to details and rigour.
Variational analysis and generalized differentiation I basic theory
Mordukhovich, Boris S
2006-01-01
Contains a study of the basic concepts and principles of variational analysis and generalized differentiation in both finite-dimensional and infinite-dimensional spaces. This title presents many applications to problems in optimization, equilibria, stability and sensitivity, control theory, economics, mechanics, and more.
Analysis of rhamnolipid biosurfactants by methylene blue complexation.
Pinzon, Neissa M; Ju, Lu-Kwang
2009-04-01
Rhamnolipids, produced by Pseudomonas aeruginosa, represent an important group of biosurfactants having various industrial, environmental, and medical applications. Current methods for rhamnolipid quantification involve the use of strong hazardous acids/chemicals, indirect measurement of the concentration of sugar moiety, or require the availability of expensive equipment (HPLC-MS). A safer, easier method that measures the whole rhamnolipid molecules would significantly enhance strain selection, metabolic engineering, and process development for economical rhamnolipid production. A semi-quantitative method was reported earlier to differentiate between the rhamnolipid-producing and non-producing strains using agar plates containing methylene blue and cetyl trimethylammonium bromide (CTAB). In this study, a rapid and simple method for rhamnolipid analysis was developed by systematically investigating the complexation of rhamnolipids and methylene blue, with and without the presence of CTAB. The method relies on measuring the absorbance (at 638 nm) of the rhamnolipid-methylene blue complex that partitions into the chloroform phase. With P. aeruginosa fermentation samples, the applicability of this method was verified by comparison of the analysis results with those obtained from the commonly used anthrone reaction technique.
Modified Homotopy Analysis Method for Nonlinear Fractional Partial Differential Equations
Directory of Open Access Journals (Sweden)
D. Ziane
2017-05-01
Full Text Available In this paper, a combined form of natural transform with homotopy analysis method is proposed to solve nonlinear fractional partial differential equations. This method is called the fractional homotopy analysis natural transform method (FHANTM. The FHANTM can easily be applied to many problems and is capable of reducing the size of computational work. The fractional derivative is described in the Caputo sense. The results show that the FHANTM is an appropriate method for solving nonlinear fractional partial differentia equation.
Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk
2013-12-01
MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified.
Pikulski, Michael; Brodbelt, Jennifer S
2003-12-01
The elucidation of flavonoid isomers is accomplished by electrospray ionization tandem mass spectrometry (ESI-MS/MS) via formation and collisional activated dissociation (CAD) of metal/flavonoid complexes containing an auxiliary ligand. Addition of a metal salt and a suitable neutral auxiliary ligand to flavonoids in solution results in the formation of [M(II) (flavonoid-H) ligand]+ complexes by ESI which, upon collisional activated dissociation, often result in more distinctive fragmentation patterns than observed for conventional protonated or deprotonated flavonoids. Previously, 2,2'-bipyridine was used as an auxiliary ligand, and now we compare and explore the use of alternative pyridyl ligands, including 4,7-diphenyl-1,10-phenanthroline. Using this technique, three groups of flavonoid glycoside isomers are differentiated, including glycosides of apigenin, quercetin, and luteolin.
Magnetic Exchange Couplings in Heterodinuclear Complexes Based on Differential Local Spin Rotations.
Joshi, Rajendra P; Phillips, Jordan J; Peralta, Juan E
2016-04-12
We analyze the performance of a new method for the calculation of magnetic exchange coupling parameters for the particular case of heterodinuclear transition metals complexes of Cu, Ni, and V. This method is based on a generalized perturbative approach which uses differential local spin rotations via formal Lagrange multipiers (Phillips, J. J.; Peralta, J. E. J. Chem. Phys. 2013, 138, 174115). The reliability of the calculated couplings has been assessed by comparing with results from traditional energy differences with different density functional approximations and with experimental values. Our results show that this method to calculate magnetic exchange couplings can be reliably used for heteronuclear transition metal complexes, and at the same time, that it is independent from the different mapping schemes used in energy difference methods.
Residual Stress Sensitivity Analysis Using a Complex Variable Finite Element Method (Postprint)
2017-08-17
differencing FD), it takes advantage of complex variable algebra to eliminate the rror developed by traditional numerical differentiation methods such s...iterative procedure for solving nonlinear prob- ems. Through the use of complex variable algebra , ZFEM overcomes he inherent truncation errors that...DTIC Document; 1972 . [23] Davis R , Keith H . Finite-element analysis of pressure vessels. J Basic Eng 1972;94(2):401–5 . [24] Chen P . Prediction of
Design and Analysis of Fully Integrated Differential VCOs
Directory of Open Access Journals (Sweden)
M. Prochaska
2005-01-01
Full Text Available Oscillators play a decisive role for electronic equipment in many fields - like communication, navigation or data processing. Especially oscillators are key building blocks in integrated transceivers for wired and wireless communication systems. In this context the study of fully integrated differential VCOs has received attention. In this paper we present an analytic analysis of the steady state oscillation of integrated differential VCOs which is based on a nonlinear model of the oscillator. The outcomes of this are design formulas for the amplitude as well as the stability of the oscillator which take the nonlinearity of the circuit into account.
Differentiation-Based Analysis of Environmental Management and Corporate Performance
Institute of Scientific and Technical Information of China (English)
SHAN Dong-ming; MU Xin
2007-01-01
By building a duopoly model based on product differentiation, both of the clean firm's and the dirty firm's performances are studied under the assumptions that consumers have different preferences for the product environmental attributes, and that the product cost increases with the environmental attribute. The analysis results show that under either the case with no environmental regulation or that with a tariff levied on the dirty product, the clean firm would always get more profit. In addition, the stricter the regulation is, the more profit the clean firm would obtain. This can verify that from the view of product differentiation, a firm could improve its corporate competitiveness with environmental management.
A complexity analysis of functional interpretations
DEFF Research Database (Denmark)
Hernest, Mircea-Dan; Kohlenbach, Ulrich
2005-01-01
Summary: We give a quantitative analysis of Gödel's functional interpretation and its monotone variant. The two have been used for the extraction of programs and numerical bounds as well as for conservation results. They apply both to (semi-)intuitionistic as well as (combined...... with negative translation) classical proofs. The proofs may be formalized in systems ranging from weak base systems to arithmetic and analysis (and numerous fragments of these). We give upper bounds in basic proof data on the depth, size, maximal type degree and maximal type arity...... of the extracted terms as well as on the depth of the verifying proof. In all cases terms of size linear in the size of the proof at input can be extracted and the corresponding extraction algorithms have cubic worst-time complexity. The verifying proofs have depth linear in the depth...
Kinetic analysis of complex metabolic networks
Energy Technology Data Exchange (ETDEWEB)
Stephanopoulos, G. [MIT, Cambridge, MA (United States)
1996-12-31
A new methodology is presented for the analysis of complex metabolic networks with the goal of metabolite overproduction. The objective is to locate a small number of reaction steps in a network that have maximum impact on network flux amplification and whose rate can also be increased without functional network derangement. This method extends the concepts of Metabolic Control Analysis to groups of reactions and offers the means for calculating group control coefficients as measures of the control exercised by groups of reactions on the overall network fluxes and intracellular metabolite pools. It is further demonstrated that the optimal strategy for the effective increase of network fluxes, while maintaining an uninterrupted supply of intermediate metabolites, is through the coordinated amplification of multiple (as opposed to a single) reaction steps. Satisfying this requirement invokes the concept of the concentration control to coefficient, which emerges as a critical parameter in the identification of feasible enzymatic modifications with maximal impact on the network flux. A case study of aromatic aminoacid production is provided to illustrate these concepts.
PRMT4 Blocks Myeloid Differentiation by Assembling a Methyl-RUNX1-Dependent Repressor Complex
Directory of Open Access Journals (Sweden)
Ly P. Vu
2013-12-01
Full Text Available Defining the role of epigenetic regulators in hematopoiesis has become critically important, because recurrent mutations or aberrant expression of these genes has been identified in both myeloid and lymphoid hematological malignancies. We found that PRMT4, a type I arginine methyltransferase whose function in normal and malignant hematopoiesis is unknown, is overexpressed in acute myelogenous leukemia patient samples. Overexpression of PRMT4 blocks the myeloid differentiation of human stem/progenitor cells (HSPCs, whereas its knockdown is sufficient to induce myeloid differentiation of HSPCs. We demonstrated that PRMT4 represses the expression of miR-223 in HSPCs via the methylation of RUNX1, which triggers the assembly of a multiprotein repressor complex that includes DPF2. As part of the feedback loop, PRMT4 expression is repressed posttranscriptionally by miR-223. Depletion of PRMT4 results in differentiation of myeloid leukemia cells in vitro and their decreased proliferation in vivo. Thus, targeting PRMT4 holds potential as a novel therapy for acute myelogenous leukemia.
Directory of Open Access Journals (Sweden)
Beatriz Cesar
2011-01-01
Full Text Available A homeopathic complex medication (HCM, with immunomodulatory properties, is recommended for patients with depressed immune systems. Previous studies demonstrated that the medication induces an increase in leukocyte number. The bone marrow microenvironment is composed of growth factors, stromal cells, an extracellular matrix and progenitor cells that differentiate into mature blood cells. Mice were our biological model used in this research. We now report in vivo immunophenotyping of total bone marrow cells and ex vivo effects of the medication on mononuclear cell differentiation at different times. Cells were examined by light microscopy and cytokine levels were measured in vitro. After in vivo treatment with HCM, a pool of cells from the new marrow microenvironment was analyzed by flow cytometry to detect any trend in cell alteration. The results showed decreases, mainly, in CD11b and TER-119 markers compared with controls. Mononuclear cells were used to analyze the effects of ex vivo HCM treatment and the number of cells showing ring nuclei, niche cells and activated macrophages increased in culture, even in the absence of macrophage colony-stimulating factor. Cytokines favoring stromal cell survival and differentiation in culture were induced in vitro. Thus, we observe that HCM is immunomodulatory, either alone or in association with other products.
Differentiation of closely related fungi by electronic nose analysis
DEFF Research Database (Denmark)
Karlshøj, Kristian; Nielsen, Per Væggemose; Larsen, Thomas Ostenfeld
2007-01-01
In this work the potential of electronic nose analysis for differentiation of closely related fun has been described. A total of 20 isolates of the cheese-associated species Geotrichum candidum, Penicillium camemberti, P.nordicum, and Proqueford and its closely related species P paneum, P carneum...... as well as the noacheese ociated P. expansum have been investigated by electronic nose, GC-MS, and LGMS analysis. The isolates were inoculated on yeast extract sucroseagar in 20-mL headspace flasks and electronicnose analysis was performed daily for a-74period. To assess which volatile metabolites...... by high pressure liquid chromatography, coupled-to a diode array detector and a time of flight mass spectrometer. Several mycotoxins were detected in samples from the specles P.nordicum, P.roqueforti, P.paneum, P.carneum, and P.expansum. Differentiation of closely related mycotoxin producing fungi...
Tensor analysis and elementary differential geometry for physicists and engineers
Nguyen-Schäfer, Hung
2014-01-01
Tensors and methods of differential geometry are very useful mathematical tools in many fields of modern physics and computational engineering including relativity physics, electrodynamics, computational fluid dynamics (CFD), continuum mechanics, aero and vibroacoustics, and cybernetics. This book comprehensively presents topics, such as bra-ket notation, tensor analysis, and elementary differential geometry of a moving surface. Moreover, authors intentionally abstain from giving mathematically rigorous definitions and derivations that are however dealt with as precisely as possible. The reader is provided with hands-on calculations and worked-out examples at which he will learn how to handle the bra-ket notation, tensors and differential geometry and to use them in the physical and engineering world. The target audience primarily comprises graduate students in physics and engineering, research scientists, and practicing engineers.
Analysis of pharmacogenomic variants associated with population differentiation.
Directory of Open Access Journals (Sweden)
Bora Yeon
Full Text Available In the present study, we systematically investigated population differentiation of drug-related (DR genes in order to identify common genetic features underlying population-specific responses to drugs. To do so, we used the International HapMap project release 27 Data and Pharmacogenomics Knowledge Base (PharmGKB database. First, we compared four measures for assessing population differentiation: the chi-square test, the analysis of variance (ANOVA F-test, Fst, and Nearest Shrunken Centroid Method (NSCM. Fst showed high sensitivity with stable specificity among varying sample sizes; thus, we selected Fst for determining population differentiation. Second, we divided DR genes from PharmGKB into two groups based on the degree of population differentiation as assessed by Fst: genes with a high level of differentiation (HD gene group and genes with a low level of differentiation (LD gene group. Last, we conducted a gene ontology (GO analysis and pathway analysis. Using all genes in the human genome as the background, the GO analysis and pathway analysis of the HD genes identified terms related to cell communication. "Cell communication" and "cell-cell signaling" had the lowest Benjamini-Hochberg's q-values (0.0002 and 0.0006, respectively, and "drug binding" was highly enriched (16.51 despite its relatively high q-value (0.0142. Among the 17 genes related to cell communication identified in the HD gene group, five genes (STX4, PPARD, DCK, GRIK4, and DRD3 contained single nucleotide polymorphisms with Fst values greater than 0.5. Specifically, the Fst values for rs10871454, rs6922548, rs3775289, rs1954787, and rs167771 were 0.682, 0.620, 0.573, 0.531, and 0.510, respectively. In the analysis using DR genes as the background, the HD gene group contained six significant terms. Five were related to reproduction, and one was "Wnt signaling pathway," which has been implicated in cancer. Our analysis suggests that the HD gene group from PharmGKB is
Differential analysis for high density tiling microarray data
Directory of Open Access Journals (Sweden)
Kapranov Philipp
2007-09-01
Full Text Available Abstract Background High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. Results We have proposed a novel approach, based on a piece-wise function – to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. Conclusion The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value -13. The prototype R code has been made available as supplementary material [see Additional file 1]. Additional file 1 gsam_prototypercode.zip. File archive comprising of prototype R code for gSAM implementation including readme and examples. Click here for file
Differential analysis for high density tiling microarray data.
Ghosh, Srinka; Hirsch, Heather A; Sekinger, Edward A; Kapranov, Philipp; Struhl, Kevin; Gingeras, Thomas R
2007-09-24
High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. We have proposed a novel approach, based on a piece-wise function - to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value < 0.003; it is most significant at the 5' end of genes, at a p-value < 10-13. The prototype R code has been made available as supplementary material [see Additional file 1].
Smitha, K A; Gupta, A K; Jayasree, R S
2015-09-07
Glioma, the heterogeneous tumors originating from glial cells, generally exhibit varied grades and are difficult to differentiate using conventional MR imaging techniques. When this differentiation is crucial in the disease prognosis and treatment, even the advanced MR imaging techniques fail to provide a higher discriminative power for the differentiation of malignant tumor from benign ones. A powerful image processing technique applied to the imaging techniques is expected to provide a better differentiation. The present study focuses on the fractal analysis of fluid attenuation inversion recovery MR images, for the differentiation of glioma. For this, we have considered the most important parameters of fractal analysis, fractal dimension and lacunarity. While fractal analysis assesses the malignancy and complexity of a fractal object, lacunarity gives an indication on the empty space and the degree of inhomogeneity in the fractal objects. Box counting method with the preprocessing steps namely binarization, dilation and outlining was used to obtain the fractal dimension and lacunarity in glioma. Statistical analysis such as one-way analysis of variance and receiver operating characteristic (ROC) curve analysis helped to compare the mean and to find discriminative sensitivity of the results. It was found that the lacunarity of low and high grade gliomas vary significantly. ROC curve analysis between low and high grade glioma for fractal dimension and lacunarity yielded 70.3% sensitivity and 66.7% specificity and 70.3% sensitivity and 88.9% specificity, respectively. The study observes that fractal dimension and lacunarity increases with an increase in the grade of glioma and lacunarity is helpful in identifying most malignant grades.
Transcriptome analysis of differentiating spermatogonia stimulated with kit ligand.
Rossi, Pellegrino; Lolicato, Francesca; Grimaldi, Paola; Dolci, Susanna; Di Sauro, Annarita; Filipponi, Doria; Geremia, Raffaele
2008-01-01
Kit ligand (KL) is a survival factor and a mitogenic stimulus for differentiating spermatogonia. However, it is not known whether KL also plays a role in the differentiative events that lead to meiotic entry of these cells. We performed a wide genome analysis of difference in gene expression induced by treatment with KL of spermatogonia from 7-day-old mice, using gene chips spanning the whole mouse genome. The analysis revealed that the pattern of RNA expression induced by KL is compatible with the qualitative changes of the cell cycle that occur during the subsequent cell divisions in type A and B spermatogonia, i.e. the progressive lengthening of the S phase and the shortening of the G2/M transition. Moreover, KL up-regulates in differentiating spermatogonia the expression of early meiotic genes (for instance: Lhx8, Nek1, Rnf141, Xrcc3, Tpo1, Tbca, Xrcc2, Mesp1, Phf7, Rtel1), whereas it down-regulates typical spermatogonial markers (for instance: Pole, Ptgs2, Zfpm2, Egr2, Egr3, Gsk3b, Hnrpa1, Fst, Ptch2). Since KL modifies the expression of several genes known to be up-regulated or down-regulated in spermatogonia during the transition from the mitotic to the meiotic cell cycle, these results are consistent with a role of the KL/kit interaction in the induction of their meiotic differentiation.
Genetic mapping of complex discrete human diseases by discriminant analysis
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
The objective of the present study is to propose and evaluate a novel multivariate approach for genetic mapping of complex categorical diseases. This approach results from an application of standard stepwise discriminant analysis to detect linkage based on the differential marker identity-by-descent (IBD) distributions among the different groups of sib pairs. Two major advantages of this method are that it allows for simultaneously testing all markers, together with other genetic and environmental factors in a single multivariate setting and it avoids explicitly modeling the complex relationship between the affection status of sib pairs and the underlying genetic determinants. The efficiency and properties of the method are demonstrated via simulations. The proposed multivariate approach has successfully located the true position(s) under various genetic scenarios. The more important finding is that using highly densely spaced markers (1～2 cM) leads to only a marginal loss of statistical efficiency of the proposed methods in terms of gene localization and statistical power. These results have well established its utility and advantages as a fine-mapping tool. A unique property of the proposed method is the ability to map multiple linked trait loci to their precise positions due to its sequential nature, as demonstrated via simulations.
McGregor, Stephen J.; Busa, Michael A.; Skufca, Joseph; Yaggie, James A.; Bollt, Erik M.
2009-06-01
Regularity statistics have been previously applied to walking gait measures in the hope of gaining insight into the complexity of gait under different conditions and in different populations. Traditional regularity statistics are subject to the requirement of stationarity, a limitation for examining changes in complexity under dynamic conditions such as exhaustive exercise. Using a novel measure, control entropy (CE), applied to triaxial continuous accelerometry, we report changes in complexity of walking and running during increasing speeds up to exhaustion in highly trained runners. We further apply Karhunen-Loeve analysis in a new and novel way to the patterns of CE responses in each of the three axes to identify dominant modes of CE responses in the vertical, mediolateral, and anterior/posterior planes. The differential CE responses observed between the different axes in this select population provide insight into the constraints of walking and running in those who may have optimized locomotion. Future comparisons between athletes, healthy untrained, and clinical populations using this approach may help elucidate differences between optimized and diseased locomotor control.
Directory of Open Access Journals (Sweden)
Treuner-Lange Anke
2010-04-01
Full Text Available Abstract Background Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of M. xanthus leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities. Results Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation per se, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate
Painlevé analysis for nonlinear partial differential equations
Musette, M
1998-01-01
The Painlevé analysis introduced by Weiss, Tabor and Carnevale (WTC) in 1983 for nonlinear partial differential equations (PDE's) is an extension of the method initiated by Painlevé and Gambier at the beginning of this century for the classification of algebraic nonlinear differential equations (ODE's) without movable critical points. In these lectures we explain the WTC method in its invariant version introduced by Conte in 1989 and its application to solitonic equations in order to find algorithmically their associated so-called ``integrable'' equations but they are generically no more valid for equations modelising physical phenomema. Belonging to this second class, some equations called ``partially integrable'' sometimes keep remnants of integrability. In that case, the singularity analysis may also be useful for building closed form analytic solutions, which necessarily % Conte agree with the singularity structure of the equations. We display the privileged role played by the Riccati equation and syste...
Directory of Open Access Journals (Sweden)
Cornelia Kranczioch
Full Text Available BACKGROUND: The neural simulation theory predicts similarity for the neural mechanisms subserving overt (motor execution and covert (movement imagination actions. Here we tested this prediction for movement preparation, a key characteristic of motor cognition. METHODOLOGY/PRINCIPAL FINDINGS: High-density electroencephalogram (EEG was recorded during covert and overt actions. Movement preparation was studied with a motor priming paradigm, which varied task complexity and amount of advance information. Participants performed simple or complex sequential finger movements either overtly or covertly. Advance information was either fully predictive or partially predictive. Stimulus-locked event-related potential (ERP data showed the typical pattern of foreperiod activation for overt and covert movements. The foreperiod contingent negative variation (CNV differed between simple and complex movements only in the execution task. ERP topographies differed between execution and imagination only when advance information was fully predictive. CONCLUSIONS/SIGNIFICANCE: Results suggest a differential contribution of the movement preparation network to action imagination and execution. Overt and covert actions seem to involve similar though not identical mechanisms, where overt actions engage a more fine-grained modulation of covert preparatory states.
A Differential Abundance Analysis of HD219175 A and B
Institute of Scientific and Technical Information of China (English)
Hua-Wei Zhang; Gang Zhao
2005-01-01
The abundances of the wide binary pair HD 219175 A and B are determined and compared using a line-by-line differential analysis. No evidence for difference has been found in the abundances of Fe, O, Na, Mg, Al, Si, K, Ca, Sc,Ti, V, Cr, Mn, Ni, Cu and Ba. Our results support a physical relation between the two components of HD 219175.
Operator Semigroups meet Complex Analysis, Harmonic Analysis and Mathematical Physics
Chill, Ralph; Tomilov, Yuri
2015-01-01
This proceedings volume originates from a conference held in Herrnhut in June 2013. It provides unique insights into the power of abstract methods and techniques in dealing successfully with numerous applications stemming from classical analysis and mathematical physics. The book features diverse topics in the area of operator semigroups, including partial differential equations, martingale and Hilbert transforms, Banach and von Neumann algebras, Schrödinger operators, maximal regularity and Fourier multipliers, interpolation, operator-theoretical problems (concerning generation, perturbation and dilation, for example), and various qualitative and quantitative Tauberian theorems with a focus on transfinite induction and magics of Cantor. The last fifteen years have seen the dawn of a new era for semigroup theory with the emphasis on applications of abstract results, often unexpected and far removed from traditional ones. The aim of the conference was to bring together prominent experts in the field of modern...
Park, Yun-Jong; Koh, Jin; Kwon, Jin Teak; Park, Yong-Seok; Yang, Lijun; Cha, Seunghee
2017-01-01
Severe xerostomia (dry mouth) compromises the quality of life in patients with Sjögren’s syndrome or radiation therapy for head and neck cancer. A clinical management of xerostomia is often unsatisfactory as most interventions are palliative with limited efficacy. Following up our previous study demonstrating that mouse BM-MSCs are capable of differentiating into salivary epithelial cells in a co-culture system, we further explored the molecular basis that governs the MSC reprogramming by utilizing high-throughput iTRAQ-2D-LC-MS/MS-based proteomics. Our data revealed the novel induction of pancreas-specific transcription factor 1a (PTF1α), muscle, intestine and stomach expression-1 (MIST-1), and achaete-scute complex homolog 3 (ASCL3) in 7 day co-cultured MSCs but not in control MSCs. More importantly, a common notion of pancreatic-specific expression of PTF1 α was challenged for the first time by our verification of PTF1 α expression in the mouse salivary glands. Furthermore, a molecular network simulation of our selected putative MSC reprogramming factors demonstrated evidence for their perspective roles in salivary gland development. In conclusion, quantitative proteomics with extensive data analyses narrowed down a set of MSC reprograming factors potentially contributing to salivary gland regeneration. Identification of their differential/synergistic impact on MSC conversion warrants further investigation. PMID:28158262
Genetic analysis of population differentiation and adaptation in Leuciscus waleckii.
Chang, Yumei; Tang, Ran; Sun, Xiaowen; Liang, Liqun; Chen, Jinping; Huang, Jinfeng; Dou, Xinjie; Tao, Ran
2013-12-01
Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.
[SADE] a Maple package for the symmetry analysis of differential equations
Rocha Filho, Tarcísio M.; Figueiredo, Annibal
2011-02-01
We present the package SADE (Symmetry Analysis of Differential Equations) for the determination of symmetries and related properties of systems of differential equations. The main methods implemented are: Lie, nonclassical, Lie-Bäcklund and potential symmetries, invariant solutions, first-integrals, Nöther theorem for both discrete and continuous systems, solution of ordinary differential equations, order and dimension reductions using Lie symmetries, classification of differential equations, Casimir invariants, and the quasi-polynomial formalism for ODE's (previously implemented by the authors in the package QPSI) for the determination of quasi-polynomial first-integrals, Lie symmetries and invariant surfaces. Examples of use of the package are given. Program summaryProgram title: SADE Catalogue identifier: AEHL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 27 704 No. of bytes in distributed program, including test data, etc.: 346 954 Distribution format: tar.gz Programming language: MAPLE 13 and MAPLE 14 Computer: PCs and workstations Operating system: UNIX/LINUX systems and WINDOWS Classification: 4.3 Nature of problem: Determination of analytical properties of systems of differential equations, including symmetry transformations, analytical solutions and conservation laws. Solution method: The package implements in MAPLE some algorithms (discussed in the text) for the study of systems of differential equations. Restrictions: Depends strongly on the system and on the algorithm required. Typical restrictions are related to the solution of a large over-determined system of linear or non-linear differential equations. Running time: Depends strongly on the order, the complexity of the differential
Mixture model analysis of complex samples
Wedel, M; ter Hofstede, F; Steenkamp, JBEM
1998-01-01
We investigate the effects of a complex sampling design on the estimation of mixture models. An approximate or pseudo likelihood approach is proposed to obtain consistent estimates of class-specific parameters when the sample arises from such a complex design. The effects of ignoring the sample desi
Complex plant traits : time for polygenic analysis
Jansen, Ritsert C.
1996-01-01
Currently, mapping of genes for complex traits is an area of active theoretical research at the interface of genetics and statistics. Much progress has been made over the past few years in handling statistically complex but realistic multilocus models. Here, I describe the state of the art and discu
Directory of Open Access Journals (Sweden)
Eine eEstrada-Mata
2016-01-01
Full Text Available The systemic infections caused by members of the Candida parapsilosis complex are currently associated to high mobility and mortality rates, and are considered as relevant as those caused by Candida albicans. Since the fungal cell wall is the first point of contact with the host cells, here we performed a comparison of this organelle in members of the C. parapsilosis complex, and its relevance during interaction with human peripheral blood mononuclear cells. We found that the wall of the C. parapsilosis complex members is similar in composition, but differs to that from C. albicans, with less mannan content and more β-glucan and porosity levels. Furthermore, lectin-based analysis showed increased chitin and β1,3-glucan exposure at the surface of C. parapsilosis sensu lato when compared to C. albicans. Yeast cells of members of the C. parapsilosis complex stimulated more cytokine production by human peripheral blood mononuclear cells than C. albicans cells; and this significantly changed upon removal of O-linked mannans, indicating this wall component plays a significant role in cytokine stimulation by C. parapsilosis sensu lato. When inner wall components were exposed on the wall surface, C. parapsilosis sensu stricto and C. metapsilosis, but not C. orthopsilosis, stimulated higher cytokine production. Moreover, we found a strong dependency on β1,3-glucan recognition for the members of the C. parapsilosis complex, but not for live C. albicans cells; whereas TLR4 was required for TNFα production by the three members of the complex, and stimulation of IL-6 by C. orthopsilosis. Mannose receptor had a significant role during TNF and IL-1β stimulation by members of the complex. Finally, we demonstrated that purified N- and O-mannans from either C. parapsilosis sensu lato or C. albicans are capable to block the recognition of these pathogens by human peripheral blood mononuclear cells. Together; our results suggest that the innate immune
Estrada-Mata, Eine; Navarro-Arias, María J; Pérez-García, Luis A; Mellado-Mojica, Erika; López, Mercedes G; Csonka, Katalin; Gacser, Attila; Mora-Montes, Héctor M
2015-01-01
The systemic infections caused by members of the Candida parapsilosis complex are currently associated to high morbility and mortality rates, and are considered as relevant as those caused by Candida albicans. Since the fungal cell wall is the first point of contact with the host cells, here we performed a comparison of this organelle in members of the C. parapsilosis complex, and its relevance during interaction with human peripheral blood mononuclear cells (PBMCs). We found that the wall of the C. parapsilosis complex members is similar in composition, but differs to that from C. albicans, with less mannan content and more β-glucan and porosity levels. Furthermore, lectin-based analysis showed increased chitin and β1,3-glucan exposure at the surface of C. parapsilosis sensu lato when compared to C. albicans. Yeast cells of members of the C. parapsilosis complex stimulated more cytokine production by human PBMCs than C. albicans cells; and this significantly changed upon removal of O-linked mannans, indicating this wall component plays a significant role in cytokine stimulation by C. parapsilosis sensu lato. When inner wall components were exposed on the wall surface, C. parapsilosis sensu stricto and C. metapsilosis, but not C. orthopsilosis, stimulated higher cytokine production. Moreover, we found a strong dependency on β1,3-glucan recognition for the members of the C. parapsilosis complex, but not for live C. albicans cells; whereas TLR4 was required for TNFα production by the three members of the complex, and stimulation of IL-6 by C. orthopsilosis. Mannose receptor had a significant role during TNFα and IL-1β stimulation by members of the complex. Finally, we demonstrated that purified N- and O-mannans from either C. parapsilosis sensu lato or C. albicans are capable to block the recognition of these pathogens by human PBMCs. Together; our results suggest that the innate immune recognition of the members of the C. parapsilosis complex is differential
Complex networks analysis in socioeconomic models
Varela, Luis M; Ausloos, Marcel; Carrete, Jesus
2014-01-01
This chapter aims at reviewing complex networks models and methods that were either developed for or applied to socioeconomic issues, and pertinent to the theme of New Economic Geography. After an introduction to the foundations of the field of complex networks, the present summary adds insights on the statistical mechanical approach, and on the most relevant computational aspects for the treatment of these systems. As the most frequently used model for interacting agent-based systems, a brief description of the statistical mechanics of the classical Ising model on regular lattices, together with recent extensions of the same model on small-world Watts-Strogatz and scale-free Albert-Barabasi complex networks is included. Other sections of the chapter are devoted to applications of complex networks to economics, finance, spreading of innovations, and regional trade and developments. The chapter also reviews results involving applications of complex networks to other relevant socioeconomic issues, including res...
On Complex Oscillation Theory of Solutions of Some Higher Order Linear Differential Equations
Institute of Scientific and Technical Information of China (English)
Jianren LONG
2012-01-01
In this paper,we shall use Nevanlinna theory of meromorphic functions to investigate the complex oscillation theory of solutions of some higher order linear differential equation.Suppose that A is a transcendental entire function with ρ(A)＜ 1/2.Suppose that k ≥ 2 and f(k)+ A(z)f =0 has a solution f with λ(f)＜ ρ(A),and suppose that A1 =A + h,where h ≠ 0 is an entire function with ρ(h)＜ ρ(A).Then g(k)+ A1(z)g =0 does not have a solution g with λ(g)＜ ∞.
Differential sensitivity of the species of Candida parapsilosis sensu lato complex against statins.
Szenzenstein, Judit; Gácser, Attila; Grózer, Zsuzsanna; Farkas, Zoltán; Nagy, Katalin; Vágvölgyi, Csaba; Márki-Zay, János; Pfeiffer, Ilona
2013-10-01
Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis are human fungal pathogens with clinical importance. The recently reclassified three closely related species have significant variation in virulence, clinical prevalence and susceptibility characteristics to different antifungal compounds. The aim of this study was to investigate the in vitro activity of atorvastatin and fluvastatin against C. metapsilosis, C. orthopsilosis and C. parapsilosis. Susceptibility tests showed that C. parapsilosis was the most sensitive while C. orthopsilosis was the least susceptible species to both drugs. On the basis of the differential sensitivity, we developed a simple, reliable and highly cost-effective plate assay to distinguish these closely related species. Applying this method, 54 isolates belonging to the C. parapsilosis sensu lato complex deposited in Szeged Microbial Collection could be sorted into the three species with 100 % probability.
Complexity Analysis and Its Application 10
Institute of Scientific and Technical Information of China (English)
JiongRUAN; WeiLIN; 等
1999-01-01
In this paper,we introduce a nonlinear method named as “Complexity Analysis”,by which we study the chaotic and other behavior in heary rate of the patients suffer from AMI,STSDS and VPB,or normal healthy subjects.The results show that the nolinear parmeter-complexity reflects the dynamic state of heart ,It can be used to measure the complexity of biologic systems quantitatively,It is possible to use such a method to analyze and diagnose cardiovascular disease in clinics.
Oda, Yuko; Chalkley, Robert J; Burlingame, Alma L; Bikle, Daniel D
2010-10-01
Mediator is a multisubunit coactivator complex that facilitates transcription of nuclear receptors. We investigated the role of the mediator complex as a coactivator for vitamin D receptor (VDR) in keratinocytes. Using VDR affinity beads, the vitamin D receptor interacting protein (DRIP)/mediator complex was purified from primary keratinocytes, and its subunit composition was determined by mass spectrometry. The complex included core subunits, such as DRIP205/MED1 (MED1), that directly binds to VDR. Additional subunits were identified that are components of the RNA polymerase II complex. The functions of different mediator components were investigated by silencing its subunits. The core subunit MED1 facilitates VDR activity and regulating keratinocyte proliferation and differentiation. A newly described subunit MED21 also has a role in promoting keratinocyte proliferation and differentiation, whereas MED10 has an inhibitory role. Blocking MED1/MED21 expression caused hyperproliferation of keratinocytes, accompanied by increases in mRNA expression of the cell cycle regulator cyclin D1 and/or glioma-associated oncogene homolog. Blocking MED1 or MED21 expression also resulted in defects in calcium-induced keratinocyte differentiation, as indicated by decreased expression of differentiation markers and decreased translocation of E-cadherin to the membrane. These results show that keratinocytes use the transcriptional coactivator mediator to regulate VDR functions and control keratinocyte proliferation and differentiation.
