Methods to mitigate data truncation artifacts in multi-contrast tomosynthesis image reconstructions

NASA Astrophysics Data System (ADS)

Garrett, John; Ge, Yongshuai; Li, Ke; Chen, Guang-Hong

2015-03-01

Differential phase contrast imaging is a promising new image modality that utilizes the refraction rather than the absorption of x-rays to image an object. A Talbot-Lau interferometer may be used to permit differential phase contrast imaging with a conventional medical x-ray source and detector. However, the current size of the gratings fabricated for these interferometers are often relatively small. As a result, data truncation image artifacts are often observed in a tomographic acquisition and reconstruction. When data are truncated in x-ray absorption imaging, the methods have been introduced to mitigate the truncation artifacts. However, the same strategy to mitigate absorption truncation artifacts may not be appropriate for differential phase contrast or dark field tomographic imaging. In this work, several new methods to mitigate data truncation artifacts in a multi-contrast imaging system have been proposed and evaluated for tomosynthesis data acquisitions. The proposed methods were validated using experimental data acquired for a bovine udder as well as several cadaver breast specimens using a benchtop system at our facility.

Correction of data truncation artifacts in differential phase contrast (DPC) tomosynthesis imaging

NASA Astrophysics Data System (ADS)

Garrett, John; Ge, Yongshuai; Li, Ke; Chen, Guang-Hong

2015-10-01

The use of grating based Talbot-Lau interferometry permits the acquisition of differential phase contrast (DPC) imaging with a conventional medical x-ray source and detector. However, due to the limited area of the gratings, limited area of the detector, or both, data truncation image artifacts are often observed in tomographic DPC acquisitions and reconstructions, such as tomosynthesis (limited-angle tomography). When data are truncated in the conventional x-ray absorption tomosynthesis imaging, a variety of methods have been developed to mitigate the truncation artifacts. However, the same strategies used to mitigate absorption truncation artifacts do not yield satisfactory reconstruction results in DPC tomosynthesis reconstruction. In this work, several new methods have been proposed to mitigate data truncation artifacts in a DPC tomosynthesis system. The proposed methods have been validated using experimental data of a mammography accreditation phantom, a bovine udder, as well as several human cadaver breast specimens using a bench-top DPC imaging system at our facility.

TRUNCATED RANDOM MEASURES

DTIC Science & Technology

2018-01-12

sequential representations, a method is required for deter- mining which to use for the application at hand and, once a representation is selected, for...DISTRIBUTION UNLIMITED Methods , Assumptions, and Procedures 3.1 Background 3.1.1 CRMs and truncation Consider a Poisson point process on R+ := [0...the heart of the study of truncated CRMs. They provide an itera- tive method that can be terminated at any point to yield a finite approximation to the

State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks. PMID:27105653

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Youfang; Terebus, Anna; Liang, Jie

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE PAGES

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-04-22

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

Scattering by truncated targets with and without boundary interactions

NASA Astrophysics Data System (ADS)

Marston, Philip L.; Baik, Kyungmin; Espana, Aubrey; Osterhoudt, Curtis F.; Morse, Scot F.; Hefner, Brian T.; Blonigen, Florian J.

2005-04-01

Ray methods have been applied to the scattering of various truncated targets having wavenumber-radius products as small as 10 [F. J. Blonigen and P. L. Marston, J. Acoust. Soc. Am. 107, 689-698 (2000); S. F. Morse and P. L. Marston, ibid. 112, 1318-1326 (2002); B. T. Hefner and P. L. Marston, ARLO 2, 55-60 (2001)]. Recent work emphasizes the exploration of scattering enhancements for other situations including plastic cylinders having curved ends, truncated plastic cones, partially exposed cylinders, and objects in simulated conditions for burial in a seabed. Enhanced scattering is often associated with a locally flat outgoing wavefront. For plastic targets it has been helpful to examine the time dependence of the backscattered envelope as a function of target tilt for targets illuminated by short tone bursts. For partially exposed objects it is helpful to examine the backscattering as a function of the target exposure. For simulated buried targets, it has been helpful to excite target resonances. [Work supported by the Office of Naval Research.

Truncated Sum Rules and Their Use in Calculating Fundamental Limits of Nonlinear Susceptibilities

NASA Astrophysics Data System (ADS)

Kuzyk, Mark G.

Truncated sum rules have been used to calculate the fundamental limits of the nonlinear susceptibilities and the results have been consistent with all measured molecules. However, given that finite-state models appear to result in inconsistencies in the sum rules, it may seem unclear why the method works. In this paper, the assumptions inherent in the truncation process are discussed and arguments based on physical grounds are presented in support of using truncated sum rules in calculating fundamental limits. The clipped harmonic oscillator is used as an illustration of how the validity of truncation can be tested and several limiting cases are discussed as examples of the nuances inherent in the method.

Multi-resolution statistical image reconstruction for mitigation of truncation effects: application to cone-beam CT of the head

NASA Astrophysics Data System (ADS)

Dang, Hao; Webster Stayman, J.; Sisniega, Alejandro; Zbijewski, Wojciech; Xu, Jennifer; Wang, Xiaohui; Foos, David H.; Aygun, Nafi; Koliatsos, Vassilis E.; Siewerdsen, Jeffrey H.

2017-01-01

A prototype cone-beam CT (CBCT) head scanner featuring model-based iterative reconstruction (MBIR) has been recently developed and demonstrated the potential for reliable detection of acute intracranial hemorrhage (ICH), which is vital to diagnosis of traumatic brain injury and hemorrhagic stroke. However, data truncation (e.g. due to the head holder) can result in artifacts that reduce image uniformity and challenge ICH detection. We propose a multi-resolution MBIR method with an extended reconstruction field of view (RFOV) to mitigate truncation effects in CBCT of the head. The image volume includes a fine voxel size in the (inner) nontruncated region and a coarse voxel size in the (outer) truncated region. This multi-resolution scheme allows extension of the RFOV to mitigate truncation effects while introducing minimal increase in computational complexity. The multi-resolution method was incorporated in a penalized weighted least-squares (PWLS) reconstruction framework previously developed for CBCT of the head. Experiments involving an anthropomorphic head phantom with truncation due to a carbon-fiber holder were shown to result in severe artifacts in conventional single-resolution PWLS, whereas extending the RFOV within the multi-resolution framework strongly reduced truncation artifacts. For the same extended RFOV, the multi-resolution approach reduced computation time compared to the single-resolution approach (viz. time reduced by 40.7%, 83.0%, and over 95% for an image volume of 6003, 8003, 10003 voxels). Algorithm parameters (e.g. regularization strength, the ratio of the fine and coarse voxel size, and RFOV size) were investigated to guide reliable parameter selection. The findings provide a promising method for truncation artifact reduction in CBCT and may be useful for other MBIR methods and applications for which truncation is a challenge.

Native thrombopoietin: structure and function.

PubMed

Kato, T; Matsumoto, A; Ogami, K; Tahara, T; Morita, H; Miyazaki, H

1998-01-01

Thrombopoietin (TPO), the c-Mpl ligand, is produced constitutively in liver and other organs, circulates in the bloodstream, and is delivered to bone marrow, where it stimulates the early development of multiple hematopoietic lineages and megakaryocytopoiesis. The concentration of TPO in blood is regulated by c-Mpl mass on platelets and megakaryocytes. In addition to regulation by the number of TPO molecules, including the possible modulation of TPO mRNA abundance in bone marrow, megakaryocytopoiesis and platelet production may be regulated as a result of modulation of TPO activity by proteolytic processing that generates truncated forms of the molecule. Characterization of TPO partially purified from human plasma, however, revealed that the full-length molecule was the predominant form in the blood of both normal individuals and thrombocytopenic patients, although small amounts of truncated species were detected. Thus, truncation of TPO, at least that in the circulation examined, does not appear to contribute to the direct regulation of platelet production in response to increased demand. Given that native TPO isolated from the plasma of thrombocytopenic animals comprises truncated forms, the truncation of TPO is likely of physiological importance in the life history of this molecule.

Apparatus, Method and Program Storage Device for Determining High-Energy Neutron/Ion Transport to a Target of Interest

NASA Technical Reports Server (NTRS)

Wilson, John W. (Inventor); Tripathi, Ram K. (Inventor); Cucinotta, Francis A. (Inventor); Badavi, Francis F. (Inventor)

2012-01-01

An apparatus, method and program storage device for determining high-energy neutron/ion transport to a target of interest. Boundaries are defined for calculation of a high-energy neutron/ion transport to a target of interest; the high-energy neutron/ion transport to the target of interest is calculated using numerical procedures selected to reduce local truncation error by including higher order terms and to allow absolute control of propagated error by ensuring truncation error is third order in step size, and using scaling procedures for flux coupling terms modified to improve computed results by adding a scaling factor to terms describing production of j-particles from collisions of k-particles; and the calculated high-energy neutron/ion transport is provided to modeling modules to control an effective radiation dose at the target of interest.

Tau truncation is a productive posttranslational modification of neurofibrillary degeneration in Alzheimer's disease.

PubMed

Kovacech, B; Novak, M

2010-12-01

Deposits of the misfolded neuronal protein tau are major hallmarks of neurodegeneration in Alzheimer's disease (AD) and other tauopathies. The etiology of the transformation process of the intrinsically disordered soluble protein tau into the insoluble misordered aggregate has attracted much attention. Tau undergoes multiple modifications in AD, most notably hyperphosphorylation and truncation. Hyperphosphorylation is widely regarded as the hottest candidate for the inducer of the neurofibrillary pathology. However, the true nature of the impetus that initiates the whole process in the human brains remains unknown. In AD, several site-specific tau cleavages were identified and became connected to the progression of the disease. In addition, western blot analyses of tau species in AD brains reveal multitudes of various truncated forms. In this review we summarize evidence showing that tau truncation alone is sufficient to induce the complete cascade of neurofibrillary pathology, including hyperphosphorylation and accumulation of misfolded insoluble forms of tau. Therefore, proteolytical abnormalities in the stressed neurons and production of aberrant tau cleavage products deserve closer attention and should be considered as early therapeutic targets for Alzheimer's disease.

Adrenodoxin supports reactions catalyzed by microsomal steroidogenic cytochrome P450s

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pechurskaya, Tatiana A.; Harnastai, Ivan N.; Grabovec, Irina P.

2007-02-16

The interaction of adrenodoxin (Adx) and NADPH cytochrome P450 reductase (CPR) with human microsomal steroidogenic cytochrome P450s was studied. It is found that Adx, mitochondrial electron transfer protein, is able to support reactions catalyzed by human microsomal P450s: full length CYP17, truncated CYP17, and truncated CYP21. CPR, but not Adx, supports activity of truncated CYP19. Truncated and the full length CYP17s show distinct preference for electron donor proteins. Truncated CYP17 has higher activity with Adx compared to CPR. The alteration in preference to electron donor does not change product profile for truncated enzymes. The electrostatic contacts play a major rolemore » in the interaction of truncated CYP17 with either CPR or Adx. Similarly electrostatic contacts are predominant in the interaction of full length CYP17 with Adx. We speculate that Adx might serve as an alternative electron donor for CYP17 at the conditions of CPR deficiency in human.« less

Estimating sales and sales market share from sales rank data for consumer appliances

NASA Astrophysics Data System (ADS)

Touzani, Samir; Van Buskirk, Robert

2016-06-01

Our motivation in this work is to find an adequate probability distribution to fit sales volumes of different appliances. This distribution allows for the translation of sales rank into sales volume. This paper shows that the log-normal distribution and specifically the truncated version are well suited for this purpose. We demonstrate that using sales proxies derived from a calibrated truncated log-normal distribution function can be used to produce realistic estimates of market average product prices, and product attributes. We show that the market averages calculated with the sales proxies derived from the calibrated, truncated log-normal distribution provide better market average estimates than sales proxies estimated with simpler distribution functions.

Truncated Gaussians as tolerance sets

NASA Technical Reports Server (NTRS)

Cozman, Fabio; Krotkov, Eric

1994-01-01

This work focuses on the use of truncated Gaussian distributions as models for bounded data measurements that are constrained to appear between fixed limits. The authors prove that the truncated Gaussian can be viewed as a maximum entropy distribution for truncated bounded data, when mean and covariance are given. The characteristic function for the truncated Gaussian is presented; from this, algorithms are derived for calculation of mean, variance, summation, application of Bayes rule and filtering with truncated Gaussians. As an example of the power of their methods, a derivation of the disparity constraint (used in computer vision) from their models is described. The authors' approach complements results in Statistics, but their proposal is not only to use the truncated Gaussian as a model for selected data; they propose to model measurements as fundamentally in terms of truncated Gaussians.

Durability of truncated dome warnings on existing curb ramps : final report.

DOT National Transportation Integrated Search

2004-12-01

In 2002 the Federal Highway Administration (FHWA) notified the Oregon Department of Transportation (ODOT) that that the state was required to use truncated dome detectable warnings on curb ramps. Products appropriate for use on cured concrete surface...

Observation of the dispersion of wedge waves propagating along cylinder wedge with different truncations by laser ultrasound technique

NASA Astrophysics Data System (ADS)

Jia, Jing; Zhang, Yu; Han, Qingbang; Jing, Xueping

2017-10-01

The research focuses on study the influence of truncations on the dispersion of wedge waves propagating along cylinder wedge with different truncations by using the laser ultrasound technique. The wedge waveguide models with different truncations were built by using finite element method (FEM). The dispersion curves were obtained by using 2D Fourier transformation method. Multiple mode wedge waves were observed, which was well agreed with the results estimated from Lagasse's empirical formula. We established cylinder wedge with radius of 3mm, 20° and 60°angle, with 0μm, 5μm, 10μm, 20μm, 30μm, 40μm, and 50μm truncations, respectively. It was found that non-ideal wedge tip caused abnormal dispersion of the mode of cylinder wedge, the modes of 20° cylinder wedge presents the characteristics of guide waves which propagating along hollow cylinder as the truncation increasing. Meanwhile, the modes of 60° cylinder wedge with truncations appears the characteristics of guide waves propagating along hollow cylinder, and its mode are observed clearly. The study can be used to evaluate and detect wedge structure.

Lamp with a truncated reflector cup

DOEpatents

Li, Ming; Allen, Steven C.; Bazydola, Sarah; Ghiu, Camil-Daniel

2013-10-15

A lamp assembly, and method for making same. The lamp assembly includes first and second truncated reflector cups. The lamp assembly also includes at least one base plate disposed between the first and second truncated reflector cups, and a light engine disposed on a top surface of the at least one base plate. The light engine is configured to emit light to be reflected by one of the first and second truncated reflector cups.

Flexible scheme to truncate the hierarchy of pure states.

PubMed

Zhang, P-P; Bentley, C D B; Eisfeld, A

2018-04-07

The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

Flexible scheme to truncate the hierarchy of pure states

NASA Astrophysics Data System (ADS)

Zhang, P.-P.; Bentley, C. D. B.; Eisfeld, A.

2018-04-01

The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

Fourier ptychographic reconstruction using Poisson maximum likelihood and truncated Wirtinger gradient.

PubMed

Bian, Liheng; Suo, Jinli; Chung, Jaebum; Ou, Xiaoze; Yang, Changhuei; Chen, Feng; Dai, Qionghai

2016-06-10

Fourier ptychographic microscopy (FPM) is a novel computational coherent imaging technique for high space-bandwidth product imaging. Mathematically, Fourier ptychographic (FP) reconstruction can be implemented as a phase retrieval optimization process, in which we only obtain low resolution intensity images corresponding to the sub-bands of the sample's high resolution (HR) spatial spectrum, and aim to retrieve the complex HR spectrum. In real setups, the measurements always suffer from various degenerations such as Gaussian noise, Poisson noise, speckle noise and pupil location error, which would largely degrade the reconstruction. To efficiently address these degenerations, we propose a novel FP reconstruction method under a gradient descent optimization framework in this paper. The technique utilizes Poisson maximum likelihood for better signal modeling, and truncated Wirtinger gradient for effective error removal. Results on both simulated data and real data captured using our laser-illuminated FPM setup show that the proposed method outperforms other state-of-the-art algorithms. Also, we have released our source code for non-commercial use.

Method for increasing thermostability in cellulase ennzymes

DOEpatents

Adney, William S.; Thomas, Steven R.; Baker, John O.; Himmel, Michael E.; Chou, Yat-Chen

1998-01-01

The gene encoding Acidothermus cellulolyticus E1 endoglucanase is cloned and expressed in Pichia pastoris. A new modified E1 endoglucanase enzyme comprising the catalytic domain of the full size E1 enzyme demonstrates enhanced thermostability and is produced by two methods. The first method of producing the new modified E1 is proteolytic cleavage to remove the cellulose binding domain and linker peptide of the full size E1. The second method of producing the new modified E1 is genetic truncation of the gene encoding the full size E1 so that the catalytic domain is expressed in the expression product.

Selective targeting of mutant adenomatous polyposis coli (APC) in colorectal cancer.

PubMed

Zhang, Lu; Theodoropoulos, Panayotis C; Eskiocak, Ugur; Wang, Wentian; Moon, Young-Ah; Posner, Bruce; Williams, Noelle S; Wright, Woodring E; Kim, Sang Bum; Nijhawan, Deepak; De Brabander, Jef K; Shay, Jerry W

2016-10-19

Mutations in the adenomatous polyposis coli (APC) gene are common in colorectal cancer (CRC), and more than 90% of those mutations generate stable truncated gene products. We describe a chemical screen using normal human colonic epithelial cells (HCECs) and a series of oncogenically progressed HCECs containing a truncated APC protein. With this screen, we identified a small molecule, TASIN-1 (truncated APC selective inhibitor-1), that specifically kills cells with APC truncations but spares normal and cancer cells with wild-type APC. TASIN-1 exerts its cytotoxic effects through inhibition of cholesterol biosynthesis. In vivo administration of TASIN-1 inhibits tumor growth of CRC cells with truncated APC but not APC wild-type CRC cells in xenograft models and in a genetically engineered CRC mouse model with minimal toxicity. TASIN-1 represents a potential therapeutic strategy for prevention and intervention in CRC with mutant APC. Copyright © 2016, American Association for the Advancement of Science.

