EpCAM Aptamer-siRNA Chimera Targets and Regress Epithelial Cancer.
Directory of Open Access Journals (Sweden)
Nithya Subramanian
Full Text Available Epithelial cell adhesion molecule (EpCAM, a cancer stem cell (CSC marker is over expressed in epithelial cancers and in retinoblastoma (RB. We fabricated an EpCAM targeting aptamer-siRNA chimera and investigated its anti-tumor property and EpCAM intracellular domain (EpICD mediated signaling in epithelial cancer. The anti-tumor efficacy of EpCAM aptamer-siEpCAM chimera (EpApt-siEp was evaluated by qPCR, northern and Western blotting in WERI-Rb1- RB cell line, primary RB tumor cells and in MCF7- breast cancer cell line. Anti-tumor activity of EpApt-siEp was studied in vivo using epithelial cancer (MCF7 mice xenograft model. The mechanism and pathways involved in the anti-tumor activity was further studied using protein arrays and qPCR. EpApt-siEp chimera was processed in vitro by dicer enzyme. Treatment of the WERI-Rb1 and MCF7 cells with EpApt-siEp revealed statistically significant down regulation of EpCAM expression (P<0.005 and concomitant reduction in cellular proliferation. In primary RB cells cultured from RB tumors, EpApt-siEp silenced EpCAM, significantly inhibited (P<0.01 cell proliferation and induced cytotoxicity. Knockdown of EpICD expressed in RB primary tumors led to repression of pluripotency markers, SOX2, OCT4, NANOG, and CD133. In vivo studies showed complete tumor growth regression without any toxicity in animals (P<0.001 and tumor tissues showed significant downregulation (P<0.05 of EpCAM, MRP1, ABCG2, stathmin, survivin and upregulation of ATM (P<0.05 leading to apoptosis by intrinsic pathway with minor alteration in cytokines. Our results revealed that EpApt-siEp potentially eradicated EpCAM positive cancer cells through CSC marker suppression and apoptosis, while sparing normal EpCAM negative adjacent cells.
Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming
DEFF Research Database (Denmark)
2016-01-01
Atherosclerosis is an inflammatory disease linked to elevated blood cholesterol concentrations. Despite ongoing advances in the prevention and treatment of atherosclerosis, cardiovascular disease remains the leading cause of death worldwide. Continuous retention of apolipoprotein B...... that increases cholesterol solubility in preventing and reversing atherosclerosis. We showed that CD treatment of murine atherosclerosis reduced atherosclerotic plaque size and CC load and promoted plaque regression even with a continued cholesterol-rich diet. Mechanistically, CD increased oxysterol production...... of CD as well as for augmented reverse cholesterol transport. Because CD treatment in humans is safe and CD beneficially affects key mechanisms of atherogenesis, it may therefore be used clinically to prevent or treat human atherosclerosis....
Energy Technology Data Exchange (ETDEWEB)
Viennot, David, E-mail: david.viennot@utinam.cnrs.fr; Aubourg, Lucile
2016-02-15
We study a theoretical model of closed quasi-hermitian chain of spins which exhibits quantum analogues of chimera states, i.e. long life classical states for which a part of an oscillator chain presents an ordered dynamics whereas another part presents a disordered dynamics. For the quantum analogue, the chimera behaviour deals with the entanglement between the spins of the chain. We discuss the entanglement properties, quantum chaos, quantum disorder and semi-classical similarity of our quantum chimera system. The quantum chimera concept is novel and induces new perspectives concerning the entanglement of multipartite systems. - Highlights: • We propose a spin chain model with long range couplings having purely quantum states similar to the classical chimera states. • The quantum chimera states are characterized by the coexistence of strongly entangled and non-entangled spins in the same chain. • The quantum chimera states present some characteristics of quantum chaos.
Esquivies, Luis; Blackler, Alissa; Peran, Macarena; Rodriguez-Esteban, Concepcion; Izpisua Belmonte, Juan Carlos; Booker, Evan; Gray, Peter C.; Ahn, Chihoon; Kwiatkowski, Witek; Choe, Senyon
2014-01-01
Nodal, a member of the TGF-β superfamily, plays an important role in vertebrate and invertebrate early development. The biochemical study of Nodal and its signaling pathway has been a challenge, mainly because of difficulties in producing the protein in sufficient quantities. We have developed a library of stable, chemically refoldable Nodal/BMP2 chimeric ligands (NB2 library). Three chimeras, named NB250, NB260, and NB264, show Nodal-like signaling properties including dependence on the co-receptor Cripto and activation of the Smad2 pathway. NB250, like Nodal, alters heart looping during the establishment of embryonic left-right asymmetry, and both NB250 and NB260, as well as Nodal, induce chondrogenic differentiation of human adipose-derived stem cells. This Nodal-induced differentiation is shown to be more efficient than BPM2-induced differentiation. Interestingly, the crystal structure of NB250 shows a backbone scaffold similar to that of BMP2. Our results show that these chimeric ligands may have therapeutic implications in cartilage injuries. PMID:24311780
Maistrenko, Yuri; Brezetsky, Serhiy; Jaros, Patrycja; Levchenko, Roman; Kapitaniak, Tomasz
2017-01-01
We demonstrate that chimera behavior can be observed in small networks consisting of three identical oscillators, with mutual all-to-all coupling. Three different types of chimeras, characterized by the coexistence of two coherent oscillators and one incoherent oscillator (i.e., rotating with another frequency) have been identified, where the oscillators show periodic (two types) and chaotic (one type) behaviors. Typical bifurcations at the transitions from full synchronization to chimera states and between different types of chimeras have been described. Parameter regions for the chimera states are obtained in the form of Arnold tongues, issued from a singular parameter point. Our analysis suggests that chimera states can be observed in small networks relevant to various real-world systems.
Gene activation regresses atherosclerosis, promotes health, and enhances longevity
Directory of Open Access Journals (Sweden)
Luoma Pauli V
2010-07-01
Full Text Available Abstract Background Lifestyle factors and pharmacological compounds activate genetic mechanisms that influence the development of atherosclerotic and other diseases. This article reviews studies on natural and pharmacological gene activation that promotes health and enhances longevity. Results Living habits including healthy diet and regular physical activity, and pharmacotherapy, upregulate genes encoding enzymes and apolipoprotein and ATP-binding cassette transporters, acting in metabolic processes that promote health and increase survival. Cytochrome P450-enzymes, physiological factors in maintaining cholesterol homeostasis, generate oxysterols for the elimination of surplus cholesterol. Hepatic CTP:phosphocholine cytidylyltransferase-α is an important regulator of plasma HDL-C level. Gene-activators produce plasma lipoprotein profile, high HDL-C, HDL2-C and HDL-C/cholesterol ratio, which is typical of low risk of atherosclerotic disease, and also of exceptional longevity together with reduced prevalence of cardiovascular, metabolic and other diseases. High HDL contributes to protection against inflammation, oxidation and thrombosis, and associates with good cognitive function in very old people. Avoiding unhealthy stress and managing it properly promotes health and increases life expectancy. Conclusions Healthy living habits and gene-activating xenobiotics upregulate mechanisms that produce lipoprotein pattern typical of very old people and enhance longevity. Lipoprotein metabolism and large HDL2 associate with the process of living a very long life. Major future goals for health promotion are the improving of commitment to both wise lifestyle choices and drug therapy, and further the developing of new and more effective and well tolerated drugs and treatments.
Multivariable Linear Regression Model for Promotional Forecasting:The Coca Cola - Morrisons Case
Zheng, Yiwei/Y
2009-01-01
This paper describes a promotional forecasting model, built by linear regression module in Microsoft Excel. It intends to provide quick and reliable forecasts with a moderate credit and to assist the CPFR between the Coca Cola Enterprises (CCE) and the Morrisons. The model is derived from previous researches and literature review on CPFR, promotion, forecasting and modelling. It is designed as a multivariable linear regression model, which involves several promotional mix as variables includi...
de Melo-Martín, Inmaculada
2008-12-01
Discussions about whether new biomedical technologies threaten or violate human dignity are now common. Indeed, appeals to human dignity have played a central role in national and international debates about whether to allow particular kinds of biomedical investigations. The focus of this paper is on chimera research. I argue here that both those who claim that particular types of human-nonhuman chimera research threaten human dignity and those who argue that such threat does not exist fail to make their case. I first introduce some of the arguments that have been offered supporting the claim that the creation of certain sorts of chimeras threatens or violates human dignity. I next present opponents' assessments of such arguments. Finally I critically analyze both the critics' and the supporters' claims about whether chimera research threatens human dignity.
A Discontinuous Galerkin Chimera Overset Solver
Galbraith, Marshall Christopher
This work summarizes the development of an accurate, efficient, and flexible Computational Fluid Dynamics computer code that is an improvement relative to the state of the art. The improved accuracy and efficiency is obtained by using a high-order discontinuous Galerkin (DG) discretization scheme. In order to maximize the computational efficiency, quadrature-free integration and numerical integration optimized as matrix-vector multiplications is employed and implemented through a pre-processor (PyDG). Using the PyDG pre-processor, a C++ polynomial library has been developed that uses overloaded operators to design an efficient Domain Specific Language (DSL) that allows expressions involving polynomials to be written as if they are scalars. The DSL, which makes the syntax of computer code legible and intuitive, promotes maintainability of the software and simplifies the development of additional capabilities. The flexibility of the code is achieved by combining the DG scheme with the Chimera overset method. The Chimera overset method produces solutions on a set of overlapping grids that communicate through an exchange of data on grid boundaries (known as artificial boundaries). Finite volume and finite difference discretizations use fringe points, which are layers of points on the artificial boundaries, to maintain the interior stencil on artificial boundaries. The fringe points receive solution values interpolated from overset grids. Proper interpolation requires fringe points to be contained in overset grids. Insufficient overlap must be corrected by modifying the grid system. The Chimera scheme can also exclude regions of grids that lie outside the computational domain; a process commonly known as hole cutting. The Chimera overset method has traditionally enabled the use of high-order finite difference and finite volume approaches such as WENO and compact differencing schemes, which require structured meshes, for modeling fluid flow associated with complex
Energy Technology Data Exchange (ETDEWEB)
Matzinger, P.; Mirkwood, G.
1978-07-01
Fully H-2 incompatible radiation chimeras were prepared using BALB congenic mice. Such chimeric mice were immunized in vivo against histocompatibility antigens of the C57BL/10Sn (B10) background in association with either the parental H-2 haplotypes, and their spleen cells subsequently boosted in vitro with the same minor antigens. Strong H-2-restricted cytotoxic activity against minor antigens was detected, and the specificity of the restriction could be to the H-2 haplotype of the donor or the host depending on the cells used for priming or boosting. Cross priming could also be demonstrated in these mice. The results show that fully allogenic radiation chimeras can produce H-2-restricted T-cell responses to minor histocompatibility (H) antigens, and are discussed in relation to contrasting results.
Chimera and other fertilization errors.
Malan, V; Vekemans, M; Turleau, C
2006-11-01
The finding of a mixture of 46,XX and 46,XY cells in an individual has been rarely reported in literature. It usually results in individuals with ambiguous genitalia. Approximately 10% of true human hermaphrodites show this type of karyotype. However, the underlying mechanisms are poorly understood. It may be the result of mosaicism or chimerism. By definition, a chimera is produced by the fusion of two different zygotes in a single embryo, while a mosaic contains genetically different cells issued from a single zygote. Several mechanisms are involved in the production of chimera. Stricto sensu, chimerism occurs from the post-zygotic fusion of two distinct embryos leading to a tetragametic chimera. In addition, there are other entities, which are also referred to as chimera: parthenogenetic chimera and chimera resulting from fertilization of the second polar body. Furthermore, a particular type of chimera called 'androgenetic chimera' recently described in fetuses with placental mesenchymal dysplasia and in rare patients with Beckwith-Wiedemann syndrome is discussed. Strategies to study mechanisms leading to the production of chimera and mosaics are also proposed.
Emergence of multicluster chimera states.
Yao, Nan; Huang, Zi-Gang; Grebogi, Celso; Lai, Ying-Cheng
2015-09-09
A remarkable phenomenon in spatiotemporal dynamical systems is chimera state, where the structurally and dynamically identical oscillators in a coupled networked system spontaneously break into two groups, one exhibiting coherent motion and another incoherent. This phenomenon was typically studied in the setting of non-local coupling configurations. We ask what can happen to chimera states under systematic changes to the network structure when links are removed from the network in an orderly fashion but the local coupling topology remains invariant with respect to an index shift. We find the emergence of multicluster chimera states. Remarkably, as a parameter characterizing the amount of link removal is increased, chimera states of distinct numbers of clusters emerge and persist in different parameter regions. We develop a phenomenological theory, based on enhanced or reduced interactions among oscillators in different spatial groups, to explain why chimera states of certain numbers of clusters occur in certain parameter regions. The theoretical prediction agrees well with numerics.
Directory of Open Access Journals (Sweden)
Yoshizawa Masato
2012-12-01
Full Text Available Abstract Background How and why animals lose eyesight during adaptation to the dark and food-limited cave environment has puzzled biologists since the time of Darwin. More recently, several different adaptive hypotheses have been proposed to explain eye degeneration based on studies in the teleost Astyanax mexicanus, which consists of blind cave-dwelling (cavefish and sighted surface-dwelling (surface fish forms. One of these hypotheses is that eye regression is the result of indirect selection for constructive characters that are negatively linked to eye development through the pleiotropic effects of Sonic Hedgehog (SHH signaling. However, subsequent genetic analyses suggested that other mechanisms also contribute to eye regression in Astyanax cavefish. Here, we introduce a new approach to this problem by investigating the phenotypic and genetic relationships between a suite of non-visual constructive traits and eye regression. Results Using quantitative genetic analysis of crosses between surface fish, the Pachón cavefish population and their hybrid progeny, we show that the adaptive vibration attraction behavior (VAB and its sensory receptors, superficial neuromasts (SN specifically found within the cavefish eye orbit (EO, are genetically correlated with reduced eye size. The quantitative trait loci (QTL for these three traits form two clusters of congruent or overlapping QTL on Astyanax linkage groups (LG 2 and 17, but not at the shh locus on LG 13. Ablation of EO SN in cavefish demonstrated a major role for these sensory receptors in VAB expression. Furthermore, experimental induction of eye regression in surface fish via shh overexpression showed that the absence of eyes was insufficient to promote the appearance of VAB or EO SN. Conclusions We conclude that natural selection for the enhancement of VAB and EO SN indirectly promotes eye regression in the Pachón cavefish population through an antagonistic relationship involving genetic
Recurrence quantification analysis of chimera states
Energy Technology Data Exchange (ETDEWEB)
Santos, M.S. [Pós-Graduação em Ciências/Física, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Szezech, J.D., E-mail: jdanilo@gmail.com [Departamento de Matemática e Estatística, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Batista, A.M., E-mail: antoniomarcosbatista@gmail.com [Departamento de Matemática e Estatística, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, 05315-970, São Paulo, SP (Brazil); Viana, R.L.; Lopes, S.R. [Departamento de Física, Universidade Federal do Paraná, 81531-990, Curitiba, PR (Brazil)
2015-10-02
Chimera states, characterised by coexistence of coherence and incoherence in coupled dynamical systems, have been found in various physical systems, such as mechanical oscillator networks and Josephson-junction arrays. We used recurrence plots to provide graphical representations of recurrent patterns and identify chimera states. Moreover, we show that recurrence plots can be used as a diagnostic of chimera states and also to identify the chimera collapse. - Highlights: • Chimera states have been found in various physical systems. • Recurrence plots is a graphical method useful to locate recurring patterns. • We used recurrence plots to identify the chimera states. • We show also the recurrence plots can identify the chimera collapse.
Crosby, Natasha M; Ghosh, Mistuni; Su, Betty; Beckstead, Jennifer A; Kamei, Ayako; Simonsen, Jens B; Luo, Bing; Gordon, Leo I; Forte, Trudy M; Ryan, Robert O
2015-08-01
A fusion protein comprising an α-CD20 single chain variable fragment (scFv) antibody, a spacer peptide, and human apolipoprotein (apo) A-I was constructed and expressed in Escherichia coli. The lipid interaction properties intrinsic to apoA-I as well as the antigen recognition properties of the scFv were retained by the chimera. scFv•apoA-I was formulated into nanoscale reconstituted high-density lipoprotein particles (termed nanodisks; ND) and incubated with cultured cells. α-CD20 scFv•apoA-I ND bound to CD20-positive non-Hodgkins lymphoma (NHL) cells (Ramos and Granta) but not to CD20-negative T lymphocytes (i.e., Jurkat). Binding to NHL cells was partially inhibited by pre-incubation with rituximab, a monoclonal antibody directed against CD20. Confocal fluorescence microscopy analysis of Granta cells following incubation with α-CD20 scFv•apoA-I ND formulated with the intrinsically fluorescent hydrophobic polyphenol, curcumin, revealed α-CD20 scFv•apoA-I localizes to the cell surface, while curcumin off-loads and gains entry to the cell. Compared to control incubations, viability of cultured NHL cells was decreased upon incubation with α-CD20 scFv•apoA-I ND harboring curcumin. Thus, formulation of curcumin ND with α-CD20 scFv•apoA-I as the scaffold component confers cell targeting and enhanced bioactive agent delivery, providing a strategy to minimize toxicity associated with chemotherapeutic agents.
Rayner, Katey J; Sheedy, Frederick J; Esau, Christine C; Hussain, Farah N; Temel, Ryan E; Parathath, Saj; van Gils, Janine M; Rayner, Alistair J; Chang, Aaron N; Suarez, Yajaira; Fernandez-Hernando, Carlos; Fisher, Edward A; Moore, Kathryn J
2011-07-01
Plasma HDL levels have a protective role in atherosclerosis, yet clinical therapies to raise HDL levels have remained elusive. Recent advances in the understanding of lipid metabolism have revealed that miR-33, an intronic microRNA located within the SREBF2 gene, suppresses expression of the cholesterol transporter ABC transporter A1 (ABCA1) and lowers HDL levels. Conversely, mechanisms that inhibit miR-33 increase ABCA1 and circulating HDL levels, suggesting that antagonism of miR-33 may be atheroprotective. As the regression of atherosclerosis is clinically desirable, we assessed the impact of miR-33 inhibition in mice deficient for the LDL receptor (Ldlr-/- mice), with established atherosclerotic plaques. Mice treated with anti-miR33 for 4 weeks showed an increase in circulating HDL levels and enhanced reverse cholesterol transport to the plasma, liver, and feces. Consistent with this, anti-miR33-treated mice showed reductions in plaque size and lipid content, increased markers of plaque stability, and decreased inflammatory gene expression. Notably, in addition to raising ABCA1 levels in the liver, anti-miR33 oligonucleotides directly targeted the plaque macrophages, in which they enhanced ABCA1 expression and cholesterol removal. These studies establish that raising HDL levels by anti-miR33 oligonucleotide treatment promotes reverse cholesterol transport and atherosclerosis regression and suggest that it may be a promising strategy to treat atherosclerotic vascular disease.
Shen, Li; Peng, Hongchun; Peng, Ran; Fan, Qingsong; Zhao, Shuiping; Xu, Danyan; Morisseau, Christophe; Chiamvimonvat, Nipavan; Hammock, Bruce D
2015-04-01
Adipose tissue is the body largest free cholesterol reservoir and abundantly expresses ATP binding cassette transporter A1 (ABCA1), which maintains plasma high-density lipoprotein (HDL) levels. HDLs have a protective role in atherosclerosis by mediating reverse cholesterol transport (RCT). Soluble epoxide hydrolase (sEH) is a cytosolic enzyme whose inhibition has various beneficial effects on cardiovascular disease. The sEH is highly expressed in adipocytes, and it converts epoxyeicosatrienoic acids (EETs) into less bioactive dihydroxyeicosatrienoic acids. We previously showed that increasing EETs levels with a sEH inhibitor (sEHI) (t-AUCB) resulted in elevated ABCA1 expression and promoted ABCA1-mediated cholesterol efflux from 3T3-L1 adipocytes. The present study investigates the impacts of t-AUCB in mice deficient for the low density lipoprotein (LDL) receptor (Ldlr(-/-) mice) with established atherosclerotic plaques. The sEH inhibitor delivered in vivo for 4 weeks decreased the activity of sEH in adipose tissue, enhanced ABCA1 expression and cholesterol efflux from adipose depots, and consequently increased HDL levels. Furthermore, t-AUCB enhanced RCT to the plasma, liver, bile and feces. It also showed the reduction of plasma LDL-C levels. Consistently, t-AUCB-treated mice showed reductions in the size of atherosclerotic plaques. These studies establish that raising adipose ABCA1 expression, cholesterol efflux, and plasma HDL levels with t-AUCB treatment promotes RCT, decreasing LDL-C and atherosclerosis regression, suggesting that sEH inhibition may be a promising strategy to treat atherosclerotic vascular disease.
Recurrence quantification analysis of chimera states
Santos, M. S.; Szezech, J. D.; Batista, A. M.; Caldas, I. L.; Viana, R. L.; Lopes, S. R.
2015-10-01
Chimera states, characterised by coexistence of coherence and incoherence in coupled dynamical systems, have been found in various physical systems, such as mechanical oscillator networks and Josephson-junction arrays. We used recurrence plots to provide graphical representations of recurrent patterns and identify chimera states. Moreover, we show that recurrence plots can be used as a diagnostic of chimera states and also to identify the chimera collapse.
Nkomo, Simbarashe; Tinsley, Mark R.; Showalter, Kenneth
2016-09-01
Chimera and chimera-like states are characterized in populations of photochemically coupled Belousov-Zhabotinsky (BZ) oscillators. Simple chimeras and chimera states with multiple and traveling phase clusters, phase-slip behavior, and chimera-like states with phase waves are described. Simulations with a realistic model of the discrete BZ system of populations of homogeneous and heterogeneous oscillators are compared with each other and with experimental behavior.
Petascale Supernova Simulation with CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Messer, Bronson [ORNL; Bruenn, S. W. [Florida Atlantic University; Blondin, J. M. [North Carolina State University; Mezzacappa, Anthony [ORNL; Hix, William Raphael [ORNL; Dirk, Charlotte [Florida Atlantic University
2007-01-01
CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. We describe some ma jor algorithmic facets of the code and briefly discuss some recent results. The multi-physics nature of the problem, and the specific implementation of that physics in CHIMERA, provide a rather straightforward path to effective use of multi-core platforms in the near future.
Petascale supernova simulation with CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Messer, O E B [National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6008 (United States); Bruenn, S W [Department of Physics, Florida Atlantic University, 777 W Glades Road, Boca Raton, FL 33431-0991 (United States); Blondin, J M [Department of Physics, North Carolina State University, Raleigh, NC 27695-8202 (United States); Hix, W R [Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6354 (United States); Mezzacappa, A [Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6354 (United States); Dirk, C J [Department of Physics, Florida Atlantic University, 777 W Glades Road, Boca Raton, FL 33431-0991 (United States)
2007-07-15
CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. We describe some major algorithmic facets of the code and briefly discuss some recent results. The multi-physics nature of the problem, and the specific implementation of that physics in CHIMERA, provide a rather straightforward path to effective use of multi-core platforms in the near future.
Ethical considerations in chimera research.
Hermerén, Göran
2015-01-01
The development of human pluripotent stem cells has opened up the possibility to analyse the function of human cells and tissues in animal hosts, thus generating chimeras. Although such lines of research have great potential for both basic and translational science, they also raise unique ethical issues that must be considered.
Constraining QGP properties with CHIMERA
Garishvili, Irakli; Abelev, Betty; Cheng, Michael; Glenn, Andrew; Soltz, Ron
2011-10-01
Understanding essential properties of strongly interacting matter is arguably the most important goal of the relativistic heavy-ion programs both at RHIC and the LHC. In particular, constraining observables such as ratio of shear viscosity to entropy density, η/s, initial temperature, Tinit, and energy density is of critical importance. For this purpose we have developed CHIMERA, Comprehensive Heavy Ion Model Reporting and Evaluation Algorithm. CHIMERA is designed to facilitate global statistical comparison of results from our multi-stage hydrodynamics/hadron cascade model of heavy ion collisions to the key soft observables (HBT, elliptic flow, spectra) measured at RHIC and the LHC. Within this framework the data representing multiple different measurements from different experiments are compiled into single format. One of the unique features of CHIMERA is, that in addition to taking into account statistical errors, it also treats different types of systematic uncertainties. The hydrodynamics/hadron cascade model used in the framework incorporates different initial state conditions, pre-equilibrium flow, the UVH2+1 viscous hydro model, Cooper-Frye freezeout, and the UrQMD hadronic cascade model. The sensitivity of the observables to the equation of state (EoS) is explored using several EoS's in the hydrodynamic evolution. The latest results from CHIMERA, including data from the LHC, will be presented.
Markova, Elena N; Kantidze, Omar L; Razin, Sergey V
2012-12-01
Chromosomal translocation t (8;21)(q22;22) is one of the most frequent cytogenetic abnormalities found in acute myeloid leukaemia (AML). It generates the AML1/ETO fusion gene, which itself supports human haematopoietic stem cell self-renewal. However, the mechanism guiding transcription of this chimeric gene remains unclear. In our work, we attempted to shed light on this essential issue. We investigated the promoter from which transcription of the AML1/ETO gene is initiated and defined the three-dimensional structure of the whole rearranged locus. Copyright © 2012 Elsevier B.V. All rights reserved.
Pinning control of chimera states
Gambuzza, Lucia Valentina; Frasca, Mattia
2016-08-01
The position of the coherent and incoherent domain of a chimera state in a ring of nonlocally coupled oscillators is strongly influenced by the initial conditions, making nontrivial the problem of confining them in a specific region of the structure. In this paper we propose the use of spatial pinning to induce a chimera state where the nodes belonging to one domain, either the coherent or the incoherent, are fixed by the control action. We design two different techniques according to the dynamics to be forced in the region of pinned nodes, and validate them on FitzHugh-Nagumo and Kuramoto oscillators. Furthermore, we introduce a suitable strategy to deal with the effects of finite size in small structures.
Recent results of CHIMERA activity
Directory of Open Access Journals (Sweden)
Pagano A.
2012-07-01
Full Text Available The experimental activity of CHIMERA in recent years has been characterized by a steady progress in the detection technique and data analysis. Since 2008 the detector system benefits of new implementations: a new reaction chamber, a new charged particle identification in silicon detector made by an extended pulse shape method and an efficient system for the identification of exotic beams produced by projectile-like fragmentation (In-flight method. These implementations appear to be promising tools in view of further exclusive experiments in the field of isospin physics. The coupling of CHIMERA with other equipments (such as interferometers and highly segmented arrays, magnetic elements, neutron detectors, etc. is also envisaged in order to extend the studies of the reaction mechanism in heavy ion physics.
2012-01-01
Abstract Background How and why animals lose eyesight during adaptation to the dark and food-limited cave environment has puzzled biologists since the time of Darwin. More recently, several different adaptive hypotheses have been proposed to explain eye degeneration based on studies in the teleost Astyanax mexicanus, which consists of blind cave-dwelling (cavefish) and sighted surface-dwelling (surface fish) forms. One of these hypotheses is that eye regression is the result of indirect selec...
Chimera states in mechanical oscillator networks
DEFF Research Database (Denmark)
Martens, Erik Andreas; Thutupalli, Shashi; Fourrière, Antoine
2013-01-01
of identical oscillators, numerous theoretical studies in recent years have revealed the intriguing possibility of "chimera states," in which the symmetry of the oscillator population is broken into a synchronous part and an asynchronous part. However, a striking lack of empirical evidence raises the question...... of whether chimeras are indeed characteristic of natural systems. This calls for a palpable realization of chimera states without any fine-tuning, from which physical mechanisms underlying their emergence can be uncovered. Here, we devise a simple experiment with mechanical oscillators coupled...... in a hierarchical network to show that chimeras emerge naturally from a competition between two antagonistic synchronization patterns. We identify a wide spectrum of complex states, encompassing and extending the set of previously described chimeras. Our mathematical model shows that the self-organization observed...
The smallest chimera state for coupled pendula
Wojewoda, Jerzy; Czolczynski, Krzysztof; Maistrenko, Yuri; Kapitaniak, Tomasz
2016-01-01
Chimera states in the systems of coupled identical oscillators are spatiotemporal patterns in which different groups of oscillators can exhibit coexisting synchronous and incoherent behaviors despite homogeneous coupling. Although these states are typically observed in large ensembles of oscillators, recently it has been suggested that chimera states may occur in the systems with small numbers of oscillators. Here, considering three coupled pendula showing chaotic behavior, we find the pattern of the smallest chimera state, which is characterized by the coexistence of two synchronized and one incoherent oscillator. We show that this chimera state can be observed in simple experiments with mechanical oscillators, which are controlled by elementary dynamical equations derived from Newton’s laws. Our finding suggests that chimera states are observable in small networks relevant to various real-world systems. PMID:27713483
The smallest chimera state for coupled pendula
Wojewoda, Jerzy; Czolczynski, Krzysztof; Maistrenko, Yuri; Kapitaniak, Tomasz
2016-10-01
Chimera states in the systems of coupled identical oscillators are spatiotemporal patterns in which different groups of oscillators can exhibit coexisting synchronous and incoherent behaviors despite homogeneous coupling. Although these states are typically observed in large ensembles of oscillators, recently it has been suggested that chimera states may occur in the systems with small numbers of oscillators. Here, considering three coupled pendula showing chaotic behavior, we find the pattern of the smallest chimera state, which is characterized by the coexistence of two synchronized and one incoherent oscillator. We show that this chimera state can be observed in simple experiments with mechanical oscillators, which are controlled by elementary dynamical equations derived from Newton’s laws. Our finding suggests that chimera states are observable in small networks relevant to various real-world systems.
Nakamura, Ryota; Suhrcke, Marc; Jebb, Susan A; Pechey, Rachel; Almiron-Roig, Eva; Marteau, Theresa M
2015-04-01
There is a growing concern, but limited evidence, that price promotions contribute to a poor diet and the social patterning of diet-related disease. We examined the following questions: 1) Are less-healthy foods more likely to be promoted than healthier foods? 2) Are consumers more responsive to promotions on less-healthy products? 3) Are there socioeconomic differences in food purchases in response to price promotions? With the use of hierarchical regression, we analyzed data on purchases of 11,323 products within 135 food and beverage categories from 26,986 households in Great Britain during 2010. Major supermarkets operated the same price promotions in all branches. The number of stores that offered price promotions on each product for each week was used to measure the frequency of price promotions. We assessed the healthiness of each product by using a nutrient profiling (NP) model. A total of 6788 products (60%) were in healthier categories and 4535 products (40%) were in less-healthy categories. There was no significant gap in the frequency of promotion by the healthiness of products neither within nor between categories. However, after we controlled for the reference price, price discount rate, and brand-specific effects, the sales uplift arising from price promotions was larger in less-healthy than in healthier categories; a 1-SD point increase in the category mean NP score, implying the category becomes less healthy, was associated with an additional 7.7-percentage point increase in sales (from 27.3% to 35.0%; P sales uplift from promotions was larger for higher-socioeconomic status (SES) groups than for lower ones (34.6% for the high-SES group, 28.1% for the middle-SES group, and 23.1% for the low-SES group). Finally, there was no significant SES gap in the absolute volume of purchases of less-healthy foods made on promotion. Attempts to limit promotions on less-healthy foods could improve the population diet but would be unlikely to reduce health
Devesa, Jesús; Alonso, Alba; López, Natalia; García, José; Puell, Carlos I.; Pablos, Tamara; Devesa, Pablo
2017-01-01
Caudal regression syndrome (CRS) is a malformation occurring during the fetal period and mainly characterized by an incomplete development of the spinal cord (SC), which is often accompanied by other developmental anomalies. We studied a 9-month old child with CRS who presented interruption of the SC at the L2–L3 level, sacral agenesis, a lack of innervation of the inferior limbs (flaccid paraplegia), and neurogenic bladder and bowel. Given the known positive effects of growth hormone (GH) on neural stem cells (NSCs), we treated him with GH and rehabilitation, trying to induce recovery from the aforementioned sequelae. The Gross Motor Function Test (GMFM)-88 test score was 12.31%. After a blood analysis, GH treatment (0.3 mg/day, 5 days/week, during 3 months and then 15 days without GH) and rehabilitation commenced. This protocol was followed for 5 years, the last GH dose being 1 mg/day. Blood analysis and physical exams were performed every 3 months initially and then every 6 months. Six months after commencing the treatment the GMFM-88 score increased to 39.48%. Responses to sensitive stimuli appeared in most of the territories explored; 18 months later sensitive innervation was complete and the patient moved all muscles over the knees and controlled his sphincters. Three years later he began to walk with crutches, there was plantar flexion, and the GMFM-88 score was 78.48%. In summary, GH plus rehabilitation may be useful for innervating distal areas below the level of the incomplete spinal cord in CRS. It is likely that GH acted on the ependymal SC NSCs, as the hormone does in the neurogenic niches of the brain, and rehabilitation helped to achieve practically full functionality. PMID:28124993
Devesa, Jesús; Alonso, Alba; López, Natalia; García, José; Puell, Carlos I; Pablos, Tamara; Devesa, Pablo
2017-01-23
Caudal regression syndrome (CRS) is a malformation occurring during the fetal period and mainly characterized by an incomplete development of the spinal cord (SC), which is often accompanied by other developmental anomalies. We studied a 9-month old child with CRS who presented interruption of the SC at the L2-L3 level, sacral agenesis, a lack of innervation of the inferior limbs (flaccid paraplegia), and neurogenic bladder and bowel. Given the known positive effects of growth hormone (GH) on neural stem cells (NSCs), we treated him with GH and rehabilitation, trying to induce recovery from the aforementioned sequelae. The Gross Motor Function Test (GMFM)-88 test score was 12.31%. After a blood analysis, GH treatment (0.3 mg/day, 5 days/week, during 3 months and then 15 days without GH) and rehabilitation commenced. This protocol was followed for 5 years, the last GH dose being 1 mg/day. Blood analysis and physical exams were performed every 3 months initially and then every 6 months. Six months after commencing the treatment the GMFM-88 score increased to 39.48%. Responses to sensitive stimuli appeared in most of the territories explored; 18 months later sensitive innervation was complete and the patient moved all muscles over the knees and controlled his sphincters. Three years later he began to walk with crutches, there was plantar flexion, and the GMFM-88 score was 78.48%. In summary, GH plus rehabilitation may be useful for innervating distal areas below the level of the incomplete spinal cord in CRS. It is likely that GH acted on the ependymal SC NSCs, as the hormone does in the neurogenic niches of the brain, and rehabilitation helped to achieve practically full functionality.
Directory of Open Access Journals (Sweden)
Jesús Devesa
2017-01-01
Full Text Available Caudal regression syndrome (CRS is a malformation occurring during the fetal period and mainly characterized by an incomplete development of the spinal cord (SC, which is often accompanied by other developmental anomalies. We studied a 9-month old child with CRS who presented interruption of the SC at the L2–L3 level, sacral agenesis, a lack of innervation of the inferior limbs (flaccid paraplegia, and neurogenic bladder and bowel. Given the known positive effects of growth hormone (GH on neural stem cells (NSCs, we treated him with GH and rehabilitation, trying to induce recovery from the aforementioned sequelae. The Gross Motor Function Test (GMFM-88 test score was 12.31%. After a blood analysis, GH treatment (0.3 mg/day, 5 days/week, during 3 months and then 15 days without GH and rehabilitation commenced. This protocol was followed for 5 years, the last GH dose being 1 mg/day. Blood analysis and physical exams were performed every 3 months initially and then every 6 months. Six months after commencing the treatment the GMFM-88 score increased to 39.48%. Responses to sensitive stimuli appeared in most of the territories explored; 18 months later sensitive innervation was complete and the patient moved all muscles over the knees and controlled his sphincters. Three years later he began to walk with crutches, there was plantar flexion, and the GMFM-88 score was 78.48%. In summary, GH plus rehabilitation may be useful for innervating distal areas below the level of the incomplete spinal cord in CRS. It is likely that GH acted on the ependymal SC NSCs, as the hormone does in the neurogenic niches of the brain, and rehabilitation helped to achieve practically full functionality.
Generation of axolotl hematopoietic chimeras
Directory of Open Access Journals (Sweden)
David Lopez
2015-02-01
Full Text Available Wound repair is an extremely complex process that requires precise coordination between various cell types including immune cells. Unfortunately, in mammals this usually results in scar formation instead of restoration of the original fully functional tissue, otherwise known as regeneration. Various animal models like frogs and salamanders are currently being studied to determine the intracellular and intercellular pathways, controlled by gene expression, that elicit cell proliferation, differentiation, and migration of cells during regenerative healing. Now, the necessary genetic tools to map regenerative pathways are becoming available for the axolotl salamander, thus allowing comparative studies between scarring and regeneration. Here, we describe in detail three methods to produce axolotl hematopoietic cell-tagged chimeras for the study of hematopoiesis and regeneration.
Directory of Open Access Journals (Sweden)
George M Philips
Full Text Available OBJECTIVE: Chronic fibrosing liver injury is a major risk factor for hepatocarcinogenesis in humans. Mice with targeted deletion of Mdr2 (the murine ortholog of MDR3 develop chronic fibrosing liver injury. Hepatocellular carcinoma (HCC emerges spontaneously in such mice by 50-60 weeks of age, providing a model of fibrosis-associated hepatocarcinogenesis. We used Mdr2(-/- mice to investigate the hypothesis that activation of the hedgehog (Hh signaling pathway promotes development of both liver fibrosis and HCC. METHODS: Hepatic injury and fibrosis, Hh pathway activation, and liver progenitor populations were compared in Mdr2(-/- mice and age-matched wild type controls. A dose finding experiment with the Hh signaling antagonist GDC-0449 was performed to optimize Hh pathway inhibition. Mice were then treated with GDC-0449 or vehicle for 9 days, and effects on liver fibrosis and tumor burden were assessed by immunohistochemistry, qRT-PCR, Western blot, and magnetic resonance imaging. RESULTS: Unlike controls, Mdr2(-/- mice consistently expressed Hh ligands and progressively accumulated Hh-responsive liver myofibroblasts and progenitors with age. Treatment of aged Mdr2-deficient mice with GDC-0449 significantly inhibited hepatic Hh activity, decreased liver myofibroblasts and progenitors, reduced liver fibrosis, promoted regression of intra-hepatic HCCs, and decreased the number of metastatic HCC without increasing mortality. CONCLUSIONS: Hh pathway activation promotes liver fibrosis and hepatocarcinogenesis, and inhibiting Hh signaling safely reverses both processes even when fibrosis and HCC are advanced.
Philips, George M; Chan, Isaac S; Swiderska, Marzena; Schroder, Vanessa T; Guy, Cynthia; Karaca, Gamze F; Moylan, Cynthia; Venkatraman, Talaignair; Feuerlein, Sebastian; Syn, Wing-Kin; Jung, Youngmi; Witek, Rafal P; Choi, Steve; Michelotti, Gregory A; Rangwala, Fatima; Merkle, Elmar; Lascola, Christopher; Diehl, Anna Mae
2011-01-01
Chronic fibrosing liver injury is a major risk factor for hepatocarcinogenesis in humans. Mice with targeted deletion of Mdr2 (the murine ortholog of MDR3) develop chronic fibrosing liver injury. Hepatocellular carcinoma (HCC) emerges spontaneously in such mice by 50-60 weeks of age, providing a model of fibrosis-associated hepatocarcinogenesis. We used Mdr2(-/-) mice to investigate the hypothesis that activation of the hedgehog (Hh) signaling pathway promotes development of both liver fibrosis and HCC. Hepatic injury and fibrosis, Hh pathway activation, and liver progenitor populations were compared in Mdr2(-/-) mice and age-matched wild type controls. A dose finding experiment with the Hh signaling antagonist GDC-0449 was performed to optimize Hh pathway inhibition. Mice were then treated with GDC-0449 or vehicle for 9 days, and effects on liver fibrosis and tumor burden were assessed by immunohistochemistry, qRT-PCR, Western blot, and magnetic resonance imaging. Unlike controls, Mdr2(-/-) mice consistently expressed Hh ligands and progressively accumulated Hh-responsive liver myofibroblasts and progenitors with age. Treatment of aged Mdr2-deficient mice with GDC-0449 significantly inhibited hepatic Hh activity, decreased liver myofibroblasts and progenitors, reduced liver fibrosis, promoted regression of intra-hepatic HCCs, and decreased the number of metastatic HCC without increasing mortality. Hh pathway activation promotes liver fibrosis and hepatocarcinogenesis, and inhibiting Hh signaling safely reverses both processes even when fibrosis and HCC are advanced.
Chimera States in Mechanical Oscillator Networks
Martens, Erik Andreas; Fourrière, Antoine; Hallatschek, Oskar
2013-01-01
The synchronization of coupled oscillators is a fascinating manifestation of self-organization that nature employs to orchestrate essential processes of life, such as the beating of the heart. While it was long thought that synchrony or disorder were mutually exclusive steady states for a network of identical oscillators, numerous theoretical studies in recent years revealed the intriguing possibility of 'chimera states', in which the symmetry of the oscillator population is broken into a synchronous and an asynchronous part. However, a striking lack of empirical evidence raises the question of whether chimeras are indeed characteristic to natural systems. This calls for a palpable realization of chimera states without any fine-tuning, from which physical mechanisms underlying their emergence can be uncovered. Here, we devise a simple experiment with mechanical oscillators coupled in a hierarchical network to show that chimeras emerge naturally from a competition between two antagonistic synchronization patte...
Transferring morality to human-nonhuman chimeras.
Piotrowska, Monika
2014-01-01
Human-nonhuman chimeras have been the focus of ethical controversies for more than a decade, yet some related issues remain unaddressed. For example, little has been said about the relationship between the origin of transferred cells and the morally relevant capacities to which they may give rise. Consider, for example, a developing mouse fetus that receives a brain stem cell transplant from a human and another that receives a brain stem cell transplant from a dolphin. If both chimeras acquire morally relevant capacities as a result of transplantation, and if those capacities are indistinguishable, should the difference in cell origin matter to how we classify these creatures? I argue that if morally relevant capacities are easy to detect, cell origin is irrelevant to how the chimera ought to be treated. However, if such capacities are hard to detect, cell origin should play a role in considerations about how to treat the chimera.
Intermittent chaotic chimeras for coupled rotators
DEFF Research Database (Denmark)
Olmi, Simona; Martens, Erik Andreas; Thutupalli, Shashi
2015-01-01
Two symmetrically coupled populations of N oscillators with inertia m display chaotic solutions with broken symmetry similar to experimental observations with mechanical pendulums. In particular, we report evidence of intermittent chaotic chimeras, where one population is synchronized and the other...
Generation of an adenovirus-parvovirus chimera with enhanced oncolytic potential.
El-Andaloussi, Nazim; Bonifati, Serena; Kaufmann, Johanna K; Mailly, Laurent; Daeffler, Laurent; Deryckère, François; Nettelbeck, Dirk M; Rommelaere, Jean; Marchini, Antonio
2012-10-01
In this study, our goal was to generate a chimeric adenovirus-parvovirus (Ad-PV) vector that combines the high-titer and efficient gene transfer of adenovirus with the anticancer potential of rodent parvovirus. To this end, the entire oncolytic PV genome was inserted into a replication-defective E1- and E3-deleted Ad5 vector genome. As we found that parvoviral NS expression inhibited Ad-PV chimera production, we engineered the parvoviral P4 early promoter, which governs NS expression, by inserting into its sequence tetracycline operator elements. As a result of these modifications, P4-driven expression was blocked in the packaging T-REx-293 cells, which constitutively express the tetracycline repressor, allowing high-yield chimera production. The chimera effectively delivered the PV genome into cancer cells, from which fully infectious replication-competent parvovirus particles were generated. Remarkably, the Ad-PV chimera exerted stronger cytotoxic activities against various cancer cell lines, compared with the PV and Ad parental viruses, while being still innocuous to a panel of tested healthy primary human cells. This Ad-PV chimera represents a novel versatile anticancer agent which can be subjected to further genetic manipulations in order to reinforce its enhanced oncolytic capacity through arming with transgenes or retargeting into tumor cells.
Imperfect traveling chimera states induced by local synaptic gradient coupling
Bera, Bidesh K.; Ghosh, Dibakar; Banerjee, Tanmoy
2016-07-01
In this paper, we report the occurrence of chimera patterns in a network of neuronal oscillators, which are coupled through local, synaptic gradient coupling. We discover a new chimera pattern, namely the imperfect traveling chimera state, where the incoherent traveling domain spreads into the coherent domain of the network. Remarkably, we also find that chimera states arise even for one-way local coupling, which is in contrast to the earlier belief that only nonlocal, global, or nearest-neighbor local coupling can give rise to chimera state; this find further relaxes the essential connectivity requirement of getting a chimera state. We choose a network of identical bursting Hindmarsh-Rose neuronal oscillators, and we show that depending upon the relative strength of the synaptic and gradient coupling, several chimera patterns emerge. We map all the spatiotemporal behaviors in parameter space and identify the transitions among several chimera patterns, an in-phase synchronized state, and a global amplitude death state.
Turbulent chimeras in large semiconductor laser arrays
Shena, Joniald; Kovanis, Vassilios; Tsironis, George P
2016-01-01
Semiconductor laser arrays have been investigated experimentally and theoretically from the viewpoint of temporal and spatial coherence for the past forty years. In this work, we are focusing on a rather novel complex collective behavior, namely chimera states, where synchronized clusters of emitters coexist with unsynchronized ones. For the first time, we find such states exist in large diode arrays based on quantum well gain media with nearest-neighbor interactions. The crucial parameters are the evanescent coupling strength and the relative optical frequency detuning between the emitters of the array. By employing a recently proposed figure of merit for classifying chimera states, we provide quantitative and qualitative evidence for the observed dynamics. The corresponding chimeras are identified as turbulent according to the irregular temporal behavior of the classification measure. Such studies may be the springboard for designing next generation photonic emitters providing on demand diverse waveforms.
Basins of Attraction for Chimera States
DEFF Research Database (Denmark)
Martens, Erik Andreas; Panaggio, Mark; Abrams, Daniel
2016-01-01
Chimera states---curious symmetry-broken states in systems of identical coupled oscillators---typically occur only for certain initial conditions. Here we analyze their basins of attraction in a simple system comprised of two populations. Using perturbative analysis and numerical simulation we...... evaluate asymptotic states and associated destination maps, and demonstrate that basins form a complex twisting structure in phase space. Understanding the basins' precise nature may help in the development of control methods to switch between chimera patterns, with possible technological and neural system...
Bistable Chimera Attractors on a Triangular Network of Oscillator Populations
DEFF Research Database (Denmark)
Martens, Erik Andreas
2010-01-01
. This triangular network is the simplest discretization of a continuous ring of oscillators. Yet it displays an unexpectedly different behavior: in contrast to the lone stable chimera observed in continuous rings of oscillators, we find that this system exhibits two coexisting stable chimeras. Both chimeras are......, as usual, born through a saddle-node bifurcation. As the coupling becomes increasingly local in nature they lose stability through a Hopf bifurcation, giving rise to breathing chimeras, which in turn get destroyed through a homoclinic bifurcation. Remarkably, one of the chimeras reemerges by a reversal...
DEFF Research Database (Denmark)
Olsen, Christian Adam; Bonke, Gitte; Vedel, Line;
2007-01-01
We describe the synthesis and characterization of the first generation of oligomers consisting of alternating repeats of a-amino acids and chiral N-alkyl-ß-alanine (ß-peptoid) residues. These chimeras are stable toward proteolysis, non-hemolytic, and possess antibacterial activity comparable...... peptidomimetic backbone construct for biologically active ligands....
CHIMERA Multidetector at Laboratori Nazionali del Sud
Energy Technology Data Exchange (ETDEWEB)
Aiello, S.; Anzalone, A.; Baldo, M.; Barna, R.; Campisi, M.g.; Cardella, G.; Cavallaro, Sl., Amico, V.D.; De Filippo, E.; DePasquale, D.; Femino, S.; Geraci, E.; Giustolisi, F.; Guazzoni, P.; Iacono-Manno, C.M.; Italiano, A.; Lanzalone, G.; Lanzano, G.; LoNigro, S.; Lombardo, U.; Manfredi, G.; Pagano, A.; Papa, M.; Pirrone, S.; Politi, G.; Porto, F.; Sambataro, S.; Sperduto, M.L.; Sutera, C.M.; Zetta, L.
2000-12-31
The installation of CHIMERA multidetector, designed in order to study central collisions in heavy ion reactions at intermediate energy, is going on at LNS and the first experiment with the forward part (688 telescopes) is running since May 1999. The aim of this contribution is to present the status of the project.
Keegan, John P.; Chan, Fong; Ditchman, Nicole; Chiu, Chung-Yi
2012-01-01
The main objective of this study was to validate Pender's Health Promotion Model (HPM) as a motivational model for exercise/physical activity self-management for people with spinal cord injuries (SCIs). Quantitative descriptive research design using hierarchical regression analysis (HRA) was used. A total of 126 individuals with SCI were recruited…
Intermittent chaotic chimeras for coupled rotators.
Olmi, Simona; Martens, Erik A; Thutupalli, Shashi; Torcini, Alessandro
2015-09-01
Two symmetrically coupled populations of N oscillators with inertia m display chaotic solutions with broken symmetry similar to experimental observations with mechanical pendulums. In particular, we report evidence of intermittent chaotic chimeras, where one population is synchronized and the other jumps erratically between laminar and turbulent phases. These states have finite lifetimes diverging as a power law with N and m. Lyapunov analyses reveal chaotic properties in quantitative agreement with theoretical predictions for globally coupled dissipative systems.
Preliminary results of Digital Pulse Shape Acquisition from Chimera
Energy Technology Data Exchange (ETDEWEB)
Alderighi, D.M.; Sechi, G. [INFN Milano and IASF, CNR, Milano (France); Anzalone, A.; Cavallaro, S.; Giustolisi, F.; Laguidara, E.; Lanzalone, G.; Porto, F. [Catania Univ., LNS and Dipartimento di Fisica (France); Bassini, R.; Boiano, C.; Guazzoni, P.; Russo, S.; Sassi, M.; Zetta, L. [Milano Univ., INFN and Dipartimento di Fisica (Italy); Cardella, G.; Defilippo, S.E.; Lanzano, G.; Paganod, A.; Papa, M.; Pirrone, S.; Politi, G. [Catania Univ., INFN and Dipartimento di Fisica (Italy); Geraci, E. [Bologna Univ., INFN and Dipartimento di Fisica (Italy)
2003-07-01
A 100 MS/s 14-bit Sampling Analog-to-Digital converter has been used to perform digital pulse-shape acquisition of signals collected from CHIMERA telescopes. The signals from a typical CHIMERA detection cell have been collected using both a standard CHIMERA electronic chain up to the amplifier, and a very simple analog front end, basically reduced to the preamplifier. The preliminary on-beam results are presented. (authors)
Coherence-Resonance Chimeras in a Network of Excitable Elements.
Semenova, Nadezhda; Zakharova, Anna; Anishchenko, Vadim; Schöll, Eckehard
2016-07-01
We demonstrate that chimera behavior can be observed in nonlocally coupled networks of excitable systems in the presence of noise. This phenomenon is distinct from classical chimeras, which occur in deterministic oscillatory systems, and it combines temporal features of coherence resonance, i.e., the constructive role of noise, and spatial properties of chimera states, i.e., the coexistence of spatially coherent and incoherent domains in a network of identical elements. Coherence-resonance chimeras are associated with alternating switching of the location of coherent and incoherent domains, which might be relevant in neuronal networks.
Rapakoulia, Trisevgeni
2017-08-09
Motivation: Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations. Results: We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens.
Assessing reprogramming by chimera formation and tetraploid complementation.
Li, Xin; Xia, Bao-long; Li, Wei; Zhou, Qi
2015-01-01
Pluripotent stem cells can be evaluated by pluripotent markers expression, embryoid body aggregation, teratoma formation, chimera contribution and even more, tetraploid complementation. Whether iPS cells in general are functionally equivalent to normal ESCs is difficult to establish. Here, we present the detailed procedure for chimera formation and tetraploid complementation, the most stringent criterion, to assessing pluripotency.
Huang, Mengmeng; Wei, Yan; Wang, Jun; Zhang, Yu
2016-09-01
We used the support vector regression (SVR) approach to predict and unravel reduction/promotion effect of characteristic flavonoids on the acrylamide formation under a low-moisture Maillard reaction system. Results demonstrated the reduction/promotion effects by flavonoids at addition levels of 1-10000 μmol/L. The maximal inhibition rates (51.7%, 68.8% and 26.1%) and promote rates (57.7%, 178.8% and 27.5%) caused by flavones, flavonols and isoflavones were observed at addition levels of 100 μmol/L and 10000 μmol/L, respectively. The reduction/promotion effects were closely related to the change of trolox equivalent antioxidant capacity (ΔTEAC) and well predicted by triple ΔTEAC measurements via SVR models (R: 0.633-0.900). Flavonols exhibit stronger effects on the acrylamide formation than flavones and isoflavones as well as their O-glycosides derivatives, which may be attributed to the number and position of phenolic and 3-enolic hydroxyls. The reduction/promotion effects were well predicted by using optimized quantitative structure-activity relationship (QSAR) descriptors and SVR models (R: 0.926-0.994). Compared to artificial neural network and multi-linear regression models, SVR models exhibited better fitting performance for both TEAC-dependent and QSAR descriptor-dependent predicting work. These observations demonstrated that the SVR models are competent for predicting our understanding on the future use of natural antioxidants for decreasing the acrylamide formation.
Solvable Model of Spiral Wave Chimeras
DEFF Research Database (Denmark)
Martens, Erik Andreas; Laing, Carlo R.; Strogatz, Steven H.
2010-01-01
Spiral waves are ubiquitous in two-dimensional systems of chemical or biological oscillators coupled locally by diffusion. At the center of such spirals is a phase singularity, a topological defect where the oscillator amplitude drops to zero. But if the coupling is nonlocal, a new kind of spiral...... can occur, with a circular core consisting of desynchronized oscillators running at full amplitude. Here, we provide the first analytical description of such a spiral wave chimera and use perturbation theory to calculate its rotation speed and the size of its incoherent core....
Metaphysical and ethical perspectives on creating animal-human chimeras.
Eberl, Jason T; Ballard, Rebecca A
2009-10-01
This paper addresses several questions related to the nature, production, and use of animal-human (a-h) chimeras. At the heart of the issue is whether certain types of a-h chimeras should be brought into existence, and, if they are, how we should treat such creatures. In our current research environment, we recognize a dichotomy between research involving nonhuman animal subjects and research involving human subjects, and the classification of a research protocol into one of these categories will trigger different ethical standards as to the moral permissibility of the research in question. Are a-h chimeras entitled to the more restrictive and protective ethical standards applied to human research subjects? We elucidate an Aristotelian-Thomistic metaphysical framework in which to argue how such chimeras ought to be defined ontologically. We then examine when the creation of, and experimentation upon, certain types of a-h chimeras may be morally permissible.