Differential Geometric Analysis of Alterations in MH α-Helices
Hischenhuber, Birgit; Havlicek, Hans; Todoric, Jelena; Höllrigl-Binder, Sonja; Schreiner, Wolfgang; Knapp, Bernhard
2013-01-01
Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α-helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α-helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α-helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α-helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α-helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α-helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α-helices for a broad range of applications. © 2013 Wiley Periodicals, Inc. PMID:23703160
Overview of Sensitivity Analysis and Shape Optimization for Complex Aerodynamic Configurations
Newman, Perry A.; Newman, James C., III; Barnwell, Richard W.; Taylor, Arthur C., III; Hou, Gene J.-W.
1998-01-01
This paper presents a brief overview of some of the more recent advances in steady aerodynamic shape-design sensitivity analysis and optimization, based on advanced computational fluid dynamics. The focus here is on those methods particularly well- suited to the study of geometrically complex configurations and their potentially complex associated flow physics. When nonlinear state equations are considered in the optimization process, difficulties are found in the application of sensitivity analysis. Some techniques for circumventing such difficulties are currently being explored and are included here. Attention is directed to methods that utilize automatic differentiation to obtain aerodynamic sensitivity derivatives for both complex configurations and complex flow physics. Various examples of shape-design sensitivity analysis for unstructured-grid computational fluid dynamics algorithms are demonstrated for different formulations of the sensitivity equations. Finally, the use of advanced, unstructured-grid computational fluid dynamics in multidisciplinary analyses and multidisciplinary sensitivity analyses within future optimization processes is recommended and encouraged.
Differential Proteomic Analysis of Carbon Ion Radiation in Sheep Sperm
Institute of Scientific and Technical Information of China (English)
HE Yu-xuan; LI Hong-yan; ZHANG Yong; HE Jian-hua; ZHANG Hong; ZHAO Xing-xu
2013-01-01
This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis (2-DE) analysis in the project of breeding a new variety of sheep. Differential expression proteins were detected using the PDQuest 8.0 software after staining with Coomassie blue. Valid spots were then analyzed through liquid chromatography tandem mass spectrometry (LC-MS/MS). Among the 480 total protein spots displayed in 2-D gels, 6 specific protein spots were observed in sperm gels. A search against protein sequences in the National Center for Biotechnology Information databases (NCBI) indicated that differentially expressed proteins correspond to two proteins, identified to be enolase and transcription factor AP-2-alpha (TFAP-2α). The two proteins were up-regulated in the irradiated sperm. To the best of our knowledge, this study is the first to identify proteomic changes induced by carbon ion radiation in sheep sperm. The analysis of differential expression protein may be useful in identifying new breeding markers in sheep reproduction and in clarifying the mechanisms involved in irradiation or space breeding.
Circadian phase has profound effects on differential expression analysis.
Directory of Open Access Journals (Sweden)
Polly Yingshan Hsu
Full Text Available Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that are generated by an endogenous clock, or oscillator. Found in diverse organisms, they are precisely controlled and provide growth and fitness benefits. Numerous microarray studies examining circadian control of gene expression have reported that a substantial fraction of the genomes of many organisms is clock-controlled. Here we show that a long-period mutant in Arabidopsis, rve8-1, has a global alteration in phase of all clock-controlled genes. After several days in constant environmental conditions, at which point the mutant and control plants have very different circadian phases, we found 1557 genes to be differentially expressed in rve8-1, almost all of which are clock-regulated. However, after adjusting for this phase difference, only a handful show overall expression level differences between rve8-1 and wild type. Thus the apparent differential expression is mainly due to the phase difference between these two genotypes. These findings prompted us to examine the effect of phase on gene expression within a single genotype. Using samples of wild-type plants harvested at thirty-minute intervals, we demonstrated that even this small difference in circadian phase significantly influences the results of differential expression analysis. Our study demonstrates the robust influence of the circadian clock on the transcriptome and provides a cautionary note for all biologists performing genome-level expression analysis.
Teacher knowledge of error analysis in differential calculus
Directory of Open Access Journals (Sweden)
Eunice K. Moru
2014-12-01
Full Text Available The study investigated teacher knowledge of error analysis in differential calculus. Two teachers were the sample of the study: one a subject specialist and the other a mathematics education specialist. Questionnaires and interviews were used for data collection. The findings of the study reflect that the teachers’ knowledge of error analysis was characterised by the following assertions, which are backed up with some evidence: (1 teachers identified the errors correctly, (2 the generalised error identification resulted in opaque analysis, (3 some of the identified errors were not interpreted from multiple perspectives, (4 teachers’ evaluation of errors was either local or global and (5 in remedying errors accuracy and efficiency were emphasised more than conceptual understanding. The implications of the findings of the study for teaching include engaging in error analysis continuously as this is one way of improving knowledge for teaching.
PC analysis of stochastic differential equations driven by Wiener noise
Le Maitre, Olivier
2015-03-01
A polynomial chaos (PC) analysis with stochastic expansion coefficients is proposed for stochastic differential equations driven by additive or multiplicative Wiener noise. It is shown that for this setting, a Galerkin formalism naturally leads to the definition of a hierarchy of stochastic differential equations governing the evolution of the PC modes. Under the mild assumption that the Wiener and uncertain parameters can be treated as independent random variables, it is also shown that the Galerkin formalism naturally separates parametric uncertainty and stochastic forcing dependences. This enables us to perform an orthogonal decomposition of the process variance, and consequently identify contributions arising from the uncertainty in parameters, the stochastic forcing, and a coupled term. Insight gained from this decomposition is illustrated in light of implementation to simplified linear and non-linear problems; the case of a stochastic bifurcation is also considered.
Quantum Analysis - Non-Commutative Differential and Integral Calculi
Suzuki, Masuo
1997-01-01
A new scheme of quantum analysis, namely a non-commutative calculus of operator derivatives and integrals is introduced. This treats differentiation of an operator-valued function with respect to the relevant operator in a Banach space. In this new scheme, operator derivatives are expressed in terms of the relevant operator and its inner derivation explicitly. Derivatives of hyperoperators are also defined. Some possible applications of the present calculus to quantum statistical physics are briefly discussed. Acknowledgements The author would like to thank Professor H. Araki, Professor K. Aomoto, Professor H. Hiai, Professor N. Obata and Dr. R.I. McLachlan for useful comments. Added in proof. Recently it has been proven that the quantum derivatives {dn f(A)/ dAn} are invariant for any choice of definitions of the differential df(A) satisfying the Leibniz rule and the linearity (M. Suzuki, J. Math. Phys.).->
Hellman, Lance M; Yin, Liusong; Wang, Yuan; Blevins, Sydney J; Riley, Timothy P; Belden, Orrin S; Spear, Timothy T; Nishimura, Michael I; Stern, Lawrence J; Baker, Brian M
2016-05-01
Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics.
Lie Symmetry Analysis of the Hopf Functional-Differential Equation
Directory of Open Access Journals (Sweden)
Daniel D. Janocha
2015-08-01
Full Text Available In this paper, we extend the classical Lie symmetry analysis from partial differential equations to integro-differential equations with functional derivatives. We continue the work of Oberlack and Wacławczyk (2006, Arch. Mech. 58, 597, (2013, J. Math. Phys. 54, 072901, where the extended Lie symmetry analysis is performed in the Fourier space. Here, we introduce a method to perform the extended Lie symmetry analysis in the physical space where we have to deal with the transformation of the integration variable in the appearing integral terms. The method is based on the transformation of the product y(xdx appearing in the integral terms and applied to the functional formulation of the viscous Burgers equation. The extended Lie symmetry analysis furnishes all known symmetries of the viscous Burgers equation and is able to provide new symmetries associated with the Hopf formulation of the viscous Burgers equation. Hence, it can be employed as an important tool for applications in continuum mechanics.
Genetic evidence for complexity in ethnic differentiation and history in East Africa.
Poloni, Estella S; Naciri, Yamama; Bucho, Rute; Niba, Régine; Kervaire, Barbara; Excoffier, Laurent; Langaney, André; Sanchez-Mazas, Alicia
2009-11-01
The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondrial DNA extracted from Nyangatom and Daasanach archival sera revealed high levels of diversity, with most sequences belonging to the L haplogroups, the basal branches of the mitochondrial phylogeny. However, in sharp contrast with other Ethiopian populations, only 5% of the Nyangatom and Daasanach sequences belong to haplogroups M and N. The Nyangatom and Daasanach were found to be significantly differentiated, while each of them displays close affinities with some Tanzanian populations. The strong genetic structure found over East Africa was neither associated with geography nor with language, a result confirmed by the analysis of 6711 HVS-I sequences of 136 populations mainly from Africa. Processes of migration, language shift and group absorption are documented by linguists and ethnographers for the Nyangatom and Daasanach, thus pointing to the probably transient and plastic nature of these ethnic groups. These processes, associated with periods of isolation, could explain the high diversity and strong genetic structure found in East Africa.
Complex analysis a modern first course in function theory
Muir, Jerry R
2015-01-01
A thorough introduction to the theory of complex functions emphasizing the beauty, power, and counterintuitive nature of the subject Written with a reader-friendly approach, Complex Analysis: A Modern First Course in Function Theory features a self-contained, concise development of the fundamental principles of complex analysis. After laying groundwork on complex numbers and the calculus and geometric mapping properties of functions of a complex variable, the author uses power series as a unifying theme to define and study the many rich and occasionally surprising properties of analytic fun
Directory of Open Access Journals (Sweden)
Xiaohong Zhou
Full Text Available Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs and differentially expressed proteins (DEPs were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq and two-dimensional electrophoresis (2-DE in conjunction with mass spectrometry (MS. A set of 4,889 DEGs and 90 DEPs were identified, respectively. Most of them are related to metabolism, chromatin assembly or disassembly and immune defense. After comparative analysis, 24 of the 90 DEPs were detected in RNA-seq and proteomics datasets simultaneously. In addition, real-time RT-PCR experiments were performed to check the differential expression of the 24 genes, and the results were consistent with the RNA-seq data. According to gene ontology (GO analysis, we found that a big part of these differentially expressed genes were related to the process of stress or immunity response. Several putative determinants and candidate effectors responsive to Agrobacterium mediated transformation of wheat cells were discussed. We speculate that some of these genes are possibly related to Agrobacterium infection. Our results will help to understand the interaction between Agrobacterium and host cells, and may facilitate developing efficient transformation strategies in cereal crops.
Complex Surveys A Guide to Analysis Using R
Lumley, Thomas
2010-01-01
A complete guide to carrying out complex survey analysis using R. As survey analysis continues to serve as a core component of sociological research, researchers are increasingly relying upon data gathered from complex surveys to carry out traditional analyses. Complex Surveys is a practical guide to the analysis of this kind of data using R, the freely available and downloadable statistical programming language. As creator of the specific survey package for R, the author provides the ultimate presentation of how to successfully use the software for analyzing data from complex surveys while al
Zhang, Li; Song, Qi-Fang; Jin, Jing-Jie; Huang, Ping; Wang, Zhou-Ping; Xie, Xiao-Fei; Gu, Xiao-Qiong; Gao, Xue-Juan; Jia, Hong-Ling
2017-08-14
Kawasaki disease, which is characterised by systemic vasculitides accompanied by acute fever, is regularly treated by intravenous immunoglobulin to avoid lesion formation in the coronary artery; however, the mechanism of intravenous immunoglobulin therapy is unclear. Hence, we aimed to analyse the global expression profile of serum exosomal proteins before and after administering intravenous immunoglobulin. Two-dimensional electrophoresis coupled with mass spectrometry analysis was used to identify the differentially expressed proteome of serum exosomes in patients with Kawasaki disease before and after intravenous immunoglobulin therapy. Our analysis revealed 69 differential protein spots in the Kawasaki disease group with changes larger than 1.5-fold and 59 differential ones in patients after intravenous immunoglobulin therapy compared with the control group. Gene ontology analysis revealed that the acute-phase response disappeared, the functions of the complement system and innate immune response were enhanced, and the antibacterial humoral response pathway of corticosteroids and cardioprotection emerged after administration of intravenous immunoglobulin. Further, we showed that complement C3 and apolipoprotein A-IV levels increased before and decreased after intravenous immunoglobulin therapy and that the insulin-like growth factor-binding protein complex acid labile subunit displayed reverse alteration before and after intravenous immunoglobulin therapy. These observations might be potential indicators of intravenous immunoglobulin function. Our results show the differential proteomic profile of serum exosomes of patients with Kawasaki disease before and after intravenous immunoglobulin therapy, such as complement C3, apolipoprotein A-IV, and insulin-like growth factor-binding protein complex acid labile subunit. These results may be useful in the identification of markers for monitoring intravenous immunoglobulin therapy in patients with Kawasaki disease.
Differential item functioning analysis by applying multiple comparison procedures.
Eusebi, Paolo; Kreiner, Svend
2015-01-01
Analysis within a Rasch measurement framework aims at development of valid and objective test score. One requirement of both validity and objectivity is that items do not show evidence of differential item functioning (DIF). A number of procedures exist for the assessment of DIF including those based on analysis of contingency tables by Mantel-Haenszel tests and partial gamma coefficients. The aim of this paper is to illustrate Multiple Comparison Procedures (MCP) for analysis of DIF relative to a variable defining a very large number of groups, with an unclear ordering with respect to the DIF effect. We propose a single step procedure controlling the false discovery rate for DIF detection. The procedure applies for both dichotomous and polytomous items. In addition to providing evidence against a hypothesis of no DIF, the procedure also provides information on subset of groups that are homogeneous with respect to the DIF effect. A stepwise MCP procedure for this purpose is also introduced.
Complex Network Characteristics and Invulnerability Simulating Analysis of Supply Chain
Hui-Huang Chen; Ai-Min Lin
2012-01-01
To study the characteristics of the complex supply chain, a invulnerability analysis method based on the complex network theory is proposed. The topological structure and dynamic characteristics of the complex supply chain network were analyzed. The fact was found that the network is with general characteristics of the complex network, and with the characteristics of small-world network and scale-free network. A simulation experiment was made on the invulnerability of the supply chain network...
Directory of Open Access Journals (Sweden)
Gisele R. de Oliveira
2007-09-01
Full Text Available The distinction of non-epileptic from epileptic events is difficult even for experienced neurologists. We retrospectively evaluated 59 dialeptic events from 27 patients admitted for video EEG monitoring to check whether heart rate (HR analysis could help in differentiating dialeptic complex partial temporal lobe seizures (TLS from dialeptic simple partial TLS, and non-epileptic dialeptic events. Baseline HR was increased in the simple partial TLS in comparison to complex partial TLS and non-epileptic groups (pA distinção entre eventos não epilépticos de epilépticos é difícil mesmo para neurologistas experientes. Analisamos 59 eventos dialéticos de 27 pacientes internados para monitorização por video-EEG para checar se a análise da frequência cardíaca (FC poderia auxiliar na diferenciação de crises dialépticas parciais complexas de crises dialépticas parciais simples e eventos dialépticos não epilépticos. A freqüência cardíaca basal estava aumentada nos pacientes com crises parciais simples em comparação com o período basal dos grupos parcial complexa e não epiléptico (p<0,05. Houve aumento da freqüência cardíaca em cada crise dialéptica parcial complexa (100% dos eventos, p<0,05, mas a FC retornou aos níveis basais na fase pós-ictal. A FC ictal não foi alterada nos grupos de crises não epiléticas e nos pacientes com crises parciais simples. Nossos achados sugerem que a taquicardia ictal com mediação central é característica de crises parciais complexas dialépticas (tanto taquicardia quanto bradicardia têm sido relatados durante crises temporais parciais complexas. Tal achado poderá ser utilizado como critério para diferenciar crises dialépticas parciais complexas de crises dialépticas parciais simples e eventos dialépticos não epilépticos.
Multivariable Discriminant Analysis for the Differential Diagnosis of Microcytic Anemia
Directory of Open Access Journals (Sweden)
Eloísa Urrechaga
2013-01-01
Full Text Available Introduction. Iron deficiency anemia and thalassemia are the most common causes of microcytic anemia. Powerful statistical computer programming enables sensitive discriminant analyses to aid in the diagnosis. We aimed at investigating the performance of the multiple discriminant analysis (MDA to the differential diagnosis of microcytic anemia. Methods. The training group was composed of 200 β-thalassemia carriers, 65 α-thalassemia carriers, 170 iron deficiency anemia (IDA, and 45 mixed cases of thalassemia and acute phase response or iron deficiency. A set of potential predictor parameters that could detect differences among groups were selected: Red Blood Cells (RBC, hemoglobin (Hb, mean cell volume (MCV, mean cell hemoglobin (MCH, and RBC distribution width (RDW. The functions obtained with MDA analysis were applied to a set of 628 consecutive patients with microcytic anemia. Results. For classifying patients into two groups (genetic anemia and acquired anemia, only one function was needed; 87.9% β-thalassemia carriers, and 83.3% α-thalassemia carriers, and 72.1% in the mixed group were correctly classified. Conclusion. Linear discriminant functions based on hemogram data can aid in differentiating between IDA and thalassemia, so samples can be efficiently selected for further analysis to confirm the presence of genetic anemia.
Numerical Analysis for Functional Differential and Integral Equations
Institute of Scientific and Technical Information of China (English)
Hermann BRUNNER; Tao TANG; Stefan VANDEWALLE
2009-01-01
@@ From December 3-6,2007,the Department of Mathematics at Hong Kong Baptist University hosted the International Workshop on Numerical Analysis and Computational Methods for Functional Differential and Integral Equations. This workshop,organized by Hermann Brunner of Memorial University of Newfoundland (Canada) & Hong Kong Baptist University,Leevan Ling and Tao Tang of Hong Kong Baptist University,and Chengjian Zhang of Huazhong University of Science and Technology (China) brought together some 40 members of research groups in Hong Kong,Taiwan and the mainland of China,Belgium,Canada,Japan,and Portugal.
Complexity analysis in particulate matter measurements
Luciano Telesca; Michele Lovallo
2011-01-01
We investigated the complex temporal fluctuations of particulate matter data recorded in London area by using the Fisher-Shannon (FS) information plane. In the FS plane the PM10 and PM2.5 data are aggregated in two different clusters, characterized by different degrees of order and organization. This results could be related to different sources of the particulate matter.
Todd, E.; Ort, M. H.
2012-12-01
Caldera collapse (˜180 km2) associated with a large Pliocene pyroclastic eruption and subsequent glacial erosion exposed an extensive and complex cross-section of pre-caldera volcanic history (at least 5 My) at the Copahue-Caviahue Eruptive Center (CCEC) in the Andean Southern Volcanic Zone (SVZ) of Argentina. Lava flows in wall exposures range from olivine-rich basaltic andesite to trachyte, are typically horizontal, vary in abundance and thickness at different wall exposures, and rarely correlate with flows in adjacent sections, although some lava and pyroclastic deposits from adjacent sections are similar in petrography, mineral assemblage, and geochemistry. Bulk-rock geochemical and isotopic data indicate at least two distinct primary melt types contributed to pre-caldera CCEC volcanism, and their differentiates produced a high-K and a low-K series. Incompatible element and isotope systematics suggest they are not related by differentiation of a common parental melt, and less-evolved examples of both types occur throughout the pre-caldera stratigraphic section, suggesting long-lived recharge of the local system by variably-sourced magmas. Petrographic and mineral chemistry evidence indicates that mixing of dissimilar magma types produced compositionally intermediate magmas. The location of the CCEC, rear of the volcanic front (VF), yet trenchward of regional backarc basin (BAB) volcanism, is reflected by the composition of CCEC lavas, which are transitional between local VF and BAB types. Thus, contrasting low- and high-K CCEC magmas in the SVZ rear-arc may reflect local focusing of VF-like (low-K) and BAB-like (high-K) melts.
Imura, Jun-ichi; Ueta, Tetsushi
2015-01-01
This book is the first to report on theoretical breakthroughs on control of complex dynamical systems developed by collaborative researchers in the two fields of dynamical systems theory and control theory. As well, its basic point of view is of three kinds of complexity: bifurcation phenomena subject to model uncertainty, complex behavior including periodic/quasi-periodic orbits as well as chaotic orbits, and network complexity emerging from dynamical interactions between subsystems. Analysis and Control of Complex Dynamical Systems offers a valuable resource for mathematicians, physicists, and biophysicists, as well as for researchers in nonlinear science and control engineering, allowing them to develop a better fundamental understanding of the analysis and control synthesis of such complex systems.
Complex Network Analysis of Brazilian Power Grid
Martins, Gabriela C; Ribeiro, Fabiano L; Forgerini, Fabricio L
2016-01-01
Power Grids and other delivery networks has been attracted some attention by the network literature last decades. Despite the Power Grids dynamics has been controlled by computer systems and human operators, the static features of this type of network can be studied and analyzed. The topology of the Brazilian Power Grid (BPG) was studied in this work. We obtained the spatial structure of the BPG from the ONS (electric systems national operator), consisting of high-voltage transmission lines, generating stations and substations. The local low-voltage substations and local power delivery as well the dynamic features of the network were neglected. We analyze the complex network of the BPG and identify the main topological information, such as the mean degree, the degree distribution, the network size and the clustering coefficient to caracterize the complex network. We also detected the critical locations on the network and, therefore, the more susceptible points to lead to a cascading failure and even to a blac...
Complex networks analysis of obstructive nephropathy data
Zanin, M.; Boccaletti, S.
2011-09-01
Congenital obstructive nephropathy (ON) is one of the most frequent and complex diseases affecting children, characterized by an abnormal flux of the urine, due to a partial or complete obstruction of the urinary tract; as a consequence, urine may accumulate in the kidney and disturb the normal operation of the organ. Despite important advances, pathological mechanisms are not yet fully understood. In this contribution, the topology of complex networks, based on vectors of features of control and ON subjects, is related with the severity of the pathology. Nodes in these networks represent genetic and metabolic profiles, while connections between them indicate an abnormal relation between their expressions. Resulting topologies allow discriminating ON subjects and detecting which genetic or metabolic elements are responsible for the malfunction.
Multivariate Complexity Analysis of Swap Bribery
Dorn, Britta; Schlotter, Ildikó
We consider the computational complexity of a problem modeling bribery in the context of voting systems. In the scenario of Swap Bribery, each voter assigns a certain price for swapping the positions of two consecutive candidates in his preference ranking. The question is whether it is possible, without exceeding a given budget, to bribe the voters in a way that the preferred candidate wins in the election.
Complexity analysis in particulate matter measurements
Directory of Open Access Journals (Sweden)
Luciano Telesca
2011-09-01
Full Text Available We investigated the complex temporal fluctuations of particulate matter data recorded in London area by using the Fisher-Shannon (FS information plane. In the FS plane the PM10 and PM2.5 data are aggregated in two different clusters, characterized by different degrees of order and organization. This results could be related to different sources of the particulate matter.
HOLOMORPHIC HARMONIC ANALYSIS ON COMPLEX REDUCTIVE GROUPS
Institute of Scientific and Technical Information of China (English)
An Jinpeng; Qian Min; Wang Zhengdong
2008-01-01
The authors define the holomorphic Fourier transform of holomorphic func-tions on complex reductive groups, prove some properties such as the Fourier inversion formula, and give some applications. The definition of the holomorphic Fourier transform makes use of the notion of K-admissible measures. The authors prove that K-admissible measures are abundant, and the definition of holomorphic Fourier transform is independent of the choice of K-admissible measures.
Modern Analysis of Protein Folding by Differential Scanning Calorimetry.
Ibarra-Molero, Beatriz; Naganathan, Athi N; Sanchez-Ruiz, Jose M; Muñoz, Victor
2016-01-01
Differential scanning calorimetry (DSC) is a very powerful tool for investigating protein folding and stability because its experimental output reflects the energetics of all conformations that become minimally populated during thermal unfolding. Accordingly, analysis of DSC experiments with simple thermodynamic models has been key for developing our understanding of protein stability during the past five decades. The discovery of ultrafast folding proteins, which have naturally broad conformational ensembles and minimally cooperative unfolding, opens the possibility of probing the complete folding free energy landscape, including those conformations at the top of the barrier to folding, via DSC. Exploiting this opportunity requires high-quality experiments and the implementation of novel analytical methods based on statistical mechanics. Here, we cover the recent exciting developments in this front, describing the new analytical procedures in detail as well as providing experimental guidelines for performing such analysis.
DEFF Research Database (Denmark)
Fournier, David A.; Skaug, Hans J.; Ancheta, Johnoel
2011-01-01
Many criteria for statistical parameter estimation, such as maximum likelihood, are formulated as a nonlinear optimization problem.Automatic Differentiation Model Builder (ADMB) is a programming framework based on automatic differentiation, aimed at highly nonlinear models with a large number...
Proteomics-based study on asthenozoospermia: differential expression of proteasome alpha complex.
Siva, Archana Bharadwaj; Kameshwari, Duvvuri Butchi; Singh, Vaibhav; Pavani, Kadupu; Sundaram, Curam Sreenivasacharlu; Rangaraj, Nandini; Deenadayal, Mamata; Shivaji, Sisinthy
2010-07-01
With a view to understand the molecular basis of sperm motility, we have tried to establish the human sperm proteome by two-dimensional PAGE MALDI MS/MS analysis. We report identification of 75 different proteins in the human spermatozoa. Comparative proteome analysis was carried out for asthenozoospermic and normozoospermic patients to understand the molecular basis of sperm motility. Analysis revealed eight proteins (including one unidentified) with altered intensity between the groups. Differential proteins distributed into three functional groups: 'energy and metabolism' (triose-phosphate isomerase, glycerol kinase 2, testis specific isoform and succinyl-CoA:3-ketoacid co-enzyme A transferase 1, mitochondrial precursor); 'movement and organization' (tubulin beta 2C and tektin 1) and 'protein turnover, folding and stress response' (proteasome alpha 3 subunit and heat shock-related 70 kDa protein 2). It was interesting to note that although the proteins falling in the functional group of 'energy and metabolism' are higher in the asthenozoospermic patients, the other two functional groups contain proteins, which are higher in the normozoospermic samples. Validation of results carried out for proteasome alpha 3 subunit by immunoblotting and confocal microscopy, confirmed significant changes in intensity of proteasome alpha 3 subunit in asthenozoospermic samples when compared with normozoospermic controls. Significant positive correlation too was found between proteasome alpha 3 subunit levels and rapid, linear progressive motility of the spermatozoa. In our understanding, this data would contribute appreciably to the presently limited information available about the proteins implicated in human sperm motility.
Differentiating salt marsh species using foreground/background analysis
Energy Technology Data Exchange (ETDEWEB)
Zhang, M.; Pinzon, J.; Ustin, S.L.; Rejmankova, E. [Univ. of California, Davis, CA (United States)
1996-10-01
Three California salt marsh plant species have distinctive morphologies that could be remotely sensed by airborne spectrometers because the architectures create differences in canopy reflectance characteristics. This paper presents a method to differentiate wetland species using a modified spectral mixture analysis termed hierarchical foreground and background analysis (HFBA). To validate this approach, the method was applied to field spectral data from several salt marshes. Foreground and background analysis allows the user to direct analysis along a specified axis of variance by identifying vectors through the n-dimensional spectral volume by identifying vectors that comprise the information of selected subset of spectra which emphasizes the presence of a discriminative signature of interest. The goal of FBA is to project spectral variation along the most relevant axis of variance that maximizes spectral differences between groups, while minimizing spectral variation within each group. For this work, we selected a training set that allowed us to create HFBA vectors which efficiently discriminate species based on canopy spectral characteristics. Results indicated that the dominant species in these salts marshes could be clearly differentiated with greater than 90% certainty from field collected canopy spectrometer data. Hundred percent of Spartina and 79% of Salicornia were correctly classified at the first level of classification. The accuracy of classification for Salicornia improved to 87% in the second level of classification. The unclassified spectral samples were related to extraordinary conditions within the wetlands such as extreme biomass, salinity and nitrogen conditions. These patterns were apparent in AVIRIS (Airborne Visible/infrared Imaging Spectrometer) images which showed distinct zonation corresponding to the distributions of these species in the marsh. Results were confirmed by field reconnaissance. 19 refs., 3 figs., 4 tabs.
Development of numerical procedures for analysis of complex structures
Gupta, K. K.
1984-01-01
The paper is concerned with the development of novel numerical procedures for the solution of static, stability, free vibration and dynamic response analysis of large, complex practical structures. Thus, details of numerical algorithms evolved for dynamic analysis of usual non-rotating and also rotating structures as well as finite dynamic elements are presented in the paper. Furthermore, the article provides some description of a general-purpose computer program STARS specifically developed for efficient analysis of complex practical structures.
DEFF Research Database (Denmark)
Manteca, Angel; Sanchez, Jesus; Jung, Hye Ryung
2010-01-01
Streptomyces species produce many clinically important secondary metabolites, including antibiotics and antitumourals. They have a complex developmental cycle that makes this bacterium a multicellular prokaryotic model including programmed cell death (PCD) phenomena. There are two differentiated...... Streptomyces coelicolor cultures using iTRAQ labelling and LC-MS/MS. A new experimental approach was developed to obtain homogeneous samples at each developmental stage (temporal protein analysis) and also to obtain membrane and cytosolic protein fractions (spatial protein analysis). A total of 345 proteins...
Energy Technology Data Exchange (ETDEWEB)
Miwa, Kenta, E-mail: kenta5710@gmail.com [Department of Nuclear Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550 (Japan); Division of Medical Quantum Science, Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Inubushi, Masayuki, E-mail: inubushi@med.kawasaki-m.ac.jp [Department of Nuclear Medicine, Kawasaki Medical School, 577 Matsushima Kurashiki, Okayama 701-0192 (Japan); Wagatsuma, Kei, E-mail: kei1192@hotmail.co.jp [Department of Nuclear Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550 (Japan); Nagao, Michinobu, E-mail: minagao@radiol.med.kyushu-u.ac.jp [Department of Molecular Imaging and Diagnosis, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Murata, Taisuke, E-mail: taisuke113@gmail.com [Department of Nuclear Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550 (Japan); Koyama, Masamichi, E-mail: masamichi.koyama@jfcr.or.jp [Department of Nuclear Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550 (Japan); Koizumi, Mitsuru, E-mail: mitsuru@jfcr.or.jp [Department of Nuclear Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550 (Japan); Sasaki, Masayuki, E-mail: msasaki@hs.med.kyushu-u.ac.jp [Division of Medical Quantum Science, Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)
2014-04-15
Purpose: The present study aimed to determine whether fractal analysis of morphological complexity and intratumoral heterogeneity of FDG uptake can help to differentiate malignant from benign pulmonary nodules. Materials and methods: We retrospectively analyzed data from 54 patients with suspected non-small cell lung cancer (NSCLC) who were examined by FDG PET/CT. Pathological assessments of biopsy specimens confirmed 35 and 19 nodules as NSCLC and inflammatory lesions, respectively. The morphological fractal dimension (m-FD), maximum standardized uptake value (SUV{sub max}) and density fractal dimension (d-FD) of target nodules were calculated from CT and PET images. Fractal dimension is a quantitative index of morphological complexity and tracer uptake heterogeneity; higher values indicate increased complexity and heterogeneity. Results: The m-FD, SUV{sub max} and d-FD significantly differed between malignant and benign pulmonary nodules (p < 0.05). Although the diagnostic ability was better for d-FD than m-FD and SUV{sub max}, the difference did not reach statistical significance. Tumor size correlated significantly with SUV{sub max} (r = 0.51, p < 0.05), but not with either m-FD or d-FD. Furthermore, m-FD combined with either SUV{sub max} or d-FD improved diagnostic accuracy to 92.6% and 94.4%, respectively. Conclusion: The d-FD of intratumoral heterogeneity of FDG uptake can help to differentially diagnose malignant and benign pulmonary nodules. The SUV{sub max} and d-FD obtained from FDG-PET images provide different types of information that are equally useful for differential diagnoses. Furthermore, the morphological complexity determined by CT combined with heterogeneous FDG uptake determined by PET improved diagnostic accuracy.
Arakel, Eric C.; Brandenburg, Sören; Uchida, Keita; Zhang, Haixia; Lin, Yu-Wen; Kohl, Tobias; Schrul, Bianca; Sulkin, Matthew S.; Efimov, Igor R.; Nichols, Colin G.; Lehnart, Stephan E.; Schwappach, Blanche
2014-01-01
ABSTRACT The copy number of membrane proteins at the cell surface is tightly regulated. Many ion channels and receptors present retrieval motifs to COPI vesicle coats and are retained in the early secretory pathway. In some cases, the interaction with COPI is prevented by binding to 14-3-3 proteins. However, the functional significance of this antagonism between COPI and 14-3-3 in terminally differentiated cells is unknown. Here, we show that ATP-sensitive K+ (KATP) channels, which are composed of Kir6.2 and SUR1 subunits, are stalled in the Golgi complex of ventricular, but not atrial, cardiomyocytes. Upon sustained β-adrenergic stimulation, which leads to activation of protein kinase A (PKA), SUR1-containing channels reach the plasma membrane of ventricular cells. We show that PKA-dependent phosphorylation of the C-terminus of Kir6.2 decreases binding to COPI and, thereby, silences the arginine-based retrieval signal. Thus, activation of the sympathetic nervous system releases this population of KATP channels from storage in the Golgi and, hence, might facilitate the adaptive response to metabolic challenges. PMID:24569881
Miyabara, Elen H; Conte, Talita C; Silva, Meiricris T; Baptista, Igor L; Bueno, Carlos; Fiamoncini, Jarlei; Lambertucci, Rafael H; Serra, Carmen S; Brum, Patricia C; Pithon-Curi, Tania; Curi, Rui; Aoki, Marcelo S; Oliveira, Antonio C; Moriscot, Anselmo S
2010-11-01
This work was undertaken to provide further insight into the role of mammalian target of rapamycin complex 1 (mTORC1) in skeletal muscle regeneration, focusing on myofiber size recovery. Rats were treated or not with rapamycin, an mTORC1 inhibitor. Soleus muscles were then subjected to cryolesion and analyzed 1, 10, and 21 days later. A decrease in soleus myofiber cross-section area on post-cryolesion days 10 and 21 was accentuated by rapamycin, which was also effective in reducing protein synthesis in these freeze-injured muscles. The incidence of proliferating satellite cells during regeneration was unaltered by rapamycin, although immunolabeling for neonatal myosin heavy chain (MHC) was weaker in cryolesion+rapamycin muscles than in cryolesion-only muscles. In addition, the decline in tetanic contraction of freeze-injured muscles was accentuated by rapamycin. This study indicates that mTORC1 plays a key role in the recovery of muscle mass and the differentiation of regenerating myofibers, independently of necrosis and satellite cell proliferation mechanisms.