Design, Construction and Cloning of Truncated ORF2 and tPAsp-PADRE-Truncated ORF2 Gene Cassette From Hepatitis E Virus in the pVAX1 Expression Vector

PubMed Central

Farshadpour, Fatemeh; Makvandi, Manoochehr; Taherkhani, Reza

2015-01-01

Background: Hepatitis E Virus (HEV) is the causative agent of enterically transmitted acute hepatitis and has high mortality rate of up to 30% among pregnant women. Therefore, development of a novel vaccine is a desirable goal. Objectives: The aim of this study was to construct tPAsp-PADRE-truncated open reading frame 2 (ORF2) and truncated ORF2 DNA plasmid, which can assist future studies with the preparation of an effective vaccine against Hepatitis E Virus. Materials and Methods: A synthetic codon-optimized gene cassette encoding tPAsp-PADRE-truncated ORF2 protein was designed, constructed and analyzed by some bioinformatics software. Furthermore, a codon-optimized truncated ORF2 gene was amplified by the polymerase chain reaction (PCR), with a specific primer from the previous construct. The constructs were sub-cloned in the pVAX1 expression vector and finally expressed in eukaryotic cells. Results: Sequence analysis and bioinformatics studies of the codon-optimized gene cassette revealed that codon adaptation index (CAI), GC content, and frequency of optimal codon usage (Fop) value were improved, and performance of the secretory signal was confirmed. Cloning and sub-cloning of the tPAsp-PADRE-truncated ORF2 gene cassette and truncated ORF2 gene were confirmed by colony PCR, restriction enzymes digestion and DNA sequencing of the recombinant plasmids pVAX-tPAsp-PADRE-truncated ORF2 (aa 112-660) and pVAX-truncated ORF2 (aa 112-660). The expression of truncated ORF2 protein in eukaryotic cells was approved by an Immunofluorescence assay (IFA) and the reverse transcriptase polymerase chain reaction (RT-PCR) method. Conclusions: The results of this study demonstrated that the tPAsp-PADRE-truncated ORF2 gene cassette and the truncated ORF2 gene in recombinant plasmids are successfully expressed in eukaryotic cells. The immunogenicity of the two recombinant plasmids with different formulations will be evaluated as a novel DNA vaccine in future investigations. PMID:26865938

Improved dual AAV vectors with reduced expression of truncated proteins are safe and effective in the retina of a mouse model of Stargardt disease

PubMed Central

Trapani, Ivana; Toriello, Elisabetta; de Simone, Sonia; Colella, Pasqualina; Iodice, Carolina; Polishchuk, Elena V.; Sommella, Andrea; Colecchi, Linda; Rossi, Settimio; Simonelli, Francesca; Giunti, Massimo; Bacci, Maria L.; Polishchuk, Roman S.; Auricchio, Alberto

2015-01-01

Stargardt disease (STGD1) due to mutations in the large ABCA4 gene is the most common inherited macular degeneration in humans. We have shown that dual adeno-associated viral (AAV) vectors effectively transfer ABCA4 to the retina of Abca4−/− mice. However, they express both lower levels of transgene compared with a single AAV and truncated proteins. To increase productive dual AAV concatemerization, which would overcome these limitations, we have explored the use of either various regions of homology or heterologous inverted terminal repeats (ITR). In addition, we tested the ability of various degradation signals to decrease the expression of truncated proteins. We found the highest levels of transgene expression using regions of homology based on either alkaline phosphatase or the F1 phage (AK). The use of heterologous ITR does not decrease the levels of truncated proteins relative to full-length ABCA4 and impairs AAV vector production. Conversely, the inclusion of the CL1 degradation signal results in the selective degradation of truncated proteins from the 5′-half without affecting full-length protein production. Therefore, we developed dual AAV hybrid ABCA4 vectors including homologous ITR2, the photoreceptor-specific G protein-coupled receptor kinase 1 promoter, the AK region of homology and the CL1 degradation signal. We show that upon subretinal administration these vectors are both safe in pigs and effective in Abca4−/− mice. Our data support the use of improved dual AAV vectors for gene therapy of STGD1. PMID:26420842

The Dynamic Response and Vibration of Functionally Graded Carbon Nanotube-Reinforced Composite (FG-CNTRC) Truncated Conical Shells Resting on Elastic Foundations

PubMed Central

Nguyen Dinh, Duc; Nguyen, Pham Dinh

2017-01-01

Based on the classical shell theory, the linear dynamic response of functionally graded carbon nanotube-reinforced composite (FG-CNTRC) truncated conical shells resting on elastic foundations subjected to dynamic loads is presented. The truncated conical shells are reinforced by single-walled carbon nanotubes (SWCNTs) that vary according to the linear functions of the shell thickness. The motion equations are solved by the Galerkin method and the fourth-order Runge–Kutta method. In numerical results, the influences of geometrical parameters, elastic foundations, natural frequency parameters, and nanotube volume fraction of FG-CNTRC truncated conical shells are investigated. The proposed results are validated by comparing them with those of other authors. PMID:29057821

Production of biodiesel by transesterification of corn and soybean oils with ethanol or butanol using resin-bound truncated Candida antarctica lipase B

USDA-ARS?s Scientific Manuscript database

Enzymatic catalysts, such as lipases, have advantages over chemical catalysts for transesterification of triglycerides to produce biodiesel. A gene encoding a synthetic truncated Candida antarctica lipase B (CALB) was generated via automated PCR and expressed in Saccharomyces cerevisiae. Western b...

Methods to compute reliabilities for genomic predictions of feed intake

USDA-ARS?s Scientific Manuscript database

For new traits without historical reference data, cross-validation is often the preferred method to validate reliability (REL). Time truncation is less useful because few animals gain substantial REL after the truncation point. Accurate cross-validation requires separating genomic gain from pedigree...

Orbit-product representation and correction of Gaussian belief propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Jason K; Chertkov, Michael; Chernyak, Vladimir

We present a new interpretation of Gaussian belief propagation (GaBP) based on the 'zeta function' representation of the determinant as a product over orbits of a graph. We show that GaBP captures back-tracking orbits of the graph and consider how to correct this estimate by accounting for non-backtracking orbits. We show that the product over non-backtracking orbits may be interpreted as the determinant of the non-backtracking adjacency matrix of the graph with edge weights based on the solution of GaBP. An efficient method is proposed to compute a truncated correction factor including all non-backtracking orbits up to a specified length.

Truncated midkine as a marker of diagnosis and detection of nodal metastases in gastrointestinal carcinomas.

PubMed Central

Aridome, K.; Takao, S.; Kaname, T.; Kadomatsu, K.; Natsugoe, S.; Kijima, F.; Aikou, T.; Muramatsu, T.

1998-01-01

Midkine (MK) is a growth factor identified as a product of a retinoic acid-responsive gene. A truncated form of MK mRNA, which lacks a sequence encoding the N-terminally located domain, was recently found in cancer cells. We investigated the expression of the truncated MK mRNA in specimens of 47 surgically removed human gastrointestinal organs using polymerase chain reaction. Truncated MK was not detected in all of the 46 corresponding non-cancerous regions. On the other hand, this short MK mRNA was expressed in the primary tumours in 12 of 16 gastric cancers, 8 of 13 colorectal carcinomas, five of nine hepatocellular carcinomas, two of two oesophageal carcinomas and one ampullary duodenal cancer. In addition, truncated MK was detectable in all of the 14 lymph node metastases but in none of three metastatic sites in the liver, suggesting that truncated MK mRNA could become a good marker of nodal metastases in gastrointestinal tract. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9716029

Analytic reconstruction algorithms for triple-source CT with horizontal data truncation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ming; Yu, Hengyong, E-mail: hengyong-yu@ieee.org

2015-10-15

Purpose: This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. Methods: The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and MATLAB. While the basic platform is constructed in MATLAB, the computationally intensive segments are coded in c + +, which are linked via a MEX interface. Results: A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle tomore » cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. Conclusions: The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units.« less

Region-of-interest image reconstruction in circular cone-beam microCT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Seungryong; Bian, Junguo; Pelizzari, Charles A.

2007-12-15

Cone-beam microcomputed tomography (microCT) is one of the most popular choices for small animal imaging which is becoming an important tool for studying animal models with transplanted diseases. Region-of-interest (ROI) imaging techniques in CT, which can reconstruct an ROI image from the projection data set of the ROI, can be used not only for reducing imaging-radiation exposure to the subject and scatters to the detector but also for potentially increasing spatial resolution of the reconstructed images. Increasing spatial resolution in microCT images can facilitate improved accuracy in many assessment tasks. A method proposed previously for increasing CT image spatial resolutionmore » entails the exploitation of the geometric magnification in cone-beam CT. Due to finite detector size, however, this method can lead to data truncation for a large geometric magnification. The Feldkamp-Davis-Kress (FDK) algorithm yields images with artifacts when truncated data are used, whereas the recently developed backprojection filtration (BPF) algorithm is capable of reconstructing ROI images without truncation artifacts from truncated cone-beam data. We apply the BPF algorithm to reconstructing ROI images from truncated data of three different objects acquired by our circular cone-beam microCT system. Reconstructed images by use of the FDK and BPF algorithms from both truncated and nontruncated cone-beam data are compared. The results of the experimental studies demonstrate that, from certain truncated data, the BPF algorithm can reconstruct ROI images with quality comparable to that reconstructed from nontruncated data. In contrast, the FDK algorithm yields ROI images with truncation artifacts. Therefore, an implication of the studies is that, when truncated data are acquired with a configuration of a large geometric magnification, the BPF algorithm can be used for effective enhancement of the spatial resolution of a ROI image.« less

Method for increasing thermostability in cellulase ennzymes

DOEpatents

Adney, W.S.; Thomas, S.R.; Baker, J.O.; Himmel, M.E.; Chou, Y.C.

1998-01-27

The gene encoding Acidothermus cellulolyticus E1 endoglucanase is cloned and expressed in Pichia pastoris. A new modified E1 endoglucanase enzyme comprising the catalytic domain of the full size E1 enzyme demonstrates enhanced thermostability and is produced by two methods. The first method of producing the new modified E1 is proteolytic cleavage to remove the cellulose binding domain and linker peptide of the full size E1. The second method of producing the new modified E1 is genetic truncation of the gene encoding the full size E1 so that the catalytic domain is expressed in the expression product. 8 figs.

Improved dual AAV vectors with reduced expression of truncated proteins are safe and effective in the retina of a mouse model of Stargardt disease.

PubMed

Trapani, Ivana; Toriello, Elisabetta; de Simone, Sonia; Colella, Pasqualina; Iodice, Carolina; Polishchuk, Elena V; Sommella, Andrea; Colecchi, Linda; Rossi, Settimio; Simonelli, Francesca; Giunti, Massimo; Bacci, Maria L; Polishchuk, Roman S; Auricchio, Alberto

2015-12-01

Stargardt disease (STGD1) due to mutations in the large ABCA4 gene is the most common inherited macular degeneration in humans. We have shown that dual adeno-associated viral (AAV) vectors effectively transfer ABCA4 to the retina of Abca4-/- mice. However, they express both lower levels of transgene compared with a single AAV and truncated proteins. To increase productive dual AAV concatemerization, which would overcome these limitations, we have explored the use of either various regions of homology or heterologous inverted terminal repeats (ITR). In addition, we tested the ability of various degradation signals to decrease the expression of truncated proteins. We found the highest levels of transgene expression using regions of homology based on either alkaline phosphatase or the F1 phage (AK). The use of heterologous ITR does not decrease the levels of truncated proteins relative to full-length ABCA4 and impairs AAV vector production. Conversely, the inclusion of the CL1 degradation signal results in the selective degradation of truncated proteins from the 5'-half without affecting full-length protein production. Therefore, we developed dual AAV hybrid ABCA4 vectors including homologous ITR2, the photoreceptor-specific G protein-coupled receptor kinase 1 promoter, the AK region of homology and the CL1 degradation signal. We show that upon subretinal administration these vectors are both safe in pigs and effective in Abca4-/- mice. Our data support the use of improved dual AAV vectors for gene therapy of STGD1. © The Author 2015. Published by Oxford University Press.

Identification of the membrane remnants of transferrin receptor with domain-specific antibodies.

PubMed

Baynes, R D; Shih, Y J; Hudson, B G; Cook, J D

1994-03-01

Tissue culture studies with K562 and HL60 cells have demonstrated the production of a soluble form of transferrin receptor identical to that identified in human serum. The present study was undertaken to search for membrane remnants of the truncated receptor with peptide antibodies specific for the extracellular and cytoplasmic domain of transferrin receptor. In cell membranes, a 105K remnant was identified that is consistent with truncation of one extracellular domain monomer of the transferrin receptor. In the exosomal fraction of the culture supernatant, a smaller 20K remnant consistent with truncation of both extracellular domains was also demonstrated. These findings provide evidence that soluble receptor is the product of proteolytic cleavage of intact membrane-bound transferrin receptor. Prior studies showing that the concentration of the extracellular domain in exosomes remained stable during incubation in culture supernatant suggest that this cleavage possibly occurs intracellularly.

Amplitude reconstruction from complete photoproduction experiments and truncated partial-wave expansions

NASA Astrophysics Data System (ADS)

Workman, R. L.; Tiator, L.; Wunderlich, Y.; Döring, M.; Haberzettl, H.

2017-01-01

We compare the methods of amplitude reconstruction, for a complete experiment and a truncated partial-wave analysis, applied to the photoproduction of pseudoscalar mesons. The approach is pedagogical, showing in detail how the amplitude reconstruction (observables measured at a single energy and angle) is related to a truncated partial-wave analysis (observables measured at a single energy and a number of angles).

Amplitude reconstruction from complete photoproduction experiments and truncated partial-wave expansions

DOE PAGES

Workman, R. L.; Tiator, L.; Wunderlich, Y.; ...

2017-01-19

Here, we compare the methods of amplitude reconstruction, for a complete experiment and a truncated partial-wave analysis, applied to the photoproduction of pseudoscalar mesons. The approach is pedagogical, showing in detail how the amplitude reconstruction (observables measured at a single energy and angle) is related to a truncated partial-wave analysis (observables measured at a single energy and a number of angles).

Comparison of extended field-of-view reconstructions in C-arm flat-detector CT using patient size, shape or attenuation information.

PubMed

Kolditz, Daniel; Meyer, Michael; Kyriakou, Yiannis; Kalender, Willi A

2011-01-07

In C-arm-based flat-detector computed tomography (FDCT) it frequently happens that the patient exceeds the scan field of view (SFOV) in the transaxial direction because of the limited detector size. This results in data truncation and CT image artefacts. In this work three truncation correction approaches for extended field-of-view (EFOV) reconstructions have been implemented and evaluated. An FDCT-based method estimates the patient size and shape from the truncated projections by fitting an elliptical model to the raw data in order to apply an extrapolation. In a camera-based approach the patient is sampled with an optical tracking system and this information is used to apply an extrapolation. In a CT-based method the projections are completed by artificial projection data obtained from the CT data acquired in an earlier exam. For all methods the extended projections are filtered and backprojected with a standard Feldkamp-type algorithm. Quantitative evaluations have been performed by simulations of voxelized phantoms on the basis of the root mean square deviation and a quality factor Q (Q = 1 represents the ideal correction). Measurements with a C-arm FDCT system have been used to validate the simulations and to investigate the practical applicability using anthropomorphic phantoms which caused truncation in all projections. The proposed approaches enlarged the FOV to cover wider patient cross-sections. Thus, image quality inside and outside the SFOV has been improved. Best results have been obtained using the CT-based method, followed by the camera-based and the FDCT-based truncation correction. For simulations, quality factors up to 0.98 have been achieved. Truncation-induced cupping artefacts have been reduced, e.g., from 218% to less than 1% for the measurements. The proposed truncation correction approaches for EFOV reconstructions are an effective way to ensure accurate CT values inside the SFOV and to recover peripheral information outside the SFOV.

Varying coefficient subdistribution regression for left-truncated semi-competing risks data.

PubMed

Li, Ruosha; Peng, Limin

2014-10-01

Semi-competing risks data frequently arise in biomedical studies when time to a disease landmark event is subject to dependent censoring by death, the observation of which however is not precluded by the occurrence of the landmark event. In observational studies, the analysis of such data can be further complicated by left truncation. In this work, we study a varying co-efficient subdistribution regression model for left-truncated semi-competing risks data. Our method appropriately accounts for the specifical truncation and censoring features of the data, and moreover has the flexibility to accommodate potentially varying covariate effects. The proposed method can be easily implemented and the resulting estimators are shown to have nice asymptotic properties. We also present inference, such as Kolmogorov-Smirnov type and Cramér Von-Mises type hypothesis testing procedures for the covariate effects. Simulation studies and an application to the Denmark diabetes registry demonstrate good finite-sample performance and practical utility of the proposed method.

Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships.

PubMed

Satz, Alexander L

2016-07-11

Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure-activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.

[Construction and transfection of eucaryotic expression recombinant vector containing truncated region of UL83 gene of human cytomegalovirus and it's sheltered effect as DNA vaccine].

PubMed

Gao, Rong-Bao; Li, Yan-Qiu; Wang, Ming-Li

2006-06-01

To construct eucaryotic expression recombinant vector containing vivo truncated region of UL83 gene of human cytomegalovirus, realize its steady expression in Hep-2 cell, and study sheltered effect of the eucaryotic expression recombinant vector as DNA vaccine. A vivo truncated UL83 gene fragment encoding for truncated HCMV pp65 was obtained by PCR from human cytomegalovirus AD169 stock genome. By gene recombinant ways, the truncated UL83 gene fragment was cloned into eucaryotic expression vector pEGFP-C1 with reported gene coding GFP to construct recombinant vector pEGFP-C1-UL83. The recombinant vector pEGFP-C1-UL83 was tested by different methods including PCR, restriction digestion and gene sequencing. Test results showed the recombinant vector was constructed successfully. After pEGFP-C1-UL83 was transfected into Hep-2 cell by lipofectin mediation, expression of GFP and truncated pp65 fusion protein in Hep-2 cell was observed at different time points by fluorescence microscope. Results showed that quantity of fusion protein expression was the highest at 36h point. Then, Hep-2 cell was cultured selectively by RPMI-1640 containing G418 (200 microg/mL) to obtain a new cell stock of expressing truncated UL83 Gene fragment steadily. RT-PCR and Western blot results showed the truncated fragment of UL83 gene could be expressed steadily in Hep-2 cell. The result showed a new cell stock of expressing Tpp65 was established. This cell stock could be useful in some HCMV research fields, for example, it could be a tool in study of pp65 and HCMV infection, and it could provide a platform for the research into the therapy of HCMV infection. Immune sheltered effect of pEGFP-C1-UL83 as DNA vaccine was studied in vivo of HCMV congenital infection mouse model. The mouse model was immunized solely by pEGFP-C1-UL83, and was immunized jointly by pEGFP-C1-UL83 and its expression product. When the mouse was pregnant and brought to bed, differential antibody of anti-HCMV pp65 was tested by indirect ELISA in mother mouse, the infectious virus was separated with the method of virus separation, and pp65 antigen was checked up by indirect immunofluorescence staining in fetal mouse. Results showed differential antibody of anti-HCMV pp65 was produced in mouse model. Tilter of the antibody was from 1:2.51 to 1:50.79. Results of virus separation and pp65 checkup of fetal mouse brain tissue were negative. So the conclusion can be reached that pEGFP-C1-UL83 as DNA vaccine in vivo has sheltered effect which can prevent HCMV vertical transmission from mother mouse to her fetus.

Using Wavelet Bases to Separate Scales in Quantum Field Theory

NASA Astrophysics Data System (ADS)

Michlin, Tracie L.