Chimera patterns in the Kuramoto-Battogtokh model
Smirnov, Lev; Osipov, Grigory; Pikovsky, Arkady
2017-02-01
Kuramoto and Battogtokh (2002 Nonlinear Phenom. Complex Syst. 5 380) discovered chimera states represented by stable coexisting synchrony and asynchrony domains in a lattice of coupled oscillators. After a reformulation in terms of a local order parameter, the problem can be reduced to partial differential equations. We find uniformly rotating, spatially periodic chimera patterns as solutions of a reversible ordinary differential equation, and demonstrate a plethora of such states. In the limit of neutral coupling they reduce to analytical solutions in the form of one- and two-point chimera patterns as well as localized chimera solitons. Patterns at weakly attracting coupling are characterized by virtue of a perturbative approach. Stability analysis reveals that only the simplest chimeras with one synchronous region are stable.
Multi-headed chimera states in coupled pendula
Jaros, P.; Borkowski, L.; Witkowski, B.; Czolczynski, K.; Kapitaniak, T.
2015-07-01
We discuss the occurrence of the chimera states in the network of coupled, excited by the clock's mechanisms pendula. We find the patterns of multi-headed chimera states in which pendula clustered in different heads behave differently (oscillate with different frequencies) and create different types of synchronous states (complete or phase synchronization). The mathematical model of the network shows that the observed chimera states are controlled by elementary dynamical equations derived from the Newton's laws that are ubiquitous in many physical and engineering systems.
Nakamura, Ryota; Suhrcke, Marc; Jebb, Susan A; Pechey, Rachel; Almiron-Roig, Eva; Marteau, Theresa M
2015-01-01
Background: There is a growing concern, but limited evidence, that price promotions contribute to a poor diet and the social patterning of diet-related disease. Objective: We examined the following questions: 1) Are less-healthy foods more likely to be promoted than healthier foods? 2) Are consumers more responsive to promotions on less-healthy products? 3) Are there socioeconomic differences in food purchases in response to price promotions? Design: With the use of hierarchical regression, we analyzed data on purchases of 11,323 products within 135 food and beverage categories from 26,986 households in Great Britain during 2010. Major supermarkets operated the same price promotions in all branches. The number of stores that offered price promotions on each product for each week was used to measure the frequency of price promotions. We assessed the healthiness of each product by using a nutrient profiling (NP) model. Results: A total of 6788 products (60%) were in healthier categories and 4535 products (40%) were in less-healthy categories. There was no significant gap in the frequency of promotion by the healthiness of products neither within nor between categories. However, after we controlled for the reference price, price discount rate, and brand-specific effects, the sales uplift arising from price promotions was larger in less-healthy than in healthier categories; a 1-SD point increase in the category mean NP score, implying the category becomes less healthy, was associated with an additional 7.7–percentage point increase in sales (from 27.3% to 35.0%; P sales uplift from promotions was larger for higher–socioeconomic status (SES) groups than for lower ones (34.6% for the high-SES group, 28.1% for the middle-SES group, and 23.1% for the low-SES group). Finally, there was no significant SES gap in the absolute volume of purchases of less-healthy foods made on promotion. Conclusion: Attempts to limit promotions on less-healthy foods could improve the
Chimeras and Mirages of the Golden Horde
Directory of Open Access Journals (Sweden)
V.A. Ivanov
2014-01-01
Full Text Available The article examines the problem of so-called “imperial culture” of the Golden Horde. The author analyzes the archaeological material regarding it as a component of “imperial culture”. The author evaluates the quality of the archaeological material as well as the breadth and intensity of its distribution among the population of the Golden Horde and the neighboring tribal areas, which the author considers a priori as consumers of this “imperial culture”. Based on this analysis, the author concludes that in general, the concept of “imperial culture” of the Golden Horde is a chimera. In turn, the expected powerful effect of “imperial culture” of the Golden Horde in the culture of neighboring peoples of the Urals and the Volga region is a mirage created by the imagination of researchers.
Fast clique minor generation in Chimera qubit connectivity graphs
Boothby, Tomas; King, Andrew D.; Roy, Aidan
2016-01-01
The current generation of D-Wave quantum annealing processor is designed to minimize the energy of an Ising spin configuration whose pairwise interactions lie on the edges of a Chimera graph C_{M,N,L}. In order to solve an Ising spin problem with arbitrary pairwise interaction structure, the corresponding graph must be minor-embedded into a Chimera graph. We define a combinatorial class of native clique minors in Chimera graphs with vertex images of uniform, near minimal size and provide a polynomial-time algorithm that finds a maximum native clique minor in a given induced subgraph of a Chimera graph. These minors allow improvement over recent work and have immediate practical applications in the field of quantum annealing.
Chimera States in Two Populations with Heterogeneous Phase-lag
DEFF Research Database (Denmark)
Martens, Erik Andreas; Bick, Christian; Panaggio, Mark
2016-01-01
The simplest network of coupled phase-oscillators exhibiting chimera states is given by two populations with disparate intra- and inter-population coupling strengths. We explore the effects of heterogeneous coupling phase-lags between the two populations. Such heterogeneity arises naturally......-uniform synchronization, including in-phase and anti-phase synchrony, full incoherence (splay state), chimera states with phase separation of 0 or π between populations, and states where both populations remain desynchronized. These desynchronized states exhibit stable, oscillatory, and even chaotic dynamics. Moreover......, we identify the bifurcations through which chimera and desynchronized states emerge. Stable chimera states and desynchronized solutions, which do not arise for homogeneous phase-lag parameters, emerge as a result of competition between synchronized in-phase, anti-phase equilibria, and fully...
La Chimera di Dino Campana e Altre Chimere
Directory of Open Access Journals (Sweden)
Lucia Wataghin
2008-08-01
Full Text Available The current article brings considerations on the results and problems of reusing material from the literary tradition in one of the most celebrated of Dino Campana’s poems, La Chimera.
Chimera in a neuronal network model of the cat brain
Santos, M. S.; Szezech Jr., J. D.; Borges, F. S.; Iarosz, K. C.; Caldas, I. L.; Batista, A. M.; Viana, R. L.; Kurths, J.
2016-01-01
Neuronal systems have been modeled by complex networks in different description levels. Recently, it has been verified that networks can simultaneously exhibit one coherent and other incoherent domain, known as chimera states. In this work, we study the existence of chimera states in a network considering the connectivity matrix based on the cat cerebral cortex. The cerebral cortex of the cat can be separated in 65 cortical areas organised into the four cognitive regions: visual, auditory, so...
Hao, Lingxin
2007-01-01
Quantile Regression, the first book of Hao and Naiman's two-book series, establishes the seldom recognized link between inequality studies and quantile regression models. Though separate methodological literature exists for each subject, the authors seek to explore the natural connections between this increasingly sought-after tool and research topics in the social sciences. Quantile regression as a method does not rely on assumptions as restrictive as those for the classical linear regression; though more traditional models such as least squares linear regression are more widely utilized, Hao
Tools for integrated sequence-structure analysis with UCSF Chimera
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Huang Conrad C
2006-07-01
Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is
Modeling Quark Gluon Plasma Using CHIMERA
Abelev, Betty
2011-09-01
We attempt to model Quark Gluon Plasma (QGP) evolution from the initial Heavy Ion collision to the final hadronic gas state by combining the Glauber model initial state conditions with eccentricity fluctuations, pre-equilibrium flow, UVH2+1 viscous hydrodynamics with lattice QCD Equation of State (EoS), a modified Cooper-Frye freeze-out and the UrQMD hadronic cascade. We then evaluate the model parameters using a comprehensive analytical framework which together with the described model we call CHIMERA. Within our framework, the initial state parameters, such as the initial temperature (Tinit), presence or absence of initial flow, viscosity over entropy density (η/S) and different Equations of State (EoS), are varied and then compared simultaneously to several experimental data observables: HBT radii, particle spectra and particle flow. χ2/nds values from comparison to the experimental data for each set of initial parameters will then used to find the optimal description of the QGP with parameters that are difficult to obtain experimentally, but are crucial to understanding of the matter produced.
Modeling Quark Gluon Plasma Using CHIMERA
Abelev, Betty B I
2011-01-01
We attempt to model Quark Gluon Plasma (QGP) evolution from the initial Heavy Ion collision to the final hadronic gas state by combining the Glauber model initial state conditions with eccentricity fluctuations, pre-equilibrium flow, UVH2+1 viscous hydrodynamics with lattice QCD Equation of State (EoS), a modified Cooper-Frye freeze-out and the UrQMD hadronic cascade. We then evaluate the model parameters using a comprehensive analytical framework which together with the described model we call CHIMERA. Within our framework, the initial state parameters, such as the initial temperature (T$_{\\mathrm{init}}$), presence or absence of initial flow, viscosity over entropy density ($\\eta$/s) and different Equations of State (EoS), are varied and then compared simultaneously to several experimental data observables: HBT radii, particle spectra and particle flow. $\\chi^2$/nds values from comparison to the experimental data for each set of initial parameters will then used to find the optimal description of the QGP wi...
Chimera states in coupled Kuramoto oscillators with inertia
Energy Technology Data Exchange (ETDEWEB)
Olmi, Simona, E-mail: simona.olmi@fi.isc.cnr.it [CNR - Consiglio Nazionale delle Ricerche - Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino (Italy); INFN Sez. Firenze, via Sansone, 1 - I-50019 Sesto Fiorentino (Italy)
2015-12-15
The dynamics of two symmetrically coupled populations of rotators is studied for different values of the inertia. The system is characterized by different types of solutions, which all coexist with the fully synchronized state. At small inertia, the system is no more chaotic and one observes mainly quasi-periodic chimeras, while the usual (stationary) chimera state is not anymore observable. At large inertia, one observes two different kind of chaotic solutions with broken symmetry: the intermittent chaotic chimera, characterized by a synchronized population and a population displaying a turbulent behaviour, and a second state where the two populations are both chaotic but whose dynamics adhere to two different macroscopic attractors. The intermittent chaotic chimeras are characterized by a finite life-time, whose duration increases as a power-law with the system size and the inertia value. Moreover, the chaotic population exhibits clear intermittent behavior, displaying a laminar phase where the two populations tend to synchronize, and a turbulent phase where the macroscopic motion of one population is definitely erratic. In the thermodynamic limit, these states survive for infinite time and the laminar regimes tends to disappear, thus giving rise to stationary chaotic solutions with broken symmetry contrary to what observed for chaotic chimeras on a ring geometry.
Institute of Scientific and Technical Information of China (English)
Qian xu; Shou-jie CHAI; Ying-ying QIAN; Min ZHANG; Kai WANG
2012-01-01
Aim: To determine the roles of breast regression protein-39 (BRP-39) in regulating dendritic cell maturation and in pathology of acute asthma.Methods: Mouse bone marrow-derived dendritic cells (BMDCs) were prepared,and infected with adenovirus over-expressing BRP-39.Ovalbumin (OVA)-induced murine model of acute asthma was made in female BALB/c mice by sensitizing and challenging with chicken OVA and Imject Alum.The transfected BMDCs were adoptively transferred into OVA-treated mice via intravenous injection.Airway hyperresponsiveness (AHR),inflammation and pulmonary histopathology were characterized.Results: The expression of BRP-39 mRNA and protein was significantly increased in lung tissues of OVA-treated mice.The BMDCs infected with adenovirus BRP-39 exhibited greater maturation and higher activity in vitro.Adoptive transfer of the cells into OVA-treated mice significantly augmented OVA-induced AHR and eosinophilic inflammation.Meanwhile,BRP-39 further enhanced the production of OVA-induced Th2 cytokines IL-4,IL-5,and IL-13,but significantly attenuated OVA-induced IFN-γ production in bronchoalveolar lavage fluid.Conclusion: In OVA-induced murine model of acute asthma,BRP-39 is over-expressed in lung tissue and augments Th2 inflammatory response and AHR.BRP-39 promotes dendritic cell maturation in vitro.Therefore,BRP-39 may be a potential therapeutic target of asthma.
Kassavou, Aikaterini; Sutton, Stephen
2017-09-12
Automated telecommunication interventions, including short message service and interactive voice response, are increasingly being used to promote adherence to medications prescribed for cardio-metabolic conditions. This systematic review aimed to comprehensively assess the effectiveness of such interventions to support medication adherence, and to identify the behaviour change techniques (BCTs) and other intervention characteristics that are positively associated with greater intervention effectiveness. Meta-analysis of 17 randomised controlled trials showed a small but statistically significant effect on medication adherence, OR = 1.89, 95% CI [1.51, 2.36], I(2) = 89%, N = 25,101. Multivariable meta-regression analysis including eight BCTs explained 88% of the observed variance in effect size (ES). The BCTs 'tailored' and 'information about health consequences' were positively and significantly associated with ES. Future studies could explore whether the inclusion of these and/or additional techniques (e.g., 'implementation intentions') would increase the effect of automated telecommunication interventions, using rigorous designs and objective outcome measures.
Deterministic and stochastic control of chimera states in delayed feedback oscillator
Energy Technology Data Exchange (ETDEWEB)
Semenov, V. [Department of Physics, Saratov State University, Astrakhanskaya Str. 83, 410012 Saratov (Russian Federation); Zakharova, A.; Schöll, E. [Institut für Theoretische Physik, TU Berlin, Hardenbergstraße 36, 10623 Berlin (Germany); Maistrenko, Y. [Institute of Mathematics and Center for Medical and Biotechnical Research, NAS of Ukraine, Tereschenkivska Str. 3, 01601 Kyiv (Ukraine)
2016-06-08
Chimera states, characterized by the coexistence of regular and chaotic dynamics, are found in a nonlinear oscillator model with negative time-delayed feedback. The control of these chimera states by external periodic forcing is demonstrated by numerical simulations. Both deterministic and stochastic external periodic forcing are considered. It is shown that multi-cluster chimeras can be achieved by adjusting the external forcing frequency to appropriate resonance conditions. The constructive role of noise in the formation of a chimera states is shown.
Kahane, Leo H
2007-01-01
Using a friendly, nontechnical approach, the Second Edition of Regression Basics introduces readers to the fundamentals of regression. Accessible to anyone with an introductory statistics background, this book builds from a simple two-variable model to a model of greater complexity. Author Leo H. Kahane weaves four engaging examples throughout the text to illustrate not only the techniques of regression but also how this empirical tool can be applied in creative ways to consider a broad array of topics. New to the Second Edition Offers greater coverage of simple panel-data estimation:
Delayed-feedback chimera states: Forced multiclusters and stochastic resonance
Semenov, V.; Zakharova, A.; Maistrenko, Y.; Schöll, E.
2016-07-01
A nonlinear oscillator model with negative time-delayed feedback is studied numerically under external deterministic and stochastic forcing. It is found that in the unforced system complex partial synchronization patterns like chimera states as well as salt-and-pepper-like solitary states arise on the route from regular dynamics to spatio-temporal chaos. The control of the dynamics by external periodic forcing is demonstrated by numerical simulations. It is shown that one-cluster and multi-cluster chimeras can be achieved by adjusting the external forcing frequency to appropriate resonance conditions. If a stochastic component is superimposed to the deterministic external forcing, chimera states can be induced in a way similar to stochastic resonance, they appear, therefore, in regimes where they do not exist without noise.
Chimera states and synchronization in magnetically driven SQUID metamaterials
Hizanidis, J.; Lazarides, N.; Neofotistos, G.; Tsironis, G. P.
2016-09-01
One-dimensional arrays of Superconducting QUantum Interference Devices (SQUIDs) form magnetic metamaterials exhibiting extraordinary properties, including tunability, dynamic multistability, negative magnetic permeability, and broadband transparency. The SQUIDs in a metamaterial interact through non-local, magnetic dipole-dipole forces, that makes it possible for multiheaded chimera states and coexisting patterns, including solitary states, to appear. The spontaneous emergence of chimera states and the role of multistability is demonstrated numerically for a SQUID metamaterial driven by an alternating magnetic field. The spatial synchronization and temporal complexity are discussed and the parameter space for the global synchronization reveals the areas of coherence-incoherence transition. Given that both one- and two-dimensional SQUID metamaterials have been already fabricated and investigated in the lab, the presence of a chimera state could in principle be detected with presently available experimental set-ups.
Chimeras in locally coupled SQUIDs: Lions, goats and snakes
Hizanidis, J; Tsironis, G P
2016-01-01
We report on the emergence of robust multi-clustered chimera states in a dissipative-driven system of symmetrically and locally coupled identical SQUID oscillators. The "snake-like" resonance curve of the single SQUID (Superconducting QUantum Interference Device) is the key to the formation of the chimera states and is responsible for the extreme multistability exhibited by the coupled system that leads to attractor crowding at the geometrical resonance frequency. Until now, chimera states were mostly believed to exist for nonlocal coupling. Our findings provide theoretical evidence that nearest neighbor interactions is indeed capable of supporting such states in a wide parameter range. SQUID metamaterials are the subject of intense experimental investigations and we are highly confident that the complex dynamics demonstrated in this manuscript can be confirmed in the laboratory.
Pulse shape method for the Chimera silicon detectors
Energy Technology Data Exchange (ETDEWEB)
Pagano, A.; Arena, N.; Cardella, G.; D' Andrea, M.; Filippo, E. de; Fichera, F.; Giudice, N.; Guardone, N.; Grimaldi, A.; Nicotra, D.; Papa, M.; Pirrone, S.; Politi, G.; Rapicavoli, C.; Rizza, G.; Russotto, P.; Sacca, G.; Urso, S.; Lanzano, G. [Catania Univ., INFN Catania and Dipartimento di Fisica e Astronomia (Italy); Alderighi, M.; Sechi, G. [INFN Milano and Istituto di Fisica Cosmica CNR, Milano (Italy); Amorini, F.; Anzalone, A.; Cali, C.; Campagna, V.; Cavallaro, S.; Di Stefano, A.; Giustolisi, F.; La Guidara, E.; Lanzalone, G.; Maiolino, C.; Porto, F.; Rizzo, F.; Salamone, S. [Catania Univ., INFN-LNS and Dipartimento di Fisica e Astronomia (Italy); Auditore, L.; Trifiro, A.; Trimarchi, M. [Messina Univ., INFN and Dipartimento di Fisica (Italy); Bassini, R.; Boiano, C.; Guazzoni, P.; Russo, S.; Sassi, M.; Zetta, L. [Milano Univ., INFN Milano and Dipartimento di Fisica (Italy); Blicharska, J.; Grzeszczuk, A. [Silesia Univ., Institute of Physics, Katowice (Poland); Chatterjee, M.B. [Saha Institute Of Nuclear Physics, Kolkata (India); Geraci, E.; Zipper, W. [Bologna Univ., INFN Bologna and Dipartimento di Fisica (Italy); Rosato, E.; Vigilante, M. [Napoli Univ., INFN and Dipartimento di Fisica (Italy); Schroder, W.U.; T-ke, J. [Rochester Univ., Dept. of Chemistry, Rochester, N.Y. (United States)
2003-07-01
Since January 2003, the 4{pi} CHIMERA (Charged Heavy Ions Mass and Energy Resolving Array) detector in its full configuration has successfully been operated at the 'Catania Laboratori Nazionali del Sud' (LNS) accelerator facility. The detector has been used with a variety of beams from the Superconducting Cyclotron in heavy-ion reaction studies at Fermi bombarding energies. Future experiments with a focus on isospin physics at Fermi energies, planned for both primary and less intense secondary particle beams, suggest the development of new and more versatile experimental particle identification methods. Recent achievements in implementing specific pulse shape particle identification methods for CHIMERA silicon detectors are reported. They suggest an upgrade of the present charge and mass identification capability of CHIMERA by a simple extension of the method. (authors)
Robust chimera states in SQUID metamaterials with local interactions
Hizanidis, J.; Lazarides, N.; Tsironis, G. P.
2016-09-01
We report on the emergence of robust multiclustered chimera states in a dissipative-driven system of symmetrically and locally coupled identical superconducting quantum interference device (SQUID) oscillators. The "snakelike" resonance curve of the single SQUID is the key to the formation of the chimera states and is responsible for the extreme multistability exhibited by the coupled system that leads to attractor crowding at the geometrical resonance (inductive-capacitive) frequency. Until now, chimera states were mostly believed to exist for nonlocal coupling. Our findings provide theoretical evidence that nearest-neighbor interactions are indeed capable of supporting such states in a wide parameter range. SQUID metamaterials are the subject of intense experimental investigations, and we are highly confident that the complex dynamics demonstrated in this paper can be confirmed in the laboratory.
Chimera-like states in modular neural networks
Hizanidis, Johanne; Zamora-López, Gorka; Díaz-Guilera, Albert; Antonopoulos, Chris G
2016-01-01
Chimera states, namely the coexistence of coherent and incoherent behavior, were previously analyzed in complex networks. However, they have not been extensively studied in modular networks. Here, we consider the neural network of the \\textit{C.elegans} soil worm, organized into six interconnected communities, where neurons obey chaotic bursting dynamics. Neurons are assumed to be connected with electrical synapses within their communities and with chemical synapses across them. As our numerical simulations reveal, the coaction of these two types of coupling can shape the dynamics in such a way that chimera-like states can happen. They consist of a fraction of synchronized neurons which belong to the larger communities, and a fraction of desynchronized neurons which are part of smaller communities. In addition to the Kuramoto order parameter $\\rho$, we also employ other measures of coherence, such as the chimera-like $\\chi$ and metastability $\\lambda$ indices, which quantify the degree of synchronization amon...
Mechanism of chimera formation during the Multiple Displacement Amplification reaction
Directory of Open Access Journals (Sweden)
Stockwell Timothy B
2007-04-01
Full Text Available Abstract Background Multiple Displacement Amplification (MDA is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.
Matson, Johnny L.; Kozlowski, Alison M.
2010-01-01
Autistic regression is one of the many mysteries in the developmental course of autism and pervasive developmental disorders not otherwise specified (PDD-NOS). Various definitions of this phenomenon have been used, further clouding the study of the topic. Despite this problem, some efforts at establishing prevalence have been made. The purpose of…
Nick, Todd G; Campbell, Kathleen M
2007-01-01
The Medical Subject Headings (MeSH) thesaurus used by the National Library of Medicine defines logistic regression models as "statistical models which describe the relationship between a qualitative dependent variable (that is, one which can take only certain discrete values, such as the presence or absence of a disease) and an independent variable." Logistic regression models are used to study effects of predictor variables on categorical outcomes and normally the outcome is binary, such as presence or absence of disease (e.g., non-Hodgkin's lymphoma), in which case the model is called a binary logistic model. When there are multiple predictors (e.g., risk factors and treatments) the model is referred to as a multiple or multivariable logistic regression model and is one of the most frequently used statistical model in medical journals. In this chapter, we examine both simple and multiple binary logistic regression models and present related issues, including interaction, categorical predictor variables, continuous predictor variables, and goodness of fit.
What’s Wrong with Human/Nonhuman Chimera Research?
Hyun, Insoo
2016-01-01
The National Institutes of Health (NIH) is poised to lift its funding moratorium on research involving chimeric human/nonhuman embryos, pending further consideration by an NIH steering committee. The kinds of ethical concerns that seem to underlie this research and chimera research more generally can be adequately addressed. PMID:27574863
Chimera states in two populations with heterogeneous phase-lag
Martens, Erik A.; Bick, Christian; Panaggio, Mark J.
2016-09-01
The simplest network of coupled phase-oscillators exhibiting chimera states is given by two populations with disparate intra- and inter-population coupling strengths. We explore the effects of heterogeneous coupling phase-lags between the two populations. Such heterogeneity arises naturally in various settings, for example, as an approximation to transmission delays, excitatory-inhibitory interactions, or as amplitude and phase responses of oscillators with electrical or mechanical coupling. We find that breaking the phase-lag symmetry results in a variety of states with uniform and non-uniform synchronization, including in-phase and anti-phase synchrony, full incoherence (splay state), chimera states with phase separation of 0 or π between populations, and states where both populations remain desynchronized. These desynchronized states exhibit stable, oscillatory, and even chaotic dynamics. Moreover, we identify the bifurcations through which chimeras emerge. Stable chimera states and desynchronized solutions, which do not arise for homogeneous phase-lag parameters, emerge as a result of competition between synchronized in-phase, anti-phase equilibria, and fully incoherent states when the phase-lags are near ± /π 2 (cosine coupling). These findings elucidate previous experimental results involving a network of mechanical oscillators and provide further insight into the breakdown of synchrony in biological systems.
CHIMERA CBRN protective suit. Advanced embodiment design. Final report
Bogerd, C.P.; Smit, B. de; Olarte, C.; Kane, G.; Bie, M. de; Megen, X. van; Schenk, J.; Hooop, J. de
2015-01-01
The Chimera project started of with the following design challenge: Designing a switchable CBRN (chemical, biological, radiological, nuclear) protective suit for soldiers, one phase being a regular work state and the other phase being a protective state to enable the soldier to get away from the tox
Use of fragmentation beams at LNS with CHIMERA detector
Directory of Open Access Journals (Sweden)
Gianí R.
2012-07-01
Full Text Available The recent intensity upgrade of the LNS fragmentation beam is discussed. The available beams, the tagging procedures and details on the beam quality are reported. The experimental program started with the CHIMERA detector using such beams is also discussed with preliminary results and future perspectives.
CHIMERA CBRN protective suit. Advanced embodiment design. Final report
Bogerd, C.P.; Smit, B. de; Olarte, C.; Kane, G.; Bie, M. de; Megen, X. van; Schenk, J.; Hooop, J. de
2015-01-01
The Chimera project started of with the following design challenge: Designing a switchable CBRN (chemical, biological, radiological, nuclear) protective suit for soldiers, one phase being a regular work state and the other phase being a protective state to enable the soldier to get away from the
Chimera: construction of chimeric sequences for phylogenetic analysis
Leunissen, J.A.M.
2003-01-01
Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output
Genetic engineering in film: the case of chimeras
Directory of Open Access Journals (Sweden)
Josep-E. BAÑOS
2016-04-01
Full Text Available The development of molecular genetics in the second half of XXth century has allowed considering situations, which were in the bioscience fiction field until then. Among them, the possibility of making chimeras using the combination of genetic material is now a real option. Movies have repeatedly shown this possibility by means of literary works o directly by screen plays. This article analyzes some films that may help to understand social beliefs on chimeras in the last century. We have considered Island of lost souls (1932, The island of doctor Moreau (1977, The fly (1958, 1986, Mimic (1997 and Splice (2009. The main conclusions of this analysis are the presence of a negative view to the possibility of making chimeras following the point of view that was used in Frankenstein. The movies also lack of a consideration of the potential benefits of using chimeras. Ethical misgivings and the vision of playing God scientists avoid a impartial view of a situation, which is already among us.
Chimera states in uncoupled neurons induced by a multilayer structure
Majhi, Soumen; Ghosh, Dibakar
2016-01-01
Spatial coexistence of coherent and incoherent dynamics in network of coupled oscillators is called a chimera state. We study such chimera states in a network of neurons without any direct interactions but connected through another medium of neurons, forming a multilayer structure. The upper layer is thus made up of uncoupled neurons and the lower layer plays the role of a medium through which the neurons in the upper layer share information among each other. Hindmarsh-Rose neurons with square wave bursting dynamics are considered as nodes in both layers. In addition, we also discuss the existence of chimera states in presence of inter layer heterogeneity. The neurons in the bottom layer are globally connected through electrical synapses, while across the two layers chemical synapses are formed. According to our research, the competing effects of these two types of synapses can lead to chimera states in the upper layer of uncoupled neurons. Remarkably, we find a density-dependent threshold for the emergence o...
Chimera states in two populations with heterogeneous phase-lag.
Martens, Erik A; Bick, Christian; Panaggio, Mark J
2016-09-01
The simplest network of coupled phase-oscillators exhibiting chimera states is given by two populations with disparate intra- and inter-population coupling strengths. We explore the effects of heterogeneous coupling phase-lags between the two populations. Such heterogeneity arises naturally in various settings, for example, as an approximation to transmission delays, excitatory-inhibitory interactions, or as amplitude and phase responses of oscillators with electrical or mechanical coupling. We find that breaking the phase-lag symmetry results in a variety of states with uniform and non-uniform synchronization, including in-phase and anti-phase synchrony, full incoherence (splay state), chimera states with phase separation of 0 or π between populations, and states where both populations remain desynchronized. These desynchronized states exhibit stable, oscillatory, and even chaotic dynamics. Moreover, we identify the bifurcations through which chimeras emerge. Stable chimera states and desynchronized solutions, which do not arise for homogeneous phase-lag parameters, emerge as a result of competition between synchronized in-phase, anti-phase equilibria, and fully incoherent states when the phase-lags are near ±π2 (cosine coupling). These findings elucidate previous experimental results involving a network of mechanical oscillators and provide further insight into the breakdown of synchrony in biological systems.
Olive, David J
2017-01-01
This text covers both multiple linear regression and some experimental design models. The text uses the response plot to visualize the model and to detect outliers, does not assume that the error distribution has a known parametric distribution, develops prediction intervals that work when the error distribution is unknown, suggests bootstrap hypothesis tests that may be useful for inference after variable selection, and develops prediction regions and large sample theory for the multivariate linear regression model that has m response variables. A relationship between multivariate prediction regions and confidence regions provides a simple way to bootstrap confidence regions. These confidence regions often provide a practical method for testing hypotheses. There is also a chapter on generalized linear models and generalized additive models. There are many R functions to produce response and residual plots, to simulate prediction intervals and hypothesis tests, to detect outliers, and to choose response trans...
Kuhn, R J; Niesters, H G; Hong, Z; Strauss, J H
1991-06-01
We have constructed a full-length cDNA clone of the virulent T48 strain of Ross River virus, a member of the alphavirus genus. Infectious RNA can be transcribed from this clone using SP6 or T7 RNA polymerase. The rescued virus has properties indistinguishable from those of the T48 strain of Ross River virus. We have used this clone, together with a full-length cDNA clone of Sindbis virus, to construct chimeric plasmids in which the 5' and the 3' nontranslated regions of the Sindbis and Ross River genomes were exchanged. The nontranslated regions of the two viral genomes differ in both size and sequence although they maintain specific conserved sequence elements. Virus was recovered from all four chimeras. Chimeras containing heterologous 3' nontranslated regions had replicative efficiencies equal to those of the parents. In contrast, the chimeras containing heterologous 5' nontranslated regions were defective in RNA synthesis and virus production, and the severity of the defect was dependent upon the host. Replication of a virus containing a heterologous 5' nontranslated region may be inefficient due to the formation of defective protein-RNA complexes, whereas, the presumptive complexes formed between host or virus proteins and the 3' nontranslated region to promote RNA synthesis appear to function normally in the chimeras.
Using CHIMERA detector at LNS for gamma-particle coincidences
Directory of Open Access Journals (Sweden)
Cardella G.
2016-01-01
Full Text Available We have recently evaluated the quality of γ-ray angular distributions that can be extracted in particle-gamma coincidence measurements using the CHIMERA detector at LNS. γ-rays have been detected using the CsI(Tl detectors of the spherical part of the CHIMERA array. Very clean γ-rays angular distributions were extracted in reactions induced by different stable beams impinging on 12C thin targets. The results evidenced an effect of projectile spin flip on the γ-rays angular distributions. γ-particle coincidence measurements were also performed in reactions induced by neutron rich exotic beams produced through in-flight fragmentation at LNS. In recent experiments also the Farcos array was used to improve energy and angular resolution measurements of the detected charged particles. Results obtained with both stable and radioactive beams are reported.
Chimera regimes in a ring of oscillators with local nonlinear interaction
Shepelev, Igor A.; Zakharova, Anna; Vadivasova, Tatiana E.
2017-03-01
One of important problems concerning chimera states is the conditions of their existence and stability. Until now, it was assumed that chimeras could arise only in ensembles with nonlocal character of interactions. However, this assumption is not exactly right. In some special cases chimeras can be realized for local type of coupling [1-3]. We propose a simple model of ensemble with local coupling when chimeras are realized. This model is a ring of linear oscillators with the local nonlinear unidirectional interaction. Chimera structures in the ring are found using computer simulations for wide area of values of parameters. Diagram of the regimes on plane of control parameters is plotted and scenario of chimera destruction are studied when the parameters are changed.
Chimera states in two populations with heterogeneous phase-lag
Martens, Erik Andreas; Bick, Christian; Panaggio, Mark J.
2016-01-01
The simplest network of coupled phase-oscillators exhibiting chimera states is given by two populations with disparate intra- and inter-population coupling strengths. We explore the effects of heterogeneous coupling phase-lags between the two populations. Such heterogeneity arises naturally in various settings, for example as an approximation to transmission delays, excitatory-inhibitory interactions, or as amplitude and phase responses of oscillators with electrical or mechanical coupling. W...
Icing modelling in NSMB with chimera overset grids
Energy Technology Data Exchange (ETDEWEB)
Pena, D. [Ècole Polytechnique de Montréal (Canada); ICUBE, Strasbourg University (France); Deloze, T.; Laurendeau, E. [Ècole Polytechnique de Montréal (Canada); Hoarau, Y. [ICUBE, Strasbourg University (France)
2015-03-10
In aerospace Engineering, the accurate simulation of ice accretion is a key element to increase flight safety and avoid accidents related to icing effects. The icing code developed in the NSMB solver is based on an Eulerian formulation for droplets tracking, an iterative Messinger model using a modified water runback scheme for ice thickness calculation and mesh deformation to track the ice/air interface through time. The whole process is parallelized with MPI and applied with chimera grids.
Anticipatory Governance: Bioethical Expertise for Human/Animal Chimeras.
Harvey, Alison; Salter, Brian
2012-09-01
The governance demands generated by the use of human/animal chimeras in scientific research offer both a challenge and an opportunity for the development of new forms of anticipatory governance through the novel application of bioethical expertise. Anticipatory governance can be seen to have three stages of development whereby bioethical experts move from a reactive to a proactive stance at the edge of what is scientifically possible. In the process, the ethicists move upstream in their engagement with the science of human-to-animal chimeras. To what extent is the anticipatory coestablishment of the principles and operational rules of governance at this early stage in the development of the human-to-animal research field likely to result in a framework for bioethical decision making that is in support of science? The process of anticipatory governance is characterised by the entwining of the scientific and the philosophical so that judgements against science are also found to be philosophically unfounded, and conversely, those activities that are permissible are deemed so on both scientific and ethical grounds. Through what is presented as an organic process, the emerging bioethical framework for human-to-animal chimera research becomes a legitimating framework within which 'good' science can safely progress. Science gives bioethical expertise access to new governance territory; bioethical expertise gives science access to political acceptability.
Streiffer, Robert
2010-01-01
Researchers are increasingly interested in creating chimeras by transplanting human embryonic stem cells (hESCs) into animals early in development. One concern is that such research could confer upon an animal the moral status of a normal human adult but then impermissibly fail to accord it the protections it merits in virtue of its enhanced moral status. Understanding the public policy implications of this ethical conclusion, though, is complicated by the fact that claims about moral status cannot play an unfettered role in public policy. Arguments like those employed in the abortion debate for the conclusion that abortion should be legally permissible even if abortion is not morally permissible also support, to a more limited degree, a liberal policy on hESC research involving the creation of chimeras.
Chimera states and the interplay between initial conditions and non-local coupling
Kalle, Peter; Sawicki, Jakub; Zakharova, Anna; Schöll, Eckehard
2017-03-01
Chimera states are complex spatio-temporal patterns that consist of coexisting domains of coherent and incoherent dynamics. We study chimera states in a network of non-locally coupled Stuart-Landau oscillators. We investigate the impact of initial conditions in combination with non-local coupling. Based on an analytical argument, we show how the coupling phase and the coupling strength are linked to the occurrence of chimera states, flipped profiles of the mean phase velocity, and the transition from a phase- to an amplitude-mediated chimera state.
Alves-Silva, Marcus Vinícius; Nico, Dirlei; Morrot, Alexandre; Palatnik, Marcos; Palatnik-de-Sousa, Clarisa B.
2017-01-01
The Leishmania donovani nucleoside hydrolase (NH36) and NH A34480 of Leishmania amazonensis share 93% of sequence identity. In mice, the NH36 induced protection against visceral leishmaniasis is mediated by a CD4+ T cell response against its C-terminal domain (F3). Besides this CD4+ Th1 response, prevention and cure of L. amazonensis infection require also additional CD8+ and regulatory T-cell responses to the NH36 N-terminal (F1 domain). We investigated if mice vaccination with F1 and F3 domains cloned in tandem, in a recombinant chimera, with saponin, optimizes the vaccine efficacy against L. amazonensis infection above the levels promoted by the two admixed domains or by each domain independently. The chimera induced the highest IgA, IgG, and IgG2a anti-NH36 antibody, IDR, IFN-γ, and IL-10 responses, while TNF-α was more secreted by mice vaccinated with F3 or all F3-contaning vaccines. Additionally, the chimera and the F1 vaccine also induced the highest proportions of CD4+ and CD8+ T cells secreting IL-2, TNF-α, or IFN-γ alone, TNF-α in combination with IL-2 or IFN-γ, and of CD4+ multifunctional cells secreting IL-2, TNF-α, and IFN-γ. Correlating with the immunological results, the strongest reductions of skin lesions sizes were determined by the admixed domains (80%) and by the chimera (84%), which also promoted the most pronounced and significant reduction of the parasite load (99.8%). Thus, the epitope presentation in a recombinant chimera optimizes immunogenicity and efficacy above the levels induced by the independent or admixed F1 and F3 domains. The multiparameter analysis disclosed that the Th1-CD4+ T helper response induced by the chimera is mainly directed against its FRYPRPKHCHTQVA epitope. Additionally, the YPPEFKTKL epitope of F1 induced the second most important CD4+ T cell response, and, followed by the DVAGIVGVPVAAGCT, FMLQILDFYTKVYE, and ELLAITTVVGNQ sequences, also the most potent CD8+ T cell responses and IL-10 secretion. Remarkably
Characteristic distribution of finite-time Lyapunov exponents for chimera states.
Botha, André E
2016-07-04
Our fascination with chimera states stems partially from the somewhat paradoxical, yet fundamental trait of identical, and identically coupled, oscillators to split into spatially separated, coherently and incoherently oscillating groups. While the list of systems for which various types of chimeras have already been detected continues to grow, there is a corresponding increase in the number of mathematical analyses aimed at elucidating the fundamental reasons for this surprising behaviour. Based on the model systems, there are strong indications that chimera states may generally be ubiquitous in naturally occurring systems containing large numbers of coupled oscillators - certain biological systems and high-Tc superconducting materials, for example. In this work we suggest a new way of detecting and characterising chimera states. Specifically, it is shown that the probability densities of finite-time Lyapunov exponents, corresponding to chimera states, have a definite characteristic shape. Such distributions could be used as signatures of chimera states, particularly in systems for which the phases of all the oscillators cannot be measured directly. For such cases, we suggest that chimera states could perhaps be detected by reconstructing the characteristic distribution via standard embedding techniques, thus making it possible to detect chimera states in systems where they could otherwise exist unnoticed.
Experimental observation of chimera and cluster states in a minimal globally coupled network
Energy Technology Data Exchange (ETDEWEB)
Hart, Joseph D. [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Bansal, Kanika [Department of Mathematics, University at Buffalo, SUNY Buffalo, New York 14260 (United States); US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Murphy, Thomas E. [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Electrical and Computer Engineering, University of Maryland, College Park, Maryland 20742 (United States); Roy, Rajarshi [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States)
2016-09-15
A “chimera state” is a dynamical pattern that occurs in a network of coupled identical oscillators when the symmetry of the oscillator population is broken into synchronous and asynchronous parts. We report the experimental observation of chimera and cluster states in a network of four globally coupled chaotic opto-electronic oscillators. This is the minimal network that can support chimera states, and our study provides new insight into the fundamental mechanisms underlying their formation. We use a unified approach to determine the stability of all the observed partially synchronous patterns, highlighting the close relationship between chimera and cluster states as belonging to the broader phenomenon of partial synchronization. Our approach is general in terms of network size and connectivity. We also find that chimera states often appear in regions of multistability between global, cluster, and desynchronized states.
Targeted chimera delivery to ovarian cancer cells by heterogeneous gold magnetic nanoparticle
Chen, Yao; Xu, Mengjiao; Guo, Yi; Tu, Keyao; Wu, Weimin; Wang, Jianjun; Tong, Xiaowen; Wu, Wenjuan; Qi, Lifeng; Shi, Donglu
2017-01-01
Efficient delivery of small interfering RNAs (siRNAs) to the targeted cells has remained a significant challenge in clinical applications. In the present study, we developed a novel aptamer-siRNA chimera delivery system mediated by cationic Au-Fe3O4 nanoparticles (NPs). The chimera constructed by VEGF RNA aptamer and Notch3 siRNA was bonded with heterogeneous Au-Fe3O4 nanoparticles by electrostatic interaction. The obtained complex exhibited much higher silencing efficiency against Notch3 gene compared with chimera alone and lipofectamine-siRNA complex, and improved the antitumor effects of the loaded chimera. Moreover, the efficient delivery of the chimera by Au-Fe3O4 NPs could reverse multi-drug resistance (MDR) of ovarian cancer cells against the chemotherapeutic drug cisplatin, indicating its potential capability for future targeted cancer therapy while overcoming MDR.
Laser chimeras as a paradigm for multistable patterns in complex systems
Larger, Laurent; Penkovsky, Bogdan; Maistrenko, Yuri
2015-07-01
A chimera state is a rich and fascinating class of self-organized solutions developed in high-dimensional networks. Necessary features of the network for the emergence of such complex but structured motions are non-local and symmetry breaking coupling. An accurate understanding of chimera states is expected to bring important insights on deterministic mechanism occurring in many structurally similar high-dimensional dynamics such as living systems, brain operation principles and even turbulence in hydrodynamics. Here we report on a powerful and highly controllable experiment based on an optoelectronic delayed feedback applied to a wavelength tuneable semiconductor laser, with which a wide variety of chimera patterns can be accurately investigated and interpreted. We uncover a cascade of higher-order chimeras as a pattern transition from N to N+1 clusters of chaoticity. Finally, we follow visually, as the gain increases, how chimera state is gradually destroyed on the way to apparent turbulence-like system behaviour.
Palacios-González, César
2015-01-01
In this paper I explore some of the moral issues that could emerge from the creation of human-nonhuman chimeras (HNH-chimeras) capable of human gamete production and human pregnancy. First I explore whether there is a cogent argument against the creation of HNH-chimeras that could produce human gametes. I conclude that so far there is none, and that in fact there is at least one good moral reason for producing such types of creatures. Afterwards I explore some of the moral problems that could emerge from the fact that a HNH-chimera could become pregnant with a human conceptus. I focus on two sets of problems: problems that would arise by virtue of the fact that a human is gestated by a nonhuman creature, and problems that would emerge from the fact that such pregnancies could affect the health of the HNH-chimera.
Rollakanti, K.; Anand, S.; Maytin, E. V.
2013-03-01
Photodynamic therapy with aminolevulinic acid can be modified by pretreatment regimens with drugs such as 5- Fluorouracil (5-FU) or Vitamin D (calcitriol) that enhance accumulation of protoporphyrin IX (PpIX) within tumor tissue which presumably will enhance the therapeutic response to light. However, histological approaches for monitoring therapeutic responses are poorly suited for studying long term survival because large numbers of mice need to be sacrificed. To address this limitation, a non-invasive model to monitor tumor regression and regrowth has been established. Breast cancer cells, stably transfected with firefly luciferase (MDA-Luc cell line), are implanted orthotopically in nude mice (0.25 - 1 x 106 cells/site), and monitored 0-60 min after s.c. injection of luciferin, with Xenogen in-vivo imaging system. Luminescence is detectable at day 1 post-implantation. Tumors are suitable for experimentation on day 6, when daily injections of pretreatment agents (5-FU, 300 mg/kg; calcitriol, 1 μg/kg) begin. On day 9, ALA (75 mg/kg i.p.) is given for 4 hr, followed by illumination (633 nm, 100 J/cm2). Tumor luminescence post- PDT is monitored daily and compared with caliper measurements. Pretreatments (5-FU, calcitriol) by themselves do not inhibit luciferase expression, and all tumors grow at a similar rate during the pretreatment period. Results from in vivo survival experiments can be correlated to survival responses of MDA-Luc cells grown in monolayer cultures +/- PDT and +/- pretreatments, and additional mechanistic information (e.g. Ki67 and E-cadherin expression) obtained. In summary, this noninvasive model will permit testing of the therapeutic survival advantages of various pretreatments during cPDT.
Ignatova, Zoya; Thakur, Ashwani K; Wetzel, Ronald; Gierasch, Lila M
2007-12-14
Toxicity in amyloid diseases is intimately linked to the nature of aggregates, with early oligomeric species believed to be more cytotoxic than later fibrillar aggregates. Yet mechanistic understanding of how aggregating species evolve with time is currently lacking. We have explored the aggregation process of a chimera composed of a globular protein (cellular retinoic acid-binding protein, CRABP) and huntingtin exon 1 with polyglutamine tracts either above (Q53) or below (Q20) the pathological threshold using Escherichia coli cells as a model intracellular environment. Previously we showed that fusion of the huntingtin exon 1 sequence with >40Q led to structural perturbation and decreased stability of CRABP (Ignatova, Z., and Gierasch, L. M. (2006) J. Biol. Chem. 281, 12959-12967). Here we report that the Q53 chimera aggregates in cells via a multistep process: early stage aggregates are spherical and detergent-soluble, characteristics of prefibrillar aggregates, and appear to be dominated structurally by CRABP, in that they can promote aggregation of a CRABP variant but not oligoglutamine aggregation, and the CRABP domain is relatively sequestered based on its protection from proteolysis. Late stage aggregates appear to be dominated by polyGln; they are fibrillar, detergent-resistant, capable of seeding aggregation of oligoglutamine but not the CRABP variant, and show relative protection of the polyglutamine-exon1 domain from proteolysis. These results point to an evolution of the dominant sequences in intracellular aggregates and may provide molecular insight into origins of toxic prefibrillar aggregates.
An Activin A/BMP2 chimera displays bone healing properties superior to those of BMP2
Yoon, Byung-Hak; Esquivies, Luis; Ahn, Chihoon; Gray, Peter C.; Ye, Sang-kyu; Kwiatkowski, Witek; Choe, Senyon
2014-01-01
Recombinant Bone Morphogenetic Protein 2 (rhBMP2) has been used clinically to treat bone fractures in human patients. However, the high doses of rhBMP2 required for a therapeutic response can cause undesirable side effects. Here, we demonstrate that a novel Activin A/BMP2 (AB2) chimera, AB204, promotes osteogenesis and bone healing much more potently and effectively than rhBMP2. Remarkably, 1 month of AB204 treatment completely heals tibial and calvarial defects of critical size in mice at a concentration 10-fold lower than a dose of rhBMP2 that only partially heals the defect. We determine the structure of AB204 to 2.3 Å that reveals a distinct BMP2-like fold in which the Activin A sequence segments confer insensitivity to the BMP2 antagonist Noggin and an affinity for the Activin/BMP type II receptor ActRII that is 100-fold greater than that of BMP2. The structure also led to our identification of a single Activin A-derived amino acid residue which when mutated to the corresponding BMP2 residue resulted in a significant increase in the affinity of AB204 for its type I receptor BMPRIa and a further enhancement in AB204's osteogenic potency. Together, these findings demonstrate that rationally designed AB2 chimeras can provide BMP2 substitutes with enhanced potency for treating non-union bone fractures. PMID:24692083
An activin A/BMP2 chimera, AB204, displays bone-healing properties superior to those of BMP2.
Yoon, Byung-Hak; Esquivies, Luis; Ahn, Chihoon; Gray, Peter C; Ye, Sang-Kyu; Kwiatkowski, Witek; Choe, Senyon
2014-09-01
Recombinant bone morphogenetic protein 2 (rhBMP2) has been used clinically to treat bone fractures in human patients. However, the high doses of rhBMP2 required for a therapeutic response can cause undesirable side effects. Here, we demonstrate that a novel Activin A/BMP2 (AB2) chimera, AB204, promotes osteogenesis and bone healing much more potently and effectively than rhBMP2. Remarkably, 1 month of AB204 treatment completely heals tibial and calvarial defects of critical size in mice at a concentration 10-fold lower than a dose of rhBMP2 that only partially heals the defect. We determine the structure of AB204 to 2.3 Å that reveals a distinct BMP2-like fold in which the Activin A sequence segments confer insensitivity to the BMP2 antagonist Noggin and an affinity for the Activin/BMP type II receptor ActRII that is 100-fold greater than that of BMP2. The structure also led to our identification of a single Activin A-derived amino acid residue, which, when mutated to the corresponding BMP2 residue, resulted in a significant increase in the affinity of AB204 for its type I receptor BMPRIa and a further enhancement in AB204's osteogenic potency. Together, these findings demonstrate that rationally designed AB2 chimeras can provide BMP2 substitutes with enhanced potency for treating non-union bone fractures.
Protein-DNA chimeras: synthesis of two-arm chimeras and non-mechanical effects of the DNA spring
Energy Technology Data Exchange (ETDEWEB)
Wang Yong; Wang, Andrew; Qu Hao; Zocchi, Giovanni, E-mail: zocchi@physics.ucla.ed [Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547 (United States)
2009-08-19
DNA molecular springs have recently been used to control the activity of enzymes and ribozymes. In this approach, the mechanical stress exerted by the molecular spring alters the enzyme's conformation and thus the enzymatic activity. Here we describe a method alternative to our previous one to attach DNA molecular springs to proteins, where two separate DNA 'arms' are coupled to the protein and subsequently ligated. We report certain non-mechanical effects associated with the DNA spring observed in some chimeras with specific DNA sequences and the nucleotide binding enzyme guanylate kinase. If a ssDNA 'arm' is attached to the protein by one end only, we find that in some cases (depending on the DNA sequence and attachment point on the protein's surface) the unhybridized DNA arm inhibits the enzyme, while hybridization of the DNA arm leads to an apparent activation of the enzyme. One interpretation is that, in these cases, hybridization of the DNA arm removes it from the vicinity of the active site of the enzyme. We show how mechanical and non-mechanical effects of the DNA spring can be distinguished. This is important if one wants to use the protein-DNA chimeras to quantitatively study the response of the enzyme to mechanical perturbations.
Chimera states in a Hodgkin-Huxley model of thermally sensitive neurons
Glaze, Tera A.; Lewis, Scott; Bahar, Sonya
2016-08-01
Chimera states occur when identically coupled groups of nonlinear oscillators exhibit radically different dynamics, with one group exhibiting synchronized oscillations and the other desynchronized behavior. This dynamical phenomenon has recently been studied in computational models and demonstrated experimentally in mechanical, optical, and chemical systems. The theoretical basis of these states is currently under active investigation. Chimera behavior is of particular relevance in the context of neural synchronization, given the phenomenon of unihemispheric sleep and the recent observation of asymmetric sleep in human patients with sleep apnea. The similarity of neural chimera states to neural "bump" states, which have been suggested as a model for working memory and visual orientation tuning in the cortex, adds to their interest as objects of study. Chimera states have been demonstrated in the FitzHugh-Nagumo model of excitable cells and in the Hindmarsh-Rose neural model. Here, we demonstrate chimera states and chimera-like behaviors in a Hodgkin-Huxley-type model of thermally sensitive neurons both in a system with Abrams-Strogatz (mean field) coupling and in a system with Kuramoto (distance-dependent) coupling. We map the regions of parameter space for which chimera behavior occurs in each of the two coupling schemes.
Energy Technology Data Exchange (ETDEWEB)
Obasaju, M.F.; Wiley, L.M.; Oudiz, D.J.; Raabe, O.; Overstreet, J.W.
1989-05-01
Male mice were divided into three experimental groups and a control group. Mice in the experimental groups received one of three doses of acute X irradiation (1.73, 0.29, and 0.05 Gy) and together with the control unirradiated mice were then mated weekly to unirradiated female mice for a 9-week experimental period. Embryos were recovered from the weekly matings at the four-cell stage and examined by the chimera assay for proliferative disadvantage. Aggregation chimeras were constructed of embryos from female mice mated to irradiated males (experimental embryos) and embryos from females mated to unexposed males (control embryos) and contained either one experimental embryo and one control embryo (heterologous chimera) or two control embryos (control chimera). The control embryo in heterologous chimeras and either embryo in control chimeras were prelabeled with the vital dye fluorescein isothiocyanate (FITC), and the chimeras were cultured for 40 h and viewed under phase-contrast and epifluorescence microscopy to obtain total embryo cell number and the cellular contribution from the FITC-labeled embryo. Experimental and control embryos that were cultured singly were also examined for embryo cell number at the end of the 40-h culture period. In control chimeras, the mean ratio of the unlabeled cells:total chimera cell number (henceforth referred to as ''mean ratio'') was 0.50 with little or no weekly variation over the 9-week experimental period. During Weeks 4-7, the mean ratios of heterologous chimeras differed significantly from the mean ratio of control chimeras with the greatest differences occurring during Week 7 (0.41 for chimeras of 0.05 Gy dose group, 0.40 for chimeras of the 0.29 Gy dose group, and 0.17 for chimeras of the 1.73 Gy dose group).
Bogomolov, Sergey A.; Slepnev, Andrei V.; Strelkova, Galina I.; Schöll, Eckehard; Anishchenko, Vadim S.
2017-02-01
We explore the bifurcation transition from coherence to incoherence in ensembles of nonlocally coupled chaotic systems. It is firstly shown that two types of chimera states, namely, amplitude and phase, can be found in a network of coupled logistic maps, while only amplitude chimera states can be observed in a ring of continuous-time chaotic systems. We reveal a bifurcation mechanism by analyzing the evolution of space-time profiles and the coupling function with varying coupling coefficient and formulate the necessary and sufficient conditions for realizing the chimera states in the ensembles.
Chimeras in a network of three oscillator populations with varying network topology
DEFF Research Database (Denmark)
Martens, Erik Andreas
2010-01-01
this system as a model system, we discuss for the first time the influence of network topology on the existence of so-called chimera states. In this context, the network with three populations represents an interesting case because the populations may either be connected as a triangle, or as a chain, thereby......-like. By showing that chimera states only exist for a bounded set of parameter values, we demonstrate that their existence depends strongly on the underlying network structures, and conclude that chimeras exist on networks with a chain-like character....
Pedrini, D. T.; Pedrini, Bonnie C.
Regression, another mechanism studied by Sigmund Freud, has had much research, e.g., hypnotic regression, frustration regression, schizophrenic regression, and infra-human-animal regression (often directly related to fixation). Many investigators worked with hypnotic age regression, which has a long history, going back to Russian reflexologists.…
Pedrini, D. T.; Pedrini, Bonnie C.
Regression, another mechanism studied by Sigmund Freud, has had much research, e.g., hypnotic regression, frustration regression, schizophrenic regression, and infra-human-animal regression (often directly related to fixation). Many investigators worked with hypnotic age regression, which has a long history, going back to Russian reflexologists.…
Linked and knotted chimera filaments in oscillatory systems.
Lau, Hon Wai; Davidsen, Jörn
2016-07-01
While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.