MacKeigan, Jeffrey P; Krueger, Darcy A
2015-12-01
Tuberous sclerosis complex (TSC) is a genetic autosomal dominant disorder characterized by benign tumor-like lesions, called hamartomas, in multiple organ systems, including the brain, skin, heart, kidneys, and lung. These hamartomas cause a diverse set of clinical problems based on their location and often result in epilepsy, learning difficulties, and behavioral problems. TSC is caused by mutations within the TSC1 or TSC2 genes that inactivate the genes' tumor-suppressive function and drive hamartomatous cell growth. In normal cells, TSC1 and TSC2 integrate growth signals and nutrient inputs to downregulate signaling to mammalian target of rapamycin (mTOR), an evolutionarily conserved serine-threonine kinase that controls cell growth and cell survival. The molecular connection between TSC and mTOR led to the clinical use of allosteric mTOR inhibitors (sirolimus and everolimus) for the treatment of TSC. Everolimus is approved for subependymal giant cell astrocytomas and renal angiomyolipomas in patients with TSC. Sirolimus, though not approved for TSC, has undergone considerable investigation to treat various aspects of the disease. Everolimus and sirolimus selectively inhibit mTOR signaling with similar molecular mechanisms, but with distinct clinical profiles. This review differentiates mTOR inhibitors in TSC while describing the molecular mechanisms, pathogenic mutations, and clinical trial outcomes for managing TSC.
Toledo-Núñez, Citlali; Vera-Robles, L Iraís; Arroyo-Maya, Izlia J; Hernández-Arana, Andrés
2016-09-15
A frequent outcome in differential scanning calorimetry (DSC) experiments carried out with large proteins is the irreversibility of the observed endothermic effects. In these cases, DSC profiles are analyzed according to methods developed for temperature-induced denaturation transitions occurring under kinetic control. In the one-step irreversible model (native → denatured) the characteristics of the observed single-peaked endotherm depend on the denaturation enthalpy and the temperature dependence of the reaction rate constant, k. Several procedures have been devised to obtain the parameters that determine the variation of k with temperature. Here, we have elaborated on one of these procedures in order to analyze more complex DSC profiles. Synthetic data for a heat capacity curve were generated according to a model with two sequential reactions; the temperature dependence of each of the two rate constants involved was determined, according to the Eyring's equation, by two fixed parameters. It was then shown that our deconvolution procedure, by making use of heat capacity data alone, permits to extract the parameter values that were initially used. Finally, experimental DSC traces showing two and three maxima were analyzed and reproduced with relative success according to two- and four-step sequential models. Copyright © 2016 Elsevier Inc. All rights reserved.
Topological analysis of complexity in multiagent systems
Abaid, Nicole; Bollt, Erik; Porfiri, Maurizio
2012-04-01
Social organisms at every level of evolutionary complexity live in groups, such as fish schools, locust swarms, and bird flocks. The complex exchange of multifaceted information across group members may result in a spectrum of salient spatiotemporal patterns characterizing collective behaviors. While instances of collective behavior in animal groups are readily identifiable by trained and untrained observers, a working definition to distinguish these patterns from raw data is not yet established. In this work, we define collective behavior as a manifestation of low-dimensional manifolds in the group motion and we quantify the complexity of such behaviors through the dimensionality of these structures. We demonstrate this definition using the ISOMAP algorithm, a data-driven machine learning algorithm for dimensionality reduction originally formulated in the context of image processing. We apply the ISOMAP algorithm to data from an interacting self-propelled particle model with additive noise, whose parameters are selected to exhibit different behavioral modalities, and from a video of a live fish school. Based on simulations of such model, we find that increasing noise in the system of particles corresponds to increasing the dimensionality of the structures underlying their motion. These low-dimensional structures are absent in simulations where particles do not interact. Applying the ISOMAP algorithm to fish school data, we identify similar low-dimensional structures, which may act as quantitative evidence for order inherent in collective behavior of animal groups. These results offer an unambiguous method for measuring order in data from large-scale biological systems and confirm the emergence of collective behavior in an applicable mathematical model, thus demonstrating that such models are capable of capturing phenomena observed in animal groups.
Modeling and analysis of retinoic acid induced differentiation of uncommitted precursor cells.
Tasseff, Ryan; Nayak, Satyaprakash; Song, Sang Ok; Yen, Andrew; Varner, Jeffrey D
2011-05-01
Manipulation of differentiation programs has therapeutic potential in a spectrum of human cancers and neurodegenerative disorders. In this study, we integrated computational and experimental methods to unravel the response of a lineage uncommitted precursor cell-line, HL-60, to Retinoic Acid (RA). HL-60 is a human myeloblastic leukemia cell-line used extensively to study human differentiation programs. Initially, we focused on the role of the BLR1 receptor in RA-induced differentiation and G1/0-arrest in HL-60. BLR1, a putative G protein-coupled receptor expressed following RA exposure, is required for RA-induced cell-cycle arrest and differentiation and causes persistent MAPK signaling. A mathematical model of RA-induced cell-cycle arrest and differentiation was formulated and tested against BLR1 wild-type (wt) knock-out and knock-in HL-60 cell-lines with and without RA. The current model described the dynamics of 729 proteins and protein complexes interconnected by 1356 interactions. An ensemble strategy was used to compensate for uncertain model parameters. The ensemble of HL-60 models recapitulated the positive feedback between BLR1 and MAPK signaling. The ensemble of models also correctly predicted Rb and p47phox regulation and the correlation between p21-CDK4-cyclin D formation and G1/0-arrest following exposure to RA. Finally, we investigated the robustness of the HL-60 network architecture to structural perturbations and generated experimentally testable hypotheses for future study. Taken together, the model presented here was a first step toward a systematic framework for analysis of programmed differentiation. These studies also demonstrated that mechanistic network modeling can help prioritize experimental directions by generating falsifiable hypotheses despite uncertainty.
cDNA cloning and function analysis of two novel erythroid differentiation related genes
Institute of Scientific and Technical Information of China (English)
WANG; Xin; (王鑫); WANG; Duncheng; (王敦成); CHEN; Xing; (陈兴),; HU; Meiru; (胡美茹); WANG; Jian'an; (王建安); LI; Yan; (黎燕); GUO; Ning; (郭宁); SHEN; Beifen; (沈倍奋)
2001-01-01
Our previous studies showed that some nuclear proteins that were expressed especially during terminal differentiation of erythroid cells might interact directly or indirectly with HS2 sequence to form the HS2-protein complexes and thus play an important role in the globin gene regulation and erythroid differentiation. Monoclonal antibodies against the nuclear proteins of terminal differentiated erythroid cells, including intermediate and late erythroblasts of human fetal liver and hemin induced K562 cells, were prepared by hybridoma technique. The monoclonal antibodies were used to screen l-gtll human cDNA expression library of fetal liver in order to obtain the rele-vant cDNA clones. By the analysis of their cDNA clones and the identification of the proteins' func-tions, the regulation mechanism of the HS2 binding proteins might be better understood. Two cDNA clones (GenBank accession number AF040247 and AF040248 respectively) were obtained and one of them owns a full length and the other encodes a protein characterized by a leucine-zipper domain. Both of them were expressed differentially in K562 cells and hemin-induced K562 cells. The evidence suggested that both of them were involved in erythroid differentiation. We investigat-ed the expression pattern of EDRF1 and EDRF2 by RT-PCR technique. The results of RT-PCR suggested that EDRF1 and EDRF2 might play a critical role in early stage of organ development and histological differentiation. EDRF1 and EDRF2 might start the program of erythroid develop-ment, and also regulate the development of erythroid tissue and the expression of globin gene at different stage of the development.
cDNA cloning and function analysis of two novel erythroid differentiation related genes
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Our previous studies showed that some nuclear proteins that wereexpressed especially during terminal differentiation of erythroid cells might interact directly or indirectly with HS2 sequence to form the HS2-protein complexes and thus play an important role in the globin gene regulation and erythroid differentiation. Monoclonal antibodies against the nuclear proteins of terminal differentiated erythroid cells, including intermediate and late erythroblasts of human fetal liver and hemin induced K562 cells, were prepared by hybridoma technique. The monoclonal antibodies were used to screen l-gtll human cDNA expression library of fetal liver in order to obtain the rele-vant cDNA clones. By the analysis of their cDNA clones and the identification of the proteins' func-tions, the regulation mechanism of the HS2 binding proteins might be better understood. Two cDNA clones (GenBank accession number AF040247 and AF040248 respectively) were obtained and one of them owns a full length and the other encodes a protein characterized by a leucine-zipper domain. Both of them were expressed differentially in K562 cells and hemin-induced K562 cells. The evidence suggested that both of them were involved in erythroid differentiation. We investigat-ed the expression pattern of EDRF1 and EDRF2 by RT-PCR technique. The results of RT-PCR suggested that EDRF1 and EDRF2 might play a critical role in early stage of organ development and histological differentiation. EDRF1 and EDRF2 might start the program of erythroid develop-ment, and also regulate the development of erythroid tissue and the expression of globin gene at different stage of the development.
A statistical framework for differential network analysis from microarray data
Directory of Open Access Journals (Sweden)
Datta Somnath
2010-02-01
Full Text Available Abstract Background It has been long well known that genes do not act alone; rather groups of genes act in consort during a biological process. Consequently, the expression levels of genes are dependent on each other. Experimental techniques to detect such interacting pairs of genes have been in place for quite some time. With the advent of microarray technology, newer computational techniques to detect such interaction or association between gene expressions are being proposed which lead to an association network. While most microarray analyses look for genes that are differentially expressed, it is of potentially greater significance to identify how entire association network structures change between two or more biological settings, say normal versus diseased cell types. Results We provide a recipe for conducting a differential analysis of networks constructed from microarray data under two experimental settings. At the core of our approach lies a connectivity score that represents the strength of genetic association or interaction between two genes. We use this score to propose formal statistical tests for each of following queries: (i whether the overall modular structures of the two networks are different, (ii whether the connectivity of a particular set of "interesting genes" has changed between the two networks, and (iii whether the connectivity of a given single gene has changed between the two networks. A number of examples of this score is provided. We carried out our method on two types of simulated data: Gaussian networks and networks based on differential equations. We show that, for appropriate choices of the connectivity scores and tuning parameters, our method works well on simulated data. We also analyze a real data set involving normal versus heavy mice and identify an interesting set of genes that may play key roles in obesity. Conclusions Examining changes in network structure can provide valuable information about the
Complex Analysis of Combat in Afghanistan
2014-12-01
South Broad Street Clinton, SC 29325 USA DRDC CORA SCIENTIFIC AUTHORITY Dr. Peter Dobias DRDC CORA 101 Colonel By Dr. Ottawa, ON, K1A 0K2...for each day. These data were provided by Dr. Peter Dobias, DRDC- CORA . Because the data record only that an event has occurred during a day, and not...abbreviations/acronyms CORA Centre for Operational Research and Analysis DFA Detrended fluctuation analysis DND Department of National Defence
Ryno, Lisa M; Levine, Yael; Iovine, Peter M
2014-01-13
The preparation and characterization of amylose-small molecule complexes is a heavily researched area. There are few reports, however, that compare complexation efficiencies across a matrix of different amylose hosts and guests. We present herein a detailed account of using microwave irradiation to prepare amylose-small molecule complexes in water. Microwave heating reduced the time required to prepare these amylose complexes from hours to minutes. We characterized not only the quantity of complex for each amylose-guest pairing but also the loading of small molecule guest in that complex. Amylose-1-naphthol complexes were found to have the highest loading density compared with other hydrophobic guests studied; in the case of 1-naphthol, there was a linear dependence of guest loading on amylose molecular weight. In addition, complexes featuring 1-naphthol were the most ordered as judged by powder X-ray diffraction (XRD) and differential scanning calorimetry. Further, powder XRD analysis of the microwave-prepared complexes revealed that many contained mixtures of V-form (single helix) and B-form (double helical) amylose. Lastly, untreated Hylon VII complexed the widest variety of small molecules with the overall greatest efficiency.
Complex noise exposures: an energy analysis.
Ahroon, W A; Hamernik, R P; Davis, R I
1993-02-01
Industrial noise environments usually present a complex stimulus to the exposed individual. These environments often contain mixtures of multiply reflected impact noises and a relatively Gaussian broadband noise. Noise exposure standards do not consider the possibility of interactions between the two classes of noise that can exacerbate the amount of hearing trauma. This paper presents the results of a large series of experiments designed to document the hazard posed to hearing from complex noise exposures. Twenty-three groups of chinchillas with 5 to 11 animals per group (total N = 135) were exposed for 5 days to either octave bands of noise, impacts alone, or combinations of impact and octave bands of noise. Evoked potential measures of hearing thresholds and cochleograms were used to quantify the noise-induced trauma. The results show that, for sound exposure levels (SEL) which produce less than approximately 10 dB PTS (permanent threshold shift) or 5% total sensory cell loss, equal-energy exposures tend to produce equivalent effects on hearing. However, there is a range of at least 10 dB in the SEL parameter where hearing loss from equal-energy exposures at a particular SEL can be exacerbated by increasing the repetition rate of the impacts or by the addition of a Gaussian low-level noise. The exacerbation of trauma from the addition of a Gaussian continuous noise is dependent upon the spectrum of that noise.
Complex system analysis using CI methods
Fathi, Madjid; Hildebrand, Lars
1999-03-01
Modern technical tasks often need the use of complex system models. In many complex cases the model parameters can be gained using neural networks, but these systems allow only a one-way simulation from the input values to the learned output values. If evaluation in the other direction is needed, these model allow no direct evaluation. This task can be solved using evolutionary algorithms, which are part of the computational intelligence. The term computational intelligence covers three special fields of the artificial intelligence, fuzzy logic, artificial neural networks and evolutionary algorithms. We will focus only on the topic of evolutionary algorithms and fuzzy logic. Evolutionary algorithms covers the fields of genetic algorithms, evolution strategies and evolutionary programming. These methods can be used to optimize technical problems. Evolutionary algorithms have certain advantages, if these problems have no mathematical properties, like steadiness or the possibility to obtain the derivatives. Fuzzy logic systems normally lack these properties. The use of a combination of evolutionary algorithms and fuzzy logic allow an evaluation of the learned simulation models in the direction form output to the input values. An example can be given from the field of screw rotor design.
Yildirim, Adem; Ozturk, Fahri Emre; Bayindir, Mehmet
2013-07-02
A novel optoelectronic nose for analysis of alcohols (ethanol and methanol) in chemically complex environments is reported. The cross-responsive sensing unit of the optoelectronic nose is an array of three distinct hollow-core infrared transmitting photonic band gap fibers, which transmit a specific band of IR light depending on their Bragg mirror structures. The presence of alcohol molecules in the optofluidic core quenches the fiber transmissions if there is an absorption band of the analyte overlapping with the transmission band of the fiber; otherwise they remain unchanged. The cumulative response data of the fiber array enables rapid, reversible, and accurate discrimination of alcohols in chemically complex backgrounds such as beer and fruit juice. In addition, we observed that humidity of the environment has no effect on the response matrix of the optoelectronic nose, which is rarely achieved in gas-sensing applications. Consequently, it can be reliably used in virtually any environment without precalibration for humidity or drying the analytes. Besides the discussed application in counterfeit alcoholic beverages, with its superior sensor parameters, this novel concept proves to be a promising contender for many other applications including food quality control, environmental monitoring, and breath analysis for disease diagnostics.
Penalized differential pathway analysis of integrative oncogenomics studies.
van Wieringen, Wessel N; van de Wiel, Mark A
2014-04-01
Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving cancer patients. The two molecular levels involved are linked through the central dogma of molecular biology. DNA copy number aberrations abound in the cancer cell. Here we investigate how these aberrations affect gene expression levels within a pathway using observational integrative genomics data of cancer patients. In particular, we aim to identify differential edges between regulatory networks of two groups involving these molecular levels. Motivated by the rate equations, the regulatory mechanism between DNA copy number aberrations and gene expression levels within a pathway is modeled by a simultaneous-equations model, for the one- and two-group case. The latter facilitates the identification of differential interactions between the two groups. Model parameters are estimated by penalized least squares using the lasso (L1) penalty to obtain a sparse pathway topology. Simulations show that the inclusion of DNA copy number data benefits the discovery of gene-gene interactions. In addition, the simulations reveal that cis-effects tend to be over-estimated in a univariate (single gene) analysis. In the application to real data from integrative oncogenomic studies we show that inclusion of prior information on the regulatory network architecture benefits the reproducibility of all edges. Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature.
Differential DNA Methylation Analysis without a Reference Genome
Directory of Open Access Journals (Sweden)
Johanna Klughammer
2015-12-01
Full Text Available Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS, which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish. Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org. The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.
Differential DNA Methylation Analysis without a Reference Genome.
Klughammer, Johanna; Datlinger, Paul; Printz, Dieter; Sheffield, Nathan C; Farlik, Matthias; Hadler, Johanna; Fritsch, Gerhard; Bock, Christoph
2015-12-22
Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.
Reddington, Kate; O'Grady, Justin; Dorai-Raj, Siobhan; Maher, Majella; van Soolingen, Dick; Barry, Thomas
2011-02-01
Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC.
DEFF Research Database (Denmark)
Czaban, Adrian; Sharma, Sapna; Byrne, Stephen
2015-01-01
-Festuca complex show very diverse phenotypes, including for many agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity. Results We have generated de novo transcriptome assemblies for four...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...
Random matrix analysis of complex networks.
Jalan, Sarika; Bandyopadhyay, Jayendra N
2007-10-01
We study complex networks under random matrix theory (RMT) framework. Using nearest-neighbor and next-nearest-neighbor spacing distributions we analyze the eigenvalues of the adjacency matrix of various model networks, namely, random, scale-free, and small-world networks. These distributions follow the Gaussian orthogonal ensemble statistic of RMT. To probe long-range correlations in the eigenvalues we study spectral rigidity via the Delta_{3} statistic of RMT as well. It follows RMT prediction of linear behavior in semilogarithmic scale with the slope being approximately 1pi;{2} . Random and scale-free networks follow RMT prediction for very large scale. A small-world network follows it for sufficiently large scale, but much less than the random and scale-free networks.
NEXCADE: perturbation analysis for complex networks.
Directory of Open Access Journals (Sweden)
Gitanjali Yadav
Full Text Available Recent advances in network theory have led to considerable progress in our understanding of complex real world systems and their behavior in response to external threats or fluctuations. Much of this research has been invigorated by demonstration of the 'robust, yet fragile' nature of cellular and large-scale systems transcending biology, sociology, and ecology, through application of the network theory to diverse interactions observed in nature such as plant-pollinator, seed-dispersal agent and host-parasite relationships. In this work, we report the development of NEXCADE, an automated and interactive program for inducing disturbances into complex systems defined by networks, focusing on the changes in global network topology and connectivity as a function of the perturbation. NEXCADE uses a graph theoretical approach to simulate perturbations in a user-defined manner, singly, in clusters, or sequentially. To demonstrate the promise it holds for broader adoption by the research community, we provide pre-simulated examples from diverse real-world networks including eukaryotic protein-protein interaction networks, fungal biochemical networks, a variety of ecological food webs in nature as well as social networks. NEXCADE not only enables network visualization at every step of the targeted attacks, but also allows risk assessment, i.e. identification of nodes critical for the robustness of the system of interest, in order to devise and implement context-based strategies for restructuring a network, or to achieve resilience against link or node failures. Source code and license for the software, designed to work on a Linux-based operating system (OS can be downloaded at http://www.nipgr.res.in/nexcade_download.html. In addition, we have developed NEXCADE as an OS-independent online web server freely available to the scientific community without any login requirement at http://www.nipgr.res.in/nexcade.html.
Energy Technology Data Exchange (ETDEWEB)
Parson, Whitney B [ORNL; Schneider, Bradley B [MDS Sciex; Kertesz, Vilmos [ORNL; Corr, Jay [AB Sciex; Covey, Thomas R. [MDS Sciex; Van Berkel, Gary J [ORNL
2011-01-01
The direct separation of isobaric glucuronide metabolites from propranolol dosed tissue extracts by differential mobility spectrometry mass spectrometry (DMS-MS) with the use of a polar gas-phase chemical modifier was demonstrated. The DMS gas-phase separation was able to resolve the isobaric metabolites with separation times on the order of ms instead of mins to hrs typically required when using pre-ionization chromatographic separation methods. Direct separation of isobaric metabolites from the complex tissue extract was validated using standards as well as implementing an HPLC separation prior to the DMS-MS analysis to pre-separate the species of interest. The ability to separate isobaric exogenous metabolites directly from a complex tissue extract is expected to facilitate the drug development process by increasing analytical throughput without the requirement for pre-ionization cleanup or separation strategies.
The shape operator for differential analysis of images.
Avants, Brian; Gee, James
2003-07-01
This work provides a new technique for surface oriented volumetric image analysis. The method makes no assumptions about topology, instead constructing a local neighborhood from image information, such as a segmentation or edge map, to define a surface patch. Neighborhood constructions using extrinsic and intrinsic distances are given. This representation allows one to estimate differential properties directly from the image's Gauss map. We develop a novel technique for this purpose which estimates the shape operator and yields both principal directions and curvatures. Only first derivatives need be estimated, making the method numerically stable. We show the use of these measures for multi-scale classification of image structure by the mean and Gaussian curvatures. Finally, we propose to register image volumes by surface curvature. This is particularly useful when geometry is the only variable. To illustrate this, we register binary segmented data by surface curvature, both rigidly and non-rigidly. A novel variant of Demons registration, extensible for use with differentiable similarity metrics, is also applied for deformable curvature-driven registration of medical images.
Differentiation of Staphylococcus spp. by high-resolution melting analysis.
Slany, Michal; Vanerkova, Martina; Nemcova, Eva; Zaloudikova, Barbora; Ruzicka, Filip; Freiberger, Tomas
2010-12-01
High-resolution melting analysis (HRMA) is a fast (post-PCR) high-throughput method to scan for sequence variations in a target gene. The aim of this study was to test the potential of HRMA to distinguish particular bacterial species of the Staphylococcus genus even when using a broad-range PCR within the 16S rRNA gene where sequence differences are minimal. Genomic DNA samples isolated from 12 reference staphylococcal strains (Staphylococcus aureus, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus intermedius, Staphylococcus saprophyticus, Staphylococcus sciuri, Staphylococcus simulans, Staphylococcus warneri, and Staphylococcus xylosus) were subjected to a real-time PCR amplification of the 16S rRNA gene in the presence of fluorescent dye EvaGreen™, followed by HRMA. Melting profiles were used as molecular fingerprints for bacterial species differentiation. HRMA of S. saprophyticus and S. xylosus resulted in undistinguishable profiles because of their identical sequences in the analyzed 16S rRNA region. The remaining reference strains were fully differentiated either directly or via high-resolution plots obtained by heteroduplex formation between coamplified PCR products of the tested staphylococcal strain and phylogenetically unrelated strain.
A Complexity Analysis of Functional Interpretations
DEFF Research Database (Denmark)
Hernest, Mircea-Dan; Kohlenbach, Ulrich
2003-01-01
We give a quantitative analysis of G ̈odel’s functional interpretation and its monotone variant. The two have been used for the extraction of programs and numerical bounds as well as for conservation results. They apply both to (semi-)intuitionistic as well as (combined with negative translation)...
A complexity analysis of functional interpretations
DEFF Research Database (Denmark)
Hernest, Mircea-Dan; Kohlenbach, Ulrich
2005-01-01
Summary: We give a quantitative analysis of Gödel's functional interpretation and its monotone variant. The two have been used for the extraction of programs and numerical bounds as well as for conservation results. They apply both to (semi-)intuitionistic as well as (combined...
Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods.
Calderhead, Ben; Girolami, Mark
2011-12-06
Mechanistic models based on systems of nonlinear differential equations can help provide a quantitative understanding of complex physical or biological phenomena. The use of such models to describe nonlinear interactions in molecular biology has a long history; however, it is only recently that advances in computing have allowed these models to be set within a statistical framework, further increasing their usefulness and binding modelling and experimental approaches more tightly together. A probabilistic approach to modelling allows us to quantify uncertainty in both the model parameters and the model predictions, as well as in the model hypotheses themselves. In this paper, the Bayesian approach to statistical inference is adopted and we examine the significant challenges that arise when performing inference over nonlinear ordinary differential equation models describing cell signalling pathways and enzymatic circadian control; in particular, we address the difficulties arising owing to strong nonlinear correlation structures, high dimensionality and non-identifiability of parameters. We demonstrate how recently introduced differential geometric Markov chain Monte Carlo methodology alleviates many of these issues by making proposals based on local sensitivity information, which ultimately allows us to perform effective statistical analysis. Along the way, we highlight the deep link between the sensitivity analysis of such dynamic system models and the underlying Riemannian geometry of the induced posterior probability distributions.
DEFF Research Database (Denmark)
Gallo, G.; Renzone, G.; Alduina, R.
2010-01-01
A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...
Lexical, Functional Grammar Analysis of Korean Complex Predicates.
Kim, Hee-Seob
The structure of complementation in complex predicates in Korean has attracted configurational analysis. Using a lexical functional grammar (LFG) framework, this paper examines the structure of complementation in complex predicates. The term "predicate" in this context is used to describe both verbs and adjectives that are assumed to…
Analysis and design of complex impedance transforming marchand baluns
DEFF Research Database (Denmark)
Michaelsen, Rasmus Schandorph; Johansen, Tom Keinicke; Tamborg, Kjeld M.
2014-01-01
A new type of Marchand balun is presented in this paper, which has the property of complex impedance transformation. To allow the Marchand balun to transform between arbitrary complex impedances, three reactances should be added to the circuit. A detailed analysis of the circuit gives the governi...
The Lsm1-7-Pat1 complex promotes viral RNA translation and replication by differential mechanisms.
Jungfleisch, Jennifer; Chowdhury, Ashis; Alves-Rodrigues, Isabel; Tharun, Sundaresan; Díez, Juana
2015-08-01
The Lsm1-7-Pat1 complex binds to the 3' end of cellular mRNAs and promotes 3' end protection and 5'-3' decay. Interestingly, this complex also specifically binds to cis-acting regulatory sequences of viral positive-strand RNA genomes promoting their translation and subsequent recruitment from translation to replication. Yet, how the Lsm1-7-Pat1 complex regulates these two processes remains elusive. Here, we show that Lsm1-7-Pat1 complex acts differentially in these processes. By using a collection of well-characterized lsm1 mutant alleles and a system that allows the replication of Brome mosaic virus (BMV) in yeast we show that the Lsm1-7-Pat1 complex integrity is essential for both, translation and recruitment. However, the intrinsic RNA-binding ability of the complex is only required for translation. Consistent with an RNA-binding-independent function of the Lsm1-7-Pat1 complex on BMV RNA recruitment, we show that the BMV 1a protein, the sole viral protein required for recruitment, interacts with this complex in an RNA-independent manner. Together, these results support a model wherein Lsm1-7-Pat1 complex binds consecutively to BMV RNA regulatory sequences and the 1a protein to promote viral RNA translation and later recruitment out of the host translation machinery to the viral replication complexes.
Empirical and theoretical analysis of complex systems
Zhao, Guannan
This thesis is an interdisciplinary work under the heading of complexity science which focuses on an arguably common "hard" problem across physics, finance and biology [1], to quantify and mimic the macroscopic "emergent phenomenon" in large-scale systems consisting of many interacting "particles" governed by microscopic rules. In contrast to traditional statistical physics, we are interested in systems whose dynamics are subject to feedback, evolution, adaption, openness, etc. Global financial markets, like the stock market and currency market, are ideal candidate systems for such a complexity study: there exists a vast amount of accurate data, which is the aggregate output of many autonomous agents continuously competing with each other. We started by examining the ultrafast "mini flash crash (MFC)" events in the US stock market. An abrupt system-wide composition transition from a mixed human machine phase to a new all-machine phase is uncovered, and a novel theory developed to explain this observation. Then in the study of FX market, we found an unexpected variation in the synchronicity of price changes in different market subsections as a function of the overall trading activity. Several survival models have been tested in analyzing the distribution of waiting times to the next price change. In the region of long waiting-times, the distribution for each currency pair exhibits a power law with exponent in the vicinity of 3.5. By contrast, for short waiting times only, the market activity can be mimicked by the fluctuations emerging from a finite resource competition model containing multiple agents with limited rationality (so called El Farol Model). Switching to the biomedical domain, we present a minimal mathematical model built around a co-evolving resource network and cell population, yielding good agreement with primary tumors in mice experiment and with clinical metastasis data. In the quest to understand contagion phenomena in systems where social group
Error analysis for a laser differential confocal radius measurement system.
Wang, Xu; Qiu, Lirong; Zhao, Weiqian; Xiao, Yang; Wang, Zhongyu
2015-02-10
In order to further improve the measurement accuracy of the laser differential confocal radius measurement system (DCRMS) developed previously, a DCRMS error compensation model is established for the error sources, including laser source offset, test sphere position adjustment offset, test sphere figure, and motion error, based on analyzing the influences of these errors on the measurement accuracy of radius of curvature. Theoretical analyses and experiments indicate that the expanded uncertainty of the DCRMS is reduced to U=0.13 μm+0.9 ppm·R (k=2) through the error compensation model. The error analysis and compensation model established in this study can provide the theoretical foundation for improving the measurement accuracy of the DCRMS.
Comparative analysis of discrete exosome fractions obtained by differential centrifugation
DEFF Research Database (Denmark)
Jeppesen, Dennis Kjølhede; Hvam, Michael L; Primdahl-Bengtson, Bjarke
2014-01-01
BACKGROUND: Cells release a mixture of extracellular vesicles, amongst these exosomes, that differ in size, density and composition. The standard isolation method for exosomes is centrifugation of fluid samples, typically at 100,000×g or above. Knowledge of the effect of discrete...... ultracentrifugation speeds on the purification from different cell types, however, is limited. METHODS: We examined the effect of applying differential centrifugation g-forces ranging from 33,000×g to 200,000×g on exosome yield and purity, using 2 unrelated human cell lines, embryonic kidney HEK293 cells and bladder...... of phenol red and cleared by 200,000×g overnight centrifugation. The centrifugation tube fill level impacted the sedimentation efficacy. Comparative analysis by NTA, protein quantification, and detection of exosomal and contamination markers identified differences in vesicle size, concentration...
Comparative analysis of discrete exosome fractions obtained by differential centrifugation
Directory of Open Access Journals (Sweden)
Dennis K. Jeppesen
2014-11-01
Full Text Available Background: Cells release a mixture of extracellular vesicles, amongst these exosomes, that differ in size, density and composition. The standard isolation method for exosomes is centrifugation of fluid samples, typically at 100,000×g or above. Knowledge of the effect of discrete ultracentrifugation speeds on the purification from different cell types, however, is limited. Methods: We examined the effect of applying differential centrifugation g-forces ranging from 33,000×g to 200,000×g on exosome yield and purity, using 2 unrelated human cell lines, embryonic kidney HEK293 cells and bladder carcinoma FL3 cells. The fractions were evaluated by nanoparticle tracking analysis (NTA, total protein quantification and immunoblotting for CD81, TSG101, syntenin, VDAC1 and calreticulin. Results: NTA revealed the lowest background particle count in Dulbecco's Modified Eagle's Medium media devoid of phenol red and cleared by 200,000×g overnight centrifugation. The centrifugation tube fill level impacted the sedimentation efficacy. Comparative analysis by NTA, protein quantification, and detection of exosomal and contamination markers identified differences in vesicle size, concentration and composition of the obtained fractions. In addition, HEK293 and FL3 vesicles displayed marked differences in sedimentation characteristics. Exosomes were pelleted already at 33,000×g, a g-force which also removed most contaminating microsomes. Optimal vesicle-to-protein yield was obtained at 67,000×g for HEK293 cells but 100,000×g for FL3 cells. Relative expression of exosomal markers (TSG101, CD81, syntenin suggested presence of exosome subpopulations with variable sedimentation characteristics. Conclusions: Specific g-force/k factor usage during differential centrifugation greatly influences the purity and yield of exosomes. The vesicle sedimentation profile differed between the 2 cell lines.
Delay Differential Analysis of Seizures in Multichannel Electrocorticography Data.
Lainscsek, Claudia; Weyhenmeyer, Jonathan; Cash, Sydney S; Sejnowski, Terrence J
2017-08-04
High-density electrocorticogram (ECoG) electrodes are capable of recording neurophysiological data with high temporal resolution with wide spatial coverage. These recordings are a window to understanding how the human brain processes information and subsequently behaves in healthy and pathologic states. Here, we describe and implement delay differential analysis (DDA) for the characterization of ECoG data obtained from human patients with intractable epilepsy. DDA is a time-domain analysis framework based on embedding theory in nonlinear dynamics that reveals the nonlinear invariant properties of an unknown dynamical system. The DDA embedding serves as a low-dimensional nonlinear dynamical basis onto which the data are mapped. This greatly reduces the risk of overfitting and improves the method's ability to fit classes of data. Since the basis is built on the dynamical structure of the data, preprocessing of the data (e.g., filtering) is not necessary. We performed a large-scale search for a DDA model that best fit ECoG recordings using a genetic algorithm to qualitatively discriminate between different cortical states and epileptic events for a set of 13 patients. A single DDA model with only three polynomial terms was identified. Singular value decomposition across the feature space of the model revealed both global and local dynamics that could differentiate electrographic and electroclinical seizures and provided insights into highly localized seizure onsets and diffuse seizure terminations. Other common ECoG features such as interictal periods, artifacts, and exogenous stimuli were also analyzed with DDA. This novel framework for signal processing of seizure information demonstrates an ability to reveal unique characteristics of the underlying dynamics of the seizure and may be useful in better understanding, detecting, and maybe even predicting seizures.
Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus
Goodwin, Zane A.; de Guzman Strong, Cristina
2017-01-01
The epidermal differentiation complex (EDC) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. Yet the EDC genes that are undergoing positive selection across mammals and in humans are not known. We sought to identify the positively selected genetic variants and determine the evolutionary events of the EDC using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (GA) branch test. Significant non-synonymous substitutions were found in filaggrin, SPRR4, LELP1, and S100A2 genes across 14 mammals. By contrast, we identified recent positive selection in SPRR4 in primates. Additionally, the GA branch test discovered lineage-specific evolution for distinct EDC genes occurring in each of the nodes in the 14-mammal phylogenetic tree. Multiple instances of positive selection for FLG, TCHHL1, SPRR4, LELP1, and S100A2 were noted among the primate branch nodes. Branch-site likelihood ratio tests further revealed positive selection in specific sites in SPRR4, LELP1, filaggrin, and repetin across 14 mammals. However, in addition to continuous evolution of SPRR4, site-specific positive selection was also found in S100A11, KPRP, SPRR1A, S100A7L2, and S100A3 in primates and filaggrin, filaggrin2, and S100A8 in great apes. Very recent human positive selection was identified in the filaggrin2 L41 site that was present in Neanderthal. Together, our results identifying recent positive selection in distinct EDC genes reveal an underappreciated evolution of epidermal skin barrier function in primates and humans. PMID:28119736
Xie, Wei; Chojnowski, Alexandre; Boudier, Thomas; Lim, John S Y; Ahmed, Sohail; Ser, Zheng; Stewart, Colin; Burke, Brian
2016-10-10
The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution.
Via, Laura E; Weiner, Danielle M; Schimel, Daniel; Lin, Philana Ling; Dayao, Emmanuel; Tankersley, Sarah L; Cai, Ying; Coleman, M Teresa; Tomko, Jaime; Paripati, Praveen; Orandle, Marlene; Kastenmayer, Robin J; Tartakovsky, Michael; Rosenthal, Alexander; Portevin, Damien; Eum, Seok Yong; Lahouar, Saher; Gagneux, Sebastien; Young, Douglas B; Flynn, Joanne L; Barry, Clifton E
2013-08-01
Existing small-animal models of tuberculosis (TB) rarely develop cavitary disease, limiting their value for assessing the biology and dynamics of this highly important feature of human disease. To develop a smaller primate model with pathology similar to that seen in humans, we experimentally infected the common marmoset (Callithrix jacchus) with diverse strains of Mycobacterium tuberculosis of various pathogenic potentials. These included recent isolates of the modern Beijing lineage, the Euro-American X lineage, and M. africanum. All three strains produced fulminant disease in this animal with a spectrum of progression rates and clinical sequelae that could be monitored in real time using 2-deoxy-2-[(18)F]fluoro-d-glucose (FDG) positron emission tomography (PET)/computed tomography (CT). Lesion pathology at sacrifice revealed the entire spectrum of lesions observed in human TB patients. The three strains produced different rates of progression to disease, various extents of extrapulmonary dissemination, and various degrees of cavitation. The majority of live births in this species are twins, and comparison of results from siblings with different infecting strains allowed us to establish that the infection was highly reproducible and that the differential virulence of strains was not simply host variation. Quantitative assessment of disease burden by FDG-PET/CT provided an accurate reflection of the pathology findings at necropsy. These results suggest that the marmoset offers an attractive small-animal model of human disease that recapitulates both the complex pathology and spectrum of disease observed in humans infected with various M. tuberculosis strain clades.
Via, Laura E.; Weiner, Danielle M.; Schimel, Daniel; Lin, Philana Ling; Dayao, Emmanuel; Tankersley, Sarah L.; Cai, Ying; Coleman, M. Teresa; Tomko, Jaime; Paripati, Praveen; Orandle, Marlene; Kastenmayer, Robin J.; Tartakovsky, Michael; Rosenthal, Alexander; Portevin, Damien; Eum, Seok Yong; Lahouar, Saher; Gagneux, Sebastien; Young, Douglas B.; Flynn, JoAnne L.
2013-01-01
Existing small-animal models of tuberculosis (TB) rarely develop cavitary disease, limiting their value for assessing the biology and dynamics of this highly important feature of human disease. To develop a smaller primate model with pathology similar to that seen in humans, we experimentally infected the common marmoset (Callithrix jacchus) with diverse strains of Mycobacterium tuberculosis of various pathogenic potentials. These included recent isolates of the modern Beijing lineage, the Euro-American X lineage, and M. africanum. All three strains produced fulminant disease in this animal with a spectrum of progression rates and clinical sequelae that could be monitored in real time using 2-deoxy-2-[18F]fluoro-d-glucose (FDG) positron emission tomography (PET)/computed tomography (CT). Lesion pathology at sacrifice revealed the entire spectrum of lesions observed in human TB patients. The three strains produced different rates of progression to disease, various extents of extrapulmonary dissemination, and various degrees of cavitation. The majority of live births in this species are twins, and comparison of results from siblings with different infecting strains allowed us to establish that the infection was highly reproducible and that the differential virulence of strains was not simply host variation. Quantitative assessment of disease burden by FDG-PET/CT provided an accurate reflection of the pathology findings at necropsy. These results suggest that the marmoset offers an attractive small-animal model of human disease that recapitulates both the complex pathology and spectrum of disease observed in humans infected with various M. tuberculosis strain clades. PMID:23716617
Coping with Complexity Model Reduction and Data Analysis
Gorban, Alexander N
2011-01-01
This volume contains the extended version of selected talks given at the international research workshop 'Coping with Complexity: Model Reduction and Data Analysis', Ambleside, UK, August 31 - September 4, 2009. This book is deliberately broad in scope and aims at promoting new ideas and methodological perspectives. The topics of the chapters range from theoretical analysis of complex and multiscale mathematical models to applications in e.g., fluid dynamics and chemical kinetics.
From quantitative protein complex analysis to disease mechanism.
Texier, Y; Kinkl, N; Boldt, K; Ueffing, M
2012-12-15
Interest in the field of cilia biology and cilia-associated diseases - ciliopathies - has strongly increased over the last few years. Proteomic technologies, especially protein complex analysis by affinity purification-based methods, have been used to decipher various basic but also disease-associated mechanisms. This review focusses on some selected recent studies using affinity purification-based protein complex analysis, thereby exemplifying the great possibilities this technology offers.
Bulgakova, Natalia A; Kempkens, Ozlem; Knust, Elisabeth
2008-06-15
Drosophila Stardust (Sdt), a member of the MAGUK family of scaffolding proteins, is a constituent of the evolutionarily conserved Crumbs-Stardust (Crb-Sdt) complex that controls epithelial cell polarity in the embryo and morphogenesis of photoreceptor cells. Although apical localisation is a hallmark of the complex in all cell types and in all organisms analysed, only little is known about how individual components are targeted to the apical membrane. We have performed a structure-function analysis of Sdt by constructing transgenic flies that express altered forms of Sdt to determine the roles of individual domains for localisation and function in photoreceptor cells. The results corroborate the observation that the organisation of the Crb-Sdt complex is differentially regulated in pupal and adult photoreceptors. In pupal photoreceptors, only the PDZ domain of Sdt - the binding site of Crb - is required for apical targeting. In adult photoreceptors, by contrast, targeting of Sdt to the stalk membrane, a distinct compartment of the apical membrane between the rhabdomere and the zonula adherens, depends on several domains, and seems to be a two-step process. The N-terminus, including the two ECR domains and a divergent N-terminal L27 domain that binds the multi-PDZ domain protein PATJ in vitro, is necessary for targeting the protein to the apical pole of the cell. The PDZ-, the SH3- and the GUK-domains are required to restrict the protein to the stalk membrane. Drosophila PATJ or Drosophila Lin-7 are stabilised whenever a Sdt variant that contains the respective binding site is present, independently of where the variant is localised. By contrast, only full-length Sdt, confined to the stalk membrane, stabilises and localises Crb, although only in reduced amounts. The amount of Crumbs recruited to the stalk membrane correlates with its length. Our results highlight the importance of the different Sdt domains and point to a more intricate regulation of the Crb
Complexity Analysis of Peat Soil Density Distribution
Sampurno, Joko; Diah Faryuni, Irfana; Dzar Eljabbar Latief, Fourier; Srigutomo, Wahyu
2016-08-01
The distributions of peat soil density have been identified using fractal analysis method. The study was conducted on 5 peat soil samples taken from a ground field in Pontianak, West Kalimantan, at the coordinates (0 ° 4 '2:27 "S, 109 ° 18' 48.59" E). In this study, we used micro computerized tomography (pCT Scanner) at 9.41 micro meter per pixel resolution under peat soil samples to provide 2-D high-resolution images L1-L5 (200 200 pixels) that were used to detect the distribution of peat soil density. The method for determining the fractal dimension and intercept was the 2-D Fourier analysis method. The method was used to obtain the log log-plot of magnitude with frequency. Fractal dimension was obtained from the straight regression line that interpolated the points in the interval with the largest coefficient determination. Intercept defined by the point of intersection on the -axis. The conclusion was that the distributions of peat soil density showing the fractal behaviour with the heterogeneity of the samples from the highest to the lowest were L5, L1, L4, L3 and L2. Meanwhile, the range of density values of the samples from the highest to the lowest was L3, L2, L4, L5 and L1. The study also concluded that the behaviour of the distribution of peat soil density was a weakly anisotropic.
Aeroelastic Analysis of Modern Complex Wings
Kapania, Rakesh K.; Bhardwaj, Manoj K.; Reichenbach, Eric; Guruswamy, Guru P.
1996-01-01
A process is presented by which aeroelastic analysis is performed by using an advanced computational fluid dynamics (CFD) code coupled with an advanced computational structural dynamics (CSD) code. The process is demonstrated on an F/A-18 Stabilator using NASTD (an in-house McDonnell Douglas Aerospace East CFD code) coupled with NASTRAN. The process is also demonstrated on an aeroelastic research wing (ARW-2) using ENSAERO (an in-house NASA Ames Research Center CFD code) coupled with a finite element wing-box structures code. Good results have been obtained for the F/A-18 Stabilator while results for the ARW-2 supercritical wing are still being obtained.
COMPUTER DATA ANALYSIS AND MODELING: COMPLEX STOCHASTIC DATA AND SYSTEMS
2010-01-01
This collection of papers includes proceedings of the Ninth International Conference “Computer Data Analysis and Modeling: Complex Stochastic Data and Systems” organized by the Belarusian State University and held in September 2010 in Minsk. The papers are devoted to the topical problems: robust and nonparametric data analysis; statistical analysis of time series and forecasting; multivariate data analysis; design of experiments; statistical signal and image processing...
Samuel A. Cushman; Andrew J. Shirk; Erin L. Landguth
2012-01-01
Little is known about how variation in landscape mosaics affects genetic differentiation. The goal of this paper is to quantify the relative importance of habitat area and configuration, as well as the contrast in resistance between habitat and non-habitat, on genetic differentiation. We hypothesized that habitat configuration would be more influential than habitat...
Vulnerability Analysis for Complex Networks Using Aggressive Abstraction
Colbaugh, Richard
2010-01-01
Large, complex networks are ubiquitous in nature and society, and there is great interest in developing rigorous, scalable methods for identifying and characterizing their vulnerabilities. This paper presents an approach for analyzing the dynamics of complex networks in which the network of interest is first abstracted to a much simpler, but mathematically equivalent, representation, the required analysis is performed on the abstraction, and analytic conclusions are then mapped back to the original network and interpreted there. We begin by identifying a broad and important class of complex networks which admit vulnerability-preserving, finite state abstractions, and develop efficient algorithms for computing these abstractions. We then propose a vulnerability analysis methodology which combines these finite state abstractions with formal analytics from theoretical computer science to yield a comprehensive vulnerability analysis process for networks of realworld scale and complexity. The potential of the prop...
ANALYSIS OF BRANCHING DISTRIBUTION IN POLYETHYLENES BY DIFFERENTIAL SCANNING CALORIMETRY
Institute of Scientific and Technical Information of China (English)
Robert Shanks; Fei Chen; Gandara Amarasinghe
2003-01-01
Short chain branching has been characterized using thermal fractionation, a stepwise isothermal crystallization technique, followed by a melting analysis scan using differential scanning calorimetry. Short chain branching distribution was also characterized by a continuous slow cooling crystallization, followed by a melting analysis scan. Four different polyethylenes were studied: Ziegler-Natta gas phase, Ziegler-Natta solution, metallocene, constrained-geometry single site catalyzed polyethylenes. The branching distribution was calculated from a calibration of branch content with melting temperature. The lamellar thickness was calculated based on the thermodynamic melting temperature of each polyethylene and the surface free energy of the crystal face. The branching distribution and lamellar thickness distribution were used to calculate weight average branch content, mean lamellar thickness, and a branch dispersity index. The results for the branch content were in good agreement with the known comonomer content of the polyethylenes. A limitation was that high branch content polyethylenes did not reach their potential crystallization at ambient temperatures. Cooling to sub-ambient was necessary to equilibrate the crystallization, but melting temperature versus branch content was not applicable after cooling to below ambient because the calibration data were not performed in this way.
ANALYSIS OF BRANCHING DISTRIBUTION IN POLYETHYLENES BY DIFFERENTIAL SCANNING CALORIMETRY
Institute of Scientific and Technical Information of China (English)
RobertShanks; FeiChan; GandaraAmarasinghe; RobertShanks
2003-01-01
Short chain branching has been characterized using thermal fractionation,a stepwise isothermal crystallization technique,followed by a melting analysis scan using differential scanning calorimetry.Short chain branching distribution was also characterized by a continuous slow cooling crystallization,followed by a melting analysis scan.Four different polyethylenes were studied:Ziegler-Natta gas phase,Ziegler-Natta solution,metallocene,constrained-geometry single site catalyzed polyethylenes.The branching distribution was calculated from a calibration of branch content with melting temperature.The lamellar thickness was calculated based on the thermodynamic melting temperature of each polyethylene and the surface free energy of the crystal face.The branching distribution and lamellar thickness distribution were used to calculate weight average branch content,mean lamellar thickness,and a branch dispersity index.The results for the branch content were in good agreement with the known comonomer content of the polyethylenes.A limitation was that high branch content polyethylenes did not reach their potential crystallization at ambient temperatures.Cooling to sub-ambient was necessary to equilibrate the crystallization,but melting temperature versus branch content was not applicable after cooling to below ambient because the calibration data were not performed in this way.
Statistical analysis of plasma thermograms measured by differential scanning calorimetry.
Fish, Daniel J; Brewood, Greg P; Kim, Jong Sung; Garbett, Nichola C; Chaires, Jonathan B; Benight, Albert S
2010-11-01
Melting curves of human plasma measured by differential scanning calorimetry (DSC), known as thermograms, have the potential to markedly impact diagnosis of human diseases. A general statistical methodology is developed to analyze and classify DSC thermograms to analyze and classify thermograms. Analysis of an acquired thermogram involves comparison with a database of empirical reference thermograms from clinically characterized diseases. Two parameters, a distance metric, P, and correlation coefficient, r, are combined to produce a 'similarity metric,' ρ, which can be used to classify unknown thermograms into pre-characterized categories. Simulated thermograms known to lie within or fall outside of the 90% quantile range around a median reference are also analyzed. Results verify the utility of the methods and establish the apparent dynamic range of the metric ρ. Methods are then applied to data obtained from a collection of plasma samples from patients clinically diagnosed with SLE (lupus). High correspondence is found between curve shapes and values of the metric ρ. In a final application, an elementary classification rule is implemented to successfully analyze and classify unlabeled thermograms. These methods constitute a set of powerful yet easy to implement tools for quantitative classification, analysis and interpretation of DSC plasma melting curves.
Analysis and differentiation of seminal plasma via polarized SERS spectroscopy
Directory of Open Access Journals (Sweden)
Chen X
2012-12-01
Full Text Available Xiwen Chen,1,* Zufang Huang,1,* Shangyuan Feng,1 Jinhua Chen,2 Lan Wang,1 Peng Lu,1 Haishan Zeng,3 Rong Chen1 1Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China; 2Fujian Provincial Hospital, Fuzhou, China; 3Imaging Unit – Integrative Oncology Department, British Columbia Cancer Agency Research Centre, Vancouver, BC, Canada*These authors contributed equally to this workAbstract: Polarized surface-enhanced Raman scattering (SERS spectroscopy was applied for obtaining biochemical information about the seminal plasma. The effect of different laser polarizations (nonpolarized, linear-polarized, right-handed circularly polarized, and left-handed circularly polarized on seminal plasma SERS spectroscopy was explored for the first time. The diagnostic performance in differentiating abnormal seminal plasma (n = 37 from normal seminal plasma (n = 24 was evaluated. A combination of principal component analysis (PCA and linear discriminant analysis (LDA was employed to develop diagnostic algorithms. Classification results of different laser polarizations demonstrated different diagnostic sensitivities and specificities, among which, left-handed circularly polarized laser excitation showed the best diagnostic result (95.8% sensitivity and 64.9% specificity. Our exploratory study demonstrated that SERS spectroscopy with left-handed circularly polarized laser excitation has the potential for becoming a new diagnostic method in semen-quality assessment.Keywords: SERS, seminal plasma, PCA-LDA, polarized laser excitation, silver nanoparticles, biomolecule chirality
Wavelet analysis on adeles and pseudo-differential operators
Khrennikov, A Yu; Shelkovich, V M
2011-01-01
This paper is devoted to wavelet analysis on adele ring $\\bA$ and the theory of pseudo-differential operators. We develop the technique which gives the possibility to generalize finite-dimensional results of wavelet analysis to the case of adeles $\\bA$ by using infinite tensor products of Hilbert spaces. The adele ring is roughly speaking a subring of the direct product of all possible ($p$-adic and Archimedean) completions $\\bQ_p$ of the field of rational numbers $\\bQ$ with some conditions at infinity. Using our technique, we prove that $L^2(\\bA)=\\otimes_{e,p\\in\\{\\infty,2,3,5,...}}L^2({\\bQ}_{p})$ is the infinite tensor product of the spaces $L^2({\\bQ}_{p})$ with a stabilization $e=(e_p)_p$, where $e_p(x)=\\Omega(|x|_p)\\in L^2({\\bQ}_{p})$, and $\\Omega$ is a characteristic function of the unit interval $[0,\\,1]$, $\\bQ_p$ is the field of $p$-adic numbers, $p=2,3,5,...$; $\\bQ_\\infty=\\bR$. This description allows us to construct an infinite family of Haar wavelet bases on $L^2(\\bA)$ which can be obtained by shifts...
Distinguishing PTSD, Complex PTSD, and Borderline Personality Disorder: A latent class analysis
Directory of Open Access Journals (Sweden)
Marylène Cloitre
2014-09-01
Full Text Available Background: There has been debate regarding whether Complex Posttraumatic Stress Disorder (Complex PTSD is distinct from Borderline Personality Disorder (BPD when the latter is comorbid with PTSD. Objective: To determine whether the patterns of symptoms endorsed by women seeking treatment for childhood abuse form classes that are consistent with diagnostic criteria for PTSD, Complex PTSD, and BPD. Method: A latent class analysis (LCA was conducted on an archival dataset of 280 women with histories of childhood abuse assessed for enrollment in a clinical trial for PTSD. Results: The LCA revealed four distinct classes of individuals: a Low Symptom class characterized by low endorsements on all symptoms; a PTSD class characterized by elevated symptoms of PTSD but low endorsement of symptoms that define the Complex PTSD and BPD diagnoses; a Complex PTSD class characterized by elevated symptoms of PTSD and self-organization symptoms that defined the Complex PTSD diagnosis but low on the symptoms of BPD; and a BPD class characterized by symptoms of BPD. Four BPD symptoms were found to greatly increase the odds of being in the BPD compared to the Complex PTSD class: frantic efforts to avoid abandonment, unstable sense of self, unstable and intense interpersonal relationships, and impulsiveness. Conclusions: Findings supported the construct validity of Complex PTSD as distinguishable from BPD. Key symptoms that distinguished between the disorders were identified, which may aid in differential diagnosis and treatment planning.
Institute of Scientific and Technical Information of China (English)
HU Yu-jia; ZHU Yuan-yuan; CHENG Chang-jun
2008-01-01
A nonlinear mathematical model for the analysis of large deformation of frame structures with discontinuity conditions and initial displacements,subject to dynamic loads is formulated with arc-coordinates.The differential quadrature element method (DQEM)is then applied to discretize the nonlinear mathematical model in the spatial domain.An effective method is presented to deal with discontinuity conditions of multivariables in the application of DQEM.A set of DQEM discretization equations are obtained,which are a set of nonlinear differential-algebraic equations with singularity in the time domain.This paper also presents a method to solve nonlinear differential-algebra equations.As application,static and dynamical analyses of large deformation of frames and combined frame structures,subjected to concentrated and distributed forces,are presented.The obtained results are compared with those in the literatares.Numerical results show that the proposed method is general,and effective in dealing with discontinuity conditions of multi-variables and solving difierential-algebraic equations.It requires only a small number of nodes and has low computation complexity with high precision and a good convergence property.
Wong, Ka H; Razmovski-Naumovski, Valentina; Li, Kong M; Li, George Q; Chan, Kelvin
2013-10-01
The aims of the study were to differentiate Pueraria lobata from its related species Pueraria thomsonii and to examine the raw herbal material used in manufacturing kudzu root granules using partial least square discriminant analysis (PLS-DA). Sixty-four raw materials of P. lobata and P. thomsonii and kudzu root-labelled granules were analysed by ultra performance liquid chromatography. To differentiate P. lobata from P. thomsonii, PLS-DA models using the variables selected from the entire chromatograms, genetic algorithm (GA), successive projection algorithm (SPA), puerarin alone and six selected peaks were employed. The models constructed by GA and SPA demonstrated superior classification ability and lower model's complexity as compared to the model based on the entire chromatographic matrix, whilst the model constructed by the six selected peaks was comparable to the entire chromatographic model. The model established by puerarin alone showed inferior classification ability. In addition, the PLS-DA models constructed by the entire chromatographic matrix, GA, SPA and the six selected peaks showed that four brands out of seventeen granules were mislabelled as P. lobata. In conclusion, PLS-DA is a promising procedure for differentiating Pueraria species and determining raw material used in commercial products.
Extending Differential Fault Analysis to Dynamic S-Box Advanced Encryption Standard Implementations
2014-09-18
EXTENDING DIFFERENTIAL FAULT ANALYSIS TO DYNAMIC S-BOX ADVANCED ENCRYPTION STANDARD IMPLEMENTATIONS THESIS Bradley M. Flamm, Civilian AFIT-ENG-T-14-S...Government and is not subject to copyright protection in the United States. AFIT-ENG-T-14-S-08 EXTENDING DIFFERENTIAL FAULT ANALYSIS TO DYNAMIC S-BOX...RELEASE; DISTRIBUTION UNLIMITED AFIT-ENG-T-14-S-08 EXTENDING DIFFERENTIAL FAULT ANALYSIS TO DYNAMIC S-BOX ADVANCED ENCRYPTION STANDARD IMPLEMENTATIONS
Pathway-based analysis tools for complex diseases: a review.
Jin, Lv; Zuo, Xiao-Yu; Su, Wei-Yang; Zhao, Xiao-Lei; Yuan, Man-Qiong; Han, Li-Zhen; Zhao, Xiang; Chen, Ye-Da; Rao, Shao-Qi
2014-10-01
Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehensive understanding of the molecular mechanisms underlying complex diseases. Extensive studies utilizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods-the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available pathway-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are discussed. This review will provide a useful guide to dissect complex diseases.
A proteomic strategy for global analysis of plant protein complexes.
Aryal, Uma K; Xiong, Yi; McBride, Zachary; Kihara, Daisuke; Xie, Jun; Hall, Mark C; Szymanski, Daniel B
2014-10-01
Global analyses of protein complex assembly, composition, and location are needed to fully understand how cells coordinate diverse metabolic, mechanical, and developmental activities. The most common methods for proteome-wide analysis of protein complexes rely on affinity purification-mass spectrometry or yeast two-hybrid approaches. These methods are time consuming and are not suitable for many plant species that are refractory to transformation or genome-wide cloning of open reading frames. Here, we describe the proof of concept for a method allowing simultaneous global analysis of endogenous protein complexes that begins with intact leaves and combines chromatographic separation of extracts from subcellular fractions with quantitative label-free protein abundance profiling by liquid chromatography-coupled mass spectrometry. Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography, we identified hundreds of cytosolic proteins that appeared to exist as components of stable protein complexes. The reliability of the method was validated by protein immunoblot analysis and comparisons with published size exclusion chromatography data and the masses of known complexes. The method can be implemented with appropriate instrumentation, is applicable to any biological system, and has the potential to be further developed to characterize the composition of protein complexes and measure the dynamics of protein complex localization and assembly under different conditions.
Directory of Open Access Journals (Sweden)
David Lagman
Full Text Available Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost-specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation.
Lagman, David; Callado-Pérez, Amalia; Franzén, Ilkin E; Larhammar, Dan; Abalo, Xesús M
2015-01-01
Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost-specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation.
Molecular electrostatic potential analysis of non-covalent complexes
Indian Academy of Sciences (India)
PADINJARE VEETIL BIJINA; CHERUMUTTATHU H SURESH
2016-10-01
Ab initio MP4/Aug-cc-pvDZ//MP2/6-311++g(d,p) level interaction energy (Eint) and molecular electrostatic potential analysis (MESP) of a large variety of non-covalent intermolecular complexes, viz. tetrel, chalcogen, pnicogen, halogen, hydrogen, dihydrogen and lithium bonded complexes have been reported. The electronic changes associated with the non-covalent complex formation is monitored in terms of MESP minimum (Vmin) in the free and complexed states of the donor and acceptor molecules as well as in terms ofMESP at the donor and acceptor atoms (Vn) of the free monomers and complexes. The change in Vmin or Vn on the donor molecule (ΔVmin(D) or ΔVn(D)) during complex formation is proportional to its electron donating ability while such a change on the acceptor molecule (ΔVmin(A) or ΔVn(A)) is proportional to its electron accepting ability. Further, the quantities ΔΔVmin = ΔVmin(D) −ΔVmin(A) and ΔΔVn = ΔVn(D) −ΔVn(A) have shown strong linear correlations with Eint of the complex (Eint values fall in the range 0.7 to 46.2 kcal/mol for 54 complexes) and suggest that the intermolecular non-covalent interactions in a wide variety of systems can be monitored and assessed in terms of change in MESP due to complex formation in the gas phase. With the incorporation of solvent effect in the calculation, charged systems showed significant deviations from the linear correlation. The MESP based analysis proposes that the large variety of intermolecular non-covalent complexes considered in this study can be grouped under the general category of electron donor-acceptor (eDA) complexes
Directory of Open Access Journals (Sweden)
Liliane Gibbs
2008-10-01
Full Text Available The diagnosis of a simple hepatic cyst is not difficult, but diagnostic confusion occurs when atypical features such as intracystic debris or extremely large size are present. In children, simple liver cysts are described as small, asymptomatic, and rarely hemorrhagic. We report an adolescent male presenting with an unusually large hepatic cyst that did not have typical imaging characteristics. The imaging findings and histology are displayed along with the differential diagnoses of complex liver cysts.
Liliane Gibbs; Peter Baron; Beverly Wood; Yolanda Bryce
2008-01-01
The diagnosis of a simple hepatic cyst is not difficult, but diagnostic confusion occurs when atypical features such as intracystic debris or extremely large size are present. In children, simple liver cysts are described as small, asymptomatic, and rarely hemorrhagic. We report an adolescent male presenting with an unusually large hepatic cyst that did not have typical imaging characteristics. The imaging findings and histology are displayed along with the differential diagnoses of complex l...
Bryce, Yolanda; Wood, Beverly; Baron, Peter; Gibbs, Liliane
2008-01-01
The diagnosis of a simple hepatic cyst is not difficult, but diagnostic confusion occurs when atypical features such as intracystic debris or extremely large size are present. In children, simple liver cysts are described as small, asymptomatic, and rarely hemorrhagic. We report an adolescent male presenting with an unusually large hepatic cyst that did not have typical imaging characteristics. The imaging findings and histology are displayed along with the differential diagnoses of complex liver cysts. PMID:22470600
Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors
Directory of Open Access Journals (Sweden)
Lamblin Anne-Francoise
2007-10-01
Full Text Available Abstract Background Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs, which alter gene expression by modifying chromatin structure. We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin. Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation. Results To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid for 18 hours in osteogenic conditions. The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays. Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR. Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1, sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4 were induced. Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1 were suppressed. We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway. Conclusion This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that
Differential diagnosis of hyperkalemia: an update to a complex problem
Eleftheriadis, T; Leivaditis, K; Antoniadi, G; Liakopoulos, V
2012-01-01
Hyperkalemia is a relative common and sometimes life threatening electorlyte disorder. Although its symptomatic treatment is relatively easy, since precise therapeutic algorithms are available, its differential diagnosis is more complicated. The present review aims to unfold the differential diagnosis of hypekalemia using a pathophysiological, albeit clinically useful, approach. The basic elements of potassium homeostasis are provided, the causes of hyperkalemia are categorized and analysed and finally the required for the diferrential diagnosis laboratory tests are mentioned. PMID:23935306
Differential diagnosis of hyperkalemia: an update to a complex problem
2012-01-01
Hyperkalemia is a relative common and sometimes life threatening electorlyte disorder. Although its symptomatic treatment is relatively easy, since precise therapeutic algorithms are available, its differential diagnosis is more complicated. The present review aims to unfold the differential diagnosis of hypekalemia using a pathophysiological, albeit clinically useful, approach. The basic elements of potassium homeostasis are provided, the causes of hyperkalemia are categorized and analysed a...
Abigail J Moore; Moore, William L.; Baldwin, Bruce G.
2014-01-01
Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations...
Gao, Jie; Buckley, Shannon M; Cimmino, Luisa; Guillamot, Maria; Strikoudis, Alexandros; Cang, Yong; Goff, Stephen P; Aifantis, Iannis
2015-11-27
Little is known on post-transcriptional regulation of adult and embryonic stem cell maintenance and differentiation. Here we characterize the role of Ddb1, a component of the CUL4-DDB1 ubiquitin ligase complex. Ddb1 is highly expressed in multipotent hematopoietic progenitors and its deletion leads to abrogation of both adult and fetal hematopoiesis, targeting specifically transiently amplifying progenitor subsets. However, Ddb1 deletion in non-dividing lymphocytes has no discernible phenotypes. Ddb1 silencing activates Trp53 pathway and leads to significant effects on cell cycle progression and rapid apoptosis. The abrogation of hematopoietic progenitor cells can be partially rescued by simultaneous deletion of Trp53. Conversely, depletion of DDB1 in embryonic stem cell (ESC) leads to differentiation albeit negative effects on cell cycle and apoptosis. Mass spectrometry reveals differing protein interactions between DDB1 and distinct DCAFs, the substrate recognizing components of the E3 complex, between cell types. Our studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation.
Energy Technology Data Exchange (ETDEWEB)
Ohsaka, Akimichi, E-mail: ohsaka@juntendo.ac.jp [Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Hirota-Komatsu, Satoko; Shibata, Miki [Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Komatsu, Norio [Department of Hematology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan)
2009-12-25
We investigated whether the gene expression of vascular endothelial growth factor (VEGF) and its receptors (VEGFR and neuropilin-1 [NRP-1]) could be specifically regulated during the megakaryocytic differentiation of human thrombopoietin (TPO)-dependent UT-7/TPO cells. Undifferentiated UT-7/TPO cells expressed a functional VEGFR-2, leading to VEGF binding and VEGF{sub 165}-induced tyrosine phosphorylation, cell proliferation, and apoptosis inhibition. The megakaryocytic differentiation of UT-7/TPO cells on treatment with phorbol myristate acetate (PMA) was accompanied by a marked up-regulation of NRP-1 mRNA and protein expression and by an increase in VEGF-binding activity, which was mainly mediated by VEGFR-2. VEGF{sub 165} promoted the formation of complexes containing NRP-1 and VEGFR-2 in undifferentiated UT-7/TPO cells in a dose-dependent manner. Unlike human umbilical vein endothelial cells, PMA-differentiated UT-7/TPO cells exhibited complex formation between NRP-1 and VEGFR-2 even in the absence of VEGF{sub 165}. These findings suggest that NRP-1-VEGFR-2-complex formation may contribute to effective cellular functions mediated by VEGF{sub 165} in megakaryocytic cells.
Ohsaka, Akimichi; Hirota-Komatsu, Satoko; Shibata, Miki; Komatsu, Norio
2009-12-25
We investigated whether the gene expression of vascular endothelial growth factor (VEGF) and its receptors (VEGFR and neuropilin-1 [NRP-1]) could be specifically regulated during the megakaryocytic differentiation of human thrombopoietin (TPO)-dependent UT-7/TPO cells. Undifferentiated UT-7/TPO cells expressed a functional VEGFR-2, leading to VEGF binding and VEGF(165)-induced tyrosine phosphorylation, cell proliferation, and apoptosis inhibition. The megakaryocytic differentiation of UT-7/TPO cells on treatment with phorbol myristate acetate (PMA) was accompanied by a marked up-regulation of NRP-1 mRNA and protein expression and by an increase in VEGF-binding activity, which was mainly mediated by VEGFR-2. VEGF(165) promoted the formation of complexes containing NRP-1 and VEGFR-2 in undifferentiated UT-7/TPO cells in a dose-dependent manner. Unlike human umbilical vein endothelial cells, PMA-differentiated UT-7/TPO cells exhibited complex formation between NRP-1 and VEGFR-2 even in the absence of VEGF(165). These findings suggest that NRP-1-VEGFR-2-complex formation may contribute to effective cellular functions mediated by VEGF(165) in megakaryocytic cells.