This thesis investigates the use of Daubechies wavelets to separate scales in local quantum field theory. Field theories have an infinite number of degrees of freedom on all distance scales. Quantum field theories are believed to describe the physics of subatomic particles. These theories have no known mathematically convergent approximation methods. Daubechies wavelet bases can be used separate degrees of freedom on different distance scales. Volume and resolution truncations lead to mathematically well-defined truncated theories that can be treated using established methods. This work demonstrates that flow equation methods can be used to block diagonalize truncated field theoretic Hamiltonians by scale. This eliminates the fine scale degrees of freedom. This may lead to approximation methods and provide an understanding of how to formulate well-defined fine resolution limits.

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

DOE PAGES

Liberton, Michelle; Chrisler, William B.; Nicora, Carrie D.; ...

2017-03-02

Here, cyanobacteria, such as Synechocystis sp. PCC 6803, utilize large antenna systems to optimize light harvesting and energy transfer to reaction centers. Understanding the structure and function of these complexes, particularly when altered, will help direct bio-design efforts to optimize biofuel production. Three specific phycobilisome (PBS) complex truncation mutants were studied, ranging from progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of all phycocyanin and allophycocyanin cores in the PAL mutant. We applied comprehensive proteomic analyses to investigate both direct and downstream molecular systems implications of each truncation. Results showed that PBS truncation inmore » Synechocystis sp. PCC 6803 dramatically alters core cellular mechanisms beyond energy capture and electron transport, placing constraints upon cellular processes that dramatically altered phenotypes. This included primarily membrane associated functions and altered regulation of cellular resources (i.e., iron, nitrite/nitrate, bicarbonate). Additionally, each PBS truncation, though progressive in nature, exhibited unique phenotypes compare to WT, and hence we assert that in the current realm of extensive bioengineering and bio-design, there remains a continuing need to assess systems-wide protein based abundances to capture potential indirect phenotypic effects.« less

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liberton, Michelle; Chrisler, William B.; Nicora, Carrie D.

Here, cyanobacteria, such as Synechocystis sp. PCC 6803, utilize large antenna systems to optimize light harvesting and energy transfer to reaction centers. Understanding the structure and function of these complexes, particularly when altered, will help direct bio-design efforts to optimize biofuel production. Three specific phycobilisome (PBS) complex truncation mutants were studied, ranging from progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of all phycocyanin and allophycocyanin cores in the PAL mutant. We applied comprehensive proteomic analyses to investigate both direct and downstream molecular systems implications of each truncation. Results showed that PBS truncation inmore » Synechocystis sp. PCC 6803 dramatically alters core cellular mechanisms beyond energy capture and electron transport, placing constraints upon cellular processes that dramatically altered phenotypes. This included primarily membrane associated functions and altered regulation of cellular resources (i.e., iron, nitrite/nitrate, bicarbonate). Additionally, each PBS truncation, though progressive in nature, exhibited unique phenotypes compare to WT, and hence we assert that in the current realm of extensive bioengineering and bio-design, there remains a continuing need to assess systems-wide protein based abundances to capture potential indirect phenotypic effects.« less

Overexpression of the truncated version of ILV2 enhances glycerol production in Saccharomyces cerevisiae.

PubMed

Murashchenko, Lidiia; Abbas, Charles; Dmytruk, Kostyantyn; Sibirny, Andriy

2016-08-01

Acetolactate synthase is a mitochondrial enzyme that catalyses the conversion of two pyruvate molecules to an acetolactate molecule with release of carbon dioxide. The overexpression of the truncated version of the corresponding gene, ILV2, that codes for presumably cytosolic acetolactate synthase in the yeast Saccharomyces cerevisiae, led to a decrease in intracellular pyruvate concentration. This recombinant strain was also characterized by a four-fold increase in glycerol production, with a concomitant 1.8-fold reduction in ethanol production, when compared to that of the wild-type strain under anaerobic conditions in a glucose alcoholic fermentation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences.

PubMed

Whitaker, Weston R; Lee, Hanson; Arkin, Adam P; Dueber, John E

2015-03-20

Genetic sequences ported into non-native hosts for synthetic biology applications can gain unexpected properties. In this study, we explored sequences functioning as ribosome binding sites (RBSs) within protein coding DNA sequences (CDSs) that cause internal translation, resulting in truncated proteins. Genome-wide prediction of bacterial RBSs, based on biophysical calculations employed by the RBS calculator, suggests a selection against internal RBSs within CDSs in Escherichia coli, but not those in Saccharomyces cerevisiae. Based on these calculations, silent mutations aimed at removing internal RBSs can effectively reduce truncation products from internal translation. However, a solution for complete elimination of internal translation initiation is not always feasible due to constraints of available coding sequences. Fluorescence assays and Western blot analysis showed that in genes with internal RBSs, increasing the strength of the intended upstream RBS had little influence on the internal translation strength. Another strategy to minimize truncated products from an internal RBS is to increase the relative strength of the upstream RBS with a concomitant reduction in promoter strength to achieve the same protein expression level. Unfortunately, lower transcription levels result in increased noise at the single cell level due to stochasticity in gene expression. At the low expression regimes desired for many synthetic biology applications, this problem becomes particularly pronounced. We found that balancing promoter strengths and upstream RBS strengths to intermediate levels can achieve the target protein concentration while avoiding both excessive noise and truncated protein.

A Support Vector Machine Approach for Truncated Fingerprint Image Detection from Sweeping Fingerprint Sensors

PubMed Central

Chen, Chi-Jim; Pai, Tun-Wen; Cheng, Mox

2015-01-01

A sweeping fingerprint sensor converts fingerprints on a row by row basis through image reconstruction techniques. However, a built fingerprint image might appear to be truncated and distorted when the finger was swept across a fingerprint sensor at a non-linear speed. If the truncated fingerprint images were enrolled as reference targets and collected by any automated fingerprint identification system (AFIS), successful prediction rates for fingerprint matching applications would be decreased significantly. In this paper, a novel and effective methodology with low time computational complexity was developed for detecting truncated fingerprints in a real time manner. Several filtering rules were implemented to validate existences of truncated fingerprints. In addition, a machine learning method of supported vector machine (SVM), based on the principle of structural risk minimization, was applied to reject pseudo truncated fingerprints containing similar characteristics of truncated ones. The experimental result has shown that an accuracy rate of 90.7% was achieved by successfully identifying truncated fingerprint images from testing images before AFIS enrollment procedures. The proposed effective and efficient methodology can be extensively applied to all existing fingerprint matching systems as a preliminary quality control prior to construction of fingerprint templates. PMID:25835186

Direct determination of one-dimensional interphase structures using normalized crystal truncation rod analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawaguchi, Tomoya; Liu, Yihua; Reiter, Anthony

Here, a one-dimensional non-iterative direct method was employed for normalized crystal truncation rod analysis. The non-iterative approach, utilizing the Kramers–Kronig relation, avoids the ambiguities due to an improper initial model or incomplete convergence in the conventional iterative methods. The validity and limitations of the present method are demonstrated through both numerical simulations and experiments with Pt(111) in a 0.1 M CsF aqueous solution. The present method is compared with conventional iterative phase-retrieval methods.

Direct determination of one-dimensional interphase structures using normalized crystal truncation rod analysis

DOE PAGES

Kawaguchi, Tomoya; Liu, Yihua; Reiter, Anthony; ...

2018-04-20

Here, a one-dimensional non-iterative direct method was employed for normalized crystal truncation rod analysis. The non-iterative approach, utilizing the Kramers–Kronig relation, avoids the ambiguities due to an improper initial model or incomplete convergence in the conventional iterative methods. The validity and limitations of the present method are demonstrated through both numerical simulations and experiments with Pt(111) in a 0.1 M CsF aqueous solution. The present method is compared with conventional iterative phase-retrieval methods.

Robust Principal Component Analysis Regularized by Truncated Nuclear Norm for Identifying Differentially Expressed Genes.

PubMed

Wang, Ya-Xuan; Gao, Ying-Lian; Liu, Jin-Xing; Kong, Xiang-Zhen; Li, Hai-Jun

2017-09-01

Identifying differentially expressed genes from the thousands of genes is a challenging task. Robust principal component analysis (RPCA) is an efficient method in the identification of differentially expressed genes. RPCA method uses nuclear norm to approximate the rank function. However, theoretical studies showed that the nuclear norm minimizes all singular values, so it may not be the best solution to approximate the rank function. The truncated nuclear norm is defined as the sum of some smaller singular values, which may achieve a better approximation of the rank function than nuclear norm. In this paper, a novel method is proposed by replacing nuclear norm of RPCA with the truncated nuclear norm, which is named robust principal component analysis regularized by truncated nuclear norm (TRPCA). The method decomposes the observation matrix of genomic data into a low-rank matrix and a sparse matrix. Because the significant genes can be considered as sparse signals, the differentially expressed genes are viewed as the sparse perturbation signals. Thus, the differentially expressed genes can be identified according to the sparse matrix. The experimental results on The Cancer Genome Atlas data illustrate that the TRPCA method outperforms other state-of-the-art methods in the identification of differentially expressed genes.

Statistical inference based on the nonparametric maximum likelihood estimator under double-truncation.

PubMed

Emura, Takeshi; Konno, Yoshihiko; Michimae, Hirofumi

2015-07-01

Doubly truncated data consist of samples whose observed values fall between the right- and left- truncation limits. With such samples, the distribution function of interest is estimated using the nonparametric maximum likelihood estimator (NPMLE) that is obtained through a self-consistency algorithm. Owing to the complicated asymptotic distribution of the NPMLE, the bootstrap method has been suggested for statistical inference. This paper proposes a closed-form estimator for the asymptotic covariance function of the NPMLE, which is computationally attractive alternative to bootstrapping. Furthermore, we develop various statistical inference procedures, such as confidence interval, goodness-of-fit tests, and confidence bands to demonstrate the usefulness of the proposed covariance estimator. Simulations are performed to compare the proposed method with both the bootstrap and jackknife methods. The methods are illustrated using the childhood cancer dataset.

Gene-Based Testing of Interactions in Association Studies of Quantitative Traits

PubMed Central

Ma, Li; Clark, Andrew G.; Keinan, Alon

2013-01-01

Various methods have been developed for identifying gene–gene interactions in genome-wide association studies (GWAS). However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene–gene interaction (GGG) tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein–protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies. PMID:23468652

Rapid one-step recombinational cloning

PubMed Central

Fu, Changlin; Wehr, Daniel R.; Edwards, Janice; Hauge, Brian

2008-01-01

As an increasing number of genes and open reading frames of unknown function are discovered, expression of the encoded proteins is critical toward establishing function. Accordingly, there is an increased need for highly efficient, high-fidelity methods for directional cloning. Among the available methods, site-specific recombination-based cloning techniques, which eliminate the use of restriction endonucleases and ligase, have been widely used for high-throughput (HTP) procedures. We have developed a recombination cloning method, which uses truncated recombination sites to clone PCR products directly into destination/expression vectors, thereby bypassing the requirement for first producing an entry clone. Cloning efficiencies in excess of 80% are obtained providing a highly efficient method for directional HTP cloning. PMID:18424799

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arakaki, Tracy; Le Trong, Isolde; Structural Genomics of Pathogenic Protozoa

2006-03-01

The crystal structure of a conserved hypothetical protein from L. major, Pfam sequence family PF04543, structural genomics target ID Lmaj006129AAA, has been determined at a resolution of 1.6 Å. The gene product of structural genomics target Lmaj006129 from Leishmania major codes for a 164-residue protein of unknown function. When SeMet expression of the full-length gene product failed, several truncation variants were created with the aid of Ginzu, a domain-prediction method. 11 truncations were selected for expression, purification and crystallization based upon secondary-structure elements and disorder. The structure of one of these variants, Lmaj006129AAH, was solved by multiple-wavelength anomalous diffraction (MAD)more » using ELVES, an automatic protein crystal structure-determination system. This model was then successfully used as a molecular-replacement probe for the parent full-length target, Lmaj006129AAA. The final structure of Lmaj006129AAA was refined to an R value of 0.185 (R{sub free} = 0.229) at 1.60 Å resolution. Structure and sequence comparisons based on Lmaj006129AAA suggest that proteins belonging to Pfam sequence families PF04543 and PF01878 may share a common ligand-binding motif.« less

Transient Expression and Purification of Horseradish Peroxidase C in Nicotiana benthamiana.

PubMed

Huddy, Suzanne M; Hitzeroth, Inga I; Meyers, Ann E; Weber, Brandon; Rybicki, Edward P

2018-01-01

Horseradish peroxidase (HRP) is a commercially important reagent enzyme used in molecular biology and in the diagnostic product industry. It is typically purified from the roots of the horseradish ( Armoracia rusticana ); however, this crop is only available seasonally, yields are variable and often low, and the product is a mixture of isoenzymes. Engineering high-level expression in transiently transformed tobacco may offer a solution to these problems. In this study, a synthetic Nicotiana benthamiana codon-adapted full-length HRP isoenzyme gene as well as C-terminally truncated and both N- and C-terminally truncated versions of the HRP C gene were synthesized, and their expression in N. benthamiana was evaluated using an Agrobacterium tumefaciens -mediated transient expression system. The influence on HRP C expression levels of co-infiltration with a silencing suppressor (NSs) construct was also evaluated. Highest HRP C levels were consistently obtained using either the full length or C-terminally truncated HRP C constructs. HRP C purification by ion exchange chromatography gave an overall yield of 54% with a Reinheitszahl value of >3 and a specific activity of 458 U/mg. The high level of HRP C production in N. benthamiana in just five days offers an alternative, viable, and scalable system for production of this commercially significant enzyme.

Transient Expression and Purification of Horseradish Peroxidase C in Nicotiana benthamiana

PubMed Central

Huddy, Suzanne M.; Hitzeroth, Inga I.; Weber, Brandon; Rybicki, Edward P.

2018-01-01

Horseradish peroxidase (HRP) is a commercially important reagent enzyme used in molecular biology and in the diagnostic product industry. It is typically purified from the roots of the horseradish (Armoracia rusticana); however, this crop is only available seasonally, yields are variable and often low, and the product is a mixture of isoenzymes. Engineering high-level expression in transiently transformed tobacco may offer a solution to these problems. In this study, a synthetic Nicotiana benthamiana codon-adapted full-length HRP isoenzyme gene as well as C-terminally truncated and both N- and C-terminally truncated versions of the HRP C gene were synthesized, and their expression in N. benthamiana was evaluated using an Agrobacterium tumefaciens-mediated transient expression system. The influence on HRP C expression levels of co-infiltration with a silencing suppressor (NSs) construct was also evaluated. Highest HRP C levels were consistently obtained using either the full length or C-terminally truncated HRP C constructs. HRP C purification by ion exchange chromatography gave an overall yield of 54% with a Reinheitszahl value of >3 and a specific activity of 458 U/mg. The high level of HRP C production in N. benthamiana in just five days offers an alternative, viable, and scalable system for production of this commercially significant enzyme. PMID:29301255

A truncated, activin-induced Smad3 isoform acts as a transcriptional repressor of FSHβ expression in mouse pituitary

PubMed Central

Kim, So-Youn; Zhu, Jie; Woodruff, Teresa K.

2011-01-01

The receptor-regulated protein Smad3 is key player in the signaling cascade stimulated by the binding of activin to its cell surface receptor. Upon phosphorylation, Smad3 forms a heterocomplex with Smad2 and Smad4, translocates to the nucleus and acts as a transcriptional co-activator. We have identified a unique isoform of Smad3 that is expressed in mature pituitary gonadotropes. 5' RACE revealed that this truncated Smad3 isoform is transcribed from an ATG site within exon 4 and consists of 7 exons encoding half of the linker region and the MH2 region. In pituitary cells, the truncated Smad3 isoform was phosphorylated upon activin treatment, in a manner that was temporally distinct from the phosphorylation of full-length Smad3. Activin-induced phosphorylation of Smad3 and the truncated Smad3 isoform was blocked by both follistatin and siRNA-mediated knockdown of Smad3. The truncated Smad3 isoform antagonized Smad3-mediated, activin-responsive promoter activity. We propose that the pituitary gonadotrope contains an ultra-short, activin-responsive feedback loop utilizing two different isoforms of Smad3, one which acts as an agonist (Smad3) and another that acts as an intracrine antagonist (truncated Smad3 isoform) to regulate FSHβ production. PMID:21664424

Estimating Patient Dose from X-ray Tube Output Metrics: Automated Measurement of Patient Size from CT Images Enables Large-scale Size-specific Dose Estimates

PubMed Central

Ikuta, Ichiro; Warden, Graham I.; Andriole, Katherine P.; Khorasani, Ramin

2014-01-01

Purpose To test the hypothesis that patient size can be accurately calculated from axial computed tomographic (CT) images, including correction for the effects of anatomy truncation that occur in routine clinical CT image reconstruction. Materials and Methods Institutional review board approval was obtained for this HIPAA-compliant study, with waiver of informed consent. Water-equivalent diameter (DW) was computed from the attenuation-area product of each image within 50 adult CT scans of the thorax and of the abdomen and pelvis and was also measured for maximal field of view (FOV) reconstructions. Linear regression models were created to compare DW with the effective diameter (Deff) used to select size-specific volume CT dose index (CTDIvol) conversion factors as defined in report 204 of the American Association of Physicists in Medicine. Linear regression models relating reductions in measured DW to a metric of anatomy truncation were used to compensate for the effects of clinical image truncation. Results In the thorax, DW versus Deff had an R2 of 0.51 (n = 200, 50 patients at four anatomic locations); in the abdomen and pelvis, R2 was 0.90 (n = 150, 50 patients at three anatomic locations). By correcting for image truncation, the proportion of clinically reconstructed images with an extracted DW within ±5% of the maximal FOV DW increased from 54% to 90% in the thorax (n = 3602 images) and from 95% to 100% in the abdomen and pelvis (6181 images). Conclusion The DW extracted from axial CT images is a reliable measure of patient size, and varying degrees of clinical image truncation can be readily corrected. Automated measurement of patient size combined with CT radiation exposure metrics may enable patient-specific dose estimation on a large scale. © RSNA, 2013 PMID:24086075

Analytic reconstruction algorithms for triple-source CT with horizontal data truncation.

PubMed

Chen, Ming; Yu, Hengyong

2015-10-01

This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and matlab. While the basic platform is constructed in matlab, the computationally intensive segments are coded in c + +, which are linked via a mex interface. A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle to cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units.

High-precision calculations in strongly coupled quantum field theory with next-to-leading-order renormalized Hamiltonian Truncation

NASA Astrophysics Data System (ADS)

Elias-Miró, Joan; Rychkov, Slava; Vitale, Lorenzo G.

2017-10-01

Hamiltonian Truncation (a.k.a. Truncated Spectrum Approach) is an efficient numerical technique to solve strongly coupled QFTs in d = 2 spacetime dimensions. Further theoretical developments are needed to increase its accuracy and the range of applicability. With this goal in mind, here we present a new variant of Hamiltonian Truncation which exhibits smaller dependence on the UV cutoff than other existing implementations, and yields more accurate spectra. The key idea for achieving this consists in integrating out exactly a certain class of high energy states, which corresponds to performing renormalization at the cubic order in the interaction strength. We test the new method on the strongly coupled two-dimensional quartic scalar theory. Our work will also be useful for the future goal of extending Hamiltonian Truncation to higher dimensions d ≥ 3.