GABAρ1/GABAAα1 receptor chimeras to study receptor desensitization
Martínez-Torres, Ataúlfo; Demuro, Angelo; Miledi, Ricardo
2000-01-01
γ-Aminobutyrate type C (GABAC) receptors are ligand-gated ion channels that are expressed preponderantly in the vertebrate retina and are characterized, among other things, by a very low rate of desensitization and resistance to the specific GABAA antagonist bicuculline. To examine which structural elements determine the nondesensitizing character of the human homomeric ρ1 receptor, we used a combination of gene chimeras and electrophysiology of receptors expressed in Xenopus oocytes. Two chimeric genes were constructed, made up of portions of the ρ1-subunit and of the α1-subunit of the GABAA receptor. When expressed in Xenopus oocytes, one chimeric gene (ρ1/α1) formed functional homooligomeric receptors that were fully resistant to bicuculline and were blocked by the specific GABAC antagonist (1,2,5,6-tetrahydropyridine-4-yl)methylphosphinic acid and by zinc. Moreover, these chimeric receptors had a fast-desensitizing component, even faster than that of heterooligomeric GABAA receptors, in striking contrast to the almost nil desensitization of wild-type ρ1 (wt ρ1) receptors. To see whether the fast-desensitizing characteristic of the chimera was determined by the amino acids forming the ion channels, we replaced the second transmembrane segment (TM2) of ρ1 by that of the α1-subunit of GABAA. Although the α1-subunit forms fast-desensitizing receptors when coexpressed with other GABAA subunits, the sole transfer of the α1TM2 segment to ρ1 was not sufficient to form desensitizing receptors. All this suggests that the slow-desensitizing trait of ρ1 receptors is determined by a combination of several interacting domains along the molecule. PMID:10725369
Laser Chimeras as a paradigm for multi-stable patterns in complex systems
Larger, Laurent; Maistrenko, Yuri
2014-01-01
Chimera is a rich and fascinating class of self-organized solutions developed in high dimensional networks having non-local and symmetry breaking coupling features. Its accurate understanding is expected to bring important insight in many phenomena observed in complex spatio-temporal dynamics, from living systems, brain operation principles, and even turbulence in hydrodynamics. In this article we report on a powerful and highly controllable experiment based on optoelectronic delayed feedback applied to a wavelength tunable semiconductor laser, with which a wide variety of Chimera patterns can be accurately investigated and interpreted. We uncover a cascade of higher order Chimeras as a pattern transition from N to N - 1 clusters of chaoticity. Finally, we follow visually, as the gain increases, how Chimera is gradually destroyed on the way to apparent turbulence-like system behaviour.
Artus, Jérôme; Hadjantonakis, Anna-Katerina
2011-01-01
From the hybrid creatures of the Greek and Egyptian mythologies, the concept of the chimera has evolved and, in modern day biology, refers to an organism comprises of at least two populations of genetically distinct cells. Mouse chimeras have proven an invaluable tool for the generation of genetically modified strains. In addition, chimeras have been extensively used in developmental biology as a powerful tool to analyze the phenotype of specific mutations, to attribute function to gene products and to address the question of cell autonomy versus noncell autonomy of gene function. This chapter describes a simple and economical technique used to generate mouse chimeras by embryo aggregation. Multiple aggregation combinations are described each of which can be tailored to answer particular biological questions.
Chimera states in a network-organized public goods game with destructive agents
Kouvaris, Nikos E.; Requejo, Rubén J.; Hizanidis, Johanne; Díaz-Guilera, Albert
2016-12-01
We found that a network-organized metapopulation of cooperators, defectors, and destructive agents playing the public goods game with mutations can collectively reach global synchronization or chimera states. Global synchronization is accompanied by a collective periodic burst of cooperation, whereas chimera states reflect the tendency of the networked metapopulation to be fragmented in clusters of synchronous and incoherent bursts of cooperation. Numerical simulations have shown that the system's dynamics switches between these two steady states through a first order transition. Depending on the parameters determining the dynamical and topological properties, chimera states with different numbers of coherent and incoherent clusters are observed. Our results present the first systematic study of chimera states and their characterization in the context of evolutionary game theory. This provides a valuable insight into the details of their occurrence, extending the relevance of such states to natural and social systems.
Effect of glycyrrhizin on pseudomonal skin infections in human-mouse chimeras.
Directory of Open Access Journals (Sweden)
Shohei Yoshida
Full Text Available In our previous studies, peripheral blood lineage(-CD34(+CD31(+ cells (CD31(+ IMC appearing in severely burned patients have been characterized as inhibitor cells for the production of β-defensins (HBDs by human epidermal keratinocytes (NHEK. In this study, the effect of glycyrrhizin on pseudomonal skin infections was studied in a chimera model of thermal injury. Two different chimera models were utilized. Patient chimeras were created in murine antimicrobial peptide-depleted NOD-SCID IL-2rγ(null mice that were grafted with unburned skin tissues of severely burned patients and inoculated with the same patient peripheral blood CD31(+ IMC. Patient chimera substitutes were created in the same mice that were grafted with NHEK and inoculated with experimentally induced CD31(+ IMC. In the results, both groups of chimeras treated with glycyrrhizin resisted a 20 LD50 dose of P. aeruginosa skin infection, while all chimeras in both groups treated with saline died within 3 days of the infection. Human antimicrobial peptides were detected from the grafted site tissues of both groups of chimeras treated with glycyrrhizin, while the peptides were not detected in the same area tissues of controls. HBD-1 was produced by keratinocytes in transwell-cultures performed with CD31(+ IMC and glycyrrhizin. Also, inhibitors (IL-10 and CCL2 of HBD-1 production by keratinocytes were not detected in cultures of patient CD31(+ IMC treated with glycyrrhizin. These results indicate that sepsis stemming from pseudomonal grafted site infections in a chimera model of burn injury is controllable by glycyrrhizin. Impaired antimicrobial peptide production at the infection site of severely burned patients may be restored after treatment with glycyrrhizin.
Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB
Energy Technology Data Exchange (ETDEWEB)
DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.
2006-02-01
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.
Schmidt, Lennart; Krischer, Katharina
2015-06-01
We study an oscillatory medium with a nonlinear global coupling that gives rise to a harmonic mean-field oscillation with constant amplitude and frequency. Two types of cluster states are found, each undergoing a symmetry-breaking transition towards a related chimera state. We demonstrate that the diffusional coupling is non-essential for these complex dynamics. Furthermore, we investigate localized turbulence and discuss whether it can be categorized as a chimera state.
TCP: a tool for designing chimera proteins based on the tertiary structure information
Directory of Open Access Journals (Sweden)
Nishida Reina
2009-01-01
Full Text Available Abstract Background Chimera proteins are widely used for the analysis of the protein-protein interaction region. One of the major issues is the epitope analysis of the monoclonal antibody. In the analysis, a continuous portion of an antigen is sequentially substituted into a different sequence. This method works well for an antibody recognizing a linear epitope, but not for that recognizing a discontinuous epitope. Although the designing the chimera proteins based on the tertiary structure information is required in such situations, there is no appropriate tool so far. Results In light of the problem, we developed a tool named TCP (standing for a Tool for designing Chimera Proteins, which extracts some sets of mutually orthogonal cutting surfaces for designing chimera proteins using a genetic algorithm. TCP can also incorporate and consider the solvent accessible surface area information calculated by a DSSP program. The test results of our method indicate that the TCP is robust and applicable to various shapes of proteins. Conclusion We developed TCP, a tool for designing chimera proteins based on the tertiary structure information. TCP is robust and possesses several favourable features, and we believe it is a useful tool for designing chimera proteins. TCP is freely available as an additional file of this manuscript for academic and non-profit organization.
Regression analysis by example
National Research Council Canada - National Science Library
Chatterjee, Samprit; Hadi, Ali S
2012-01-01
.... The emphasis continues to be on exploratory data analysis rather than statistical theory. The coverage offers in-depth treatment of regression diagnostics, transformation, multicollinearity, logistic regression, and robust regression...
DEFF Research Database (Denmark)
Klco, Jeffery M; Sen, Saurabh; Hansen, Jakob L
2009-01-01
. Despite relatively conservative substitutions, the lipid-facing chimeras (TM1, TM2, TM4, TM5, TM6 or TM7) were retained in the endoplasmic reticulum/cis-Golgi network. With the exception of the TM7 chimera that did not bind ligand, the lipid-facing chimeras bound ligand with low affinity, but similar...... oligomerization studies demonstrated energy transfer between the wild-type complement factor 5a receptor and the lipid-facing chimeras, suggesting that the lipid-facing residues within a single TM segment are not essential for oligomerization. These studies highlight the importance of the lipid-facing residues...
DEFF Research Database (Denmark)
Johansen, Søren
2008-01-01
The reduced rank regression model is a multivariate regression model with a coefficient matrix with reduced rank. The reduced rank regression algorithm is an estimation procedure, which estimates the reduced rank regression model. It is related to canonical correlations and involves calculating e...
Directory of Open Access Journals (Sweden)
Daar Abdallah S
2010-05-01
Full Text Available Abstract Background In recent years, the field of vaccines for diseases such as Human Immunodeficiency Virus (HIV which take a heavy toll in developing countries has faced major failures. This has led to a call for more basic science research, and development as well as evaluation of new vaccine candidates. Human-animal chimeras, developed with a 'humanized' immune system could be useful to study infectious diseases, including many neglected diseases. These would also serve as an important tool for the efficient testing of new vaccine candidates to streamline promising candidates for further trials in humans. However, developing human-animal chimeras has proved to be controversial. Discussion Development of human-animal chimeras for vaccine development has been slowed down because of opposition by some philosophers, ethicists and policy makers in the west-they question the moral status of such animals, and also express discomfort about transgression of species barriers. Such opposition often uses a contemporary western world view as a reference point. Human-animal chimeras are often being created for diseases which cause significantly higher morbidity and mortality in the developing world as compared to the developed world. We argue in our commentary that given this high disease burden, we should look at socio-cultural perspectives on human-animal chimera like beings in the developing world. On examination, it's clear that such beings have been part of mythology and cultural descriptions in many countries in the developing world. Summary To ensure that important research on diseases afflicting millions like malaria, HIV, Hepatitis-C and dengue continues to progress, we recommend supporting human-animal chimera research for vaccine development in developing countries (especially China and India which have growing technical expertise in the area. The negative perceptions in some parts of the west about human-animal chimeras can be used as an
Present status of the Chimera-Isospin experiment
Energy Technology Data Exchange (ETDEWEB)
Politi, G.; Arena, N.; Cardella, G.; DeFilippo, E.; Lanzano, G.; Nigro, S.L.; Pagano, A.; Papa, M.; Pirrone, S.; Russotto, P. [Catania Univ., INFN (Italy); Alderighi, M.; Sechi, G.; Sperduto, M.L. [Milano Univ., INFN, CNR (Italy); Amorini, F.; Anzalone, A.; Baran, V.; Bonasera, A.; Cavallaro, S.L.; Colonna, M.; Di Toro, M.; LaGuidara, E.; Lanzalone, G.; IaconoManno, M.; Giustolisi, F.; Maiolino, C.; Porto, F.; Rizzo, F.; Trifiro, A.; Trimarchi, M. [Catania Univ., INFN, Lab. Nazionali del Sud (Italy); Auditore, L.; Barna, R.; DePasquale, D. [Messina Univ., INFN (Italy); Berceanu, I.; Petrovici, M.; Pop, A. [Inst. for Physics and Nuclear Engineering, Bucharest (Romania); Blicharska, J.; Grzeszczuk, A.; Kowalski, S.; Zipper, W. [Univ. of Silesia, Inst. of Physics, Katowice (Poland); Borderie, B.; LeNeindre, N.; Rivet, M.F. [Paris-11 Univ., IPN-IN2P3-CNRS, 91 - Orsay (France); Bougault, R. [Caen Univ., LPC-ISMRA (France); Briczycnski, J.; Gawlikowicz, W.; Majka, Z.; Planeta, R. [M. Smoluchowski Inst. of Physics, Jagellonian Univ., Cracow (Poland); Bruno, M.; D' Agostino, M.; Fuschini, E.; Geraci, E.; Vannini, G. [Bologna Univ., INFN (Italy); Chatterjee, M.B. [Saha Inst. of Nuclear Physics, NIS Div., Kolkata (India); Chbihi, A.; Wieleczko, J.P. [GANIL -CEA-IN2P3-CNRS, 14 - Caen (France); Cibor, J. [H.Niewodniczanski Inst. of Nuclear Physics, Cracow (Poland); Dayras, R. [CEA Saclay, Dept. d' Astrophysique, de Physique des Particules, de Physique Nucleaire et de l' Instrumentation Associee, SPhN, 91- Gif sur Yvette (France); Guazzoni, P.; Russo, S.; Sassi, M.; Zetta, L. [Milano Univ., INFN (Italy); Guinet, D. [Univ. Claude Bernard, IPN-IN2P3-CNRS, 69 - Lyon (France); Li, S.; Wu, H.; Xiao, Z. [Inst. of Modern Physics, Lanzhou (China); Nicolis, N.G. [Ioannina Univ., Dept. of Physics (Greece); Piasecki, E.; Swiderski, L.; Siwek-Wilczynska, K.; Skwira, I. [Warsaw Univ., Inst. for Experimental Physics (Poland); Rosato, E.; Vigilante, M.; Wilczynski, J.
2003-07-01
The CHIMERA detector was designed to significantly contribute to multifragmentation studies in the field of heavy ion collisions at intermediate energies. The device has been used at 'Laboratori Nazionali del Sud' (LNS) in Catania (Italy) to study different aspects of the relevant nuclear reaction mechanism, in two different campaigns: the first one in 2000, by using the forward part (1 - 30 degrees) of the device, and the second one in 2003, by using the 4{pi} geometry. The experimental results have confirmed the capability of the apparatus for good isotopic identification of light charged particles and light fragments (3
Formyl peptide receptor chimeras define domains involved in ligand binding.
Perez, H D; Holmes, R; Vilander, L R; Adams, R R; Manzana, W; Jolley, D; Andrews, W H
1993-02-05
We have begun to study the structural requirements for the binding of formyl peptides to their specific receptors. As an initial approach, we constructed C5a-formyl peptide receptor chimeras. Unique (and identical) restriction sites were introduced within the transmembrane domains of these receptors that allowed for the exchange of specific areas. Four types of chimeric receptors were generated. 1) The C5a receptor was progressively substituted by the formyl peptide receptor. 2) The formyl peptide receptor was progressively substituted by the C5a receptor. 3) Specific domains of the C5a receptor were substituted by the corresponding domain of the formyl peptide receptor. 4) Specific domains of the formyl peptide receptor were replaced by the same corresponding domain of the C5a receptor. Wild type and chimeric receptors were transfected into COS 7 cells and their ability to bind formyl peptide determined, taking into account efficiency of transfection and expression of chimeric protein. Based on these results, a ligand binding model is presented in which the second, third, and fourth extracellular (and/or their transmembrane) domains together with the first transmembrane domain form a ligand binding pocket for formyl peptides. It is proposed that the amino-terminal domain plays a role by presumably providing a "lid" to the pocket. The carboxyl-terminal cytoplasmic tail appears to modulate ligand binding by regulating receptor affinity.
Chimera-like states in a neuronal network model of the cat brain
Santos, M. S.; Szezech, J. D.; Borges, F. S.; Iarosz, K. C.; Caldas, I. L.; Batista, A. M.; Viana, R. L.; Kurths, J.
2017-08-01
Neuronal systems have been modeled by complex networks in different description levels. Recently, it has been verified that networks can simultaneously exhibit one coherent and other incoherent domain, known as chimera states. In this work, we study the existence of chimera states in a network considering the connectivity matrix based on the cat cerebral cortex. The cerebral cortex of the cat can be separated in 65 cortical areas organised into the four cognitive regions: visual, auditory, somatosensory-motor and frontolimbic. We consider a network where the local dynamics is given by the Hindmarsh-Rose model. The Hindmarsh-Rose equations are a well known model of neuronal activity that has been considered to simulate membrane potential in neuron. Here, we analyse under which conditions chimera states are present, as well as the affects induced by intensity of coupling on them. We observe the existence of chimera states in that incoherent structure can be composed of desynchronised spikes or desynchronised bursts. Moreover, we find that chimera states with desynchronised bursts are more robust to neuronal noise than with desynchronised spikes.
Dodhia, Vikash Rajnikant; Fantuzzi, Andrea; Gilardi, Gianfranco
2006-10-01
The membrane-bound human cytochrome P450s have essential roles in the metabolism of endogenous compounds and drugs. Presented here are the results on the construction and characterization of three fusion proteins containing the N-terminally modified human cytochrome P450s CYP2C9, CY2C19 and CYP3A4 fused to the soluble NADPH-dependent oxidoreductase domain of CYP102A1 from Bacillus megaterium. The constructs, CYP2C9/BMR, CYP2C19/BMR and CYP3A4/BMR are well expressed in Escherichia coli as holo proteins. The chimeras can be purified in the absence of detergent and the purified enzymes are both active and correctly folded in the absence of detergent, as demonstrated by circular dichroism and functional studies. Additionally, in comparison with the parent P450 enzyme, these chimeras have greatly improved solubility properties. The chimeras are catalytically self-sufficient and present turnover rates similar to those reported for the native enzymes in reconstituted systems, unlike previously reported mammalian cytochrome P450 fusion proteins. Furthermore the specific activities of these chimeras are not dependent on the enzyme concentration present in the reaction buffer and they do not require the addition of accessory proteins, detergents or phospholipids to be fully active. The solubility, catalytic self-sufficiency and wild-type like activities of these chimeras would greatly simplify the studies of cytochrome P450 mediated drug metabolism in solution.
Regression analysis by example
Chatterjee, Samprit
2012-01-01
Praise for the Fourth Edition: ""This book is . . . an excellent source of examples for regression analysis. It has been and still is readily readable and understandable."" -Journal of the American Statistical Association Regression analysis is a conceptually simple method for investigating relationships among variables. Carrying out a successful application of regression analysis, however, requires a balance of theoretical results, empirical rules, and subjective judgment. Regression Analysis by Example, Fifth Edition has been expanded
Unitary Response Regression Models
Lipovetsky, S.
2007-01-01
The dependent variable in a regular linear regression is a numerical variable, and in a logistic regression it is a binary or categorical variable. In these models the dependent variable has varying values. However, there are problems yielding an identity output of a constant value which can also be modelled in a linear or logistic regression with…
Flexible survival regression modelling
DEFF Research Database (Denmark)
Cortese, Giuliana; Scheike, Thomas H; Martinussen, Torben
2009-01-01
Regression analysis of survival data, and more generally event history data, is typically based on Cox's regression model. We here review some recent methodology, focusing on the limitations of Cox's regression model. The key limitation is that the model is not well suited to represent time-varyi...
DEFF Research Database (Denmark)
Fitzenberger, Bernd; Wilke, Ralf Andreas
2015-01-01
Quantile regression is emerging as a popular statistical approach, which complements the estimation of conditional mean models. While the latter only focuses on one aspect of the conditional distribution of the dependent variable, the mean, quantile regression provides more detailed insights by m...... treatment of the topic is based on the perspective of applied researchers using quantile regression in their empirical work....
Status and perspectives of fragmentation beams at LNS with CHIMERA detector
Directory of Open Access Journals (Sweden)
Cardella G.
2015-01-01
Full Text Available Relatively large yields of various exotic beams produced through in-flight fragmentation are available at LNS. Using the CHIMERA detector, we performed various experiments to study elastic and inelastic scattering, transfer, break-up, and reaction dynamics with targets from proton and deuteron to carbon and heavier. For reactions with relatively light systems we used the kinematical coincidence method to extract high resolution angular distributions of binary reactions from the measured light particle energy spectra. We also used the CsI detectors of CHIMERA to detect gamma rays emitted in the reactions. Some of most recent results are presented together with future perspectives with the coupling of CHIMERA with FARCOS array.
The Influence of the Resonant Frequency on the Presence Of Chimera State
Directory of Open Access Journals (Sweden)
Phablo Ramos Carvalho
2016-04-01
Full Text Available The Chimera State could be a result of the interaction between the resonant frequency and the synchronization process in a network of identical oscillators. The target of this paper is to do the numerically investigation of the chimera occurrence in a model with fifteen metronomes on each swing and two coupled swings Therefore, changing the value of metronomes oscillation frequency one can observe the level of synchronization between the two populations of metronomes through the Kuramoto complex order parameter. This analysis was conducted considering three different values of the connecting spring’s stiffness among the swings. Thus, a relation between the presence of chimera state and the system resonant frequency was observed
A Multitier System for the Verification, Visualization and Management of CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Lingerfelt, Eric J [ORNL; Messer, Bronson [ORNL; Osborne, James A [National Institute for Computational Sciences (NICS); Budiardja, R. D. [University of Tennessee, Knoxville (UTK); Mezzacappa, Anthony [ORNL
2011-01-01
CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. Given CHIMERA s complexity and pace of ongoing development, a new support system, Bellerophon, has been designed and implemented to perform automated verification, visualization and management tasks while integrating with other workflow systems utilized by CHIMERA s development group. In order to achieve these goals, a multitier approach has been adopted. By integrating supercomputing platforms, visualization clusters, a dedicated web server and a client-side desktop application, this system attempts to provide an encapsulated, end-to-end solution to these needs.
The Chimera II Real-Time Operating System for advanced sensor-based control applications
Stewart, David B.; Schmitz, Donald E.; Khosla, Pradeep K.
1992-01-01
Attention is given to the Chimera II Real-Time Operating System, which has been developed for advanced sensor-based control applications. The Chimera II provides a high-performance real-time kernel and a variety of IPC features. The hardware platform required to run Chimera II consists of commercially available hardware, and allows custom hardware to be easily integrated. The design allows it to be used with almost any type of VMEbus-based processors and devices. It allows radially differing hardware to be programmed using a common system, thus providing a first and necessary step towards the standardization of reconfigurable systems that results in a reduction of development time and cost.
Multicluster and traveling chimera states in nonlocal phase-coupled oscillators.
Xie, Jianbo; Knobloch, Edgar; Kao, Hsien-Ching
2014-08-01
Chimera states consisting of domains of coherently and incoherently oscillating identical oscillators with nonlocal coupling are studied. These states usually coexist with the fully synchronized state and have a small basin of attraction. We propose a nonlocal phase-coupled model in which chimera states develop from random initial conditions. Several classes of chimera states have been found: (a) stationary multicluster states with evenly distributed coherent clusters, (b) stationary multicluster states with unevenly distributed clusters, and (c) a single cluster state traveling with a constant speed across the system. Traveling coherent states are also identified. A self-consistent continuum description of these states is provided and their stability properties analyzed through a combination of linear stability analysis and numerical simulation.
Liu, Yamei; Stepanov, Victor G; Strych, Ulrich; Willson, Richard C; Jackson, George W; Fox, George E
2010-12-06
Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA) was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.
Katzgraber, Helmut G.; Hamze, Firas; Andrist, Ruben S.
2014-04-01
Recently, a programmable quantum annealing machine has been built that minimizes the cost function of hard optimization problems by, in principle, adiabatically quenching quantum fluctuations. Tests performed by different research teams have shown that, indeed, the machine seems to exploit quantum effects. However, experiments on a class of random-bond instances have not yet demonstrated an advantage over classical optimization algorithms on traditional computer hardware. Here, we present evidence as to why this might be the case. These engineered quantum annealing machines effectively operate coupled to a decohering thermal bath. Therefore, we study the finite-temperature critical behavior of the standard benchmark problem used to assess the computational capabilities of these complex machines. We simulate both random-bond Ising models and spin glasses with bimodal and Gaussian disorder on the D-Wave Chimera topology. Our results show that while the worst-case complexity of finding a ground state of an Ising spin glass on the Chimera graph is not polynomial, the finite-temperature phase space is likely rather simple because spin glasses on Chimera have only a zero-temperature transition. This means that benchmarking optimization methods using spin glasses on the Chimera graph might not be the best benchmark problems to test quantum speedup. We propose alternative benchmarks by embedding potentially harder problems on the Chimera topology. Finally, we also study the (reentrant) disorder-temperature phase diagram of the random-bond Ising model on the Chimera graph and show that a finite-temperature ferromagnetic phase is stable up to 19.85(15)% antiferromagnetic bonds. Beyond this threshold, the system only displays a zero-temperature spin-glass phase. Our results therefore show that a careful design of the hardware architecture and benchmark problems is key when building quantum annealing machines.
Directory of Open Access Journals (Sweden)
Helmut G. Katzgraber
2014-04-01
Full Text Available Recently, a programmable quantum annealing machine has been built that minimizes the cost function of hard optimization problems by, in principle, adiabatically quenching quantum fluctuations. Tests performed by different research teams have shown that, indeed, the machine seems to exploit quantum effects. However, experiments on a class of random-bond instances have not yet demonstrated an advantage over classical optimization algorithms on traditional computer hardware. Here, we present evidence as to why this might be the case. These engineered quantum annealing machines effectively operate coupled to a decohering thermal bath. Therefore, we study the finite-temperature critical behavior of the standard benchmark problem used to assess the computational capabilities of these complex machines. We simulate both random-bond Ising models and spin glasses with bimodal and Gaussian disorder on the D-Wave Chimera topology. Our results show that while the worst-case complexity of finding a ground state of an Ising spin glass on the Chimera graph is not polynomial, the finite-temperature phase space is likely rather simple because spin glasses on Chimera have only a zero-temperature transition. This means that benchmarking optimization methods using spin glasses on the Chimera graph might not be the best benchmark problems to test quantum speedup. We propose alternative benchmarks by embedding potentially harder problems on the Chimera topology. Finally, we also study the (reentrant disorder-temperature phase diagram of the random-bond Ising model on the Chimera graph and show that a finite-temperature ferromagnetic phase is stable up to 19.85(15% antiferromagnetic bonds. Beyond this threshold, the system only displays a zero-temperature spin-glass phase. Our results therefore show that a careful design of the hardware architecture and benchmark problems is key when building quantum annealing machines.
Naghshpour, Shahdad
2012-01-01
Regression analysis is the most commonly used statistical method in the world. Although few would characterize this technique as simple, regression is in fact both simple and elegant. The complexity that many attribute to regression analysis is often a reflection of their lack of familiarity with the language of mathematics. But regression analysis can be understood even without a mastery of sophisticated mathematical concepts. This book provides the foundation and will help demystify regression analysis using examples from economics and with real data to show the applications of the method. T
Chimera states in a population of identical oscillators under planar cross-coupling
Indian Academy of Sciences (India)
C R Hens; A Mishra; P K Roy; A Sen; S K Dana
2015-02-01
We report the existence of chimera states in an assembly of identical nonlinear oscillators that are globally linked to each other in a simple planar cross-coupled form. The rotational symmetry breaking of the coupling term appears to be responsible for the emergence of these collective states that display a characteristic coexistence of coherent and incoherent behaviour. The finding, observed in both a collection of van der Pol oscillators and chaotic Rössler oscillators, further simplifies the existence criterion for chimeras, thereby broadens the range of their applicability to real-world situations.
Greengenes, a Chimera-checked 16S rRNA gene database and workbenchcompatible with ARB
Energy Technology Data Exchange (ETDEWEB)
DeSantis, Todd Z.; Hugenholtz, Philip; Larsen, Neils; Rojas,Mark; Brodie, Eoin L.; Keller, Keith; Huber, Thomas; Dalevi, Daniel; Hu,Ping; Andersen, Gary L.
2006-04-10
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that in congruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3 percent of environmental sequences and 0.2 percent of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.
Marginal chimera state at cross-frequency locking of pulse-coupled neural networks
Bolotov, M. I.; Osipov, G. V.; Pikovsky, A.
2016-03-01
We consider two coupled populations of leaky integrate-and-fire neurons. Depending on the coupling strength, mean fields generated by these populations can have incommensurate frequencies or become frequency locked. In the observed 2:1 locking state of the mean fields, individual neurons in one population are asynchronous with the mean fields, while in another population they have the same frequency as the mean field. These synchronous neurons form a chimera state, where part of them build a fully synchronized cluster, while other remain scattered. We explain this chimera as a marginal one, caused by a self-organized neutral dynamics of the effective circle map.
Autistic epileptiform regression.
Canitano, Roberto; Zappella, Michele
2006-01-01
Autistic regression is a well known condition that occurs in one third of children with pervasive developmental disorders, who, after normal development in the first year of life, undergo a global regression during the second year that encompasses language, social skills and play. In a portion of these subjects, epileptiform abnormalities are present with or without seizures, resembling, in some respects, other epileptiform regressions of language and behaviour such as Landau-Kleffner syndrome. In these cases, for a more accurate definition of the clinical entity, the term autistic epileptifom regression has been suggested. As in other epileptic syndromes with regression, the relationships between EEG abnormalities, language and behaviour, in autism, are still unclear. We describe two cases of autistic epileptiform regression selected from a larger group of children with autistic spectrum disorders, with the aim of discussing the clinical features of the condition, the therapeutic approach and the outcome.
Scaled Sparse Linear Regression
Sun, Tingni
2011-01-01
Scaled sparse linear regression jointly estimates the regression coefficients and noise level in a linear model. It chooses an equilibrium with a sparse regression method by iteratively estimating the noise level via the mean residual squares and scaling the penalty in proportion to the estimated noise level. The iterative algorithm costs nearly nothing beyond the computation of a path of the sparse regression estimator for penalty levels above a threshold. For the scaled Lasso, the algorithm is a gradient descent in a convex minimization of a penalized joint loss function for the regression coefficients and noise level. Under mild regularity conditions, we prove that the method yields simultaneously an estimator for the noise level and an estimated coefficient vector in the Lasso path satisfying certain oracle inequalities for the estimation of the noise level, prediction, and the estimation of regression coefficients. These oracle inequalities provide sufficient conditions for the consistency and asymptotic...
Rolling Regressions with Stata
Kit Baum
2004-01-01
This talk will describe some work underway to add a "rolling regression" capability to Stata's suite of time series features. Although commands such as "statsby" permit analysis of non-overlapping subsamples in the time domain, they are not suited to the analysis of overlapping (e.g. "moving window") samples. Both moving-window and widening-window techniques are often used to judge the stability of time series regression relationships. We will present an implementation of a rolling regression...
Institute of Scientific and Technical Information of China (English)
Guijun YANG; Lu LIN; Runchu ZHANG
2007-01-01
Quasi-regression, motivated by the problems arising in the computer experiments, focuses mainly on speeding up evaluation. However, its theoretical properties are unexplored systemically. This paper shows that quasi-regression is unbiased, strong convergent and asymptotic normal for parameter estimations but it is biased for the fitting of curve. Furthermore, a new method called unbiased quasi-regression is proposed. In addition to retaining the above asymptotic behaviors of parameter estimations, unbiased quasi-regression is unbiased for the fitting of curve.
Introduction to regression graphics
Cook, R Dennis
2009-01-01
Covers the use of dynamic and interactive computer graphics in linear regression analysis, focusing on analytical graphics. Features new techniques like plot rotation. The authors have composed their own regression code, using Xlisp-Stat language called R-code, which is a nearly complete system for linear regression analysis and can be utilized as the main computer program in a linear regression course. The accompanying disks, for both Macintosh and Windows computers, contain the R-code and Xlisp-Stat. An Instructor's Manual presenting detailed solutions to all the problems in the book is ava
Weisberg, Sanford
2005-01-01
Master linear regression techniques with a new edition of a classic text Reviews of the Second Edition: ""I found it enjoyable reading and so full of interesting material that even the well-informed reader will probably find something new . . . a necessity for all of those who do linear regression."" -Technometrics, February 1987 ""Overall, I feel that the book is a valuable addition to the now considerable list of texts on applied linear regression. It should be a strong contender as the leading text for a first serious course in regression analysis."" -American Scientist, May-June 1987
Occurrence and stability of chimera states in coupled externally excited oscillators
Dudkowski, Dawid; Maistrenko, Yuri; Kapitaniak, Tomasz
2016-11-01
We studied the phenomenon of chimera states in networks of non-locally coupled externally excited oscillators. Units of the considered networks are bi-stable, having two co-existing attractors of different types (chaotic and periodic). The occurrence of chimeras is discussed, and the influence of coupling radius and coupling strength on their co-existence is analyzed (including typical bifurcation scenarios). We present a statistical analysis and investigate sensitivity of the probability of observing chimeras to the initial conditions and parameter values. Due to the fact that each unit of the considered networks is individually excited, we study the influence of the excitation failure on stability of observed states. Typical transitions are shown, and changes in network's dynamics are discussed. We analyze systems of coupled van der Pol-Duffing oscillators and the Duffing ones. Described chimera states are robust as they are observed in the wide regions of parameter values, as well as in other networks of coupled forced oscillators.
"American Chimera: The Ever-Present Domination of Whiteness, Patriarchy, and Capitalism…A Parable"
Montoya, Roberto; Matias, Cheryl E.; Nishi, Naomi W. M.; Sarcedo, Geneva L.
2016-01-01
In Greek mythology, the Chimera is a fire-breathing monster with three heads: one of a lion, one of a horned goat, and one of a powerful dragon. Of similar construction is the presence of three structures in US society, whiteness, patriarchy, and capitalism, which are overwhelmingly represented, valued, and espoused when examining areas of…
CHIMERA: Clustering of Heterogeneous Disease Effects via Distribution Matching of Imaging Patterns.
Dong, Aoyan; Honnorat, Nicolas; Gaonkar, Bilwaj; Davatzikos, Christos
2016-02-01
Many brain disorders and diseases exhibit heterogeneous symptoms and imaging characteristics. This heterogeneity is typically not captured by commonly adopted neuroimaging analyses that seek only a main imaging pattern when two groups need to be differentiated (e.g., patients and controls, or clinical progressors and non-progressors). We propose a novel probabilistic clustering approach, CHIMERA, modeling the pathological process by a combination of multiple regularized transformations from normal/control population to the patient population, thereby seeking to identify multiple imaging patterns that relate to disease effects and to better characterize disease heterogeneity. In our framework, normal and patient populations are considered as point distributions that are matched by a variant of the coherent point drift algorithm. We explain how the posterior probabilities produced during the MAP optimization of CHIMERA can be used for clustering the patients into groups and identifying disease subtypes. CHIMERA was first validated on a synthetic dataset and then on a clinical dataset mixing 317 control subjects and patients suffering from Alzheimer's Disease (AD) and Parkison's Disease (PD). CHIMERA produced better clustering results compared to two standard clustering approaches. We further analyzed 390 T1 MRI scans from Alzheimer's patients. We discovered two main and reproducible AD subtypes displaying significant differences in cognitive performance.
"American Chimera: The Ever-Present Domination of Whiteness, Patriarchy, and Capitalism…A Parable"
Montoya, Roberto; Matias, Cheryl E.; Nishi, Naomi W. M.; Sarcedo, Geneva L.
2016-01-01
In Greek mythology, the Chimera is a fire-breathing monster with three heads: one of a lion, one of a horned goat, and one of a powerful dragon. Of similar construction is the presence of three structures in US society, whiteness, patriarchy, and capitalism, which are overwhelmingly represented, valued, and espoused when examining areas of…
Incoherent chimera and glassy states in coupled oscillators with frustrated interactions
Choe, Chol-Ung; Ri, Ji-Song; Kim, Ryong-Son
2016-09-01
We suggest a site disorder model that describes the population of identical oscillators with quenched random interactions for both the coupling strength and coupling phase. We obtain the reduced equations for the suborder parameters, on the basis of Ott-Antonsen ansatz theory, and present a complete bifurcation analysis of the reduced system. New effects include the appearance of the incoherent chimera and glassy state, both of which are caused by heterogeneity of the coupling phases. In the incoherent chimera state, the system displays an exotic symmetry-breaking behavior in spite of the apparent structural symmetry where the oscillators for both of the two subpopulations are in a frustrated state, while the phase distribution for each subpopulation approaches a steady state that differs from each other. When the incoherent chimera undergoes Hopf bifurcation, the system displays a breathing incoherent chimera. The glassy state that occurs on a surface of three-dimensional parameter space exhibits a continuum of metastable states with zero value of the global order parameter. Explicit formulas are derived for the system's Hopf, saddle-node, and transcritical bifurcation curves, as well as the codimension-2 crossing points, including the Takens-Bogdanov point.
Producing The New Regressive Left
DEFF Research Database (Denmark)
Crone, Christine
to be a committed artist, and how that translates into supporting al-Assad’s rule in Syria; the Ramadan programme Harrir Aqlak’s attempt to relaunch an intellectual renaissance and to promote religious pluralism; and finally, al-Mayadeen’s cooperation with the pan-Latin American TV station TeleSur and its ambitions...... becomes clear from the analytical chapters is the emergence of the new cross-ideological alliance of The New Regressive Left. This emerging coalition between Shia Muslims, religious minorities, parts of the Arab Left, secular cultural producers, and the remnants of the political,strategic resistance...... coalition (Iran, Hizbollah, Syria), capitalises on a series of factors that bring them together in spite of their otherwise diverse worldviews and agendas. The New Regressive Left is united by resistance against the growing influence of Saudi Arabia in the religious, cultural, political, economic...
Energy Technology Data Exchange (ETDEWEB)
Gerber, Samuel [Univ. of Utah, Salt Lake City, UT (United States); Rubel, Oliver [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Univ. of Utah, Salt Lake City, UT (United States); Whitaker, Ross T. [Univ. of Utah, Salt Lake City, UT (United States)
2012-01-19
This paper introduces a novel partition-based regression approach that incorporates topological information. Partition-based regression typically introduces a quality-of-fit-driven decomposition of the domain. The emphasis in this work is on a topologically meaningful segmentation. Thus, the proposed regression approach is based on a segmentation induced by a discrete approximation of the Morse–Smale complex. This yields a segmentation with partitions corresponding to regions of the function with a single minimum and maximum that are often well approximated by a linear model. This approach yields regression models that are amenable to interpretation and have good predictive capacity. Typically, regression estimates are quantified by their geometrical accuracy. For the proposed regression, an important aspect is the quality of the segmentation itself. Thus, this article introduces a new criterion that measures the topological accuracy of the estimate. The topological accuracy provides a complementary measure to the classical geometrical error measures and is very sensitive to overfitting. The Morse–Smale regression is compared to state-of-the-art approaches in terms of geometry and topology and yields comparable or improved fits in many cases. Finally, a detailed study on climate-simulation data demonstrates the application of the Morse–Smale regression. Supplementary Materials are available online and contain an implementation of the proposed approach in the R package msr, an analysis and simulations on the stability of the Morse–Smale complex approximation, and additional tables for the climate-simulation study.
DEFF Research Database (Denmark)
Bordacconi, Mats Joe; Larsen, Martin Vinæs
2014-01-01
Humans are fundamentally primed for making causal attributions based on correlations. This implies that researchers must be careful to present their results in a manner that inhibits unwarranted causal attribution. In this paper, we present the results of an experiment that suggests regression...... models – one of the primary vehicles for analyzing statistical results in political science – encourage causal interpretation. Specifically, we demonstrate that presenting observational results in a regression model, rather than as a simple comparison of means, makes causal interpretation of the results...... of equivalent results presented as either regression models or as a test of two sample means. Our experiment shows that the subjects who were presented with results as estimates from a regression model were more inclined to interpret these results causally. Our experiment implies that scholars using regression...
Embryonic stem cells contribute to mouse chimeras in the absence of detectable cell fusion.
Kidder, Benjamin L; Oseth, Leann; Miller, Shanna; Hirsch, Betsy; Verfaillie, Catherine; Coucouvanis, Electra
2008-06-01
Embryonic stem (ES) cells are capable of differentiating into all embryonic and adult cell types following mouse chimera production. Although injection of diploid ES cells into tetraploid blastocysts suggests that tetraploid cells have a selective disadvantage in the developing embryo, tetraploid hybrid cells, formed by cell fusion between ES cells and somatic cells, have been reported to contribute to mouse chimeras. In addition, other examples of apparent stem cell plasticity have recently been shown to be the result of cell fusion. Here we investigate whether ES cells contribute to mouse chimeras through a cell fusion mechanism. Fluorescence in situ hybridization (FISH) analysis for X and Y chromosomes was performed on dissociated tissues from embryonic, neonatal, and adult wild-type, and chimeric mice to follow the ploidy distributions of cells from various tissues. FISH analysis showed that the ploidy distributions in dissociated tissues, notably the tetraploid cell number, did not differ between chimeric and wild-type tissues. To address the possibility that early cell fusion events are hidden by subsequent reductive divisions or other changes in cell ploidy, we injected Z/EG (lacZ/EGFP) ES cells into ACTB-cre blastocysts. Recombination can only occur as the result of cell fusion, and the recombined allele should persist through any subsequent changes in cell ploidy. We did not detect evidence of fusion in embryonic chimeras either by direct fluorescence microscopy for GFP or by PCR amplification of the recombined Z/EG locus on genomic DNA from ACTB-cre::Z/EG chimeric embryos. Our results argue strongly against cell fusion as a mechanism by which ES cells contribute to chimeras.
Directory of Open Access Journals (Sweden)
Matthias Schmid
Full Text Available Regression analysis with a bounded outcome is a common problem in applied statistics. Typical examples include regression models for percentage outcomes and the analysis of ratings that are measured on a bounded scale. In this paper, we consider beta regression, which is a generalization of logit models to situations where the response is continuous on the interval (0,1. Consequently, beta regression is a convenient tool for analyzing percentage responses. The classical approach to fit a beta regression model is to use maximum likelihood estimation with subsequent AIC-based variable selection. As an alternative to this established - yet unstable - approach, we propose a new estimation technique called boosted beta regression. With boosted beta regression estimation and variable selection can be carried out simultaneously in a highly efficient way. Additionally, both the mean and the variance of a percentage response can be modeled using flexible nonlinear covariate effects. As a consequence, the new method accounts for common problems such as overdispersion and non-binomial variance structures.
Hosmer, David W; Sturdivant, Rodney X
2013-01-01
A new edition of the definitive guide to logistic regression modeling for health science and other applications This thoroughly expanded Third Edition provides an easily accessible introduction to the logistic regression (LR) model and highlights the power of this model by examining the relationship between a dichotomous outcome and a set of covariables. Applied Logistic Regression, Third Edition emphasizes applications in the health sciences and handpicks topics that best suit the use of modern statistical software. The book provides readers with state-of-
Weisberg, Sanford
2013-01-01
Praise for the Third Edition ""...this is an excellent book which could easily be used as a course text...""-International Statistical Institute The Fourth Edition of Applied Linear Regression provides a thorough update of the basic theory and methodology of linear regression modeling. Demonstrating the practical applications of linear regression analysis techniques, the Fourth Edition uses interesting, real-world exercises and examples. Stressing central concepts such as model building, understanding parameters, assessing fit and reliability, and drawing conclusions, the new edition illus
Transductive Ordinal Regression
Seah, Chun-Wei; Ong, Yew-Soon
2011-01-01
Ordinal regression is commonly formulated as a multi-class problem with ordinal constraints. The challenge of designing accurate classifiers for ordinal regression generally increases with the number of classes involved, due to the large number of labeled patterns that are needed. The availability of ordinal class labels, however, are often costly to calibrate or difficult to obtain. Unlabeled patterns, on the other hand, often exist in much greater abundance and are freely available. To take benefits from the abundance of unlabeled patterns, we present a novel transductive learning paradigm for ordinal regression in this paper, namely Transductive Ordinal Regression (TOR). The key challenge of the present study lies in the precise estimation of both the ordinal class label of the unlabeled data and the decision functions of the ordinal classes, simultaneously. The core elements of the proposed TOR include an objective function that caters to several commonly used loss functions casted in transductive setting...
Nonparametric Predictive Regression
Ioannis Kasparis; Elena Andreou; Phillips, Peter C.B.
2012-01-01
A unifying framework for inference is developed in predictive regressions where the predictor has unknown integration properties and may be stationary or nonstationary. Two easily implemented nonparametric F-tests are proposed. The test statistics are related to those of Kasparis and Phillips (2012) and are obtained by kernel regression. The limit distribution of these predictive tests holds for a wide range of predictors including stationary as well as non-stationary fractional and near unit...
Energy Technology Data Exchange (ETDEWEB)
Beschorner, W.E.; Tutschka, P.J.; Santos, G.W.
1982-04-01
The clinical features, pathology, and immunopathology of chronic graft-versus-host disease (GVHD) developing in the long-term rat radiation chimera are described. At 6 to 12 months post-transplant, the previously stable ACI/LEW chimeras developed patchy to diffuse severe hair loss and thickened skin folds, and had microscopic features resembling scleroderma, Sjogren's syndrome, and chronic hepatitis. Skin histology showed dermal inflammation and acanthosis with atrophy of the appendages, with progression to dermal sclerosis. The liver revealed chronic hepatitis with bile duct injury and proliferation and periportal piecemeal necrosis. The tongue had considerable submucosal inflammation, muscular necrosis, and atrophy and arteritis. The serous salivary glands, lacrimal glands, and bronchi had lymphocytic inflammation and injury to duct, acinar, and mucosal columnar epithelium. The thymus had lymphocyte depletion of the medulla with prominent epithelium. The spleen and lymph nodes had poorly developed germinal centers but increased numbers of plasma cells. IgM was observed along the basement membrane and around the basal cells of the skin and tongue and along the basement membrane of the bile ducts. IgM was present also in the arteries of the tongue. Immunoglobulins eluted from the skin, cross-reacted with the bile duct epithelium and usually with both ACI and Lewis skin. Increased titers of speckled antinuclear antibodies were present in the serum of rats with chronic (GVHD). Chronic GVHD in the long-term rat radiation chimera is very similar to human chronic GVHD and is a potentially excellent model for autoimmune disorders including scleroderma, Sjorgren's syndrome, and chronic hepatitis.
[Understanding logistic regression].
El Sanharawi, M; Naudet, F
2013-10-01
Logistic regression is one of the most common multivariate analysis models utilized in epidemiology. It allows the measurement of the association between the occurrence of an event (qualitative dependent variable) and factors susceptible to influence it (explicative variables). The choice of explicative variables that should be included in the logistic regression model is based on prior knowledge of the disease physiopathology and the statistical association between the variable and the event, as measured by the odds ratio. The main steps for the procedure, the conditions of application, and the essential tools for its interpretation are discussed concisely. We also discuss the importance of the choice of variables that must be included and retained in the regression model in order to avoid the omission of important confounding factors. Finally, by way of illustration, we provide an example from the literature, which should help the reader test his or her knowledge.
Constrained Sparse Galerkin Regression
Loiseau, Jean-Christophe
2016-01-01
In this work, we demonstrate the use of sparse regression techniques from machine learning to identify nonlinear low-order models of a fluid system purely from measurement data. In particular, we extend the sparse identification of nonlinear dynamics (SINDy) algorithm to enforce physical constraints in the regression, leading to energy conservation. The resulting models are closely related to Galerkin projection models, but the present method does not require the use of a full-order or high-fidelity Navier-Stokes solver to project onto basis modes. Instead, the most parsimonious nonlinear model is determined that is consistent with observed measurement data and satisfies necessary constraints. The constrained Galerkin regression algorithm is implemented on the fluid flow past a circular cylinder, demonstrating the ability to accurately construct models from data.
Energy Technology Data Exchange (ETDEWEB)
Tutschka, P.J.; Ki, P.F.; Beschorner, W.E.; Hess, A.D.; Santos, G.W.
1981-10-01
Histoincompatible bone marrow allografts were established in lethally irradiated rats. At various times after transplantation, the spleen cells were harvested, subjected to mixed lymphocyte cultures, and assayed for suppressor cells in vitro and in vivo by adoptive transfer studies. Alloantigen-nonspecific suppressor cells appeared in the chimera at 40 days after grafting, coinciding with the resolution of graft-versus-host disease (GVHD). At 250 days the nonspecific suppressor cells were replaced by suppressor cells specifically suppressing donor-versus-host alloantigen responses. At 720 days suppressor cells could no longer be identified by in vitro methods but were identified by in vivo adoptive transfer of transplantation tolerance. After injection of host-type antigen into chimeras, the suppressor cells could be again demonstrated by in vitro methods.
Energy Technology Data Exchange (ETDEWEB)
Tutschka, P.J.; Ki, P.F.; Beschorner, W.E.; Hess, A.D.; Santos, G.W.
1981-10-01
Histoincompatible bone marrow allografts were established in lethally irradiated rats. At various times after transplantation, the spleen cells were harvested, subjected to mixed lymphocyte cultures, and assayed for suppressor cells in vitro and in vivo by adoptive transfer studies. Alloantigen-nonspecific suppressor cells appeared in the chimera at 40 days after grafting, coinciding with the resolution of graft-versus-host disease (GVHD). At 250 days the nonspecific suppressor cells were replaced by suppressor cells specifically suppressing donor-versus-host alloantigen responses. At 720 days suppressor cells could no longer be identified by in vitro methods but were identified by in vivo adoptive transfer of transplantation tolerance. After injection of host-type antigen into chimeras, the suppressor cells could be again demonstrated by in vitro methods.
Chimera patterns induced by distance-dependent power-law coupling in ecological networks
Banerjee, Tanmoy; Dutta, Partha Sharathi; Zakharova, Anna; Schöll, Eckehard
2016-09-01
This paper reports the occurrence of several chimera patterns and the associated transitions among them in a network of coupled oscillators, which are connected by a long-range interaction that obeys a distance-dependent power law. This type of interaction is common in physics and biology and constitutes a general form of coupling scheme, where by tuning the power-law exponent of the long-range interaction the coupling topology can be varied from local via nonlocal to global coupling. To explore the effect of the power-law coupling on collective dynamics, we consider a network consisting of a realistic ecological model of oscillating populations, namely the Rosenzweig-MacArthur model, and show that the variation of the power-law exponent mediates transitions between spatial synchrony and various chimera patterns. We map the possible spatiotemporal states and their scenarios that arise due to the interplay between the coupling strength and the power-law exponent.
Practical Session: Logistic Regression
Clausel, M.; Grégoire, G.
2014-12-01
An exercise is proposed to illustrate the logistic regression. One investigates the different risk factors in the apparition of coronary heart disease. It has been proposed in Chapter 5 of the book of D.G. Kleinbaum and M. Klein, "Logistic Regression", Statistics for Biology and Health, Springer Science Business Media, LLC (2010) and also by D. Chessel and A.B. Dufour in Lyon 1 (see Sect. 6 of http://pbil.univ-lyon1.fr/R/pdf/tdr341.pdf). This example is based on data given in the file evans.txt coming from http://www.sph.emory.edu/dkleinb/logreg3.htm#data.
DEFF Research Database (Denmark)
Bache, Stefan Holst
A new and alternative quantile regression estimator is developed and it is shown that the estimator is root n-consistent and asymptotically normal. The estimator is based on a minimax ‘deviance function’ and has asymptotically equivalent properties to the usual quantile regression estimator. It is......, however, a different and therefore new estimator. It allows for both linear- and nonlinear model specifications. A simple algorithm for computing the estimates is proposed. It seems to work quite well in practice but whether it has theoretical justification is still an open question....
Impact of hyperbolicity on chimera states in ensembles of nonlocally coupled chaotic oscillators
Energy Technology Data Exchange (ETDEWEB)
Semenova, N.; Anishchenko, V. [Department of Physics, Saratov State University, Astrakhanskaya Str. 83, 410012 Saratov (Russian Federation); Zakharova, A.; Schöll, E. [Institut für Theoretische Physik, TU Berlin, Hardenbergstraße 36, 10623 Berlin (Germany)
2016-06-08
In this work we analyse nonlocally coupled networks of identical chaotic oscillators. We study both time-discrete and time-continuous systems (Henon map, Lozi map, Lorenz system). We hypothesize that chimera states, in which spatial domains of coherent (synchronous) and incoherent (desynchronized) dynamics coexist, can be obtained only in networks of chaotic non-hyperbolic systems and cannot be found in networks of hyperbolic systems. This hypothesis is supported by numerical simulations for hyperbolic and non-hyperbolic cases.
Mass and charge identification of fragments detected with the Chimera Silicon-CsI(Tl) telescopes
Energy Technology Data Exchange (ETDEWEB)
Le Neindre, N.; Alderighi, M.; Anzalone, A.; Barna, R.; Bartolucci, M.; Berceanu, I.; Borderie, B.; Bougault, R.; Bruno, M.; Cardella, G.; Cavallaro, S.; D' Agostino, M. E-mail: dagostino@bo.infn.it; Dayras, R.; De Filippo, E.; De Pasquale, D.; Geraci, E.; Giustolisi, F.; Grzeszczuk, A.; Guazzoni, P.; Guinet, D.; Iacono-Manno, M.; Italiano, A.; Kowalski, S.; Lanchais, A.; Lanzano, G.; Lanzalone, G.; Li, S.; Lo Nigro, S.; Maiolino, C.; Manfredi, G.; Moisa, D.; Pagano, A.; Papa, M.; Paduszynski, T.; Petrovici, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Pop, A.; Porto, F.; Rivet, M.F.; Rosato, E.; Russo, S.; Sambataro, S.; Sechi, G.; Simion, V.; Sperduto, M.L.; Steckmeyer, J.C.; Sutera, C.; Trifiro, A.; Tassan-Got, L.; Trimarchi, M.; Vannini, G.; Vigilante, M.; Wilczynski, J.; Wu, H.; Xiao, Z.; Zetta, L.; Zipper, W
2002-09-01
Mass and charge identification of charged products detected with Silicon-CsI(Tl) telescopes of the Chimera apparatus are presented. An identification function, based on the Bethe-Bloch formula, is used to fit empirical correlations between {delta}E and E ADC readings, in order to determine, event by event, the atomic and mass numbers of the detected charged reaction products prior to energy calibration.
Functional prokaryotic-eukaryotic chimera from the pentameric ligand-gated ion channel family.
Duret, Guillaume; Van Renterghem, Catherine; Weng, Yun; Prevost, Marie; Moraga-Cid, Gustavo; Huon, Christèle; Sonner, James M; Corringer, Pierre-Jean
2011-07-19
Pentameric ligand-gated ion channels (pLGICs), which mediate chemo-electric signal transduction in animals, have been recently found in bacteria. Despite clear sequence and 3D structure homology, the phylogenetic distance between prokaryotic and eukaryotic homologs suggests significant structural divergences, especially at the interface between the extracellular (ECD) and the transmembrane (TMD) domains. To challenge this possibility, we constructed a chimera in which the ECD of the bacterial protein GLIC is fused to the TMD of the human α1 glycine receptor (α1GlyR). Electrophysiology in Xenopus oocytes shows that it functions as a proton-gated ion channel, thereby locating the proton activation site(s) of GLIC in its ECD. Patch-clamp experiments in BHK cells show that the ion channel displays an anionic selectivity with a unitary conductance identical to that of the α1GlyR. In addition, pharmacological investigations result in transmembrane allosteric modulation similar to the one observed on α1GlyR. Indeed, the clinically active drugs propofol, four volatile general anesthetics, alcohols, and ivermectin all potentiate the chimera while they inhibit GLIC. Collectively, this work shows the compatibility between GLIC and α1GlyR domains and points to conservation of the ion channel and transmembrane allosteric regulatory sites in the chimera. This provides evidence that GLIC and α1GlyR share a highly homologous 3D structure. GLIC is thus a relevant model of eukaryotic pLGICs, at least from the anionic type. In addition, the chimera is a good candidate for mass production in Escherichia coli, opening the way for investigations of "druggable" eukaryotic allosteric sites by X-ray crystallography.