Institute of Scientific and Technical Information of China (English)
LI Shoufu
2005-01-01
A series of stability, contractivity and asymptotic stability results of the solutions to nonlinear stiff Volterra functional differential equations (VFDEs) in Banach spaces is obtained, which provides the unified theoretical foundation for the stability analysis of solutions to nonlinear stiff problems in ordinary differential equations(ODEs), delay differential equations(DDEs), integro-differential equations(IDEs) and VFDEs of other type which appear in practice.
Reliability analysis of large, complex systems using ASSIST
Johnson, Sally C.
1988-01-01
The SURE reliability analysis program is discussed as well as the ASSIST model generation program. It is found that semi-Markov modeling using model reduction strategies with the ASSIST program can be used to accurately solve problems at least as complex as other reliability analysis tools can solve. Moreover, semi-Markov analysis provides the flexibility needed for modeling realistic fault-tolerant systems.
Analysis of macromolecules, ligands and macromolecule-ligand complexes
Von Dreele, Robert B [Los Alamos, NM
2008-12-23
A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.
A Functional Complexity Framework for the Analysis of Telecommunication Networks
Dzaferagic, Merim; Macaluso, Irene; Marchetti, Nicola
2016-01-01
The rapid evolution of network services demands new paradigms for studying and designing networks. In order to understand the underlying mechanisms that provide network functions, we propose a framework which enables the functional analysis of telecommunication networks. This framework allows us to isolate and analyse a network function as a complex system. We propose functional topologies to visualise the relationships between system entities and enable the systematic study of interactions between them. We also define a complexity metric $C_F$ (functional complexity) which quantifies the variety of structural patterns and roles of nodes in the topology. This complexity metric provides a wholly new approach to study the operation of telecommunication networks. We study the relationship between $C_F$ and different graph structures by analysing graph theory metrics in order to recognize complex organisations. $C_F$ is equal to zero for both a full mesh topology and a disconnected topology. We show that complexi...
Conservation laws, differential identities, and constraints of partial differential equations
Zharinov, V. V.
2015-11-01
We consider specific cohomological properties such as low-dimensional conservation laws and differential identities of systems of partial differential equations (PDEs). We show that such properties are inherent to complex systems such as evolution systems with constraints. The mathematical tools used here are the algebraic analysis of PDEs and cohomologies over differential algebras and modules.
Dynamic analysis of biochemical network using complex network method
Directory of Open Access Journals (Sweden)
Wang Shuqiang
2015-01-01
Full Text Available In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.
Differential role of lipocalin-2 during immune-complex mediated acute and chronic inflammation
Shashidharamurthy, Rangaiah; Machiah, Deepa; Aitken, Jesse D; Putty, Kalyani; Srinivasan, Gayathri; Chassaing, Benoit; Parkos, Charles A; Selvaraj, Periasamy; Vijay-Kumar, Matam
2013-01-01
Objectives Lipocalin-2 (Lcn2) is an innate immune protein expressed by a variety of cells and is highly upregulated during several pathological conditions including immune-complex (IC) mediated inflammatory/autoimmune disorders. However, the function of Lcn2 during IC-mediated inflammation is largely unknown. Therefore our objective was to investigate the role of Lcn2 in IC-mediated diseases. Methods The upregulation of Lcn2 was determined by ELISA in three different mouse models of IC-mediated autoimmune disease: systemic lupus erythematosus, collagen-induced arthritis and serum-induced arthritis. The in vivo role of Lcn2 during IC-mediated inflammation was investigated using Lcn2 knockout (Lcn2KO) mice and their wild type (WT) littermates. Results Lcn2 levels were significantly elevated in all the three autoimmune disease models. Further, in an acute skin inflammation model, Lcn2KO mice demonstrated a 50% reduction in inflammation with histopathological analysis revealing strikingly reduced immune cell infiltration compared to WT mice. Administration of recombinant Lcn2 to Lcn2KO mice restored inflammation to levels observed in WT mice. Neutralization of Lcn2 using a monoclonal antibody significantly reduced inflammation in WT mice. In contrast, Lcn2KO mice developed more severe serum-induced arthritis compared to WT mice. Histological analysis revealed extensive tissue and bone destruction with significantly reduced neutrophil infiltration but considerably more macrophage migration in Lcn2KO mice when compared to WT. Conclusion These results demonstrate that Lcn2 may regulate immune cell recruitment to the site of inflammation, a process essential for the controlled initiation, perpetuation and resolution of inflammatory processes. Thus, Lcn2 may present a promising target in the treatment of IC-mediated inflammatory/autoimmune diseases. PMID:23280250
Feng, Xiaobo; Wu, Zengbin; Ling, Bo; Pan, Shuming; Liao, Wanqing; Pan, Weihua; Yao, Zhirong
2014-05-01
The Candida parapsilosis complex is composed of Candida parapsilosis sensu stricto, Candida orthopsilosis, Candida metapsilosis, and the closely related species Lodderomyces elongisporus. An exon-primed intron-crossing PCR assay was developed here to distinguish the members of the species complex on the basis of the distinct sizes of amplicons, and Candida orthopsilosis and Candida metapsilosis were further discriminated by restriction enzyme analysis.
Single-strand conformation polymorphism analysis for differentiating phytoplasma strains.
Musić, Martina Seruga; Skorić, Dijana
2013-01-01
Single-strand conformation polymorphism (SSCP) analysis is a sensitive and rapid technique for detecting DNA polymorphisms and mutations in PCR-amplified fragments. Due to its technical simplicity, it is widely used as a screening tool in various investigations, ranging from clinical diagnosis of human hereditary diseases to the characterization of microbial communities. This method can also be used successfully on phytoplasmas as a tool for the detection of molecular variability in conserved housekeeping genes such as 16S rRNA and tuf, as well as in more variable genes, revealing the presence of polymorphisms undetected by routine RFLP analyses. The reliability of SSCP has been confirmed by multiple alignments and phylogenetic analyses of representative sequences showing different SSCP profiles. However, it is not broadly applied in phytoplasma research yet. The technique provides an inexpensive, convenient, and sensitive method for determining sequence variation and to differentiate phytoplasma strains, and is particularly suitable for epidemiological studies or as a fast screening, typing tool when dealing with a large number of field samples.
Differential expression analysis for RNAseq using Poisson mixed models.
Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang
2017-06-20
Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid.
Zhang, Xiaoshen; Deng, Minjie; Fan, Guoqiang
2014-03-21
Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx). About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST) search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI) non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.
Differentially Private Data Analysis of Social Networks via Restricted Sensitivity
Blocki, Jeremiah; Datta, Anupam; Sheffet, Or
2012-01-01
We introduce the notion of restricted sensitivity as an alternative to global and smooth sensitivity to improve accuracy in differentially private data analysis. The definition of restricted sensitivity is similar to that of global sensitivity except that instead of quantifying over all possible datasets, we take advantage of any beliefs about the dataset that a querier may have, to quantify over a restricted class of datasets. Specifically, given a query f and a hypothesis H about the structure of a dataset D, we show generically how to transform f into a new query f_H whose global sensitivity (over all datasets including those that do not satisfy H) matches the restricted sensitivity of the query f. Moreover, if the belief of the querier is correct (i.e., D is in H) then f_H(D) = f(D). If the belief is incorrect, then f_H(D) may be inaccurate. We demonstrate the usefulness of this notion by considering the task of answering queries regarding social-networks, which we model as a combination of a graph and a ...
Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid
Directory of Open Access Journals (Sweden)
Xiaoshen Zhang
2014-03-01
Full Text Available Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx. About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.
Analysis of differential infrared thermography for boundary layer transition detection
Gardner, A. D.; Eder, C.; Wolf, C. C.; Raffel, M.
2017-09-01
This paper presents an analysis of the differential infrared thermography (DIT) technique, a contactless method of measuring the unsteady movement of the boundary layer transition position on an unprepared surface. DIT has been shown to measure boundary layer transition positions which correlate well with those from other measurement methods. In this paper unsteady aerodynamics from a 2D URANS solution are used and the resulting wall temperatures computed. It is shown that the peak of the temperature difference signal correlates well with the boundary layer transition position, but that the start and end of boundary layer transition cannot be extracted. A small systematic time-lag cannot be reduced by using different surface materials, but the signal strength can be improved by reducing the heat capacity and heat transfer of the surface layer, for example by using a thin plastic coating. Reducing the image time separation used to produce the difference images reduces the time-lag and also the signal level, thus the optimum is when the signal to noise ratio is at the minimum which can be evaluated.
Chou, Loke Ming; Toh, Tai Chong; Toh, Kok Ben; Ng, Chin Soon Lionel; Cabaitan, Patrick; Tun, Karenne; Goh, Eugene; Afiq-Rosli, Lutfi; Taira, Daisuke; Du, Rosa Celia Poquita; Loke, Hai Xin; Khalis, Aizat; Li, Jinghan; Song, Tiancheng
2016-01-01
Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera-Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change.
Directory of Open Access Journals (Sweden)
Loke Ming Chou
Full Text Available Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera-Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached. The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change.
Complex analysis with applications to flows and fields
Braga da Costa Campos, Luis Manuel
2012-01-01
Complex Analysis with Applications to Flows and Fields presents the theory of functions of a complex variable, from the complex plane to the calculus of residues to power series to conformal mapping. The book explores numerous physical and engineering applications concerning potential flows, the gravity field, electro- and magnetostatics, steady heat conduction, and other problems. It provides the mathematical results to sufficiently justify the solution of these problems, eliminating the need to consult external references.The book is conveniently divided into four parts. In each part, the ma
Engineering Complex Systems: Multiscale Analysis and Evolutionary Engineering
Bar-Yam, Yaneer
We describe an analytic approach, multiscale analysis, that can demonstrate the fundamental limitations of decomposition based engineering for the development of highly complex systems. The interdependence of components and communication between design teams limits any planning based process. Recognizing this limitation, we found that a new strategy for constructing many highly complex systems should be modeled after biological evolution, or market economies, where multiple design efforts compete in parallel for adoption through testing in actual use. Evolution is the only process that is known to create highly complex systems.
Analysis of Caputo Impulsive Fractional Order Differential Equations with Applications
Directory of Open Access Journals (Sweden)
Lakshman Mahto
2013-01-01
Full Text Available We use Sadovskii's fixed point method to investigate the existence and uniqueness of solutions of Caputo impulsive fractional differential equations of order with one example of impulsive logistic model and few other examples as well. We also discuss Caputo impulsive fractional differential equations with finite delay. The results proven are new and compliment the existing one.
Diagnosability Analysis Considering Causal Interpretations for Differential Constraints
2012-01-01
This paper is focused on structural approaches to study diagnosability properties given a system model taking into account, both simultaneously or separately, integral and differential causal interpretations for differential constraints. We develop a model characterization and corresponding algorithms, for studying system diagnosability using a structural decomposition that avoids generating the full set of system analytical redundancy relations. Simultaneous application of integral and diffe...
Analysis of Caputo impulsive fractional order differential equations with applications
Mahto, Lakshman; Favini, Angelo
2012-01-01
We use Sadavoskii's fixed point method to investigate the existence and uniqueness of solutions of Caputo impulsive fractional differential equations of order \\alpha between 0 and 1 with one example of impulsive logistic model and few other examples as well. We also discuss Caputo impulsive fractional differential equations with finite delay. The results proven are new and complement the existing one.
Partial differential equation transform - Variational formulation and Fourier analysis.
Wang, Yang; Wei, Guo-Wei; Yang, Siyang
2011-12-01
Nonlinear partial differential equation (PDE) models are established approaches for image/signal processing, data analysis and surface construction. Most previous geometric PDEs are utilized as low-pass filters which give rise to image trend information. In an earlier work, we introduced mode decomposition evolution equations (MoDEEs), which behave like high-pass filters and are able to systematically provide intrinsic mode functions (IMFs) of signals and images. Due to their tunable time-frequency localization and perfect reconstruction, the operation of MoDEEs is called a PDE transform. By appropriate selection of PDE transform parameters, we can tune IMFs into trends, edges, textures, noise etc., which can be further utilized in the secondary processing for various purposes. This work introduces the variational formulation, performs the Fourier analysis, and conducts biomedical and biological applications of the proposed PDE transform. The variational formulation offers an algorithm to incorporate two image functions and two sets of low-pass PDE operators in the total energy functional. Two low-pass PDE operators have different signs, leading to energy disparity, while a coupling term, acting as a relative fidelity of two image functions, is introduced to reduce the disparity of two energy components. We construct variational PDE transforms by using Euler-Lagrange equation and artificial time propagation. Fourier analysis of a simplified PDE transform is presented to shed light on the filter properties of high order PDE transforms. Such an analysis also offers insight on the parameter selection of the PDE transform. The proposed PDE transform algorithm is validated by numerous benchmark tests. In one selected challenging example, we illustrate the ability of PDE transform to separate two adjacent frequencies of sin(x) and sin(1.1x). Such an ability is due to PDE transform's controllable frequency localization obtained by adjusting the order of PDEs. The
Complexity of software trustworthiness and its dynamical statistical analysis methods
Institute of Scientific and Technical Information of China (English)
ZHENG ZhiMing; MA ShiLong; LI Wei; JIANG Xin; WEI Wei; MA LiLi; TANG ShaoTing
2009-01-01
Developing trusted softwares has become an important trend and a natural choice in the development of software technology and applications.At present,the method of measurement and assessment of software trustworthiness cannot guarantee safe and reliable operations of software systems completely and effectively.Based on the dynamical system study,this paper interprets the characteristics of behaviors of software systems and the basic scientific problems of software trustworthiness complexity,analyzes the characteristics of complexity of software trustworthiness,and proposes to study the software trustworthiness measurement in terms of the complexity of software trustworthiness.Using the dynamical statistical analysis methods,the paper advances an invariant-measure based assessment method of software trustworthiness by statistical indices,and hereby provides a dynamical criterion for the untrustworthiness of software systems.By an example,the feasibility of the proposed dynamical statistical analysis method in software trustworthiness measurement is demonstrated using numerical simulations and theoretical analysis.
Tyler, Glenn A.; Brennan, Terry J.; Browne, Stephen L.; Dueck, Robert H.; Lodin, Michael S.; Roberts, Phillip H.; Vaughn, Jeffrey L.
1997-08-01
This paper describes the differential phase experiment (DPE) which formed a major part of the ABLE ACE suite of experiments conducted by the Air Force. The work described covers the rationale for the experiment, the basic experimental concept, the analysis of the differential phase, the optical and software design analysis, a discussion of the polarization scrambling characteristics of the optics, calibration of the equipment and a presentation of some of the major results of the data reduction effort to date. The DPE was a propagation experiment conducted between two aircraft flying at an altitude of 40,000 feet whose purpose was to measure the phase difference between two beams propagating at slightly different angels through the atmosphere. A four bin polarization interferometer was used to measure the differential phase. Due to the high level of scintillation that was presented branch points were present in the phase function. Rytov theory, wave optics simulation and the experimental measurements are in general agreement. Self consistency checks that were performed on the data indicate a high level of confidence in the results. Values of Cn2 that are consistent with the measurements of the differential phase agree with simultaneous scintillometer measurement taken long the same path in levels of turbulence where the scintillometer is not saturated. These differential phase based Cn2 estimates do not appear to saturate as is typical of scintillometer measurements and appear to extend the range over which high levels of Cn2 can be estimated. In addition the differential phase and anisoplanatic Strehl computed from the data is consistent with Rytov theory and wave optics simulations.
Visual analysis and exploration of complex corporate shareholder networks
Tekušová, Tatiana; Kohlhammer, Jörn
2008-01-01
The analysis of large corporate shareholder network structures is an important task in corporate governance, in financing, and in financial investment domains. In a modern economy, large structures of cross-corporation, cross-border shareholder relationships exist, forming complex networks. These networks are often difficult to analyze with traditional approaches. An efficient visualization of the networks helps to reveal the interdependent shareholding formations and the controlling patterns. In this paper, we propose an effective visualization tool that supports the financial analyst in understanding complex shareholding networks. We develop an interactive visual analysis system by combining state-of-the-art visualization technologies with economic analysis methods. Our system is capable to reveal patterns in large corporate shareholder networks, allows the visual identification of the ultimate shareholders, and supports the visual analysis of integrated cash flow and control rights. We apply our system on an extensive real-world database of shareholder relationships, showing its usefulness for effective visual analysis.
In situ structural analysis of the human nuclear pore complex.
von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin
2015-10-01
Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.
Chen, Lu; Bush, Stephen J; Tovar-Corona, Jaime M.; Castillo-Morales, Atahualpa; Urrutia, Araxi O.
2014-01-01
What at the genomic level underlies organism complexity? Although several genomic features have been associated with organism complexity, in the case of alternative splicing, which has long been proposed to explain the variation in complexity, no such link has been established. Here, we analyzed over 39 million expressed sequence tags available for 47 eukaryotic species with fully sequenced genomes to obtain a comparable index of alternative splicing estimates, which corrects for the distorti...
Differential Bees Flux Balance Analysis with OptKnock for in silico microbial strains optimization.
Directory of Open Access Journals (Sweden)
Yee Wen Choon
Full Text Available Microbial strains optimization for the overproduction of desired phenotype has been a popular topic in recent years. The strains can be optimized through several techniques in the field of genetic engineering. Gene knockout is a genetic engineering technique that can engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, the complexities of the metabolic networks have made the process to identify the effects of genetic modification on the desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to the combinatorial problem in obtaining optimal gene deletion strategy. Basically, the size of a genome-scale metabolic model is usually large. As the size of the problem increases, the computation time increases exponentially. In this paper, we propose Differential Bees Flux Balance Analysis (DBFBA with OptKnock to identify optimal gene knockout strategies for maximizing the production yield of desired phenotypes while sustaining the growth rate. This proposed method functions by improving the performance of a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA by hybridizing Differential Evolution (DE algorithm into neighborhood searching strategy of BAFBA. In addition, DBFBA is integrated with OptKnock to validate the results for improving the reliability the work. Through several experiments conducted on Escherichia coli, Bacillus subtilis, and Clostridium thermocellum as the model organisms, DBFBA has shown a better performance in terms of computational time, stability, growth rate, and production yield of desired phenotypes compared to the methods used in previous works.
Directory of Open Access Journals (Sweden)
Lijun Li
2012-01-01
Full Text Available Five sterically hindered platinum(II complexes with tetradentate schiff bases as ligands, [Pt(L] (L= N,N′-bisalicylidene-1,2-ethylenediamine (L1, N,N′-bisalicylidene-1,2-cyclohexanediamine (L2, N,N′-bis(5-hydroxyl-salicylidene-1,2-cyclohexanediamine (L3, N,N′-bisalicylidene-1,2-diphenyl-ethylenediamine (L4 and N,N′-bis(3-tert-butyl-5-methyl-salicylidene-1,2-diphenylethylenediamine (L5 have been synthesized and characterized by IR spectroscopy and elemental analysis. The sterical hindrance of antitumor drug candidates potentially makes them less susceptible to deactivation by sulphur containing proteins and helping to overcome resistance mechanisms. The interaction of these metal complexes with fish sperm single-stranded DNA (ssDNA was studied electrochemically based on the oxidation signals of guanine and adenine. Differential pulse voltammetry was employed to monitor the DNA interaction in solution by using renewable pencil graphite electrode. The results indicate that ligands with different groups can strongly affect the interaction between [Pt(L] complexes and ssDNA due to sterical hindrances and complex [Pt(L1] has the best interaction with DNA among the five complexes.
The ultrasonographic features of endometriomas: morphologic analysis and differential diagnosis
Energy Technology Data Exchange (ETDEWEB)
Kim, Mi Sung; Park, Chan Sup; Song, Soon Young; Lee, Eun Ja; Park, No Hyuck [College of Medicine, Kwandong Univ., Koyang (Korea, Republic of); Park, Cheol Min [College of Medicine, Korea Univ., Seoul (Korea, Republic of); Kim, Bo Hyun; Kim, Chan Kyo [College of Medicine, Sungkyunkwan Univ., Seoul (Korea, Republic of)
2003-12-01
To analyze the sonographic, morphologic, and internal echo patterns of endometriomas, and thus determine which ultrasonographic (US) findings assist diagnosis. One hundred and forty-seven eases of pathologically proven adnexal masses in 130 women were divided into three groups: group I, in which endometriomas were diagnosed at both preoperative US and surgery (true positive) (n=97); group II, in which endometriomas were misdiagnosed at preoperative US, and were confirmed after surgery to be other pathologic entities (false positive) (n=10); group III, in which other adnexal masses were misdiagnosed at preoperative US, but were proven after surgery to be endometriomas (false negative) (n=40). The US findings in these cases were retrospectively reviewed in terms of (a) morphologic type: unilocular, multiseptated, multilobulated, solid and cystic, or mixed; (b) internal echo pattern: homogeneous fine, anechoic, fine septation, or complex; (c) size; (d) wall thickness; (e) the presence or absence of septation; (f) wall nodularity; (g) echogenic wall foci; and (h) a solid area. In group I, the most common morphological type was unilocular cyst (n=63; 65%). In lesions most commonly emitted homogeneous fine echoes (n=76; 78%). In this group, most masses (86%) were less than 10 cm in diameter and the wall thickness in 65% of cases was less than 3 mm. Additionally, internal septation, wall nodularity, focal echogenic wall foci, and a solid area were observed at US. Group II, cases were pathologically confirmed as mucinous cystadenoma (n=3), mucinous cystadenoma with borderline malignancy, hemorrhagic cyst, functional cyst, endometrioid carcinoma, and hematoma. In group III, cases were misdiagnosed as cystadenoma (n=15), hemorrhagic cyst, teratoma, ovarian cancer, functional cyst and ectopic pregnancy at preoperative US. There were no significant differences in size or wall thickness between groups II and III, and group I. At US, groups II and III also showed internal
Prandini, Tâmara Heloísa Rocha; Theodoro, Raquel Cordeiro; Bruder-Nascimento, Ariane C M O; Scheel, Christina M; Bagagli, Eduardo
2013-09-01
Inteins are coding sequences that are transcribed and translated with flanking sequences and then are excised by an autocatalytic process. There are two types of inteins in fungi, mini-inteins and full-length inteins, both of which present a splicing domain containing well-conserved amino acid sequences. Full-length inteins also present a homing endonuclease domain that makes the intein a mobile genetic element. These parasitic genetic elements are located in highly conserved genes and may allow for the differentiation of closely related species of the Candida parapsilosis (psilosis) complex. The correct identification of the three psilosis complex species C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis is very important in the clinical setting for improving antifungal therapy and patient care. In this work, we analyzed inteins that are present in the vacuolar ATPase gene VMA and in the threonyl-tRNA synthetase gene ThrRS in 85 strains of the Candida psilosis complex (46 C. parapsilosis, 17 C. metapsilosis, and 22 C. orthopsilosis). Here, we describe an accessible and accurate technique based on a single PCR that is able to differentiate the psilosis complex based on the VMA intein. Although the ThrRS intein does not distinguish the three species of the psilosis complex by PCR product size, it can differentiate them by sequencing and phylogenetic analysis. Furthermore, this intein is unusually present as both mini- and full-length forms in C. orthopsilosis. Additional population studies should be performed to address whether this represents a common intraspecific variability or the presence of subspecies within C. orthopsilosis.
Integral formulas for differential forms of type(p,q)on complex Finsler manifolds
Institute of Scientific and Technical Information of China (English)
QIU; Chunhui; ZHONG; Tongde
2004-01-01
Using the invariant integral kernel introduced by Demailly and Laurent-Thiebaut,complex Finsler metric and nonlinear connection associating with Chern-Finsler connection, we research the integral representation theory on complex Finsler manifolds. The Koppelman and Koppelman-Leray formulas are obtained, and the (θ)-equations are solved.
Demonstration of a Safety Analysis on a Complex System
Leveson, Nancy; Alfaro, Liliana; Alvarado, Christine; Brown, Molly; Hunt, Earl B.; Jaffe, Matt; Joslyn, Susan; Pinnell, Denise; Reese, Jon; Samarziya, Jeffrey; Sandys, Sean; Shaw, Alan; Zabinsky, Zelda
1997-01-01
For the past 17 years, Professor Leveson and her graduate students have been developing a theoretical foundation for safety in complex systems and building a methodology upon that foundation. The methodology includes special management structures and procedures, system hazard analyses, software hazard analysis, requirements modeling and analysis for completeness and safety, special software design techniques including the design of human-machine interaction, verification, operational feedback, and change analysis. The Safeware methodology is based on system safety techniques that are extended to deal with software and human error. Automation is used to enhance our ability to cope with complex systems. Identification, classification, and evaluation of hazards is done using modeling and analysis. To be effective, the models and analysis tools must consider the hardware, software, and human components in these systems. They also need to include a variety of analysis techniques and orthogonal approaches: There exists no single safety analysis or evaluation technique that can handle all aspects of complex systems. Applying only one or two may make us feel satisfied, but will produce limited results. We report here on a demonstration, performed as part of a contract with NASA Langley Research Center, of the Safeware methodology on the Center-TRACON Automation System (CTAS) portion of the air traffic control (ATC) system and procedures currently employed at the Dallas/Fort Worth (DFW) TRACON (Terminal Radar Approach CONtrol). CTAS is an automated system to assist controllers in handling arrival traffic in the DFW area. Safety is a system property, not a component property, so our safety analysis considers the entire system and not simply the automated components. Because safety analysis of a complex system is an interdisciplinary effort, our team included system engineers, software engineers, human factors experts, and cognitive psychologists.
Directory of Open Access Journals (Sweden)
A. G. Polyakova
2013-01-01
Full Text Available Goal of research: analysis of the effectiveness of Biofeedback therapy is differentiated depending on the clinical forms of autonomic dysfunction. Exchange rate control efficacy of biofeedback hardware was conducted on the dynamics of clinical andl aboratory data, surveys and assessment of the functional State of the SNC using heart rate variability, vegetative resonance test, Kerdo index definition, as well as èlektrokardiografiče applications and questionnaires, characterizing the State of psychoemotional sphere (Spilbergera–Hanina, test, Luscher. Laboratory tests include a complete blood count with evaluation of Adaptive reactions of the organism. The results of the rehabilitation complex of the patients with the use of biofeedback have confirmed its effectiveness.
Quantifying ligand adsorption to nanoparticles using tandem differential mobility mass analysis.
Guha, Suvajyoti; Ma, Xiaofei; Tarlov, Michael J; Zachariah, Michael R
2012-08-07
Although electrospray-differential mobility analyzers (ES-DMA) have been previously employed to characterize ligand binding to nanoparticles, absolute quantification of surface coverage can be inaccurate at times because of ligand conformational effects. In this Letter, we report a quantitative technique by in-flight coupling of a particle mass analyzer (APM) with ES-DMA, thus enabling a direct quantitative analysis of mass independent of particle size, material, morphology and conformation. We demonstrate the utility of ES-DMA-APM by studying two model complex systems (gold nanoparticle-bovine serum albumin and polystyrene bead-antibody) as a function of concentration and pH. Our results obtained with ES-DMA-APM are in excellent agreement with prior work. We anticipate that this will enhance the capabilities of online quantitative characterization of ligand binding to nanoparticles.
Differential association of protein subunits with the human RNase MRP and RNase P complexes.
Welting, Tim J M; Kikkert, Bastiaan J; van Venrooij, Walther J; Pruijn, Ger J M
2006-07-01
RNase MRP is a eukaryotic endoribonuclease involved in nucleolar and mitochondrial RNA processing events. RNase MRP is a ribonucleoprotein particle, which is structurally related to RNase P, an endoribonuclease involved in pre-tRNA processing. Most of the protein components of RNase MRP have been reported to be associated with RNase P as well. In this study we determined the association of these protein subunits with the human RNase MRP and RNase P particles by glycerol gradient sedimentation and coimmunoprecipitation. In agreement with previous studies, RNase MRP sedimented at 12S and 60-80S. In contrast, only a single major peak was observed for RNase P at 12S. The analysis of individual protein subunits revealed that hPop4 (also known as Rpp29), Rpp21, Rpp20, and Rpp25 only sedimented in 12S fractions, whereas hPop1, Rpp40, Rpp38, and Rpp30 were also found in 60-80S fractions. In agreement with their cosedimentation with RNase P RNA in the 12S peak, coimmunoprecipitation with VSV-epitope-tagged protein subunits revealed that hPop4, Rpp21, and in addition Rpp14 preferentially associate with RNase P. These data show that hPop4, Rpp21, and Rpp14 may not be associated with RNase MRP. Furthermore, Rpp20 and Rpp25 appear to be associated with only a subset of RNase MRP particles, in contrast to hPop1, Rpp40, Rpp38, and Rpp30 (and possibly also hPop5), which are probably associated with all RNase MRP complexes. Our data are consistent with a transient association of Rpp20 and Rpp25 with RNase MRP, which may be inversely correlated to its involvement in pre-rRNA processing.
Directory of Open Access Journals (Sweden)
Mihailović Dragutin T.
2015-01-01
Full Text Available We propose novel metrics based on the Kolmogorov complexity for use in complex system behavior studies and time series analysis. We consider the origins of the Kolmogorov complexity and discuss its physical meaning. To get better insights into the nature of complex systems and time series analysis we introduce three novel measures based on the Kolmogorov complexity: (i the Kolmogorov complexity spectrum, (ii the Kolmogorov complexity spectrum highest value and (iii the overall Kolmogorov complexity. The characteristics of these measures have been tested using a generalized logistic equation. Finally, the proposed measures have been applied to different time series originating from: a model output (the biochemical substance exchange in a multi-cell system, four different geophysical phenomena (dynamics of: river flow, long term precipitation, indoor 222Rn concentration and UV radiation dose and the economy (stock price dynamics. The results obtained offer deeper insights into the complexity of system dynamics and time series analysis with the proposed complexity measures.
Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven
2016-04-26
The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.
Several Indicators of Critical Transitions for Complex Diseases Based on Stochastic Analysis.
Wang, Gang; Li, Yuanyuan; Zou, Xiufen
2017-01-01
Many complex diseases (chronic disease onset, development and differentiation, self-assembly, etc.) are reminiscent of phase transitions in a dynamical system: quantitative changes accumulate largely unnoticed until a critical threshold is reached, which causes abrupt qualitative changes of the system. Understanding such nonlinear behaviors is critical to dissect the multiple genetic/environmental factors that together shape the genetic and physiological landscape underlying basic biological functions and to identify the key driving molecules. Based on stochastic differential equation (SDE) model, we theoretically derive three statistical indicators, that is, coefficient of variation (CV), transformed Pearson's correlation coefficient (TPC), and transformed probability distribution (TPD), to identify critical transitions and detect the early-warning signals of the phase transition in complex diseases. To verify the effectiveness of these early-warning indexes, we use high-throughput data for three complex diseases, including influenza caused by either H3N2 or H1N1 and acute lung injury, to extract the dynamical network biomarkers (DNBs) responsible for catastrophic transition into the disease state from predisease state. The numerical results indicate that the derived indicators provide a data-based quantitative analysis for early-warning signals for critical transitions in complex diseases or other dynamical systems.
Stepanova, Anna; Shurubor, Yevgeniya; Valsecchi, Federica; Manfredi, Giovanni; Galkin, Alexander
2016-09-01
Mitochondrial Complex II is a key mitochondrial enzyme connecting the tricarboxylic acid (TCA) cycle and the electron transport chain. Studies of complex II are clinically important since new roles for this enzyme have recently emerged in cell signalling, cancer biology, immune response and neurodegeneration. Oxaloacetate (OAA) is an intermediate of the TCA cycle and at the same time is an inhibitor of complex II with high affinity (Kd~10(-8)M). Whether or not OAA inhibition of complex II is a physiologically relevant process is a significant, but still controversial topic. We found that complex II from mouse heart and brain tissue has similar affinity to OAA and that only a fraction of the enzyme in isolated mitochondrial membranes (30.2±6.0% and 56.4±5.6% in the heart and brain, respectively) is in the free, active form. Since OAA could bind to complex II during isolation, we established a novel approach to deplete OAA in the homogenates at the early stages of isolation. In heart, this treatment significantly increased the fraction of free enzyme, indicating that OAA binds to complex II during isolation. In brain the OAA-depleting system did not significantly change the amount of free enzyme, indicating that a large fraction of complex II is already in the OAA-bound inactive form. Furthermore, short-term ischemia resulted in a dramatic decline of OAA in tissues, but it did not change the amount of free complex II. Our data show that in brain OAA is an endogenous effector of complex II, potentially capable of modulating the activity of the enzyme.
Estimation and analysis of Galileo differential code biases
Li, Min; Yuan, Yunbin; Wang, Ningbo; Li, Zishen; Li, Ying; Huo, Xingliang
2017-03-01
When sensing the Earth's ionosphere using dual-frequency pseudorange observations of global navigation satellite systems (GNSS), the satellite and receiver differential code biases (DCBs) account for one of the main sources of error. For the Galileo system, limited knowledge is available about the determination and characteristic analysis of the satellite and receiver DCBs. To better understand the characteristics of satellite and receiver DCBs of Galileo, the IGGDCB (IGG, Institute of Geodesy and Geophysics, Wuhan, China) method is extended to estimate the satellite and receiver DCBs of Galileo, with the combined use of GPS and Galileo observations. The experimental data were collected from the Multi-GNSS Experiment network, covering the period of 2013-2015. The stability of both Galileo satellite and receiver DCBs over a time period of 36 months was thereby analyzed for the current state of the Galileo system. Good agreement of Galileo satellite DCBs is found between the IGGDCB-based DCB estimates and those from the German Aerospace Center (DLR), at the level of 0.22 ns. Moreover, high-level stability of the Galileo satellite DCB estimates is obtained over the selected time span (less than 0.25 ns in terms of standard deviation) by both IGGDCB and DLR algorithms. The Galileo receiver DCB estimates are also relatively stable for the case in which the receiver hardware device stays unchanged. It can also be concluded that the receiver DCB estimates are rather sensitive to the change of the firmware version and that the receiver antenna type has no great impact on receiver DCBs.
Differential proteome analysis of chikungunya virus infection on host cells.