Manufacturing Methods and Technology Engineering (MM&TE) Program for the Establishment of Production Techniques for High Density Thick Film Circuits Used in Crystal Oscillators. Volume I.

DTIC Science & Technology

1980-04-01

incorporate the high reliability ceramic-packaged quartz crystal resonator developed at ERADCOM, and utilize beam -leaded devices wherever possible...the form of a truncated cylinder. The rather complex module outline is best accomplished through the use of a precast potting shell filled with a low...crossover connections are achieved by means of thick-film dielectric material. Chip components attached to the metallized substrate complete the circuits

Targeted mass spectrometric analysis of N-terminally truncated isoforms generated via alternative translation initiation.

PubMed

Kobayashi, Ryuji; Patenia, Rebecca; Ashizawa, Satoshi; Vykoukal, Jody

2009-07-21

Alternative translation initiation is a mechanism whereby functionally altered proteins are produced from a single mRNA. Internal initiation of translation generates N-terminally truncated protein isoforms, but such isoforms observed in immunoblot analysis are often overlooked or dismissed as degradation products. We identified an N-terminally truncated isoform of human Dok-1 with N-terminal acetylation as seen in the wild-type. This Dok-1 isoform exhibited distinct perinuclear localization whereas the wild-type protein was distributed throughout the cytoplasm. Targeted analysis of blocked N-terminal peptides provides rapid identification of protein isoforms and could be widely applied for the general evaluation of perplexing immunoblot bands.

Forward Looking Radar Imaging by Truncated Singular Value Decomposition and Its Application for Adverse Weather Aircraft Landing.

PubMed

Huang, Yulin; Zha, Yuebo; Wang, Yue; Yang, Jianyu

2015-06-18

The forward looking radar imaging task is a practical and challenging problem for adverse weather aircraft landing industry. Deconvolution method can realize the forward looking imaging but it often leads to the noise amplification in the radar image. In this paper, a forward looking radar imaging based on deconvolution method is presented for adverse weather aircraft landing. We first present the theoretical background of forward looking radar imaging task and its application for aircraft landing. Then, we convert the forward looking radar imaging task into a corresponding deconvolution problem, which is solved in the framework of algebraic theory using truncated singular decomposition method. The key issue regarding the selecting of the truncated parameter is addressed using generalized cross validation approach. Simulation and experimental results demonstrate that the proposed method is effective in achieving angular resolution enhancement with suppressing the noise amplification in forward looking radar imaging.

Meshfree truncated hierarchical refinement for isogeometric analysis

NASA Astrophysics Data System (ADS)

Atri, H. R.; Shojaee, S.

2018-05-01

In this paper truncated hierarchical B-spline (THB-spline) is coupled with reproducing kernel particle method (RKPM) to blend advantages of the isogeometric analysis and meshfree methods. Since under certain conditions, the isogeometric B-spline and NURBS basis functions are exactly represented by reproducing kernel meshfree shape functions, recursive process of producing isogeometric bases can be omitted. More importantly, a seamless link between meshfree methods and isogeometric analysis can be easily defined which provide an authentic meshfree approach to refine the model locally in isogeometric analysis. This procedure can be accomplished using truncated hierarchical B-splines to construct new bases and adaptively refine them. It is also shown that the THB-RKPM method can provide efficient approximation schemes for numerical simulations and represent a promising performance in adaptive refinement of partial differential equations via isogeometric analysis. The proposed approach for adaptive locally refinement is presented in detail and its effectiveness is investigated through well-known benchmark examples.

The effect of acceleration versus displacement methods on steady-state boundary forces

NASA Technical Reports Server (NTRS)

Mcghee, D. S.

1992-01-01

This study describes the acceleration and displacement methods for use in the recovery of coupled system boundary forces. A simple two degree of freedom system has been used for illustration. The effect of the choice of method for use with indeterminate or over-constrained boundaries has been investigated. It has specifically looked at results from a simple two dimensional beam problem using both methods. Much work has been done on the effect of Craig-Bampton modal truncation system displacements and forces, however, little work has been done on system level modal truncation. The findings of this study indicate that the effect of this system level truncation is significant. This may be particularly true for the 35 Hz system cutoff frequency that is required by the space shuttle. From this study's findings, recommendations for areas of study with space shuttle payload systems are made.

Ensemble Kalman filtering in presence of inequality constraints

NASA Astrophysics Data System (ADS)

van Leeuwen, P. J.

2009-04-01

Kalman filtering is presence of constraints is an active area of research. Based on the Gaussian assumption for the probability-density functions, it looks hard to bring in extra constraints in the formalism. On the other hand, in geophysical systems we often encounter constraints related to e.g. the underlying physics or chemistry, which are violated by the Gaussian assumption. For instance, concentrations are always non-negative, model layers have non-negative thickness, and sea-ice concentration is between 0 and 1. Several methods to bring inequality constraints into the Kalman-filter formalism have been proposed. One of them is probability density function (pdf) truncation, in which the Gaussian mass from the non-allowed part of the variables is just equally distributed over the pdf where the variables are alolwed, as proposed by Shimada et al. 1998. However, a problem with this method is that the probability that e.g. the sea-ice concentration is zero, is zero! The new method proposed here does not have this drawback. It assumes that the probability-density function is a truncated Gaussian, but the truncated mass is not distributed equally over all allowed values of the variables, but put into a delta distribution at the truncation point. This delta distribution can easily be handled with in Bayes theorem, leading to posterior probability density functions that are also truncated Gaussians with delta distributions at the truncation location. In this way a much better representation of the system is obtained, while still keeping most of the benefits of the Kalman-filter formalism. In the full Kalman filter the formalism is prohibitively expensive in large-scale systems, but efficient implementation is possible in ensemble variants of the kalman filter. Applications to low-dimensional systems and large-scale systems will be discussed.

``Dressing'' lines and vertices in calculations of matrix elements with the coupled-cluster method and determination of Cs atomic properties

NASA Astrophysics Data System (ADS)

Derevianko, Andrei; Porsev, Sergey G.

2005-03-01

We consider evaluation of matrix elements with the coupled-cluster method. Such calculations formally involve infinite number of terms and we devise a method of partial summation (dressing) of the resulting series. Our formalism is built upon an expansion of the product C†C of cluster amplitudes C into a sum of n -body insertions. We consider two types of insertions: particle (hole) line insertion and two-particle (two-hole) random-phase-approximation-like insertion. We demonstrate how to “dress” these insertions and formulate iterative equations. We illustrate the dressing equations in the case when the cluster operator is truncated at single and double excitations. Using univalent systems as an example, we upgrade coupled-cluster diagrams for matrix elements with the dressed insertions and highlight a relation to pertinent fourth-order diagrams. We illustrate our formalism with relativistic calculations of the hyperfine constant A(6s) and the 6s1/2-6p1/2 electric-dipole transition amplitude for the Cs atom. Finally, we augment the truncated coupled-cluster calculations with otherwise omitted fourth order diagrams. The resulting analysis for Cs is complete through the fourth order of many-body perturbation theory and reveals an important role of triple and disconnected quadruple excitations.

Prediction of the moments in advection-diffusion lattice Boltzmann method. I. Truncation dispersion, skewness, and kurtosis

NASA Astrophysics Data System (ADS)

Ginzburg, Irina

2017-01-01

The effect of the heterogeneity in the soil structure or the nonuniformity of the velocity field on the modeled resident time distribution (RTD) and breakthrough curves is quantified by their moments. While the first moment provides the effective velocity, the second moment is related to the longitudinal dispersion coefficient (kT) in the developed Taylor regime; the third and fourth moments are characterized by their normalized values skewness (Sk) and kurtosis (Ku), respectively. The purpose of this investigation is to examine the role of the truncation corrections of the numerical scheme in kT, Sk, and Ku because of their interference with the second moment, in the form of the numerical dispersion, and in the higher-order moments, by their definition. Our symbolic procedure is based on the recently proposed extended method of moments (EMM). Originally, the EMM restores any-order physical moments of the RTD or averaged distributions assuming that the solute concentration obeys the advection-diffusion equation in multidimensional steady-state velocity field, in streamwise-periodic heterogeneous structure. In our work, the EMM is generalized to the fourth-order-accurate apparent mass-conservation equation in two- and three-dimensional duct flows. The method looks for the solution of the transport equation as the product of a long harmonic wave and a spatially periodic oscillating component; the moments of the given numerical scheme are derived from a chain of the steady-state fourth-order equations at a single cell. This mathematical technique is exemplified for the truncation terms of the two-relaxation-time lattice Boltzmann scheme, using plug and parabolic flow in straight channel and cylindrical capillary with the d2Q9 and d3Q15 discrete velocity sets as simple but illustrative examples. The derived symbolic dependencies can be readily extended for advection by another, Newtonian or non-Newtonian, flow profile in any-shape open-tabular conduits. It is established that the truncation errors in the three transport coefficients kT, Sk, and Ku decay with the second-order accuracy. While the physical values of the three transport coefficients are set by Péclet number, their truncation corrections additionally depend on the two adjustable relaxation rates and the two adjustable equilibrium weight families which independently determine the convective and diffusion discretization stencils. We identify flow- and dimension-independent optimal strategies for adjustable parameters and confront them to stability requirements. Through specific choices of two relaxation rates and weights, we expect our results be directly applicable to forward-time central differences and leap-frog central-convective Du Fort-Frankel-diffusion schemes. In straight channel, a quasi-exact validation of the truncation predictions through the numerical moments becomes possible thanks to the specular-forward no-flux boundary rule. In the staircase description of a cylindrical capillary, we account for the spurious boundary-layer diffusion and dispersion because of the tangential constraint of the bounce-back no-flux boundary rule.

Higher-order stochastic differential equations and the positive Wigner function

NASA Astrophysics Data System (ADS)

Drummond, P. D.

2017-12-01

General higher-order stochastic processes that correspond to any diffusion-type tensor of higher than second order are obtained. The relationship of multivariate higher-order stochastic differential equations with tensor decomposition theory and tensor rank is explained. Techniques for generating the requisite complex higher-order noise are proved to exist either using polar coordinates and γ distributions, or from products of Gaussian variates. This method is shown to allow the calculation of the dynamics of the Wigner function, after it is extended to a complex phase space. The results are illustrated physically through dynamical calculations of the positive Wigner distribution for three-mode parametric downconversion, widely used in quantum optics. The approach eliminates paradoxes arising from truncation of the higher derivative terms in Wigner function time evolution. Anomalous results of negative populations and vacuum scattering found in truncated Wigner quantum simulations in quantum optics and Bose-Einstein condensate dynamics are shown not to occur with this type of stochastic theory.

Controlled synthesis and visible light photocatalytic activity of Bi12GeO20 uniform microcrystals

PubMed Central

Wan, Zhen; Zhang, Gaoke

2014-01-01

We successfully synthesized uniform Bi12GeO20 microspheres and microtetrahedrons enclosed by four {111} facets using a controlled hydrothermal method for the first time. The photocatalytic activity of these regular-shaped products was further investigated by the degradation of RhB and gaseous formaldehyde under visible light irradiation (λ>420 nm). The Bi12GeO20 microtetrahedrons (s) exhibited enhanced photocatalytic activity and stability which is closely related to the high capacity of exposed {111} facets for uptake of O2. The formation mechanism studies indicate that the Bi12GeO20 seeds were directed to grow into truncated microcubes, truncated microtetrahedrons, and then microtetrahedrons when the NaOH concentration was 5 M. The same batch of seeds only evolved into microspheres when the NaOH concentration was switched to 3 M. The difference in Bi12GeO20 morphology could be attributed to the rates of both crystal nucleation and crystal growth. PMID:25199641

The effect of truncation on very small cardiac SPECT camerasystems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohmer, Damien; Eisner, Robert L.; Gullberg, Grant T.

2006-08-01

Background: The limited transaxial field-of-view (FOV) of avery small cardiac SPECT camera system causes view-dependent truncationof the projection of structures exterior to, but near the heart. Basictomographic principles suggest that the reconstruction of non-attenuatedtruncated data gives a distortion-free image in the interior of thetruncated region, but the DC term of the Fourier spectrum of thereconstructed image is incorrect, meaning that the intensity scale of thereconstruction is inaccurate. The purpose of this study was tocharacterize the reconstructed image artifacts from truncated data, andto quantify their effects on the measurement of tracer uptake in themyocardial. Particular attention was given to instances wheremore » the heartwall is close to hot structures (structures of high activity uptake).Methods: The MCAT phantom was used to simulate a 2D slice of the heartregion. Truncated and non-truncated projections were formed both with andwithout attenuation. The reconstructions were analyzed for artifacts inthe myocardium caused by truncation, and for the effect that attenuationhas relative to increasing those artifacts. Results: The inaccuracy dueto truncation is primarily caused by an incorrect DC component. Forvisualizing theleft ventricular wall, this error is not worse than theeffect of attenuation. The addition of a small hot bowel-like structurenear the left ventricle causes few changes in counts on the wall. Largerartifacts due to the truncation are located at the boundary of thetruncation and can be eliminated by sinogram interpolation. Finally,algebraic reconstruction methods are shown to give better reconstructionresults than an analytical filtered back-projection reconstructionalgorithm. Conclusion: Small inaccuracies in reconstructed images fromsmall FOV camera systems should have little effect on clinicalinterpretation. However, changes in the degree of inaccuracy in countsfrom slice toslice are due to changes in the truncated structures. Thesecan result in a visual 3-dimensional distortion. As with conventionallarge FOV systems attenuation effects have a much more significant effecton image accuracy.« less

A Gauss-Newton full-waveform inversion in PML-truncated domains using scalar probing waves

NASA Astrophysics Data System (ADS)

Pakravan, Alireza; Kang, Jun Won; Newtson, Craig M.

2017-12-01

This study considers the characterization of subsurface shear wave velocity profiles in semi-infinite media using scalar waves. Using surficial responses caused by probing waves, a reconstruction of the material profile is sought using a Gauss-Newton full-waveform inversion method in a two-dimensional domain truncated by perfectly matched layer (PML) wave-absorbing boundaries. The PML is introduced to limit the semi-infinite extent of the half-space and to prevent reflections from the truncated boundaries. A hybrid unsplit-field PML is formulated in the inversion framework to enable more efficient wave simulations than with a fully mixed PML. The full-waveform inversion method is based on a constrained optimization framework that is implemented using Karush-Kuhn-Tucker (KKT) optimality conditions to minimize the objective functional augmented by PML-endowed wave equations via Lagrange multipliers. The KKT conditions consist of state, adjoint, and control problems, and are solved iteratively to update the shear wave velocity profile of the PML-truncated domain. Numerical examples show that the developed Gauss-Newton inversion method is accurate enough and more efficient than another inversion method. The algorithm's performance is demonstrated by the numerical examples including the case of noisy measurement responses and the case of reduced number of sources and receivers.

A truncated, activin-induced Smad3 isoform acts as a transcriptional repressor of FSHβ expression in mouse pituitary.

PubMed

Kim, So-Youn; Zhu, Jie; Woodruff, Teresa K

2011-08-06

The receptor-regulated protein Smad3 is key player in the signaling cascade stimulated by the binding of activin to its cell surface receptor. Upon phosphorylation, Smad3 forms a heterocomplex with Smad2 and Smad4, translocates to the nucleus and acts as a transcriptional co-activator. We have identified a unique isoform of Smad3 that is expressed in mature pituitary gonadotropes. 5' RACE revealed that this truncated Smad3 isoform is transcribed from an ATG site within exon 4 and consists of 7 exons encoding half of the linker region and the MH2 region. In pituitary cells, the truncated Smad3 isoform was phosphorylated upon activin treatment, in a manner that was temporally distinct from the phosphorylation of full-length Smad3. Activin-induced phosphorylation of Smad3 and the truncated Smad3 isoform was blocked by both follistatin and siRNA-mediated knockdown of Smad3. The truncated Smad3 isoform antagonized Smad3-mediated, activin-responsive promoter activity. We propose that the pituitary gonadotrope contains an ultra-short, activin-responsive feedback loop utilizing two different isoforms of Smad3, one which acts as an agonist (Smad3) and another that acts as an intracrine antagonist (truncated Smad3 isoform) to regulate FSHβ production. Copyright © 2011 Elsevier Ltd. All rights reserved.

Zero-truncated panel Poisson mixture models: Estimating the impact on tourism benefits in Fukushima Prefecture.

PubMed

Narukawa, Masaki; Nohara, Katsuhito

2018-04-01

This study proposes an estimation approach to panel count data, truncated at zero, in order to apply a contingent behavior travel cost method to revealed and stated preference data collected via a web-based survey. We develop zero-truncated panel Poisson mixture models by focusing on respondents who visited a site. In addition, we introduce an inverse Gaussian distribution to unobserved individual heterogeneity as an alternative to a popular gamma distribution, making it possible to capture effectively the long tail typically observed in trip data. We apply the proposed method to estimate the impact on tourism benefits in Fukushima Prefecture as a result of the Fukushima Nuclear Power Plant No. 1 accident. Copyright © 2018 Elsevier Ltd. All rights reserved.

Detecting and correcting for publication bias in meta-analysis - A truncated normal distribution approach.

PubMed

Zhu, Qiaohao; Carriere, K C

2016-01-01

Publication bias can significantly limit the validity of meta-analysis when trying to draw conclusion about a research question from independent studies. Most research on detection and correction for publication bias in meta-analysis focus mainly on funnel plot-based methodologies or selection models. In this paper, we formulate publication bias as a truncated distribution problem, and propose new parametric solutions. We develop methodologies of estimating the underlying overall effect size and the severity of publication bias. We distinguish the two major situations, in which publication bias may be induced by: (1) small effect size or (2) large p-value. We consider both fixed and random effects models, and derive estimators for the overall mean and the truncation proportion. These estimators will be obtained using maximum likelihood estimation and method of moments under fixed- and random-effects models, respectively. We carried out extensive simulation studies to evaluate the performance of our methodology, and to compare with the non-parametric Trim and Fill method based on funnel plot. We find that our methods based on truncated normal distribution perform consistently well, both in detecting and correcting publication bias under various situations.

Geminal-spanning orbitals make explicitly correlated reduced-scaling coupled-cluster methods robust, yet simple

NASA Astrophysics Data System (ADS)

Pavošević, Fabijan; Neese, Frank; Valeev, Edward F.

2014-08-01

We present a production implementation of reduced-scaling explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) method based on pair-natural orbitals (PNOs). A key feature is the reformulation of the explicitly correlated terms using geminal-spanning orbitals that greatly reduce the truncation errors of the F12 contribution. For the standard S66 benchmark of weak intermolecular interactions, the cc-pVDZ-F12 PNO CCSD F12 interaction energies reproduce the complete basis set CCSD limit with mean absolute error <0.1 kcal/mol, and at a greatly reduced cost compared to the conventional CCSD F12.

Expression of a truncated form of the endoplasmic reticulum chaperone protein, σ1 receptor, promotes mitochondrial energy depletion and apoptosis.