Neddersen, Mara; Elleuche, Skander
2015-12-01
Degradation of complex plant biomass demands a fine-regulated portfolio of glycoside hydrolases. The LE (LguI/Eco81I)-cloning approach was used to produce two enzyme chimeras CB and BC composed of an endoglucanase Cel5A (C) from the extreme thermophilic bacterium Fervidobacterium gondwanense and an archaeal β-glucosidase Bgl1 (B) derived from a hydrothermal spring metagenome. Recombinant chimeras and parental enzymes were produced in Escherichia coli and purified using a two-step affinity chromatography approach. Enzymatic properties revealed that both chimeras closely resemble the parental enzymes and physical mixtures, but Cel5A displayed lower temperature tolerance at 100°C when fused to Bgl1 independent of the conformational order. Moreover, the determination of enzymatic performances resulted in the detection of additive effects in case of BC fusion chimera. Kinetic measurements in combination with HPLC-mediated product analyses and site-directed mutation constructs indicated that Cel5A was strongly impaired when fused at the N-terminus, while activity was reduced to a slighter extend as C-terminal fusion partner. In contrast to these results, catalytic activity of Bgl1 at the N-terminus was improved 1.2-fold, effectively counteracting the slightly reduced activity of Cel5A by converting cellobiose into glucose. In addition, cellobiose exhibited inhibitory effects on Cel5A, resulting in a higher yield of cellobiose and glucose by application of an enzyme mixture (53.1%) compared to cellobiose produced from endoglucanase alone (10.9%). However, the overall release of cellobiose and glucose was even increased by catalytic action of BC (59.2%). These results indicate possible advantages of easily produced bifunctional fusion enzymes for the improved conversion of complex polysaccharide plant materials.
Cabrera Trujillo, Laura Yenisa; Engel-Glatter, Sabrina
2015-06-01
Research with human-animal chimera raises a number of ethical concerns, especially when neural stem cells are transplanted into the brains of non-human primates (NHPs). Besides animal welfare concerns and ethical issues associated with the use of embryonic stem cells, the research is also regarded as controversial from the standpoint of NHPs developing cognitive or behavioural capabilities that are regarded as "unique" to humans. However, scientists are urging to test new therapeutic approaches for neurological diseases in primate models as they better mimic human physiology than all current animal models. As a response, various countries have issued reports on the topic. Our paper summarizes the ethical issues raised by research with human-animal brain chimeras and compares the relevant regulatory instruments and different recommendations issued in national reports from three important European research nations: Germany, Switzerland and the United Kingdom. We assess and discuss the focus and priorities set by the different reports, review various reasons for and perspectives on the importance of the brain in chimera research, and identify critical points in the reports that warrant further specification and debate.
Paul, Sibasish; Caruthers, Marvin H
2016-12-07
Phosphorodiamidate morpholinos (PMOs) and PMO-DNA chimeras have been prepared on DNA synthesizers using phosphoramidite chemistry. This was possible by first generating boranephosphoroamidate morpholino internucleotide linkages followed by oxidative substitution with four different amines: N,N-dimethylamine, N-methylamine, ammonia, and morpholine. When compared to a natural DNA duplex, the amino modified PMO was found to have a higher melting temperature with either complementary DNA or RNA, whereas the remaining PMO analogues having morpholino, dimethylamino, or N-methylamino phosphorodiamidate linkages had melting temperatures that were either comparable or reduced. Additionally the N,N-dimethylamino PMO-DNA chimeras were found to stimulate RNaseH1 activity. Treatment of HeLa cells with fluorescently labeled PMO chimeras demonstrated that these analogues were efficiently taken up by cells in the presence of a lipid transfection reagent. Because of the simplistic synthesis procedures, various PMO analogues are now readily available and should therefore open new pathways for research into the antisense, diagnostic, and nanotechnology oligonucleotide fields.
Flexible and rapid construction of viral chimeras applied to hepatitis C virus.
McClure, C Patrick; Urbanowicz, Richard A; King, Barnabas J; Cano-Crespo, Sara; Tarr, Alexander W; Ball, Jonathan K
2016-09-01
A novel and broadly applicable strategy combining site-directed mutagenesis and DNA assembly for constructing seamless viral chimeras is described using hepatitis C virus (HCV) as an exemplar. Full-length HCV genomic cloning cassettes, which contained flexibly situated restriction endonuclease sites, were prepared via a single, site-directed mutagenesis reaction and digested to receive PCR-amplified virus envelope genes by In-Fusion cloning. Using this method, we were able to construct gene-shuttle cassettes for generation of cell culture-infectious JFH-1-based chimeras containing genotype 1-3 E1E2 genes. Importantly, using this method we also show that E1E2 clones that were not able to support cell entry in the HCV pseudoparticle assay did confer entry when shuttled into the chimeric cell culture chimera system. This method can be easily applied to other genes of study and other viruses and, as such, will greatly simplify reverse genetics studies of variable viruses.
Ritz, Christian; Parmigiani, Giovanni
2009-01-01
R is a rapidly evolving lingua franca of graphical display and statistical analysis of experiments from the applied sciences. This book provides a coherent treatment of nonlinear regression with R by means of examples from a diversity of applied sciences such as biology, chemistry, engineering, medicine and toxicology.
Multiple linear regression analysis
Edwards, T. R.
1980-01-01
Program rapidly selects best-suited set of coefficients. User supplies only vectors of independent and dependent data and specifies confidence level required. Program uses stepwise statistical procedure for relating minimal set of variables to set of observations; final regression contains only most statistically significant coefficients. Program is written in FORTRAN IV for batch execution and has been implemented on NOVA 1200.
Adaptive metric kernel regression
DEFF Research Database (Denmark)
Goutte, Cyril; Larsen, Jan
2000-01-01
regression by minimising a cross-validation estimate of the generalisation error. This allows to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms...
Software Regression Verification
2013-12-11
of recursive procedures. Acta Informatica , 45(6):403 – 439, 2008. [GS11] Benny Godlin and Ofer Strichman. Regression verifica- tion. Technical Report...functions. Therefore, we need to rede - fine m-term. – Mutual termination. If either function f or function f ′ (or both) is non- deterministic, then their
Seber, George A F
2012-01-01
Concise, mathematically clear, and comprehensive treatment of the subject.* Expanded coverage of diagnostics and methods of model fitting.* Requires no specialized knowledge beyond a good grasp of matrix algebra and some acquaintance with straight-line regression and simple analysis of variance models.* More than 200 problems throughout the book plus outline solutions for the exercises.* This revision has been extensively class-tested.
Low rank Multivariate regression
Giraud, Christophe
2010-01-01
We consider in this paper the multivariate regression problem, when the target regression matrix $A$ is close to a low rank matrix. Our primary interest in on the practical case where the variance of the noise is unknown. Our main contribution is to propose in this setting a criterion to select among a family of low rank estimators and prove a non-asymptotic oracle inequality for the resulting estimator. We also investigate the easier case where the variance of the noise is known and outline that the penalties appearing in our criterions are minimal (in some sense). These penalties involve the expected value of the Ky-Fan quasi-norm of some random matrices. These quantities can be evaluated easily in practice and upper-bounds can be derived from recent results in random matrix theory.
Subset selection in regression
Miller, Alan
2002-01-01
Originally published in 1990, the first edition of Subset Selection in Regression filled a significant gap in the literature, and its critical and popular success has continued for more than a decade. Thoroughly revised to reflect progress in theory, methods, and computing power, the second edition promises to continue that tradition. The author has thoroughly updated each chapter, incorporated new material on recent developments, and included more examples and references. New in the Second Edition:A separate chapter on Bayesian methodsComplete revision of the chapter on estimationA major example from the field of near infrared spectroscopyMore emphasis on cross-validationGreater focus on bootstrappingStochastic algorithms for finding good subsets from large numbers of predictors when an exhaustive search is not feasible Software available on the Internet for implementing many of the algorithms presentedMore examplesSubset Selection in Regression, Second Edition remains dedicated to the techniques for fitting...
Classification and regression trees
Breiman, Leo; Olshen, Richard A; Stone, Charles J
1984-01-01
The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.
DEFF Research Database (Denmark)
Hansen, Henrik; Tarp, Finn
2001-01-01
. There are, however, decreasing returns to aid, and the estimated effectiveness of aid is highly sensitive to the choice of estimator and the set of control variables. When investment and human capital are controlled for, no positive effect of aid is found. Yet, aid continues to impact on growth via...... investment. We conclude by stressing the need for more theoretical work before this kind of cross-country regressions are used for policy purposes....
Robust Nonstationary Regression
1993-01-01
This paper provides a robust statistical approach to nonstationary time series regression and inference. Fully modified extensions of traditional robust statistical procedures are developed which allow for endogeneities in the nonstationary regressors and serial dependence in the shocks that drive the regressors and the errors that appear in the equation being estimated. The suggested estimators involve semiparametric corrections to accommodate these possibilities and they belong to the same ...
TWO REGRESSION CREDIBILITY MODELS
Directory of Open Access Journals (Sweden)
Constanţa-Nicoleta BODEA
2010-03-01
Full Text Available In this communication we will discuss two regression credibility models from Non – Life Insurance Mathematics that can be solved by means of matrix theory. In the first regression credibility model, starting from a well-known representation formula of the inverse for a special class of matrices a risk premium will be calculated for a contract with risk parameter θ. In the next regression credibility model, we will obtain a credibility solution in the form of a linear combination of the individual estimate (based on the data of a particular state and the collective estimate (based on aggregate USA data. To illustrate the solution with the properties mentioned above, we shall need the well-known representation theorem for a special class of matrices, the properties of the trace for a square matrix, the scalar product of two vectors, the norm with respect to a positive definite matrix given in advance and the complicated mathematical properties of conditional expectations and of conditional covariances.
Directory of Open Access Journals (Sweden)
Willson Richard C
2010-12-01
Full Text Available Abstract Background Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use
Sipo, I; Wang, X; Hurtado Picó, A; Suckau, L; Weger, S; Poller, W; Fechner, H
2006-01-01
Pharmacological control is a desirable safety feature of oncolytic adenoviruses (oAdV). It has recently been shown that oAdV replication may be controlled by drug-dependent transcriptional regulation of E1A expression. Here, we present a novel concept that relies on tamoxifen-dependent regulation of E1A activity through functional linkage to the mutated hormone-binding domain of the murine estrogen receptor (Mer). Four different E1A-Mer chimeras (ME, EM, E(DeltaNLS)M, MEM) were constructed and inserted into the adenoviral genome under control of a lung-specific surfactant protein B promoter. The highest degree of regulation in vitro was seen for the corresponding oAdVs Ad.E(DeltaNLS)M and Ad.MEM, which exhibited an up to 100-fold higher oAdV replication in the presence as compared with the absence of 4-OH-tamoxifen. Moreover, destruction of nontarget cells was six- and 13-fold reduced for Ad.E(DeltaNLS)M and Ad.MEM, respectively, as compared with Ad.E. Further investigations supported tamoxifen-dependent regulation of Ad.E(DeltaNLS)M and Ad.MEM in vivo. Induction of Ad.E(DeltaNLS)M inhibited growth of H441 lung tumors as efficient as a control oAdV expressing E1A. E(DeltaNLS)M and the MEM chimeras can be easily inserted into a single vector genome, which extends their application to existing oAdVs and strongly facilitates in vivo application.
Tinker, Juliette K; Davis, Chadwick T; Arlian, Britni M
2010-11-01
Yersinia pestis is a virulent human pathogen and potential biological weapon. Despite a long history of research on this organism, there is no licensed vaccine to protect against pneumonic forms of Y. pestis disease. In the present study, plasmids were constructed to express cholera toxin A(2)/B chimeric molecules containing the LcrV protective antigen from Yersinia enterocolitica and Y. pestis. These chimeras were expressed and purified to high yields from the supernatant of transformed Escherichia coli. Western and GM(1) ELISA assays were used to characterize the composition, receptor-binding and relative stability of the LcrV-CTA(2)/B chimera in comparison to cholera toxin. In addition, we investigated the ability of the Y. pestis LcrV-CTA(2)/B chimera to bind to and internalize into cultured epithelial cells and macrophages by confocal microscopy. These studies indicate that the uptake and trafficking of the LcrV antigen from the chimera is comparable to the trafficking of native toxin. Together these findings report that stable, receptor-binding, non-toxic LcrV-cholera toxin A(2)/B chimeras can be expressed at high levels in E. coli and purified from the supernatant. In addition, the internalization of antigen in vitro reported here supports the development of these molecules as novel mucosal vaccine candidates. Copyright 2010 Elsevier Inc. All rights reserved.
DEFF Research Database (Denmark)
Ussing, Anne Phaff; Prause, J.U.; Sørensen, Inger
1992-01-01
Autoimmune disease, primary Sjögren's syndrome, transplantation chimeras, experimental model, exocrinopathy, inbred mouse strains......Autoimmune disease, primary Sjögren's syndrome, transplantation chimeras, experimental model, exocrinopathy, inbred mouse strains...
Institute of Scientific and Technical Information of China (English)
XING FeiYue; LIU Jing; YU Zhe; JI YuHua
2008-01-01
A soluble Jagged 1/Fc chimera protein (Jagged 1/Fc) was directly used to induce differentiation and maturation of bone marrow-derived dendritic cells (DCs) in mice in vitro. A model of inducing and am-plifying DCs in vitro was established. The effect of Jagged 1/Fc on morphology of DCs induced by both rmGM-CSF and rmlL-4 was observed under a confocal microscope. A fluorescein-labeled monoclonal antibody staining combined with flow cytometry was applied to detect the effect of Jagged 1/Fc on the expression of CD11c, MHC-Ⅱ, CD86, CD80 and CD40 molecules on the surface of DCs. The results showed that Jagged 1/Fc did not affect the morphological properties of DC differentiation induced by both rmGM-CSF and rmlL-4. But it could promote the differentiation and maturation of DCs induced by both. The effect of it was strikingly different in the expression profile of co-stimulating molecules and the morphologic properties of DCs from lipopolysaccharide (LPS). The levels of MHC-Ⅱ and CD40 molecule expression on the surface of DCs stimulated by Jagged 1/Fc were significantly lower than those stimulated by LPS, and the level of CD80 expression on the surface of DCs induced by Jagged 1/Fc was near to that induced by LPS. Jagged 1/Fc had no influence on the expression of CD86 mole-cule on the surface of DCs. Jagged 1/Fc when used alone could not maintain the growth, differentiation and maturation of DCs. All the findings indicate that Jagged 1/Fc influences the differentiation and maturation of DCs, which is not markedly similar to LPS, providing important evidence for its devel-opment and application as a novel immunosuppressant.
Institute of Scientific and Technical Information of China (English)
Hong-Li YAN; Wei-Ting WANG; Yan HE; Zhuan-You ZHAO; Yuan-Jian GAO; Yi ZHANG; Shu-Han SUN
2004-01-01
To produce a thrombi-targeting plasminogen activator,low molecular weight single-chain urokinase gene(scuPA32k)was spliced with the full-length cDNA of annexin B 1 gene(anxB1)by overlap extension method.The fused gene anxBlscuPA was ligated into pET28a vector,transformed into E.coli BL21-RIL,and then induced to express under the control of T7 promoter.The AnxB 1ScuPA protein expressed amounted to 22% of the total bacterial proteins.The product was refolded,and then purified by using DEAE Sepharose fast flow ion-exchange column and Superdex S-200 gel-filtration column.HPLC analysis revealed that the final purity is about 95%.The specific activity ofAnxB 1ScuPA,measured as amidolytic activity,reached 100,000 IU/mg.It had a similar S2444 catalytic efficiency(kcat/Km)to ScuPA32k,and also showed high activated-platelet membrane-binding activity and anticoagulant activity,indicating that the chimera fully retained the components of enzymatic and membrane-binding activities of the parent molecules.In vivo test revealed that,the dogs administered with AnxB 1ScuPA had less reperfusion time,higher reperfusion ratio,and less bleeding effects than those with urokinase.These findings indicated that AnxB 1ScuPAmight have advantages over current available thrombolytic agents.
Anti-bacterial immunity to Listeria monocytogenes in allogeneic bone marrow chimera in mice
Energy Technology Data Exchange (ETDEWEB)
Onoe, K.; Good, R.A.; Yamamoto, K.
1986-06-01
Protection and delayed-type hypersensitivity (DTH) to the facultative intracellular bacterium Listeria monocytogenes (L.m.) were studied in allogeneic and syngeneic bone marrow chimeras. Lethally irradiated AKR (H-2k) mice were successfully reconstituted with marrow cells from C57BL/10 (B10) (H-2b), B10 H-2-recombinant strains or syngeneic mice. Irradiated AKR mice reconstituted with marrow cells from H-2-compatible B10.BR mice, (BR----AKR), as well as syngeneic marrow cells, (AKR----AKR), showed a normal level of responsiveness to the challenge stimulation with the listeria antigens when DTH was evaluated by footpad reactions. These mice also showed vigorous activities in acquired resistance to the L.m. By contrast, chimeric mice that had total or partial histoincompatibility at the H-2 determinants between donor and recipient, (B10----AKR), (B10.AQR----AKR), (B10.A(4R)----AKR), or (B10.A(5R)----AKR), were almost completely unresponsive in DTH and antibacterial immunity. However, when (B10----AKR) H-2-incompatible chimeras had been immunized with killed L.m. before challenge with live L.m., these mice manifested considerable DTH and resistance to L.m. These observations suggest that compatibility at the entire MHC between donor and recipient is required for bone marrow chimeras to be able to manifest DTH and protection against L.m. after a short-term immunization schedule. However, this requirement is overcome by a preceding or more prolonged period of immunization with L.m. antigens. These antigens, together with marrow-derived antigen-presenting cells, can then stimulate and expand cell populations that are restricted to the MHC (H-2) products of the donor type.
Directory of Open Access Journals (Sweden)
Kostaman T
2014-03-01
Full Text Available Formation of germline chimeras by transfer of chicken primordial germ cells (PGCs is one of the effective techniques for preservation and regeneration of genetic resources in chickens. This study attempted to form germline chimeras of Gaok chicken buy purifying circulated PGCs of donor embryo before it is transferred to the recipient (White Leghorn chickens=WL and studied the ability of recipient embryo on survival in incubators, and hatchability. This study used 200 fertile eggs of Gaok and 90 fertile WL breed all of the eggs was incubated at 380C and 60% humidity in a portable incubator. PGCs-circulation of the blood collected Gaok embryos at stage 14-16 were taken from the dorsal aorta, and then purified by centrifugation method using nycodenz. PGCs-circulation results further purification frozen in liquid nitrogen before being transferred to the recipient embryo. The results showed that for the development of embryos transferred to the fresh circulation of PGCs-circulation as many as 25 cells can survive up to day 14, while one of the transferred of 50 and 100 cells into recipient embryos was hatched (10%. On the contrari recipient embryos that are transferred to the frozen PGCs-circulation the embryos development was shorter, and only survived until day 10th (treatment 25 cells, day 14th (treatment of 50 cells and day 17th (treatment of 100 cells. It is concluded that the amount of PGCs-circulation embryos transferred to the recipient is one factor that influence the success of the development germline chimeras.
Caro-Aguilar, Ivette; Rodríguez, Alexandra; Calvo-Calle, J. Mauricio; Guzmán, Fanny; De la Vega, Patricia; Elkin Patarroyo, Manuel; Galinski, Mary R.; Moreno, Alberto
2002-01-01
Clinical trials of malaria vaccines have confirmed that parasite-derived T-cell epitopes are required to elicit consistent and long-lasting immune responses. We report here the identification and functional characterization of six T-cell epitopes that are present in the merozoite surface protein-1 of Plasmodium vivax (PvMSP-1) and bind promiscuously to four different HLA-DRB1∗ alleles. Each of these peptides induced lymphoproliferative responses in cells from individuals with previous P. vivax infections. Furthermore, linear-peptide chimeras containing the promiscuous PvMSP-1 T-cell epitopes, synthesized in tandem with the Plasmodium falciparum immunodominant circumsporozoite protein (CSP) B-cell epitope, induced high specific antibody titers, cytokine production, long-lasting immune responses, and immunoglobulin G isotype class switching in BALB/c mice. A linear-peptide chimera containing an allele-restricted P. falciparum T-cell epitope with the CSP B-cell epitope was not effective. Two out of the six promiscuous T-cell epitopes exhibiting the highest anti-peptide response also contain B-cell epitopes. Antisera generated against these B-cell epitopes recognize P. vivax merozoites in immunofluorescence assays. Importantly, the anti-peptide antibodies generated to the CSP B-cell epitope inhibited the invasion of P. falciparum sporozoites into human hepatocytes. These data and the simplicity of design of the chimeric constructs highlight the potential of multimeric, multistage, and multispecies linear-peptide chimeras containing parasite promiscuous T-cell epitopes for malaria vaccine development. PMID:12065487
Resurrecting the chimera: Progressions in parenting and peer processes.
Forgatch, Marion S; Snyder, James J; Patterson, Gerald R; Pauldine, Michael R; Chaw, Yvonne; Elish, Katie; Harris, Jasmine B; Richardson, Eric B
2016-08-01
This report uses 6-year outcomes of the Oregon Divorce Study to examine the processes by which parenting practices affect deviant peer association during two developmental stages: early to middle childhood and late childhood to early adolescence. The participants were 238 newly divorced mothers and their 5- to 8-year-old sons who were randomly assigned to Parent Management Training-Oregon Model (PMTO®) or to a no-treatment control group. Parenting practices, child delinquent behavior, and deviant peer association were repeatedly assessed from baseline to 6 years after baseline using multiple methods and informants. PMTO had a beneficial effect on parenting practices relative to the control group. Two stage models linking changes in parenting generated by PMTO to children's growth in deviant peer association were supported. During the early to middle childhood stage, the relationship of improved parenting practices on deviant peer association was moderated by family socioeconomic status (SES); effective parenting was particularly important in mitigating deviant peer association for lower SES families whose children experience higher densities of deviant peers in schools and neighborhoods. During late childhood and early adolescence, the relationship of improved parenting to youths' growth in deviant peer association was mediated by reductions in the growth of delinquency during childhood; higher levels of early delinquency are likely to promote deviant peer association through processes of selective affiliation and reciprocal deviancy training. The results are discussed in terms of multilevel developmental progressions of diminished parenting, child involvement in deviancy producing processes in peer groups, and increased variety and severity of antisocial behavior, all exacerbated by ecological risks associated with low family SES.
Modified Regression Correlation Coefficient for Poisson Regression Model
Kaengthong, Nattacha; Domthong, Uthumporn
2017-09-01
This study gives attention to indicators in predictive power of the Generalized Linear Model (GLM) which are widely used; however, often having some restrictions. We are interested in regression correlation coefficient for a Poisson regression model. This is a measure of predictive power, and defined by the relationship between the dependent variable (Y) and the expected value of the dependent variable given the independent variables [E(Y|X)] for the Poisson regression model. The dependent variable is distributed as Poisson. The purpose of this research was modifying regression correlation coefficient for Poisson regression model. We also compare the proposed modified regression correlation coefficient with the traditional regression correlation coefficient in the case of two or more independent variables, and having multicollinearity in independent variables. The result shows that the proposed regression correlation coefficient is better than the traditional regression correlation coefficient based on Bias and the Root Mean Square Error (RMSE).
Directory of Open Access Journals (Sweden)
Karim Hardani*
2012-05-01
Full Text Available A 10-month-old baby presented with developmental delay. He had flaccid paralysis on physical examination.An MRI of the spine revealed malformation of the ninth and tenth thoracic vertebral bodies with complete agenesis of the rest of the spine down that level. The thoracic spinal cord ends at the level of the fifth thoracic vertebra with agenesis of the posterior arches of the eighth, ninth and tenth thoracic vertebral bodies. The roots of the cauda equina appear tightened down and backward and ended into a subdermal fibrous fatty tissue at the level of the ninth and tenth thoracic vertebral bodies (closed meningocele. These findings are consistent with caudal regression syndrome.
Energy Technology Data Exchange (ETDEWEB)
Hinrichs, D.J.; Wegmann, K.W.; Dietsch, G.N.
1987-12-01
The adoptive transfer of clinical and histopathologic signs of experimental allergic encephalomyelitis (EAE) requires MHC compatibility between cell donor and cell recipient. The results of adoptive transfer studies using F1 to parent bone marrow chimeras as recipients of parental-derived BP-sensitive spleen cells indicate that this restriction is not expressed at the level of the endothelial cell but is confined to the cells of bone marrow derivation. Furthermore, these results indicate that the development of EAE is not dependent on the activity of MHC-restricted cytotoxic cells.
Core Collapse Supernovae Using CHIMERA: Gravitational Radiation from Non-Rotating Progenitors
Energy Technology Data Exchange (ETDEWEB)
Yakunin, Konstantin [Florida Atlantic University; Marronetti, Pedro [Florida Atlantic University; Mezzacappa, Anthony [ORNL; Bruenn, S. W. [Florida Atlantic University; Lee, Ching-Tsai [University of Tennessee, Knoxville (UTK); Chertkow, Merek A [ORNL; Hix, William Raphael [ORNL; Blondin, J. M. [North Carolina State University; Lentz, Eric J [ORNL; Messer, Bronson [ORNL; Yoshida, S. [University of Tokyo, Tokyo, Japan
2011-01-01
The CHIMERA code is a multi-dimensional multi-physics engine dedicated primarily to the simulation of core collapse supernova explosions. One of the most important aspects of these explosions is their capacity to produce gravitational radiation that is detectable by earth-based laser-interferometric gravitational wave observatories such as LIGO and VIRGO. We present here preliminary gravitational signatures of two-dimensional models with non-rotating progenitors. These simulations exhibit explosions, which are followed for more than half a second after stellar core bounce.
Self-renewal of pulmonary alveolar macrophages: evidence from radiation chimera studies
Energy Technology Data Exchange (ETDEWEB)
Tarling, J.D.; Lin, H.S.; Hsu, S.
1987-11-01
Radiation-induced chimeric mice were used to study the origin of pulmonary alveolar macrophages. Unlike in other studies, these radiation chimeras were prepared by using a special fractionated irradiation regimen to minimize the killing of alveolar macrophage colony-forming cells, putative local stem cells. For this study CBA mice with or without T6 chromosome marker were used. Under this experimental condition, the majority of alveolar macrophages in mitosis are of host origin even after 45 weeks. These data suggest that alveolar macrophages are a self-renewing population under normal steady-state conditions.
Kruglova, A A; Kizilova, E A; Zhelezova, A I; Gridina, M M; Golubitsa, A N; Serov, O L
2008-12-01
Ten primary clones of hybrid cells were produced by the fusion of diploid embryonic stem (ES) cells, viz., line E14Tg2aSc4TP6.3 marked by green fluorescent protein (GFP), with diploid embryonic or adult fibroblasts derived from DD/c mice. All the hybrid clones had many characteristics similar to those of ES cells and were positive for GFP. Five hybrid clones having ploidy close to tetraploidy (over 80% of cells had 76-80 chromosomes) were chosen for the generation of chimeras via injection into C57BL blastocysts. These hybrid clones also contained microsatellites marking all ES cell and fibroblast chromosomes judging from microsatellite analysis. Twenty chimeric embryos at 11-13 days post-conception were obtained after injection of hybrid cells derived from two of three clones. Many embryos showed a high content of GFP-positive descendents of the tested hybrid cells. Twenty one adult chimeras were generated by the injection of hybrid cells derived from three clones. The contribution of GFP-labeled hybrid cells was significant and comparable with that of diploid E14Tg2aSc4TP6.3 cells. Cytogenetic and microsatellite analyses of cell cultures derived from chimeric embryos or adults indicated that the initial karyotype of the tested hybrid cells remained stable during the development of the chimeras, i.e., the hybrid cells were mainly responsible for the generation of the chimeras. Thus, ES cell/fibroblast hybrid cells with near-tetraploid karyotype are able to generate chimeras at a high rate, and many adult chimeras contain a high percentage of descendants of the hybrid cells.
Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera.
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Andrew Wang
Full Text Available We present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. We construct a channel-DNA chimera with the KvAP potassium channel reconstituted in an artificial membrane. The channel is functional and the single channel ion conductivity unperturbed by the presence of the DNA. However, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the DNA and the voltage sensing domain of the protein. Different hybridization states of the chimera DNA thus lead to different response curves of the channel.
Energy Technology Data Exchange (ETDEWEB)
Joysey, H.S.; Wakelin, D.; Rose, M.E.
1988-05-01
The course of infection with Eimeria vermiformis was determined in BALB/b, BALB/c, and C57BL/10ScSn (B10) mice and in radiation chimeras prepared from the H-2-compatible BALB/b and B10 mice. The BALB strains, irrespective of H-2 haplotype, were resistant, the B10 mice were susceptible, and in the chimeras infection was characterized by the genotype of the donated bone-marrow cells and not by the phenotype of the recipient. Thus, the genetic control of relative resistance or susceptibility to infection with this parasite is expressed through bone-marrow-derived cells.
Transient scaling and resurgence of chimera states in networks of Boolean phase oscillators
Rosin, David P.; Rontani, Damien; Haynes, Nicholas D.; Schöll, Eckehard; Gauthier, Daniel J.
2014-09-01
We study networks of nonlocally coupled electronic oscillators that can be described approximately by a Kuramoto-like model. The experimental networks show long complex transients from random initial conditions on the route to network synchronization. The transients display complex behaviors, including resurgence of chimera states, which are network dynamics where order and disorder coexists. The spatial domain of the chimera state moves around the network and alternates with desynchronized dynamics. The fast time scale of our oscillators (on the order of 100ns) allows us to study the scaling of the transient time of large networks of more than a hundred nodes, which has not yet been confirmed previously in an experiment and could potentially be important in many natural networks. We find that the average transient time increases exponentially with the network size and can be modeled as a Poisson process in experiment and simulation. This exponential scaling is a result of a synchronization rate that follows a power law of the phase-space volume.
Kuzmenkov, Alexey I; Nekrasova, Oksana V; Kudryashova, Kseniya S; Peigneur, Steve; Tytgat, Jan; Stepanov, Alexey V; Kirpichnikov, Mikhail P; Grishin, Eugene V; Feofanov, Alexey V; Vassilevski, Alexander A
2016-09-21
Ion channels play a central role in a host of physiological and pathological processes and are the second largest target for existing drugs. There is an increasing need for reliable tools to detect and visualize particular ion channels, but existing solutions suffer from a number of limitations such as high price, poor specificity, and complicated protocols. As an alternative, we produced recombinant chimeric constructs (FP-Tx) consisting of fluorescent proteins (FP) fused with potassium channel toxins from scorpion venom (Tx). In particular, we used two FP, eGFP and TagRFP, and two Tx, OSK1 and AgTx2, to create eGFP-OSK1 and RFP-AgTx2. We show that these chimeras largely retain the high affinity of natural toxins and display selectivity to particular ion channel subtypes. FP-Tx are displaced by other potassium channel blockers and can be used as an imaging tool in ion channel ligand screening setups. We believe FP-Tx chimeras represent a new efficient molecular tool for neurobiology.
Crystal structure of the minimalist Max-E47 protein chimera.
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Faraz Ahmadpour
Full Text Available Max-E47 is a protein chimera generated from the fusion of the DNA-binding basic region of Max and the dimerization region of E47, both members of the basic region/helix-loop-helix (bHLH superfamily of transcription factors. Like native Max, Max-E47 binds with high affinity and specificity to the E-box site, 5'-CACGTG, both in vivo and in vitro. We have determined the crystal structure of Max-E47 at 1.7 Å resolution, and found that it associates to form a well-structured dimer even in the absence of its cognate DNA. Analytical ultracentrifugation confirms that Max-E47 is dimeric even at low micromolar concentrations, indicating that the Max-E47 dimer is stable in the absence of DNA. Circular dichroism analysis demonstrates that both non-specific DNA and the E-box site induce similar levels of helical secondary structure in Max-E47. These results suggest that Max-E47 may bind to the E-box following the two-step mechanism proposed for other bHLH proteins. In this mechanism, a rapid step where protein binds to DNA without sequence specificity is followed by a slow step where specific protein:DNA interactions are fine-tuned, leading to sequence-specific recognition. Collectively, these results show that the designed Max-E47 protein chimera behaves both structurally and functionally like its native counterparts.
Prototype and Chimera-Type Galectins in Placentas with Spontaneous and Recurrent Miscarriages
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Laura Unverdorben
2016-04-01
Full Text Available Galectins are galactose binding proteins and, in addition, factors for a wide range of pathologies in pregnancy. We have analyzed the expression of prototype (gal-1, -2, -7, -10 and chimera-type (gal-3 galectins in the placenta in cases of spontaneous abortions (SPA and recurrent abortions (RA in the first trimester. Fifteen placental samples from healthy pregnancies were used as a control group. Nine placentas were examined for spontaneous abortions, and 12 placentas for recurrent abortions. For differentiation and evaluation of different cell types of galectin-expression in the decidua, immunofluorescence was used. For all investigated prototype galectins (gal-1, -2, -7, -10 in SPA and RA placenta trophoblast cells the expression is significantly decreased. In the decidua/extravillous trophoblast only gal-2 expression was significantly lowered, which could be connected to its role in angiogenesis. In trophoblasts in first-trimester placentas and in cases of SPA and RA, prototype galectins are altered in the same way. We suspect prototype galectins have a similar function in placental tissue because of their common biochemical structure. Expression of galectin 3 as a chimera type galectin was not found to be significantly altered in abortive placentas.
Directory of Open Access Journals (Sweden)
Juanjuan Yu
2016-03-01
Full Text Available Leaf color change of variegated leaves from chimera species is regulated by fine-tuned molecular mechanisms. Hosta “Gold Standard” is a typical chimera Hosta species with golden-green variegated leaves, which is an ideal material to investigate the molecular mechanisms of leaf variegation. In this study, the margin and center regions of young and mature leaves from Hosta “Gold Standard”, as well as the leaves from plants after excess nitrogen fertilization were studied using physiological and comparative proteomic approaches. We identified 31 differentially expressed proteins in various regions and development stages of variegated leaves. Some of them may be related to the leaf color regulation in Hosta “Gold Standard”. For example, cytosolic glutamine synthetase (GS1, heat shock protein 70 (Hsp70, and chloroplastic elongation factor G (cpEF-G were involved in pigment-related nitrogen synthesis as well as protein synthesis and processing. By integrating the proteomics data with physiological results, we revealed the metabolic patterns of nitrogen metabolism, photosynthesis, energy supply, as well as chloroplast protein synthesis, import and processing in various leaf regions at different development stages. Additionally, chloroplast-localized proteoforms involved in nitrogen metabolism, photosynthesis and protein processing implied that post-translational modifications were crucial for leaf color regulation. These results provide new clues toward understanding the mechanisms of leaf color regulation in variegated leaves.
Crystal Structure of the Minimalist Max-E47 Protein Chimera
Energy Technology Data Exchange (ETDEWEB)
Ahmadpour, Faraz [McMaster Univ., Hamilton, ON (Canada); Ghirlando, Rodolfo [National Inst. of Health (NIH), Bethesda, MD (United States); De Jong, Antonia T. [Univ. of Toronto, ON (Canada); Gloyd, Melanie [McMaster Univ., Hamilton, ON (Canada); Shin, Jumi A. [Univ. of Toronto, ON (Canada); Guarné, Alba [McMaster Univ., Hamilton, ON (Canada)
2012-02-28
Max-E47 is a protein chimera generated from the fusion of the DNA-binding basic region of Max and the dimerization region of E47, both members of the basic region/helix-loop-helix (bHLH) superfamily of transcription factors. Like native Max, Max-E47 binds with high affinity and specificity to the E-box site, 5'-CACGTG, both in vivo and in vitro. We have determined the crystal structure of Max-E47 at 1.7 Å resolution, and found that it associates to form a well-structured dimer even in the absence of its cognate DNA. Analytical ultracentrifugation confirms that Max-E47 is dimeric even at low micromolar concentrations, indicating that the Max-E47 dimer is stable in the absence of DNA. Circular dichroism analysis demonstrates that both non-specific DNA and the E-box site induce similar levels of helical secondary structure in Max-E47. These results suggest that Max-E47 may bind to the E-box following the two-step mechanism proposed for other bHLH proteins. In this mechanism, a rapid step where protein binds to DNA without sequence specificity is followed by a slow step where specific protein:DNA interactions are fine-tuned, leading to sequence-specific recognition. Collectively, these results show that the designed Max-E47 protein chimera behaves both structurally and functionally like its native counterparts.
Ethical questions concerning research on human embryos, embryonic stem cells and chimeras.
Bobbert, Monika
2006-12-01
Research using human embryos and embryonic stem cells is viewed as important for various reasons. Apart from questions concerning legal regulations, numerous ethical objections are raised pertaining to the use of surplus embryos from reproductive medicine as well as the creation of embryos and stem cells through cloning. In the hopes of avoiding ethical problems, alternatives have been proposed including the extraction of egg cells from "dead" embryos derived from in vitro fertilization procedures, the extraction of pluripotent stem cells from blastocysts, technologies such as "altered nuclear transfer" (ANT) and "oocyte-assisted reprogramming" (ANT-OAR) as well as parthenogenesis. Initial ethical assessments show that certain questions pertaining to such strategies have remained unanswered. Furthermore, with the help of new or more differentiated biotechnological procedures, it is possible to create chimeras and hybrids in which human and non-human cells are combined. Human-animal chimeras, in which gametes or embryonic tissue have been mixed with embryonic or adult stem cells, demonstrate a different "quality" and "degree of penetration" from those produced in previous experiments. Not only does this have consequences regarding questions of patentability, this situation also raises fundamental questions concerning the human being's self image, the concept of person, identity and species and the moral rights and duties that are connected with such concepts. There is a need for legal regulation, on the national as well as the international level.
Recursive Algorithm For Linear Regression
Varanasi, S. V.
1988-01-01
Order of model determined easily. Linear-regression algorithhm includes recursive equations for coefficients of model of increased order. Algorithm eliminates duplicative calculations, facilitates search for minimum order of linear-regression model fitting set of data satisfactory.
Szymkowiak, E J; Sussex, I M
1992-01-01
Cell-cell interactions are important during plant development. We have generated periclinal chimeras between plants that differ in the number of carpels per flower to determine the roles of cells occupying specific positions in the floral meristem in determining the number of carpels initiated. Intraspecific chimeras were generated between tomato (Lycopersicon esculentum) expressing the mutation fasciated, which causes an increased number of floral organs per whorl, and tomato wild type for fasciated. Interspecific chimeras were generated between tomato and L. peruvianum, which differ in number of carpels per flower. In both sets of chimeras, carpel number as well as the size of the floral meristem during carpel initiation were not determined by the genotype of cells in the outer two layers of the meristem (L1 and L2) but were determined by the genotype of cells occupying the inner layer (L3) of the meristem. We concluded from these experiments that during floral organ initiation, cells in certain layers of the meristem respond to information supplied to them from other cells in the meristem. PMID:1392610
Laender, de F.; Brink, van den P.J.; Janssen, C.R.; Guardo, Di A.
2014-01-01
Current techniques for the ecological risk assessment of chemical substances are often criticised for their lack of environmental realism, ecological relevance and methodological accuracy. ChimERA is a 3-year project (2013-2016), funded by Cefic's Long Range Initiative (LRI) that aims to address som
Laender, de F.; Brink, van den P.J.; Janssen, C.R.; Guardo, Di A.
2014-01-01
Current techniques for the ecological risk assessment of chemical substances are often criticised for their lack of environmental realism, ecological relevance and methodological accuracy. ChimERA is a 3-year project (2013-2016), funded by Cefic's Long Range Initiative (LRI) that aims to address
DEFF Research Database (Denmark)
Guilfoyle, Amy P.; Deshpande, Chandrika N.; Font Sadurni, Josep
2014-01-01
for GDP release, or, alternatively, the movement is a consequence of release. To gain additional insight into the sequence of events leading to GDP release, we have created a chimeric protein comprised of Escherichia coli NFeoB and the G5 loop from the human Giα1 protein. The protein chimera retains...
Energy Technology Data Exchange (ETDEWEB)
Beschorner, W.E.; Tutschka, P.J.; Santos, G.W.
1983-03-01
Although chronic graft-versus-host disease (GVHD) frequently develops in the long-term rat radiation chimera, we present three additional models in which a histologically similar disease is rapidly induced. These include adoptive transfer of spleen and bone marrow from rats with spontaneous chronic GVHD into lethally irradiated rats of the primary host strain; sublethal irradiation of stable chimeras followed by a booster transplant; and transfer of spleen cells of chimeras recovering from acute GVHD into second-party (primary recipient strain) or third-party hosts. Some immunopathologic and immune abnormalities associated with spontaneous chronic GVHD were not observed in one or more of the induced models. Thus, IgM deposition in the skin, antinuclear antibodies, and vasculitis appear to be paraphenomena. On the other hand, lymphoid hypocellularity of the thymic medulla, immaturity of splenic follicles, and nonspecific suppressor cells were consistently present in the long term chimeras, and in all models. These abnormalities therefore may be pathogenetically important, or closely related to the development of chronic GVHD.
Regression in autistic spectrum disorders.
Stefanatos, Gerry A
2008-12-01
A significant proportion of children diagnosed with Autistic Spectrum Disorder experience a developmental regression characterized by a loss of previously-acquired skills. This may involve a loss of speech or social responsitivity, but often entails both. This paper critically reviews the phenomena of regression in autistic spectrum disorders, highlighting the characteristics of regression, age of onset, temporal course, and long-term outcome. Important considerations for diagnosis are discussed and multiple etiological factors currently hypothesized to underlie the phenomenon are reviewed. It is argued that regressive autistic spectrum disorders can be conceptualized on a spectrum with other regressive disorders that may share common pathophysiological features. The implications of this viewpoint are discussed.
Combining Alphas via Bounded Regression
Directory of Open Access Journals (Sweden)
Zura Kakushadze
2015-11-01
Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.
Linear regression in astronomy. I
Isobe, Takashi; Feigelson, Eric D.; Akritas, Michael G.; Babu, Gutti Jogesh
1990-01-01
Five methods for obtaining linear regression fits to bivariate data with unknown or insignificant measurement errors are discussed: ordinary least-squares (OLS) regression of Y on X, OLS regression of X on Y, the bisector of the two OLS lines, orthogonal regression, and 'reduced major-axis' regression. These methods have been used by various researchers in observational astronomy, most importantly in cosmic distance scale applications. Formulas for calculating the slope and intercept coefficients and their uncertainties are given for all the methods, including a new general form of the OLS variance estimates. The accuracy of the formulas was confirmed using numerical simulations. The applicability of the procedures is discussed with respect to their mathematical properties, the nature of the astronomical data under consideration, and the scientific purpose of the regression. It is found that, for problems needing symmetrical treatment of the variables, the OLS bisector performs significantly better than orthogonal or reduced major-axis regression.
FBH1 Catalyzes Regression of Stalled Replication Forks
DEFF Research Database (Denmark)
Fugger, Kasper; Mistrik, Martin; Neelsen, Kai J
2015-01-01
DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression...... a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks....... of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity...
Generating porcine chimeras using inner cell mass cells and parthenogenetic preimplantation embryos.
Directory of Open Access Journals (Sweden)
Kazuaki Nakano
Full Text Available BACKGROUND: The development and validation of stem cell therapies using induced pluripotent stem (iPS cells can be optimized through translational research using pigs as large animal models, because pigs have the closest characteristics to humans among non-primate animals. As the recent investigations have been heading for establishment of the human iPS cells with naïve type characteristics, it is an indispensable challenge to develop naïve type porcine iPS cells. The pluripotency of the porcine iPS cells can be evaluated using their abilities to form chimeras. Here, we describe a simple aggregation method using parthenogenetic host embryos that offers a reliable and effective means of determining the chimera formation ability of pluripotent porcine cells. METHODOLOGY/SIGNIFICANT PRINCIPAL FINDINGS: In this study, we show that a high yield of chimeric blastocysts can be achieved by aggregating the inner cell mass (ICM from porcine blastocysts with parthenogenetic porcine embryos. ICMs cultured with morulae or 4-8 cell-stage parthenogenetic embryos derived from in vitro-matured (IVM oocytes can aggregate to form chimeric blastocysts that can develop into chimeric fetuses after transfer. The rate of production of chimeric blastocysts after aggregation with host morulae (20/24, 83.3% was similar to that after the injection of ICMs into morulae (24/29, 82.8%. We also found that 4-8 cell-stage embryos could be used; chimeric blastocysts were produced with a similar efficiency (17/26, 65.4%. After transfer into recipients, these blastocysts yielded chimeric fetuses at frequencies of 36.0% and 13.6%, respectively. CONCLUSION/SIGNIFICANCE: Our findings indicate that the aggregation method using parthenogenetic morulae or 4-8 cell-stage embryos offers a highly reproducible approach for producing chimeric fetuses from porcine pluripotent cells. This method provides a practical and highly accurate system for evaluating pluripotency of undifferentiated
Generating Porcine Chimeras Using Inner Cell Mass Cells and Parthenogenetic Preimplantation Embryos
Nakano, Kazuaki; Watanabe, Masahito; Matsunari, Hitomi; Matsuda, Taisuke; Honda, Kasumi; Maehara, Miki; Kanai, Takahiro; Hayashida, Gota; Kobayashi, Mirina; Kuramoto, Momoko; Arai, Yoshikazu; Umeyama, Kazuhiro; Fujishiro, Shuh-hei; Mizukami, Yoshihisa; Nagaya, Masaki; Hanazono, Yutaka; Nagashima, Hiroshi
2013-01-01
Background The development and validation of stem cell therapies using induced pluripotent stem (iPS) cells can be optimized through translational research using pigs as large animal models, because pigs have the closest characteristics to humans among non-primate animals. As the recent investigations have been heading for establishment of the human iPS cells with naïve type characteristics, it is an indispensable challenge to develop naïve type porcine iPS cells. The pluripotency of the porcine iPS cells can be evaluated using their abilities to form chimeras. Here, we describe a simple aggregation method using parthenogenetic host embryos that offers a reliable and effective means of determining the chimera formation ability of pluripotent porcine cells. Methodology/Significant Principal Findings In this study, we show that a high yield of chimeric blastocysts can be achieved by aggregating the inner cell mass (ICM) from porcine blastocysts with parthenogenetic porcine embryos. ICMs cultured with morulae or 4–8 cell-stage parthenogenetic embryos derived from in vitro-matured (IVM) oocytes can aggregate to form chimeric blastocysts that can develop into chimeric fetuses after transfer. The rate of production of chimeric blastocysts after aggregation with host morulae (20/24, 83.3%) was similar to that after the injection of ICMs into morulae (24/29, 82.8%). We also found that 4–8 cell-stage embryos could be used; chimeric blastocysts were produced with a similar efficiency (17/26, 65.4%). After transfer into recipients, these blastocysts yielded chimeric fetuses at frequencies of 36.0% and 13.6%, respectively. Conclusion/Significance Our findings indicate that the aggregation method using parthenogenetic morulae or 4–8 cell-stage embryos offers a highly reproducible approach for producing chimeric fetuses from porcine pluripotent cells. This method provides a practical and highly accurate system for evaluating pluripotency of undifferentiated cells, such
Time-adaptive quantile regression
DEFF Research Database (Denmark)
Møller, Jan Kloppenborg; Nielsen, Henrik Aalborg; Madsen, Henrik
2008-01-01
An algorithm for time-adaptive quantile regression is presented. The algorithm is based on the simplex algorithm, and the linear optimization formulation of the quantile regression problem is given. The observations have been split to allow a direct use of the simplex algorithm. The simplex method...... and an updating procedure are combined into a new algorithm for time-adaptive quantile regression, which generates new solutions on the basis of the old solution, leading to savings in computation time. The suggested algorithm is tested against a static quantile regression model on a data set with wind power...... production, where the models combine splines and quantile regression. The comparison indicates superior performance for the time-adaptive quantile regression in all the performance parameters considered....
Linear regression in astronomy. II
Feigelson, Eric D.; Babu, Gutti J.
1992-01-01
A wide variety of least-squares linear regression procedures used in observational astronomy, particularly investigations of the cosmic distance scale, are presented and discussed. The classes of linear models considered are (1) unweighted regression lines, with bootstrap and jackknife resampling; (2) regression solutions when measurement error, in one or both variables, dominates the scatter; (3) methods to apply a calibration line to new data; (4) truncated regression models, which apply to flux-limited data sets; and (5) censored regression models, which apply when nondetections are present. For the calibration problem we develop two new procedures: a formula for the intercept offset between two parallel data sets, which propagates slope errors from one regression to the other; and a generalization of the Working-Hotelling confidence bands to nonstandard least-squares lines. They can provide improved error analysis for Faber-Jackson, Tully-Fisher, and similar cosmic distance scale relations.
Chimera distribution amplitudes for the pion and the longitudinally polarized ρ-meson
Energy Technology Data Exchange (ETDEWEB)
Stefanis, N.G., E-mail: stefanis@tp2.ruhr-uni-bochum.de [Institut für Theoretische Physik II, Ruhr-Universität Bochum, D-44780 Bochum (Germany); Pimikov, A.V., E-mail: pimikov@theor.jinr.ru [Bogoliubov Laboratory of Theoretical Physics, JINR, 141980 Dubna (Russian Federation); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000 (China)
2016-01-15
Using QCD sum rules with nonlocal condensates, we show that the distribution amplitude of the longitudinally polarized ρ-meson may have a shorttailed platykurtic profile in close analogy to our recently proposed platykurtic distribution amplitude for the pion. Such a chimera distribution de facto amalgamates the broad unimodal profile of the distribution amplitude, obtained with a Dyson–Schwinger equations-based computational scheme, with the suppressed tails characterizing the bimodal distribution amplitudes derived from QCD sum rules with nonlocal condensates. We argue that pattern formation, emerging from the collective synchronization of coupled oscillators, can provide a single theoretical scaffolding to study unimodal and bimodal distribution amplitudes of light mesons without recourse to particular computational schemes and the reasons for them.
2D and 3D Core-Collapse Supernovae Simulation Results Obtained with the CHIMERA Code
Bruenn, S W; Hix, W R; Blondin, J M; Marronetti, P; Messer, O E B; Dirk, C J; Yoshida, S
2010-01-01
Much progress in realistic modeling of core-collapse supernovae has occurred recently through the availability of multi-teraflop machines and the increasing sophistication of supernova codes. These improvements are enabling simulations with enough realism that the explosion mechanism, long a mystery, may soon be delineated. We briefly describe the CHIMERA code, a supernova code we have developed to simulate core-collapse supernovae in 1, 2, and 3 spatial dimensions. We then describe the results of an ongoing suite of 2D simulations initiated from a 12, 15, 20, and 25 solar mass progenitor. These have all exhibited explosions and are currently in the expanding phase with the shock at between 5,000 and 20,000 km. We also briefly describe an ongoing simulation in 3 spatial dimensions initiated from the 15 solar mass progenitor.
Monsters, dreams and madness: Commentary on 'The arms of the chimeras'.
Reis, Bruce
2016-04-01
Considering Freudian and Post-Freudian approaches to the intersubjective Beatrice Ithier puts the work of Michel de M'Uzan and Thomas Ogden in comparison. To this comparison I add a consideration of the work of Christopher Bollas. The highly creative clinical approaches these three theorists take is shown to be informed by their elaborations of the Freudian notion of unconscious communication and by new approaches to the issue of identity. Attention is paid to differentiating traumatic from fanciful chimeras; and to the experience of the analyst undergoing the sorts of transformations requisite to entering this psychic space marked by fluid exchanges of being and becoming, wherein analyst becomes patient, new subjects are created through shared dreams, and through which monsters appear. Copyright © 2016 Institute of Psychoanalysis.
THE KEY TO THE TREASURE IS THE TREASURE: BARTH’S METAFICTION IN CHIMERA
Directory of Open Access Journals (Sweden)
Katarina Drzajic
2014-11-01
Full Text Available John Barth, one of the most prominent postmodern authors, is famous for his creative literary games: while his favorite tool, metafiction, is at times hard to comprehend, he is almost always both the writer and a character of his stories. “Everyone is necessarily the hero of his own life story,” he said, thus confirming the quite loose difference between reality and fiction in post-modernism. Bearing in mind that the story within a story is a common characteristic of his work, in this paper we shall analyze the most interesting points at which we encounter this phenomenon an d discover what actually represents the treasure in one of his most perplexing, yet incredibly captivating novels, Chimera.
Novel type of chimera spiral waves arising from decoupling of a diffusible component
Energy Technology Data Exchange (ETDEWEB)
Tang, Xiaodong; Yang, Tao; Liu, Yang; Zhao, Yuemin; Gao, Qingyu, E-mail: epstein@brandeis.edu, E-mail: gaoqy@cumt.edu.cn [College of Chemical Engineering, China University of Mining and Technology, Xuzhou 221008 (China); Epstein, Irving R., E-mail: epstein@brandeis.edu, E-mail: gaoqy@cumt.edu.cn [Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, Massachusetts 02454-9110 (United States)
2014-07-14
Spiral waves composed of coherent traveling waves surrounding a core containing stochastically distributed stationary areas are found in numerical simulations of a three-variable reaction-diffusion system with one diffusible species. In the spiral core, diffusion of this component (w) mediates transitions between dynamic states of the subsystem formed by the other two components, whose dynamics is more rapid than that of w. Diffusive coupling between adjacent sites can be “on” or “off” depending on the subsystem state. The incoherent structures in the spiral core are produced by this decoupling of the slow diffusive component from the fast non-diffusing subsystem. The phase diagram reveals that the region of incoherent behavior in chimera spirals grows drastically, leading to modulation and breakup of the spirals, in the transition zones between 1{sup n-1} and 1{sup n} local mixed-mode oscillations.
Two- and three-dimensional simulations of core-collapse supernovae with CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Lentz, Eric J [ORNL; Bruenn, S. W. [Florida Atlantic University, Boca Raton; Harris, James A [ORNL; Chertkow, Merek A [ORNL; Hix, William Raphael [ORNL; Mezzacappa, Anthony [ORNL; Messer, Bronson [ORNL; Blondin, J. M. [North Carolina State University; Marronetti, Pedro [Florida Atlantic University, Boca Raton; Mauney, Christopher M [ORNL; Yakunin, Konstantin [Florida Atlantic University, Boca Raton
2012-01-01
Ascertaining the core-collapse supernova mechanism is a complex, and yet unsolved, problem dependent on the interaction of general relativity, hydrodynamics, neutrino transport, neutrino-matter interactions, and nuclear equations of state and reaction kinetics. Ab initio modeling of core-collapse supernovae and their nucleosynthetic outcomes requires care in the coupling and approximations of the physical components. We have built our multi-physics CHIMERA code for supernova modeling in 1-, 2-, and 3-D, using ray-by-ray neutrino transport, approximate general relativity, and detailed neutrino and nuclear physics. We discuss some early results from our current series of exploding 2D simulations and our work to perform computationally tractable simulations in 3D using the ``Yin--Yang'' grid.
2D and 3D core-collapse supernovae simulation results obtained with the CHIMERA code
Energy Technology Data Exchange (ETDEWEB)
Bruenn, S W; Marronetti, P; Dirk, C J [Physics Department, Florida Atlantic University, 777 W. Glades Road, Boca Raton, FL 33431-0991 (United States); Mezzacappa, A; Hix, W R [Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6354 (United States); Blondin, J M [Department of Physics, North Carolina State University, Raleigh, NC 27695-8202 (United States); Messer, O E B [Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6354 (United States); Yoshida, S, E-mail: bruenn@fau.ed [Max-Planck-Institut fur Gravitationsphysik, Albert Einstein Institut, Golm (Germany)
2009-07-01
Much progress in realistic modeling of core-collapse supernovae has occurred recently through the availability of multi-teraflop machines and the increasing sophistication of supernova codes. These improvements are enabling simulations with enough realism that the explosion mechanism, long a mystery, may soon be delineated. We briefly describe the CHIMERA code, a supernova code we have developed to simulate core-collapse supernovae in 1, 2, and 3 spatial dimensions. We then describe the results of an ongoing suite of 2D simulations initiated from a 12, 15, 20, and 25 M{sub o-dot} progenitor. These have all exhibited explosions and are currently in the expanding phase with the shock at between 5,000 and 20,000 km. We also briefly describe an ongoing simulation in 3 spatial dimensions initiated from the 15 M{sub o-dot} progenitor.