Directory of Open Access Journals (Sweden)
Christina Li-Ping Thio
Full Text Available BACKGROUND: Chikungunya virus (CHIKV is an emerging mosquito-borne alphavirus that has caused multiple unprecedented and re-emerging outbreaks in both tropical and temperate countries. Despite ongoing research efforts, the underlying factors involved in facilitating CHIKV replication during early infection remains ill-characterized. The present study serves to identify host proteins modulated in response to early CHIKV infection using a proteomics approach. METHODOLOGY AND PRINCIPAL FINDINGS: The whole cell proteome profiles of CHIKV-infected and mock control WRL-68 cells were compared and analyzed using two-dimensional gel electrophoresis (2-DGE. Fifty-three spots were found to be differentially modulated and 50 were successfully identified by MALDI-TOF/TOF. Eight were significantly up-regulated and 42 were down-regulated. The mRNA expressions of 15 genes were also found to correlate with the corresponding protein expression. STRING network analysis identified several biological processes to be affected, including mRNA processing, translation, energy production and cellular metabolism, ubiquitin-proteasome pathway (UPP and cell cycle regulation. CONCLUSION/SIGNIFICANCE: This study constitutes a first attempt to investigate alteration of the host cellular proteome during early CHIKV infection. Our proteomics data showed that during early infection, CHIKV affected the expression of proteins that are involved in mRNA processing, host metabolic machinery, UPP, and cyclin-dependent kinase 1 (CDK1 regulation (in favour of virus survival, replication and transmission. While results from this study complement the proteomics results obtained from previous late host response studies, functional characterization of these proteins is warranted to reinforce our understanding of their roles during early CHIKV infection in humans.
The retinoblastoma-histone deacetylase 3 complex inhibits PPARgamma and adipocyte differentiation
DEFF Research Database (Denmark)
Fajas, Lluis; Egler, Viviane; Reiter, Raphael
2002-01-01
The retinoblastoma protein (RB) has previously been shown to facilitate adipocyte differentiation by inducing cell cycle arrest and enhancing the transactivation by the adipogenic CCAAT/enhancer binding proteins (C/EBP). We show here that the peroxisome proliferator-activated receptor gamma...
Solving Second-Order Ordinary Differential Equations without Using Complex Numbers
Kougias, Ioannis E.
2009-01-01
Ordinary differential equations (ODEs) is a subject with a wide range of applications and the need of introducing it to students often arises in the last year of high school, as well as in the early stages of tertiary education. The usual methods of solving second-order ODEs with constant coefficients, among others, rely upon the use of complex…
Growth of Logarithmic Derivatives and Their Applications in Complex Differential Equations
Directory of Open Access Journals (Sweden)
Zinelâabidine Latreuch
2014-01-01
of their logarithmic derivatives. We also give an estimate of the growth of the quotient of two differential polynomials generated by solutions of the equation f″+A(zf′+B(zf=0, where A(z and B(z are entire functions.
Ray, Sudipta; Saha, Sandeep
2016-11-01
Numerical solution of engineering problems with interfacial discontinuities requires exact implementation of the jump conditions else the accuracy deteriorates significantly; particularly, achieving spectral accuracy has been limited due to complex interface geometry and Gibbs phenomenon. We adopt a novel implementation of the immersed-interface method that satisfies the jump conditions at the interfaces exactly, in conjunction with the Chebyshev-collocation method. We consider solutions to linear second order ordinary and partial differential equations having a discontinuity in their zeroth and first derivatives across an interface traced by a complex curve. The solutions obtained demonstrate the ability of the proposed method to achieve spectral accuracy for discontinuous solutions across tortuous interfaces. The solution methodology is illustrated using two model problems: (i) an ordinary differential equation with jump conditions forced by an infinitely differentiable function, (ii) Poisson's equation having a discontinuous solution across interfaces that are ellipses of varying aspect ratio. The use of more polynomials in the direction of the major axis than the minor axis of the ellipse increases the convergence rate of the solution.
CSF neurofilament protein analysis in the differential diagnosis of ALS.
Reijn, T.S.M.; Abdo, W.; Schelhaas, H.J.; Verbeek, M.M.
2009-01-01
BACKGROUND: Cerebrospinal fluid (CSF) biomarkers have been studied to differentiate between patients with ALS and neurological controls, but not in comparison to clinically more relevant disorders mimicking ALS. METHODS: In this retrospective study, CSF concentrations of various brain-specific
Genome wide molecular analysis of minimally differentiated acute myeloid leukemia
Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline
2009-01-01
Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other
Genome wide molecular analysis of minimally differentiated acute myeloid leukemia
Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline
2009-01-01
Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other criteri
Graph theory and stability analysis of protein complex interaction networks.
Huang, Chien-Hung; Chen, Teng-Hung; Ng, Ka-Lok
2016-04-01
Protein complexes play an essential role in many biological processes. Complexes can interact with other complexes to form protein complex interaction network (PCIN) that involves in important cellular processes. There are relatively few studies on examining the interaction topology among protein complexes; and little is known about the stability of PCIN under perturbations. We employed graph theoretical approach to reveal hidden properties and features of four species PCINs. Two main issues are addressed, (i) the global and local network topological properties, and (ii) the stability of the networks under 12 types of perturbations. According to the topological parameter classification, we identified some critical protein complexes and validated that the topological analysis approach could provide meaningful biological interpretations of the protein complex systems. Through the Kolmogorov-Smimov test, we showed that local topological parameters are good indicators to characterise the structure of PCINs. We further demonstrated the effectiveness of the current approach by performing the scalability and data normalization tests. To measure the robustness of PCINs, we proposed to consider eight topological-based perturbations, which are specifically applicable in scenarios of targeted, sustained attacks. We found that the degree-based, betweenness-based and brokering-coefficient-based perturbations have the largest effect on network stability.
Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae
Uthe, Henriette; Vanselow, Jens T.; Schlosser, Andreas
2017-01-01
Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis. PMID:28240253
Shen, Jiacheng; Igathinathane, C; Yu, Manlu; Pothula, Anand Kumar
2015-06-01
Integral reaction heats of switchgrass, big bluestem, and corn stalks were determined using thermogravimetric analysis/differential scanning calorimetry (TGA/DSC). Iso-conversion differential reaction heats using TGA/DSC pyrolysis and combustion of biomass were not available, despite reports available on heats required and released. A concept of iso-conversion differential reaction heats was used to determine the differential reaction heats of each thermal characteristics segment of these materials. Results showed that the integral reaction heats were endothermic from 30 to 700°C for pyrolysis of switchgrass and big bluestem, but they were exothermic for corn stalks prior to 587°C. However, the integral reaction heats for combustion of the materials followed an endothermic to exothermic transition. The differential reaction heats of switchgrass pyrolysis were predominantly endothermic in the fraction of mass loss (0.0536-0.975), and were exothermic for corn stalks (0.0885-0.850) and big bluestem (0.736-0.919). Study results provided better insight into biomass thermal mechanism. Published by Elsevier Ltd.
Finite element analysis to model complex mitral valve repair.
Labrosse, Michel; Mesana, Thierry; Baxter, Ian; Chan, Vincent
2016-01-01
Although finite element analysis has been used to model simple mitral repair, it has not been used to model complex repair. A virtual mitral valve model was successful in simulating normal and abnormal valve function. Models were then developed to simulate an edge-to-edge repair and repair employing quadrangular resection. Stress contour plots demonstrated increased stresses along the mitral annulus, corresponding to the annuloplasty. The role of finite element analysis in guiding clinical practice remains undetermined.
Big and complex data analysis methodologies and applications
2017-01-01
This volume conveys some of the surprises, puzzles and success stories in high-dimensional and complex data analysis and related fields. Its peer-reviewed contributions showcase recent advances in variable selection, estimation and prediction strategies for a host of useful models, as well as essential new developments in the field. The continued and rapid advancement of modern technology now allows scientists to collect data of increasingly unprecedented size and complexity. Examples include epigenomic data, genomic data, proteomic data, high-resolution image data, high-frequency financial data, functional and longitudinal data, and network data. Simultaneous variable selection and estimation is one of the key statistical problems involved in analyzing such big and complex data. The purpose of this book is to stimulate research and foster interaction between researchers in the area of high-dimensional data analysis. More concretely, its goals are to: 1) highlight and expand the breadth of existing methods in...
Directory of Open Access Journals (Sweden)
Shaheed N. Huseen
2013-01-01
Full Text Available A modified q-homotopy analysis method (mq-HAM was proposed for solving nth-order nonlinear differential equations. This method improves the convergence of the series solution in the nHAM which was proposed in (see Hassan and El-Tawil 2011, 2012. The proposed method provides an approximate solution by rewriting the nth-order nonlinear differential equation in the form of n first-order differential equations. The solution of these n differential equations is obtained as a power series solution. This scheme is tested on two nonlinear exactly solvable differential equations. The results demonstrate the reliability and efficiency of the algorithm developed.
Simplified Worst-Case Analysis of Complex Systems
Pond, C. L.
1985-01-01
Statistical method avoids excessive computer time. Technique involves simplified Monte Carlo simulation of system with randomly chosen parameters and comparison of tolerance extremes of several of worst-case situations found. Resulting combination of tolerance extremes then used in detailed analysis - one that makes use of full complex nonlinear model capable of accurate simulations.
Mihailovic, Dragutin T; Nikolic-Djoric, Emilija; Arsenic, Ilija
2013-01-01
We have proposed novel measures based on the Kolmogorov complexity for use in complex system behavior studies and time series analysis. We have considered background of the Kolmogorov complexity and also we have discussed meaning of the physical as well as other complexities. To get better insights into the complexity of complex systems and time series analysis we have introduced the three novel measures based on the Kolmogorov complexity: (i) the Kolmogorov complexity spectrum, (ii) the Kolmogorov complexity spectrum highest value and (iii) the overall Kolmogorov complexity. The characteristics of these measures have been tested using a generalized logistic equation. Finally, the proposed measures have been applied on different time series originating from: the model output (the biochemical substance exchange in a multi-cell system), four different geophysical phenomena (dynamics of: river flow, long term precipitation, indoor 222Rn concentration and UV radiation dose) and economy (stock prices dynamics). Re...
Fractal Analysis Based on Hierarchical Scaling in Complex Systems
Chen, Yanguang
2016-01-01
A fractal is in essence a hierarchy with cascade structure, which can be described with a set of exponential functions. From these exponential functions, a set of power laws indicative of scaling can be derived. Hierarchy structure and spatial network proved to be associated with one another. This paper is devoted to exploring the theory of fractal analysis of complex systems by means of hierarchical scaling. Two research methods are utilized to make this study, including logic analysis method and empirical analysis method. The main results are as follows. First, a fractal system such as Cantor set is described from the hierarchical angle of view; based on hierarchical structure, three approaches are proposed to estimate fractal dimension. Second, the hierarchical scaling can be generalized to describe multifractals, fractal complementary sets, and self-similar curve such as logarithmic spiral. Third, complex systems such as urban system are demonstrated to be a self-similar hierarchy. The human settlements i...
Considering Complexity: Toward A Strategy for Non-linear Analysis
Directory of Open Access Journals (Sweden)
Ken Hatt
2009-01-01
Full Text Available This paper explores complexity and a strategy for non-linear analysis with a consistent ontological, epistemological and methodological orientation. Complexity is defined and approaches in the natural sciences, ecosystems research, discursive studies and the social sciences are reviewed. In social science, theoretical efforts associated with problems of social order (Luhmann, critical sociology (Byrne and post-structuralism (Cilliers as well as representative studies are examined. The review concludes that there is need for an approach that will address morphogenesis and facilitate analysis of multilateral mutual causal relations. The remainder of the paper approaches these matters by outlining Archer’s approach to morphogenesis, Maruyama’s morphogenetic casual-loop model of epistemology and illustrating Maruyama’s method for analysis which employs both positive and negative feedback loops. The result is a strategy based on morphogenetic causal loop models that can be used to analyze structuring and the connections through which structures may be reproduced or transformed.
Analysis of an operator-differential model for magnetostrictive energy harvesting
Davino, D.; Krejčí, P.; Pimenov, A.; Rachinskii, D.; Visone, C.
2016-10-01
We present a model of, and analysis of an optimization problem for, a magnetostrictive harvesting device which converts mechanical energy of the repetitive process such as vibrations of the smart material to electrical energy that is then supplied to an electric load. The model combines a lumped differential equation for a simple electronic circuit with an operator model for the complex constitutive law of the magnetostrictive material. The operator based on the formalism of the phenomenological Preisach model describes nonlinear saturation effects and hysteresis losses typical of magnetostrictive materials in a thermodynamically consistent fashion. We prove well-posedness of the full operator-differential system and establish global asymptotic stability of the periodic regime under periodic mechanical forcing that represents mechanical vibrations due to varying environmental conditions. Then we show the existence of an optimal solution for the problem of maximization of the output power with respect to a set of controllable parameters (for the periodically forced system). Analytical results are illustrated with numerical examples of an optimal solution.
Dynamic analysis of the human brain with complex cerebral sulci.
Tseng, Jung-Ge; Huang, Bo-Wun; Ou, Yi-Wen; Yen, Ke-Tien; Wu, Yi-Te
2016-07-03
The brain is one of the most vulnerable organs inside the human body. Head accidents often appear in daily life and are easy to cause different level of brain damage inside the skull. Once the brain suffered intense locomotive impact, external injuries, falls, or other accidents, it will result in different degrees of concussion. This study employs finite element analysis to compare the dynamic characteristics between the geometric models of an assumed simple brain tissue and a brain tissue with complex cerebral sulci. It is aimed to understand the free vibration of the internal brain tissue and then to protect the brain from injury caused by external influences. Reverse engineering method is used for a Classic 5-Part Brain (C18) model produced by 3B Scientific Corporation. 3D optical scanner is employed to scan the human brain structure model with complex cerebral sulci and imported into 3D graphics software to construct a solid brain model to simulate the real complex brain tissue. Obtaining the normal mode analysis by inputting the material properties of the true human brain into finite element analysis software, and then to compare the simplified and the complex of brain models.
DEFF Research Database (Denmark)
Kjeldsen, Marianne Kirstine; Bek, Dorte; Rasmussen, Erik Michael;
2009-01-01
A line probe assay (GenoType MTBC) was evaluated for species differentiation within the Mycobacterium tuberculosis complex (MTBC). We included 387 MTBC isolates, 43 IS6110 low-copy MTBC isolates, 28 clinical specimens with varying microscopy grade, and 30 isolates of non-tuberculous mycobacteria....... The assay was 100% specific and identified all 387 isolates and 98% of all IS6110 low-copy strains in concordance with the gold standard. The 2% discrepancy was caused by 1 isolate showing a faint restriction fragment length polymorphism (RFLP) pattern. The assay could provide specifies identification in 13...
Structural dynamic responses analysis applying differential quadrature method
Institute of Scientific and Technical Information of China (English)
PU Jun-ping; ZHENG Jian-jun
2006-01-01
Unconditionally stable higher-order accurate time step integration algorithms based on the differential quadrature method (DQM) for second-order initial value problems were applied and the quadrature rules of DQM, computing of the weighting coefficients and choices of sampling grid points were discussed. Some numerical examples dealing with the heat transfer problem, the second-order differential equation of imposed vibration of linear single-degree-of-freedom systems and double-degree-of-freedom systems, the nonlinear move differential equation and a beam forced by a changing load were computed,respectively. The results indicated that the algorithm can produce highly accurate solutions with minimal time consumption, and that the system total energy can remain conservative in the numerical computation.
A uranium (VI) complex: Synthesis, structural and thermal kinetic analysis
Goel, Nidhi
2016-08-01
A new complex [UO2(2,6-DNP)2phen] (1) (2,6-DNP = 2,6-dinitrophenol, phen = 1,10-phenanthroline) was synthesized, and identified by elemental analysis, IR, Powder XRD and single crystal X-ray crystallography. Crystal structure provides the abundant information's about the bonding and geometry around the U(VI) metal center. The thermal decomposition was studied by TG-DSC, and the kinetics of thermolysis was investigated by applying model fitting as well as isoconversional methods. Explosion delay measurement (De) was also evaluated to determine the response of this complex under the condition of rapid heating.
International Winter Workshop on Differential Equations and Numerical Analysis
Miller, John; Narasimhan, Ramanujam; Mathiazhagan, Paramasivam; Victor, Franklin
2016-01-01
This book offers an ideal introduction to singular perturbation problems, and a valuable guide for researchers in the field of differential equations. It also includes chapters on new contributions to both fields: differential equations and singular perturbation problems. Written by experts who are active researchers in the related fields, the book serves as a comprehensive source of information on the underlying ideas in the construction of numerical methods to address different classes of problems with solutions of different behaviors, which will ultimately help researchers to design and assess numerical methods for solving new problems. All the chapters presented in the volume are complemented by illustrations in the form of tables and graphs.
Optimization and Performance Analysis of Bulk-Driven Differential Amplifier
Directory of Open Access Journals (Sweden)
Antarpreet kaur
2014-04-01
Full Text Available In recent years, there has been an increasing demand for high-speed digital circuits at low power consumption. This paper presents a design of input stage of Operational Amplifier i.e cascode differential amplifier using a standard 65nm CMOS Technology.A comparison betweem gate-driven, bulk-driven and cascode bulk driven bulk-driven differential amplifier is described. The Results demonstrate that CMMR is 83.98 dB, 3-dB Bandwidth is 1.04 MHz. The circuit dissipate power of 28uWunder single supply of 1.0V.
CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences
Directory of Open Access Journals (Sweden)
Charalambos Chrysostomou
2015-01-01
Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.
Differential evolution based on the node degree of its complex network: Initial study
Skanderova, Lenka; Zelinka, Ivan
2016-06-01
In this paper is reported our progress in the synthesis of two partially different areas of research: complex networks and evolutionary computation. Ideas and results reported and mentioned here are based on our previous results and experiments. The main core of our participation is an evolutionary algorithm performance improvement by means of complex network use. Complex network is related to the evolutionary dynamics and reflect it. We report here our latest results as well as propositions on further research that is in process in our group (http://navy.cs.vsb.cz/). Only the main ideas and results are reported here, for more details it is recommended to read related literature of our previous research and results.
Uebelacker, James W.
This module considers ordinary linear differential equations with constant coefficients. The "complex method" used to find solutions is discussed, with numerous examples. The unit includes both problem sets and an exam, with answers provided for both. (MP)
Bound anions differentially stabilize multiprotein complexes in the absence of bulk solvent.
Han, Linjie; Hyung, Suk-Joon; Mayers, Jonathan J S; Ruotolo, Brandon T
2011-07-27
The combination of ion mobility separation with mass spectrometry is an emergent and powerful structural biology tool, capable of simultaneously assessing the structure, topology, dynamics, and composition of large protein assemblies within complex mixtures. An integral part of the ion mobility-mass spectrometry measurement is the ionization of intact multiprotein complexes and their removal from bulk solvent. This process, during which a substantial portion of protein structure and organization is likely to be preserved, imposes a foreign environment on proteins that may cause structural rearrangements to occur. Thus, a general means must be identified to stabilize protein structures in the absence of bulk solvent. Our approach to this problem involves the protection of protein complex structure through the addition of salts in solution prior to desorption/ionization. Anionic components of the added salts bind to the complex either in solution or during the electrospray process, and those that remain bound in the gas phase tend to have high gas phase acidities. The resulting 'shell' of counterions is able to carry away excess energy from the protein complex ion upon activation and can result in significant structural stabilization of the gas-phase protein assembly overall. By using ion mobility-mass spectrometry, we observe both the dissociation and unfolding transitions for four tetrameric protein complexes bound to populations of 12 different anions using collisional activation. The data presented here quantifies, for the first time, the influence of a large range of counterions on gas-phase protein structure and allows us to rank and classify counterions as structure stabilizers in the absence of bulk solvent. Our measurements indicate that tartrate, citrate, chloride, and nitrate anions are among the strongest stabilizers of gas-phase protein structure identified in this screen. The rank order determined by our data is substantially different when compared to
Indian Academy of Sciences (India)
O P Singh; Geeta Goswami; N Nanda; K Raghavendra; D Chandra; S K Subbarao
2004-09-01
Anopheles culicifacies, the principal vector of malaria in India, is a complex of five cryptic species which are morphologically indistinguishable at any stage of life. In view of the practical difficulties associated with classical cytotaxonomic method for the identification of members of the complex, an allele-specific polymerase chain reaction (ASPCR) assay targeted to the D3 domain of 28S ribosomal DNA was developed. The assay discriminates An. culicifacies species A and D from species B, C and E. The assay was validated using chromosomally-identified specimens of An. culicifacies from different geographical regions of India representing different sympatric associations. The assay correctly differentiates species A and D from species B, C and E. The possible use of this diagnostic assay in disease vector control programmes is discussed.
Partial differential equations with variable exponents variational methods and qualitative analysis
Radulescu, Vicentiu D
2015-01-01
Partial Differential Equations with Variable Exponents: Variational Methods and Qualitative Analysis provides researchers and graduate students with a thorough introduction to the theory of nonlinear partial differential equations (PDEs) with a variable exponent, particularly those of elliptic type. The book presents the most important variational methods for elliptic PDEs described by nonhomogeneous differential operators and containing one or more power-type nonlinearities with a variable exponent. The authors give a systematic treatment of the basic mathematical theory and constructive meth
Free Vibration Analysis of Laminated Composite Beams Using Differential Quadrature Method
Institute of Scientific and Technical Information of China (English)
冯丽娟; 钟宏志; 郝照平; 吴德隆
2002-01-01
A higher-order theory for laminated composite beams is used to study the free vibration of laminated composite beams, and the differential quadrature method is employed to obtain the numerical solution of the governing differential equations. Free vibration analysis of beams with rectangular cross-section for various combinations of end conditions is studied. The results show that the differential quadrature method is reliable and accurate compared with other available results.
Probabilistic Analysis Techniques Applied to Complex Spacecraft Power System Modeling
Hojnicki, Jeffrey S.; Rusick, Jeffrey J.
2005-01-01
Electric power system performance predictions are critical to spacecraft, such as the International Space Station (ISS), to ensure that sufficient power is available to support all the spacecraft s power needs. In the case of the ISS power system, analyses to date have been deterministic, meaning that each analysis produces a single-valued result for power capability because of the complexity and large size of the model. As a result, the deterministic ISS analyses did not account for the sensitivity of the power capability to uncertainties in model input variables. Over the last 10 years, the NASA Glenn Research Center has developed advanced, computationally fast, probabilistic analysis techniques and successfully applied them to large (thousands of nodes) complex structural analysis models. These same techniques were recently applied to large, complex ISS power system models. This new application enables probabilistic power analyses that account for input uncertainties and produce results that include variations caused by these uncertainties. Specifically, N&R Engineering, under contract to NASA, integrated these advanced probabilistic techniques with Glenn s internationally recognized ISS power system model, System Power Analysis for Capability Evaluation (SPACE).
An Analysis on the Differentiation between Diglossia and Bilingualism
Institute of Scientific and Technical Information of China (English)
ZHANG Ying
2014-01-01
Despite a hot and sensitive topic in China, the practice and education of bilingualism has been misunderstood in some areas because people have little sense of it. This paper is to differentiate the diglossia and the bilingualism to make it clear that it is important and necessary to put into practice the bilingualism and bilingual education in parts of China.
Thermogravimetric and differential thermal analysis of potassium bicarbonate contaminated cellulose
A. Broido
1966-01-01
When samples undergo a complicated set of simultaneous and sequential reactions, as cellulose does on heating, results of thermogravimetric and differential thermal analyses are difficult to interpret. Nevertheless, careful comparison of pure and contaminated samples, pyrolyzed under identical conditions, can yield useful information. In these experiments TGA and DTA...
Analysis of Differential Item Functioning in the NAEP History Assessment.
Zwick, Rebecca; Ercikan, Kadriye
The Mantel-Haenszel approach for investigating differential item functioning (DIF) was applied to U.S. history items that were administered as part of the National Assessment of Educational Progress (NAEP). DIF analyses were based on the responses of 7,743 students in grade 11. On some items, Blacks, Hispanics, and females performed more poorly…
Stability analysis of a class of fractional delay differential equations
Indian Academy of Sciences (India)
Sachin B Bhalekar
2013-08-01
In this paper we analyse stability of nonlinear fractional order delay differential equations of the form $D^{} y(t) = af(y(t - )) - {\\text{by}} (t)$, where $D^{}$ is a Caputo fractional derivative of order 0 < ≤ 1. We describe stability regions using critical curves. To explain the proposed theory, we discuss fractional order logistic equation with delay.
Differential Protein Network Analysis of the Immune Cell Lineage
Directory of Open Access Journals (Sweden)
Trevor Clancy
2014-01-01
Full Text Available Recently, the Immunological Genome Project (ImmGen completed the first phase of the goal to understand the molecular circuitry underlying the immune cell lineage in mice. That milestone resulted in the creation of the most comprehensive collection of gene expression profiles in the immune cell lineage in any model organism of human disease. There is now a requisite to examine this resource using bioinformatics integration with other molecular information, with the aim of gaining deeper insights into the underlying processes that characterize this immune cell lineage. We present here a bioinformatics approach to study differential protein interaction mechanisms across the entire immune cell lineage, achieved using affinity propagation applied to a protein interaction network similarity matrix. We demonstrate that the integration of protein interaction networks with the most comprehensive database of gene expression profiles of the immune cells can be used to generate hypotheses into the underlying mechanisms governing the differentiation and the differential functional activity across the immune cell lineage. This approach may not only serve as a hypothesis engine to derive understanding of differentiation and mechanisms across the immune cell lineage, but also help identify possible immune lineage specific and common lineage mechanism in the cells protein networks.
Progress toward the analysis of complex propulsion installation flow phenomenon
Kern, P. R. A.; Hopcroft, R. G.
1983-01-01
A trend toward replacement of parametric model testing with parametric analysis for the design of aircraft is driven by the rapidly escalating cost of wind tunnel testing, the increasing availability of large fast computers, and powerful numerical flow algorithms. In connection with the complex flow phenomena characteristic of propulsion installations, it is now necessary to employ both parametric analysis and testing for design procedures. Powerful flow analysis techniques are available to predict local flow phenomena. However, the employment of these techniques is very expensive. It is, therefore, necessary to link these analyses with less powerful and less expensive procedures for an accurate analysis of propulsion installation flowfields. However, the interfacing and coupling processes needed are not available. The present investigation is concerned with progress made regarding the development of suitable linking methods. Attention is given to methods of analysis for predicting the flow around a nacelle coupled to a highly swept wing.
Complexity of carbon market from multi-scale entropy analysis
Fan, Xinghua; Li, Shasha; Tian, Lixin
2016-06-01
Complexity of carbon market is the consequence of economic dynamics and extreme social political events in global carbon markets. The multi-scale entropy can measure the long-term structures in the daily price return time series. By using multi-scale entropy analysis, we explore the complexity of carbon market and mean reversion trend of daily price return. The logarithmic difference of data Dec16 from August 6, 2010 to May 22, 2015 is selected as the sample. The entropy is higher in small time scale, while lower in large. The dependence of the entropy on the time scale reveals the mean reversion of carbon prices return in the long run. A relatively great fluctuation over some short time period indicates that the complexity of carbon market evolves consistently with economic development track and the events of international climate conferences.
Nostradamus 2014 prediction, modeling and analysis of complex systems
Suganthan, Ponnuthurai; Chen, Guanrong; Snasel, Vaclav; Abraham, Ajith; Rössler, Otto
2014-01-01
The prediction of behavior of complex systems, analysis and modeling of its structure is a vitally important problem in engineering, economy and generally in science today. Examples of such systems can be seen in the world around us (including our bodies) and of course in almost every scientific discipline including such “exotic” domains as the earth’s atmosphere, turbulent fluids, economics (exchange rate and stock markets), population growth, physics (control of plasma), information flow in social networks and its dynamics, chemistry and complex networks. To understand such complex dynamics, which often exhibit strange behavior, and to use it in research or industrial applications, it is paramount to create its models. For this purpose there exists a rich spectrum of methods, from classical such as ARMA models or Box Jenkins method to modern ones like evolutionary computation, neural networks, fuzzy logic, geometry, deterministic chaos amongst others. This proceedings book is a collection of accepted ...
The differential effects of task complexity on domain-specific and peer assessment skills
Sluijsmans, Dominique; Zundert, Marjo van; Könings, K.; Merriënboer, J.J.G. van
2012-01-01
In this study the relationship between domain-specific skills and peer assessment skills as a function of task complexity is investigated. We hypothesised that peer assessment skills were superposed on domain-specific skills and will therefore suffer more when higher cognitive load is induced by inc
Differential regulation of adhesion complex turnover by ROCK1 and ROCK2.
Directory of Open Access Journals (Sweden)
Frances E Lock
Full Text Available BACKGROUND: ROCK1 and ROCK2 are serine/threonine kinases that function downstream of the small GTP-binding protein RhoA. Rho signalling via ROCK regulates a number of cellular functions including organisation of the actin cytoskeleton, cell adhesion and cell migration. METHODOLOGY/PRINCIPAL FINDINGS: In this study we use RNAi to specifically knockdown ROCK1 and ROCK2 and analyse their role in assembly of adhesion complexes in human epidermal keratinocytes. We observe that loss of ROCK1 inhibits signalling via focal adhesion kinase resulting in a failure of immature adhesion complexes to form mature stable focal adhesions. In contrast, loss of ROCK2 expression results in a significant reduction in adhesion complex turnover leading to formation of large, stable focal adhesions. Interestingly, loss of either ROCK1 or ROCK2 expression significantly impairs cell migration indicating both ROCK isoforms are required for normal keratinocyte migration. CONCLUSIONS: ROCK1 and ROCK2 have distinct and separate roles in adhesion complex assembly and turnover in human epidermal keratinocytes.
Debourgogne, A.; Gueidan, C.; Hennequin, C.; Contet-Audonneau, N.; de Hoog, S.; Machouart, M.
2010-01-01
Fungi belonging to the Fusarium solani Species Complex (FSSC) are well known plant pathogens. In addition to being the causative agent of some superficial infections, FSSC has recently emerged as a group of common opportunistic moulds, mainly in patients with haematological malignancies. Molecular
Directory of Open Access Journals (Sweden)
Jeongah Yoon
Full Text Available Cell growth critically depends on signalling pathways whose regulation is the focus of intense research. Without utilizing a priori knowledge of the relative importance of pathway components, we have applied in silico computational methods to the EGF-induced MAPK cascade. Specifically, we systematically perturbed the entire parameter space, including initial conditions, using a Monte Carlo approach, and investigate which protein components or kinetic reaction steps contribute to the differentiation of ERK responses. The model, based on previous work by Brightman and Fell (2000, is composed of 28 reactions, 27 protein molecules, and 48 parameters from both mass action and Michaelis-Menten kinetics. Our multi-parametric systems analysis confirms that Raf inactivation is one of the key steps regulating ERK responses to be either transient or sustained. Furthermore, the results of amplitude-differential ERK phosphorylations within the transient case are mainly attributed to the balance between activation and inactivation of Ras while duration-differential ERK responses for the sustained case are, in addition to Ras, markedly affected by dephospho-/phosphorylation of both MEK and ERK. Our sub-module perturbations showed that MEK and ERK's contribution to this differential ERK activation originates from fluctuations in intermediate pathway module components such as Ras and Raf, implicating a cooperative regulatory mode among the key components. The initial protein concentrations of corresponding reactions such as Ras, GAP, and Raf also influence the distinct signalling outputs of ERK activation. We then compare these results with those obtained from a single-parametric perturbation approach using an overall state sensitivity (OSS analysis. The OSS findings indicate a more pronounced role of ERK's inhibitory feedback effect on catalysing the dissociation of the SOS complex. Both approaches reveal the presence of multiple specific reactions involved in
Linear systems approach to analysis of complex dynamic behaviours in biochemical networks.
Schmidt, H; Jacobsen, E W
2004-06-01
Central functions in the cell are often linked to complex dynamic behaviours, such as sustained oscillations and multistability, in a biochemical reaction network. Determination of the specific mechanisms underlying such behaviours is important, e.g. to determine sensitivity, robustness, and modelling requirements of given cell functions. In this work we adopt a systems approach to the analysis of complex behaviours in intracellular reaction networks, described by ordinary differential equations with known kinetic parameters. We propose to decompose the overall system into a number of low complexity subsystems, and consider the importance of interactions between these in generating specific behaviours. Rather than analysing the network in a state corresponding to the complex non-linear behaviour, we move the system to the underlying unstable steady state, and focus on the mechanisms causing destabilisation of this steady state. This is motivated by the fact that all complex behaviours in unforced systems can be traced to destabilisation (bifurcation) of some steady state, and hence enables us to use tools from linear system theory to qualitatively analyse the sources of given network behaviours. One important objective of the present study is to see how far one can come with a relatively simple approach to the analysis of highly complex biochemical networks. The proposed method is demonstrated by application to a model of mitotic control in Xenopus frog eggs, and to a model of circadian oscillations in Drosophila. In both examples we are able to identify the subsystems, and the related interactions, which are instrumental in generating the observed complex non-linear behaviours.
KatG protein: A novel marker for differential diagnosis of Myobacterium avium complex infection
Directory of Open Access Journals (Sweden)
Gupta K
2010-01-01
Full Text Available Purpose: Biochemical or nucleic acid based diagnostic techniques for MAC infection are unsatisfactory. This study aims to identify and evaluate M. avium secretory protein(s of diagnostic potential, so as to develop a rapid and simple method for diagnosis of MAC infection. Material and Methods: Initially, a specific protein band of ~80-85 kDa was recognised by differential immunoblotting; which was subjected to anion exchange column chromatography for purification of proteins. After fractionisation using SDS-PAGE and electroelution, blast search was carried out. Further immunoreactivity studies were done with M. avium and Mtb infected mice sera. Clinical utilisation of separated protein was evaluated by conducting indirect ELISA with serum samples from mycobacterial infected patients. Results: A specific 81.6 kDa protein, shown to be catalase-peroxidase protein (KatG by blast search was separated. Immunoreactivity studies of purified KatG proteins with mice sera confirmed it to be specific for M. avium infection. Indirect ELISA with patient samples further confirmed it to be M. avium infection specific. Conclusion: KatG protein is specifically recognised by MAC patients and can be used as a marker for simple and rapid ELISA based tests for differential diagnosis of M. avium infection.