PubMed

Shioda, Norifumi; Ishikawa, Kiyoshi; Tagashira, Hideaki; Ishizuka, Toru; Yawo, Hiromu; Fukunaga, Kohji

2012-07-06

The σ1 receptor (σ(1)R) regulates endoplasmic reticulum (ER)/mitochondrial interorganellar Ca(2+) mobilization through the inositol 1,4,5-trisphosphate receptor (IP(3)R). Here, we observed that expression of a novel splice variant of σ(1)R, termed short form σ(1)R (σ(1)SR), has a detrimental effect on mitochondrial energy production and cell survival. σ(1)SR mRNA lacks 47 ribonucleotides encoding exon 2, resulting in a frameshift and formation of a truncated receptor. σ(1)SR localizes primarily in the ER at perinuclear regions and forms a complex with σ(1)R but not with IP(3)R in the mitochondrion-associated ER membrane. Overexpression of both σ(1)R and the truncated isoform promotes mitochondrial elongation with increased ER mitochondrial contact surface. σ(1)R overexpression increases the efficiency of mitochondrial Ca(2+) uptake in response to IP(3)R-driven stimuli, whereas σ(1)SR overexpression reduces it. Most importantly, σ(1)R promotes ATP production via increased mitochondrial Ca(2+) uptake, promoting cell survival in the presence of ER stress. By contrast, σ(1)SR suppresses ATP production following ER stress, enhancing cell death. Taken together, the newly identified σ(1)SR isoform interferes with σ(1)R function relevant to mitochondrial energy production under ER stress conditions, promoting cellular apoptosis.

Errors due to the truncation of the computational domain in static three-dimensional electrical impedance tomography.

PubMed

Vauhkonen, P J; Vauhkonen, M; Kaipio, J P

2000-02-01

In electrical impedance tomography (EIT), an approximation for the internal resistivity distribution is computed based on the knowledge of the injected currents and measured voltages on the surface of the body. The currents spread out in three dimensions and therefore off-plane structures have a significant effect on the reconstructed images. A question arises: how far from the current carrying electrodes should the discretized model of the object be extended? If the model is truncated too near the electrodes, errors are produced in the reconstructed images. On the other hand if the model is extended very far from the electrodes the computational time may become too long in practice. In this paper the model truncation problem is studied with the extended finite element method. Forward solutions obtained using so-called infinite elements, long finite elements and separable long finite elements are compared to the correct solution. The effects of the truncation of the computational domain on the reconstructed images are also discussed and results from the three-dimensional (3D) sensitivity analysis are given. We show that if the finite element method with ordinary elements is used in static 3D EIT, the dimension of the problem can become fairly large if the errors associated with the domain truncation are to be avoided.

N-terminally truncated GADD34 proteins are convenient translation enhancers in a human cell-derived in vitro protein synthesis system.

PubMed

Mikami, Satoshi; Kobayashi, Tominari; Machida, Kodai; Masutani, Mamiko; Yokoyama, Shigeyuki; Imataka, Hiroaki

2010-07-01

Human cell-derived in vitro protein synthesis systems are useful for the production of recombinant proteins. Productivity can be increased by supplementation with GADD34, a protein that is difficult to express in and purify from E. coli. Deletion of the N-terminal 120 or 240 amino acids of GADD34 improves recovery of this protein from E. coli without compromising its ability to boost protein synthesis in an in vitro protein synthesis system. The use of N-terminally truncated GADD34 proteins in place of full-length GADD34 should improve the utility of human cell-based cell-free protein synthesis systems.

Low field magnetic resonance imaging

DOEpatents

Pines, Alexander; Sakellariou, Dimitrios; Meriles, Carlos A.; Trabesinger, Andreas H.

2010-07-13

A method and system of magnetic resonance imaging does not need a large homogenous field to truncate a gradient field. Spatial information is encoded into the spin magnetization by allowing the magnetization to evolve in a non-truncated gradient field and inducing a set of 180 degree rotations prior to signal acquisition.

Discovery of Genomic Breakpoints Affecting Breast Cancer Progression and Prognosis

DTIC Science & Technology

2010-10-01

mutations compared to those detected by the 5Kbp method alone. Fosmid diTag method also reveals much higher proportion of gene fusions and truncations...observed highly similar structural mutational spectra affecting different sets of genes , pointing to similar histories of genomic instability against... mutations have been identified in non-BRCA1/2 multiethnic breast cancer cases (45,46), no truncating mutation of the RAP80 gene in breast cancer has

Causal analysis of ordinal treatments and binary outcomes under truncation by death.

PubMed

Wang, Linbo; Richardson, Thomas S; Zhou, Xiao-Hua

2017-06-01

It is common that in multi-arm randomized trials, the outcome of interest is "truncated by death," meaning that it is only observed or well-defined conditioning on an intermediate outcome. In this case, in addition to pairwise contrasts, the joint inference for all treatment arms is also of interest. Under a monotonicity assumption we present methods for both pairwise and joint causal analyses of ordinal treatments and binary outcomes in presence of truncation by death. We illustrate via examples the appropriateness of our assumptions in different scientific contexts.

Differential Expression of Zinc Transporters in Prostate Epithelia of Racial Groups

DTIC Science & Technology

2010-09-01

mitochondria inhibits terminal oxidation, truncating the Krebs cycle , hence decreasing the ATP-based energy production and resulting in less growth...as a major component of prostatic fluid [7,10]. In addition, high Zn levels in the mitochondria inhibits terminal oxidation, truncat- ing the Krebs ...PCR (MJR/Bio-Rod – Twin Tower, PTC 200, Waltham, MA). The two cycles were programmed for 30 min at 50 C, then 95 C for 5 min (for cDNA step), and

Modified truncated randomized singular value decomposition (MTRSVD) algorithms for large scale discrete ill-posed problems with general-form regularization

NASA Astrophysics Data System (ADS)

Jia, Zhongxiao; Yang, Yanfei

2018-05-01

In this paper, we propose new randomization based algorithms for large scale linear discrete ill-posed problems with general-form regularization: subject to , where L is a regularization matrix. Our algorithms are inspired by the modified truncated singular value decomposition (MTSVD) method, which suits only for small to medium scale problems, and randomized SVD (RSVD) algorithms that generate good low rank approximations to A. We use rank-k truncated randomized SVD (TRSVD) approximations to A by truncating the rank- RSVD approximations to A, where q is an oversampling parameter. The resulting algorithms are called modified TRSVD (MTRSVD) methods. At every step, we use the LSQR algorithm to solve the resulting inner least squares problem, which is proved to become better conditioned as k increases so that LSQR converges faster. We present sharp bounds for the approximation accuracy of the RSVDs and TRSVDs for severely, moderately and mildly ill-posed problems, and substantially improve a known basic bound for TRSVD approximations. We prove how to choose the stopping tolerance for LSQR in order to guarantee that the computed and exact best regularized solutions have the same accuracy. Numerical experiments illustrate that the best regularized solutions by MTRSVD are as accurate as the ones by the truncated generalized singular value decomposition (TGSVD) algorithm, and at least as accurate as those by some existing truncated randomized generalized singular value decomposition (TRGSVD) algorithms. This work was supported in part by the National Science Foundation of China (Nos. 11771249 and 11371219).

Piecewise-Constant-Model-Based Interior Tomography Applied to Dentin Tubules

DOE PAGES

He, Peng; Wei, Biao; Wang, Steve; ...

2013-01-01

Dentin is a hierarchically structured biomineralized composite material, and dentin’s tubules are difficult to study in situ. Nano-CT provides the requisite resolution, but the field of view typically contains only a few tubules. Using a plate-like specimen allows reconstruction of a volume containing specific tubules from a number of truncated projections typically collected over an angular range of about 140°, which is practically accessible. Classical computed tomography (CT) theory cannot exactly reconstruct an object only from truncated projections, needless to say a limited angular range. Recently, interior tomography was developed to reconstruct a region-of-interest (ROI) from truncated data in amore » theoretically exact fashion via the total variation (TV) minimization under the condition that the ROI is piecewise constant. In this paper, we employ a TV minimization interior tomography algorithm to reconstruct interior microstructures in dentin from truncated projections over a limited angular range. Compared to the filtered backprojection (FBP) reconstruction, our reconstruction method reduces noise and suppresses artifacts. Volume rendering confirms the merits of our method in terms of preserving the interior microstructure of the dentin specimen.« less

Quantum corrections of the truncated Wigner approximation applied to an exciton transport model.

PubMed

Ivanov, Anton; Breuer, Heinz-Peter

2017-04-01

We modify the path integral representation of exciton transport in open quantum systems such that an exact description of the quantum fluctuations around the classical evolution of the system is possible. As a consequence, the time evolution of the system observables is obtained by calculating the average of a stochastic difference equation which is weighted with a product of pseudoprobability density functions. From the exact equation of motion one can clearly identify the terms that are also present if we apply the truncated Wigner approximation. This description of the problem is used as a basis for the derivation of a new approximation, whose validity goes beyond the truncated Wigner approximation. To demonstrate this we apply the formalism to a donor-acceptor transport model.

Fabrication of large-area nano-scale patterned sapphire substrate with laser interference lithography

NASA Astrophysics Data System (ADS)

Xuan, Ming-dong; Dai, Long-gui; Jia, Hai-qiang; Chen, Hong

2014-01-01

Periodic triangle truncated pyramid arrays are successfully fabricated on the sapphire substrate by a low-cost and high-efficiency laser interference lithography (LIL) system. Through the combination of dry etching and wet etching techniques, the nano-scale patterned sapphire substrate (NPSS) with uniform size is prepared. The period of the patterns is 460 nm as designed to match the wavelength of blue light emitting diode (LED). By improving the stability of the LIL system and optimizing the process parameters, well-defined triangle truncated pyramid arrays can be achieved on the sapphire substrate with diameter of 50.8 mm. The deviation of the bottom width of the triangle truncated pyramid arrays is 6.8%, which is close to the industrial production level of 3%.

In silico and in vivo studies of truncated forms of flagellin (FliC) of enteroaggregative Escherichia coli fused to FimH from uropathogenic Escherichia coli as a vaccine candidate against urinary tract infections.

PubMed

Savar, Nastaran Sadat; Jahanian-Najafabadi, Ali; Mahdavi, Mehdi; Shokrgozar, Mohammad Ali; Jafari, Anis; Bouzari, Saeid

2014-04-10

The new generation of vaccines against infectious diseases is based on recombinant fusion proteins. Flagellin (FliC) of enteroaggregative Escherichia coli (EAEC) could be considered as a potent adjuvant in designing new vaccines. However, because of its large size, incorporation of this protein with a vaccine antigen might negatively influence recognition of the vaccine epitopes by the immune system. Designing the truncated forms of FliC, capable of inducing innate immune response, enhances the immune responses to the target antigen. We have previously shown that two truncated forms of FliC are able to induce Interleukine-8 production in HT-29 epithelial cell line. In this study we designed recombinant vaccine against urinary tract infections (UTIs) using truncated forms of FliC and type 1 fimbrial FimH adhesin from uropathogenic Escherichia coli (UPEC) and studied their in silico interactions with Toll-like receptor 5 (TLR-5) via docking protocols. The best fusion protein was subjected to cloning and expression. The ability of the recombinant vaccine and the truncated forms in inducing immune responses was investigated. Our results showed that truncated forms are capable of inducing Th1 (forms A and B) and Th2 (form A) responses and fusion vaccine induced strong cellular and humoral immune responses. Copyright © 2014 Elsevier B.V. All rights reserved.

De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome

PubMed Central

2013-01-01

Background Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel syndrome, likely caused by de novo truncating mutations in ASXL3, which shares characteristics with Bohring-Opitz syndrome, a disease associated with de novo truncating mutations in ASXL1. Methods We used whole-genome and whole-exome sequencing to interrogate the genomes of four subjects with an undiagnosed syndrome. Results Using genome-wide sequencing, we identified heterozygous, de novo truncating mutations in ASXL3, a transcriptional repressor related to ASXL1, in four unrelated probands. We found that these probands shared similar phenotypes, including severe feeding difficulties, failure to thrive, and neurologic abnormalities with significant developmental delay. Further, they showed less phenotypic overlap with patients who had de novo truncating mutations in ASXL1. Conclusion We have identified truncating mutations in ASXL3 as the likely cause of a novel syndrome with phenotypic overlap with Bohring-Opitz syndrome. PMID:23383720

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

A key, yet often neglected, component of digital evolution and evolutionary models is the ‘selection method’ which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations’ average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics. PMID:24152811

The expression of full length Gp91-phox protein is associated with reduced amphotropic retroviral production.

PubMed

Bellantuono, I; Lashford, L S; Rafferty, J A; Fairbairn, L J

2000-05-01

As a single gene defect in mature bone marrow cells, chronic granulomatous disease (X-CGD) represents a disorder which may be amenable to gene therapy by the transfer of the missing subunit into hemopoietic stem cells. In the majority of cases lack of Gp91-phox causes the disease. So far, studies involving transfer of Gp91-phox cDNA, including a phase I clinical trial, have yielded disappointing results. Most often, low titers of virus have been reported. In the present study we investigated the possible reasons for low titer amphotropic viral production. To investigate the effect of Gp91 cDNA on the efficiency of retroviral production from the packaging cell line, GP+envAm12, we constructed vectors containing either the native cDNA, truncated versions of the cDNA or a mutated form (LATG) in which the natural translational start codon was changed to a stop codon. Following derivation of clonal packaging cell lines, these were assessed for viral titer by RNA slot blot and analyzed by non-parametrical statistical analysis (Whitney-Mann U-test). An improvement in viral titer of just over two-fold was found in packaging cells containing the start-codon mutant of Gp91 and no evidence of truncated viral RNA was seen in these cells. Further analysis revealed the presence of rearranged forms of the provirus in Gp91-expressing cells, and the production of truncated, unpackaged viral RNA. Protein analysis revealed that LATG-transduced cells did not express full-length Gp91-phox, whereas those containing the wild-type cDNA did. However, a truncated protein was seen in ATG-transduced cells which was also present in wild type cells. No evidence for the presence of a negative transcriptional regulatory element was found from studies with the deletion mutants. A statistically significant effect of protein production on the production of virus from Gp91-expressing cells was found. Our data point to a need to restrict expression of the Gp91-phox protein and its derivatives in order to enhance retroviral production and suggest that improvements in current vectors for CGD gene therapy may need to include controlled, directed expression only in mature neutrophils.

Modifications of Geometric Truncation of the Scattering Phase Function

NASA Astrophysics Data System (ADS)

Radkevich, A.

2017-12-01

Phase function (PF) of light scattering on large atmospheric particles has very strong peak in forward direction constituting a challenge for accurate numerical calculations of radiance. Such accurate (and fast) evaluations are important in the problems of remote sensing of the atmosphere. Scaling transformation replaces original PF with a sum of the delta function and a new regular smooth PF. A number of methods to construct such a PF were suggested. Delta-M and delta-fit methods require evaluation of the PF moments which imposes a numerical problem if strongly anisotropic PF is given as a function of angle. Geometric truncation keeps the original PF unchanged outside the forward peak cone replacing it with a constant within the cone. This approach is designed to preserve the asymmetry parameter. It has two disadvantages: 1) PF has discontinuity at the cone; 2) the choice of the cone is subjective, no recommendations were provided on the choice of the truncation angle. This choice affects both truncation fraction and the value of the phase function within the forward cone. Both issues are addressed in this study. A simple functional form of the replacement PF is suggested. This functional form allows for a number of modifications. This study consider 3 versions providing continuous PF. The considered modifications also bear either of three properties: preserve asymmetry parameter, provide continuity of the 1st derivative of the PF, and preserve mean scattering angle. The second problem mentioned above is addressed with a heuristic approach providing unambiguous criterion of selection of the truncation angle. The approach showed good performance on liquid water and ice clouds with different particle size distributions. Suggested modifications were tested on different cloud PFs using both discrete ordinates and Monte Carlo methods. It was showed that the modifications provide better accuracy of the radiance computation compare to the original geometric truncation.

Matrix product algorithm for stochastic dynamics on networks applied to nonequilibrium Glauber dynamics

NASA Astrophysics Data System (ADS)

Barthel, Thomas; De Bacco, Caterina; Franz, Silvio

2018-01-01

We introduce and apply an efficient method for the precise simulation of stochastic dynamical processes on locally treelike graphs. Networks with cycles are treated in the framework of the cavity method. Such models correspond, for example, to spin-glass systems, Boolean networks, neural networks, or other technological, biological, and social networks. Building upon ideas from quantum many-body theory, our approach is based on a matrix product approximation of the so-called edge messages—conditional probabilities of vertex variable trajectories. Computation costs and accuracy can be tuned by controlling the matrix dimensions of the matrix product edge messages (MPEM) in truncations. In contrast to Monte Carlo simulations, the algorithm has a better error scaling and works for both single instances as well as the thermodynamic limit. We employ it to examine prototypical nonequilibrium Glauber dynamics in the kinetic Ising model. Because of the absence of cancellation effects, observables with small expectation values can be evaluated accurately, allowing for the study of decay processes and temporal correlations.

A Truncated Nuclear Norm Regularization Method Based on Weighted Residual Error for Matrix Completion.

PubMed

Qing Liu; Zhihui Lai; Zongwei Zhou; Fangjun Kuang; Zhong Jin

2016-01-01

Low-rank matrix completion aims to recover a matrix from a small subset of its entries and has received much attention in the field of computer vision. Most existing methods formulate the task as a low-rank matrix approximation problem. A truncated nuclear norm has recently been proposed as a better approximation to the rank of matrix than a nuclear norm. The corresponding optimization method, truncated nuclear norm regularization (TNNR), converges better than the nuclear norm minimization-based methods. However, it is not robust to the number of subtracted singular values and requires a large number of iterations to converge. In this paper, a TNNR method based on weighted residual error (TNNR-WRE) for matrix completion and its extension model (ETNNR-WRE) are proposed. TNNR-WRE assigns different weights to the rows of the residual error matrix in an augmented Lagrange function to accelerate the convergence of the TNNR method. The ETNNR-WRE is much more robust to the number of subtracted singular values than the TNNR-WRE, TNNR alternating direction method of multipliers, and TNNR accelerated proximal gradient with Line search methods. Experimental results using both synthetic and real visual data sets show that the proposed TNNR-WRE and ETNNR-WRE methods perform better than TNNR and Iteratively Reweighted Nuclear Norm (IRNN) methods.

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga

2013-11-01

Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

Measuring the Social Recreation Per-Day Net Benefit of the Wildlife Amenities of a National Park: A Count-Data Travel-Cost Approach

NASA Astrophysics Data System (ADS)

Mendes, Isabel; Proença, Isabel

2011-11-01

In this article, we apply count-data travel-cost methods to a truncated sample of visitors to estimate the Peneda-Gerês National Park (PGNP) average consumer surplus (CS) for each day of visit. The measurement of recreation demand is highly specific because it is calculated by number of days of stay per visit. We therefore propose the application of altered truncated count-data models or truncated count-data models on grouped data to estimate a single, on-site individual recreation demand function, with the price (cost) of each recreation day per trip equal to out-of-pocket and time travel plus out-of-pocket and on-site time costs. We further check the sensitivity of coefficient estimations to alternative models and analyse the welfare measure precision by using the delta and simulation methods by Creel and Loomis. With simulated limits, CS is estimated to be €194 (range €116 to €448). This information is of use in the quest to improve government policy and PNPG management and conservation as well as promote nature-based tourism. To our knowledge, this is the first attempt to measure the average recreation net benefits of each day of stay generated by a national park by using truncated altered and truncated grouped count-data travel-cost models based on observing the individual number of days of stay.