Chimera distribution amplitudes for the pion and the longitudinally polarized $\\rho$-meson
Stefanis, N G
2016-01-01
Using QCD sum rules with nonlocal condensates, we show that the distribution amplitude of the longitudinally polarized $\\rho$-meson may have a shorttailed platykurtic profile in close analogy to our recently proposed platykurtic distribution amplitude for the pion. Such a chimera distribution de facto amalgamates the broad unimodal profile of the distribution amplitude, obtained with a Dyson-Schwinger equations-based computational scheme, with the suppressed tails characterizing the bimodal distribution amplitudes derived from QCD sum rules with nonlocal condensates. We argue that pattern formation, emerging from the collective synchronization of coupled oscillators, can provide a single theoretical scaffolding to study unimodal and bimodal distribution amplitudes of light mesons without recourse to particular computational schemes and the reasons for them.
TRAPS, CHIMERAS AND PATHWAYS: THREE APPROACHES OF ART IN CONTEMPORARY ANTHROPOLOGY
Directory of Open Access Journals (Sweden)
André Demarchi
2009-12-01
Full Text Available Based upon the concepts of traps, chimera and pathways proposed by Alfred Gell, Carlo Severi and Els Lagrou respectively, this bibliographic essay presents the characteristics, similarities and specificities of three approaches on art in contemporary anthropology. The work focuses on the ruptures created by these approaches, concerning the symbolic analysis that has long dominated the anthropological art studies. Breaking away from the conception of art as a symbolic language, the studies we analyzed emphasized, in different ways, the cognitive action of art in native contexts, privileging categories such as agency, efficacy, counter-intuitiveness, and presentification. In the conclusion, we demonstrate how these categories are applied to Amerindian Art through the work of Els Lagrou on Cashinahua Art.
Polynomial Regression on Riemannian Manifolds
Hinkle, Jacob; Fletcher, P Thomas; Joshi, Sarang
2012-01-01
In this paper we develop the theory of parametric polynomial regression in Riemannian manifolds and Lie groups. We show application of Riemannian polynomial regression to shape analysis in Kendall shape space. Results are presented, showing the power of polynomial regression on the classic rat skull growth data of Bookstein as well as the analysis of the shape changes associated with aging of the corpus callosum from the OASIS Alzheimer's study.
Evaluating Differential Effects Using Regression Interactions and Regression Mixture Models
Van Horn, M. Lee; Jaki, Thomas; Masyn, Katherine; Howe, George; Feaster, Daniel J.; Lamont, Andrea E.; George, Melissa R. W.; Kim, Minjung
2015-01-01
Research increasingly emphasizes understanding differential effects. This article focuses on understanding regression mixture models, which are relatively new statistical methods for assessing differential effects by comparing results to using an interactive term in linear regression. The research questions which each model answers, their…
Energy Technology Data Exchange (ETDEWEB)
Yamamoto, H.; Bitoh, S.; Fujimoto, S.
1987-01-15
Immunization of BALB/c mice with MOPC-104E myeloma protein induced idiotype-specific enhancing B cells that acted on anti-dextran antibody producing B cells. The enhancing cells have the surface phenotype of B cells. With the use of several H-2 or Igh congenic mice, it was found that the cooperation among B cells was controlled by both the major histocompatibility complex (MHC) and Igh. The capability to generate enhancing B cell activity was analyzed by using tetraparental bone marrow chimeras. (C57BL/6 X BALB/c)F1 mice, for example, were lethally irradiated and were reconstituted with C57BL/6 and BALB/c bone marrow cells. Nine to 12 wk after the reconstitution, the chimeras were immunized with the myeloma protein and were tested for their enhancing B cell activity. After the removal of C57BL/6 origin cells by treatment with anti-H-2b + complement, residual cells exhibited enhancing B cell activity on BALB.B, as well as BALB/c antidextran antibody response. This indicates that the generation of H-2-restricted, idiotype-specific enhancing B cell activity differentiated adaptively so as to recognize foreign MHC as self under chimeric conditions. On the other hand, splenic B cells treated with anti-H-2d + complement did not enhance the responses of BALB/c or BALB.B. Even in a chimeric environment, the B cells of C57BL/6 origin could not obtain the ability to generate enhancing B cell activity upon immunization of the idiotype. The results described here, taken in conjunction with our previous studies, suggest that the Ig heavy chain gene(s) predominantly control the Igh restriction properties of enhancing B cells, and the capability of MHC recognition by B cells is selected under chimeric conditions.
Cross-reactivity of hypervariable region 1 chimera of hepatitis C virus
Institute of Scientific and Technical Information of China (English)
Bing-Shui Xiu; Shi-Gan Ling; Xiao-Guo Song; He-Qiu Zhang; Kun Chen; Cui-Xia Zhu
2003-01-01
AIM: To analyze the amino acid sequences of hypervariable region 1 (HVR1) of HCV isolates in China and to construct a combinatorial chimeric HVR1 protein having a very broad high cross-reactivity. METHODS: All of the published HVR1 sequences from China were collected and processed with a computer program.Several representative HVR1's sequences were formulated based on a consensus profile and homology within certain subdivision. A few reported HVR1 mimotope sequences were also included for a broader representation. All of them were cloned and expressed in E.coli. The cross-reactivity of the purified recombinant HVR1 antigens was tested by ELISA with a panel of sera from HCV infected patients in China.Some of them were further ligated together to form a combinatorial HVR1 chimera. RESULTS: Altogether 12 HVR1s were selected and expressed in E. coli and purified to homogeneity. All of these purified antigens showed some cross-reactivity with sera in a 27 HCV positive panel. Recombinant HVR1s of No. 1, 2, 4, and 8# showing broad cross-reactivities and complementarity with each other, were selected for the ligation elements. The chimera containing these 4 HVR1s was highly expressed in E. coli. The purified chimeric antigen could react not only with all the HCV antibody positive sera in the panel but also with 90/91 sera of HCV -infected patients. CONCLUSION: The chimeric antigen was shown to have a broad cross-reactivity. It may be helpful for solving the problem caused by high variability of HCV, and in the efforts for a novel vaccine against the virus.
Karagenç, Levent; Sandikci, Mustafa
2010-01-01
The objective of the current study was to determine the tissue distribution of cells derived from the area opaca in heterospecific quail-chick blastodermal chimeras. Quail-chick chimeras were constructed by transferring dissociated cells from the area opaca of the stage X-XII (EG&K) quail embryo into the subgerminal cavity of the unincubated chick blastoderm. The distribution of quail cells in embryonic as well as extra-embryonic tissues of the recipient embryo were examined using the QCPN monoclonal antibody after 6 days of incubation in serial sections taken at 100-mum intervals. Data gathered in the present study demonstrated that, when introduced into the subgerminal cavity of a recipient embryo, cells of the area opaca are able to populate not only extra-embryonic structures such as the amnion and the yolk sac, but also various embryonic tissues derived from the ectoderm and less frequently the mesoderm. Ectodermal chimerism was confined mainly to the head region and was observed in tissues derived from the neural ectoderm and the surface ectoderm, including the optic cup, diencephalon and lens. Although the possibility of random incorporation of transplanted cells into these embryonic structures cannot be excluded, these results would suggest that area opaca, a peripheral ring of cells in the avian embryo destined to form the extra-embryonic ectoderm and endoderm of the yolk sac, might harbor cells that have the potential to give rise to various cell types in the recipient chick embryo, including those derived from the surface ectoderm and neural ectoderm.
Quantile regression theory and applications
Davino, Cristina; Vistocco, Domenico
2013-01-01
A guide to the implementation and interpretation of Quantile Regression models This book explores the theory and numerous applications of quantile regression, offering empirical data analysis as well as the software tools to implement the methods. The main focus of this book is to provide the reader with a comprehensivedescription of the main issues concerning quantile regression; these include basic modeling, geometrical interpretation, estimation and inference for quantile regression, as well as issues on validity of the model, diagnostic tools. Each methodological aspect is explored and
Business applications of multiple regression
Richardson, Ronny
2015-01-01
This second edition of Business Applications of Multiple Regression describes the use of the statistical procedure called multiple regression in business situations, including forecasting and understanding the relationships between variables. The book assumes a basic understanding of statistics but reviews correlation analysis and simple regression to prepare the reader to understand and use multiple regression. The techniques described in the book are illustrated using both Microsoft Excel and a professional statistical program. Along the way, several real-world data sets are analyzed in deta
DEFF Research Database (Denmark)
Hein-Kristensen, Line; Knapp, Kolja M; Franzyk, Henrik;
2011-01-01
, and this was parallel by the largest reduction in number of viable bacteria. CONCLUSION: We found that chain length but not type of cationic amino acid influenced the antibacterial activity of a series of synthetic α-peptide/β-peptoid chimeras. The synthetic chimeras exert their killing effect by permeabilization......BACKGROUND: Characterization and use of antimicrobial peptides (AMPs) requires that their mode of action is determined. The interaction of membrane-active peptides with their target is often established using model membranes, however, the actual permeabilization of live bacterial cells...... acid only had a minor effect on MIC values, whereas chain length had a profound influence on activity. All chimeras were less active against Serratia marcescens (MICs above 46 μM). The chimeras were bactericidal and induced leakage of ATP from Staphylococcus aureus and S. marcescens with similar time...
Testing discontinuities in nonparametric regression
Dai, Wenlin
2017-01-19
In nonparametric regression, it is often needed to detect whether there are jump discontinuities in the mean function. In this paper, we revisit the difference-based method in [13 H.-G. Müller and U. Stadtmüller, Discontinuous versus smooth regression, Ann. Stat. 27 (1999), pp. 299–337. doi: 10.1214/aos/1018031100
Logistic Regression: Concept and Application
Cokluk, Omay
2010-01-01
The main focus of logistic regression analysis is classification of individuals in different groups. The aim of the present study is to explain basic concepts and processes of binary logistic regression analysis intended to determine the combination of independent variables which best explain the membership in certain groups called dichotomous…
LENUS (Irish Health Repository)
Connolly, Mary
2010-06-01
Serum amyloid A (A-SAA), an acute-phase protein with cytokine-like properties, is expressed at sites of inflammation. This study investigated the effects of A-SAA on chemokine-regulated migration and angiogenesis using rheumatoid arthritis (RA) cells and whole-tissue explants in vitro, ex vivo, and in vivo. A-SAA levels were measured by real-time PCR and ELISA. IL-8 and MCP-1 expression was examined in RA synovial fibroblasts, human microvascular endothelial cells, and RA synovial explants by ELISA. Neutrophil transendothelial cell migration, cell adhesion, invasion, and migration were examined using transwell leukocyte\\/monocyte migration assays, invasion assays, and adhesion assays with or without anti-MCP-1\\/anti-IL-8. NF-kappaB was examined using a specific inhibitor and Western blotting. An RA synovial\\/SCID mouse chimera model was used to examine the effects of A-SAA on cell migration, proliferation, and angiogenesis in vivo. High expression of A-SAA was demonstrated in RA patients (p < 0.05). A-SAA induced chemokine expression in a time- and dose-dependent manner (p < 0.05). Blockade with anti-scavenger receptor class B member 1 and lipoxin A4 (A-SAA receptors) significantly reduced chemokine expression in RA synovial tissue explants (p < 0.05). A-SAA induced cell invasion, neutrophil-transendothelial cell migration, monocyte migration, and adhesion (all p < 0.05), effects that were blocked by anti-IL-8 or anti-MCP-1. A-SAA-induced chemokine expression was mediated through NF-kappaB in RA explants (p < 0.05). Finally, in the RA synovial\\/SCID mouse chimera model, we demonstrated for the first time in vivo that A-SAA directly induces monocyte migration from the murine circulation into RA synovial grafts, synovial cell proliferation, and angiogenesis (p < 0.05). A-SAA promotes cell migrational mechanisms and angiogenesis critical to RA pathogenesis.
Kutsuzawa, K; Chowdhury, E H; Nagaoka, M; Maruyama, K; Akiyama, Y; Akaike, T
2006-11-24
Stem cells holding great promises in regenerative medicine have the potential to be differentiated to a specific cell type through genetic manipulation. However, conventional ways of gene transfer to such progenitor cells suffer from a number of disadvantages particularly involving safety and efficacy issues. Here, we report on the development of a bio-functionalized inorganic nano-carrier of DNA by embedding fibronectin and E-cadherin chimera on the carrier, leading to its high affinity interactions with embryonic stem cell surface and accelerated trans-gene delivery for subsequent expression. While only apatite nano-particles were very inefficient in transfecting embryonic stem cells, fibronectin-anchored particles and to a more significant extent, fibronectin and E-cadherin-Fc-associated particles dramatically enhanced trans-gene delivery with a value notably higher than that of commercially available lipofection system. The involvement of both cell surface integrin and E-cadherin in mediating intracellular localization of the hybrid carrier was verified by blocking integrin binding site with excess free fibronectin and up-regulating both integrin and E-cadherin through PKC activation. Thus, the new establishment of a bio-functional hybrid gene-carrier would promote and facilitate development of stem cell-based therapy in regenerative medicine.
Fungible weights in logistic regression.
Jones, Jeff A; Waller, Niels G
2016-06-01
In this article we develop methods for assessing parameter sensitivity in logistic regression models. To set the stage for this work, we first review Waller's (2008) equations for computing fungible weights in linear regression. Next, we describe 2 methods for computing fungible weights in logistic regression. To demonstrate the utility of these methods, we compute fungible logistic regression weights using data from the Centers for Disease Control and Prevention's (2010) Youth Risk Behavior Surveillance Survey, and we illustrate how these alternate weights can be used to evaluate parameter sensitivity. To make our work accessible to the research community, we provide R code (R Core Team, 2015) that will generate both kinds of fungible logistic regression weights. (PsycINFO Database Record
Regression Testing Cost Reduction Suite
Directory of Open Access Journals (Sweden)
Mohamed Alaa El-Din
2014-08-01
Full Text Available The estimated cost of software maintenance exceeds 70 percent of total software costs [1], and large portion of this maintenance expenses is devoted to regression testing. Regression testing is an expensive and frequently executed maintenance activity used to revalidate the modified software. Any reduction in the cost of regression testing would help to reduce the software maintenance cost. Test suites once developed are reused and updated frequently as the software evolves. As a result, some test cases in the test suite may become redundant when the software is modified over time since the requirements covered by them are also covered by other test cases. Due to the resource and time constraints for re-executing large test suites, it is important to develop techniques to minimize available test suites by removing redundant test cases. In general, the test suite minimization problem is NP complete. This paper focuses on proposing an effective approach for reducing the cost of regression testing process. The proposed approach is applied on real-time case study. It was found that the reduction in cost of regression testing for each regression testing cycle is ranging highly improved in the case of programs containing high number of selected statements which in turn maximize the benefits of using it in regression testing of complex software systems. The reduction in the regression test suite size will reduce the effort and time required by the testing teams to execute the regression test suite. Since regression testing is done more frequently in software maintenance phase, the overall software maintenance cost can be reduced considerably by applying the proposed approach.
Rank regression: an alternative regression approach for data with outliers.
Chen, Tian; Tang, Wan; Lu, Ying; Tu, Xin
2014-10-01
Linear regression models are widely used in mental health and related health services research. However, the classic linear regression analysis assumes that the data are normally distributed, an assumption that is not met by the data obtained in many studies. One method of dealing with this problem is to use semi-parametric models, which do not require that the data be normally distributed. But semi-parametric models are quite sensitive to outlying observations, so the generated estimates are unreliable when study data includes outliers. In this situation, some researchers trim the extreme values prior to conducting the analysis, but the ad-hoc rules used for data trimming are based on subjective criteria so different methods of adjustment can yield different results. Rank regression provides a more objective approach to dealing with non-normal data that includes outliers. This paper uses simulated and real data to illustrate this useful regression approach for dealing with outliers and compares it to the results generated using classical regression models and semi-parametric regression models.
Directory of Open Access Journals (Sweden)
S. Więckowski
2015-01-01
Full Text Available The assimilatory pigment composition, photosynthetic activity and ultrastructure of chloroplasts were studied in the chlorophyll - deficient chimera of Acer platanoides L. Part of the crown of this chimera is a virescent mutant with variegated leaves. It was found that there exists no qualitative difference in the pigment composition between normal and variegated leaves. The accumulation of chlorophyll in the mutated part is more delayed that the accumulation of carotenoids. The photosynthetic rate on a chlorophyll basis is much higher in variegated than in green leaves. This difference gradually falls off with development. In the early spring, chloroplasts from the yellow spots of leaf blade have no lamellar system but only many vesicles are dispersed in the stroma. Occasionally also a single granum consisting of a few thylakoids occurs in the stroma. At the end of summer chloroplasts from yellow spots of variegated leaves possess a poorly developed lamellar system.
Matveeva, Natalia M; Kizilova, Elena A; Serov, Oleg L
2015-01-01
The in vitro long-term cultivation of embryonic stem (ES) cells derived from pre-implantation embryos offers the unique possibility of combining ES cells with pre-implantation embryos to generate chimeras, thus facilitating the creation of a bridge between in vitro and in vivo investigations. Genomic manipulation using ES cells and homologous recombination is one of the most outstanding scientific achievements, resulting in the generation of animals with desirable genome modifications. As such, the generation of ES cells with different ploidy via cell fusion also deserves much attention because this approach allows for the production of chimeras that contain somatic cells with various ploidy. Therefore, this is a powerful tool that can be used to study the role of polyploidy in the normal development of mammals.
Energy Technology Data Exchange (ETDEWEB)
Shepelev, I.A., E-mail: igor_sar@li.ru; Vadivasova, T.E., E-mail: vadivasovate@yandex.ru; Bukh, A.V., E-mail: buh.andrey@yandex.ru; Strelkova, G.I., E-mail: strelkovagi@info.sgu.ru; Anishchenko, V.S., E-mail: wadim@info.sgu.ru
2017-04-25
We study the spatiotemporal dynamics of a ring of nonlocally coupled FitzHugh–Nagumo oscillators in the bistable regime. A new type of chimera patterns has been found in the noise-free network and when isolated elements do not oscillate. The region of existence of these structures has been explored when the coupling range and the coupling strength between the network elements are varied. - Highlights: • Dynamics of a ring of nonlocally coupled FitzHugh–Nagumo oscillators in the bistable regime is studied. • A new type of chimera patterns has been found in the noise-free network. • The region of existence of new structures has been explored when varying the coupling parameters.
Shepelev, I. A.; Vadivasova, T. E.; Bukh, A. V.; Strelkova, G. I.; Anishchenko, V. S.
2017-04-01
We study the spatiotemporal dynamics of a ring of nonlocally coupled FitzHugh-Nagumo oscillators in the bistable regime. A new type of chimera patterns has been found in the noise-free network and when isolated elements do not oscillate. The region of existence of these structures has been explored when the coupling range and the coupling strength between the network elements are varied.
Lapelosa, Mauro; Arnold, Gail Ferstandig; Gallicchio, Emilio; Arnold, Eddy; Levy, Ronald M
2010-04-02
The development of an effective AIDS vaccine remains the most promising long-term strategy to combat human immunodeficiency virus (HIV)/AIDS. Here, we report favorable antigenic characteristics of vaccine candidates isolated from a combinatorial library of human rhinoviruses displaying the ELDKWA epitope of the gp41 glycoprotein of HIV-1. The design principles of this library emerged from the application of molecular modeling calculations in conjunction with our knowledge of previously obtained ELDKWA-displaying chimeras, including knowledge of a chimera with one of the best 2F5-binding characteristics obtained to date. The molecular modeling calculations identified the energetic and structural factors affecting the ability of the epitope to assume conformations capable of fitting into the complementarity determining region of the ELDKWA-binding, broadly neutralizing human mAb 2F5. Individual viruses were isolated from the library following competitive immunoselection and were tested using ELISA and fluorescence quenching experiments. Dissociation constants obtained using both techniques revealed that some of the newly isolated chimeras bind 2F5 with greater affinity than previously identified chimeric rhinoviruses. Molecular dynamics simulations of two of these same chimeras confirmed that their HIV inserts were partially preorganized for binding, which is largely responsible for their corresponding gains in binding affinity. The study illustrates the utility of combining structure-based experiments with computational modeling approaches for improving the odds of selecting vaccine component designs with preferred antigenic characteristics. The results obtained also confirm the flexibility of HRV as a presentation vehicle for HIV epitopes and the potential of this platform for the development of vaccine components against AIDS.
Qiu, X; Wu, L; Huang, H; McDonel, P E; Palumbo, A V; Tiedje, J M; Zhou, J
2001-02-01
To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Taq DNA polymerases examined: 20% for Z-Taq, with the highest processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies.
Nasution, Inggrita Gusti Sari; Muchtar, Yasmin Chairunnisa
2013-01-01
This research is to study the factors which influence the business success of small business ‘processed rotan’. The data employed in the study are primary data within the period of July to August 2013, 30 research observations through census method. Method of analysis used in the study is multiple linear regressions. The results of analysis showed that the factors of labor, innovation and promotion have positive and significant influence on the business success of small busine...
ORDINAL REGRESSION FOR INFORMATION RETRIEVAL
Institute of Scientific and Technical Information of China (English)
无
2008-01-01
This letter presents a new discriminative model for Information Retrieval (IR), referred to as Ordinal Regression Model (ORM). ORM is different from most existing models in that it views IR as ordinal regression problem (i.e. ranking problem) instead of binary classification. It is noted that the task of IR is to rank documents according to the user information needed, so IR can be viewed as ordinal regression problem. Two parameter learning algorithms for ORM are presented. One is a perceptron-based algorithm. The other is the ranking Support Vector Machine (SVM). The effectiveness of the proposed approach has been evaluated on the task of ad hoc retrieval using three English Text REtrieval Conference (TREC) sets and two Chinese TREC sets. Results show that ORM significantly outperforms the state-of-the-art language model approaches and OKAPI system in all test sets; and it is more appropriate to view IR as ordinal regression other than binary classification.
Multiple Regression and Its Discontents
Snell, Joel C.; Marsh, Mitchell
2012-01-01
Multiple regression is part of a larger statistical strategy originated by Gauss. The authors raise questions about the theory and suggest some changes that would make room for Mandelbrot and Serendipity.
Multiple Regression and Its Discontents
Snell, Joel C.; Marsh, Mitchell
2012-01-01
Multiple regression is part of a larger statistical strategy originated by Gauss. The authors raise questions about the theory and suggest some changes that would make room for Mandelbrot and Serendipity.
A Direct Mapping of Max k-SAT and High Order Parity Checks to a Chimera Graph
Chancellor, N.; Zohren, S.; Warburton, P. A.; Benjamin, S. C.; Roberts, S.
2016-11-01
We demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a similar class of maximum satisfiability problems where the clauses are replaced by parity checks over potentially large numbers of bits. The latter is of specific interest for applications in decoding for communication. We discuss an example in which the decoding of a turbo code, which has been demonstrated to perform near the Shannon limit, can be mapped to a Chimera graph. The weighted max k-SAT problem is the most general class of satisfiability problems, so our result effectively demonstrates how any satisfiability problem may be directly mapped to a Chimera graph. Our methods faithfully reproduce the low energy spectrum of the target problems, so therefore may also be used for maximum entropy inference.
Directory of Open Access Journals (Sweden)
Tomoko Lee
2017-02-01
Full Text Available Duchenne muscular dystrophy (DMD is a fatal muscle-wasting disease characterized by dystrophin deficiency from mutations in the dystrophin gene. Antisense oligonucleotide (AO-mediated exon skipping targets restoration of the dystrophin reading frame to allow production of an internally deleted dystrophin protein with functional benefit for DMD patients who have out-of-frame deletions. After accelerated US approval of eteplirsen (Exondys 51, which targets dystrophin exon 51 for skipping, efforts are now focused on targeting other exons. For improved clinical benefits, this strategy requires more studies of the delivery method and modification of nucleic acids. We studied a nucleotide with a 2′-O,4′-C-ethylene-bridged nucleic acid (ENA, which shows high nuclease resistance and high affinity for complementary RNA strands. Here, we describe the process of developing a 2′-O-methyl RNA(2′-OMeRNA/ENA chimera AO to induce dystrophin exon 45 skipping. One 18-mer 2′-OMeRNA/ENA chimera (AO85 had the most potent activity for inducing exon 45 skipping in cultured myotubes. AO85 was administered to mdx mice without significant side effects. AO85 transfection into cultured myotubes from 13 DMD patients induced exon 45 skipping in all samples at different levels and dystrophin expression in 11 patients. These results suggest the possible efficacy of AO-mediated exon skipping changes in individual patients and highlight the 2′-OMeRNA/ENA chimera AO as a potential fundamental treatment for DMD.
The ethics of killing human/great-ape chimeras for their organs: a reply to Shaw et al.
Palacios-González, César
2016-06-01
The aim of this paper is to critically examine David Shaw, Wybo Dondorp, and Guido de Wert's arguments in favour of the procurement of human organs from human/nonhuman-primate chimeras, specifically from great-ape/human chimeras. My main claim is that their arguments fail and are in need of substantial revision. To prove this I first introduce the topic, and then reconstruct Shaw et al.'s position and arguments. Next, I show that Shaw et al.: (1) failed to properly apply the subsidiarity and proportionality principles; (2) neglected species overlapping cases in their ethical assessment; (3) ignored the ethics literature on borderline persons; and (4) misunderstood McMahan's two-tiered moral theory. These mistakes render an important part of their conclusions either false or problematic to the point that they would no longer endorse them. Finally I will briefly mention a possible multipolar solution to the human organ shortage problem that would reduce the need for chimeras' organs.
Karagenç, Levent; Sandikci, Mustafa
2013-01-01
The current study has two main objectives: first, to determine if cells derived from the area pellucida are able to populate extraembryonic membranes, and second, to determine if donor cells have the potential to differentiate to endothelial (EC) and hematopoietic cells (HC) in the yolk sac and allantois, the two extraembryonic membranes functioning as hematopoietic organs in the avian embryo. To this end, quail chick chimeras were constructed by transferring dissociated cells from the areae pellucidae of the stage X-XII (EG&K) quail embryo into the subgerminal cavity of the unincubated chick blastoderm. The distribution of quail cells in the allantois, yolk sac, amnion, and chorion of resulting putative chimeras was examined using quail cell-specific antibody against a perinuclear antigen (QCPN) after 6 days of incubation. The presence of EC, HC, and smooth muscle cells among the QCPN(+) donor cells was examined using QH-1, a quail-specific marker identifying HC and EC and an anti-α-smooth muscle actin antibody. Evidence gathered in the present study demonstrates that quail cells derived from the areae pellucidae are able to populate all of the extraembryonic membranes of resulting heterospecific quail chick chimeras and, most importantly, give rise to HC, EC, and smooth muscle cells, all of the three main mesodermal lineages derived from the posterior mesoderm both in the yolk sac and allantois.
Regression methods for medical research
Tai, Bee Choo
2013-01-01
Regression Methods for Medical Research provides medical researchers with the skills they need to critically read and interpret research using more advanced statistical methods. The statistical requirements of interpreting and publishing in medical journals, together with rapid changes in science and technology, increasingly demands an understanding of more complex and sophisticated analytic procedures.The text explains the application of statistical models to a wide variety of practical medical investigative studies and clinical trials. Regression methods are used to appropriately answer the
Forecasting with Dynamic Regression Models
Pankratz, Alan
2012-01-01
One of the most widely used tools in statistical forecasting, single equation regression models is examined here. A companion to the author's earlier work, Forecasting with Univariate Box-Jenkins Models: Concepts and Cases, the present text pulls together recent time series ideas and gives special attention to possible intertemporal patterns, distributed lag responses of output to input series and the auto correlation patterns of regression disturbance. It also includes six case studies.
Wrong Signs in Regression Coefficients
McGee, Holly
1999-01-01
When using parametric cost estimation, it is important to note the possibility of the regression coefficients having the wrong sign. A wrong sign is defined as a sign on the regression coefficient opposite to the researcher's intuition and experience. Some possible causes for the wrong sign discussed in this paper are a small range of x's, leverage points, missing variables, multicollinearity, and computational error. Additionally, techniques for determining the cause of the wrong sign are given.
From Rasch scores to regression
DEFF Research Database (Denmark)
Christensen, Karl Bang
2006-01-01
Rasch models provide a framework for measurement and modelling latent variables. Having measured a latent variable in a population a comparison of groups will often be of interest. For this purpose the use of observed raw scores will often be inadequate because these lack interval scale propertie....... This paper compares two approaches to group comparison: linear regression models using estimated person locations as outcome variables and latent regression models based on the distribution of the score....
FBH1 Catalyzes Regression of Stalled Replication Forks
Directory of Open Access Journals (Sweden)
Kasper Fugger
2015-03-01
Full Text Available DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity, is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks.
A Matlab program for stepwise regression
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Yanhong Qi
2016-03-01
Full Text Available The stepwise linear regression is a multi-variable regression for identifying statistically significant variables in the linear regression equation. In present study, we presented the Matlab program of stepwise regression.
XRA image segmentation using regression
Jin, Jesse S.
1996-04-01
Segmentation is an important step in image analysis. Thresholding is one of the most important approaches. There are several difficulties in segmentation, such as automatic selecting threshold, dealing with intensity distortion and noise removal. We have developed an adaptive segmentation scheme by applying the Central Limit Theorem in regression. A Gaussian regression is used to separate the distribution of background from foreground in a single peak histogram. The separation will help to automatically determine the threshold. A small 3 by 3 widow is applied and the modal of the local histogram is used to overcome noise. Thresholding is based on local weighting, where regression is used again for parameter estimation. A connectivity test is applied to the final results to remove impulse noise. We have applied the algorithm to x-ray angiogram images to extract brain arteries. The algorithm works well for single peak distribution where there is no valley in the histogram. The regression provides a method to apply knowledge in clustering. Extending regression for multiple-level segmentation needs further investigation.
Chimeras in leaky integrate-and-fire neural networks: effects of reflecting connectivities
Tsigkri-DeSmedt, Nefeli Dimitra; Hizanidis, Johanne; Schöll, Eckehard; Hövel, Philipp; Provata, Astero
2017-07-01
The effects of attracting-nonlocal and reflecting connectivity are investigated in coupled Leaky Integrate-and-Fire (LIF) elements, which model the exchange of electrical signals between neurons. Earlier investigations have demonstrated that repulsive-nonlocal and hierarchical network connectivity can induce complex synchronization patterns and chimera states in systems of coupled oscillators. In the LIF system we show that if the elements are nonlocally linked with positive diffusive coupling on a ring network, the system splits into a number of alternating domains. Half of these domains contain elements whose potential stays near the threshold and they are interrupted by active domains where the elements perform regular LIF oscillations. The active domains travel along the ring with constant velocity, depending on the system parameters. When we introduce reflecting coupling in LIF networks unexpected complex spatio-temporal structures arise. For relatively extensive ranges of parameter values, the system splits into two coexisting domains: one where all elements stay near the threshold and one where incoherent states develop, characterized by multi-leveled mean phase velocity profiles.
T and B lymphocytes in the marmoset: a natural haemopoietic chimera
Energy Technology Data Exchange (ETDEWEB)
Niblack, G.D.; Gengozian, N.
1976-01-01
The thymus-derived (T) lymphocyte and bone marrow-derived (B) lymphocyte populations of the marmoset were characterized using specific cell surface markers. Approximately 85% of the thymocytes formed rosettes with neuraminidase-treated sheep erythrocytes (E/sub n/). The percentage (approximately 69%) of peripheral blood lymphocytes (PBL) forming rosettes with E/sub n/ was the same as that which stained with fluorescently labelled goat anti-marmoset thymocyte serum (ATS). These two assays identified the same cell population since treatment of cells with ATS and complement resulted in a concomitant decrease in E/sub n/ rosette formation. Marmoset PBL also formed rosettes with human erythrocytes sensitized with antibody and complement (HEAC); since the percentage (approximately 20%) HEAC rosette was the same as that of cells stained with fluorescently labelled goat anti-marmoset IgG, these cells were considered to be B cells. A small percentage of cells (aproximately 1.5%) possessed both types of receptors. The mean percentages of T and B cells present in PBL of single-born, presumably non-chimeric animals, were the same as that of isosexual and heterosexual chimeras.
Aerodynamic study of sounding rocket flows using Chimera and patched multiblock meshes
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João Alves de Oliveira Neto
2011-01-01
Full Text Available Aerodynamic flow simulations over a typical sounding rocket are presented in this paper. The work is inserted in the effort of developing computational tools necessary to simulate aerodynamic flows over configurations of interest for Instituto de Aeronáutica e Espaço of Departamento de Ciência e Tecnologia Aeroespacial. Sounding rocket configurations usually require fairly large fins and, quite frequently, have more than one set of fins. In order to be able to handle such configurations, the present paper presents a novel methodology which combines both Chimera and patched multiblock grids in the discretization of the computational domain. The flows of interest are modeled using the 3-D Euler equations and the work describes the details of discretization procedure, which uses a finite difference approach for structure, body-conforming, multiblock grids. The method is used to calculate the aerodynamics of a sounding rocket vehicle. The results indicate that the present approach can be a powerful aerodynamic analysis and design tool.
The data acquisition and control system for the 4{pi} detector CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Aiello, S.; Anzalone, A.; Cardella, G. [Ist. Nazionale di Fisica Nucleare, Catania (Italy)] [and others
1998-08-01
CHIMERA (Charged Heavy Ions Mass and Energy Resolving Array), a new 4{pi} detector for charged particles is under development at various sites of the Istituto Nazionale di Fisica Nucleare. This paper describes the new data acquisition system built to handle the signals coming out from the detector with a rate up to 1 kHz on almost 5000 electronic channels. The required average throughput for the system is in the order of the 1 MB/s. The used converters allow double-range conversion on 15 bits, in less than 50 {micro}s for all the 64 channels. The FDL link connects the different VME 9U crates performing a programmable hardware readout with a rate up to 100 MB/s. It uses a fast hardware protocol (Sparse Data Scan) to read the data buffers and send them to a FIC 8243 CPU board. A FIC 8243 dual-processor board forwards data (through Ethernet) to the analysis station (266 Mhz Digital AlphaStation or Sun Sparcstation). A DLT (Digital Linear Tape) unit connected to analysis station is used to store data. The new data acquisition system has been tested under beam conditions at the Laboratorio Nazionale del Sud (Catania, Italy) and at GANIL (Caen, France).
Fragmentation studies with the CHIMERA detector at LNS in Catania: recent progress
Energy Technology Data Exchange (ETDEWEB)
Pagano, A.; Alderighi, M.; Amorini, F.; Anzalone, A.; Arena, L.; Auditore, L.; Baran, V.; Bartolucci, M.; Berceanu, I.; Blicharska, J.; Brzychczyk, J.; Bonasera, A.; Borderie, B.; Bougault, R.; Bruno, M.; Cardella, G.; Cavallaro, S.; Chatterjee, M.B.; Chbihi, A.; Cibor, J.; Colonna, M.; D' Agostino, M.; Dayras, R.; De Filippo, E.; Di Toro, M.; Gawlikowicz, W.; Geraci, E.; Giustolisi, F.; Grzeszczuk, A.; Guazzoni, P.; Guinet, D.; Iacono-Manno, M.; Kowalski, S.; La Guidara, E.; Lanzano, G.; Lanzalone, G.; Le Neindre, N.; Li, S.; Lo Nigro, S.; Maiolino, C.; Majka, Z.; Manfredi, G.; Paduszynski, T.; Papa, M.; Petrovici, M.; Piasecki, E.; Pirrone, S.; Planeta, R.; Politi, G.; Pop, A.; Porto, F.; Rivet, M.F.; Rosato, E.; Rizzo, F.; Russo, S.; Russotto, P.; Sassi, M.; Sechi, G.; Simion, V.; Siwek-Wilczynska, K.; Skwira, I.; Sperduto, M.L.; Steckmeyer, J.C.; Swiderski, L.; Trifiro, A.; Trimarchi, M.; Vannini, G.; Vigilante, M.; Wieleczko, J.P.; Wilczynski, J.; Wu, H.; Xiao, Z.; Zetta, L.; Zipper, W
2004-04-05
The new detector CHIMERA, in its final 4{pi} configuration, has been installed at Laboratori Nazionali del Sud (LNS) in Catania in January 2003. Beams of different energies ranging from protons to Au ions were delivered by the Tandem and the Super Conducting Cyclotron for nuclear reaction studies, in agreement with the approval of the Scientific Advisory Committee of LNS. Recent experimental results confirm very low energy thresholds of the trigger (below 0.5 MeV/nucleon), ensured within a wide dynamical range. Good characteristics of identification of light charged particles and heavy fragments have been obtained by using three detection techniques: {delta}E-E, {delta}E-time of flight, and the Pulse-Shape discrimination method. We present results of recent analysis concerning the production of intermediate mass fragments (IMF) in semi-peripheral collisions. Our results combined with theoretical Boltzmann-Nordheim-Vlasov simulations clearly demonstrate the presence of very fast processes of IMF production in the overlapping region of the target and projectile nuclei during re-separation, i.e. in the time scale comparable with the collision time. Evidence for slower, sequential-like production of IMF's is also shown.
Directory of Open Access Journals (Sweden)
Mahesh Wickramasinghe
Full Text Available Dynamical processes in many engineered and living systems take place on complex networks of discrete dynamical units. We present laboratory experiments with a networked chemical system of nickel electrodissolution in which synchronization patterns are recorded in systems with smooth periodic, relaxation periodic, and chaotic oscillators organized in networks composed of up to twenty dynamical units and 140 connections. The reaction system formed domains of synchronization patterns that are strongly affected by the architecture of the network. Spatially organized partial synchronization could be observed either due to densely connected network nodes or through the 'chimera' symmetry breaking mechanism. Relaxation periodic and chaotic oscillators formed structures by dynamical differentiation. We have identified effects of network structure on pattern selection (through permutation symmetry and coupling directness and on formation of hierarchical and 'fuzzy' clusters. With chaotic oscillators we provide experimental evidence that critical coupling strengths at which transition to identical synchronization occurs can be interpreted by experiments with a pair of oscillators and analysis of the eigenvalues of the Laplacian connectivity matrix. The experiments thus provide an insight into the extent of the impact of the architecture of a network on self-organized synchronization patterns.
Establishment of rat embryonic stem cells and making of chimera rats.
Directory of Open Access Journals (Sweden)
Shinobu Ueda
Full Text Available The rat is a reference animal model for physiological studies and for the analysis of multigenic human diseases such as hypertension, diabetes, neurological disorders, and cancer. The rats have long been used in extensive chemical carcinogenesis studies. Thus, the rat embryonic stem (rES cell is an important resource for the study of disease models. Attempts to derive ES cells from various mammals, including the rat, have not succeeded. Here we have established two independent rES cells from Wister rat blastocysts that have undifferentiated characters such as Nanog and Oct3/4 genes expression and they have stage-specific embryonic antigen (SSEA -1, -3, -4, and TRA-1-81 expression. The cells were successfully cultured in an undifferentiated state and can be possible over 18 passages with maintaining more than 40% of normal karyotype. Their pluripotent potential was confirmed by the differentiation into derivatives of the endoderm, mesoderm, and ectoderm. Most importantly, the rES cells are capable of producing chimera rats. Therefore, we established pluripotent rES cell lines that are widely used to produce genetically modified experimental rats for study of human diseases.
Human-animal chimeras: ethical issues about farming chimeric animals bearing human organs.
Bourret, Rodolphe; Martinez, Eric; Vialla, François; Giquel, Chloé; Thonnat-Marin, Aurélie; De Vos, John
2016-06-29
Recent advances in stem cells and gene engineering have paved the way for the generation of interspecies chimeras, such as animals bearing an organ from another species. The production of a rat pancreas by a mouse has demonstrated the feasibility of this approach. The next step will be the generation of larger chimeric animals, such as pigs bearing human organs. Because of the dramatic organ shortage for transplantation, the medical needs for such a transgressive practice are indisputable. However, there are serious technical barriers and complex ethical issues that must be discussed and solved before producing human organs in animals. The main ethical issues are the risks of consciousness and of human features in the chimeric animal due to a too high contribution of human cells to the brain, in the first case, or for instance to limbs, in the second. Another critical point concerns the production of human gametes by such chimeric animals. These worst-case scenarios are obviously unacceptable and must be strictly monitored by careful risk assessment, and, if necessary, technically prevented. The public must be associated with this ethical debate. Scientists and physicians have a critical role in explaining the medical needs, the advantages and limits of this potential medical procedure, and the ethical boundaries that must not be trespassed. If these prerequisites are met, acceptance of such a new, borderline medical procedure may prevail, as happened before for in-vitro fertilization or preimplantation genetic diagnosis.
Mouse embryos and chimera cloned from neural cells in the postnatal cerebral cortex.
Makino, Hatsune; Yamazaki, Yukiko; Hirabayashi, Takahiro; Kaneko, Ryosuke; Hamada, Shun; Kawamura, Yoshimi; Osada, Tomoharu; Yanagimachi, Ryuzo; Yagi, Takeshi
2005-01-01
Cloning of mice has been achieved by transferring nuclei of various types of somatic cell nuclei into enucleated oocytes. However, all attempts to produce live cloned offspring using the nuclei of neurons from adult cerebral cortex have failed. Previously we obtained cloned mice using the nuclei of neural cells collected from fetal cerebral cortex. Here, we attempted to generate cloned mice using differentiated neurons from the cerebral cortex of postnatal (day 0-4) mice. Although we were unable to obtain live cloned pups, many fetuses reached day 10.5 days of development. These fetuses showed various abnormalities such as spherical omission of the neuroepithelium, collapsed lumen of neural tube, and aberrant expressions of marker proteins of neurons. We produced chimeric mice in which some hair cells and kidney cells were originated from differentiated neurons. In chimeric fetuses, LacZ-positive donor cells were in all three germ cell layers. However, chimeras with large contribution of donor-derived cells were not obtained. These results indicate that nuclei of differentiated neurons have lost their developmental totipotency. In other words, the conventional nuclear transfer technique does not allow nuclei of differentiated neurons to undergo complete genomic reprogramming required for normal embryonic development.
Clonal and territorial development of the pancreas as revealed by eGFP-labelled mouse chimeras.
Eberhard, Daniel; Jockusch, Harald
2010-10-01
The clonal structure of the pancreas was analysed in neonatal and adult mouse chimeras in which one partner displayed cell patches expressing green fluorescent protein (eGFP). Coherent growth during pancreatic histogenesis was suggested by the presence of large eGFP-labelled acinar clusters rather than a scattered distribution of individual labelled acinar cells. The adult chimeric pancreas contained monophenotypic acini, whereas surprisingly 5% of acini in neonates were polyclonal. Monophenotypic acini presumably arose by coherent expansion leading to large 3D patches and may not be monoclonal. Islets of Langerhans were oligoclonal at both ages investigated. The proportion of eGFP positive cells within islets did not correlate with that of the surrounding acinar tissue indicating clonal independence of islets from their neighbourhood. The patterns observed argue against a secondary contribution of blood-borne progenitor/stem cells to the acinar compartment during tissue turnover. The different clonal origins of acini and islets are integrated into a model of pancreatic histogenesis.
Dechorionation of medaka embryos and cell transplantation for the generation of chimeras.
Porazinski, Sean R; Wang, Huijia; Furutani-Seiki, Makoto
2010-12-22
Medaka is a small egg-laying freshwater fish that allows both genetic and embryological analyses and is one of the three vertebrate model organisms in which genome-wide phenotype-driven mutant screens were carried out (1). Divergence of functional overlap of related genes between medaka and zebrafish allows identification of novel phenotypes that are unidentifiable in a single species (2), thus medaka and zebrafish are complementary for genetic dissection of the vertebrate genome functions. Manipulation of medaka embryos, such as dechorionation, mounting embryos for imaging and cell transplantation, are key procedures to work on both medaka and zebrafish in a laboratory. Cell transplantation examines cell autonomy of medaka mutations. Chimeras are generated by transplanting labeled cells from donor embryos into unlabeled recipient embryos. Donor cells can be transplanted to specific areas of the recipient embryos based on the fate maps (3) so that clones from transplanted cells can be integrated in the tissue of interest during development. Due to the hard chorion and soft embryos, manipulation of medaka embryos is more involved than in zebrafish. In this video, we show detailed procedures to manipulate medaka embryos.
Biplots in Reduced-Rank Regression
Braak, ter C.J.F.; Looman, C.W.N.
1994-01-01
Regression problems with a number of related response variables are typically analyzed by separate multiple regressions. This paper shows how these regressions can be visualized jointly in a biplot based on reduced-rank regression. Reduced-rank regression combines multiple regression and principal c
Interpretation of Standardized Regression Coefficients in Multiple Regression.
Thayer, Jerome D.
The extent to which standardized regression coefficients (beta values) can be used to determine the importance of a variable in an equation was explored. The beta value and the part correlation coefficient--also called the semi-partial correlation coefficient and reported in squared form as the incremental "r squared"--were compared for…
Inferential Models for Linear Regression
Directory of Open Access Journals (Sweden)
Zuoyi Zhang
2011-09-01
Full Text Available Linear regression is arguably one of the most widely used statistical methods in applications. However, important problems, especially variable selection, remain a challenge for classical modes of inference. This paper develops a recently proposed framework of inferential models (IMs in the linear regression context. In general, an IM is able to produce meaningful probabilistic summaries of the statistical evidence for and against assertions about the unknown parameter of interest and, moreover, these summaries are shown to be properly calibrated in a frequentist sense. Here we demonstrate, using simple examples, that the IM framework is promising for linear regression analysis --- including model checking, variable selection, and prediction --- and for uncertain inference in general.
[Is regression of atherosclerosis possible?].
Thomas, D; Richard, J L; Emmerich, J; Bruckert, E; Delahaye, F
1992-10-01
Experimental studies have shown the regression of atherosclerosis in animals given a cholesterol-rich diet and then given a normal diet or hypolipidemic therapy. Despite favourable results of clinical trials of primary prevention modifying the lipid profile, the concept of atherosclerosis regression in man remains very controversial. The methodological approach is difficult: this is based on angiographic data and requires strict standardisation of angiographic views and reliable quantitative techniques of analysis which are available with image processing. Several methodologically acceptable clinical coronary studies have shown not only stabilisation but also regression of atherosclerotic lesions with reductions of about 25% in total cholesterol levels and of about 40% in LDL cholesterol levels. These reductions were obtained either by drugs as in CLAS (Cholesterol Lowering Atherosclerosis Study), FATS (Familial Atherosclerosis Treatment Study) and SCOR (Specialized Center of Research Intervention Trial), by profound modifications in dietary habits as in the Lifestyle Heart Trial, or by surgery (ileo-caecal bypass) as in POSCH (Program On the Surgical Control of the Hyperlipidemias). On the other hand, trials with non-lipid lowering drugs such as the calcium antagonists (INTACT, MHIS) have not shown significant regression of existing atherosclerotic lesions but only a decrease on the number of new lesions. The clinical benefits of these regression studies are difficult to demonstrate given the limited period of observation, relatively small population numbers and the fact that in some cases the subjects were asymptomatic. The decrease in the number of cardiovascular events therefore seems relatively modest and concerns essentially subjects who were symptomatic initially. The clinical repercussion of studies of prevention involving a single lipid factor is probably partially due to the reduction in progression and anatomical regression of the atherosclerotic plaque
Nonparametric regression with filtered data
Linton, Oliver; Nielsen, Jens Perch; Van Keilegom, Ingrid; 10.3150/10-BEJ260
2011-01-01
We present a general principle for estimating a regression function nonparametrically, allowing for a wide variety of data filtering, for example, repeated left truncation and right censoring. Both the mean and the median regression cases are considered. The method works by first estimating the conditional hazard function or conditional survivor function and then integrating. We also investigate improved methods that take account of model structure such as independent errors and show that such methods can improve performance when the model structure is true. We establish the pointwise asymptotic normality of our estimators.
Logistic regression for circular data
Al-Daffaie, Kadhem; Khan, Shahjahan
2017-05-01
This paper considers the relationship between a binary response and a circular predictor. It develops the logistic regression model by employing the linear-circular regression approach. The maximum likelihood method is used to estimate the parameters. The Newton-Raphson numerical method is used to find the estimated values of the parameters. A data set from weather records of Toowoomba city is analysed by the proposed methods. Moreover, a simulation study is considered. The R software is used for all computations and simulations.
Quasi-least squares regression
Shults, Justine
2014-01-01
Drawing on the authors' substantial expertise in modeling longitudinal and clustered data, Quasi-Least Squares Regression provides a thorough treatment of quasi-least squares (QLS) regression-a computational approach for the estimation of correlation parameters within the framework of generalized estimating equations (GEEs). The authors present a detailed evaluation of QLS methodology, demonstrating the advantages of QLS in comparison with alternative methods. They describe how QLS can be used to extend the application of the traditional GEE approach to the analysis of unequally spaced longitu
Regression of lumbar disk herniation
Directory of Open Access Journals (Sweden)
G. Yu Evzikov
2015-01-01
Full Text Available Compression of the spinal nerve root, giving rise to pain and sensory and motor disorders in the area of its innervation is the most vivid manifestation of herniated intervertebral disk. Different treatment modalities, including neurosurgery, for evolving these conditions are discussed. There has been recent evidence that spontaneous regression of disk herniation can regress. The paper describes a female patient with large lateralized disc extrusion that has caused compression of the nerve root S1, leading to obvious myotonic and radicular syndrome. Magnetic resonance imaging has shown that the clinical manifestations of discogenic radiculopathy, as well myotonic syndrome and morphological changes completely regressed 8 months later. The likely mechanism is inflammation-induced resorption of a large herniated disk fragment, which agrees with the data available in the literature. A decision to perform neurosurgery for which the patient had indications was made during her first consultation. After regression of discogenic radiculopathy, there was only moderate pain caused by musculoskeletal diseases (facet syndrome, piriformis syndrome that were successfully eliminated by minimally invasive techniques.
Heteroscedasticity checks for regression models
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
For checking on heteroscedasticity in regression models, a unified approach is proposed to constructing test statistics in parametric and nonparametric regression models. For nonparametric regression, the test is not affected sensitively by the choice of smoothing parameters which are involved in estimation of the nonparametric regression function. The limiting null distribution of the test statistic remains the same in a wide range of the smoothing parameters. When the covariate is one-dimensional, the tests are, under some conditions, asymptotically distribution-free. In the high-dimensional cases, the validity of bootstrap approximations is investigated. It is shown that a variant of the wild bootstrap is consistent while the classical bootstrap is not in the general case, but is applicable if some extra assumption on conditional variance of the squared error is imposed. A simulation study is performed to provide evidence of how the tests work and compare with tests that have appeared in the literature. The approach may readily be extended to handle partial linear, and linear autoregressive models.
Cactus: An Introduction to Regression
Hyde, Hartley
2008-01-01
When the author first used "VisiCalc," the author thought it a very useful tool when he had the formulas. But how could he design a spreadsheet if there was no known formula for the quantities he was trying to predict? A few months later, the author relates he learned to use multiple linear regression software and suddenly it all clicked into…
Growth Regression and Economic Theory
Elbers, Chris; Gunning, Jan Willem
2002-01-01
In this note we show that the standard, loglinear growth regression specificationis consistent with one and only one model in the class of stochastic Ramsey models. Thismodel is highly restrictive: it requires a Cobb-Douglas technology and a 100% depreciationrate and it implies that risk does not af
Correlation Weights in Multiple Regression
Waller, Niels G.; Jones, Jeff A.
2010-01-01
A general theory on the use of correlation weights in linear prediction has yet to be proposed. In this paper we take initial steps in developing such a theory by describing the conditions under which correlation weights perform well in population regression models. Using OLS weights as a comparison, we define cases in which the two weighting…
Ridge Regression for Interactive Models.
Tate, Richard L.
1988-01-01
An exploratory study of the value of ridge regression for interactive models is reported. Assuming that the linear terms in a simple interactive model are centered to eliminate non-essential multicollinearity, a variety of common models, representing both ordinal and disordinal interactions, are shown to have "orientations" that are favorable to…
Logistic regression: a brief primer.
Stoltzfus, Jill C
2011-10-01
Regression techniques are versatile in their application to medical research because they can measure associations, predict outcomes, and control for confounding variable effects. As one such technique, logistic regression is an efficient and powerful way to analyze the effect of a group of independent variables on a binary outcome by quantifying each independent variable's unique contribution. Using components of linear regression reflected in the logit scale, logistic regression iteratively identifies the strongest linear combination of variables with the greatest probability of detecting the observed outcome. Important considerations when conducting logistic regression include selecting independent variables, ensuring that relevant assumptions are met, and choosing an appropriate model building strategy. For independent variable selection, one should be guided by such factors as accepted theory, previous empirical investigations, clinical considerations, and univariate statistical analyses, with acknowledgement of potential confounding variables that should be accounted for. Basic assumptions that must be met for logistic regression include independence of errors, linearity in the logit for continuous variables, absence of multicollinearity, and lack of strongly influential outliers. Additionally, there should be an adequate number of events per independent variable to avoid an overfit model, with commonly recommended minimum "rules of thumb" ranging from 10 to 20 events per covariate. Regarding model building strategies, the three general types are direct/standard, sequential/hierarchical, and stepwise/statistical, with each having a different emphasis and purpose. Before reaching definitive conclusions from the results of any of these methods, one should formally quantify the model's internal validity (i.e., replicability within the same data set) and external validity (i.e., generalizability beyond the current sample). The resulting logistic regression model
Regression Verification Using Impact Summaries
Backes, John; Person, Suzette J.; Rungta, Neha; Thachuk, Oksana
2013-01-01
Regression verification techniques are used to prove equivalence of syntactically similar programs. Checking equivalence of large programs, however, can be computationally expensive. Existing regression verification techniques rely on abstraction and decomposition techniques to reduce the computational effort of checking equivalence of the entire program. These techniques are sound but not complete. In this work, we propose a novel approach to improve scalability of regression verification by classifying the program behaviors generated during symbolic execution as either impacted or unimpacted. Our technique uses a combination of static analysis and symbolic execution to generate summaries of impacted program behaviors. The impact summaries are then checked for equivalence using an o-the-shelf decision procedure. We prove that our approach is both sound and complete for sequential programs, with respect to the depth bound of symbolic execution. Our evaluation on a set of sequential C artifacts shows that reducing the size of the summaries can help reduce the cost of software equivalence checking. Various reduction, abstraction, and compositional techniques have been developed to help scale software verification techniques to industrial-sized systems. Although such techniques have greatly increased the size and complexity of systems that can be checked, analysis of large software systems remains costly. Regression analysis techniques, e.g., regression testing [16], regression model checking [22], and regression verification [19], restrict the scope of the analysis by leveraging the differences between program versions. These techniques are based on the idea that if code is checked early in development, then subsequent versions can be checked against a prior (checked) version, leveraging the results of the previous analysis to reduce analysis cost of the current version. Regression verification addresses the problem of proving equivalence of closely related program
CONSTRUCTION OF HU-PBL/SCID CHIMERAS AND DEVELOPMENT OF EBV-RELATED LYMPHOMAS
Institute of Scientific and Technical Information of China (English)
Run-liang Gan; Ke Lan; Zhi-hua Yin; Li-jiang Wang; Ying Song; Kai-tai Yao
2005-01-01
Objective To construct hu-PBL/SCID chimeras and to investigate the development of lymphoma and oncogenicity of the Epstein-Barr virus (EBV).Mtehods Human peripheral blood lymphocytes (PBLs) were isolated from healthy adult donors and transplanted intraperitoneally into severe combined immunodeficient (SCID) mice. Mice with hu-PBL engraftment from healthy EBV seronegative donors were injected intraperitoneally with EBV-containing supematant from suspension culture of B95-8 cell line (active infection), whereas mice receiving lymphocytes from healthy EBV seropositive donors were not re-infected with B95-8 derived EBV (latent infection). Pathological examination and molecular analysis were performed on experimental animals and induced neoplasms.Results In the early stage of this experiment, 12 mice died of acute graft-versus-host disease, mortality was 34.3%(12/35 mice) with an average life span of 17.5 days. In 19 survival hu-PBL/SCID chimeric recipients from 12 healthy donors,tumor incidence was 84.2% (16/19 mice). The average survival time of tumor-bearing mice was 65.5 days. EBV-related neoplasms in SCID mice were nodular tumors with aggressive and fatal features. Histological morphology of tumors exhibited diffuse large cell lymphomas. Immunohistochemistry revealed that LCA (CD45) and L26 (CD20) were positive, but both PS1 (CD3) and UCHL-1 (CD45RO) were negative, and EBV products ZEBRA, LMP1, and EBNA2 were expressed in a small number of tumor cells. EB virus particles were seen in the nuclei of some tumor cells by electron microscopy, and EBV DNA could be amplified in the tumor tissues by PCR. In situ hybridization indicated that the nuclei of tumor cells contained human-specific Alu sequence.Conclusions EBV-induced tumors were human B-cell malignant lymphomas. We obtained direct causative evidence dealing with EBV-associated tumor deriving from normal human cells.