Lee, Seungkoo; Bang, Seunghyun; Song, Kyuyoung; Lee, Inchul
2006-10-01
The majority of colon cancers develop from pre-existing adenomas. We analyzed the expression profiles in the sequence of normal colon crypts, adenomas and early-stage carcinomas using microdissected cells from tubular adenomas with foci of malignant transformation. Differentially expressed genes were detected between normal-adenoma and adenoma-carcinoma, and were grouped according to the patterns of expression changes in the sequence. Down-regulated genes in the sequence included PLA2G2A, TSPAN1, PDCD4, FCGBP, AATK, EPLIN, FABP1, AGR2, MTUS1, TSC1, galectin 4 and MT1F. PLA2G2A has been shown to suppress colon tumorigenesis in mice, but the pathobiological role in humans has been controversial. Our data showed continuous down-regulation of PLA2G2A in the sequence supporting an implication in human colon cancer. Tumor suppressor and/ or proapoptotic activities have also been reported in other genes. Up-regulated genes included ribosomal proteins, IER3 and TPR. TGF-beta2 and matrix metalloproteinase 23B were up-regulated in carcinoma but not in adenoma, supporting the pathobiological roles in malignant transformation. Differentially expressed genes partly coincided with those in the adenoma-carcinoma sequence of the stomach, which was published previously, suggesting a partial overlap between the adenoma-carcinoma sequences of the colon and stomach.
Sumantran, Venil N; Mishra, Pratik; Sudhakar, N
2015-04-01
A new hallmark of cancer involves acquisition of a lipogenic phenotype which promotes tumorigenesis. Little is known about lipid metabolism in melanomas. Therefore, we used BRB (Biometrics Research Branch) class comparison tool with multivariate analysis to identify differentially expressed genes in human cutaneous melanomas, compared with benign nevi and normal skin derived from the microarray dataset (GDS1375). The methods were validated by identifying known melanoma biomarkers (CITED1, FGFR2, PTPRF, LICAM, SPP1 and PHACTR1) in our results. Eighteen genes regulating metabolism of fatty acids, lipid second messengers and gangliosides were 2-9 fold upregulated in melanomas of GDS-1375. Out of the 18 genes, 13 were confirmed by KEGG pathway analysis and 10 were also significantly upregulated in human melanoma cell lines of NCI-60 Cell Miner database. Results showed that melanomas upregulated PPARGC1A transcription factor and its target genes regulating synthesis of fatty acids (SCD) and complex lipids (FABP3 and ACSL3). Melanoma also upregulated genes which prevented lipotoxicity (CPT2 and ACOT7) and regulated lipid second messengers, such as phosphatidic acid (AGPAT-4, PLD3) and inositol triphosphate (ITPKB, ITPR3). Genes for synthesis of pro-tumorigenic GM3 and GD3 gangliosides (UGCG, HEXA, ST3GAL5 and ST8SIA1) were also upregulated in melanoma. Overall, the microarray analysis of GDS-1375 dataset indicated that melanomas can become lipogenic by upregulating genes, leading to increase in fatty acid metabolism, metabolism of specific lipid second messengers, and ganglioside synthesis.
SPR imaging based electronic tongue via landscape images for complex mixture analysis.
Genua, Maria; Garçon, Laurie-Amandine; Mounier, Violette; Wehry, Hillary; Buhot, Arnaud; Billon, Martial; Calemczuk, Roberto; Bonnaffé, David; Hou, Yanxia; Livache, Thierry
2014-12-01
Electronic noses/tongues (eN/eT) have emerged as promising alternatives for analysis of complex mixtures in the domain of food and beverage quality control. We have recently developed an electronic tongue by combining surface plasmon resonance imaging (SPRi) with an array of non-specific and cross-reactive receptors prepared by simply mixing two small molecules in varying and controlled proportions and allowing the mixtures to self-assemble on the SPRi prism surface. The obtained eT generated novel and unique 2D continuous evolution profiles (CEPs) and 3D continuous evolution landscapes (CELs) based on which the differentiation of complex mixtures such as red wine, beer and milk were successful. The preliminary experiments performed for monitoring the deterioration of UHT milk demonstrated its potential for quality control applications. Furthermore, the eT exhibited good repeatability and stability, capable of operating after a minimum storage period of 5 months.
Outlier-resilient complexity analysis of heartbeat dynamics
Lo, Men-Tzung; Chang, Yi-Chung; Lin, Chen; Young, Hsu-Wen Vincent; Lin, Yen-Hung; Ho, Yi-Lwun; Peng, Chung-Kang; Hu, Kun
2015-03-01
Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals with outliers remains a major barrier for translating this novel concept of nonlinear dynamic theory to clinical practice. Here we propose a new approach to estimate the complexity in a signal by analyzing the irregularity of the sign time series of its coarse-grained time series at different time scales. Using surrogate data, we show that the method can reliably assess the complexity in noisy data while being highly resilient to outliers. We further apply this method to the analysis of human heartbeat recordings. Without removing any outliers due to ectopic beats, the method is able to detect a degradation of cardiac control in patients with congestive heart failure and a more degradation in critically ill patients whose life continuation relies on extracorporeal membrane oxygenator (ECMO). Moreover, the derived complexity measures can predict the mortality of ECMO patients. These results indicate that the proposed method may serve as a promising tool for monitoring cardiac function of patients in clinical settings.
Marín-Buera, Lorena; García-Bartolomé, Alberto; Morán, María; López-Bernardo, Elia; Cadenas, Susana; Hidalgo, Beatriz; Sánchez, Ricardo; Seneca, Sara; Arenas, Joaquín; Martín, Miguel A; Ugalde, Cristina
2015-01-15
We have analyzed the cellular pathways and metabolic adaptations that take place in primary skin fibroblasts from patients with mutations in BCS1L, a major genetic cause of mitochondrial complex III enzyme deficiency. Mutant fibroblasts exhibited low oxygen consumption rates and intracellular ATP levels, indicating that the main altered molecular event probably is a limited respiration-coupled ATP production through the OXPHOS system. Two-dimensional DIGE and MALDI-TOF/TOF mass spectrometry analyses unambiguously identified 39 proteins whose expression was significantly altered in complex III-deficient fibroblasts. Extensive statistical and cluster analyses revealed a protein profile characteristic for the BCS1L mutant fibroblasts that included alterations in energy metabolism, cell signaling and gene expression regulation, cytoskeleton formation and maintenance, and intracellular stress responses. The physiological validation of the predicted functional adaptations of human cultured fibroblasts to complex III deficiency confirmed the up-regulation of glycolytic enzyme activities and the accumulation of branched-chain among other amino acids, suggesting the activation of anaerobic glycolysis and cellular catabolic states, in particular protein catabolism, together with autophagy as adaptive responses to mitochondrial respiratory chain dysfunction and ATP deficiency. Our data point to an overall metabolic and genetic reprogramming that could contribute to explain the clinical manifestations of complex III deficiency in patients. Despite considerable knowledge about their genetic origins, the pathophysiological mechanisms that contribute to the clinical manifestations of mitochondrial disorders remain poorly understood. We have investigated the molecular pathways and metabolic adaptations that take place in primary skin fibroblasts from patients with mutations in the BCS1L gene, a primary cause of mitochondrial complex III enzyme deficiency. Two-dimensional DIGE
Modeling data irregularities and structural complexities in data envelopment analysis
Zhu, Joe
2007-01-01
In a relatively short period of time, Data Envelopment Analysis (DEA) has grown into a powerful quantitative, analytical tool for measuring and evaluating performance. It has been successfully applied to a whole variety of problems in many different contexts worldwide. This book deals with the micro aspects of handling and modeling data issues in modeling DEA problems. DEA's use has grown with its capability of dealing with complex "service industry" and the "public service domain" types of problems that require modeling of both qualitative and quantitative data. This handbook treatment deals with specific data problems including: imprecise or inaccurate data; missing data; qualitative data; outliers; undesirable outputs; quality data; statistical analysis; software and other data aspects of modeling complex DEA problems. In addition, the book will demonstrate how to visualize DEA results when the data is more than 3-dimensional, and how to identify efficiency units quickly and accurately.
Complexity, Analysis and Control of Singular Biological Systems
Zhang, Qingling; Zhang, Xue
2012-01-01
Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...
Analysis and perturbation of degree correlation in complex networks
Xiang, Ju; Hu, Tao; Zhang, Yan
2015-01-01
Degree correlation is an important topological property common to many real-world networks. In this paper, the statistical measures for characterizing the degree correlation in networks are investigated analytically. We give an exact proof of the consistency for the statistical measures, reveal the general linear relation in the degree correlation, which provide a simple and interesting perspective on the analysis of the degree correlation in complex networks. By using the general linear analysis, we investigate the perturbation of the degree correlation in complex networks caused by the addition of few nodes and the rich club. The results show that the assortativity of homogeneous networks such as the ER graphs is easily to be affected strongly by the simple structural changes, while it has only slight variation for heterogeneous networks with broad degree distribution such as the scale-free networks. Clearly, the homogeneous networks are more sensitive for the perturbation than the heterogeneous networks.
Synthesis, molecular spectroscopy and thermal analysis of some cefepime complexes
Masoud, Mamdouh S.; Ali, Alaa E.; Ghareeb, Doaa A.; Nasr, Nessma M.
2016-03-01
The metal complexes of cefepime with Cr (III), Mn (II), Fe (III), Co (II), Cu (II), Zn (II), Cd (II), Hg (II) and mixed metals (Fe, Ni) or (Cu, Fe) were synthesized, the suggested structures of the complexes are based on the results of the elemental analysis, infrared, UV-visible, mass and HNMR spectra, effective magnetic moment as well as the thermal analysis (DTA, TGA & DSC) and characterized by energy dispersive x-ray (EDX) and scanning electron microscopy (SEM). The results obtained suggested that cefepime reacted with metal ions as bidentate ligand through the nitrogen of the β-lactone thiozolidine ring and carboxylate ion forming a five membered ring. The kinetic thermodynamic parameters were estimated from the DTA curves.
Transonic analysis of complex configurations using TRANAIR program
Saaris, G. R.; Gilkey, R. D.; Smit, K. L.; Tinoco, E. N.
1989-01-01
The application of a three-dimensional transonic flow analysis method, TRANAIR, is explored from the point of view of a user. Detailed features of the program are outlined to give a better understanding of capability. Numerous results are presented to show some of the complex configurations which have been analyzed. In particular, examples are provided which show the application to turbofan engine installation on transport aircraft.
Coupled dark energy: a dynamical analysis with complex scalar field
Energy Technology Data Exchange (ETDEWEB)
Landim, Ricardo C.G. [Universidade de Sao Paulo, Instituto de Fisica, Caixa Postal 66318, Sao Paulo, SP (Brazil)
2016-01-15
The dynamical analysis for coupled dark energy with dark matter is presented, where a complex scalar field is taken into account and it is considered in the presence of a barothropic fluid. We consider three dark-energy candidates: quintessence, phantom, and tachyon. The critical points are found and their stabilities analyzed, leading to the three cosmological eras (radiation, matter, and dark energy), for a generic potential. The results presented here extend the previous analyses found in the literature. (orig.)
Complex signal amplitude analysis for complete fusion nuclear reaction products
Tsyganov, Yu S
2015-01-01
A complex analysis has been performed on the energy amplitude signals corresponding to events of Z=117 element measured in the 249Bk+48Ca complete fusion nuclear reaction. These signals were detected with PIPS position sensitive detector. The significant values of pulse height defect both for recoils (ER) and fission fragments (FF) were measured. Comparison with the computer simulations and empirical formulae has been performed both for ER and FF signals.
Differential patterns of cortical activation as a function of fluid reasoning complexity.
Perfetti, Bernardo; Saggino, Aristide; Ferretti, Antonio; Caulo, Massimo; Romani, Gian Luca; Onofrj, Marco
2009-02-01
Fluid intelligence (gf) refers to abstract reasoning and problem solving abilities. It is considered a human higher cognitive factor central to general intelligence (g). The regions of the cortex supporting gf have been revealed by recent bioimaging studies and valuable hypothesis on the neural correlates of individual differences have been proposed. However, little is known about the interaction between individual variability in gf and variation in cortical activity following task complexity increase. To further investigate this, two samples of participants (high-IQ, N = 8; low-IQ, N = 10) with significant differences in gf underwent two reasoning (moderate and complex) tasks and a control task adapted from the Raven progressive matrices. Functional magnetic resonance was used and the recorded signal analyzed between and within the groups. The present study revealed two opposite patterns of neural activity variation which were probably a reflection of the overall differences in cognitive resource modulation: when complexity increased, high-IQ subjects showed a signal enhancement in some frontal and parietal regions, whereas low-IQ subjects revealed a decreased activity in the same areas. Moreover, a direct comparison between the groups' activation patterns revealed a greater neural activity in the low-IQ sample when conducting moderate task, with a strong involvement of medial and lateral frontal regions thus suggesting that the recruitment of executive functioning might be different between the groups. This study provides evidence for neural differences in facing reasoning complexity among subjects with different gf level that are mediated by specific patterns of activation of the underlying fronto-parietal network.
Calculation of photoionization differential cross sections using complex Gauss-type orbitals.
Matsuzaki, Rei; Yabushita, Satoshi
2017-09-05
Accurate theoretical calculation of photoelectron angular distributions for general molecules is becoming an important tool to image various chemical reactions in real time. We show in this article that not only photoionization total cross sections but also photoelectron angular distributions can be accurately calculated using complex Gauss-type orbital (cGTO) basis functions. Our method can be easily combined with existing quantum chemistry techniques including electron correlation effects, and applied to various molecules. The so-called two-potential formula is applied to represent the transition dipole moment from an initial bound state to a final continuum state in the molecular coordinate frame. The two required continuum functions, the zeroth-order final continuum state and the first-order wave function induced by the photon field, have been variationally obtained using the complex basis function method with a mixture of appropriate cGTOs and conventional real Gauss-type orbitals (GTOs) to represent the continuum orbitals as well as the remaining bound orbitals. The complex orbital exponents of the cGTOs are optimized by fitting to the outgoing Coulomb functions. The efficiency of the current method is demonstrated through the calculations of the asymmetry parameters and molecular-frame photoelectron angular distributions of H2+ and H2 . In the calculations of H2 , the static exchange and random phase approximations are employed, and the dependence of the results on the basis functions is discussed. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Analysis III analytic and differential functions, manifolds and Riemann surfaces
Godement, Roger
2015-01-01
Volume III sets out classical Cauchy theory. It is much more geared towards its innumerable applications than towards a more or less complete theory of analytic functions. Cauchy-type curvilinear integrals are then shown to generalize to any number of real variables (differential forms, Stokes-type formulas). The fundamentals of the theory of manifolds are then presented, mainly to provide the reader with a "canonical'' language and with some important theorems (change of variables in integration, differential equations). A final chapter shows how these theorems can be used to construct the compact Riemann surface of an algebraic function, a subject that is rarely addressed in the general literature though it only requires elementary techniques. Besides the Lebesgue integral, Volume IV will set out a piece of specialized mathematics towards which the entire content of the previous volumes will converge: Jacobi, Riemann, Dedekind series and infinite products, elliptic functions, classical theory of modular fun...
Directory of Open Access Journals (Sweden)
Xiubi Wu
2015-05-01
Full Text Available The classical problem of finding conditions on the entire coefficients A(z and B(z guaranteeing that all nontrivial solutions of $f''+A(zf'+B(zf=0$ are of infinite order is discussed. Two distinct approaches are used. In the first approach the coefficient A(z itself is a solution of a differential equation $w''+P(zw=0$, where P(z is a polynomial. This assumption yields stability on the behavior of A(z via Hille's classical method on asymptotic integration. In this case A(z is a special function of which the Airy integral is one example. The second approach involves extremal functions. It is assumed that either A(z is extremal for Yang's inequality or B(z is extremal for Denjoy's conjecture. A combination of these two approaches is also discussed.
Stability analysis of linear multistep methods for delay differential equations
Directory of Open Access Journals (Sweden)
V. L. Bakke
1986-01-01
Full Text Available Stability properties of linear multistep methods for delay differential equations with respect to the test equation y′(t=ay(λt+by(t, t≥0,0<λ<1, are investigated. It is known that the solution of this equation is bounded if and only if |a|<−b and we examine whether this property is inherited by multistep methods with Lagrange interpolation and by parametrized Adams methods.
A stability analysis for a semilinear parabolic partial differential equation
Chafee, N.
1973-01-01
The parabolic partial differential equation considered is u sub t = u sub xx + f(u), where minus infinity x plus infinity and o t plus infinity. Under suitable hypotheses pertaining to f, a class of initial data is exhibited: phi(x), minus infinity x plus infinity, for which the corresponding solutions u(x,t) appraoch zero as t approaches the limit of plus infinity. This convergence is uniform with respect to x on any compact subinterval of the real axis.
Microarray expression analysis of epithelial ovarian cancer with distinct differentiation
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
To identify gene expression profiling in epithelial ovarian cancer and to explore its correlation with histopathology characterization and prognosis. Gene expression profiles were generated from 10 human ovarian frozen tissue specimens using Agilent Human 1A microarrays. Strikingly, clear differences of gene expression patterns were observed in ovarian cancer as compared to normal tissues. Unique gene profiles were observed in moderately and poorly differentiated epithelial ovarian cancer. It is concluded that different histopathology characterization likely exists extensive molecular heterogeneity.
Triangular Differential Quadrature for Bending Analysis of Reissner Plates with Curved Boundaries
Institute of Scientific and Technical Information of China (English)
华永霞; 钟宏志
2003-01-01
The recently proposed concept of the triangular differential quadrature method (TDQM) is applied to the bending analysis of Reissner plates with various curvilinear geometries subjected to various combinations of boundary conditions. A unit isosceles right triangle is used as the standard triangle for all the derivatives expressed using the triangular differential quadrature rule. Geometric transformations are introduced using basis functions to determine the weighting coefficients for the triangular differential quadrature to map an arbitrary curvilinear triangle into the standard triangle. The triangular differential quadrature method provides good accuracy and rapid convergence relative to other available exact and numerical results.
[SADE] A Maple package for the Symmetry Analysis of Differential Equations
Filho, Tarcí sio M Rocha
2010-01-01
We present the package SADE (Symmetry Analysis of Differential Equations) for the determination of symmetries and related properties of systems of differential equations. The main methods implemented are: Lie, nonclassical, Lie-B\\"acklund and potential symmetries, invariant solutions, first-integrals, N\\"other theorem for both discrete and continuous systems, solution of ordinary differential equations, reduction of order or dimension using Lie symmetries, classification of differential equations, Casimir invariants, and the quasi-polynomial formalism for ODE's (previously implemented in the package QPSI by the authors) for the determination of quasi-polynomial first-integrals, Lie symmetries and invariant surfaces. Examples of use of the package are given.
Lie group analysis method for two classes of fractional partial differential equations
Chen, Cheng; Jiang, Yao-Lin
2015-09-01
In this paper we deal with two classes of fractional partial differential equation: n order linear fractional partial differential equation and nonlinear fractional reaction diffusion convection equation, by using the Lie group analysis method. The infinitesimal generators general formula of n order linear fractional partial differential equation is obtained. For nonlinear fractional reaction diffusion convection equation, the properties of their infinitesimal generators are considered. The four special cases are exhaustively investigated respectively. At the same time some examples of the corresponding case are also given. So it is very convenient to solve the infinitesimal generator of some fractional partial differential equation.
Hoshide, Takashi; Obata, Masaaki; Akatsuka, Takashi
2006-01-01
The Murotomisaki Gabbroic Complex is a sill-like layered intrusion of up to 220 m in thickness and is located at Cape Muroto, Kochi Prefecture, Japan. There are several olivine-rich zones within the intrusion, which may have been formed through accumulation of olivine crystals. However, up to now it has not been clear as to whether all of the olivine-rich zones formed in this way. To clarify this, we reinvestigated the layered structure by collecting a consistent data set of modal composition...
Differential Regulation of Adhesion Complex Turnover by ROCK1 and ROCK2
Lock, Frances E.; Katie R Ryan; Poulter, Natalie S.; Maddy Parsons; Hotchin, Neil A
2012-01-01
BACKGROUND: ROCK1 and ROCK2 are serine/threonine kinases that function downstream of the small GTP-binding protein RhoA. Rho signalling via ROCK regulates a number of cellular functions including organisation of the actin cytoskeleton, cell adhesion and cell migration. METHODOLOGY/PRINCIPAL FINDINGS: In this study we use RNAi to specifically knockdown ROCK1 and ROCK2 and analyse their role in assembly of adhesion complexes in human epidermal keratinocytes. We observe that loss of ROCK1 inhibi...
Analysis of oocyte-like cells differentiated from porcine fetal skin-derived stem cells.
Dyce, Paul W; Shen, Wei; Huynh, Evanna; Shao, Hua; Villagómez, Daniel A F; Kidder, Gerald M; King, W Allan; Li, Julang
2011-05-01
We previously reported the differentiation of cells derived from porcine female fetal skin into cells resembling germ cells and oocytes. A subpopulation of these cells expressed germ cell markers and formed aggregates resembling cumulus-oocyte complexes. Some of these aggregates extruded large oocyte-like cells (OLCs) that expressed markers consistent with those of oocytes. The objective of the current study was to further characterize OLCs differentiated from porcine skin-derived stem cells. Reverse transcriptase (RT)-polymerase chain reaction and Western blot revealed the expression of connexin37 and connexin43, both of which are characteristic of ovarian follicles. The expression of meiosis markers DMC1 and synaptonemal complex protein, but not STRA8 and REC8, was detected in the OLC cultures. Immunofluorescence with an antibody against synaptonemal complex protein on chromosome spreads revealed a very small subpopulation of stained OLCs that had a similar pattern to leptotene, zytotene, or pachytene nuclei during prophase I of meiosis. Sodium bisulfite sequencing of the differentially methylated region of H19 indicated that this region is almost completely demethylated in OLCs, similar to in vivo-derived oocytes. We also investigated the differentiation potential of male skin-derived stem cells in the same differentiation medium. Large cells with oocyte morphology were generated in the male stem cell differentiation cultures. These OLCs expressed oocyte genes such as octamer-binding transcription factor 4 (OCT4), growth differentiation factor-9b (GDF9B), deleted in azoospermia-like (DAZL), VASA, zona pellucida B (ZPB), and zona pellucida C (ZPC). It was concluded that skin-derived stem cells from both male and female porcine fetuses are capable of entering an oocyte differentiation pathway, but the culture system currently in place is inadequate to support the complete development of competent oocytes.
Directory of Open Access Journals (Sweden)
Eun Ju Lee
Full Text Available BACKGROUND: The expression of myogenic regulatory factors (MRFs consisting of MyoD, Myf5, myogenin (MyoG and MRF4 characterizes various phases of skeletal muscle development including myoblast proliferation, cell-cycle exit, cell fusion and the maturation of myotubes to form myofibers. Although it is well known that the function of MyoG cannot be compensated for other MRFs, the molecular mechanism by which MyoG controls muscle cell differentiation is still unclear. Therefore, in this study, RNA-Seq technology was applied to profile changes in gene expression in response to MyoG knock-down (MyoGkd in primary bovine muscle satellite cells (MSCs. RESULTS: About 61-64% of the reads of over 42 million total reads were mapped to more than 13,000 genes in the reference bovine genome. RNA-Seq analysis identified 8,469 unique genes that were differentially expressed in MyoGkd. Among these genes, 230 were up-regulated and 224 were down-regulated by at least four-fold. DAVID Functional Annotation Cluster (FAC and pathway analysis of all up- and down-regulated genes identified overrepresentation for cell cycle and division, DNA replication, mitosis, organelle lumen, nucleoplasm and cytosol, phosphate metabolic process, phosphoprotein phosphatase activity, cytoskeleton and cell morphogenesis, signifying the functional implication of these processes and pathways during skeletal muscle development. The RNA-Seq data was validated by real time RT-PCR analysis for eight out of ten genes as well as five marker genes investigated. CONCLUSIONS: This study is the first RNA-Seq based gene expression analysis of MyoGkd undertaken in primary bovine MSCs. Computational analysis of the differentially expressed genes has identified the significance of genes such as SAP30-like (SAP30L, Protein lyl-1 (LYL1, various matrix metalloproteinases, and several glycogenes in myogenesis. The results of the present study widen our knowledge of the molecular basis of skeletal muscle
Reddington, K.; O'Grady, J.; Dorai-Raj, S.; Maher, M.; Soolingen, D. van; Barry, T.
2011-01-01
Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treat
Understanding the specificity of serpin-protease complexes through interface analysis.
Rashid, Qudsia; Kapil, Charu; Singh, Poonam; Kumari, Vineeta; Jairajpuri, Mohamad Aman
2015-01-01
Serpins such as antithrombin, heparin cofactor II, plasminogen activator inhibitor, antitrypsin, antichymotrypsin, and neuroserpin are involved in important biological processes by inhibiting specific serine proteases. Initially, the protease recognizes the mobile reactive loop of the serpin eliciting conformational changes, where the cleaved loop together with the protease inserts into β-sheet A, translocating the protease to the opposite side of inhibitor leading to its inactivation. Serpin interaction with proteases is governed mainly by the reactive center loop residues (RCL). However, in some inhibitory serpins, exosite residues apart from RCL have been shown to confer protease specificity. Further, this forms the basis of multi-specificity of some serpins, but the residues and their dimension at interface in serpin-protease complexes remain elusive. Here, we present a comprehensive structural analysis of the serpin-protease interfaces using bio COmplexes COntact MAPS (COCOMAPS), PRotein Interface Conservation and Energetics (PRICE), and ProFace programs. We have carried out interface, burial, and evolutionary analysis of different serpin-protease complexes. Among the studied complexes, non-inhibitory serpins exhibit larger interface region with greater number of residue involvement as compared to the inhibitory serpins. On comparing the multi-specific serpins (antithrombin and antitrypsin), a difference in the interface area and residue number was observed, suggestive of a differential mechanism of action of these serpins in regulating their different target proteases. Further, detailed study of these multi-specific serpins listed few essential residues (common in all the complexes) and certain specificity (unique to each complex) determining residues at their interfaces. Structural mapping of interface residues suggested that individual patches with evolutionary conserved residues in specific serpins determine their specificity towards a particular protease.
Krendl, Anne C; Rule, Nicholas O; Ambady, Nalini
2014-09-01
Young adults can be surprisingly accurate at making inferences about people from their faces. Although these first impressions have important consequences for both the perceiver and the target, it remains an open question whether first impression accuracy is preserved with age. Specifically, could age differences in impressions toward others stem from age-related deficits in accurately detecting complex social cues? Research on aging and impression formation suggests that young and older adults show relative consensus in their first impressions, but it is unknown whether they differ in accuracy. It has been widely shown that aging disrupts emotion recognition accuracy, and that these impairments may predict deficits in other social judgments, such as detecting deceit. However, it is unclear whether general impression formation accuracy (e.g., emotion recognition accuracy, detecting complex social cues) relies on similar or distinct mechanisms. It is important to examine this question to evaluate how, if at all, aging might affect overall accuracy. Here, we examined whether aging impaired first impression accuracy in predicting real-world outcomes and categorizing social group membership. Specifically, we studied whether emotion recognition accuracy and age-related cognitive decline (which has been implicated in exacerbating deficits in emotion recognition) predict first impression accuracy. Our results revealed that emotion recognition accuracy did not predict first impression accuracy, nor did age-related cognitive decline impair it. These findings suggest that domains of social perception outside of emotion recognition may rely on mechanisms that are relatively unimpaired by aging.
Spectroscopic analysis of protein Fe-NO complexes.
Bellota-Antón, César; Munnoch, John; Robb, Kirsty; Adamczyk, Katrin; Candelaresi, Marco; Parker, Anthony W; Dixon, Ray; Hutchings, Matthew I; Hunt, Neil T; Tucker, Nicholas P
2011-10-01
The toxic free radical NO (nitric oxide) has diverse biological roles in eukaryotes and bacteria, being involved in signalling, vasodilation, blood clotting and immunity, and as an intermediate in microbial denitrification. The predominant biological mechanism of detecting NO is through the formation of iron nitrosyl complexes, although this is a deleterious process for other iron-containing enzymes. We have previously applied techniques such as UV-visible and EPR spectroscopy to the analysis of protein Fe-NO complex formation in order to study how NO controls the activity of the bacterial transcriptional regulators NorR and NsrR. These studies have analysed NO-dependent biological activity both in vitro and in vivo using diverse biochemical, molecular and spectroscopic methods. Recently, we have applied ultrafast 2D-IR (two-dimensional IR) spectroscopy to the analysis of NO-protein interactions using Mb (myoglobin) and Cc (cytochrome c) as model haem proteins. The ultrafast fluctuations of Cc and Mb show marked differences, indicating altered flexibility of the haem pockets. We have extended this analysis to bacterial catalase enzymes that are known to play a role in the nitrosative stress response by detoxifying peroxynitrite. The first 2D-IR analysis of haem nitrosylation and perspectives for the future are discussed.
Model Analysis of Complex Systems Behavior using MADS
Vesselinov, V. V.; O'Malley, D.
2016-12-01
Evaluation of robustness (reliability) of model predictions is challenging for models representing complex system behavior. Frequently in science and engineering applications related to complex systems, several alternative physics models may describe the available data equally well and are physically reasonable based on the available conceptual understanding. However, these alternative models could give very different predictions about the future states of the analyzed system. Furthermore, in the case of complex systems, we often must do modeling with an incomplete understanding of the underlying physical processes and model parameters. The analyses of model predictions representing complex system behavior are particularly challenging when we are quantifying uncertainties of rare events in the model prediction space that can have major consequences (also called "black swans"). These types of analyses are also computationally challenging. Here, we demonstrate the application of a general high-performance computational tool for Model Analysis & Decision Support (MADS; http://mads.lanl.gov) which can be applied to perform analyses using any external physics or systems model. The coupling between MADS and the external model can be performed using different methods. MADS is implemented in Julia, a high-level, high-performance dynamic programming language for technical computing (http://mads.lanl.gov/, https://github.com/madsjulia/Mads.jl, http://mads.readthedocs.org). MADS has been applied to perform analyses for environmental-management and water-energy-food nexus problems. To demonstrate MADS capabilities and functionalities, we analyze a series of synthetic problems consistent with actual real-world problems.
De Meester, N; Gingold, R; Rigaux, A; Derycke, S; Moens, T
2016-10-01
Marine ecosystems are experiencing accelerating population and species loss. Some ecosystem functions are decreasing and there is growing interest in the link between biodiversity and ecosystem functioning. The role of cryptic (morphologically identical but genetically distinct) species in this biodiversity-ecosystem functioning link is unclear and has not yet been formally tested. We tested if there is a differential effect of four cryptic species of the bacterivorous nematode Litoditis marina on the decomposition process of macroalgae. Bacterivorous nematodes can stimulate or slow down bacterial activity and modify the bacterial assemblage composition. Moreover, we tested if interspecific interactions among the four cryptic species influence the decomposition process. A laboratory experiment with both mono- and multispecific nematode cultures was conducted, and loss of organic matter and the activity of two key extracellular enzymes for the degradation of phytodetritus were assessed. L. marina mainly influenced qualitative aspects of the decomposition process rather than its overall rate: an effect of the nematodes on the enzymatic activities became manifest, although no clear nematode effect on bulk organic matter weight loss was found. We also demonstrated that species-specific effects on the decomposition process existed. Combining the four cryptic species resulted in high competition, with one dominant species, but without complete exclusion of other species. These interspecific interactions translated into different effects on the decomposition process. The species-specific differences indicated that each cryptic species may play an important and distinct role in ecosystem functioning. Functional differences may result in coexistence among very similar species.
Multiscale differential phase contrast analysis with a unitary detector
Lopatin, Sergei
2015-12-30
A new approach to generate differential phase contrast (DPC) images for the visualization and quantification of local magnetic fields in a wide range of modern nano materials is reported. In contrast to conventional DPC methods our technique utilizes the idea of a unitary detector under bright field conditions, making it immediately usable by a majority of modern transmission electron microscopes. The approach is put on test to characterize the local magnetization of cylindrical nanowires and their 3D ordered arrays, revealing high sensitivity of our method in a combination with nanometer-scale spatial resolution.
Introduction to stochastic analysis integrals and differential equations
Mackevicius, Vigirdas
2013-01-01
This is an introduction to stochastic integration and stochastic differential equations written in an understandable way for a wide audience, from students of mathematics to practitioners in biology, chemistry, physics, and finances. The presentation is based on the naïve stochastic integration, rather than on abstract theories of measure and stochastic processes. The proofs are rather simple for practitioners and, at the same time, rather rigorous for mathematicians. Detailed application examples in natural sciences and finance are presented. Much attention is paid to simulation diffusion pro
State analysis requirements database for engineering complex embedded systems
Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.
2004-01-01
It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.
Fire hazard analysis for Plutonium Finishing Plant complex
Energy Technology Data Exchange (ETDEWEB)
MCKINNIS, D.L.
1999-02-23
A fire hazards analysis (FHA) was performed for the Plutonium Finishing Plant (PFP) Complex at the Department of Energy (DOE) Hanford site. The scope of the FHA focuses on the nuclear facilities/structures in the Complex. The analysis was conducted in accordance with RLID 5480.7, [DOE Directive RLID 5480.7, 1/17/94] and DOE Order 5480.7A, ''Fire Protection'' [DOE Order 5480.7A, 2/17/93] and addresses each of the sixteen principle elements outlined in paragraph 9.a(3) of the Order. The elements are addressed in terms of the fire protection objectives stated in paragraph 4 of DOE 5480.7A. In addition, the FHA also complies with WHC-CM-4-41, Fire Protection Program Manual, Section 3.4 [1994] and WHC-SD-GN-FHA-30001, Rev. 0 [WHC, 1994]. Objectives of the FHA are to determine: (1) the fire hazards that expose the PFP facilities, or that are inherent in the building operations, (2) the adequacy of the fire safety features currently located in the PFP Complex, and (3) the degree of compliance of the facility with specific fire safety provisions in DOE orders, related engineering codes, and standards.
State analysis requirements database for engineering complex embedded systems
Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.
2004-01-01
It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.