Measuring the social recreation per-day net benefit of the wildlife amenities of a national park: a count-data travel-cost approach.

PubMed

Mendes, Isabel; Proença, Isabel

2011-11-01

In this article, we apply count-data travel-cost methods to a truncated sample of visitors to estimate the Peneda-Gerês National Park (PGNP) average consumer surplus (CS) for each day of visit. The measurement of recreation demand is highly specific because it is calculated by number of days of stay per visit. We therefore propose the application of altered truncated count-data models or truncated count-data models on grouped data to estimate a single, on-site individual recreation demand function, with the price (cost) of each recreation day per trip equal to out-of-pocket and time travel plus out-of-pocket and on-site time costs. We further check the sensitivity of coefficient estimations to alternative models and analyse the welfare measure precision by using the delta and simulation methods by Creel and Loomis. With simulated limits, CS is estimated to be 194 (range 116 to 448). This information is of use in the quest to improve government policy and PNPG management and conservation as well as promote nature-based tourism. To our knowledge, this is the first attempt to measure the average recreation net benefits of each day of stay generated by a national park by using truncated altered and truncated grouped count-data travel-cost models based on observing the individual number of days of stay.

Preserving Symmetry in Preconditioned Krylov Subspace Methods

NASA Technical Reports Server (NTRS)

Chan, Tony F.; Chow, E.; Saad, Y.; Yeung, M. C.

1996-01-01

We consider the problem of solving a linear system Ax = b when A is nearly symmetric and when the system is preconditioned by a symmetric positive definite matrix M. In the symmetric case, one can recover symmetry by using M-inner products in the conjugate gradient (CG) algorithm. This idea can also be used in the nonsymmetric case, and near symmetry can be preserved similarly. Like CG, the new algorithms are mathematically equivalent to split preconditioning, but do not require M to be factored. Better robustness in a specific sense can also be observed. When combined with truncated versions of iterative methods, tests show that this is more effective than the common practice of forfeiting near-symmetry altogether.

Analytical and experimental studies of natural vibrations modes of ring-stiffened truncated-cone shells with variable theoretical ring fixity

NASA Technical Reports Server (NTRS)

Naumann, E. C.; Catherines, D. S.; Walton, W. C., Jr.

1971-01-01

Experimental and analytical investigations of the vibratory behavior of ring-stiffened truncated-cone shells are described. Vibration tests were conducted on 60 deg conical shells having up to four ring stiffeners and for free-free and clamped-free edge constraints and 9 deg conical shells, for two thicknesses, each with two angle rings and for free-free, free-clamped, and clamped-clamped edge constraints. The analytical method is based on linear thin shell theory, employing the Rayleigh-Ritz method. Discrete rings are represented as composed of one or more segments, each of which is a short truncated-cone shell of uniform thickness. Equations of constraint are used to join a ring and shell along a circumferential line connection. Excellent agreement was obtained for comparisons of experimental and calculated frequencies.

Digestion proteomics: tracking lactoferrin truncation and peptide release during simulated gastric digestion.

PubMed

Grosvenor, Anita J; Haigh, Brendan J; Dyer, Jolon M

2014-11-01

The extent to which nutritional and functional benefit is derived from proteins in food is related to its breakdown and digestion in the body after consumption. Further, detailed information about food protein truncation during digestion is critical to understanding and optimising the availability of bioactives, in controlling and limiting allergen release, and in minimising or monitoring the effects of processing and food preparation. However, tracking the complex array of products formed during the digestion of proteins is not easily accomplished using classical proteomics. We here present and develop a novel proteomic approach using isobaric labelling to mapping and tracking protein truncation and peptide release during simulated gastric digestion, using bovine lactoferrin as a model food protein. The relative abundance of related peptides was tracked throughout a digestion time course, and the effect of pasteurisation on peptide release assessed. The new approach to food digestion proteomics developed here therefore appears to be highly suitable not only for tracking the truncation and relative abundance of released peptides during gastric digestion, but also for determining the effects of protein modification on digestibility and potential bioavailability.

Isobaric Quantification of Cerebrospinal Fluid Amyloid-β Peptides in Alzheimer's Disease: C-Terminal Truncation Relates to Early Measures of Neurodegeneration.

PubMed

Rogeberg, Magnus; Almdahl, Ina Selseth; Wettergreen, Marianne; Nilsson, Lars N G; Fladby, Tormod

2015-11-06

The amyloid beta (Aβ) peptide is the main constituent of the plaques characteristic of Alzheimer's disease (AD). Measurement of Aβ1-42 in cerebrospinal fluid (CSF) is a valuable marker in AD research, where low levels indicate AD. Although the use of immunoassays measuring Aβ1-38 and Aβ1-40 in addition to Aβ1-42 has increased, quantitative assays of other Aβ peptides remain rarely explored. We recently discovered novel Aβ peptides in CSF using antibodies recognizing the Aβ mid-domain region. Here we have developed a method using both Aβ N-terminal and mid-domain antibodies for immunoprecipitation in combination with isobaric labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for relative quantification of endogenous Aβ peptides in CSF. The developed method was used in a pilot study to produce Aβ peptide profiles from 38 CSF samples. Statistical comparison between CSF samples from 19 AD patients and 19 cognitively healthy controls revealed no significant differences at group level. A significant correlation was found between several larger C-terminally truncated Aβ peptides and protein biomarkers for neuronal damage, particularly prominent in the control group. Comparison of the isobaric quantification with immunoassays measuring Aβ1-38 or Aβ1-40 showed good correlation (r(2) = 0.84 and 0.85, respectively) between the two analysis methods. The developed method could be used to assess disease-modifying therapies directed at Aβ production or degradation.

The finite scaling for S = 1 XXZ chains with uniaxial single-ion-type anisotropy

NASA Astrophysics Data System (ADS)

Wang, Honglei; Xiong, Xingliang

2014-03-01

The scaling behavior of criticality for spin-1 XXZ chains with uniaxial single-ion-type anisotropy is investigated by employing the infinite matrix product state representation with the infinite time evolving block decimation method. At criticality, the accuracy of the ground state of a system is limited by the truncation dimension χ of the local Hilbert space. We present four evidences for the scaling of the entanglement entropy, the largest eigenvalue of the Schmidt decomposition, the correlation length, and the connection between the actual correlation length ξ and the energy. The result shows that the finite scalings are governed by the central charge of the critical system. Also, it demonstrates that the infinite time evolving block decimation algorithm by the infinite matrix product state representation can be a quite accurate method to simulate the critical properties at criticality.

Exact Fan-Beam Reconstruction With Arbitrary Object Translations and Truncated Projections

NASA Astrophysics Data System (ADS)

Hoskovec, Jan; Clackdoyle, Rolf; Desbat, Laurent; Rit, Simon

2016-06-01

This article proposes a new method for reconstructing two-dimensional (2D) computed tomography (CT) images from truncated and motion contaminated sinograms. The type of motion considered here is a sequence of rigid translations which are assumed to be known. The algorithm first identifies the sufficiency of angular coverage in each 2D point of the CT image to calculate the Hilbert transform from the local “virtual” trajectory which accounts for the motion and the truncation. By taking advantage of data redundancy in the full circular scan, our method expands the reconstructible region beyond the one obtained with chord-based methods. The proposed direct reconstruction algorithm is based on the Differentiated Back-Projection with Hilbert filtering (DBP-H). The motion is taken into account during backprojection which is the first step of our direct reconstruction, before taking the derivatives and inverting the finite Hilbert transform. The algorithm has been tested in a proof-of-concept study on Shepp-Logan phantom simulations with several motion cases and detector sizes.

Vibration suppression for large scale adaptive truss structures using direct output feedback control

NASA Technical Reports Server (NTRS)

Lu, Lyan-Ywan; Utku, Senol; Wada, Ben K.

1993-01-01

In this article, the vibration control of adaptive truss structures, where the control actuation is provided by length adjustable active members, is formulated as a direct output feedback control problem. A control method named Model Truncated Output Feedback (MTOF) is presented. The method allows the control feedback gain to be determined in a decoupled and truncated modal space in which only the critical vibration modes are retained. The on-board computation required by MTOF is minimal; thus, the method is favorable for the applications of vibration control of large scale structures. The truncation of the modal space inevitably introduces spillover effect during the control process. In this article, the effect is quantified in terms of active member locations, and it is shown that the optimal placement of active members, which minimizes the spillover effect (and thus, maximizes the control performance) can be sought. The problem of optimally selecting the locations of active members is also treated.

A novel hybrid scattering order-dependent variance reduction method for Monte Carlo simulations of radiative transfer in cloudy atmosphere

NASA Astrophysics Data System (ADS)

Wang, Zhen; Cui, Shengcheng; Yang, Jun; Gao, Haiyang; Liu, Chao; Zhang, Zhibo

2017-03-01

We present a novel hybrid scattering order-dependent variance reduction method to accelerate the convergence rate in both forward and backward Monte Carlo radiative transfer simulations involving highly forward-peaked scattering phase function. This method is built upon a newly developed theoretical framework that not only unifies both forward and backward radiative transfer in scattering-order-dependent integral equation, but also generalizes the variance reduction formalism in a wide range of simulation scenarios. In previous studies, variance reduction is achieved either by using the scattering phase function forward truncation technique or the target directional importance sampling technique. Our method combines both of them. A novel feature of our method is that all the tuning parameters used for phase function truncation and importance sampling techniques at each order of scattering are automatically optimized by the scattering order-dependent numerical evaluation experiments. To make such experiments feasible, we present a new scattering order sampling algorithm by remodeling integral radiative transfer kernel for the phase function truncation method. The presented method has been implemented in our Multiple-Scaling-based Cloudy Atmospheric Radiative Transfer (MSCART) model for validation and evaluation. The main advantage of the method is that it greatly improves the trade-off between numerical efficiency and accuracy order by order.

Selective object encryption for privacy protection

NASA Astrophysics Data System (ADS)

Zhou, Yicong; Panetta, Karen; Cherukuri, Ravindranath; Agaian, Sos

2009-05-01

This paper introduces a new recursive sequence called the truncated P-Fibonacci sequence, its corresponding binary code called the truncated Fibonacci p-code and a new bit-plane decomposition method using the truncated Fibonacci pcode. In addition, a new lossless image encryption algorithm is presented that can encrypt a selected object using this new decomposition method for privacy protection. The user has the flexibility (1) to define the object to be protected as an object in an image or in a specific part of the image, a selected region of an image, or an entire image, (2) to utilize any new or existing method for edge detection or segmentation to extract the selected object from an image or a specific part/region of the image, (3) to select any new or existing method for the shuffling process. The algorithm can be used in many different areas such as wireless networking, mobile phone services and applications in homeland security and medical imaging. Simulation results and analysis verify that the algorithm shows good performance in object/image encryption and can withstand plaintext attacks.

Sonar Imaging of Elastic Fluid-Filled Cylindrical Shells.

NASA Astrophysics Data System (ADS)

Dodd, Stirling Scott

1995-01-01

Previously a method of describing spherical acoustic waves in cylindrical coordinates was applied to the problem of point source scattering by an elastic infinite fluid -filled cylindrical shell (S. Dodd and C. Loeffler, J. Acoust. Soc. Am. 97, 3284(A) (1995)). This method is applied to numerically model monostatic oblique incidence scattering from a truncated cylinder by a narrow-beam high-frequency imaging sonar. The narrow beam solution results from integrating the point source solution over the spatial extent of a line source and line receiver. The cylinder truncation is treated by the method of images, and assumes that the reflection coefficient at the truncation is unity. The scattering form functions, calculated using this method, are applied as filters to a narrow bandwidth, high ka pulse to find the time domain scattering response. The time domain pulses are further processed and displayed in the form of a sonar image. These images compare favorably to experimentally obtained images (G. Kaduchak and C. Loeffler, J. Acoust. Soc. Am. 97, 3289(A) (1995)). The impact of the s_{ rm o} and a_{rm o} Lamb waves is vividly apparent in the images.

Interior tomography in microscopic CT with image reconstruction constrained by full field of view scan at low spatial resolution

NASA Astrophysics Data System (ADS)

Luo, Shouhua; Shen, Tao; Sun, Yi; Li, Jing; Li, Guang; Tang, Xiangyang

2018-04-01

In high resolution (microscopic) CT applications, the scan field of view should cover the entire specimen or sample to allow complete data acquisition and image reconstruction. However, truncation may occur in projection data and results in artifacts in reconstructed images. In this study, we propose a low resolution image constrained reconstruction algorithm (LRICR) for interior tomography in microscopic CT at high resolution. In general, the multi-resolution acquisition based methods can be employed to solve the data truncation problem if the project data acquired at low resolution are utilized to fill up the truncated projection data acquired at high resolution. However, most existing methods place quite strict restrictions on the data acquisition geometry, which greatly limits their utility in practice. In the proposed LRICR algorithm, full and partial data acquisition (scan) at low and high resolutions, respectively, are carried out. Using the image reconstructed from sparse projection data acquired at low resolution as the prior, a microscopic image at high resolution is reconstructed from the truncated projection data acquired at high resolution. Two synthesized digital phantoms, a raw bamboo culm and a specimen of mouse femur, were utilized to evaluate and verify performance of the proposed LRICR algorithm. Compared with the conventional TV minimization based algorithm and the multi-resolution scout-reconstruction algorithm, the proposed LRICR algorithm shows significant improvement in reduction of the artifacts caused by data truncation, providing a practical solution for high quality and reliable interior tomography in microscopic CT applications. The proposed LRICR algorithm outperforms the multi-resolution scout-reconstruction method and the TV minimization based reconstruction for interior tomography in microscopic CT.

Pulmonary MRA: Differentiation of pulmonary embolism from truncation artifact

PubMed Central

Bannas, Peter; Schiebler, Mark L; Motosugi, Utaroh; François, Christopher J; Reeder, Scott B; Nagle, Scott K

2015-01-01

Purpose Truncation artifact (Gibbs ringing) causes central signal drop within vessels in pulmonary MRA that can be mistaken for emboli, reducing the diagnostic accuracy for pulmonary embolism (PE). We propose a quantitative approach to differentiate truncation artifact from PE. Methods Twenty-eight patients who underwent pulmonary CTA for suspected PE were recruited for pulmonary MRA. Signal intensity drops within pulmonary arteries that persisted on both arterial-phase and delayed-phase MRA were identified. The percent signal loss between the vessel lumen and central drop was measured. CTA served as the reference standard for presence of pulmonary emboli. Results A total of 65 signal intensity drops were identified on MRA. 48 (74%) of these were artifact and 17 (26%) were PE, as confirmed by CTA. Truncation artifacts had a significantly lower median signal drop than PE at both arterial-phase (26% [range 12–58%] vs. 85% [range 53–91%]) and at delayed-phase MRA (26% [range 11–55%] vs. 77% [range 47–89%]), p<0.0001 for both. ROC analyses revealed a threshold value of 51% (arterial-phase) and 47%-signal drop (delayed-phase) to differentiate between truncation artifact and PE with 100% sensitivity and >90% specificity. Conclusion Quantitative signal drop is an objective tool to help differentiate truncation artifact and pulmonary embolism in pulmonary MRA. PMID:24863886

Propagation of coherently combined truncated laser beam arrays with beam distortions in non-Kolmogorov turbulence.

PubMed

Tao, Rumao; Si, Lei; Ma, Yanxing; Zhou, Pu; Liu, Zejin

2012-08-10

The propagation properties of coherently combined truncated laser beam arrays with beam distortions through non-Kolmogorov turbulence are studied in detail both analytically and numerically. The analytical expressions for the average intensity and the beam width of coherently combined truncated laser beam arrays with beam distortions propagating through turbulence are derived based on the combination of statistical optics methods and the extended Huygens-Fresnel principle. The effect of beam distortions, such as amplitude modulation and phase fluctuation, is studied by numerical examples. The numerical results reveal that phase fluctuations have significant influence on the spreading of coherently combined truncated laser beam arrays in non-Kolmogorov turbulence, and the effects of the phase fluctuations can be negligible as long as the phase fluctuations are controlled under a certain level, i.e., a>0.05 for the situation considered in the paper. Furthermore, large phase fluctuations can convert the beam distribution rapidly to a Gaussian form, vary the spreading, weaken the optimum truncation effects, and suppress the dependence of spreading on the parameters of the non-Kolmogorov turbulence.

10 CFR Appendix C to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of Dishwashers

Code of Federal Regulations, 2011 CFR

2011-01-01

... electrically heated, gas-heated, or oil-heated water. The water consumption for the sensor normal cycle, V, is.... 1.16Truncated sensor heavy response means the sensor heavy response interrupted to eliminate the power-dry feature after the termination of the last rinse operation. 1.17Truncated sensor light response...

10 CFR Appendix C to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of Dishwashers

Code of Federal Regulations, 2010 CFR

2010-01-01

... electrically heated, gas-heated, or oil-heated water. The water consumption for the sensor normal cycle, V, is.... 1.16Truncated sensor heavy response means the sensor heavy response interrupted to eliminate the power-dry feature after the termination of the last rinse operation. 1.17Truncated sensor light response...

Volterra series truncation and kernel estimation of nonlinear systems in the frequency domain

NASA Astrophysics Data System (ADS)

Zhang, B.; Billings, S. A.

2017-02-01

The Volterra series model is a direct generalisation of the linear convolution integral and is capable of displaying the intrinsic features of a nonlinear system in a simple and easy to apply way. Nonlinear system analysis using Volterra series is normally based on the analysis of its frequency-domain kernels and a truncated description. But the estimation of Volterra kernels and the truncation of Volterra series are coupled with each other. In this paper, a novel complex-valued orthogonal least squares algorithm is developed. The new algorithm provides a powerful tool to determine which terms should be included in the Volterra series expansion and to estimate the kernels and thus solves the two problems all together. The estimated results are compared with those determined using the analytical expressions of the kernels to validate the method. To further evaluate the effectiveness of the method, the physical parameters of the system are also extracted from the measured kernels. Simulation studies demonstrates that the new approach not only can truncate the Volterra series expansion and estimate the kernels of a weakly nonlinear system, but also can indicate the applicability of the Volterra series analysis in a severely nonlinear system case.

An Improved Extrapolation Scheme for Truncated CT Data Using 2D Fourier-Based Helgason-Ludwig Consistency Conditions.