Magnetorotational dynamo chimeras. The missing link to turbulent accretion disk dynamo models?
Riols, A.; Rincon, F.; Cossu, C.; Lesur, G.; Ogilvie, G. I.; Longaretti, P.-Y.
2017-02-01
In Keplerian accretion disks, turbulence and magnetic fields may be jointly excited through a subcritical dynamo mechanisminvolving magnetorotational instability (MRI). This dynamo may notably contribute to explaining the time-variability of various accreting systems, as high-resolution simulations of MRI dynamo turbulence exhibit statistical self-organization into large-scale cyclic dynamics. However, understanding the physics underlying these statistical states and assessing their exact astrophysical relevance is theoretically challenging. The study of simple periodic nonlinear MRI dynamo solutions has recently proven useful in this respect, and has highlighted the role of turbulent magnetic diffusion in the seeming impossibility of a dynamo at low magnetic Prandtl number (Pm), a common regime in disks. Arguably though, these simple laminar structures may not be fully representative of the complex, statistically self-organized states expected in astrophysical regimes. Here, we aim at closing this seeming discrepancy by reporting the numerical discovery of exactly periodic, yet semi-statistical "chimeral MRI dynamo states" which are the organized outcome of a succession of MRI-unstable, non-axisymmetric dynamical stages of different forms and amplitudes. Interestingly, these states, while reminiscent of the statistical complexity of turbulent simulations, involve the same physical principles as simpler laminar cycles, and their analysis further confirms the theory that subcritical turbulent magnetic diffusion impedes the sustainment of an MRI dynamo at low Pm. Overall, chimera dynamo cycles therefore offer an unprecedented dual physical and statistical perspective on dynamos in rotating shear flows, which may prove useful in devising more accurate, yet intuitive mean-field models of time-dependent turbulent disk dynamos. Movies associated to Fig. 1 are available at http://www.aanda.org
Polynomial Regressions and Nonsense Inference
Directory of Open Access Journals (Sweden)
Daniel Ventosa-Santaulària
2013-11-01
Full Text Available Polynomial specifications are widely used, not only in applied economics, but also in epidemiology, physics, political analysis and psychology, just to mention a few examples. In many cases, the data employed to estimate such specifications are time series that may exhibit stochastic nonstationary behavior. We extend Phillips’ results (Phillips, P. Understanding spurious regressions in econometrics. J. Econom. 1986, 33, 311–340. by proving that an inference drawn from polynomial specifications, under stochastic nonstationarity, is misleading unless the variables cointegrate. We use a generalized polynomial specification as a vehicle to study its asymptotic and finite-sample properties. Our results, therefore, lead to a call to be cautious whenever practitioners estimate polynomial regressions.
Quantile Regression With Measurement Error
Wei, Ying
2009-08-27
Regression quantiles can be substantially biased when the covariates are measured with error. In this paper we propose a new method that produces consistent linear quantile estimation in the presence of covariate measurement error. The method corrects the measurement error induced bias by constructing joint estimating equations that simultaneously hold for all the quantile levels. An iterative EM-type estimation algorithm to obtain the solutions to such joint estimation equations is provided. The finite sample performance of the proposed method is investigated in a simulation study, and compared to the standard regression calibration approach. Finally, we apply our methodology to part of the National Collaborative Perinatal Project growth data, a longitudinal study with an unusual measurement error structure. © 2009 American Statistical Association.
Heteroscedasticity checks for regression models
Institute of Scientific and Technical Information of China (English)
ZHU; Lixing
2001-01-01
［1］Carroll, R. J., Ruppert, D., Transformation and Weighting in Regression, New York: Chapman and Hall, 1988.［2］Cook, R. D., Weisberg, S., Diagnostics for heteroscedasticity in regression, Biometrika, 1988, 70: 1—10.［3］Davidian, M., Carroll, R. J., Variance function estimation, J. Amer. Statist. Assoc., 1987, 82: 1079—1091.［4］Bickel, P., Using residuals robustly I: Tests for heteroscedasticity, Ann. Statist., 1978, 6: 266—291.［5］Carroll, R. J., Ruppert, D., On robust tests for heteroscedasticity, Ann. Statist., 1981, 9: 205—209.［6］Eubank, R. L., Thomas, W., Detecting heteroscedasticity in nonparametric regression, J. Roy. Statist. Soc., Ser. B, 1993, 55: 145—155.［7］Diblasi, A., Bowman, A., Testing for constant variance in a linear model, Statist. and Probab. Letters, 1997, 33: 95—103.［8］Dette, H., Munk, A., Testing heteoscedasticity in nonparametric regression, J. R. Statist. Soc. B, 1998, 60: 693—708.［9］Müller, H. G., Zhao, P. L., On a semi-parametric variance function model and a test for heteroscedasticity, Ann. Statist., 1995, 23: 946—967.［10］Stute, W., Manteiga, G., Quindimil, M. P., Bootstrap approximations in model checks for regression, J. Amer. Statist. Asso., 1998, 93: 141—149.［11］Stute, W., Thies, G., Zhu, L. X., Model checks for regression: An innovation approach, Ann. Statist., 1998, 26: 1916—1939.［12］Shorack, G. R., Wellner, J. A., Empirical Processes with Applications to Statistics, New York: Wiley, 1986.［13］Efron, B., Bootstrap methods: Another look at the jackknife, Ann. Statist., 1979, 7: 1—26.［14］Wu, C. F. J., Jackknife, bootstrap and other re-sampling methods in regression analysis, Ann. Statist., 1986, 14: 1261—1295.［15］H rdle, W., Mammen, E., Comparing non-parametric versus parametric regression fits, Ann. Statist., 1993, 21: 1926—1947.［16］Liu, R. Y., Bootstrap procedures under some non-i.i.d. models, Ann. Statist., 1988, 16: 1696—1708.［17
Clustered regression with unknown clusters
Barman, Kishor
2011-01-01
We consider a collection of prediction experiments, which are clustered in the sense that groups of experiments ex- hibit similar relationship between the predictor and response variables. The experiment clusters as well as the regres- sion relationships are unknown. The regression relation- ships define the experiment clusters, and in general, the predictor and response variables may not exhibit any clus- tering. We call this prediction problem clustered regres- sion with unknown clusters (CRUC) and in this paper we focus on linear regression. We study and compare several methods for CRUC, demonstrate their applicability to the Yahoo Learning-to-rank Challenge (YLRC) dataset, and in- vestigate an associated mathematical model. CRUC is at the crossroads of many prior works and we study several prediction algorithms with diverse origins: an adaptation of the expectation-maximization algorithm, an approach in- spired by K-means clustering, the singular value threshold- ing approach to matrix rank minimization u...
Immunogenicity of a West Nile Virus DIII-Cholera Toxin A2/B Chimera after Intranasal Delivery
Directory of Open Access Journals (Sweden)
Juliette K. Tinker
2014-04-01
Full Text Available West Nile virus (WNV causes potentially fatal neuroinvasive disease and persists at endemic levels in many parts of the world. Despite advances in our understanding of WNV pathogenesis, there remains a significant need for a human vaccine. The domain III (DIII region of the WNV envelope protein contains epitopes that are the target of neutralizing antibodies. We have constructed a chimeric fusion of the non-toxic cholera toxin (CT CTA2/B domains to DIII for investigation as a novel mucosally-delivered WNV vaccine. Purification and assembly of the chimera, as well as receptor-binding and antigen delivery, were verified by western blot, GM1 ELISA and confocal microscopy. Groups of BALB/c mice were immunized intranasally with DIII-CTA2/B, DIII, DIII mixed with CTA2/B, or CTA2/B control, and boosted at 10 days. Analysis of serum IgG after 14 and 45 days revealed that mucosal immunization with DIII-CTA2/B induced significant DIII-specific humoral immunity and drove isotype switching to IgG2a. The DIII-CTA2/B chimera also induced antigen-specific IgM and IgA responses. Bactericidal assays indicate that the DIII-CTA2/B immunized mice produced DIII-specific antibodies that can trigger complement-mediated killing. A dose escalation resulted in increased DIII-specific serum IgG titers on day 45. DIII antigen alone, in the absence of adjuvant, also induced significant systemic responses after intranasal delivery. Our results indicate that the DIII-CTA2/B chimera is immunogenic after intranasal delivery and merits further investigation as a novel WNV vaccine candidate.
Guo, S; Ives, D H
1998-10-01
The heterodimeric subunits of deoxyadenosine kinase (dAK)-deoxyguanosine kinase (dGK) from Lactobacillus acidophilus R-26 exhibit contrasting conformations manifested in the nearly unidirectional heterotropic activation of dAK when dGK binds deoxyguanosine. This is mediated, in part, by the conserved Ras switch I-like sequence (residues 153-161) [Guo et al. (1997) J. Biol. Chem. 272, 6890-6897]. In an attempt to identify domains differentiating the specificities of dAK and dGK, we constructed several chimeras splicing heterodimeric dAK within this region. In Chimera-III, dAK residues 120-170 were replaced by the homologous section of dGK. dAK activity was elevated 40%, but although it retained its original specificity and Km values, it could no longer be activated by deoxyguanosine. Moreover, both the activated dAK and the "dAK" of Chimera-III exhibited (i) an increased Ks for the leading substrate ATP-Mg2+, suggesting the formation of intermediate enzyme species along their respective kinetic pathways, and (ii) broadened and lower pH optima for the dAK activities. These observations further indicate the importance of dAK residues 120-170, including the Ras-like segment, in catalysis and heterotropic activation. The other conformational properties of dAK (e.g. self-inactivity and MgATP being the leading substrate) were unaltered by this substitution, thus localizing the responsible domains even further upstream.
Immunogenicity of a West Nile virus DIII-cholera toxin A2/B chimera after intranasal delivery.
Tinker, Juliette K; Yan, Jie; Knippel, Reece J; Panayiotou, Panos; Cornell, Kenneth A
2014-04-22
West Nile virus (WNV) causes potentially fatal neuroinvasive disease and persists at endemic levels in many parts of the world. Despite advances in our understanding of WNV pathogenesis, there remains a significant need for a human vaccine. The domain III (DIII) region of the WNV envelope protein contains epitopes that are the target of neutralizing antibodies. We have constructed a chimeric fusion of the non-toxic cholera toxin (CT) CTA2/B domains to DIII for investigation as a novel mucosally-delivered WNV vaccine. Purification and assembly of the chimera, as well as receptor-binding and antigen delivery, were verified by western blot, GM1 ELISA and confocal microscopy. Groups of BALB/c mice were immunized intranasally with DIII-CTA2/B, DIII, DIII mixed with CTA2/B, or CTA2/B control, and boosted at 10 days. Analysis of serum IgG after 14 and 45 days revealed that mucosal immunization with DIII-CTA2/B induced significant DIII-specific humoral immunity and drove isotype switching to IgG2a. The DIII-CTA2/B chimera also induced antigen-specific IgM and IgA responses. Bactericidal assays indicate that the DIII-CTA2/B immunized mice produced DIII-specific antibodies that can trigger complement-mediated killing. A dose escalation resulted in increased DIII-specific serum IgG titers on day 45. DIII antigen alone, in the absence of adjuvant, also induced significant systemic responses after intranasal delivery. Our results indicate that the DIII-CTA2/B chimera is immunogenic after intranasal delivery and merits further investigation as a novel WNV vaccine candidate.
Robust nonlinear regression in applications
Lim, Changwon; Sen, Pranab K.; Peddada, Shyamal D.
2013-01-01
Robust statistical methods, such as M-estimators, are needed for nonlinear regression models because of the presence of outliers/influential observations and heteroscedasticity. Outliers and influential observations are commonly observed in many applications, especially in toxicology and agricultural experiments. For example, dose response studies, which are routinely conducted in toxicology and agriculture, sometimes result in potential outliers, especially in the high dose gr...
DEFF Research Database (Denmark)
Pedersen, Lene; Johann, Stephen V; van Zeijl, Marja
1995-01-01
in several of their predicted extracellular loops, with the highest degree of divergence in region A. Chimeras were made between the two genes to further investigate the role of Glvr1 region A in defining receptor specificity for GALV and FeLV-B and to map which regions of Glvr2 control receptor specificity...... for A-MLVs. Region A from Glvr1 was sufficient to confer receptor specificity for GALV upon Glvr2, with the same chimera failing to act as a receptor for FeLV-B. However, introduction of additional N- or C-terminal Glvr1-encoding sequences in addition to Glvr1 region A-encoding sequences resulted......-MLV infection upon Glvr1. Surprisingly, though GALV/FeLV-B and A-MLV belong to different interference groups, some chimeras functioned as receptors for all three viruses...
DEFF Research Database (Denmark)
Jensen, Anne Bjørnskov; Hoestgaard-Jensen, Kirsten; Jensen, Anders A.
2014-01-01
by their inefficient functional expression in vitro. In the present study we have characterized and compared the pharmacological properties displayed by α6β4 and α6β4β3 nicotinic acetylcholine receptors assembled in tsA201 cells from the classical α6/α3 chimera (C1) and two novel α6/α3 chimeras (C6F223L and C16F223L...... should be made keeping the molecular modifications in the α6 surrogate subunits in mind, this study sheds light on the pharmacological properties of α6β4⁎ nicotinic acetylcholine receptors and demonstrates the applicability of the C6F223L and C16F223L chimeras for studies of these receptors....
Astronomical Methods for Nonparametric Regression
Steinhardt, Charles L.; Jermyn, Adam
2017-01-01
I will discuss commonly used techniques for nonparametric regression in astronomy. We find that several of them, particularly running averages and running medians, are generically biased, asymmetric between dependent and independent variables, and perform poorly in recovering the underlying function, even when errors are present only in one variable. We then examine less-commonly used techniques such as Multivariate Adaptive Regressive Splines and Boosted Trees and find them superior in bias, asymmetry, and variance both theoretically and in practice under a wide range of numerical benchmarks. In this context the chief advantage of the common techniques is runtime, which even for large datasets is now measured in microseconds compared with milliseconds for the more statistically robust techniques. This points to a tradeoff between bias, variance, and computational resources which in recent years has shifted heavily in favor of the more advanced methods, primarily driven by Moore's Law. Along these lines, we also propose a new algorithm which has better overall statistical properties than all techniques examined thus far, at the cost of significantly worse runtime, in addition to providing guidance on choosing the nonparametric regression technique most suitable to any specific problem. We then examine the more general problem of errors in both variables and provide a new algorithm which performs well in most cases and lacks the clear asymmetry of existing non-parametric methods, which fail to account for errors in both variables.
Hagan-Brown, Abena; Favaretto, Maddalena; Borry, Pascal
2017-07-01
A recently published article in the journal Cell by scientists from the Salk Institute highlighted the successful integration of stem cells from humans in pig embryos. This marks the first step toward the goal of growing human organs in animals for transplantation. There has, to date, been no research performed on the presentation of this breakthrough in the media. We thus assessed early newspaper coverage of the chimera study, looking into the descriptions as well as the benefits and concerns raised by the study mentioned by newspaper sources. We looked at newspaper coverage of the human-pig chimera study in the two weeks after the publication of the article describing the breakthrough in Cell. This time period spanned from January 26 to February 9, 2017. We used the LexisNexis Academic database and identified articles using the search string "hybrid OR chimera AND pig OR human OR embryo." The relevant articles were analyzed using qualitative content analysis. Two researchers openly coded the articles independently using themes that emerged from the raw texts. Our search yielded 31 unique articles, after extensive screening for relevance and duplicates. Through our analysis, we were able to identify several themes in a majority of the texts. Almost every article gave descriptive information about the chimera experiment with details about the study findings. All of the articles mentioned the benefits of the study, citing both immediate- and long-term goals, which included creating transplantable human organs, disease and drug development, and personalized medicine, among others. Some of the articles highlighted some ethical, social, and health concerns that the study and its future implications pose. Many of the articles also offered reassurances over the concerns brought up by the experiment. Our results appeared to align with similar research performed on the media representation of sensitive scientific news coverage. We also explored the inconsistency between
Particle identification method in the CsI(Tl) scintillator used for the CHIMERA 4{pi} detector
Energy Technology Data Exchange (ETDEWEB)
Alderighi, M.; Anzalone, A.; Basssini, R.; Berceanu, I.; Blicharska, J.; Boiano, C.; Borderie, B.; Bougault, R.; Bruno, M.; Cali, C.; Cardella, G. E-mail: cardella@ct.infn.it; Cavallaro, Sl.; D' Agostino, M.; D' Andrea, M.; Dayras, R.; De Filippo, E.; Fichera, F.; Geraci, E.; Giustolisi, F.; Grzeszczuk, A.; Guardone, N.; Guazzoni, P.; Guinet, D.; Iacono-Manno, C.M.; Kowalski, S.; La Guidara, E.; Lanchais, A.L.; Lanzalone, G.; Lanzano, G.; Le Neindre, N.; Li, S.; Maiolino, C.; Majka, Z.; Manfredi, G.; Nicotra, D.; Paduszynski, T.; Pagano, A.; Papa, M.; Petrovici, C.M.; Piasecki, E.; Pirrone, S.; Politi, G.; Pop, A.; Porto, F.; Rivet, M.F.; Rosato, E.; Sacca, G.; Sechi, G.; Simion, V.; Sperduto, M.L.; Steckmeyer, J.C.; Trifiro, A.; Trimarchi, M.; Urso, S.; Vannini, G.; Vigilante, M.; Wilczynski, J.; Wu, H.; Xiao, Z.; Zetta, L.; Zipper, W
2002-08-21
The charged particle identification obtained by the analysis of signals coming from the CsI(Tl) detectors of the CHIMERA 4{pi} heavy-ion detector is presented. A simple double-gate integration method, with the use of the cyclotron radiofrequency as reference time, results in low thresholds for isotopic particle identification. The dependence of the identification quality on the gate generation timing is discussed. Isotopic identification of light ions up to Beryllium is clearly seen. For the first time also the identification of Z=5 particles is observed. The identification of neutrons interacting with CsI(Tl) by (n,{alpha}) and (n,{gamma}) reactions is also discussed.
Particle identification method in the CsI(Tl) scintillator used for the CHIMERA 4 pi detector
Alderighi, M; Basssini, R; Berceanu, I; Blicharska, J; Boiano, C; Borderie, B; Bougault, R; Bruno, M; Cali, C; Cardella, G; Cavallaro, S; D'Agostino, M; D'andrea, M; Dayras, R; De Filippo, E; Fichera, F; Geraci, E; Giustolisi, F; Grzeszczuk, A; Guardone, N; Guazzoni, P; Guinet, D; Iacono-Manno, M; Kowalski, S; La Guidara, E; Lanchais, A L; Lanzalone, G; Lanzanò, G; Le Neindre, N; Li, S; Maiolino, C; Majka, Z; Manfredi, G; Nicotra, D; Paduszynski, T; Pagano, A; Papa, M; Petrovici, C M; Piasecki, E; Pirrone, S; Politi, G; Pop, A; Porto, F; Rivet, M F; Rosato, E; Sacca, G; Sechi, G; Simion, V; Sperduto, M L; Steckmeyer, J C; Trifiró, A; Trimarchi, M; Urso, S; Vannini, G; Vigilante, M; Wilczynski, J; Wu, H; Xiao, Z; Zetta, L; Zipper, W
2002-01-01
The charged particle identification obtained by the analysis of signals coming from the CsI(Tl) detectors of the CHIMERA 4 pi heavy-ion detector is presented. A simple double-gate integration method, with the use of the cyclotron radiofrequency as reference time, results in low thresholds for isotopic particle identification. The dependence of the identification quality on the gate generation timing is discussed. Isotopic identification of light ions up to Beryllium is clearly seen. For the first time also the identification of Z=5 particles is observed. The identification of neutrons interacting with CsI(Tl) by (n,alpha) and (n,gamma) reactions is also discussed.
Genetics Home Reference: caudal regression syndrome
... Twitter Home Health Conditions caudal regression syndrome caudal regression syndrome Enable Javascript to view the expand/collapse ... Download PDF Open All Close All Description Caudal regression syndrome is a disorder that impairs the development ...
On Weighted Support Vector Regression
DEFF Research Database (Denmark)
Han, Xixuan; Clemmensen, Line Katrine Harder
2014-01-01
We propose a new type of weighted support vector regression (SVR), motivated by modeling local dependencies in time and space in prediction of house prices. The classic weights of the weighted SVR are added to the slack variables in the objective function (OF‐weights). This procedure directly...... the differences and similarities of the two types of weights by demonstrating the connection between the Least Absolute Shrinkage and Selection Operator (LASSO) and the SVR. We show that an SVR problem can be transformed to a LASSO problem plus a linear constraint and a box constraint. We demonstrate...
Multiatlas segmentation as nonparametric regression.
Awate, Suyash P; Whitaker, Ross T
2014-09-01
This paper proposes a novel theoretical framework to model and analyze the statistical characteristics of a wide range of segmentation methods that incorporate a database of label maps or atlases; such methods are termed as label fusion or multiatlas segmentation. We model these multiatlas segmentation problems as nonparametric regression problems in the high-dimensional space of image patches. We analyze the nonparametric estimator's convergence behavior that characterizes expected segmentation error as a function of the size of the multiatlas database. We show that this error has an analytic form involving several parameters that are fundamental to the specific segmentation problem (determined by the chosen anatomical structure, imaging modality, registration algorithm, and label-fusion algorithm). We describe how to estimate these parameters and show that several human anatomical structures exhibit the trends modeled analytically. We use these parameter estimates to optimize the regression estimator. We show that the expected error for large database sizes is well predicted by models learned on small databases. Thus, a few expert segmentations can help predict the database sizes required to keep the expected error below a specified tolerance level. Such cost-benefit analysis is crucial for deploying clinical multiatlas segmentation systems.
Premalatha, K; Chandrasekar, V K; Senthilvelan, M; Lakshmanan, M
2016-07-01
We investigate the emergence of different kinds of imperfectly synchronized states and chimera states in two interacting populations of nonlocally coupled Stuart-Landau oscillators. We find that the complete synchronization in population I and existence of solitary oscillators which escape from the synchronized group in population II lead to imperfectly synchronized states for sufficiently small values of nonisochronicity parameter. Interestingly, upon increasing the strength of this parameter further there occurs an onset of mixed imperfectly synchronized states where the solitary oscillators occur from both the populations. Synchronized oscillators from both the populations are locked to a common average frequency. In both cases of imperfectly synchronized states, synchronized oscillators exhibit periodic motion while the solitary oscillators are quasiperiodic in nature. In this region, for spatially prepared initial conditions, we can observe the mixed chimera states where the coexistence of synchronized and desynchronized oscillations occur from both the populations. On the other hand, imperfectly synchronized states are not always stable, and they can drift aperiodically due to instability caused by an increase of nonisochronicity parameter. We observe that these states are robust to the introduction of frequency mismatch between the two populations.
Ho, Michelle L; Adler, Benjamin A; Torre, Michael L; Silberg, Jonathan J; Suh, Junghae
2013-12-20
Adeno-associated virus (AAV) recombination can result in chimeric capsid protein subunits whose ability to assemble into an oligomeric capsid, package a genome, and transduce cells depends on the inheritance of sequence from different AAV parents. To develop quantitative design principles for guiding site-directed recombination of AAV capsids, we have examined how capsid structural perturbations predicted by the SCHEMA algorithm correlate with experimental measurements of disruption in seventeen chimeric capsid proteins. In our small chimera population, created by recombining AAV serotypes 2 and 4, we found that protection of viral genomes and cellular transduction were inversely related to calculated disruption of the capsid structure. Interestingly, however, we did not observe a correlation between genome packaging and calculated structural disruption; a majority of the chimeric capsid proteins formed at least partially assembled capsids and more than half packaged genomes, including those with the highest SCHEMA disruption. These results suggest that the sequence space accessed by recombination of divergent AAV serotypes is rich in capsid chimeras that assemble into 60-mer capsids and package viral genomes. Overall, the SCHEMA algorithm may be useful for delineating quantitative design principles to guide the creation of libraries enriched in genome-protecting virus nanoparticles that can effectively transduce cells. Such improvements to the virus design process may help advance not only gene therapy applications but also other bionanotechnologies dependent upon the development of viruses with new sequences and functions.
Krishnarjuna, Bankala; Andrew, Dean; MacRaild, Christopher A.; Morales, Rodrigo A. V.; Beeson, James G.; Anders, Robin F.; Richards, Jack S.; Norton, Raymond S.
2016-01-01
MSP2 is an intrinsically disordered protein that is abundant on the merozoite surface and essential to the parasite Plasmodium falciparum. Naturally-acquired antibody responses to MSP2 are biased towards dimorphic sequences within the central variable region of MSP2 and have been linked to naturally-acquired protection from malaria. In a phase IIb study, an MSP2-containing vaccine induced an immune response that reduced parasitemias in a strain-specific manner. A subsequent phase I study of a vaccine that contained both dimorphic forms of MSP2 induced antibodies that exhibited functional activity in vitro. We have assessed the contribution of the conserved and variable regions of MSP2 to the generation of a strain-transcending antibody response by generating MSP2 chimeras that included conserved and variable regions of the 3D7 and FC27 alleles. Robust anti-MSP2 antibody responses targeting both conserved and variable regions were generated in mice, although the fine specificity and the balance of responses to these regions differed amongst the constructs tested. We observed significant differences in antibody subclass distribution in the responses to these chimeras. Our results suggest that chimeric MSP2 antigens can elicit a broad immune response suitable for protection against different strains of P. falciparum. PMID:26865062
New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.
Ashelford, Kevin E; Chuzhanova, Nadia A; Fry, John C; Jones, Antonia J; Weightman, Andrew J
2006-09-01
A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.
CHIMERA: a wide-field, multi-color, high-speed photometer at the prime focus of the Hale telescope
Harding, Leon K; Milburn, Jennifer; Gardner, Paul; Konidaris, Nick; Singh, Navtej; Shao, Michael; Sandhu, Jagmit; Kyne, Gillian; Schlichting, Hilke E
2016-01-01
The Caltech HIgh-speed Multi-color camERA (CHIMERA) is a new instrument that has been developed for use at the prime focus of the Hale 200-inch telescope. Simultaneous optical imaging in two bands is enabled by a dichroic beam splitter centered at 567 nm, with Sloan u' and g' bands available on the blue arm and Sloan r', i' and z_s' bands available on the red arm. Additional narrow-band filters will also become available as required. An Electron Multiplying CCD (EMCCD) detector is employed for both optical channels, each capable of simultaneously delivering sub-electron effective read noise under multiplication gain and frame rates of up to 26 fps full frame (several 1000 fps windowed), over a fully corrected 5 x 5 arcmin field of view. CHIMERA was primarily developed to enable the characterization of the size distribution of sub-km Kuiper Belt Objects via stellar occultation, a science case that motivates the frame-rate, the simultaneous multi-color imaging and the wide field of view of the instrument. In ad...
Kawakami, Yutaka; Goto-Kazeto, Rie; Saito, Taiju; Fujimoto, Takafumi; Higaki, Shogo; Takahashi, Yoshiyuki; Arai, Katsutoshi; Yamaha, Etsuro
2010-01-01
Primordial germ cells (PGCs) are the only cells in developing embryos with the potential to transmit genetic information to the next generation. In our previous study, a single PGC transplanted into a host differentiated into fertile gametes and produced germ-line chimeras of cyprinid fish, including zebrafish. In this study, we aimed to induce germ-line chimeras by transplanting donor PGCs from various sources (normal embryos at different stages, dissociated blastomeres, embryoids, or embryoids cryopreserved by vitrification) into host blastulae, and compare the migration rates of the PGCs towards the gonadal ridge. Isolated, cultured blastomeres not subject to mesodermal induction were able to differentiate into PGCs that retained their motility. Moreover, these PGCs successfully migrated towards the gonadal ridge of the host and formed viable gametes. Motility depended on developmental stage and culture duration: PGCs obtained at earlier developmental stages and with shorter cultivation periods showed an increased rate of migration to the gonadal ridge. Offspring were obtained from natural spawning between normal females and chimeric males. These results provide the basis for new methods of gene preservation in zebrafish.
Regression of Pathological Cardiac Hypertrophy: Signaling Pathways and Therapeutic Targets
Hou, Jianglong; Kang, Y. James
2012-01-01
Pathological cardiac hypertrophy is a key risk factor for heart failure. It is associated with increased interstitial fibrosis, cell death and cardiac dysfunction. The progression of pathological cardiac hypertrophy has long been considered as irreversible. However, recent clinical observations and experimental studies have produced evidence showing the reversal of pathological cardiac hypertrophy. Left ventricle assist devices used in heart failure patients for bridging to transplantation not only improve peripheral circulation but also often cause reverse remodeling of the geometry and recovery of the function of the heart. Dietary supplementation with physiologically relevant levels of copper can reverse pathological cardiac hypertrophy in mice. Angiogenesis is essential and vascular endothelial growth factor (VEGF) is a constitutive factor for the regression. The action of VEGF is mediated by VEGF receptor-1, whose activation is linked to cyclic GMP-dependent protein kinase-1 (PKG-1) signaling pathways, and inhibition of cyclic GMP degradation leads to regression of pathological cardiac hypertrophy. Most of these pathways are regulated by hypoxia-inducible factor. Potential therapeutic targets for promoting the regression include: promotion of angiogenesis, selective enhancement of VEGF receptor-1 signaling pathways, stimulation of PKG-1 pathways, and sustention of hypoxia-inducible factor transcriptional activity. More exciting insights into the regression of pathological cardiac hypertrophy are emerging. The time of translating the concept of regression of pathological cardiac hypertrophy to clinical practice is coming. PMID:22750195
Prediction, Regression and Critical Realism
DEFF Research Database (Denmark)
Næss, Petter
2004-01-01
This paper considers the possibility of prediction in land use planning, and the use of statistical research methods in analyses of relationships between urban form and travel behaviour. Influential writers within the tradition of critical realism reject the possibility of predicting social...... of prediction necessary and possible in spatial planning of urban development. Finally, the political implications of positions within theory of science rejecting the possibility of predictions about social phenomena are addressed....... phenomena. This position is fundamentally problematic to public planning. Without at least some ability to predict the likely consequences of different proposals, the justification for public sector intervention into market mechanisms will be frail. Statistical methods like regression analyses are commonly...
Nonparametric Regression with Common Shocks
Directory of Open Access Journals (Sweden)
Eduardo A. Souza-Rodrigues
2016-09-01
Full Text Available This paper considers a nonparametric regression model for cross-sectional data in the presence of common shocks. Common shocks are allowed to be very general in nature; they do not need to be finite dimensional with a known (small number of factors. I investigate the properties of the Nadaraya-Watson kernel estimator and determine how general the common shocks can be while still obtaining meaningful kernel estimates. Restrictions on the common shocks are necessary because kernel estimators typically manipulate conditional densities, and conditional densities do not necessarily exist in the present case. By appealing to disintegration theory, I provide sufficient conditions for the existence of such conditional densities and show that the estimator converges in probability to the Kolmogorov conditional expectation given the sigma-field generated by the common shocks. I also establish the rate of convergence and the asymptotic distribution of the kernel estimator.
Practical Session: Multiple Linear Regression
Clausel, M.; Grégoire, G.
2014-12-01
Three exercises are proposed to illustrate the simple linear regression. In the first one investigates the influence of several factors on atmospheric pollution. It has been proposed by D. Chessel and A.B. Dufour in Lyon 1 (see Sect. 6 of http://pbil.univ-lyon1.fr/R/pdf/tdr33.pdf) and is based on data coming from 20 cities of U.S. Exercise 2 is an introduction to model selection whereas Exercise 3 provides a first example of analysis of variance. Exercises 2 and 3 have been proposed by A. Dalalyan at ENPC (see Exercises 2 and 3 of http://certis.enpc.fr/~dalalyan/Download/TP_ENPC_5.pdf).
Lumbar herniated disc: spontaneous regression
Yüksel, Kasım Zafer
2017-01-01
Background Low back pain is a frequent condition that results in substantial disability and causes admission of patients to neurosurgery clinics. To evaluate and present the therapeutic outcomes in lumbar disc hernia (LDH) patients treated by means of a conservative approach, consisting of bed rest and medical therapy. Methods This retrospective cohort was carried out in the neurosurgery departments of hospitals in Kahramanmaraş city and 23 patients diagnosed with LDH at the levels of L3−L4, L4−L5 or L5−S1 were enrolled. Results The average age was 38.4 ± 8.0 and the chief complaint was low back pain and sciatica radiating to one or both lower extremities. Conservative treatment was administered. Neurological examination findings, durations of treatment and intervals until symptomatic recovery were recorded. Laségue tests and neurosensory examination revealed that mild neurological deficits existed in 16 of our patients. Previously, 5 patients had received physiotherapy and 7 patients had been on medical treatment. The number of patients with LDH at the level of L3−L4, L4−L5, and L5−S1 were 1, 13, and 9, respectively. All patients reported that they had benefit from medical treatment and bed rest, and radiologic improvement was observed simultaneously on MRI scans. The average duration until symptomatic recovery and/or regression of LDH symptoms was 13.6 ± 5.4 months (range: 5−22). Conclusions It should be kept in mind that lumbar disc hernias could regress with medical treatment and rest without surgery, and there should be an awareness that these patients could recover radiologically. This condition must be taken into account during decision making for surgical intervention in LDH patients devoid of indications for emergent surgery. PMID:28119770
Credit Scoring Problem Based on Regression Analysis
Khassawneh, Bashar Suhil Jad Allah
2014-01-01
ABSTRACT: This thesis provides an explanatory introduction to the regression models of data mining and contains basic definitions of key terms in the linear, multiple and logistic regression models. Meanwhile, the aim of this study is to illustrate fitting models for the credit scoring problem using simple linear, multiple linear and logistic regression models and also to analyze the found model functions by statistical tools. Keywords: Data mining, linear regression, logistic regression....
Varying-coefficient functional linear regression
Wu, Yichao; Müller, Hans-Georg; 10.3150/09-BEJ231
2011-01-01
Functional linear regression analysis aims to model regression relations which include a functional predictor. The analog of the regression parameter vector or matrix in conventional multivariate or multiple-response linear regression models is a regression parameter function in one or two arguments. If, in addition, one has scalar predictors, as is often the case in applications to longitudinal studies, the question arises how to incorporate these into a functional regression model. We study a varying-coefficient approach where the scalar covariates are modeled as additional arguments of the regression parameter function. This extension of the functional linear regression model is analogous to the extension of conventional linear regression models to varying-coefficient models and shares its advantages, such as increased flexibility; however, the details of this extension are more challenging in the functional case. Our methodology combines smoothing methods with regularization by truncation at a finite numb...
Functional Regression for Quasar Spectra
Ciollaro, Mattia; Freeman, Peter; Genovese, Christopher; Lei, Jing; O'Connell, Ross; Wasserman, Larry
2014-01-01
The Lyman-alpha forest is a portion of the observed light spectrum of distant galactic nuclei which allows us to probe remote regions of the Universe that are otherwise inaccessible. The observed Lyman-alpha forest of a quasar light spectrum can be modeled as a noisy realization of a smooth curve that is affected by a `damping effect' which occurs whenever the light emitted by the quasar travels through regions of the Universe with higher matter concentration. To decode the information conveyed by the Lyman-alpha forest about the matter distribution, we must be able to separate the smooth `continuum' from the noise and the contribution of the damping effect in the quasar light spectra. To predict the continuum in the Lyman-alpha forest, we use a nonparametric functional regression model in which both the response and the predictor variable (the smooth part of the damping-free portion of the spectrum) are function-valued random variables. We demonstrate that the proposed method accurately predicts the unobserv...
Knowledge and Awareness: Linear Regression
Directory of Open Access Journals (Sweden)
Monika Raghuvanshi
2016-12-01
Full Text Available Knowledge and awareness are factors guiding development of an individual. These may seem simple and practicable, but in reality a proper combination of these is a complex task. Economically driven state of development in younger generations is an impediment to the correct manner of development. As youths are at the learning phase, they can be molded to follow a correct lifestyle. Awareness and knowledge are important components of any formal or informal environmental education. The purpose of this study is to evaluate the relationship of these components among students of secondary/ senior secondary schools who have undergone a formal study of environment in their curricula. A suitable instrument is developed in order to measure the elements of Awareness and Knowledge among the participants of the study. Data was collected from various secondary and senior secondary school students in the age group 14 to 20 years using cluster sampling technique from the city of Bikaner, India. Linear regression analysis was performed using IBM SPSS 23 statistical tool. There exists a weak relation between knowledge and awareness about environmental issues, caused due to routine practices mishandling; hence one component can be complemented by other for improvement in both. Knowledge and awareness are crucial factors and can provide huge opportunities in any field. Resource utilization for economic solutions may pave the way for eco-friendly products and practices. If green practices are inculcated at the learning phase, they may become normal routine. This will also help in repletion of the environment.
Streamflow forecasting using functional regression
Masselot, Pierre; Dabo-Niang, Sophie; Chebana, Fateh; Ouarda, Taha B. M. J.
2016-07-01
Streamflow, as a natural phenomenon, is continuous in time and so are the meteorological variables which influence its variability. In practice, it can be of interest to forecast the whole flow curve instead of points (daily or hourly). To this end, this paper introduces the functional linear models and adapts it to hydrological forecasting. More precisely, functional linear models are regression models based on curves instead of single values. They allow to consider the whole process instead of a limited number of time points or features. We apply these models to analyse the flow volume and the whole streamflow curve during a given period by using precipitations curves. The functional model is shown to lead to encouraging results. The potential of functional linear models to detect special features that would have been hard to see otherwise is pointed out. The functional model is also compared to the artificial neural network approach and the advantages and disadvantages of both models are discussed. Finally, future research directions involving the functional model in hydrology are presented.
Principal component regression analysis with SPSS.
Liu, R X; Kuang, J; Gong, Q; Hou, X L
2003-06-01
The paper introduces all indices of multicollinearity diagnoses, the basic principle of principal component regression and determination of 'best' equation method. The paper uses an example to describe how to do principal component regression analysis with SPSS 10.0: including all calculating processes of the principal component regression and all operations of linear regression, factor analysis, descriptives, compute variable and bivariate correlations procedures in SPSS 10.0. The principal component regression analysis can be used to overcome disturbance of the multicollinearity. The simplified, speeded up and accurate statistical effect is reached through the principal component regression analysis with SPSS.
Spontaneous Regression of an Incidental Spinal Meningioma
National Research Council Canada - National Science Library
Yilmaz, Ali; Kizilay, Zahir; Sair, Ahmet; Avcil, Mucahit; Ozkul, Ayca
2015-01-01
AIM: The regression of meningioma has been reported in literature before. In spite of the fact that the regression may be involved by hemorrhage, calcification or some drugs withdrawal, it is rarely observed spontaneously. CASE REPORT...
Common pitfalls in statistical analysis: Logistic regression.
Ranganathan, Priya; Pramesh, C S; Aggarwal, Rakesh
2017-01-01
Logistic regression analysis is a statistical technique to evaluate the relationship between various predictor variables (either categorical or continuous) and an outcome which is binary (dichotomous). In this article, we discuss logistic regression analysis and the limitations of this technique.
Semiparametric regression during 2003–2007
Ruppert, David
2009-01-01
Semiparametric regression is a fusion between parametric regression and nonparametric regression that integrates low-rank penalized splines, mixed model and hierarchical Bayesian methodology – thus allowing more streamlined handling of longitudinal and spatial correlation. We review progress in the field over the five-year period between 2003 and 2007. We find semiparametric regression to be a vibrant field with substantial involvement and activity, continual enhancement and widespread application.
Unbalanced Regressions and the Predictive Equation
DEFF Research Database (Denmark)
Osterrieder, Daniela; Ventosa-Santaulària, Daniel; Vera-Valdés, J. Eduardo
Predictive return regressions with persistent regressors are typically plagued by (asymptotically) biased/inconsistent estimates of the slope, non-standard or potentially even spurious statistical inference, and regression unbalancedness. We alleviate the problem of unbalancedness in the theoreti......Predictive return regressions with persistent regressors are typically plagued by (asymptotically) biased/inconsistent estimates of the slope, non-standard or potentially even spurious statistical inference, and regression unbalancedness. We alleviate the problem of unbalancedness...
Directory of Open Access Journals (Sweden)
Dhananjay R Namjoshi
Full Text Available Concussion is a serious health concern. Concussion in athletes is of particular interest with respect to the relationship of concussion exposure to risk of chronic traumatic encephalopathy (CTE, a neurodegenerative condition associated with altered cognitive and psychiatric functions and profound tauopathy. However, much remains to be learned about factors other than cumulative exposure that could influence concussion pathogenesis. Approximately 20% of CTE cases report a history of substance use including androgenic-anabolic steroids (AAS. How acute, chronic, or historical AAS use may affect the vulnerability of the brain to concussion is unknown. We therefore tested whether antecedent AAS exposure in young, male C57Bl/6 mice affects acute behavioral and neuropathological responses to mild traumatic brain injury (TBI induced with the CHIMERA (Closed Head Impact Model of Engineered Rotational Acceleration platform. Male C57Bl/6 mice received either vehicle or a cocktail of three AAS (testosterone, nandrolone and 17α-methyltestosterone from 8-16 weeks of age. At the end of the 7th week of treatment, mice underwent two closed-head TBI or sham procedures spaced 24 h apart using CHIMERA. Post-repetitive TBI (rTBI behavior was assessed for 7 d followed by tissue collection. AAS treatment induced the expected physiological changes including increased body weight, testicular atrophy, aggression and downregulation of brain 5-HT1B receptor expression. rTBI induced behavioral deficits, widespread axonal injury and white matter microgliosis. While AAS treatment did not worsen post-rTBI behavioral changes, AAS-treated mice exhibited significantly exacerbated axonal injury and microgliosis, indicating that AAS exposure can alter neuronal and innate immune responses to concussive TBI.
Iannaccone, Stephen; Zhou, Yue; Walterhouse, David; Taborn, Greg; Landini, Gabriel; Iannaccone, Philip
2012-01-01
The production of organ parenchyma in a rapid and reproducible manner is critical to normal development. In chimeras produced by the combination of genetically distinguishable tissues, mosaic patterns of cells derived from the combined genotypes can be visualized. These patterns comprise patches of contiguously similar genotypes and are different in different organs but similar in a given organ from individual to individual. Thus, the processes that produce the patterns are regulated and conserved. We have previously established that mosaic patches in multiple tissues are fractal, consistent with an iterative, recursive growth model with simple stereotypical division rules. Fractal dimensions of various tissues are consistent with algorithmic models in which changing a single variable (e.g. daughter cell placement after division) switches the mosaic pattern from islands to stripes of cells. Here we show that the spiral pattern previously observed in mouse cornea can also be visualized in rat chimeras. While it is generally held that the pattern is induced by stem cell division dynamics, there is an unexplained discrepancy in the speed of cellular migration and the emergence of the pattern. We demonstrate in chimeric rat corneas both island and striped patterns exist depending on the age of the animal. The patches that comprise the pattern are fractal, and the fractal dimension changes with the age of the animal and indicates the constraint in patch complexity as the spiral pattern emerges. The spiral patterns are consistent with a loxodrome. Such data are likely to be relevant to growth and cell division in organ systems and will help in understanding how organ parenchyma are generated and maintained from multipotent stem cell populations located in specific topographical locations within the organ. Ultimately, understanding algorithmic growth is likely to be essential in achieving organ regeneration in vivo or in vitro from stem cell populations.
Directory of Open Access Journals (Sweden)
Stephen Iannaccone
Full Text Available The production of organ parenchyma in a rapid and reproducible manner is critical to normal development. In chimeras produced by the combination of genetically distinguishable tissues, mosaic patterns of cells derived from the combined genotypes can be visualized. These patterns comprise patches of contiguously similar genotypes and are different in different organs but similar in a given organ from individual to individual. Thus, the processes that produce the patterns are regulated and conserved. We have previously established that mosaic patches in multiple tissues are fractal, consistent with an iterative, recursive growth model with simple stereotypical division rules. Fractal dimensions of various tissues are consistent with algorithmic models in which changing a single variable (e.g. daughter cell placement after division switches the mosaic pattern from islands to stripes of cells. Here we show that the spiral pattern previously observed in mouse cornea can also be visualized in rat chimeras. While it is generally held that the pattern is induced by stem cell division dynamics, there is an unexplained discrepancy in the speed of cellular migration and the emergence of the pattern. We demonstrate in chimeric rat corneas both island and striped patterns exist depending on the age of the animal. The patches that comprise the pattern are fractal, and the fractal dimension changes with the age of the animal and indicates the constraint in patch complexity as the spiral pattern emerges. The spiral patterns are consistent with a loxodrome. Such data are likely to be relevant to growth and cell division in organ systems and will help in understanding how organ parenchyma are generated and maintained from multipotent stem cell populations located in specific topographical locations within the organ. Ultimately, understanding algorithmic growth is likely to be essential in achieving organ regeneration in vivo or in vitro from stem cell populations.
Standards for Standardized Logistic Regression Coefficients
Menard, Scott
2011-01-01
Standardized coefficients in logistic regression analysis have the same utility as standardized coefficients in linear regression analysis. Although there has been no consensus on the best way to construct standardized logistic regression coefficients, there is now sufficient evidence to suggest a single best approach to the construction of a…
Synthesizing Regression Results: A Factored Likelihood Method
Wu, Meng-Jia; Becker, Betsy Jane
2013-01-01
Regression methods are widely used by researchers in many fields, yet methods for synthesizing regression results are scarce. This study proposes using a factored likelihood method, originally developed to handle missing data, to appropriately synthesize regression models involving different predictors. This method uses the correlations reported…
Regression Analysis by Example. 5th Edition
Chatterjee, Samprit; Hadi, Ali S.
2012-01-01
Regression analysis is a conceptually simple method for investigating relationships among variables. Carrying out a successful application of regression analysis, however, requires a balance of theoretical results, empirical rules, and subjective judgment. "Regression Analysis by Example, Fifth Edition" has been expanded and thoroughly…
Regression with Sparse Approximations of Data
DEFF Research Database (Denmark)
Noorzad, Pardis; Sturm, Bob L.
2012-01-01
We propose sparse approximation weighted regression (SPARROW), a method for local estimation of the regression function that uses sparse approximation with a dictionary of measurements. SPARROW estimates the regression function at a point with a linear combination of a few regressands selected by...
Standards for Standardized Logistic Regression Coefficients
Menard, Scott
2011-01-01
Standardized coefficients in logistic regression analysis have the same utility as standardized coefficients in linear regression analysis. Although there has been no consensus on the best way to construct standardized logistic regression coefficients, there is now sufficient evidence to suggest a single best approach to the construction of a…
Regression with Sparse Approximations of Data
DEFF Research Database (Denmark)
Noorzad, Pardis; Sturm, Bob L.
2012-01-01
We propose sparse approximation weighted regression (SPARROW), a method for local estimation of the regression function that uses sparse approximation with a dictionary of measurements. SPARROW estimates the regression function at a point with a linear combination of a few regressands selected...... by a sparse approximation of the point in terms of the regressors. We show SPARROW can be considered a variant of \\(k\\)-nearest neighbors regression (\\(k\\)-NNR), and more generally, local polynomial kernel regression. Unlike \\(k\\)-NNR, however, SPARROW can adapt the number of regressors to use based...
Assumptions of Multiple Regression: Correcting Two Misconceptions
Directory of Open Access Journals (Sweden)
Matt N. Williams
2013-09-01
Full Text Available In 2002, an article entitled - Four assumptions of multiple regression that researchers should always test- by.Osborne and Waters was published in PARE. This article has gone on to be viewed more than 275,000 times.(as of August 2013, and it is one of the first results displayed in a Google search for - regression.assumptions- . While Osborne and Waters' efforts in raising awareness of the need to check assumptions.when using regression are laudable, we note that the original article contained at least two fairly important.misconceptions about the assumptions of multiple regression: Firstly, that multiple regression requires the.assumption of normally distributed variables; and secondly, that measurement errors necessarily cause.underestimation of simple regression coefficients. In this article, we clarify that multiple regression models.estimated using ordinary least squares require the assumption of normally distributed errors in order for.trustworthy inferences, at least in small samples, but not the assumption of normally distributed response or.predictor variables. Secondly, we point out that regression coefficients in simple regression models will be.biased (toward zero estimates of the relationships between variables of interest when measurement error is.uncorrelated across those variables, but that when correlated measurement error is present, regression.coefficients may be either upwardly or downwardly biased. We conclude with a brief corrected summary of.the assumptions of multiple regression when using ordinary least squares.
Functional linear regression via canonical analysis
He, Guozhong; Wang, Jane-Ling; Yang, Wenjing; 10.3150/09-BEJ228
2011-01-01
We study regression models for the situation where both dependent and independent variables are square-integrable stochastic processes. Questions concerning the definition and existence of the corresponding functional linear regression models and some basic properties are explored for this situation. We derive a representation of the regression parameter function in terms of the canonical components of the processes involved. This representation establishes a connection between functional regression and functional canonical analysis and suggests alternative approaches for the implementation of functional linear regression analysis. A specific procedure for the estimation of the regression parameter function using canonical expansions is proposed and compared with an established functional principal component regression approach. As an example of an application, we present an analysis of mortality data for cohorts of medflies, obtained in experimental studies of aging and longevity.
Henrard, S; Speybroeck, N; Hermans, C
2015-11-01
Haemophilia is a rare genetic haemorrhagic disease characterized by partial or complete deficiency of coagulation factor VIII, for haemophilia A, or IX, for haemophilia B. As in any other medical research domain, the field of haemophilia research is increasingly concerned with finding factors associated with binary or continuous outcomes through multivariable models. Traditional models include multiple logistic regressions, for binary outcomes, and multiple linear regressions for continuous outcomes. Yet these regression models are at times difficult to implement, especially for non-statisticians, and can be difficult to interpret. The present paper sought to didactically explain how, why, and when to use classification and regression tree (CART) analysis for haemophilia research. The CART method is non-parametric and non-linear, based on the repeated partitioning of a sample into subgroups based on a certain criterion. Breiman developed this method in 1984. Classification trees (CTs) are used to analyse categorical outcomes and regression trees (RTs) to analyse continuous ones. The CART methodology has become increasingly popular in the medical field, yet only a few examples of studies using this methodology specifically in haemophilia have to date been published. Two examples using CART analysis and previously published in this field are didactically explained in details. There is increasing interest in using CART analysis in the health domain, primarily due to its ease of implementation, use, and interpretation, thus facilitating medical decision-making. This method should be promoted for analysing continuous or categorical outcomes in haemophilia, when applicable. © 2015 John Wiley & Sons Ltd.
Regression in children with autism spectrum disorders.
Malhi, Prahbhjot; Singhi, Pratibha
2012-10-01
To understand the characteristics of autistic regression and to compare the clinical and developmental profile of children with autism spectrum disorders (ASD) in whom parents report developmental regression with age matched ASD children in whom no regression is reported. Participants were 35 (Mean age = 3.57 y, SD = 1.09) children with ASD in whom parents reported developmental regression before age 3 y and a group of age and IQ matched 35 ASD children in whom parents did not report regression. All children were recruited from the outpatient Child Psychology Clinic of the Department of Pediatrics of a tertiary care teaching hospital in North India. Multi-disciplinary evaluations including neurological, diagnostic, cognitive, and behavioral assessments were done. Parents were asked in detail about the age at onset of regression, type of regression, milestones lost, and event, if any, related to the regression. In addition, the Childhood Autism Rating Scale (CARS) was administered to assess symptom severity. The mean age at regression was 22.43 mo (SD = 6.57) and large majority (66.7%) of the parents reported regression between 12 and 24 mo. Most (75%) of the parents of the regression-autistic group reported regression in the language domain, particularly in the expressive language sector, usually between 18 and 24 mo of age. Regression of language was not an isolated phenomenon and regression in other domains was also reported including social skills (75%), cognition (31.25%). In majority of the cases (75%) the regression reported was slow and subtle. There were no significant differences in the motor, social, self help, and communication functioning between the two groups as measured by the DP II.There were also no significant differences between the two groups on the total CARS score and total number of DSM IV symptoms endorsed. However, the regressed children had significantly (t = 2.36, P = .021) more social deficits as per the DSM IV as
DEFF Research Database (Denmark)
Lenhard, Boris; Sandelin, Albin Gustav; Carninci, Piero
2012-01-01
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory elements, sequence motifs, the choice of transcription start sites and other features. Several technologies that harness next-generation sequencing have enabled recent advances in identifying promoters...... and their features, helping researchers who are investigating functional categories of promoters and their modes of regulation. Additional features of promoters that are being characterized include types of histone modifications, nucleosome positioning, RNA polymerase pausing and novel small RNAs. In this Review, we...... discuss recent findings relating to metazoan promoters and how these findings are leading to a revised picture of what a gene promoter is and how it works....
Using Regression Mixture Analysis in Educational Research
Directory of Open Access Journals (Sweden)
Cody S. Ding
2006-11-01
Full Text Available Conventional regression analysis is typically used in educational research. Usually such an analysis implicitly assumes that a common set of regression parameter estimates captures the population characteristics represented in the sample. In some situations, however, this implicit assumption may not be realistic, and the sample may contain several subpopulations such as high math achievers and low math achievers. In these cases, conventional regression models may provide biased estimates since the parameter estimates are constrained to be the same across subpopulations. This paper advocates the applications of regression mixture models, also known as latent class regression analysis, in educational research. Regression mixture analysis is more flexible than conventional regression analysis in that latent classes in the data can be identified and regression parameter estimates can vary within each latent class. An illustration of regression mixture analysis is provided based on a dataset of authentic data. The strengths and limitations of the regression mixture models are discussed in the context of educational research.