Ciucci, Sara; Ge, Yan; Durán, Claudio; Palladini, Alessandra; Jiménez-Jiménez, Víctor; Martínez-Sánchez, Luisa María; Wang, Yuting; Sales, Susanne; Shevchenko, Andrej; Poser, Steven W.; Herbig, Maik; Otto, Oliver; Androutsellis-Theotokis, Andreas; Guck, Jochen; Gerl, Mathias J.; Cannistraci, Carlo Vittorio
2017-01-01
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics. PMID:28287094
Directory of Open Access Journals (Sweden)
ECOBICI MIHAELA LOREDANA
2016-12-01
Full Text Available Product quality has been and will remain one of the most important indicators of increasing economic and financial performance of a company. Quality is that which ensures the greatest part of the competitiveness of a product or service, this being the result of some important aspects such as: products and services of quality to meet consumers requirements, low costs without affecting the quality level, the performance of contractual obligations, customer satisfaction and last but not least obtaining profit. Research and results concerning this issue will result in the prerequisites in the process for quality assurance that can develop both internally and externally. The purpose of this article lies in the approach and illustration of the aspects of products differentiated and non-differentiated in quality classes. In launching this research I will try to highlight some aspects that most efficiently the indicators mentioned above, indicators that read to what extent a certain product meets the characteristics specified to its destination.
Energy Technology Data Exchange (ETDEWEB)
Aube, Michel, E-mail: 4aubem@videotron.ca [Axe de recherche en sante des populations et environnementale, Centre de recherche du Centre hospitalier universitaire de Quebec and Universite Laval, 2875 Boulevard Laurier, Edifice Delta 2, bureau 600, Quebec, QC, Canada G1V 2M2 (Canada); Larochelle, Christian, E-mail: christian.larochelle@inspq.qc.ca [Axe de recherche en sante des populations et environnementale, Centre de recherche du Centre hospitalier universitaire de Quebec and Universite Laval, 2875 Boulevard Laurier, Edifice Delta 2, bureau 600, Quebec, QC, Canada G1V 2M2 (Canada); Ayotte, Pierre, E-mail: pierre.ayotte@inspq.qc.ca [Axe de recherche en sante des populations et environnementale, Centre de recherche du Centre hospitalier universitaire de Quebec and Universite Laval, 2875 Boulevard Laurier, Edifice Delta 2, bureau 600, Quebec, QC, Canada G1V 2M2 (Canada); Laboratoire de Toxicologie, Institut national de sante publique du Quebec, 945 avenue Wolfe, Quebec, QC, Canada G1V 5B3 (Canada)
2011-04-15
Organochlorine compounds (OCs) are a group of persistent chemicals that accumulate in fatty tissues with age. Although OCs has been tested individually for their capacity to induce breast cancer cell proliferation, few studies examined the effect of complex mixtures that comprise compounds frequently detected in the serum of women. We constituted such an OC mixture containing 15 different components in environmentally relevant proportions and assessed its proliferative effects in four breast cancer cell lines (MCF-7, T47D, CAMA-1, MDAMB231) and in non-cancerous CV-1 cells. We also determined the capacity of the mixture to modulate cell cycle stage of breast cancer cells and to induce estrogenic and antiandrogenic effects using gene reporter assays. We observed that low concentrations of the mixture (100x10{sup 3} and 50x10{sup 3} dilutions) stimulated the proliferation of MCF-7 cells while higher concentrations (10x10{sup 3} and 5x10{sup 3} dilutions) had the opposite effect. In contrast, the mixture inhibited the proliferation of non-hormone-dependent cell lines. The mixture significantly increased the number of MCF-7 cells entering the S phase, an effect that was blocked by the antiestrogen ICI 182,780. Low concentrations of the mixture also caused an increase in CAMA-1 cell proliferation but only in the presence estradiol and dihydrotestosterone (p<0.05 at the 50x10{sup 3} dilution). DDT analogs and polychlorinated biphenyls all had the capacity to stimulate the proliferation of CAMA-1 cells in the presence of sex steroids. Reporter gene assays further revealed that the mixture and several of its constituents (DDT analogs, aldrin, dieldrin, {beta}-hexachlorocyclohexane, toxaphene) induced estrogenic effects, whereas the mixture and several components (DDT analogs, aldrin, dieldrin and PCBs) inhibited the androgen signaling pathway. Our results indicate that the complex OC mixture increases the proliferation of MCF-7 cells due to its estrogenic potential. The
Kafle, Amol; Coy, Stephen L; Wong, Bryan M; Fornace, Albert J; Glick, James J; Vouros, Paul
2014-07-01
A systematic study involving the use and optimization of gas-phase modifiers in quantitative differential mobility-mass spectrometry (DMS-MS) analysis is presented using nucleoside-adduct biomarkers of DNA damage as an important reference point for analysis in complex matrices. Commonly used polar protic and polar aprotic modifiers have been screened for use against two deoxyguanosine adducts of DNA: N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG-C8-4-ABP) and N-(deoxyguanosin-8-y1)-2-amino-l-methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-PhIP). Particular attention was paid to compensation voltage (CoV) shifts, peak shapes, and product ion signal intensities while optimizing the DMS-MS conditions. The optimized parameters were then applied to rapid quantitation of the DNA adducts in calf thymus DNA. After a protein precipitation step, adduct levels corresponding to less than one modification in 10(6) normal DNA bases were detected using the DMS-MS platform. Based on DMS fundamentals and ab initio thermochemical results, we interpret the complexity of DMS modifier responses in terms of thermal activation and the development of solvent shells. At very high bulk gas temperature, modifier dipole moment may be the most important factor in cluster formation and cluster geometry, but at lower temperatures, multi-neutral clusters are important and less predictable. This work provides a useful protocol for targeted DNA adduct quantitation and a basis for future work on DMS modifier effects.
Control capability analysis for complex spacecraft thruster configurations
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
The set of forces and moments that can be generated by thrusters of a spacecraft is called the"control capability"with respect to the thruster configuration.If the control capability of a thruster configuration is adequate to fulfill a given space mission,we say this configuration is a feasible one with respect to the task.This study proposed a new way to analyze the control capability of the complex thruster configuration.Precise mathematical definitions of feasibility were proposed,based on which a criterion to judge the feasibility of the thruster configuration was presented through calculating the shortest distance to the boundary of the controllable region as a function of the thruster configuration.Finally,control capability analysis for the complex thruster configuration based on its feasibility with respect to the space mission was given followed by a 2-D thruster configuration example to demonstrate its validity.
Entropy-complexity analysis in some globally-coupled systems
Chrisment, Antoine M.; Firpo, Marie-Christine
2016-10-01
Globally-coupled N-body systems are well known to possess an intricate dynamics. When N is large, collective effects may drastically lower the effective dimension of the dynamics breaking the conditions on ergodicity necessary for the applicability of statistical mechanics. These problems are here illustrated and discussed through an entropy-complexity analysis of the repulsive Hamiltonian mean-field model. Using a Poincaré section of the mean-field time series provides a natural sampling time in the entropy-complexity treatment. This approach is shown to single-out the out-of-equilibrium dynamical features and to uncover a transition of the system dynamics from low-energy non-Boltzmann quasi-stationary states to high-energy stochastic-like behavior.
Institute of Scientific and Technical Information of China (English)
Jungsug Gwak; Dong-Eun Kim; Jeong Woo Cho; Sangtaek Oh; Sun Gwan Hwang; Hyung-Soon Park; Sang Rak Choi; Sun-Hee Park; Hyunjoon Kim; Nam-Chul Ha; Sung Jin Bae; Jin-Kwan Han
2012-01-01
The Wnt/β-catenin pathway plays important roles in the differentiation of multiple cell types,including mesenchymal stem cells.Using a cell-based chemical screening assay with a synthetic chemical library of 270 000 compounds,we identified the compound SKL2001 as a novel agonist of the Wnt/β-catenin pathway and uncovered its molecular mechanism of action.SKL2001 upregulated β-catenin responsive transcription by increasing the intracellular β-catenin protein level and inhibited the phosphorylation of β-catenin at residues Ser33/37/Thr41 and Ser45,which would mark it for proteasomal degradation,without affecting CK1 and GSK-3β enzyme activities.Biochemical analysis revealed that SKL2001 disrupted the Axin/β-catenin interaction,which is a critical step for CK1- and GSK-3β-mediated phosphorylation of β-catenin at Ser33/37/Thr41 and Ser45.The treatment of mesenchymal stem cells with SKL2001 promoted osteoblastogenesis and suppressed adipocyte differentiation,both of which were accompanied by the activation of Wnt/β-catenin pathway.Our findings provide a new strategy to regulate mesenchymal stem cell differentiation by modulation of the Wnt/β-catenin pathway.
Structure analysis of growing network based on partial differential equations
Junbo JIA; Jin, Zhen
2016-01-01
The topological structure is one of the most important contents in the complex network research. Therein the node degree and the degree distribution are the most basic characteristic quantities to describe topological structure. In order to calculate the degree distribution, first of all, the node degree is considered as a continuous variable. Then, according to the Markov Property of growing network, the cumulative distribution function's evolution equation with time can be obtained. Finally...
Taylor, Arthur C., III; Newman, James C., III; Barnwell, Richard W.
1997-01-01
A three-dimensional unstructured grid approach to aerodynamic shape sensitivity analysis and design optimization has been developed and is extended to model geometrically complex configurations. The advantage of unstructured grids (when compared with a structured-grid approach) is their inherent ability to discretize irregularly shaped domains with greater efficiency and less effort. Hence, this approach is ideally suited for geometrically complex configurations of practical interest. In this work the nonlinear Euler equations are solved using an upwind, cell-centered, finite-volume scheme. The discrete, linearized systems which result from this scheme are solved iteratively by a preconditioned conjugate-gradient-like algorithm known as GMRES for the two-dimensional geometry and a Gauss-Seidel algorithm for the three-dimensional; similar procedures are used to solve the accompanying linear aerodynamic sensitivity equations in incremental iterative form. As shown, this particular form of the sensitivity equation makes large-scale gradient-based aerodynamic optimization possible by taking advantage of memory efficient methods to construct exact Jacobian matrix-vector products. Simple parameterization techniques are utilized for demonstrative purposes. Once the surface has been deformed, the unstructured grid is adapted by considering the mesh as a system of interconnected springs. Grid sensitivities are obtained by differentiating the surface parameterization and the grid adaptation algorithms with ADIFOR (which is an advanced automatic-differentiation software tool). To demonstrate the ability of this procedure to analyze and design complex configurations of practical interest, the sensitivity analysis and shape optimization has been performed for a two-dimensional high-lift multielement airfoil and for a three-dimensional Boeing 747-200 aircraft.
Claycomb, Meredith A; Charak, Ruby; Kaplow, Julie; Layne, Christopher M; Pynoos, Robert; Elhai, Jon D
2016-10-01
Persistent Complex Bereavement Disorder (PCBD) is a newly proposed diagnosis placed in the Appendix of the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) as an invitation for further research. To date, no studies have examined the dimensionality of PCBD or explored whether different PCBD criteria domains relate in similar, versus differential, ways to other psychological conditions common to war-exposed bereaved youth, including symptoms of Posttraumatic Stress Disorder (PTSD) and depression. We evaluated the dimensionality of proposed PCBD B and C symptom domains, and their respective relations with measures of PTSD and depression, in 1142 bereaved Bosnian adolescents exposed to the 1992-1995 Bosnian civil war. Instruments included the UCLA PTSD Reaction Index, the Depression Self-Rating Scale, and the UCLA Grief Screening Scale (a prototype measure of PCBD symptoms). We investigated potential differences in grief, PTSD, and depression scores as a function of cause of death. We then examined hypothesized differential relations between PCBD B and C symptom domain subscales and selected external correlates, specifically measures of depression and the four-factor emotional numbing model of PTSD. Results of both analyses provide preliminary evidence of a multidimensional structure for PCBD in this population, in that the PCBD Criterion C subscale score covaried more strongly with each of the four PTSD factors and with depression than did PCBD Criterion B. We conclude by discussing theoretical, methodological, clinical, and policy-related implications linked to the ongoing study of essential features of PCBD.
Proteomic analysis of osteogenic differentiation of dental follicle precursor cells
DEFF Research Database (Denmark)
Morsczeck, Christian; Petersen, Jørgen; Völlner, Florian
2009-01-01
proteins, plastin 3 T-isoform, beta-actin, superoxide dismutases, and transgelin were found to be highly up-regulated, whereas cofilin-1, pro-alpha 1 collagen, destrin, prolyl 4-hydrolase and dihydrolipoamide dehydrogenase were found to be highly down-regulated. The group of up-regulated proteins...... is associated with actin-bundling and defence against oxidative cellular stress, whereas down-regulated proteins were associated with collagen biosynthesis. Bioinformatic analyses of the entire data set confirmed these findings that represent significant steps towards the understanding of DFPC differentiation....... The bioinformatic analyses suggest that proteins associated with cell cycle progression and protein metabolism were down-regulated and proteins involved in catabolism, cell motility and biological quality were up-regulated. These results display the general physiological state of DFPCs before and after osteogenic...
Inverse spectral analysis for singular differential operators with matrix coefficients
Directory of Open Access Journals (Sweden)
Nour el Houda Mahmoud
2006-02-01
Full Text Available Let $L_alpha$ be the Bessel operator with matrix coefficients defined on $(0,infty$ by $$ L_alpha U(t = U''(t+ {I/4-alpha^2over t^2}U(t, $$ where $alpha$ is a fixed diagonal matrix. The aim of this study, is to determine, on the positive half axis, a singular second-order differential operator of $L_alpha+Q$ kind and its various properties from only its spectral characteristics. Here $Q$ is a matrix-valued function. Under suitable circumstances, the solution is constructed by means of the spectral function, with the help of the Gelfund-Levitan process. The hypothesis on the spectral function are inspired on the results of some direct problems. Also the resolution of Fredholm's equations and properties of Fourier-Bessel transforms are used here.
ANALYSIS OF A HEAT-FLUX DIFFERENTIAL SCANNING CALORIMETRY INSTRUMENTS
Energy Technology Data Exchange (ETDEWEB)
Sabau, Adrian S [ORNL; Porter, Wallace D [ORNL
2007-01-01
Differential Scanning Calorimetry (DSC) measurements are used to estimate the fractional latent heat release during phase changes. There are temperature lags inherent to the instruments due to the temperature measurement at a different location than that of the sample and reference materials. Recently, Dong and Hunt[1] showed that significant improvement in estimating the fractional latent heat can be obtained when detailed simulations of the heat transfer within the instrument are performed. The Netzsch DSC 404C instrument, with a high accuracy heat capacity sensor, is considered in this study. This instrument had a different configuration than that studied by Dong and Hunt[1]. The applicability of Dong and Hunt's approach to this instrument is investigated. It was found that the DSC instrument could be described by numerous parameters but that model parameters were difficult to estimate. Numerical simulation results are presented and compared with experimental results for the fractional latent heat of a commercial A356 aluminum alloy.
Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomics.
Liu, Xiaoyun; Afrane, Mary; Clemmer, David E; Zhong, Guangming; Nelson, David E
2010-06-01
The extracellular chlamydial infectious particle, or elementary body (EB), is enveloped by an intra- and intermolecular cysteine cross-linked protein shell called the chlamydial outer membrane complex (COMC). A few abundant proteins, including the major outer membrane protein and cysteine-rich proteins (OmcA and OmcB), constitute the overwhelming majority of COMC proteins. The identification of less-abundant COMC proteins has been complicated by limitations of proteomic methodologies and the contamination of COMC fractions with abundant EB proteins. Here, we used parallel liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analyses of Chlamydia trachomatis serovar L2 434/Bu EB, COMC, and Sarkosyl-soluble EB fractions to identify proteins enriched or depleted from COMC. All well-described COMC proteins were specifically enriched in the COMC fraction. In contrast, multiple COMC-associated proteins found in previous studies were strongly enriched in the Sarkosyl-soluble fraction, suggesting that these proteins are not COMC components or are not stably associated with COMC. Importantly, we also identified novel proteins enriched in COMC. The list of COMC proteins identified in this study has provided reliable information for further understanding chlamydial protein secretion systems and modeling COMC and EB structures.
Magnetic resonance velocity imaging derived pressure differential using control volume analysis
Directory of Open Access Journals (Sweden)
Cohen Benjamin
2011-03-01
Full Text Available Abstract Background Diagnosis and treatment of hydrocephalus is hindered by a lack of systemic understanding of the interrelationships between pressures and flow of cerebrospinal fluid in the brain. Control volume analysis provides a fluid physics approach to quantify and relate pressure and flow information. The objective of this study was to use control volume analysis and magnetic resonance velocity imaging to non-invasively estimate pressure differentials in vitro. Method A flow phantom was constructed and water was the experimental fluid. The phantom was connected to a high-resolution differential pressure sensor and a computer controlled pump producing sinusoidal flow. Magnetic resonance velocity measurements were taken and subsequently analyzed to derive pressure differential waveforms using momentum conservation principles. Independent sensor measurements were obtained for comparison. Results Using magnetic resonance data the momentum balance in the phantom was computed. The measured differential pressure force had amplitude of 14.4 dynes (pressure gradient amplitude 0.30 Pa/cm. A 12.5% normalized root mean square deviation between derived and directly measured pressure differential was obtained. These experiments demonstrate one example of the potential utility of control volume analysis and the concepts involved in its application. Conclusions This study validates a non-invasive measurement technique for relating velocity measurements to pressure differential. These methods may be applied to clinical measurements to estimate pressure differentials in vivo which could not be obtained with current clinical sensors.
Statistical energy analysis of complex structures, phase 2
Trudell, R. W.; Yano, L. I.
1980-01-01
A method for estimating the structural vibration properties of complex systems in high frequency environments was investigated. The structure analyzed was the Materials Experiment Assembly, (MEA), which is a portion of the OST-2A payload for the space transportation system. Statistical energy analysis (SEA) techniques were used to model the structure and predict the structural element response to acoustic excitation. A comparison of the intial response predictions and measured acoustic test data is presented. The conclusions indicate that: the SEA predicted the response of primary structure to acoustic excitation over a wide range of frequencies; and the contribution of mechanically induced random vibration to the total MEA is not significant.
Analysis and visualization of complex unsteady three-dimensional flows
Van Dalsem, William R.; Buning, Pieter G.; Dougherty, F. Carroll; Smith, Merritt H.
1989-01-01
Flow field animation is the natural choice as a tool in the analysis of the numerical simulations of complex unsteady three-dimensional flows. The PLOT4D extension of the widely used PLOT3D code to allow the interactive animation of a broad range of flow variables was developed and is presented. To allow direct comparison with unsteady experimental smoke and dye flow visualization, the code STREAKER was developed to produce time accurate streaklines. Considerations regarding the development of PLOT4D and STREAKER, and example results are presented.
Rajesh, Ramanna Valmiki; Heo, Gang-Nyung; Park, Mi-Rim; Nam, Jin-Seon; Kim, Nam-Kuk; Yoon, Duhak; Kim, Tae-Hun; Lee, Hyun-Jeong
2010-09-01
Given the substantial rise in obesity, depot-specific fat accumulation and its associated diseases like diabetes, it is important to understand the molecular basis of depot-specific adipocyte differentiation. Many studies have successfully exploited the adipocyte differentiation, but most of them were not related to depot-specificity, particularly using freshly isolated primary preadipocytes. Using 2-dimensional polyacrylamide gel electrophoresis coupled with sequencing mass spectrometry, we searched and compared the proteins differentially expressed in undifferentiated and differentiated preadipocytes from bovine omental, subcutaneous and intramuscular adipose depots. Our proteome mapping strategy to identify differentially expressed intracellular proteins during adipogenic conversion revealed 65 different proteins that were found to be common for the three depots. Further, we validated the differential expression for a subset of proteins by immunoblotting analyses. The results demonstrated that many structural proteins were down-regulated during differentiation of preadipocytes from all the depots. Most up-regulated proteins like Ubiquinol-cytochrome-c reductase complex core protein I (UQCRC1), ATP synthase D chain, Superoxide dismutase (SOD), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Sulfotransferase 1A1 (SULT1A1), Carnitine O-palmitoyltransferase 2 (CPT2) and Heat-shock protein beta 1 (HSPB1) across the three depots were found to be associated with lipid metabolism and metabolic activity. Further, all the up-regulated proteins were found to have higher protein expression in omental than subcutaneous or intramuscular depots.
Wu, Licia N Y; Genge, Brian R; Wuthier, Roy E
2009-07-01
Mg(2+) and Zn(2+) are present in the mineral of matrix vesicles (MVs) and biological apatites, and are known to influence the onset and progression of mineral formation by amorphous calcium phosphate (ACP) and hydroxyapatite (HAP). However, neither has been studied systematically for its effect on mineral formation by phosphatidylserine-Ca(2+)-Pi complexes (PS-CPLX), an important constituent of the MV nucleation core. Presented here are studies on the effects of increasing levels of Mg(2+) and Zn(2+) on the process of mineral formation, either when present in synthetic cartilage lymph (SCL), or when incorporated during the formation of PS-CPLX. Pure HAP and PS-CPLX proved to be powerful nucleators, but ACP took much longer to induce mineral formation. In SCL, Mg(2+) and Zn(2+) had significantly different inhibitory effects on the onset and amount of mineral formation; HAP and PS-CPLX were less affected than ACP. Mg(2+) and Zn(2+) caused similar reductions in the rate and length of rapid mineral formation, but Zn(2+) was a more potent inhibitor on a molar basis. When incorporated into PS-CPLX, Mg(2+) and Zn(2+) caused significantly different effects than when present in SCL. Even low, subphysiological levels of Mg(2+) altered the inherent structure of PS-CPLX and markedly reduced its ability to induce and propagate mineral formation. Incorporated Zn(2+) caused significantly less effect, low (<20 microM) levels causing almost no inhibition. Levels of Zn(2+) present in MVs do not appear to inhibit their nucleational activity.
Differential predictors of DSM-5 PTSD and ICD-11 complex PTSD among African American women.
Powers, Abigail; Fani, Negar; Carter, Sierra; Cross, Dorthie; Cloitre, Marylene; Bradley, Bekh
2017-01-01
Background: Complex posttraumatic stress disorder (CPTSD) is proposed for inclusion in the ICD-11 as a diagnosis distinct from posttraumatic stress disorder (PTSD), reflecting deficits in affective, self-concept, and relational domains. There remains significant controversy over whether CPTSD provides useful diagnostic information beyond PTSD and other comorbid conditions, such as depression or substance use disorders. Objective: The present study examined differences in psychiatric presentation for three groups: traumatized controls, DSM-5 PTSD subjects, and ICD-11 CPTSD subjects. Method: The sample included 190 African American women recruited from an urban public hospital where rates of trauma exposure are high. PTSD was measured using Clinician Administered PTSD Scale for DSM-5 and CPTSD was measured using clinician administered ICD-Trauma Interview. Psychiatric diagnoses and emotion dysregulation were also assessed. In a subset of women (n = 60), emotion recognition was measured using the Penn Emotion Recognition Task. Results: There were significant differences across groups on current and lifetime major depression (p PTSD and depression symptoms and, as expected, more severe emotion dysregulation and dissociation, compared to DSM-5 PTSD and traumatized control groups. Individuals with CPTSD also had higher levels of emotion recognition to faces on a computer-based behavioural assessment, which may be related to heightened vigilance toward emotional cues from others. CPTSD women had better facial emotion recognition on a computer-based assessment, which may suggest heightened vigilance toward emotional cues. Conclusions: Our results suggest clear, clinically-relevant differences between PTSD and CPTSD, and highlight the need for further research on this topic with other traumatized populations, particularly studies that combine clinical and neurobiological data.
Sebastiani, F; Meiswinkel, R; Gomulski, L M; Guglielmino, C R; Mellor, P S; Malacrida, A R; Gasperi, G
2001-07-01
Samples of seven of the 10 morphological species of midges of the Culicoides imicola complex were considered. The importance of this species complex is connected to its vectorial capacity for African horse sickness virus (AHSV) and bluetongue virus (BTV). Consequently, the risk of transmission may vary dramatically, depending upon the particular cryptic species present in a given area. The species complex is confined to the Old World and our samples were collected in Southern Africa, Madagascar and the Ivory Coast. Genomic DNA of 350 randomly sampled individual midges from 19 populations was amplified using four 20-mer primers by the random amplified polymorphic DNA (RAPD) technique. One hundred and ninety-six interpretable polymorphic bands were obtained. Species-specific RAPD profiles were defined and for five species diagnostic RAPD fragments were identified. A high degree of polymorphism was detected in the species complex, most of which was observed within populations (from 64 to 76%). Principal coordinate analysis (PCO) and cluster analysis provided an estimate of the degree of variation between and within populations and species. There was substantial concordance between the taxonomies derived from morphological and molecular data. The amount and the different distributions of genetic (RAPD) variation among the taxa can be associated to their life histories, i.e. the abundance and distribution of the larval breeding sites and their seasonality.
Optimal fatigue analysis of structures during complex loadings
Directory of Open Access Journals (Sweden)
Karaouni Habib
2016-01-01
Full Text Available A new framework for high cycle fatigue analysis of metallic structures under complex multi-parameter loadings was here developed. This allows to reduce the analysis on a 2-D window with a characterized one-parameter cyclic loading thanks to an equivalence rule relative to damage between any two loadings. The simplified inelastic analysis introduced by J. Zarka [J. Zarka et al. 1990. A new approach in inelastic analysis of structures. CADLM] was used to find the limit state of the structure. A new design rules for fatigue analysis by utilizing automatic learning systems was successfully performed. A database was built by coupling numerical simulations and experimental results on several welded specimens which are considered as a general structure in the proposed approach. This could be possible by the introduction of an intelligent description of a general fatigue case based on the actual theories and models. A software, FATPRO [M.I. Systems, FatPro, available at http://www.mzintsys.com/our_products_fatpro.html], based on this work has been developed at MZ Intelligent Systems.
RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq.
Directory of Open Access Journals (Sweden)
Yafang Li
Full Text Available Alternative splicing is an important biological process in the generation of multiple functional transcripts from the same genomic sequences. Differential analysis of splice junctions (SJs and intron retentions (IRs is helpful in the detection of alternative splicing events. In this study, we conducted differential analysis of SJs and IRs by use of DEXSeq, a Bioconductor package originally designed for differential exon usage analysis in RNA-seq data analysis. We set up an analysis pipeline including mapping of RNA-seq reads, the preparation of count tables of SJs and IRs as the input files, and the differential analysis in DEXSeq. We analyzed the public RNA-seq datasets generated from RNAi experiments on Drosophila melanogaster S2-DRSC cells to deplete RNA-binding proteins (GSE18508. The analysis confirmed previous findings on the alternative splicing of the trol and Ant2 (sesB genes in the CG8144 (ps-depletion experiment and identified some new alternative splicing events in other RNAi experiments. We also identified IRs that were confirmed in our SJ analysis. The proposed method used in our study can output the genomic coordinates of differentially used SJs and thus enable sequence motif search. Sequence motif search and gene function annotation analysis helped us infer the underlying mechanism in alternative splicing events. To further evaluate this method, we also applied the method to public RNA-seq data from human breast cancer (GSE45419 and the plant Arabidopsis (SRP008262. In conclusion, our study showed that DEXSeq can be adapted to differential analysis of SJs and IRs, which will facilitate the identification of alternative splicing events and provide insights into the molecular mechanisms of transcription processes and disease development.
RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq
Li, Yafang; Rao, Xiayu; Mattox, William W.; Amos, Christopher I.; Liu, Bin
2015-01-01
Alternative splicing is an important biological process in the generation of multiple functional transcripts from the same genomic sequences. Differential analysis of splice junctions (SJs) and intron retentions (IRs) is helpful in the detection of alternative splicing events. In this study, we conducted differential analysis of SJs and IRs by use of DEXSeq, a Bioconductor package originally designed for differential exon usage analysis in RNA-seq data analysis. We set up an analysis pipeline including mapping of RNA-seq reads, the preparation of count tables of SJs and IRs as the input files, and the differential analysis in DEXSeq. We analyzed the public RNA-seq datasets generated from RNAi experiments on Drosophila melanogaster S2-DRSC cells to deplete RNA-binding proteins (GSE18508). The analysis confirmed previous findings on the alternative splicing of the trol and Ant2 (sesB) genes in the CG8144 (ps)-depletion experiment and identified some new alternative splicing events in other RNAi experiments. We also identified IRs that were confirmed in our SJ analysis. The proposed method used in our study can output the genomic coordinates of differentially used SJs and thus enable sequence motif search. Sequence motif search and gene function annotation analysis helped us infer the underlying mechanism in alternative splicing events. To further evaluate this method, we also applied the method to public RNA-seq data from human breast cancer (GSE45419) and the plant Arabidopsis (SRP008262). In conclusion, our study showed that DEXSeq can be adapted to differential analysis of SJs and IRs, which will facilitate the identification of alternative splicing events and provide insights into the molecular mechanisms of transcription processes and disease development. PMID:26327458
Complex Networks Analysis of Manual and Machine Translations
Amancio, Diego R.; Antiqueira, Lucas; Pardo, Thiago A. S.; da F. Costa, Luciano; Oliveira, Osvaldo N.; Nunes, Maria G. V.
Complex networks have been increasingly used in text analysis, including in connection with natural language processing tools, as important text features appear to be captured by the topology and dynamics of the networks. Following previous works that apply complex networks concepts to text quality measurement, summary evaluation, and author characterization, we now focus on machine translation (MT). In this paper we assess the possible representation of texts as complex networks to evaluate cross-linguistic issues inherent in manual and machine translation. We show that different quality translations generated by MT tools can be distinguished from their manual counterparts by means of metrics such as in- (ID) and out-degrees (OD), clustering coefficient (CC), and shortest paths (SP). For instance, we demonstrate that the average OD in networks of automatic translations consistently exceeds the values obtained for manual ones, and that the CC values of source texts are not preserved for manual translations, but are for good automatic translations. This probably reflects the text rearrangements humans perform during manual translation. We envisage that such findings could lead to better MT tools and automatic evaluation metrics.
Sandbox algorithm for multifractal analysis of complex networks
Liu, Jin-Long; Anh, Vo
2014-01-01
Complex networks have attracted much attention in diverse areas of science and technology. Multifractal analysis (MFA) is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns. In this paper, we introduce a new algorithm --- the sandbox (SB) algorithm, for MFA of complex networks. First we compare the SB algorithm with two existing algorithms of MFA for complex networks: the compact-box-burning (CBB) algorithm proposed by Furuya and Yakubo ( Phys. Rev. E, 84 (2011) 036118), and the improved box-counting (BC) algorithm proposed by Li et al. ( J. Stat. Mech.: Theor. Exp., 2014 (2014) P02020) by calculating the mass exponents tau(q) of some deterministic model networks. We make a detailed comparison between the numerical and theoretical results of these model networks. The comparison results show that the SB algorithm is the most effective and feasible algorithm to calculate the mass exponents tau(q) and to explore the multifractal behavior of com...
Christensen, Claire Petra
Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author
Discrete Fourier Transform Analysis in a Complex Vector Space
Dean, Bruce H.
2009-01-01
Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.
Calculation and Analysis of Differential Corrections for BeiDou
Yang, Sainan; Chen, Junping; Zhang, Yize
2015-04-01
BeiDou Satellite Navigation System has been providing service forAsia-Pacific area. BeiDou uses observations of regional monitoring network to determine satellite orbit, which limits the satellite orbit accuracy. And the satellite clock error is produced by time synchronization system. The time synchronization delay of antenna device is general obtained through prior Calibration, and the residual calibration error is included in the satellite clock, which affects the prediction accuracy of satellite clock error. In this paper, we study the algorithms of Beidou differential corrections to improve the accuracy of satellite signals to improve the user positioning accuracy. In this algorithm, both pseudo-range and phase observations are used to calculate differential corrections. We process pseudo-range observations to obtain equivalent satellite clock error, which include satellite clock errors and orbit radial errors, as well as the average projection of orbit tangential and normal errors in combination. And the epoch-difference of phase observations are processed to eliminate the ambiguity which simplifies algorithms and ensure the relative accuracy (corrections variety between the epochs). Observations more than 10 stations in China are processed, and the equivalent clock error calculation results are analyzed, which shows that the satellite UDRE are significantly reduced and user location accuracy improves when the equivalent clock error corrections are applied. The residuals deducting equivalent satellite clock error contains the projection difference of satellite orbit error in all station (tangential and normal errors are main). We utilize the residuals to solve the tangential and normal orbit errors which cause the projection difference. The same observation data is processed. The results show that after calculating three-dimensional corrections, the satellite UDRE doesn't improve significantly compared to equivalent satellite clock error corrections and user
Ohsaka, Akimichi; Hirota-Komatsu, Satoko; Araki, Marito; Komatsu, Norio
2015-04-10
Neuropilin-1 (NRP-1) is involved in angiogenesis, but the role of NRP-1 in megakaryocytopoiesis is not yet fully understood. In this study, we investigated whether thrombopoietin (TPO) regulates the expression of platelet-derived growth factor (PDGF) and its receptors (PDGFRs) on TPO-dependent UT-7/TPO cells and whether PDGFRs and NRP-1 on UT-7/TPO cells form complexes during megakaryocytic differentiation. When UT-7/TPO cells were starved of TPO for 24 h and then stimulated with 5 ng/ml TPO, the expression of PDGF-B, PDGFRα, and PDGFRβ were significantly up-regulated after the addition of TPO. TPO also induced tyrosine phosphorylation of PDGFRα but not PDGFRβ, and promoted the formation of PDGFRαβ heterodimer complexes. Furthermore, megakaryocytic differentiation of UT-7/TPO cells on treatment with phorbol myristate acetate (PMA) was accompanied by a marked up-regulation of PDGFRβ and NRP-1 protein expression, complex formation between PDGFRs and NRP-1, PDGFRαβ heterodimer complexes, and an increase in PDGF-BB-binding activity. Immunocytochemistry confirmed complex formation between PDGFRs and NRP-1 and PDGFRαβ heterodimer complexes in PMA-differentiated UT-7/TPO cells. Our observations suggest that NRP-1 is involved in megakaryocytopoiesis through complex formation with PDGFRs, and that NRP-1-PDGFR-complexes may contribute to effective cellular functions mediated by TPO and PDGF in megakaryocytic cells.
Informational analysis involving application of complex information system
Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael
The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.