PubMed

Xia, Yan; Berger, Martin; Bauer, Sebastian; Hu, Shiyang; Aichert, Andre; Maier, Andreas

2017-01-01

We improve data extrapolation for truncated computed tomography (CT) projections by using Helgason-Ludwig (HL) consistency conditions that mathematically describe the overlap of information between projections. First, we theoretically derive a 2D Fourier representation of the HL consistency conditions from their original formulation (projection moment theorem), for both parallel-beam and fan-beam imaging geometry. The derivation result indicates that there is a zero energy region forming a double-wedge shape in 2D Fourier domain. This observation is also referred to as the Fourier property of a sinogram in the previous literature. The major benefit of this representation is that the consistency conditions can be efficiently evaluated via 2D fast Fourier transform (FFT). Then, we suggest a method that extrapolates the truncated projections with data from a uniform ellipse of which the parameters are determined by optimizing these consistency conditions. The forward projection of the optimized ellipse can be used to complete the truncation data. The proposed algorithm is evaluated using simulated data and reprojections of clinical data. Results show that the root mean square error (RMSE) is reduced substantially, compared to a state-of-the-art extrapolation method.

An Improved Extrapolation Scheme for Truncated CT Data Using 2D Fourier-Based Helgason-Ludwig Consistency Conditions

PubMed Central

Berger, Martin; Bauer, Sebastian; Hu, Shiyang; Aichert, Andre

2017-01-01

We improve data extrapolation for truncated computed tomography (CT) projections by using Helgason-Ludwig (HL) consistency conditions that mathematically describe the overlap of information between projections. First, we theoretically derive a 2D Fourier representation of the HL consistency conditions from their original formulation (projection moment theorem), for both parallel-beam and fan-beam imaging geometry. The derivation result indicates that there is a zero energy region forming a double-wedge shape in 2D Fourier domain. This observation is also referred to as the Fourier property of a sinogram in the previous literature. The major benefit of this representation is that the consistency conditions can be efficiently evaluated via 2D fast Fourier transform (FFT). Then, we suggest a method that extrapolates the truncated projections with data from a uniform ellipse of which the parameters are determined by optimizing these consistency conditions. The forward projection of the optimized ellipse can be used to complete the truncation data. The proposed algorithm is evaluated using simulated data and reprojections of clinical data. Results show that the root mean square error (RMSE) is reduced substantially, compared to a state-of-the-art extrapolation method. PMID:28808441

Phase gradient imaging for positive contrast generation to superparamagnetic iron oxide nanoparticle-labeled targets in magnetic resonance imaging.

PubMed

Zhu, Haitao; Demachi, Kazuyuki; Sekino, Masaki

2011-09-01

Positive contrast imaging methods produce enhanced signal at large magnetic field gradient in magnetic resonance imaging. Several postprocessing algorithms, such as susceptibility gradient mapping and phase gradient mapping methods, have been applied for positive contrast generation to detect the cells targeted by superparamagnetic iron oxide nanoparticles. In the phase gradient mapping methods, smoothness condition has to be satisfied to keep the phase gradient unwrapped. Moreover, there has been no discussion about the truncation artifact associated with the algorithm of differentiation that is performed in k-space by the multiplication with frequency value. In this work, phase gradient methods are discussed by considering the wrapping problem when the smoothness condition is not satisfied. A region-growing unwrapping algorithm is used in the phase gradient image to solve the problem. In order to reduce the truncation artifact, a cosine function is multiplied in the k-space to eliminate the abrupt change at the boundaries. Simulation, phantom and in vivo experimental results demonstrate that the modified phase gradient mapping methods may produce improved positive contrast effects by reducing truncation or wrapping artifacts. Copyright © 2011 Elsevier Inc. All rights reserved.

Growth, Uplift and Truncation of Indo-Burman Anticlines Paced By Glacial-Interglacial Sea Level Change

NASA Astrophysics Data System (ADS)

Gale, J.; Steckler, M. S.; Sousa, D.; Seeber, L.; Goodbred, S. L., Jr.; Ferguson, E. K.

2014-12-01

The Ganges-Brahmaputra Delta abuts the Indo-Burman Arc on the east. Subduction of the thick delta strata has generated a large subaerial accretionary prism, up to 250 km wide, with multiple ranges of anticlines composed of the folded and faulted delta sediments. As the wedge has grown, the exposed anticlines have become subject to erosion by the rivers draining the Himalaya, a local Indo-Burman drainage network, and coastal processes. Multiple lines of geophysical, geologic, and geomorphologic evidence indicate anticline truncation as a result of interaction with the rivers of the delta and sea level. Seismic lines, geologic mapping, and geomorphology reveal truncated anticlines with angular unconformities that have been arched due to continued growth of the anticline. Buried, truncated anticlines have been identified by seismic lines, tube well logs, and resistivity measurements. The truncation of these anticlines also appears to provide a pathway for high-As Holocene groundwater into the generally low-As Pleistocene groundwater. Overall, the distribution of anticline erosion and elevation in the fold belt appears to be consistent with glacial-interglacial changes in river behavior in the delta. The anticline crests are eroded during sea level highstands as rivers and the coastline sweep across the region, and excavated by local drainage during lowstands. With continued growth, the anticlines are uplifted above the delta and "survive" as topographic features. As a result, the maximum elevations of the anticlines are clustered in a pattern suggesting continued growth since their last glacial highstand truncation. An uplift rate is calculated from this paced truncation and growth that is consistent with other measurements of Indo-Burman wedge advance. This rate, combined with the proposed method of truncation, give further evidence of dynamic fluvial changes in the delta between glacial and interglacial times.

Optical asymmetric cryptography based on elliptical polarized light linear truncation and a numerical reconstruction technique.

PubMed

Lin, Chao; Shen, Xueju; Wang, Zhisong; Zhao, Cheng

2014-06-20

We demonstrate a novel optical asymmetric cryptosystem based on the principle of elliptical polarized light linear truncation and a numerical reconstruction technique. The device of an array of linear polarizers is introduced to achieve linear truncation on the spatially resolved elliptical polarization distribution during image encryption. This encoding process can be characterized as confusion-based optical cryptography that involves no Fourier lens and diffusion operation. Based on the Jones matrix formalism, the intensity transmittance for this truncation is deduced to perform elliptical polarized light reconstruction based on two intensity measurements. Use of a quick response code makes the proposed cryptosystem practical, with versatile key sensitivity and fault tolerance. Both simulation and preliminary experimental results that support theoretical analysis are presented. An analysis of the resistance of the proposed method on a known public key attack is also provided.

Adaptive bit plane quadtree-based block truncation coding for image compression

NASA Astrophysics Data System (ADS)

Li, Shenda; Wang, Jin; Zhu, Qing

2018-04-01

Block truncation coding (BTC) is a fast image compression technique applied in spatial domain. Traditional BTC and its variants mainly focus on reducing computational complexity for low bit rate compression, at the cost of lower quality of decoded images, especially for images with rich texture. To solve this problem, in this paper, a quadtree-based block truncation coding algorithm combined with adaptive bit plane transmission is proposed. First, the direction of edge in each block is detected using Sobel operator. For the block with minimal size, adaptive bit plane is utilized to optimize the BTC, which depends on its MSE loss encoded by absolute moment block truncation coding (AMBTC). Extensive experimental results show that our method gains 0.85 dB PSNR on average compare to some other state-of-the-art BTC variants. So it is desirable for real time image compression applications.

Analytical and experimental study of axisymmetric truncated plug nozzle flow fields

NASA Technical Reports Server (NTRS)

Muller, T. J.; Sule, W. P.; Fanning, A. E.; Giel, T. V.; Galanga, F. L.

1972-01-01

Experimental and analytical investigation of the flow field and base pressure of internal-external-expansion truncated plug nozzles are discussed. Experimental results for two axisymmetric, conical plug-cylindrical shroud, truncated plug nozzles are presented for both open and closed wake operations. These results include extensive optical and pressure data covering nozzle flow field and base pressure characteristics, diffuser effects, lip shock strength, Mach disc behaviour, and the recompression and reverse flow regions. Transonic experiments for a special planar transonic section are presented. An extension of the analytical method of Hall and Mueller to include the internal shock wave from the shroud exit is presented for closed wake operation. Results of this analysis include effects on the flow field and base pressure of ambient pressure ratio, nozzle geometry, and the ratio of specific heats. Static thrust is presented as a function of ambient pressure ratio and nozzle geometry. A new transonic solution method is also presented.

Nonlocal symmetry and explicit solutions from the CRE method of the Boussinesq equation

NASA Astrophysics Data System (ADS)

Zhao, Zhonglong; Han, Bo

2018-04-01

In this paper, we analyze the integrability of the Boussinesq equation by using the truncated Painlevé expansion and the CRE method. Based on the truncated Painlevé expansion, the nonlocal symmetry and Bäcklund transformation of this equation are obtained. A prolonged system is introduced to localize the nonlocal symmetry to the local Lie point symmetry. It is proved that the Boussinesq equation is CRE solvable. The two-solitary-wave fusion solutions, single soliton solutions and soliton-cnoidal wave solutions are presented by means of the Bäcklund transformations.

Two Dimensional Finite Element Based Magnetotelluric Inversion using Singular Value Decomposition Method on Transverse Electric Mode

NASA Astrophysics Data System (ADS)

Tjong, Tiffany; Yihaa’ Roodhiyah, Lisa; Nurhasan; Sutarno, Doddy

2018-04-01

In this work, an inversion scheme was performed using a vector finite element (VFE) based 2-D magnetotelluric (MT) forward modelling. We use an inversion scheme with Singular value decomposition (SVD) method toimprove the accuracy of MT inversion.The inversion scheme was applied to transverse electric (TE) mode of MT. SVD method was used in this inversion to decompose the Jacobian matrices. Singular values which obtained from the decomposition process were analyzed. This enabled us to determine the importance of data and therefore to define a threshold for truncation process. The truncation of singular value in inversion processcould improve the resulted model.

In Glaucoma the Upregulated Truncated TrkC.T1 Receptor Isoform in Glia Causes Increased TNF-α Production, Leading to Retinal Ganglion Cell Death

PubMed Central

Bai, Yujing; Shi, ZhiHua; Zhuo, Yehong; Liu, Jing; Malakhov, Andrey; Ko, Eunhwa; Burgess, Kevin; Schaefer, Henry; Esteban, Pedro F.; Tessarollo, Lino; Saragovi, H. Uri

2010-01-01

Purpose. Glaucoma is a distinct neuropathy characterized by the chronic and progressive death of retinal ganglion cells (RGCs). The etiology of RGC death remains unknown. Risk factors for glaucomatous RGC death are elevated intraocular pressure and glial production of tumor necrosis factor-alpha (TNF-α). Previously, the authors showed that glaucoma causes a rapid upregulation of a neurotrophin receptor truncated isoform lacking the kinase domain, TrkC.T1, in retina. Here they examined the biological role of TrkC.T1 during glaucoma progression. Methods. Rat and mouse models of chronic ocular hypertension were used. Immunofluorescence Western blot analysis and in situ mRNA hybridization were used to identify cells upregulating TrkC.T1. A genetic model of engineered mice lacking TrkC.T1 (TrkC.T1−/−) was used to validate a role for this receptor in glaucoma. Pharmacologic studies were conducted to evaluate intravitreal delivery of agonists or antagonists of TrkC.T1, compared with controls, during glaucoma. Surviving RGCs were quantified by retrograde-labeling techniques. Production of neurotoxic TNF-α and α2 macroglobulin were quantified. Results. TrkC.T1 was upregulated in retinal glia, with a pattern similar to that of TNF-α. TrkC.T1−/− mice had normal retinas. However, during experimental glaucoma, TrkC.T1−/− mice had lower rates of RGC death and produced less TNF-α than wild-type littermates. In rats with glaucoma, the pharmacologic use of TrkC antagonists delayed RGC death and reduced the production of retinal TNF-α. Conclusions. TrkC.T1 is implicated in glaucomatous RGC death through the control of glial TNF-α production. Overall, the data point to a paracrine mechanism whereby elevated intraocular pressure upregulated glial TrkC.T1 expression in glia; TrkC.T1 controlled glial TNF-α production, and TNF-α caused RGC death. PMID:20574020

Production of Truncated Candida antarctica Lipase B Gene Using Automated PCR Gene Assembly Protocol and Expression in Yeast for use in Ethanol and Biodiesel Production.

USDA-ARS?s Scientific Manuscript database

An improved column-based process for production of biodiesel was developed using a column containing a strongly basic anion-exchange resin in sequence with a column containing a resin to which a lipase biocatalyst is bound. Currently most biodiesel is produced by transesterification of triglyceride...

MO-DE-207A-06: ECG-Gated CT Reconstruction for a C-Arm Inverse Geometry X-Ray System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slagowski, JM; Dunkerley, DAP

2016-06-15

Purpose: To obtain ECG-gated CT images from truncated projection data acquired with a C-arm based inverse geometry fluoroscopy system, for the purpose of cardiac chamber mapping in interventional procedures. Methods: Scanning-beam digital x-ray (SBDX) is an inverse geometry fluoroscopy system with a scanned multisource x-ray tube and a photon-counting detector mounted to a C-arm. In the proposed method, SBDX short-scan rotational acquisition is performed followed by inverse geometry CT (IGCT) reconstruction and segmentation of contrast-enhanced objects. The prior image constrained compressed sensing (PICCS) framework was adapted for IGCT reconstruction to mitigate artifacts arising from data truncation and angular undersampling duemore » to cardiac gating. The performance of the reconstruction algorithm was evaluated in numerical simulations of truncated and non-truncated thorax phantoms containing a dynamic ellipsoid to represent a moving cardiac chamber. The eccentricity of the ellipsoid was varied at frequencies from 1–1.5 Hz. Projection data were retrospectively sorted into 13 cardiac phases. Each phase was reconstructed using IGCT-PICCS, with a nongated gridded FBP (gFBP) prior image. Surface accuracy was determined using Dice similarity coefficient and a histogram of the point distances between the segmented surface and ground truth surface. Results: The gated IGCT-PICCS algorithm improved surface accuracy and reduced streaking and truncation artifacts when compared to nongated gFBP. For the non-truncated thorax with 1.25 Hz motion, 99% of segmented surface points were within 0.3 mm of the 15 mm diameter ground truth ellipse, versus 1.0 mm for gFBP. For the truncated thorax phantom with a 40 mm diameter ellipse, IGCT-PICCS surface accuracy measured 0.3 mm versus 7.8 mm for gFBP. Dice similarity coefficient was 0.99–1.00 (IGCT-PICCS) versus 0.63–0.75 (gFBP) for intensity-based segmentation thresholds ranging from 25–75% maximum contrast. Conclusions: The PICCS algorithm was successfully applied to reconstruct truncated IGCT projection data with angular undersampling resulting from simulated cardiac gating. Research supported by the National Heart, Lung, and Blood Institute of the NIH under award number R01HL084022. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.« less

Truncation effects in computing free wobble/nutation modes explored using a simple Earth model

NASA Astrophysics Data System (ADS)

Seyed-Mahmoud, Behnam; Rochester, Michael G.; Rogers, Christopher M.

2017-06-01

The displacement field accompanying the wobble/nutation of the Earth is conventionally represented by an infinite chain of toroidal and spheroidal vector spherical harmonics, coupled by rotation and ellipticity. Numerical solutions for the eigenperiods require truncation of that chain, and the standard approaches using the linear momentum description (LMD) of deformation during wobble/nutation have truncated it at very low degrees, usually degree 3 or 4, and at most degree 5. The effects of such heavy truncation on the computed eigenperiods have hardly been examined. We here investigate the truncation effects on the periods of the free wobble/nutation modes using a simplified Earth model consisting of a homogeneous incompressible inviscid liquid outer core with a rigid (but not fixed) inner core and mantle. A novel Galerkin method is implemented using a Clairaut coordinate system to solve the classic Poincaré problem in the liquid core and, to close the problem, we use the Lagrangean formulation of the Liouville equation for each of the solid parts of the Earth model. We find that, except for the free inner core nutation (FICN), the periods of the free rotational modes converge rather quickly. The period of the tiltover mode is found to excellent accuracy. The computed periods of the Chandler wobble and free core nutation are nearly identical to the values cited in the literature for similar Earth models, but that for the inner core wobble is slightly different. Truncation at low-degree harmonics causes the FICN period to fluctuate over a range as large as 90 sd, with different values at different truncation levels. For example, truncation at degree 6 gives a period of 752 sd (almost identical with the value cited in the literature for such an Earth model) but truncation at degree 24 is required to obtain convergence, and the resulting period is 746 ± 1 sd, as more terms are included, with no guarantee that its proximity to earlier values is other than fortuitous. We conclude that the heavy truncation necessitated by the conventional LMD is unsatisfactory for the FICN.

Truncation Effects in Computing Free Wobble/Nutation Modes Explored Using a Simple Earth Model

NASA Astrophysics Data System (ADS)

Seyed-Mahmoud, B.; Rochester, M. G.; Rogers, C. M.

2016-12-01

The displacement field accompanying the wobble/nutation of the Earth is conventionally represented by an infinite chain of toroidal and spheroidal vector spherical harmonics, coupled by rotation and ellipticity. Numerical solutions for the eigenperiods require truncation of that chain, and the standard approaches using the linear momentum description (LMD) of deformation during wobble/nutation have truncated it at very low degrees, usually degree 3 or 4, and at most degree 5. The effects of such heavy truncation on the computed eigenperiods have hardly been examined. We here investigate the truncation effects on the periods of the free wobble/nutation modes using a simplified Earth model consisting of a homogeneous incompressible inviscid liquid outer core with a rigid (but not fixed) inner core and mantle. A novel Galerkin method is implemented using a Clairaut coordinate system to solve the classic Poincare problem in the liquid core and, to close the problem, we use the Lagrangean formulation of the Liouville equation for each of the solid parts of the Earth model. We find that, except for the free inner core nutation (FICN), the periods of the free rotational modes converge rather quickly. The period of the tiltover mode (TOM) is found to excellent accuracy. The computed periods of the Chandler wobble (CW) and free core nutation (FCN) are nearly identical to the values cited in the literature for similar Earth models, but that for the inner core wobble (ICW) is slightly different. Truncation at low-degree harmonics causes the FICN period to fluctuate over a range as large as 90 sd, with different values at different truncation levels. For example, truncation at degree 6 gives a period of 752 sd (almost identical with the value cited in the literature for such an Earth model) but truncation at degree 24 is required to obtain convergence, and the resulting period is 746 sd, with no guarantee that its proximity to earlier values is other than fortuitous. We conclude that the heavy truncation necessitated by the conventional LMD is unsatisfactory for the FICN.