Regression modeling methods, theory, and computation with SAS
Panik, Michael
2009-01-01
Regression Modeling: Methods, Theory, and Computation with SAS provides an introduction to a diverse assortment of regression techniques using SAS to solve a wide variety of regression problems. The author fully documents the SAS programs and thoroughly explains the output produced by the programs.The text presents the popular ordinary least squares (OLS) approach before introducing many alternative regression methods. It covers nonparametric regression, logistic regression (including Poisson regression), Bayesian regression, robust regression, fuzzy regression, random coefficients regression,
Indian Academy of Sciences (India)
A Prakash; Durgadas P Kasbekar
2002-03-01
The human gene TM7SF2 encodes a polypeptide (SR-1) with high sequence similarity to sterol C-14 reductase, a key sterol biosynthetic enzyme in fungi, plants and mammals. In Neurospora and yeast this enzyme is encoded by the erg-3 and erg24 genes respectively. In an effort to demonstrate sterol C-14 reductase activity for SR-1 we constructed six recombinant genes coding for chimeras of the Neurospora erg-3 and SR-1 protein sequences and tested them for complementation of the Neurospora erg-3 mutant. To our surprise, all the chimeras failed to complement erg-3. A few of the chimeric proteins were also tested against the yeast erg24 mutant, but again there was no complementation. We discuss some reasons that might account for these unexpected findings.
Energy Technology Data Exchange (ETDEWEB)
Straume, T. [University of California Lawrence Livermore National Laboratory, Livermore, CA (United States); Raabe, O.G.; Walsh, K.J.; Wiley, L.M. [Institute of Toxicology and Environmental Health, Davis, CA (United States)
1996-09-23
A previous study using the mouse-preimplantation-embryo-chimera assay demonstrated a reproducible transmitted effect (proliferation disadvantage observed in early embryos) from females irradiated as 49-day-old adults using 0.15 Gy of gamma rays and then mated seven weeks later, i.e., embryos were from oocytes that were immature at time of irradiation. Because mouse immature oocytes are known to be much more radiosensitive to cell killing in juveniles than in adults, a follow-on study was performed here using 14-day-old juvenile mice. In contrast to adults, the exposure of juveniles to 0.15 Gy of gamma rays did not result in a detectable transmitted proliferation disadvantage when animals were mated 7 or 12 weeks later. This observation is discussed in light of previous studies on mouse immature oocytes and embryo chimeras.
Beta blockers & left ventricular hypertrophy regression.
George, Thomas; Ajit, Mullasari S; Abraham, Georgi
2010-01-01
Left ventricular hypertrophy (LVH) particularly in hypertensive patients is a strong predictor of adverse cardiovascular events. Identifying LVH not only helps in the prognostication but also in the choice of therapeutic drugs. The prevalence of LVH is age linked and has a direct correlation to the severity of hypertension. Adequate control of blood pressure, most importantly central aortic pressure and blocking the effects of cardiomyocyte stimulatory growth factors like Angiotensin II helps in regression of LVH. Among the various antihypertensives ACE-inhibitors and angiotensin receptor blockers are more potent than other drugs in regressing LVH. Beta blockers especially the newer cardio selective ones do still have a role in regressing LVH albeit a minor one. A meta-analysis of various studies on LVH regression shows many lacunae. There have been no consistent criteria for defining LVH and documenting LVH regression. This article reviews current evidence on the role of Beta Blockers in LVH regression.
Applied regression analysis a research tool
Pantula, Sastry; Dickey, David
1998-01-01
Least squares estimation, when used appropriately, is a powerful research tool. A deeper understanding of the regression concepts is essential for achieving optimal benefits from a least squares analysis. This book builds on the fundamentals of statistical methods and provides appropriate concepts that will allow a scientist to use least squares as an effective research tool. Applied Regression Analysis is aimed at the scientist who wishes to gain a working knowledge of regression analysis. The basic purpose of this book is to develop an understanding of least squares and related statistical methods without becoming excessively mathematical. It is the outgrowth of more than 30 years of consulting experience with scientists and many years of teaching an applied regression course to graduate students. Applied Regression Analysis serves as an excellent text for a service course on regression for non-statisticians and as a reference for researchers. It also provides a bridge between a two-semester introduction to...
High-dimensional regression with unknown variance
Giraud, Christophe; Verzelen, Nicolas
2011-01-01
We review recent results for high-dimensional sparse linear regression in the practical case of unknown variance. Different sparsity settings are covered, including coordinate-sparsity, group-sparsity and variation-sparsity. The emphasize is put on non-asymptotic analyses and feasible procedures. In addition, a small numerical study compares the practical performance of three schemes for tuning the Lasso esti- mator and some references are collected for some more general models, including multivariate regression and nonparametric regression.
DEFF Research Database (Denmark)
Pedersen, Stine F; King, Scott A; Nygaard, Eva B
2007-01-01
NHE1). Although highly homologous to the amiloride- and HOE-sensitive human NHE1 (hNHE1), AtNHE1 is insensitive to HOE-type and PaNHE1 to both amiloride- and HOE-type compounds. Here we generated chimeras to "knock in" amiloride and HOE sensitivity to PaNHE1, and we thereby identified several NHE1...
Pluchino, Kristen M; Hall, Matthew D; Moen, Janna K; Chufan, Eduardo E; Fetsch, Patricia A; Shukla, Suneet; Gill, Deborah R; Hyde, Stephen C; Xia, Di; Ambudkar, Suresh V; Gottesman, Michael M
2016-02-23
The efflux transporter P-glycoprotein (P-gp) plays a vital role in the transport of molecules across cell membranes and has been shown to interact with a panoply of functionally and structurally unrelated compounds. How human P-gp interacts with this large number of drugs has not been well understood, although structural flexibility has been implicated. To gain insight into this transporter's broad substrate specificity and to assess its ability to accommodate a variety of molecular and structural changes, we generated human-mouse P-gp chimeras by the exchange of homologous transmembrane and nucleotide-binding domains. High-level expression of these chimeras by BacMam- and baculovirus-mediated transduction in mammalian (HeLa) and insect cells, respectively, was achieved. There were no detectable differences between wild-type and chimeric P-gp in terms of cell surface expression, ability to efflux the P-gp substrates rhodamine 123, calcein-AM, and JC-1, or to be inhibited by the substrate cyclosporine A and the inhibitors tariquidar and elacridar. Additionally, expression of chimeric P-gp was able to confer a paclitaxel-resistant phenotype to HeLa cells characteristic of P-gp-mediated drug resistance. P-gp ATPase assays and photo-cross-linking with [(125)I]iodoarylazidoprazosin confirmed that transport and biochemical properties of P-gp chimeras were similar to those of wild-type P-gp, although differences in drug binding were detected when human and mouse transmembrane domains were combined. Overall, chimeras with one or two mouse P-gp domains were deemed functionally equivalent to human wild-type P-gp, demonstrating the ability of human P-gp to tolerate major structural changes.
Whetsell, M; Mosley, R L; Whetsell, L; Schaefer, F V; Miller, K S; Klein, J R
1991-12-01
The molecular organization of rearranged T-cell receptor (TCR) gamma genes intraepithelial lymphocytes (IEL) was studied in athymic radiation chimeras and was compared with the organization of gamma gene rearrangements in IEL from thymus-bearing animals by polymerase chain reaction and by sequence analyses of DNA spanning the junction of the variable (V) and joining (J) genes. In both thymus-bearing mice and athymic chimeras, IEL V-J gamma-gene rearrangements occurred for V gamma 1.2, V gamma 2, and V gamma 5 but not for V gamma 3 or V gamma 4. Sequence analyses of cloned V-J polymerase chain reaction-amplified products indicated that in both thymus-bearing mice and athymic chimeras, rearrangement of V gamma 1.2 and V gamma 5 resulted in in-frame as well as out-of-frame genes, whereas nearly all V gamma 2 rearrangements were out of frame from either type of animal. V-segment nucleotide removal occurred in most V gamma 1.2, V gamma 2, and V gamma 5 rearrangements; J-segment nucleotide removal was common in V gamma 1.2 but not in V gamma 2 or V gamma 5 rearrangements. N-segment nucleotide insertions were present in V gamma 1.2, V gamma 2, and V gamma 5 IEL rearrangements in both thymus-bearing mice and athymic chimeras, resulting in a predominant in-frame sequence for V gamma 5 and a predominant out-of-frame sequence for V gamma 2 genes. These findings demonstrate that (i) TCR gamma-gene rearrangement occurs extrathymically in IEL, (ii) rearrangements of TCR gamma genes involve the same V gene regardless of thymus influence; and (iii) the thymus does not determine the degree to which functional or nonfunctional rearrangements occur in IEL.
Directory of Open Access Journals (Sweden)
Esther Ndungo
2012-10-01
Full Text Available We recently demonstrated that Niemann-Pick C1 (NPC1, a ubiquitous 13-pass cellular membrane protein involved in lysosomal cholesterol transport, is a critical entry receptor for filoviruses. Here we show that Niemann-Pick C1-like1 (NPC1L1, an NPC1 paralog and hepatitis C virus entry factor, lacks filovirus receptor activity. We exploited the structural similarity between NPC1 and NPC1L1 to construct and analyze a panel of chimeras in which NPC1L1 sequences were replaced with cognate sequences from NPC1. Only one chimera, NPC1L1 containing the second luminal domain (C of NPC1 in place of its own, bound to the viral glycoprotein, GP. This engineered protein mediated authentic filovirus infection nearly as well as wild-type NPC1, and more efficiently than did a minimal NPC1 domain C-based receptor recently described by us. A reciprocal chimera, NPC1 containing NPC1L1’s domain C, was completely inactive. Remarkably, an intra-domain NPC1L1-NPC1 chimera bearing only a ~130-amino acid N–terminal region of NPC1 domain C could confer substantial viral receptor activity on NPC1L1. Taken together, these findings account for the failure of NPC1L1 to serve as a filovirus receptor, highlight the central role of the luminal domain C of NPC1 in filovirus entry, and reveal the direct involvement of N–terminal domain C sequences in NPC1’s function as a filovirus receptor.
Regression calibration with heteroscedastic error variance.
Spiegelman, Donna; Logan, Roger; Grove, Douglas
2011-01-01
The problem of covariate measurement error with heteroscedastic measurement error variance is considered. Standard regression calibration assumes that the measurement error has a homoscedastic measurement error variance. An estimator is proposed to correct regression coefficients for covariate measurement error with heteroscedastic variance. Point and interval estimates are derived. Validation data containing the gold standard must be available. This estimator is a closed-form correction of the uncorrected primary regression coefficients, which may be of logistic or Cox proportional hazards model form, and is closely related to the version of regression calibration developed by Rosner et al. (1990). The primary regression model can include multiple covariates measured without error. The use of these estimators is illustrated in two data sets, one taken from occupational epidemiology (the ACE study) and one taken from nutritional epidemiology (the Nurses' Health Study). In both cases, although there was evidence of moderate heteroscedasticity, there was little difference in estimation or inference using this new procedure compared to standard regression calibration. It is shown theoretically that unless the relative risk is large or measurement error severe, standard regression calibration approximations will typically be adequate, even with moderate heteroscedasticity in the measurement error model variance. In a detailed simulation study, standard regression calibration performed either as well as or better than the new estimator. When the disease is rare and the errors normally distributed, or when measurement error is moderate, standard regression calibration remains the method of choice.
Enhanced piecewise regression based on deterministic annealing
Institute of Scientific and Technical Information of China (English)
ZHANG JiangShe; YANG YuQian; CHEN XiaoWen; ZHOU ChengHu
2008-01-01
Regression is one of the important problems in statistical learning theory. This paper proves the global convergence of the piecewise regression algorithm based on deterministic annealing and continuity of global minimum of free energy w.r.t temperature, and derives a new simplified formula to compute the initial critical temperature. A new enhanced piecewise regression algorithm by using "migration of prototypes" is proposed to eliminate "empty cell" in the annealing process. Numerical experiments on several benchmark datasets show that the new algo-rithm can remove redundancy and improve generalization of the piecewise regres-sion model.
Geodesic least squares regression on information manifolds
Energy Technology Data Exchange (ETDEWEB)
Verdoolaege, Geert, E-mail: geert.verdoolaege@ugent.be [Department of Applied Physics, Ghent University, Ghent, Belgium and Laboratory for Plasma Physics, Royal Military Academy, Brussels (Belgium)
2014-12-05
We present a novel regression method targeted at situations with significant uncertainty on both the dependent and independent variables or with non-Gaussian distribution models. Unlike the classic regression model, the conditional distribution of the response variable suggested by the data need not be the same as the modeled distribution. Instead they are matched by minimizing the Rao geodesic distance between them. This yields a more flexible regression method that is less constrained by the assumptions imposed through the regression model. As an example, we demonstrate the improved resistance of our method against some flawed model assumptions and we apply this to scaling laws in magnetic confinement fusion.
[From clinical judgment to linear regression model.
Palacios-Cruz, Lino; Pérez, Marcela; Rivas-Ruiz, Rodolfo; Talavera, Juan O
2013-01-01
When we think about mathematical models, such as linear regression model, we think that these terms are only used by those engaged in research, a notion that is far from the truth. Legendre described the first mathematical model in 1805, and Galton introduced the formal term in 1886. Linear regression is one of the most commonly used regression models in clinical practice. It is useful to predict or show the relationship between two or more variables as long as the dependent variable is quantitative and has normal distribution. Stated in another way, the regression is used to predict a measure based on the knowledge of at least one other variable. Linear regression has as it's first objective to determine the slope or inclination of the regression line: Y = a + bx, where "a" is the intercept or regression constant and it is equivalent to "Y" value when "X" equals 0 and "b" (also called slope) indicates the increase or decrease that occurs when the variable "x" increases or decreases in one unit. In the regression line, "b" is called regression coefficient. The coefficient of determination (R(2)) indicates the importance of independent variables in the outcome.
Logistic Regression for Evolving Data Streams Classification
Institute of Scientific and Technical Information of China (English)
YIN Zhi-wu; HUANG Shang-teng; XUE Gui-rong
2007-01-01
Logistic regression is a fast classifier and can achieve higher accuracy on small training data. Moreover,it can work on both discrete and continuous attributes with nonlinear patterns. Based on these properties of logistic regression, this paper proposed an algorithm, called evolutionary logistical regression classifier (ELRClass), to solve the classification of evolving data streams. This algorithm applies logistic regression repeatedly to a sliding window of samples in order to update the existing classifier, to keep this classifier if its performance is deteriorated by the reason of bursting noise, or to construct a new classifier if a major concept drift is detected. The intensive experimental results demonstrate the effectiveness of this algorithm.
New ridge parameters for ridge regression
Directory of Open Access Journals (Sweden)
A.V. Dorugade
2014-04-01
Full Text Available Hoerl and Kennard (1970a introduced the ridge regression estimator as an alternative to the ordinary least squares (OLS estimator in the presence of multicollinearity. In ridge regression, ridge parameter plays an important role in parameter estimation. In this article, a new method for estimating ridge parameters in both situations of ordinary ridge regression (ORR and generalized ridge regression (GRR is proposed. The simulation study evaluates the performance of the proposed estimator based on the mean squared error (MSE criterion and indicates that under certain conditions the proposed estimators perform well compared to OLS and other well-known estimators reviewed in this article.
Bulcock, J. W.
The problem of model estimation when the data are collinear was examined. Though the ridge regression (RR) outperforms ordinary least squares (OLS) regression in the presence of acute multicollinearity, it is not a problem free technique for reducing the variance of the estimates. It is a stochastic procedure when it should be nonstochastic and it…
Incremental Net Effects in Multiple Regression
Lipovetsky, Stan; Conklin, Michael
2005-01-01
A regular problem in regression analysis is estimating the comparative importance of the predictors in the model. This work considers the 'net effects', or shares of the predictors in the coefficient of the multiple determination, which is a widely used characteristic of the quality of a regression model. Estimation of the net effects can be a…
Regression Analysis and the Sociological Imagination
De Maio, Fernando
2014-01-01
Regression analysis is an important aspect of most introductory statistics courses in sociology but is often presented in contexts divorced from the central concerns that bring students into the discipline. Consequently, we present five lesson ideas that emerge from a regression analysis of income inequality and mortality in the USA and Canada.
Dealing with Outliers: Robust, Resistant Regression
Glasser, Leslie
2007-01-01
Least-squares linear regression is the best of statistics and it is the worst of statistics. The reasons for this paradoxical claim, arising from possible inapplicability of the method and the excessive influence of "outliers", are discussed and substitute regression methods based on median selection, which is both robust and resistant, are…
Competing Risks Quantile Regression at Work
DEFF Research Database (Denmark)
Dlugosz, Stephan; Lo, Simon M. S.; Wilke, Ralf
2017-01-01
Despite its emergence as a frequently used method for the empirical analysis of multivariate data, quantile regression is yet to become a mainstream tool for the analysis of duration data. We present a pioneering empirical study on the grounds of a competing risks quantile regression model. We use...
Implementing Variable Selection Techniques in Regression.
Thayer, Jerome D.
Variable selection techniques in stepwise regression analysis are discussed. In stepwise regression, variables are added or deleted from a model in sequence to produce a final "good" or "best" predictive model. Stepwise computer programs are discussed and four different variable selection strategies are described. These…
Regression Model With Elliptically Contoured Errors
Arashi, M; Tabatabaey, S M M
2012-01-01
For the regression model where the errors follow the elliptically contoured distribution (ECD), we consider the least squares (LS), restricted LS (RLS), preliminary test (PT), Stein-type shrinkage (S) and positive-rule shrinkage (PRS) estimators for the regression parameters. We compare the quadratic risks of the estimators to determine the relative dominance properties of the five estimators.
Regression Analysis and the Sociological Imagination
De Maio, Fernando
2014-01-01
Regression analysis is an important aspect of most introductory statistics courses in sociology but is often presented in contexts divorced from the central concerns that bring students into the discipline. Consequently, we present five lesson ideas that emerge from a regression analysis of income inequality and mortality in the USA and Canada.
A Simulation Investigation of Principal Component Regression.
Allen, David E.
Regression analysis is one of the more common analytic tools used by researchers. However, multicollinearity between the predictor variables can cause problems in using the results of regression analyses. Problems associated with multicollinearity include entanglement of relative influences of variables due to reduced precision of estimation,…
Zhu, Feng; Feng, Weiyue; Wang, Huajian; Huang, Shaosen; Lv, Yisong; Chen, Yong
2013-01-01
X-ray spectral imaging provides quantitative imaging of trace elements in biological sample with high sensitivity. We propose a novel algorithm to promote the signal-to-noise ratio (SNR) of X-ray spectral images that have low photon counts. Firstly, we estimate the image data area that belongs to the homogeneous parts through confidence interval testing. Then, we apply the Poisson regression through its maximum likelihood estimation on this area to estimate the true photon counts from the Poisson noise corrupted data. Unlike other denoising methods based on regression analysis, we use the bootstrap resampling methods to ensure the accuracy of regression estimation. Finally, we use a robust local nonparametric regression method to estimate the baseline and subsequently subtract it from the X-ray spectral data to further improve the SNR of the data. Experiments on several real samples show that the proposed method performs better than some state-of-the-art approaches to ensure accuracy and precision for quantit...
Should metacognition be measured by logistic regression?
Rausch, Manuel; Zehetleitner, Michael
2017-03-01
Are logistic regression slopes suitable to quantify metacognitive sensitivity, i.e. the efficiency with which subjective reports differentiate between correct and incorrect task responses? We analytically show that logistic regression slopes are independent from rating criteria in one specific model of metacognition, which assumes (i) that rating decisions are based on sensory evidence generated independently of the sensory evidence used for primary task responses and (ii) that the distributions of evidence are logistic. Given a hierarchical model of metacognition, logistic regression slopes depend on rating criteria. According to all considered models, regression slopes depend on the primary task criterion. A reanalysis of previous data revealed that massive numbers of trials are required to distinguish between hierarchical and independent models with tolerable accuracy. It is argued that researchers who wish to use logistic regression as measure of metacognitive sensitivity need to control the primary task criterion and rating criteria. Copyright © 2017 Elsevier Inc. All rights reserved.
Atherosclerotic plaque regression: fact or fiction?
Shanmugam, Nesan; Román-Rego, Ana; Ong, Peter; Kaski, Juan Carlos
2010-08-01
Coronary artery disease is the major cause of death in the western world. The formation and rapid progression of atheromatous plaques can lead to serious cardiovascular events in patients with atherosclerosis. The better understanding, in recent years, of the mechanisms leading to atheromatous plaque growth and disruption and the availability of powerful HMG CoA-reductase inhibitors (statins) has permitted the consideration of plaque regression as a realistic therapeutic goal. This article reviews the existing evidence underpinning current therapeutic strategies aimed at achieving atherosclerotic plaque regression. In this review we also discuss imaging modalities for the assessment of plaque regression, predictors of regression and whether plaque regression is associated with a survival benefit.
Pathological assessment of liver fibrosis regression
Directory of Open Access Journals (Sweden)
WANG Bingqiong
2017-03-01
Full Text Available Hepatic fibrosis is the common pathological outcome of chronic hepatic diseases. An accurate assessment of fibrosis degree provides an important reference for a definite diagnosis of diseases, treatment decision-making, treatment outcome monitoring, and prognostic evaluation. At present, many clinical studies have proven that regression of hepatic fibrosis and early-stage liver cirrhosis can be achieved by effective treatment, and a correct evaluation of fibrosis regression has become a hot topic in clinical research. Liver biopsy has long been regarded as the gold standard for the assessment of hepatic fibrosis, and thus it plays an important role in the evaluation of fibrosis regression. This article reviews the clinical application of current pathological staging systems in the evaluation of fibrosis regression from the perspectives of semi-quantitative scoring system, quantitative approach, and qualitative approach, in order to propose a better pathological evaluation system for the assessment of fibrosis regression.
Aronoff-Spencer, Eliah; Venkatesh, A G; Sun, Alex; Brickner, Howard; Looney, David; Hall, Drew A
2016-12-15
Yeast cell lines were genetically engineered to display Hepatitis C virus (HCV) core antigen linked to gold binding peptide (GBP) as a dual-affinity biobrick chimera. These multifunctional yeast cells adhere to the gold sensor surface while simultaneously acting as a "renewable" capture reagent for anti-HCV core antibody. This streamlined functionalization and detection strategy removes the need for traditional purification and immobilization techniques. With this biobrick construct, both optical and electrochemical immunoassays were developed. The optical immunoassays demonstrated detection of anti-HCV core antibody down to 12.3pM concentrations while the electrochemical assay demonstrated higher binding constants and dynamic range. The electrochemical format and a custom, low-cost smartphone-based potentiostat ($20 USD) yielded comparable results to assays performed on a state-of-the-art electrochemical workstation. We propose this combination of synthetic biology and scalable, point-of-care sensing has potential to provide low-cost, cutting edge diagnostic capability for many pathogens in a variety of settings.
Dong, Jinhua; Otsuki, Takahiro; Kato, Tatsuya; Park, Enoch Y
2014-03-01
Neosporosis, an infectious disease of cattle and dogs, causes an abortion in cattle, which has a major damage on the dairy industry worldwide. Tracking of Neospora caninum parasite that is responsible for neosporosis is required for the prevention of this infectious disease. We developed three chimera monoclonal antibodies consist of variable regions of murine antibody and constant regions of human antibody against N. caninum. Recombinant surface antigen-related sequence 2 (rNcSRS2) of N. caninum was expressed in silkworm larvae, and immunized in mice to obtain phage displaying antibody library. Through three rounds of selection, three antibodies, A6, E1 and H3, were isolated and bound to rNcSRS2 with nanomolar to micromolar affinity. In immunofluorescent staining assays, A6 and E1 bound to N. caninum strain Nc-Liv, demonstrating a successful tracking of the parasite. H3 clone bound to rNcSRS2 but not to a truncated protein without glycosylphosphatidylinositol (GPI) anchor domain in the carboxyl terminal. Amino acid sequences of A6 and E1 were similar, but that of H3 differed in the CDR-H1 region, which might be the reason of their difference of affinity. These antibodies are thought to be useful for prevention of cattle from neosporosis.
Chen, Chun-Chun; Balaban, Evan; Jarvis, Erich D
2012-01-01
Like humans, birds that exhibit vocal learning have relatively delayed telencephalon maturation, resulting in a disproportionately smaller brain prenatally but enlarged telencephalon in adulthood relative to vocal non-learning birds. To determine if this size difference results from evolutionary changes in cell-autonomous or cell-interdependent developmental processes, we transplanted telencephala from zebra finch donors (a vocal-learning species) into Japanese quail hosts (a vocal non-learning species) during the early neural tube stage (day 2 of incubation), and harvested the chimeras at later embryonic stages (between 9-12 days of incubation). The donor and host tissues fused well with each other, with known major fiber pathways connecting the zebra finch and quail parts of the brain. However, the overall sizes of chimeric finch telencephala were larger than non-transplanted finch telencephala at the same developmental stages, even though the proportional sizes of telencephalic subregions and fiber tracts were similar to normal finches. There were no significant changes in the size of chimeric quail host midbrains, even though they were innervated by the physically smaller zebra finch brain, including the smaller retinae of the finch eyes. Chimeric zebra finch telencephala had a decreased cell density relative to normal finches. However, cell nucleus size differences between each species were maintained as in normal birds. These results suggest that telencephalic size development is partially cell-interdependent, and that the mechanisms controlling the size of different brain regions may be functionally independent.
Directory of Open Access Journals (Sweden)
Chun-Chun Chen
Full Text Available Like humans, birds that exhibit vocal learning have relatively delayed telencephalon maturation, resulting in a disproportionately smaller brain prenatally but enlarged telencephalon in adulthood relative to vocal non-learning birds. To determine if this size difference results from evolutionary changes in cell-autonomous or cell-interdependent developmental processes, we transplanted telencephala from zebra finch donors (a vocal-learning species into Japanese quail hosts (a vocal non-learning species during the early neural tube stage (day 2 of incubation, and harvested the chimeras at later embryonic stages (between 9-12 days of incubation. The donor and host tissues fused well with each other, with known major fiber pathways connecting the zebra finch and quail parts of the brain. However, the overall sizes of chimeric finch telencephala were larger than non-transplanted finch telencephala at the same developmental stages, even though the proportional sizes of telencephalic subregions and fiber tracts were similar to normal finches. There were no significant changes in the size of chimeric quail host midbrains, even though they were innervated by the physically smaller zebra finch brain, including the smaller retinae of the finch eyes. Chimeric zebra finch telencephala had a decreased cell density relative to normal finches. However, cell nucleus size differences between each species were maintained as in normal birds. These results suggest that telencephalic size development is partially cell-interdependent, and that the mechanisms controlling the size of different brain regions may be functionally independent.
Rao, Harita; Damian, Mariana S; Alshiekh, Alak; Elmroth, Sofi K C; Diederichsen, Ulf
2015-12-28
Conjugation of metal complexes with peptide scaffolds possessing high DNA binding affinity has shown to modulate their biological activities and to enhance their interaction with DNA. In this work, a platinum complex/peptide chimera was synthesized based on a model of the Integration Host Factor (IHF), an architectural protein possessing sequence specific DNA binding and bending abilities through its interaction with a minor groove. The model peptide consists of a cyclic unit resembling the minor grove binding subdomain of IHF, a positively charged lysine dendrimer for electrostatic interactions with the DNA phosphate backbone and a flexible glycine linker tethering the two units. A norvaline derived artificial amino acid was designed to contain a dimethylethylenediamine as a bidentate platinum chelating unit, and introduced into the IHF mimicking peptides. The interaction of the chimeric peptides with various DNA sequences was studied by utilizing the following experiments: thermal melting studies, agarose gel electrophoresis for plasmid DNA unwinding experiments, and native and denaturing gel electrophoresis to visualize non-covalent and covalent peptide-DNA adducts, respectively. By incorporation of the platinum metal center within the model peptide mimicking IHF we have attempted to improve its specificity and DNA targeting ability, particularly towards those sequences containing adjacent guanine residues.
Particle gamma correlations in {sup 12}C measured with the CsI(Tl) based detector array CHIMERA
Energy Technology Data Exchange (ETDEWEB)
Cardella, G., E-mail: cardella@ct.infn.it [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); Acosta, L. [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); Amorini, F. [INFN - Laboratori Nazionali del Sud, Via S. Sofia, Catania (Italy); Auditore, L. [INFN Gruppo collegato di Messina and Dip. di Fisica e Scienze della Terra, Università di Messina (Italy); Berceanu, I. [Institute for Physics and Nuclear Engineering, Bucharest (Romania); Castoldi, A. [INFN Sezione di Milano e Politecnico Milano (Italy); De Filippo, E. [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); Dell' Aquila, D. [Dipartimento di scienze Fisiche, Università Federico II and INFN Sezione di Napoli (Italy); Francalanza, L. [INFN - Laboratori Nazionali del Sud, Via S. Sofia, Catania (Italy); Dip. di Fisica e Astronomia, Università di Catania, Via S. Sofia, Catania (Italy); Gnoffo, B. [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); Guazzoni, C. [INFN Sezione di Milano e Politecnico Milano (Italy); Lanzalone, G. [INFN - Laboratori Nazionali del Sud, Via S. Sofia, Catania (Italy); Facoltà di Ingegneria e Architettura, Università Kore, Enna (Italy); Lombardo, I. [Dipartimento di scienze Fisiche, Università Federico II and INFN Sezione di Napoli (Italy); Minniti, T.; Morgana, E.; Norella, S. [INFN Gruppo collegato di Messina and Dip. di Fisica e Scienze della Terra, Università di Messina (Italy); Pagano, A. [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); Pagano, E.V. [INFN - Laboratori Nazionali del Sud, Via S. Sofia, Catania (Italy); Dip. di Fisica e Astronomia, Università di Catania, Via S. Sofia, Catania (Italy); Papa, M.; Pirrone, S. [INFN - Sezione di Catania, Via S. Sofia, 95123 Catania (Italy); and others
2015-11-01
The gamma decay of the first excited 4.44 MeV 2+level of {sup 12}C, populated by inelastic scattering of proton and {sup 16}O beams at various energies was studied in order to test γ-ray detection efficiency and the quality of angular distribution information given by the CsI(Tl) detectors of the 4π CHIMERA array. The γ-decay was measured in coincidence with ejectile scattered particles in an approximately 4π geometry allowing to extract the angular distribution in the reference frame of recoiling {sup 12}C target. The typical sin{sup 2} (2θ) behavior of angular distribution was observed in the case of {sup 16}O beam. Besides that, for the proton beam, in order to explain the observed distribution, the addition of an incoherent flat contribution was required. This latter is the effect of proton spin flip events allowing the population of M=±1 magnetic substates, that is not possible in reactions induced by {sup 16}O beam. A comparison with previously collected data, obtained measuring only in and out of plane proton-γ-ray coincidences, confirms the good quality of the angular distribution information given by the apparatus. Possible applications with radioactive beams are outlined.
Directory of Open Access Journals (Sweden)
Li-Min Yang
2013-02-01
Full Text Available MscL, the highly conserved bacterial mechanosensitive channel of large conductance, serves as an osmotic “emergency release valve,” is among the best-studied mechanosensors, and is a paradigm of how a channel senses and responds to membrane tension. Although all homologs tested thus far encode channel activity, many show functional differences. We tested Escherichia coli and Staphylococcus aureus chimeras and found that the periplasmic region of the protein, particularly E. coli I49 and the equivalent S. aureus F47 at the periplasmic lipid-aqueous interface of the first transmembrane domain, drastically influences both the open dwell time and the threshold of channel opening. One mutant shows a severe hysteresis, confirming the importance of this residue in determining the energy barriers for channel gating. We propose that this site acts similarly to a spring for a clasp knife, adjusting the resistance for obtaining and stabilizing an open or closed channel structure.
Quantile regression applied to spectral distance decay
Rocchini, D.; Cade, B.S.
2008-01-01
Remotely sensed imagery has long been recognized as a powerful support for characterizing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance allows us to quantitatively estimate the amount of turnover in species composition with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological data sets are characterized by a high number of zeroes that add noise to the regression model. Quantile regressions can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this letter, we used ordinary least squares (OLS) and quantile regressions to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p species similarity when habitats are more similar. In this letter, we demonstrated the power of using quantile regressions applied to spectral distance decay to reveal species diversity patterns otherwise lost or underestimated by OLS regression. ?? 2008 IEEE.
Hypotheses testing for fuzzy robust regression parameters
Energy Technology Data Exchange (ETDEWEB)
Kula, Kamile Sanli [Ahi Evran University, Department of Mathematics, 40200 Kirsehir (Turkey)], E-mail: sanli2004@hotmail.com; Apaydin, Aysen [Ankara University, Department of Statistics, 06100 Ankara (Turkey)], E-mail: apaydin@science.ankara.edu.tr
2009-11-30
The classical least squares (LS) method is widely used in regression analysis because computing its estimate is easy and traditional. However, LS estimators are very sensitive to outliers and to other deviations from basic assumptions of normal theory [Huynh H. A comparison of four approaches to robust regression. Psychol Bull 1982;92:505-12; Stephenson D. 2000. Available from: (http://folk.uib.no/ngbnk/kurs/notes/node38.html); Xu R, Li C. Multidimensional least-squares fitting with a fuzzy model. Fuzzy Sets and Systems 2001;119:215-23.]. If there exists outliers in the data set, robust methods are preferred to estimate parameters values. We proposed a fuzzy robust regression method by using fuzzy numbers when x is crisp and Y is a triangular fuzzy number and in case of outliers in the data set, a weight matrix was defined by the membership function of the residuals. In the fuzzy robust regression, fuzzy sets and fuzzy regression analysis was used in ranking of residuals and in estimation of regression parameters, respectively [Sanli K, Apaydin A. Fuzzy robust regression analysis based on the ranking of fuzzy sets. Inernat. J. Uncertainty Fuzziness and Knowledge-Based Syst 2008;16:663-81.]. In this study, standard deviation estimations are obtained for the parameters by the defined weight matrix. Moreover, we propose another point of view in hypotheses testing for parameters.
Regression modeling of ground-water flow
Cooley, R.L.; Naff, R.L.
1985-01-01
Nonlinear multiple regression methods are developed to model and analyze groundwater flow systems. Complete descriptions of regression methodology as applied to groundwater flow models allow scientists and engineers engaged in flow modeling to apply the methods to a wide range of problems. Organization of the text proceeds from an introduction that discusses the general topic of groundwater flow modeling, to a review of basic statistics necessary to properly apply regression techniques, and then to the main topic: exposition and use of linear and nonlinear regression to model groundwater flow. Statistical procedures are given to analyze and use the regression models. A number of exercises and answers are included to exercise the student on nearly all the methods that are presented for modeling and statistical analysis. Three computer programs implement the more complex methods. These three are a general two-dimensional, steady-state regression model for flow in an anisotropic, heterogeneous porous medium, a program to calculate a measure of model nonlinearity with respect to the regression parameters, and a program to analyze model errors in computed dependent variables such as hydraulic head. (USGS)
Relative risk regression analysis of epidemiologic data.
Prentice, R L
1985-11-01
Relative risk regression methods are described. These methods provide a unified approach to a range of data analysis problems in environmental risk assessment and in the study of disease risk factors more generally. Relative risk regression methods are most readily viewed as an outgrowth of Cox's regression and life model. They can also be viewed as a regression generalization of more classical epidemiologic procedures, such as that due to Mantel and Haenszel. In the context of an epidemiologic cohort study, relative risk regression methods extend conventional survival data methods and binary response (e.g., logistic) regression models by taking explicit account of the time to disease occurrence while allowing arbitrary baseline disease rates, general censorship, and time-varying risk factors. This latter feature is particularly relevant to many environmental risk assessment problems wherein one wishes to relate disease rates at a particular point in time to aspects of a preceding risk factor history. Relative risk regression methods also adapt readily to time-matched case-control studies and to certain less standard designs. The uses of relative risk regression methods are illustrated and the state of development of these procedures is discussed. It is argued that asymptotic partial likelihood estimation techniques are now well developed in the important special case in which the disease rates of interest have interpretations as counting process intensity functions. Estimation of relative risks processes corresponding to disease rates falling outside this class has, however, received limited attention. The general area of relative risk regression model criticism has, as yet, not been thoroughly studied, though a number of statistical groups are studying such features as tests of fit, residuals, diagnostics and graphical procedures. Most such studies have been restricted to exponential form relative risks as have simulation studies of relative risk estimation
Variable and subset selection in PLS regression
DEFF Research Database (Denmark)
Høskuldsson, Agnar
2001-01-01
The purpose of this paper is to present some useful methods for introductory analysis of variables and subsets in relation to PLS regression. We present here methods that are efficient in finding the appropriate variables or subset to use in the PLS regression. The general conclusion...... is that variable selection is important for successful analysis of chemometric data. An important aspect of the results presented is that lack of variable selection can spoil the PLS regression, and that cross-validation measures using a test set can show larger variation, when we use different subsets of X, than...
Applied Regression Modeling A Business Approach
Pardoe, Iain
2012-01-01
An applied and concise treatment of statistical regression techniques for business students and professionals who have little or no background in calculusRegression analysis is an invaluable statistical methodology in business settings and is vital to model the relationship between a response variable and one or more predictor variables, as well as the prediction of a response value given values of the predictors. In view of the inherent uncertainty of business processes, such as the volatility of consumer spending and the presence of market uncertainty, business professionals use regression a
Regressive language in severe head injury.
Thomsen, I V; Skinhoj, E
1976-09-01
In a follow-up study of 50 patients with severe head injuries three patients had echolalia. One patient with initially global aphasia had echolalia for some weeks when he started talking. Another patient with severe diffuse brain damage, dementia, and emotional regression had echolalia. The dysfunction was considered a detour performance. In the third patient echolalia and palilalia were details in a total pattern of regression lasting for months. The patient, who had extensive frontal atrophy secondary to a very severe head trauma, presented an extreme state of regression returning to a foetal-body pattern and behaving like a baby.
Regression of altitude-produced cardiac hypertrophy.
Sizemore, D. A.; Mcintyre, T. W.; Van Liere, E. J.; Wilson , M. F.
1973-01-01
The rate of regression of cardiac hypertrophy with time has been determined in adult male albino rats. The hypertrophy was induced by intermittent exposure to simulated high altitude. The percentage hypertrophy was much greater (46%) in the right ventricle than in the left (16%). The regression could be adequately fitted to a single exponential function with a half-time of 6.73 plus or minus 0.71 days (90% CI). There was no significant difference in the rates of regression for the two ventricles.
Regression of altitude-produced cardiac hypertrophy.
Sizemore, D. A.; Mcintyre, T. W.; Van Liere, E. J.; Wilson , M. F.
1973-01-01
The rate of regression of cardiac hypertrophy with time has been determined in adult male albino rats. The hypertrophy was induced by intermittent exposure to simulated high altitude. The percentage hypertrophy was much greater (46%) in the right ventricle than in the left (16%). The regression could be adequately fitted to a single exponential function with a half-time of 6.73 plus or minus 0.71 days (90% CI). There was no significant difference in the rates of regression for the two ventricles.
In precision agriculture regression has been used widely to quality the relationship between soil attributes and other environmental variables. However, spatial correlation existing in soil samples usually makes the regression model suboptimal. In this study, a regression-kriging method was attemp...
DEFF Research Database (Denmark)
Povlsen, Lene; Borup, I.
2015-01-01
In 1953 when the Nordic School of Public Health was founded, the aim of public health programmes was disease prevention more than health promotion. This was not unusual, since at this time health usually was seen as the opposite of disease and illness. However, with the Ottawa Charter of 1986......, the World Health Organization made a crucial change to view health not as a goal in itself but as the means to a full life. In this way, health promotion became a first priority and fundamental action for the modern society. This insight eventually reached NHV and in 2002 - 50 years after the foundation...... - an associate professorship was established with a focus on health promotion. Nevertheless, the concept of health promotion had been integrated with or mentioned in courses run prior to the new post. Subsequently, a wide spectrum of courses in health promotion was introduced, such as Empowerment for Child...
Multiple Instance Regression with Structured Data
Wagstaff, Kiri L.; Lane, Terran; Roper, Alex
2008-01-01
This slide presentation reviews the use of multiple instance regression with structured data from multiple and related data sets. It applies the concept to a practical problem, that of estimating crop yield using remote sensed country wide weekly observations.
Prediction of Dynamical Systems by Symbolic Regression
Quade, Markus; Shafi, Kamran; Niven, Robert K; Noack, Bernd R
2016-01-01
We study the modeling and prediction of dynamical systems based on conventional models derived from measurements. Such algorithms are highly desirable in situations where the underlying dynamics are hard to model from physical principles or simplified models need to be found. We focus on symbolic regression methods as a part of machine learning. These algorithms are capable of learning an analytically tractable model from data, a highly valuable property. Symbolic regression methods can be considered as generalized regression methods. We investigate two particular algorithms, the so-called fast function extraction which is a generalized linear regression algorithm, and genetic programming which is a very general method. Both are able to combine functions in a certain way such that a good model for the prediction of the temporal evolution of a dynamical system can be identified. We illustrate the algorithms by finding a prediction for the evolution of a harmonic oscillator based on measurements, by detecting a...
Some Simple Computational Formulas for Multiple Regression
Aiken, Lewis R., Jr.
1974-01-01
Short-cut formulas are presented for direct computation of the beta weights, the standard errors of the beta weights, and the multiple correlation coefficient for multiple regression problems involving three independent variables and one dependent variable. (Author)
Spontaneous Regression of an Incidental Spinal Meningioma
Directory of Open Access Journals (Sweden)
Ali Yilmaz
2015-12-01
Full Text Available AIM: The regression of meningioma has been reported in literature before. In spite of the fact that the regression may be involved by hemorrhage, calcification or some drugs withdrawal, it is rarely observed spontaneously. CASE REPORT: We report a 17 year old man with a cervical meningioma which was incidentally detected. In his cervical MRI an extradural, cranio-caudal contrast enchanced lesion at C2-C3 levels of the cervical spinal cord was detected. Despite the slight compression towards the spinal cord, he had no symptoms and refused any kind of surgical approach. The meningioma was followed by control MRI and it spontaneously regressed within six months. There were no signs of hemorrhage or calcification. CONCLUSION: Although it is a rare condition, the clinicians should consider that meningiomas especially incidentally diagnosed may be regressed spontaneously.
Spontaneous Regression of an Incidental Spinal Meningioma.
Yilmaz, Ali; Kizilay, Zahir; Sair, Ahmet; Avcil, Mucahit; Ozkul, Ayca
2016-03-15
The regression of meningioma has been reported in literature before. In spite of the fact that the regression may be involved by hemorrhage, calcification or some drugs withdrawal, it is rarely observed spontaneously. We report a 17 year old man with a cervical meningioma which was incidentally detected. In his cervical MRI an extradural, cranio-caudal contrast enchanced lesion at C2-C3 levels of the cervical spinal cord was detected. Despite the slight compression towards the spinal cord, he had no symptoms and refused any kind of surgical approach. The meningioma was followed by control MRI and it spontaneously regressed within six months. There were no signs of hemorrhage or calcification. Although it is a rare condition, the clinicians should consider that meningiomas especially incidentally diagnosed may be regressed spontaneously.
Vectors, a tool in statistical regression theory
Corsten, L.C.A.
1958-01-01
Using linear algebra this thesis developed linear regression analysis including analysis of variance, covariance analysis, special experimental designs, linear and fertility adjustments, analysis of experiments at different places and times. The determination of the orthogonal projection, yielding e
Patterns of Regression in Rett Syndrome
Directory of Open Access Journals (Sweden)
J Gordon Millichap
2002-10-01
Full Text Available Patterns and features of regression in a case series of 53 girls and women with Rett syndrome were studied at the Institute of Child Health and Great Ormond Street Children’s Hospital, London, UK.
A new bivariate negative binomial regression model
Faroughi, Pouya; Ismail, Noriszura
2014-12-01
This paper introduces a new form of bivariate negative binomial (BNB-1) regression which can be fitted to bivariate and correlated count data with covariates. The BNB regression discussed in this study can be fitted to bivariate and overdispersed count data with positive, zero or negative correlations. The joint p.m.f. of the BNB1 distribution is derived from the product of two negative binomial marginals with a multiplicative factor parameter. Several testing methods were used to check overdispersion and goodness-of-fit of the model. Application of BNB-1 regression is illustrated on Malaysian motor insurance dataset. The results indicated that BNB-1 regression has better fit than bivariate Poisson and BNB-2 models with regards to Akaike information criterion.
Heteroscedastic regression analysis method for mixed data
Institute of Scientific and Technical Information of China (English)
FU Hui-min; YUE Xiao-rui
2011-01-01
The heteroscedastic regression model was established and the heteroscedastic regression analysis method was presented for mixed data composed of complete data, type- I censored data and type- Ⅱ censored data from the location-scale distribution. The best unbiased estimations of regression coefficients, as well as the confidence limits of the location parameter and scale parameter were given. Furthermore, the point estimations and confidence limits of percentiles were obtained. Thus, the traditional multiple regression analysis method which is only suitable to the complete data from normal distribution can be extended to the cases of heteroscedastic mixed data and the location-scale distribution. So the presented method has a broad range of promising applications.
Superquantile Regression: Theory, Algorithms, and Applications
2014-12-01
Isabel. I love having you in my arms, and although you are still too young to understand what a hug is, your warmth has given me the strength and...squares and the quantile regression models adjust to changes in the data set, denoted by the red dots. Notice that the observa- tions are moved upwards...model hardly changes. If we change this observation in red even further upwards, we would notice no more changes in the quantile regression function
Marginal longitudinal semiparametric regression via penalized splines
Al Kadiri, M.
2010-08-01
We study the marginal longitudinal nonparametric regression problem and some of its semiparametric extensions. We point out that, while several elaborate proposals for efficient estimation have been proposed, a relative simple and straightforward one, based on penalized splines, has not. After describing our approach, we then explain how Gibbs sampling and the BUGS software can be used to achieve quick and effective implementation. Illustrations are provided for nonparametric regression and additive models.
Boosted regression tree, table, and figure data
Spreadsheets are included here to support the manuscript Boosted Regression Tree Models to Explain Watershed Nutrient Concentrations and Biological Condition. This dataset is associated with the following publication:Golden , H., C. Lane , A. Prues, and E. D'Amico. Boosted Regression Tree Models to Explain Watershed Nutrient Concentrations and Biological Condition. JAWRA. American Water Resources Association, Middleburg, VA, USA, 52(5): 1251-1274, (2016).
Fuzzy multiple linear regression: A computational approach
Juang, C. H.; Huang, X. H.; Fleming, J. W.
1992-01-01
This paper presents a new computational approach for performing fuzzy regression. In contrast to Bardossy's approach, the new approach, while dealing with fuzzy variables, closely follows the conventional regression technique. In this approach, treatment of fuzzy input is more 'computational' than 'symbolic.' The following sections first outline the formulation of the new approach, then deal with the implementation and computational scheme, and this is followed by examples to illustrate the new procedure.
Discriminative Elastic-Net Regularized Linear Regression.
Zhang, Zheng; Lai, Zhihui; Xu, Yong; Shao, Ling; Wu, Jian; Xie, Guo-Sen
2017-03-01
In this paper, we aim at learning compact and discriminative linear regression models. Linear regression has been widely used in different problems. However, most of the existing linear regression methods exploit the conventional zero-one matrix as the regression targets, which greatly narrows the flexibility of the regression model. Another major limitation of these methods is that the learned projection matrix fails to precisely project the image features to the target space due to their weak discriminative capability. To this end, we present an elastic-net regularized linear regression (ENLR) framework, and develop two robust linear regression models which possess the following special characteristics. First, our methods exploit two particular strategies to enlarge the margins of different classes by relaxing the strict binary targets into a more feasible variable matrix. Second, a robust elastic-net regularization of singular values is introduced to enhance the compactness and effectiveness of the learned projection matrix. Third, the resulting optimization problem of ENLR has a closed-form solution in each iteration, which can be solved efficiently. Finally, rather than directly exploiting the projection matrix for recognition, our methods employ the transformed features as the new discriminate representations to make final image classification. Compared with the traditional linear regression model and some of its variants, our method is much more accurate in image classification. Extensive experiments conducted on publicly available data sets well demonstrate that the proposed framework can outperform the state-of-the-art methods. The MATLAB codes of our methods can be available at http://www.yongxu.org/lunwen.html.
Spontaneous regression of metastatic Merkel cell carcinoma.
LENUS (Irish Health Repository)
Hassan, S J
2010-01-01
Merkel cell carcinoma is a rare aggressive neuroendocrine carcinoma of the skin predominantly affecting elderly Caucasians. It has a high rate of local recurrence and regional lymph node metastases. It is associated with a poor prognosis. Complete spontaneous regression of Merkel cell carcinoma has been reported but is a poorly understood phenomenon. Here we present a case of complete spontaneous regression of metastatic Merkel cell carcinoma demonstrating a markedly different pattern of events from those previously published.
The Infinite Hierarchical Factor Regression Model
Rai, Piyush
2009-01-01
We propose a nonparametric Bayesian factor regression model that accounts for uncertainty in the number of factors, and the relationship between factors. To accomplish this, we propose a sparse variant of the Indian Buffet Process and couple this with a hierarchical model over factors, based on Kingman's coalescent. We apply this model to two problems (factor analysis and factor regression) in gene-expression data analysis.
Marginal longitudinal semiparametric regression via penalized splines.
Kadiri, M Al; Carroll, R J; Wand, M P
2010-08-01
We study the marginal longitudinal nonparametric regression problem and some of its semiparametric extensions. We point out that, while several elaborate proposals for efficient estimation have been proposed, a relative simple and straightforward one, based on penalized splines, has not. After describing our approach, we then explain how Gibbs sampling and the BUGS software can be used to achieve quick and effective implementation. Illustrations are provided for nonparametric regression and additive models.
Multiple-Instance Regression with Structured Data
Wagstaff, Kiri L.; Lane, Terran; Roper, Alex
2008-01-01
We present a multiple-instance regression algorithm that models internal bag structure to identify the items most relevant to the bag labels. Multiple-instance regression (MIR) operates on a set of bags with real-valued labels, each containing a set of unlabeled items, in which the relevance of each item to its bag label is unknown. The goal is to predict the labels of new bags from their contents. Unlike previous MIR methods, MI-ClusterRegress can operate on bags that are structured in that they contain items drawn from a number of distinct (but unknown) distributions. MI-ClusterRegress simultaneously learns a model of the bag's internal structure, the relevance of each item, and a regression model that accurately predicts labels for new bags. We evaluated this approach on the challenging MIR problem of crop yield prediction from remote sensing data. MI-ClusterRegress provided predictions that were more accurate than those obtained with non-multiple-instance approaches or MIR methods that do not model the bag structure.
[Iris movement mediates pupillary membrane regression].
Morizane, Yuki
2007-11-01
In the course of mammalian lens development, a transient capillary meshwork called as the pupillary membrane (PM) forms. It is located in the pupil area to nourish the anterior surface of the lens, and then regresses to clear the optical path. Although the involvement of the apoptotic process has been reported in PM regression, the initiating factor remains unknown. We initially found that regression of the PM coincided with the development of iris motility, and that iris movement caused cessation and resumption of blood flow within the PM. Therefore, we investigated whether the development of the capacity of the iris to constrict and dilate can function as an essential signal that induces apoptosis in the PM. Continuous inhibition of iris movement with mydriatic agents suppressed apoptosis of the PM and resulted in the persistence of PM in rats. The distribution of apoptotic cells in the regressing PM was diffuse and showed no apparent localization. These results indicated that iris movement induced regression of the PM by changing the blood flow within it. This study suggests the importance of the physiological interactions between tissues-in this case, the iris and the PM-as a signal to advance vascular regression during organ development.
Post-processing through linear regression
Directory of Open Access Journals (Sweden)
B. Van Schaeybroeck
2011-03-01
Full Text Available Various post-processing techniques are compared for both deterministic and ensemble forecasts, all based on linear regression between forecast data and observations. In order to evaluate the quality of the regression methods, three criteria are proposed, related to the effective correction of forecast error, the optimal variability of the corrected forecast and multicollinearity. The regression schemes under consideration include the ordinary least-square (OLS method, a new time-dependent Tikhonov regularization (TDTR method, the total least-square method, a new geometric-mean regression (GM, a recently introduced error-in-variables (EVMOS method and, finally, a "best member" OLS method. The advantages and drawbacks of each method are clarified.
These techniques are applied in the context of the 63 Lorenz system, whose model version is affected by both initial condition and model errors. For short forecast lead times, the number and choice of predictors plays an important role. Contrarily to the other techniques, GM degrades when the number of predictors increases. At intermediate lead times, linear regression is unable to provide corrections to the forecast and can sometimes degrade the performance (GM and the best member OLS with noise. At long lead times the regression schemes (EVMOS, TDTR which yield the correct variability and the largest correlation between ensemble error and spread, should be preferred.
Post-processing through linear regression
van Schaeybroeck, B.; Vannitsem, S.
2011-03-01
Various post-processing techniques are compared for both deterministic and ensemble forecasts, all based on linear regression between forecast data and observations. In order to evaluate the quality of the regression methods, three criteria are proposed, related to the effective correction of forecast error, the optimal variability of the corrected forecast and multicollinearity. The regression schemes under consideration include the ordinary least-square (OLS) method, a new time-dependent Tikhonov regularization (TDTR) method, the total least-square method, a new geometric-mean regression (GM), a recently introduced error-in-variables (EVMOS) method and, finally, a "best member" OLS method. The advantages and drawbacks of each method are clarified. These techniques are applied in the context of the 63 Lorenz system, whose model version is affected by both initial condition and model errors. For short forecast lead times, the number and choice of predictors plays an important role. Contrarily to the other techniques, GM degrades when the number of predictors increases. At intermediate lead times, linear regression is unable to provide corrections to the forecast and can sometimes degrade the performance (GM and the best member OLS with noise). At long lead times the regression schemes (EVMOS, TDTR) which yield the correct variability and the largest correlation between ensemble error and spread, should be preferred.
Labunskaia, E A; Zhigalova, T V; Chub, V V
2007-01-01
Leaf anatomy was studied in the mosaic Ficus benjamina cv. Starlight and non-chimeric Ficus benjamina cv. Daniel. The number of chloroplasts in a white, chlorophyll-deficient tissue declines as compared to the green tissue. However, their functional activity is retained. The leaf of the mosaic F. benjamina contains two or, sometimes, three subepidermal layers. Mesophyll forms one layer in the green and white parts of leaf palisade and one white and one green layer in the transitional zone (edge). In the transitional zone, green spongy mesophyll is located between two white spongy layers and the proportion of photosynthesizing cells varies. In cv. Daniel, there are two subepidermal layers and one layer of columnar mesophyll cells. According to the morphometry data, the proportion of white zone in the leaf correlates with the leaf position in the whole shoot: the higher the branch order, the larger the proportion of white zone. The total leaf area depends also on its position in the shoot. No such correlation was found in non-chimeric F. benjamina cv. Daniel. In the mosaic chimera, the source-sink status appears to depend on the leaf position in the shoot. Experiments with individual shoots of the same order and elimination of all lateral shoots have shown that the proportion of white zone in new leaves on the shoot increases with the total area of green zone. Thus, the area of assimilating shoot surface affects the formation of leaves in the meristem. A hypothesis was put forward that the source-sink state affects the ratio of green and white parts in the leaf primordium. Products of photosynthesis (carbohydrates) are a possible metabolic signal affecting the meristem. It cannot be excluded as well that the hormonal state undergoes changes in the chimeric plant.
Energy Technology Data Exchange (ETDEWEB)
NONE
1995-10-01
The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.
Franke, R.
2016-11-01
In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.
Energy Technology Data Exchange (ETDEWEB)
NONE
1995-10-01
The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.
An Analysis of Bank Service Satisfaction Based on Quantile Regression and Grey Relational Analysis
Directory of Open Access Journals (Sweden)
Wen-Tsao Pan
2016-01-01
Full Text Available Bank service satisfaction is vital to the success of a bank. In this paper, we propose to use the grey relational analysis to gauge the levels of service satisfaction of the banks. With the grey relational analysis, we compared the effects of different variables on service satisfaction. We gave ranks to the banks according to their levels of service satisfaction. We further used the quantile regression model to find the variables that affected the satisfaction of a customer at a specific quantile of satisfaction level. The result of the quantile regression analysis provided a bank manager with information to formulate policies to further promote satisfaction of the customers at different quantiles of satisfaction level. We also compared the prediction accuracies of the regression models at different quantiles. The experiment result showed that, among the seven quantile regression models, the median regression model has the best performance in terms of RMSE, RTIC, and CE performance measures.
Regression Test Selection for C# Programs
Directory of Open Access Journals (Sweden)
Nashat Mansour
2009-01-01
Full Text Available We present a regression test selection technique for C# programs. C# is fairly new and is often used within the Microsoft .Net framework to give programmers a solid base to develop a variety of applications. Regression testing is done after modifying a program. Regression test selection refers to selecting a suitable subset of test cases from the original test suite in order to be rerun. It aims to provide confidence that the modifications are correct and did not affect other unmodified parts of the program. The regression test selection technique presented in this paper accounts for C#.Net specific features. Our technique is based on three phases; the first phase builds an Affected Class Diagram consisting of classes that are affected by the change in the source code. The second phase builds a C# Interclass Graph (CIG from the affected class diagram based on C# specific features. In this phase, we reduce the number of selected test cases. The third phase involves further reduction and a new metric for assigning weights to test cases for prioritizing the selected test cases. We have empirically validated the proposed technique by using case studies. The empirical results show the usefulness of the proposed regression testing technique for C#.Net programs.
Regression analysis using dependent Polya trees.
Schörgendorfer, Angela; Branscum, Adam J
2013-11-30
Many commonly used models for linear regression analysis force overly simplistic shape and scale constraints on the residual structure of data. We propose a semiparametric Bayesian model for regression analysis that produces data-driven inference by using a new type of dependent Polya tree prior to model arbitrary residual distributions that are allowed to evolve across increasing levels of an ordinal covariate (e.g., time, in repeated measurement studies). By modeling residual distributions at consecutive covariate levels or time points using separate, but dependent Polya tree priors, distributional information is pooled while allowing for broad pliability to accommodate many types of changing residual distributions. We can use the proposed dependent residual structure in a wide range of regression settings, including fixed-effects and mixed-effects linear and nonlinear models for cross-sectional, prospective, and repeated measurement data. A simulation study illustrates the flexibility of our novel semiparametric regression model to accurately capture evolving residual distributions. In an application to immune development data on immunoglobulin G antibodies in children, our new model outperforms several contemporary semiparametric regression models based on a predictive model selection criterion. Copyright © 2013 John Wiley & Sons, Ltd.
Hyperglycemia impairs atherosclerosis regression in mice.
Gaudreault, Nathalie; Kumar, Nikit; Olivas, Victor R; Eberlé, Delphine; Stephens, Kyle; Raffai, Robert L
2013-12-01
Diabetic patients are known to be more susceptible to atherosclerosis and its associated cardiovascular complications. However, the effects of hyperglycemia on atherosclerosis regression remain unclear. We hypothesized that hyperglycemia impairs atherosclerosis regression by modulating the biological function of lesional macrophages. HypoE (Apoe(h/h)Mx1-Cre) mice express low levels of apolipoprotein E (apoE) and develop atherosclerosis when fed a high-fat diet. Atherosclerosis regression occurs in these mice upon plasma lipid lowering induced by a change in diet and the restoration of apoE expression. We examined the morphological characteristics of regressed lesions and assessed the biological function of lesional macrophages isolated with laser-capture microdissection in euglycemic and hyperglycemic HypoE mice. Hyperglycemia induced by streptozotocin treatment impaired lesion size reduction (36% versus 14%) and lipid loss (38% versus 26%) after the reversal of hyperlipidemia. However, decreases in lesional macrophage content and remodeling in both groups of mice were similar. Gene expression analysis revealed that hyperglycemia impaired cholesterol transport by modulating ATP-binding cassette A1, ATP-binding cassette G1, scavenger receptor class B family member (CD36), scavenger receptor class B1, and wound healing pathways in lesional macrophages during atherosclerosis regression. Hyperglycemia impairs both reduction in size and loss of lipids from atherosclerotic lesions upon plasma lipid lowering without significantly affecting the remodeling of the vascular wall.
Razza, Eduardo M; Satrapa, Rafael A; Emanuelli, Isabele P; Barros, Ciro M; Nogueira, Marcelo F G
2016-03-01
The aggregation of a tetraploid zebu embryo (Bos indicus, a thermotolerant breed) with a diploid taurine embryo (Bos taurus, a thermosensitive breed) should create a complete taurine fetus, whose extra-embryonic components, e.g., the chorion, is derived mainly from the zebu embryo. These zebu-derived extra-embryonic components may interact positively with the taurine embryo/fetus during pregnancy in a tropical environment. We tested different parameters for the production of tetraploid Nelore (Bos indicus) embryos to be combined via aggregation with crossbred Bos taurus (diploid) embryos in order to produce viable chimeric blastocysts. Bovine (Bos indicus or crossbred Bos taurus) embryos were produced in vitro according to standard procedures. Two-cell Bos indicus embryos were submitted to electrofusion with varying numbers of pulses (1 or 2), voltages (0.4, 0.5, 0.75, 1.0, 1.4 and 5.0 kV/cm) and time (20, 25, 50 and 60 μs) to produce tetraploid embryos. Electrofused embryos were cultured with crossbred non-fused embryos to form chimeras that developed until the blastocyst stage. The best fusion parameter was 0.75 kV/cm for 60 μs. Four chimeric blastocysts (tetraploid Nelore with diploid crossbred Holstein) were formed after 31 attempts in 4 replicates (13%). We established an optimal procedure for the production of tetraploid Bos indicus (4n) embryos and embryonic chimeras by aggregation of crossbred Bos taurus (2n) with Bos indicus (4n) embryos. This technique would be valid in applied research, by producing exclusively taurine calves, but with placental elements from the Bos indicus breed, following transfer of these chimeras into recipient cows.
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Cesidio Giuliani
2016-07-01
Full Text Available Since the discovery 60 years ago of the long-acting thyroid stimulator by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH receptor autoantibodies (TRAbs in Graves’ disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves’ disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies against the TSH receptor. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves’ disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSH receptor, the Kohn laboratory constructed human TSH receptor–rat luteinizing hormone/ chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of nonthyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves’ disease. This review also describes the main contributions made by others researchers in TSH receptor molecular biology and TRAbs assay, especially with the development of highly potent monoclonal antibodies. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided.
Giuliani, Cesidio; Saji, Motoyasu; Bucci, Ines; Napolitano, Giorgio
2016-01-01
Since the discovery 60 years ago of the “long-acting thyroid stimulator” by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH) receptor (TSHR) autoantibodies (TRAbs) in Graves’ disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves’ disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies (moAbs) against the TSHR. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves’ disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSHR, the Kohn laboratory constructed human TSHR–rat luteinizing hormone/chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of non-thyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves’ disease. This review also describes the main contributions made by other researchers in TSHR molecular biology and TRAbs assay, especially with the development of highly potent moAbs. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided. PMID:27504107
Kylefjord, Helen; Danielsson, Axel; Sedig, Susanne; Belda, Oscar; Wiktelius, Daniel; Vrang, Lotta; Targett-Adams, Paul
2014-01-01
Although hepatitis C virus (HCV) is a pathogen of global significance, experimental therapies in current clinical development include highly efficacious all-oral combinations of HCV direct-acting antivirals (DAAs). If approved for use, these new treatment regimens will impact dramatically upon our capacity to eradicate HCV in the majority of virus-infected patients. However, recent data from late-stage clinical evaluations demonstrated that individuals infected with HCV genotype (GT) 3 responded less well to all-oral DAA combinations than patients infected with other HCV GTs. In light of these observations, the present study sought to expand the number of molecular tools available to investigate small molecule-mediated inhibition of HCV GT3 NS5A and NS5B proteins in preclinical tissue-culture systems. Accordingly, a novel subgenomic HCV replicon chimera was created by utilizing a GT1b backbone modified to produce NS5A and NS5B proteins from a consensus sequence generated from HCV GT3a genomic sequences deposited online at the European Hepatitis C Virus database. This approach avoided the need to isolate and amplify HCV genomes from sera derived from HCV-infected patients. The replicon chimera, together with a version engineered to express NS5A encoding a Y93H mutation, demonstrated levels of replication in transient assays robust enough to assess accurate antiviral activities of inhibitors representing different HCV DAA classes. Thus, the replicon chimera represents a new simple molecular tool suitable for drug discovery programmes aimed at investigating, understanding, and improving GT3a activities of HCV DAAs targeting NS5A or NS5B.
Giuliani, Cesidio; Saji, Motoyasu; Bucci, Ines; Napolitano, Giorgio
2016-01-01
Since the discovery 60 years ago of the "long-acting thyroid stimulator" by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH) receptor (TSHR) autoantibodies (TRAbs) in Graves' disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves' disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies (moAbs) against the TSHR. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves' disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSHR, the Kohn laboratory constructed human TSHR-rat luteinizing hormone/chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of non-thyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves' disease. This review also describes the main contributions made by other researchers in TSHR molecular biology and TRAbs assay, especially with the development of highly potent moAbs. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided.
Hajimorad, M R; Eggenberger, A L; Hill, J H
2008-07-01
In Rsv1-genotype soybean, Soybean mosaic virus (SMV)-N (an avirulent isolate of strain G2) elicits extreme resistance (ER) whereas strain SMV-G7 provokes a lethal systemic hypersensitive response (LSHR). SMV-G7d, an experimentally evolved variant of SMV-G7, induces systemic mosaic. Thus, for Rsv1-genotype soybean, SMV-N is avirulent whereas SMV-G7 and SMV-G7d are both virulent. Exploiting these differential interactions, we recently mapped the elicitor functions of SMV provoking Rsv1-mediated ER and LSHR to the N-terminal 271 amino acids of P3 from SMV-N and SMV-G7, respectively. The phenotype of both SMV-G7 and SMV-G7d were rendered avirulent on Rsv1-genotype soybean when the part of the genome encoding the N-terminus or the entire P3 cistron was replaced with that from SMV-N; however, reciprocal exchanges did not confer virulence to SMV-N-derived P3 chimeras. Here, we describe virulent SMV-N-derived P3 chimeras containing the full-length or the N-terminal P3 from SMV-G7 or SMV-G7d, with or without additional mutations in P3, that were selected on Rsv1-genotype soybean by sequential transfers on rsv1 and Rsv1-genotype soybean. Sequence analyses of the P3 and helper-component proteinase (HC-Pro) cistrons of progeny recovered from Rsv1-genotype soybean consistently revealed the presence of mutations in HC-Pro. Interestingly, the precise mutations in HC-Pro required for the adaptation varied among the chimeras. No mutation was detected in the HC-Pro of progeny passaged continuously in rsv1-genotype soybean, suggesting that selection is a consequence of pressure imposed by Rsv1. Mutations in HC-Pro alone failed to confer virulence to SMV-N; however, reconstruction of mutations in HC-Pro of the SMV-N-derived P3 chimeras resulted in virulence. Taken together, the data suggest that HC-Pro complementation of P3 is essential for SMV virulence on Rsv1-genotype soybean.
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Priya Chikhlikar
Full Text Available Previous studies of HIV-1 p55Gag immunization of mice have demonstrated the usefulness of targeting antigens to the cellular compartment containing the major histocompatibility complex type II (MHC II complex molecules by use of a DNA antigen formulation encoding Gag as a chimera with the mouse lysosome-associated membrane protein (mLAMP/gag. In the present study, we have analyzed the magnitude and breadth of Gag-specific T-lymphocyte and antibody responses elicited in Rhesus macaques after immunization with DNA encoding a human LAMP/gag (hLAMP/gag chimera. ELISPOT analyses indicated that the average Gag-specific IFN-gamma response elicited by the hLAMP/gag chimera was detectable after only two or three naked DNA immunizations in all five immunized macaques and reached an average of 1000 spot-forming cells (SFC/10(6 PBMCs. High IFN-gamma ELISPOT responses were detected in CD8(+-depleted cells, indicating that CD4(+ T-cells play a major role in these responses. The T-cell responses of four of the macaques were also tested by use of ELISPOT to 12 overlapping 15-amino acids (aa peptide pools containing ten peptides each, encompassing the complete Gag protein sequence. The two Mamu 08 immunized macaques responded to eight and twelve of the pools, the Mamu B01 to six, and the other macaque to five pools indicating that the hLAMP/gag DNA antigen formulation elicits a broad T-cell response against Gag. Additionally, there was a strong HIV-1-specific IgG response. The IgG antibody titers increased after each DNA injection, indicating a strong amnestic B-cell response, and were highly elevated in all the macaques after three immunizations. Moreover, the serum of each macaque recognized 13 of the 49 peptides of a 20-aa peptide library covering the complete Gag amino acid sequence. In addition, HIV-1-specific IgA antibodies were present in the plasma and external secretions, including nasal washes. These data support the findings of increased
Competing Risks Quantile Regression at Work
DEFF Research Database (Denmark)
Dlugosz, Stephan; Lo, Simon M. S.; Wilke, Ralf
2017-01-01
Despite its emergence as a frequently used method for the empirical analysis of multivariate data, quantile regression is yet to become a mainstream tool for the analysis of duration data. We present a pioneering empirical study on the grounds of a competing risks quantile regression model. We us...... into the distribution of transitions out of maternity leave. It is found that cumulative incidences implied by the quantile regression model differ from those implied by a proportional hazards model. To foster the use of the model, we make an R-package (cmprskQR) available....... large-scale maternity duration data with multiple competing risks derived from German linked social security records to analyse how public policies are related to the length of economic inactivity of young mothers after giving birth. Our results show that the model delivers detailed insights...
SMOOTH TRANSITION LOGISTIC REGRESSION MODEL TREE
RODRIGO PINTO MOREIRA
2008-01-01
Este trabalho tem como objetivo principal adaptar o modelo STR-Tree, o qual é a combinação de um modelo Smooth Transition Regression com Classification and Regression Tree (CART), a fim de utilizá-lo em Classificação. Para isto algumas alterações foram realizadas em sua forma estrutural e na estimação. Devido ao fato de estarmos fazendo classificação de variáveis dependentes binárias, se faz necessária a utilização das técnicas empregadas em Regressão Logística, dessa forma a estimação dos pa...
Unsupervised K-Nearest Neighbor Regression
Kramer, Oliver
2011-01-01
In many scientific disciplines structures in high-dimensional data have to be found, e.g., in stellar spectra, in genome data, or for face recognition tasks. In this work we present a novel approach to non-linear dimensionality reduction. It is based on fitting K-nearest neighbor regression to the unsupervised regression framework for learning of low-dimensional manifolds. Similar to related approaches that are mostly based on kernel methods, unsupervised K-nearest neighbor (UKNN) regression optimizes latent variables w.r.t. the data space reconstruction error employing the K-nearest neighbor heuristic. The problem of optimizing latent neighborhoods is difficult to solve, but the UKNN formulation allows an efficient strategy of iteratively embedding latent points to fixed neighborhood topologies. The approaches will be tested experimentally.
LINEAR REGRESSION WITH R AND HADOOP
Directory of Open Access Journals (Sweden)
Bogdan OANCEA
2015-07-01
Full Text Available In this paper we present a way to solve the linear regression model with R and Hadoop using the Rhadoop library. We show how the linear regression model can be solved even for very large models that require special technologies. For storing the data we used Hadoop and for computation we used R. The interface between R and Hadoop is the open source library RHadoop. We present the main features of the Hadoop and R software systems and the way of interconnecting them. We then show how the least squares solution for the linear regression problem could be expressed in terms of map-reduce programming paradigm and how could be implemented using the Rhadoop library.
Rapidly Regressive Unilateral Fetal Pleural Effusion
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Tuncay Yuce
2015-03-01
Full Text Available Intrauterine pleural effusion of fetal lungs rarely regresses without intervention. In our case we treated a women at 32th weeks of gestation. Her pregnancy was complicated with fetal pleural effusion and polyhydramniosis. A therapeutic thoracocentesis was planned and she received two courses of betamethasone prior to procedure. On the day of planned procedure, a substantial regression of pleural effusion was observed and procedure was postponed. During her antenatal follow-up a complete regression of pleural effusion was observed. After delivery pleural effusion did not relapse. These findings hint there may be a role of antenatal steroids in treatment of fetal pleural effusion, which is known to be resistant to treatment modalities both during antenatal and postnatal period. [Cukurova Med J 2015; 40(Suppl 1: 25-28
Uncertainty quantification in DIC with Kriging regression
Wang, Dezhi; DiazDelaO, F. A.; Wang, Weizhuo; Lin, Xiaoshan; Patterson, Eann A.; Mottershead, John E.
2016-03-01
A Kriging regression model is developed as a post-processing technique for the treatment of measurement uncertainty in classical subset-based Digital Image Correlation (DIC). Regression is achieved by regularising the sample-point correlation matrix using a local, subset-based, assessment of the measurement error with assumed statistical normality and based on the Sum of Squared Differences (SSD) criterion. This leads to a Kriging-regression model in the form of a Gaussian process representing uncertainty on the Kriging estimate of the measured displacement field. The method is demonstrated using numerical and experimental examples. Kriging estimates of displacement fields are shown to be in excellent agreement with 'true' values for the numerical cases and in the experimental example uncertainty quantification is carried out using the Gaussian random process that forms part of the Kriging model. The root mean square error (RMSE) on the estimated displacements is produced and standard deviations on local strain estimates are determined.
KINERJA JACKKNIFE RIDGE REGRESSION DALAM MENGATASI MULTIKOLINEARITAS
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HANY DEVITA
2015-02-01
Full Text Available Ordinary least square is a parameter estimations for minimizing residual sum of squares. If the multicollinearity was found in the data, unbias estimator with minimum variance could not be reached. Multicollinearity is a linear correlation between independent variabels in model. Jackknife Ridge Regression(JRR as an extension of Generalized Ridge Regression (GRR for solving multicollinearity. Generalized Ridge Regression is used to overcome the bias of estimators caused of presents multicollinearity by adding different bias parameter for each independent variabel in least square equation after transforming the data into an orthoghonal form. Beside that, JRR can reduce the bias of the ridge estimator. The result showed that JRR model out performs GRR model.
On Solving Lq-Penalized Regressions
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Tracy Zhou Wu
2007-01-01
Full Text Available Lq-penalized regression arises in multidimensional statistical modelling where all or part of the regression coefficients are penalized to achieve both accuracy and parsimony of statistical models. There is often substantial computational difficulty except for the quadratic penalty case. The difficulty is partly due to the nonsmoothness of the objective function inherited from the use of the absolute value. We propose a new solution method for the general Lq-penalized regression problem based on space transformation and thus efficient optimization algorithms. The new method has immediate applications in statistics, notably in penalized spline smoothing problems. In particular, the LASSO problem is shown to be polynomial time solvable. Numerical studies show promise of our approach.
Principal component regression for crop yield estimation
Suryanarayana, T M V
2016-01-01
This book highlights the estimation of crop yield in Central Gujarat, especially with regard to the development of Multiple Regression Models and Principal Component Regression (PCR) models using climatological parameters as independent variables and crop yield as a dependent variable. It subsequently compares the multiple linear regression (MLR) and PCR results, and discusses the significance of PCR for crop yield estimation. In this context, the book also covers Principal Component Analysis (PCA), a statistical procedure used to reduce a number of correlated variables into a smaller number of uncorrelated variables called principal components (PC). This book will be helpful to the students and researchers, starting their works on climate and agriculture, mainly focussing on estimation models. The flow of chapters takes the readers in a smooth path, in understanding climate and weather and impact of climate change, and gradually proceeds towards downscaling techniques and then finally towards development of ...
A tutorial on Bayesian Normal linear regression
Klauenberg, Katy; Wübbeler, Gerd; Mickan, Bodo; Harris, Peter; Elster, Clemens
2015-12-01
Regression is a common task in metrology and often applied to calibrate instruments, evaluate inter-laboratory comparisons or determine fundamental constants, for example. Yet, a regression model cannot be uniquely formulated as a measurement function, and consequently the Guide to the Expression of Uncertainty in Measurement (GUM) and its supplements are not applicable directly. Bayesian inference, however, is well suited to regression tasks, and has the advantage of accounting for additional a priori information, which typically robustifies analyses. Furthermore, it is anticipated that future revisions of the GUM shall also embrace the Bayesian view. Guidance on Bayesian inference for regression tasks is largely lacking in metrology. For linear regression models with Gaussian measurement errors this tutorial gives explicit guidance. Divided into three steps, the tutorial first illustrates how a priori knowledge, which is available from previous experiments, can be translated into prior distributions from a specific class. These prior distributions have the advantage of yielding analytical, closed form results, thus avoiding the need to apply numerical methods such as Markov Chain Monte Carlo. Secondly, formulas for the posterior results are given, explained and illustrated, and software implementations are provided. In the third step, Bayesian tools are used to assess the assumptions behind the suggested approach. These three steps (prior elicitation, posterior calculation, and robustness to prior uncertainty and model adequacy) are critical to Bayesian inference. The general guidance given here for Normal linear regression tasks is accompanied by a simple, but real-world, metrological example. The calibration of a flow device serves as a running example and illustrates the three steps. It is shown that prior knowledge from previous calibrations of the same sonic nozzle enables robust predictions even for extrapolations.
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
Detecting plant health conditions plays a key role in farm pest management and crop protection. In this study,measurement of hyperspectral leaf reflectance in rice crop (Oryzasativa L.) was conducted on groups of healthy and infected leaves by the fungus Bipolaris oryzae (Helminthosporium oryzae Breda. de Hann) through the wavelength range from 350 to 2 500 nm. The percentage of leaf surface lesions was estimated and defined as the disease severity. Statistical methods like multiple stepwise regression, principal component analysis and partial least-square regression were utilized to calculate and estimate the disease severity of rice brown spot at the leaf level. Our results revealed that multiple stepwise linear regressions could efficiently estimate disease severity with three wavebands in seven steps. The root mean square errors (RMSEs) for training (n=210) and testing (n=53) dataset were 6.5% and 5.8%, respectively. Principal component analysis showed that the first principal component could explain approximately 80% of the variance of the original hyperspectral reflectance. The regression model with the first two principal components predicted a disease severity with RMSEs of 16.3% and 13.9% for the training and testing dataset, respectively. Partial least-square regression with seven extracted factors could most effectively predict disease severity compared with other statistical methods with RMSEs of 4.1% and 2.0% for the training and testing dataset, respectively. Our research demonstrates that it is feasible to estimate the disease severity office brown spot using hyperspectral reflectance data at the leaf level.
Removing Malmquist bias from linear regressions
Verter, Frances
1993-01-01
Malmquist bias is present in all astronomical surveys where sources are observed above an apparent brightness threshold. Those sources which can be detected at progressively larger distances are progressively more limited to the intrinsically luminous portion of the true distribution. This bias does not distort any of the measurements, but distorts the sample composition. We have developed the first treatment to correct for Malmquist bias in linear regressions of astronomical data. A demonstration of the corrected linear regression that is computed in four steps is presented.
Multicollinearity in cross-sectional regressions
Lauridsen, Jørgen; Mur, Jesùs
2006-10-01
The paper examines robustness of results from cross-sectional regression paying attention to the impact of multicollinearity. It is well known that the reliability of estimators (least-squares or maximum-likelihood) gets worse as the linear relationships between the regressors become more acute. We resolve the discussion in a spatial context, looking closely into the behaviour shown, under several unfavourable conditions, by the most outstanding misspecification tests when collinear variables are added to the regression. A Monte Carlo simulation is performed. The conclusions point to the fact that these statistics react in different ways to the problems posed.
Institute of Scientific and Technical Information of China (English)
林成华; 洪成文
2015-01-01
The eXplosion of international financial crisis in 2008 makes the growing of university students’em-ployment problems become a worldwide problem that impacts the development of higher education and social stabili-ty. The Federal Government of USA had issued many acts to solve the problem of university students’employment, and positive results had been obtained. From the perspective of the logic framework,value orientation and the base of theory,the university students’employment promotion policy during the financial crisis in USA was analyzed. It was found that under the impact of the Keynesian,American government adopted the combination of the short term strategy and long term strategy,mainly including the crisis emergency relief,eXpanding labor demand,improving the labor supply,promoting the match of demand and supply to promote the university students’employment,dis-playing the development tendency of combination of Keynesian and Neoliberalism. The short term strategy is mainly presented in the emergency relief policy at the beginning of the crisis,paying attention to the short term efficiency of the policy,to promote the social fairness as the value orientation,through the increasing government public fun-ding,developing the Green economy,directly purchasing the public service,supporting the development of middle and small enterprises and so on,to arouse the employment demand,solve the contradiction of supply and demand and promote the increasing of employment. The middle and longer term strategy is mainly presented in the function-al policy in the middle and later period of crisis,paying attention to the sustainable development of economy and society,and the long term efficiency of the policy,to promote the employment demand,labor force supply,match of the demand and supply as the value orientation,reforming the talents training mode,strengthening the occupa-tional training and human resources tactic reservation,also improving the national university
Directory of Open Access Journals (Sweden)
Federico A. Sturzeneger
1992-03-01
Full Text Available Currency Substitution and the Regressivity of Inflationary Taxation The purpose of this paper is to show that in the presence of financial adaptation or currency substitution. the inflation tax is extremely regressive. This regressivity arises from the existence of a fixed cost of switching to inflation-proof transactions technologies. This fixed cost makes it optimal only for those agents with sufficiently high incomes to switch out of domestic currency. The effects are illustrated and quantified for a particular case.
Demonstration of a Fiber Optic Regression Probe
Korman, Valentin; Polzin, Kurt A.
2010-01-01
The capability to provide localized, real-time monitoring of material regression rates in various applications has the potential to provide a new stream of data for development testing of various components and systems, as well as serving as a monitoring tool in flight applications. These applications include, but are not limited to, the regression of a combusting solid fuel surface, the ablation of the throat in a chemical rocket or the heat shield of an aeroshell, and the monitoring of erosion in long-life plasma thrusters. The rate of regression in the first application is very fast, while the second and third are increasingly slower. A recent fundamental sensor development effort has led to a novel regression, erosion, and ablation sensor technology (REAST). The REAST sensor allows for measurement of real-time surface erosion rates at a discrete surface location. The sensor is optical, using two different, co-located fiber-optics to perform the regression measurement. The disparate optical transmission properties of the two fiber-optics makes it possible to measure the regression rate by monitoring the relative light attenuation through the fibers. As the fibers regress along with the parent material in which they are embedded, the relative light intensities through the two fibers changes, providing a measure of the regression rate. The optical nature of the system makes it relatively easy to use in a variety of harsh, high temperature environments, and it is also unaffected by the presence of electric and magnetic fields. In addition, the sensor could be used to perform optical spectroscopy on the light emitted by a process and collected by fibers, giving localized measurements of various properties. The capability to perform an in-situ measurement of material regression rates is useful in addressing a variety of physical issues in various applications. An in-situ measurement allows for real-time data regarding the erosion rates, providing a quick method for
Li, Qin; Zhao, Yongxin; Wu, Xiaofeng; Liu, Si
There can be multitudinous models specifying aspects of the same system. Each model has a bias towards one aspect. These models often override in specific aspects though they have different expressions. A specification written in one model can be refined by introducing additional information from other models. The paper proposes a concept of promoting models which is a methodology to obtain refinements with support from cooperating models. It refines a primary model by integrating the information from a secondary model. The promotion principle is not merely an academic point, but also a reliable and robust engineering technique which can be used to develop software and hardware systems. It can also check the consistency between two specifications from different models. A case of modeling a simple online shopping system with the cooperation of the guarded design model and CSP model illustrates the practicability of the promotion principle.
A Skew-Normal Mixture Regression Model
Liu, Min; Lin, Tsung-I
2014-01-01
A challenge associated with traditional mixture regression models (MRMs), which rest on the assumption of normally distributed errors, is determining the number of unobserved groups. Specifically, even slight deviations from normality can lead to the detection of spurious classes. The current work aims to (a) examine how sensitive the commonly…
Predicting Social Trust with Binary Logistic Regression
Adwere-Boamah, Joseph; Hufstedler, Shirley
2015-01-01
This study used binary logistic regression to predict social trust with five demographic variables from a national sample of adult individuals who participated in The General Social Survey (GSS) in 2012. The five predictor variables were respondents' highest degree earned, race, sex, general happiness and the importance of personally assisting…
The Geometry of Enhancement in Multiple Regression.
Waller, Niels G
2011-10-01
In linear multiple regression, "enhancement" is said to occur when R (2)=b'r>r'r, where b is a p×1 vector of standardized regression coefficients and r is a p×1 vector of correlations between a criterion y and a set of standardized regressors, x. When p=1 then b≡r and enhancement cannot occur. When p=2, for all full-rank R xx≠I, R xx=E[xx']=V Λ V' (where V Λ V' denotes the eigen decomposition of R xx; λ 1>λ 2), the set [Formula: see text] contains four vectors; the set [Formula: see text]; [Formula: see text] contains an infinite number of vectors. When p≥3 (and λ 1>λ 2>⋯>λ p ), both sets contain an uncountably infinite number of vectors. Geometrical arguments demonstrate that B 1 occurs at the intersection of two hyper-ellipsoids in ℝ (p) . Equations are provided for populating the sets B 1 and B 2 and for demonstrating that maximum enhancement occurs when b is collinear with the eigenvector that is associated with λ p (the smallest eigenvalue of the predictor correlation matrix). These equations are used to illustrate the logic and the underlying geometry of enhancement in population, multiple-regression models. R code for simulating population regression models that exhibit enhancement of any degree and any number of predictors is included in Appendices A and B.
Regression Segmentation for M³ Spinal Images.
Wang, Zhijie; Zhen, Xiantong; Tay, KengYeow; Osman, Said; Romano, Walter; Li, Shuo
2015-08-01
Clinical routine often requires to analyze spinal images of multiple anatomic structures in multiple anatomic planes from multiple imaging modalities (M(3)). Unfortunately, existing methods for segmenting spinal images are still limited to one specific structure, in one specific plane or from one specific modality (S(3)). In this paper, we propose a novel approach, Regression Segmentation, that is for the first time able to segment M(3) spinal images in one single unified framework. This approach formulates the segmentation task innovatively as a boundary regression problem: modeling a highly nonlinear mapping function from substantially diverse M(3) images directly to desired object boundaries. Leveraging the advancement of sparse kernel machines, regression segmentation is fulfilled by a multi-dimensional support vector regressor (MSVR) which operates in an implicit, high dimensional feature space where M(3) diversity and specificity can be systematically categorized, extracted, and handled. The proposed regression segmentation approach was thoroughly tested on images from 113 clinical subjects including both disc and vertebral structures, in both sagittal and axial planes, and from both MRI and CT modalities. The overall result reaches a high dice similarity index (DSI) 0.912 and a low boundary distance (BD) 0.928 mm. With our unified and expendable framework, an efficient clinical tool for M(3) spinal image segmentation can be easily achieved, and will substantially benefit the diagnosis and treatment of spinal diseases.
A Spline Regression Model for Latent Variables
Harring, Jeffrey R.
2014-01-01
Spline (or piecewise) regression models have been used in the past to account for patterns in observed data that exhibit distinct phases. The changepoint or knot marking the shift from one phase to the other, in many applications, is an unknown parameter to be estimated. As an extension of this framework, this research considers modeling the…
Assessing risk factors for periodontitis using regression
Lobo Pereira, J. A.; Ferreira, Maria Cristina; Oliveira, Teresa
2013-10-01
Multivariate statistical analysis is indispensable to assess the associations and interactions between different factors and the risk of periodontitis. Among others, regression analysis is a statistical technique widely used in healthcare to investigate and model the relationship between variables. In our work we study the impact of socio-demographic, medical and behavioral factors on periodontal health. Using regression, linear and logistic models, we can assess the relevance, as risk factors for periodontitis disease, of the following independent variables (IVs): Age, Gender, Diabetic Status, Education, Smoking status and Plaque Index. The multiple linear regression analysis model was built to evaluate the influence of IVs on mean Attachment Loss (AL). Thus, the regression coefficients along with respective p-values will be obtained as well as the respective p-values from the significance tests. The classification of a case (individual) adopted in the logistic model was the extent of the destruction of periodontal tissues defined by an Attachment Loss greater than or equal to 4 mm in 25% (AL≥4mm/≥25%) of sites surveyed. The association measures include the Odds Ratios together with the correspondent 95% confidence intervals.
Selecting a Regression Saturated by Indicators
DEFF Research Database (Denmark)
Hendry, David F.; Johansen, Søren; Santos, Carlos
We consider selecting a regression model, using a variant of Gets, when there are more variables than observations, in the special case that the variables are impulse dummies (indicators) for every observation. We show that the setting is unproblematic if tackled appropriately, and obtain...
Functional data analysis of generalized regression quantiles
Guo, Mengmeng
2013-11-05
Generalized regression quantiles, including the conditional quantiles and expectiles as special cases, are useful alternatives to the conditional means for characterizing a conditional distribution, especially when the interest lies in the tails. We develop a functional data analysis approach to jointly estimate a family of generalized regression quantiles. Our approach assumes that the generalized regression quantiles share some common features that can be summarized by a small number of principal component functions. The principal component functions are modeled as splines and are estimated by minimizing a penalized asymmetric loss measure. An iterative least asymmetrically weighted squares algorithm is developed for computation. While separate estimation of individual generalized regression quantiles usually suffers from large variability due to lack of sufficient data, by borrowing strength across data sets, our joint estimation approach significantly improves the estimation efficiency, which is demonstrated in a simulation study. The proposed method is applied to data from 159 weather stations in China to obtain the generalized quantile curves of the volatility of the temperature at these stations. © 2013 Springer Science+Business Media New York.
Nonparametric regression with martingale increment errors
Delattre, Sylvain
2010-01-01
We consider the problem of adaptive estimation of the regression function in a framework where we replace ergodicity assumptions (such as independence or mixing) by another structural assumption on the model. Namely, we propose adaptive upper bounds for kernel estimators with data-driven bandwidth (Lepski's selection rule) in a regression model where the noise is an increment of martingale. It includes, as very particular cases, the usual i.i.d. regression and auto-regressive models. The cornerstone tool for this study is a new result for self-normalized martingales, called ``stability'', which is of independent interest. In a first part, we only use the martingale increment structure of the noise. We give an adaptive upper bound using a random rate, that involves the occupation time near the estimation point. Thanks to this approach, the theoretical study of the statistical procedure is disconnected from usual ergodicity properties like mixing. Then, in a second part, we make a link with the usual minimax th...
Finite Algorithms for Robust Linear Regression
DEFF Research Database (Denmark)
Madsen, Kaj; Nielsen, Hans Bruun
1990-01-01
The Huber M-estimator for robust linear regression is analyzed. Newton type methods for solution of the problem are defined and analyzed, and finite convergence is proved. Numerical experiments with a large number of test problems demonstrate efficiency and indicate that this kind of approach may...
Finite Algorithms for Robust Linear Regression
DEFF Research Database (Denmark)
Madsen, Kaj; Nielsen, Hans Bruun
1990-01-01
The Huber M-estimator for robust linear regression is analyzed. Newton type methods for solution of the problem are defined and analyzed, and finite convergence is proved. Numerical experiments with a large number of test problems demonstrate efficiency and indicate that this kind of approach may...
Modeling confounding by half-sibling regression
DEFF Research Database (Denmark)
Schölkopf, Bernhard; Hogg, David W; Wang, Dun
2016-01-01
We describe a method for removing the effect of confounders to reconstruct a latent quantity of interest. The method, referred to as "half-sibling regression," is inspired by recent work in causal inference using additive noise models. We provide a theoretical justification, discussing both...
Selecting a Regression Saturated by Indicators
DEFF Research Database (Denmark)
Hendry, David F.; Johansen, Søren; Santos, Carlos
We consider selecting a regression model, using a variant of Gets, when there are more variables than observations, in the special case that the variables are impulse dummies (indicators) for every observation. We show that the setting is unproblematic if tackled appropriately, and obtain...
Structural Break Tests Robust to Regression Misspecification
Abi Morshed, Alaa; Andreou, E.; Boldea, Otilia
2016-01-01
Structural break tests developed in the literature for regression models are sensitive to model misspecification. We show - analytically and through simulations - that the sup Wald test for breaks in the conditional mean and variance of a time series process exhibits severe size distortions when the
Panel data specifications in nonparametric kernel regression
DEFF Research Database (Denmark)
Czekaj, Tomasz Gerard; Henningsen, Arne
parametric panel data estimators to analyse the production technology of Polish crop farms. The results of our nonparametric kernel regressions generally differ from the estimates of the parametric models but they only slightly depend on the choice of the kernel functions. Based on economic reasoning, we...
The M Word: Multicollinearity in Multiple Regression.
Morrow-Howell, Nancy
1994-01-01
Notes that existence of substantial correlation between two or more independent variables creates problems of multicollinearity in multiple regression. Discusses multicollinearity problem in social work research in which independent variables are usually intercorrelated. Clarifies problems created by multicollinearity, explains detection of…
Genetic Programming Transforms in Linear Regression Situations
Castillo, Flor; Kordon, Arthur; Villa, Carlos
The chapter summarizes the use of Genetic Programming (GP) inMultiple Linear Regression (MLR) to address multicollinearity and Lack of Fit (LOF). The basis of the proposed method is applying appropriate input transforms (model respecification) that deal with these issues while preserving the information content of the original variables. The transforms are selected from symbolic regression models with optimal trade-off between accuracy of prediction and expressional complexity, generated by multiobjective Pareto-front GP. The chapter includes a comparative study of the GP-generated transforms with Ridge Regression, a variant of ordinary Multiple Linear Regression, which has been a useful and commonly employed approach for reducing multicollinearity. The advantages of GP-generated model respecification are clearly defined and demonstrated. Some recommendations for transforms selection are given as well. The application benefits of the proposed approach are illustrated with a real industrial application in one of the broadest empirical modeling areas in manufacturing - robust inferential sensors. The chapter contributes to increasing the awareness of the potential of GP in statistical model building by MLR.
Macroeconomic Forecasting Using Penalized Regression Methods
Smeekes, Stephan; Wijler, Etiënne
2016-01-01
We study the suitability of lasso-type penalized regression techniques when applied to macroeconomic forecasting with high-dimensional datasets. We consider performance of the lasso-type methods when the true DGP is a factor model, contradicting the sparsity assumption underlying penalized regressio
Deriving the Regression Line with Algebra
Quintanilla, John A.
2017-01-01
Exploration with spreadsheets and reliance on previous skills can lead students to determine the line of best fit. To perform linear regression on a set of data, students in Algebra 2 (or, in principle, Algebra 1) do not have to settle for using the mysterious "black box" of their graphing calculators (or other classroom technologies).…
Prediction of dynamical systems by symbolic regression
Quade, Markus; Abel, Markus; Shafi, Kamran; Niven, Robert K.; Noack, Bernd R.
2016-07-01
We study the modeling and prediction of dynamical systems based on conventional models derived from measurements. Such algorithms are highly desirable in situations where the underlying dynamics are hard to model from physical principles or simplified models need to be found. We focus on symbolic regression methods as a part of machine learning. These algorithms are capable of learning an analytically tractable model from data, a highly valuable property. Symbolic regression methods can be considered as generalized regression methods. We investigate two particular algorithms, the so-called fast function extraction which is a generalized linear regression algorithm, and genetic programming which is a very general method. Both are able to combine functions in a certain way such that a good model for the prediction of the temporal evolution of a dynamical system can be identified. We illustrate the algorithms by finding a prediction for the evolution of a harmonic oscillator based on measurements, by detecting an arriving front in an excitable system, and as a real-world application, the prediction of solar power production based on energy production observations at a given site together with the weather forecast.
Chen, Rui; Wang, Zhe; Chen, Jing; Qiao, Ge-Xia
2015-08-25
It is known that PCR amplification of highly homologous genes from complex DNA mixtures can generate a significant proportion of chimeric sequences. The 16S rRNA gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions. In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae. These chimeras are hybrid products of multiple parent sequences from the dominant species of endosymbionts in each corresponding host. It is difficult to identify the chimeric sequences of a new or unidentified species due to the high variability of their main parent, Buchnera aphidicola, and because the chimeric sequences can confuse the phylogenetic analysis of 16S rRNA gene sequences. These chimeras present a challenge to Buchnera-based phylogenetic research in aphids. Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.
Directory of Open Access Journals (Sweden)
Qi Zhao
Full Text Available Pre-clinical and clinical studies of therapeutic antibodies require highly specific reagents to examine their immune responses, bio-distributions, immunogenicity, and pharmacodynamics in patients. Selective antigen-mimicking anti-idiotype antibody facilitates the assessment of therapeutic antibody in the detection, quantitation and characterization of antibody immune responses. Using mouse specific degenerate primer pairs and splenocytic RNA, we generated an idiotype antibody-immunized phage-displayed scFv library in which an anti-idiotype antibody against the therapeutic chimera anti-CD22 antibody SM03 was isolated. The anti-idiotype scFv recognized the idiotype of anti-CD22 antibody and inhibited binding of SM03 to CD22 on Raji cell surface. The anti-idiotype scFv was subsequently classified as Ab2γ type. Moreover, our results also demonstrated firstly that the anti-idiotype scFv could be used for pharmacokinetic measurement of circulating residual antibody in lymphoma patients treated with chimera anti-CD22 monoclonal antibody SM03. Of important, the present approach could be easily adopted to generate anti-idiotype antibodies for therapeutic antibodies targeting membrane proteins, saving the cost and time for producing a soluble antigen.
Progression and regression of the atherosclerotic plaque.
de Feyter, P J; Vos, J; Deckers, J W
1995-08-01
In animals in which atherosclerosis was induced experimentally (by a high cholesterol diet) regression of the atherosclerotic lesion was demonstrated after serum cholesterol was reduced by cholesterol- lowering drugs or a low-fat diet. Whether regression of advanced coronary arterly lesions also takes place in humans after a similar intervention remains conjectural. However, several randomized studies, primarily employing lipid-lowering intervention or comprehensive changes in lifestyle, have demonstrated, using serial angiograms, that it is possible to achieve less progression, arrest or even (small) regression of atherosclerotic lesions. The lipid-lowering trials (NHBLI, CLAS, POSCH, FATS, SCOR and STARS) studied 1240 symptomatic patients, mostly men, with moderately elevated cholesterol levels and moderately severe angiographic-proven coronary artery disease. A variety of lipid-lowering drugs, in addition to a diet, were used over an intervention period ranging from 2 to 3 years. In all but one study (NHBLI), the progression of coronary atherosclerosis was less in the treated group, but regression was induced in only a few patients. The overall relative risk of progression of coronary atherosclerosis was 0 x 62 and 2 x 13, respectively. The induced angiographic differences were small and did not produce any significant haemodynamic benefit. The most important result was tht the disease process could be stabilized in the majority of patients. Three comprehensive lifestyle change trials (the Lifestyle Heart study, STARS and the Heidelberg Study) studied 183 patients, who were subjected to stress management, and/or intensive exercise, in addition to a low fat diet, over a period ranging from 1 to 3 years. All three trials demonstrated less progression, and more regression with overall relative risks of 0 x 40 and 2 x 35 respectively, in the intervention groups. Angiographic trials demonstrated that retardation or arrest of coronary atherosclerosis was possible
Logistic regression when binary predictor variables are highly correlated.
Barker, L; Brown, C
Standard logistic regression can produce estimates having large mean square error when predictor variables are multicollinear. Ridge regression and principal components regression can reduce the impact of multicollinearity in ordinary least squares regression. Generalizations of these, applicable in the logistic regression framework, are alternatives to standard logistic regression. It is shown that estimates obtained via ridge and principal components logistic regression can have smaller mean square error than estimates obtained through standard logistic regression. Recommendations for choosing among standard, ridge and principal components logistic regression are developed. Published in 2001 by John Wiley & Sons, Ltd.
Model selection in kernel ridge regression
DEFF Research Database (Denmark)
Exterkate, Peter
2013-01-01
Kernel ridge regression is a technique to perform ridge regression with a potentially infinite number of nonlinear transformations of the independent variables as regressors. This method is gaining popularity as a data-rich nonlinear forecasting tool, which is applicable in many different contexts....... The influence of the choice of kernel and the setting of tuning parameters on forecast accuracy is investigated. Several popular kernels are reviewed, including polynomial kernels, the Gaussian kernel, and the Sinc kernel. The latter two kernels are interpreted in terms of their smoothing properties......, and the tuning parameters associated to all these kernels are related to smoothness measures of the prediction function and to the signal-to-noise ratio. Based on these interpretations, guidelines are provided for selecting the tuning parameters from small grids using cross-validation. A Monte Carlo study...
Online support vector regression for reinforcement learning
Institute of Scientific and Technical Information of China (English)
Yu Zhenhua; Cai Yuanli
2007-01-01
The goal in reinforcement learning is to learn the value of state-action pair in order to maximize the total reward. For continuous states and actions in the real world, the representation of value functions is critical. Furthermore, the samples in value functions are sequentially obtained. Therefore, an online support vector regression (OSVR) is set up, which is a function approximator to estimate value functions in reinforcement learning. OSVR updates the regression function by analyzing the possible variation of support vector sets after new samples are inserted to the training set. To evaluate the OSVR learning ability, it is applied to the mountain-car task. The simulation results indicate that the OSVR has a preferable convergence speed and can solve continuous problems that are infeasible using lookup table.
Constrained regression models for optimization and forecasting
Directory of Open Access Journals (Sweden)
P.J.S. Bruwer
2003-12-01
Full Text Available Linear regression models and the interpretation of such models are investigated. In practice problems often arise with the interpretation and use of a given regression model in spite of the fact that researchers may be quite "satisfied" with the model. In this article methods are proposed which overcome these problems. This is achieved by constructing a model where the "area of experience" of the researcher is taken into account. This area of experience is represented as a convex hull of available data points. With the aid of a linear programming model it is shown how conclusions can be formed in a practical way regarding aspects such as optimal levels of decision variables and forecasting.
Controlling attribute effect in linear regression
Calders, Toon
2013-12-01
In data mining we often have to learn from biased data, because, for instance, data comes from different batches or there was a gender or racial bias in the collection of social data. In some applications it may be necessary to explicitly control this bias in the models we learn from the data. This paper is the first to study learning linear regression models under constraints that control the biasing effect of a given attribute such as gender or batch number. We show how propensity modeling can be used for factoring out the part of the bias that can be justified by externally provided explanatory attributes. Then we analytically derive linear models that minimize squared error while controlling the bias by imposing constraints on the mean outcome or residuals of the models. Experiments with discrimination-aware crime prediction and batch effect normalization tasks show that the proposed techniques are successful in controlling attribute effects in linear regression models. © 2013 IEEE.
Multiple Kernel Spectral Regression for Dimensionality Reduction
Directory of Open Access Journals (Sweden)
Bing Liu
2013-01-01
Full Text Available Traditional manifold learning algorithms, such as locally linear embedding, Isomap, and Laplacian eigenmap, only provide the embedding results of the training samples. To solve the out-of-sample extension problem, spectral regression (SR solves the problem of learning an embedding function by establishing a regression framework, which can avoid eigen-decomposition of dense matrices. Motivated by the effectiveness of SR, we incorporate multiple kernel learning (MKL into SR for dimensionality reduction. The proposed approach (termed MKL-SR seeks an embedding function in the Reproducing Kernel Hilbert Space (RKHS induced by the multiple base kernels. An MKL-SR algorithm is proposed to improve the performance of kernel-based SR (KSR further. Furthermore, the proposed MKL-SR algorithm can be performed in the supervised, unsupervised, and semi-supervised situation. Experimental results on supervised classification and semi-supervised classification demonstrate the effectiveness and efficiency of our algorithm.
A Gibbs Sampler for Multivariate Linear Regression
Mantz, Adam B
2015-01-01
Kelly (2007, hereafter K07) described an efficient algorithm, using Gibbs sampling, for performing linear regression in the fairly general case where non-zero measurement errors exist for both the covariates and response variables, where these measurements may be correlated (for the same data point), where the response variable is affected by intrinsic scatter in addition to measurement error, and where the prior distribution of covariates is modeled by a flexible mixture of Gaussians rather than assumed to be uniform. Here I extend the K07 algorithm in two ways. First, the procedure is generalized to the case of multiple response variables. Second, I describe how to model the prior distribution of covariates using a Dirichlet process, which can be thought of as a Gaussian mixture where the number of mixture components is learned from the data. I present an example of multivariate regression using the extended algorithm, namely fitting scaling relations of the gas mass, temperature, and luminosity of dynamica...
Wavelet Scattering Regression of Quantum Chemical Energies
Hirn, Matthew; Poilvert, Nicolas
2016-01-01
We introduce multiscale invariant dictionaries to estimate quantum chemical energies of organic molecules, from training databases. Molecular energies are invariant to isometric atomic displacements, and are Lipschitz continuous to molecular deformations. Similarly to density functional theory (DFT), the molecule is represented by an electronic density function. A multiscale invariant dictionary is calculated with wavelet scattering invariants. It cascades a first wavelet transform which separates scales, with a second wavelet transform which computes interactions across scales. Sparse scattering regressions give state of the art results over two databases of organic planar molecules. On these databases, the regression error is of the order of the error produced by DFT codes, but at a fraction of the computational cost.
Are increases in cigarette taxation regressive?
Borren, P; Sutton, M
1992-12-01
Using the latest published data from Tobacco Advisory Council surveys, this paper re-evaluates the question of whether or not increases in cigarette taxation are regressive in the United Kingdom. The extended data set shows no evidence of increasing price-elasticity by social class as found in a major previous study. To the contrary, there appears to be no clear pattern in the price responsiveness of smoking behaviour across different social classes. Increases in cigarette taxation, while reducing smoking levels in all groups, fall most heavily on men and women in the lowest social class. Men and women in social class five can expect to pay eight and eleven times more of a tax increase respectively, than their social class one counterparts. Taken as a proportion of relative incomes, the regressive nature of increases in cigarette taxation is even more pronounced.
Nonexistence in Reciprocal and Logarithmic Regression
Institute of Scientific and Technical Information of China (English)
Josef Bukac
2003-01-01
Fitting logarithmic b ln(clx), a+bln(c+x) or reciprocal b/(c+x), a+b/(c+x) regression models to data by the least squares method asks for the determination of the closure of the set of each type of these functions defined on a finite domain. It follows that a minimal solution may not exist. But it does exist when the closure is considered.
Logistic regression a self-learning text
Kleinbaum, David G
1994-01-01
This textbook provides students and professionals in the health sciences with a presentation of the use of logistic regression in research. The text is self-contained, and designed to be used both in class or as a tool for self-study. It arises from the author's many years of experience teaching this material and the notes on which it is based have been extensively used throughout the world.
Curvatures for Parameter Subsets in Nonlinear Regression
1986-01-01
The relative curvature measures of nonlinearity proposed by Bates and Watts (1980) are extended to an arbitrary subset of the parameters in a normal, nonlinear regression model. In particular, the subset curvatures proposed indicate the validity of linearization-based approximate confidence intervals for single parameters. The derivation produces the original Bates-Watts measures directly from the likelihood function. When the intrinsic curvature is negligible, the Bates-Watts parameter-effec...
Realization of Ridge Regression in MATLAB
Dimitrov, S.; Kovacheva, S.; Prodanova, K.
2008-10-01
The least square estimator (LSE) of the coefficients in the classical linear regression models is unbiased. In the case of multicollinearity of the vectors of design matrix, LSE has very big variance, i.e., the estimator is unstable. A more stable estimator (but biased) can be constructed using ridge-estimator (RE). In this paper the basic methods of obtaining of Ridge-estimators and numerical procedures of its realization in MATLAB are considered. An application to Pharmacokinetics problem is considered.
Bayesian Inference of a Multivariate Regression Model
Directory of Open Access Journals (Sweden)
Marick S. Sinay
2014-01-01
Full Text Available We explore Bayesian inference of a multivariate linear regression model with use of a flexible prior for the covariance structure. The commonly adopted Bayesian setup involves the conjugate prior, multivariate normal distribution for the regression coefficients and inverse Wishart specification for the covariance matrix. Here we depart from this approach and propose a novel Bayesian estimator for the covariance. A multivariate normal prior for the unique elements of the matrix logarithm of the covariance matrix is considered. Such structure allows for a richer class of prior distributions for the covariance, with respect to strength of beliefs in prior location hyperparameters, as well as the added ability, to model potential correlation amongst the covariance structure. The posterior moments of all relevant parameters of interest are calculated based upon numerical results via a Markov chain Monte Carlo procedure. The Metropolis-Hastings-within-Gibbs algorithm is invoked to account for the construction of a proposal density that closely matches the shape of the target posterior distribution. As an application of the proposed technique, we investigate a multiple regression based upon the 1980 High School and Beyond Survey.
Leukemia prediction using sparse logistic regression.
Directory of Open Access Journals (Sweden)
Tapio Manninen
Full Text Available We describe a supervised prediction method for diagnosis of acute myeloid leukemia (AML from patient samples based on flow cytometry measurements. We use a data driven approach with machine learning methods to train a computational model that takes in flow cytometry measurements from a single patient and gives a confidence score of the patient being AML-positive. Our solution is based on an [Formula: see text] regularized logistic regression model that aggregates AML test statistics calculated from individual test tubes with different cell populations and fluorescent markers. The model construction is entirely data driven and no prior biological knowledge is used. The described solution scored a 100% classification accuracy in the DREAM6/FlowCAP2 Molecular Classification of Acute Myeloid Leukaemia Challenge against a golden standard consisting of 20 AML-positive and 160 healthy patients. Here we perform a more extensive validation of the prediction model performance and further improve and simplify our original method showing that statistically equal results can be obtained by using simple average marker intensities as features in the logistic regression model. In addition to the logistic regression based model, we also present other classification models and compare their performance quantitatively. The key benefit in our prediction method compared to other solutions with similar performance is that our model only uses a small fraction of the flow cytometry measurements making our solution highly economical.
Outlier Detection Using Nonconvex Penalized Regression
She, Yiyuan
2010-01-01
This paper studies the outlier detection problem from the point of view of penalized regressions. Our regression model adds one mean shift parameter for each of the $n$ data points. We then apply a regularization favoring a sparse vector of mean shift parameters. The usual $L_1$ penalty yields a convex criterion, but we find that it fails to deliver a robust estimator. The $L_1$ penalty corresponds to soft thresholding. We introduce a thresholding (denoted by $\\Theta$) based iterative procedure for outlier detection ($\\Theta$-IPOD). A version based on hard thresholding correctly identifies outliers on some hard test problems. We find that $\\Theta$-IPOD is much faster than iteratively reweighted least squares for large data because each iteration costs at most $O(np)$ (and sometimes much less) avoiding an $O(np^2)$ least squares estimate. We describe the connection between $\\Theta$-IPOD and $M$-estimators. Our proposed method has one tuning parameter with which to both identify outliers and estimate regression...