Estimation of gestational age in early pregnancy from crown-rump length when gestational age range is truncated: the case study of the INTERGROWTH-21st Project

PubMed Central

2013-01-01

Background Fetal ultrasound scanning is considered vital for routine antenatal care with first trimester scans recommended for accurate estimation of gestational age (GA). A reliable estimate of gestational age is key information underpinning clinical care and allows estimation of expected date of delivery. Fetal crown-rump length (CRL) is recommended over last menstrual period for estimating GA when measured in early pregnancy i.e. 9+0-13+6 weeks. Methods The INTERGROWTH-21st Project is the largest prospective study to collect data on CRL in geographically diverse populations and with a high level of quality control measures in place. We aim to develop a new gestational age estimation equation based on the crown-rump length (CRL) from women recruited between 9+0-13+6 weeks. The main statistical challenge is modelling data when the outcome variable (GA) is truncated at both ends, i.e. at 9 and 14 weeks. We explored three alternative statistical approaches to overcome the truncation of GA. To evaluate these strategies we generated a data set with no truncation of GA that was similar to the INTERGROWTH-21st Project CRL data, which we used to explore the performance of different methods of analysis of these data when we imposed truncation at 9 and 14 weeks of gestation. These 3 methods were first tested in a simulation based study using a previously published dating equation by Verburg et al. and evaluated how well each of them performed in relation to the model from which the data were generated. After evaluating the 3 approaches using simulated data based on the Verburg equations, the best approach will be applied to the INTERGROWTH-21st Project data to estimate GA from CRL. Results Results of these rather “ad hoc” statistical methods correspond very closely to the “real data” for Verburg, a data set that is similar to the INTERGROWTH-21st project CRL data set. Conclusions We are confident that we can use these approaches to get reliable estimates based on INTERGROWTH-21st Project CRL data. These approaches may be a solution to other truncation problems involving similar data though their application to other settings would need to be evaluated. PMID:24314232

Particulate-matter content of 11 cephalosporin injections: conformance with USP limits.

PubMed

Parkins, D A; Taylor, A J

1987-05-01

The particulate-matter content of 11 dry-powder cephalosporin injections was determined using a modified version of the official United States Pharmacopeial Convention (USP) method for particulate matter in small-volume injections (SVIs). Ten vials of each cephalosporin product were each constituted with 10 mL of Water for Injections BP that had been filtered through a 0.22-micron membrane. The pooled contents of the 10 vials for each product were allowed to stand under reduced pressure to ensure removal of gas bubbles. Particulate-matter content was determined using a HIAC/Royco particle counter on six 10-mL samples obtained from the pooled solutions for each product. All solution preparation and particle counting was performed in a horizontal-laminar-airflow hood. Modifications of the USP method used in this study included the use of six rather than two samples from each pooled solution, the addition of diluent to the injections through the rubber closure with a needle instead of into the open container, and changes in the degassing method. Particle counts for all products examined were lower than USP limits for SVIs. All but two products contained less than 15% of USP limits for particles greater than or equal to 10 microns in effective diameter and particles greater than or equal to 25 microns in effective diameter. The standard USP method for degassing (standing for two minutes) was inadequate. Application of reduced pressure for up to 10 minutes was necessary for thorough degassing of products.(ABSTRACT TRUNCATED AT 250 WORDS)

Truncated hexa-octahedral magnetite crystals in ALH84001: Presumptive biosignatures

PubMed Central

Thomas-Keprta, Kathie L.; Clemett, Simon J.; Bazylinski, Dennis A.; Kirschvink, Joseph L.; McKay, David S.; Wentworth, Susan J.; Vali, Hojatollah; Gibson, Everett K.; McKay, Mary Fae; Romanek, Christopher S.

2001-01-01

McKay et al. [(1996) Science 273, 924–930] suggested that carbonate globules in the meteorite ALH84001 contained the fossil remains of Martian microbes. We have characterized a subpopulation of magnetite (Fe3O4) crystals present in abundance within the Fe-rich rims of these carbonate globules. We find these Martian magnetites to be both chemically and physically identical to terrestrial, biogenically precipitated, intracellular magnetites produced by magnetotactic bacteria strain MV-1. Specifically, both magnetite populations are single-domain and chemically pure, and exhibit a unique crystal habit we describe as truncated hexa-octahedral. There are no known reports of inorganic processes to explain the observation of truncated hexa-octahedral magnetites in a terrestrial sample. In bacteria strain MV-1 their presence is therefore likely a product of Natural Selection. Unless there is an unknown and unexplained inorganic process on Mars that is conspicuously absent on the Earth and forms truncated hexa-octahedral magnetites, we suggest that these magnetite crystals in the Martian meteorite ALH84001 were likely produced by a biogenic process. As such, these crystals are interpreted as Martian magnetofossils and constitute evidence of the oldest life yet found. PMID:11226210

Truncated hexa-octahedral magnetite crystals in ALH84001: presumptive biosignatures

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; Clemett, S. J.; Bazylinski, D. A.; Kirschvink, J. L.; McKay, D. S.; Wentworth, S. J.; Vali, H.; Gibson, E. K. Jr; McKay, M. F.; Romanek, C. S.

2001-01-01

McKay et al. [(1996) Science 273, 924-930] suggested that carbonate globules in the meteorite ALH84001 contained the fossil remains of Martian microbes. We have characterized a subpopulation of magnetite (Fe(3)O(4)) crystals present in abundance within the Fe-rich rims of these carbonate globules. We find these Martian magnetites to be both chemically and physically identical to terrestrial, biogenically precipitated, intracellular magnetites produced by magnetotactic bacteria strain MV-1. Specifically, both magnetite populations are single-domain and chemically pure, and exhibit a unique crystal habit we describe as truncated hexa-octahedral. There are no known reports of inorganic processes to explain the observation of truncated hexa-octahedral magnetites in a terrestrial sample. In bacteria strain MV-1 their presence is therefore likely a product of Natural Selection. Unless there is an unknown and unexplained inorganic process on Mars that is conspicuously absent on the Earth and forms truncated hexa-octahedral magnetites, we suggest that these magnetite crystals in the Martian meteorite ALH84001 were likely produced by a biogenic process. As such, these crystals are interpreted as Martian magnetofossils and constitute evidence of the oldest life yet found.

Wulff polyhedra derived from morse potentials and crystal habits of bcc and fcc metal particles

NASA Astrophysics Data System (ADS)

Saito, Yahachi

1981-05-01

Using the broken-bond method and the pairwise potentials of Morse type, relative surface energies were calculated to derive the Wulff polyhedra for bcc and fcc metals. When only the first and the second nearest neighbour interactions are taken into account, the resulting Wulff polyhedron is a rhombic dodecahedron truncated by {100} faces and an octahedron truncated by {100} and {100} faces for bcc and fcc metals, respectively. The truncation degrees calculated are in good agreement with those measured from smoke particles grown in an atmosphere of rarefied inactive gas. The effect of the higher order terms of interactions is simply to make the edges and corners round.

The functional equation truncation method for approximating slow invariant manifolds: a rapid method for computing intrinsic low-dimensional manifolds.

PubMed

Roussel, Marc R; Tang, Terry

2006-12-07

A slow manifold is a low-dimensional invariant manifold to which trajectories nearby are rapidly attracted on the way to the equilibrium point. The exact computation of the slow manifold simplifies the model without sacrificing accuracy on the slow time scales of the system. The Maas-Pope intrinsic low-dimensional manifold (ILDM) [Combust. Flame 88, 239 (1992)] is frequently used as an approximation to the slow manifold. This approximation is based on a linearized analysis of the differential equations and thus neglects curvature. We present here an efficient way to calculate an approximation equivalent to the ILDM. Our method, called functional equation truncation (FET), first develops a hierarchy of functional equations involving higher derivatives which can then be truncated at second-derivative terms to explicitly neglect the curvature. We prove that the ILDM and FET-approximated (FETA) manifolds are identical for the one-dimensional slow manifold of any planar system. In higher-dimensional spaces, the ILDM and FETA manifolds agree to numerical accuracy almost everywhere. Solution of the FET equations is, however, expected to generally be faster than the ILDM method.

Preserving temporal relations in clinical data while maintaining privacy

PubMed Central

Mirhaji, Parsa; Low, Alexander FH; Malin, Bradley A

2016-01-01

Objective Maintaining patient privacy is a challenge in large-scale observational research. To assist in reducing the risk of identifying study subjects through publicly available data, we introduce a method for obscuring date information for clinical events and patient characteristics. Methods The method, which we call Shift and Truncate (SANT), obscures date information to any desired granularity. Shift and Truncate first assigns each patient a random shift value, such that all dates in that patient’s record are shifted by that amount. Data are then truncated from the beginning and end of the data set. Results The data set can be proven to not disclose temporal information finer than the chosen granularity. Unlike previous strategies such as a simple shift, it remains robust to frequent – even daily – updates and robust to inferring dates at the beginning and end of date-shifted data sets. Time-of-day may be retained or obscured, depending on the goal and anticipated knowledge of the data recipient. Conclusions The method can be useful as a scientific approach for reducing re-identification risk under the Privacy Rule of the Health Insurance Portability and Accountability Act and may contribute to qualification for the Safe Harbor implementation. PMID:27013522

Helical cone beam CT with an asymmetrical detector.

PubMed

Zamyatin, Alexander A; Taguchi, Katsuyuki; Silver, Michael D

2005-10-01

If a multislice or other area detector is shifted to one side to cover a larger field of view, then the data are truncated on one side. We propose a method to restore the missing data in helical cone-beam acquisitions that uses measured data on the longer side of the asymmetric detector array. The method is based on the idea of complementary rays, which is well known in fan beam geometry; in this paper we extend this concept to the cone-beam case. Different cases of complementary data coverage and dependence on the helical pitch are considered. The proposed method is used in our prototype 16-row CT scanner with an asymmetric detector and a 700 mm field of view. For evaluation we used scanned body phantom data and computer-simulated data. To simulate asymmetric truncation, the full, symmetric datasets were truncated by dropping either 22.5% or 45% from one side of the detector. Reconstructed images from the prototype scanner with the asymmetrical detector show excellent image quality in the extended field of view. The proposed method allows flexible helical pitch selection and can be used with overscan, short-scan, and super-short-scan reconstructions.

Cloning and expression of soluble truncated variants of Borrelia OspA, OspB and Vmp7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, J.J.; Barbour, A.G.

1996-11-05

A method is provided for preparing soluble recombinant variations of Borrelia lipoproteins such as Borrelia burgdorferi outer surface protein A (OspA) and outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The method includes synthesizing a set of oligonucleotide primers, amplifying the template DNA utilizing the PCR, purifying the amplification products, cloning the amplification products into a suitable expression vector, transforming a suitable host utilizing the cloned expression vector, cultivating the transformed host for protein production and subsequently isolating and purifying the resulting protein. Also provided are soluble, recombinant variations of Borrelia burgdorferi outer surface proteinmore » A (OspA), outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The expression vectors harboring DNA encoding the recombinant variations, pET9-OspA, pET9-OspB and pET9-Vmp7, as well as the E. coli host BL21(DE3)/pLysS transformed with each of these vectors, are also disclosed. 38 figs.« less

Cloning and expression of soluble truncated variants of Borrelia OspA, OspB and Vmp7

DOEpatents

Dunn, John J.; Barbour, Alan G.

1996-11-05

A method is provided herein for preparing soluble recombinant variations of Borrelia lipoproteins such as Borrelia burgdorferi outer surface protein A (OspA) and outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The method includes synthesizing a set of oligonucleotide primers, amplifying the template DNA utilizing the PCR, purifying the amplification products, cloning the amplification products into a suitable expression vector, transforming a suitable host utilizing the cloned expression vector, cultivating the transformed host for protein production and subsequently isolating and purifying the resulting protein. Also provided are soluble, recombinant variations of Borrelia burgdorferi outer surface protein A (OspA), outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The expression vectors harboring DNA encoding the recombinant variations, pET9-OspA, pET9-OspB and pET9-Vmp7, as well as the E. coli host BL21(DE3)/pLysS transformed with each of these vectors, are also disclosed.

Cloning and expression of soluble truncated variants of Borrelia OspA, OspB and Vmp7

DOEpatents

Dunn, J.J.; Barbour, A.G.

1996-11-05

A method is provided for preparing soluble recombinant variations of Borrelia lipoproteins such as Borrelia burgdorferi outer surface protein A (OspA) and outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The method includes synthesizing a set of oligonucleotide primers, amplifying the template DNA utilizing the PCR, purifying the amplification products, cloning the amplification products into a suitable expression vector, transforming a suitable host utilizing the cloned expression vector, cultivating the transformed host for protein production and subsequently isolating and purifying the resulting protein. Also provided are soluble, recombinant variations of Borrelia burgdorferi outer surface protein A (OspA), outer surface protein B (OspB), and B. hermsii variable major protein 7 (Vmp7). The expression vectors harboring DNA encoding the recombinant variations, pET9-OspA, pET9-OspB and pET9-Vmp7, as well as the E. coli host BL21(DE3)/pLysS transformed with each of these vectors, are also disclosed. 38 figs.

Projection-free approximate balanced truncation of large unstable systems

NASA Astrophysics Data System (ADS)

Flinois, Thibault L. B.; Morgans, Aimee S.; Schmid, Peter J.

2015-08-01

In this article, we show that the projection-free, snapshot-based, balanced truncation method can be applied directly to unstable systems. We prove that even for unstable systems, the unmodified balanced proper orthogonal decomposition algorithm theoretically yields a converged transformation that balances the Gramians (including the unstable subspace). We then apply the method to a spatially developing unstable system and show that it results in reduced-order models of similar quality to the ones obtained with existing methods. Due to the unbounded growth of unstable modes, a practical restriction on the final impulse response simulation time appears, which can be adjusted depending on the desired order of the reduced-order model. Recommendations are given to further reduce the cost of the method if the system is large and to improve the performance of the method if it does not yield acceptable results in its unmodified form. Finally, the method is applied to the linearized flow around a cylinder at Re = 100 to show that it actually is able to accurately reproduce impulse responses for more realistic unstable large-scale systems in practice. The well-established approximate balanced truncation numerical framework therefore can be safely applied to unstable systems without any modifications. Additionally, balanced reduced-order models can readily be obtained even for large systems, where the computational cost of existing methods is prohibitive.

Trading Land: A Review of Approaches to Accounting for Upstream Land Requirements of Traded Products.

PubMed

Schaffartzik, Anke; Haberl, Helmut; Kastner, Thomas; Wiedenhofer, Dominik; Eisenmenger, Nina; Erb, Karl-Heinz

2015-10-01

Land use is recognized as a pervasive driver of environmental impacts, including climate change and biodiversity loss. Global trade leads to "telecoupling" between the land use of production and the consumption of biomass-based goods and services. Telecoupling is captured by accounts of the upstream land requirements associated with traded products, also commonly referred to as land footprints. These accounts face challenges in two main areas: (1) the allocation of land to products traded and consumed and (2) the metrics to account for differences in land quality and land-use intensity. For two main families of accounting approaches (biophysical, factor-based and environmentally extended input-output analysis), this review discusses conceptual differences and compares results for land footprints. Biophysical approaches are able to capture a large number of products and different land uses, but suffer from a truncation problem. Economic approaches solve the truncation problem, but are hampered by the limited disaggregation of sectors and products. In light of the conceptual differences, the overall similarity of results generated by both types of approaches is remarkable. Diametrically opposed results for some of the world's largest producers and consumers of biomass-based products, however, make interpretation difficult. This review aims to provide clarity on some of the underlying conceptual issues of accounting for land footprints.

Stochastic static fault slip inversion from geodetic data with non-negativity and bound constraints

NASA Astrophysics Data System (ADS)

Nocquet, J.-M.

2018-07-01

Despite surface displacements observed by geodesy are linear combinations of slip at faults in an elastic medium, determining the spatial distribution of fault slip remains a ill-posed inverse problem. A widely used approach to circumvent the illness of the inversion is to add regularization constraints in terms of smoothing and/or damping so that the linear system becomes invertible. However, the choice of regularization parameters is often arbitrary, and sometimes leads to significantly different results. Furthermore, the resolution analysis is usually empirical and cannot be made independently of the regularization. The stochastic approach of inverse problems provides a rigorous framework where the a priori information about the searched parameters is combined with the observations in order to derive posterior probabilities of the unkown parameters. Here, I investigate an approach where the prior probability density function (pdf) is a multivariate Gaussian function, with single truncation to impose positivity of slip or double truncation to impose positivity and upper bounds on slip for interseismic modelling. I show that the joint posterior pdf is similar to the linear untruncated Gaussian case and can be expressed as a truncated multivariate normal (TMVN) distribution. The TMVN form can then be used to obtain semi-analytical formulae for the single, 2-D or n-D marginal pdf. The semi-analytical formula involves the product of a Gaussian by an integral term that can be evaluated using recent developments in TMVN probabilities calculations. Posterior mean and covariance can also be efficiently derived. I show that the maximum posterior (MAP) can be obtained using a non-negative least-squares algorithm for the single truncated case or using the bounded-variable least-squares algorithm for the double truncated case. I show that the case of independent uniform priors can be approximated using TMVN. The numerical equivalence to Bayesian inversions using Monte Carlo Markov chain (MCMC) sampling is shown for a synthetic example and a real case for interseismic modelling in Central Peru. The TMVN method overcomes several limitations of the Bayesian approach using MCMC sampling. First, the need of computer power is largely reduced. Second, unlike Bayesian MCMC-based approach, marginal pdf, mean, variance or covariance are obtained independently one from each other. Third, the probability and cumulative density functions can be obtained with any density of points. Finally, determining the MAP is extremely fast.

Adaptive truncation of matrix decompositions and efficient estimation of NMR relaxation distributions

NASA Astrophysics Data System (ADS)

Teal, Paul D.; Eccles, Craig

2015-04-01

The two most successful methods of estimating the distribution of nuclear magnetic resonance relaxation times from two dimensional data are data compression followed by application of the Butler-Reeds-Dawson algorithm, and a primal-dual interior point method using preconditioned conjugate gradient. Both of these methods have previously been presented using a truncated singular value decomposition of matrices representing the exponential kernel. In this paper it is shown that other matrix factorizations are applicable to each of these algorithms, and that these illustrate the different fundamental principles behind the operation of the algorithms. These are the rank-revealing QR (RRQR) factorization and the LDL factorization with diagonal pivoting, also known as the Bunch-Kaufman-Parlett factorization. It is shown that both algorithms can be improved by adaptation of the truncation as the optimization process progresses, improving the accuracy as the optimal value is approached. A variation on the interior method viz, the use of barrier function instead of the primal-dual approach, is found to offer considerable improvement in terms of speed and reliability. A third type of algorithm, related to the algorithm known as Fast iterative shrinkage-thresholding algorithm, is applied to the problem. This method can be efficiently formulated without the use of a matrix decomposition.

Automatic estimation of detector radial position for contoured SPECT acquisition using CT images on a SPECT/CT system.

PubMed

Liu, Ruijie Rachel; Erwin, William D

2006-08-01

An algorithm was developed to estimate noncircular orbit (NCO) single-photon emission computed tomography (SPECT) detector radius on a SPECT/CT imaging system using the CT images, for incorporation into collimator resolution modeling for iterative SPECT reconstruction. Simulated male abdominal (arms up), male head and neck (arms down) and female chest (arms down) anthropomorphic phantom, and ten patient, medium-energy SPECT/CT scans were acquired on a hybrid imaging system. The algorithm simulated inward SPECT detector radial motion and object contour detection at each projection angle, employing the calculated average CT image and a fixed Hounsfield unit (HU) threshold. Calculated radii were compared to the observed true radii, and optimal CT threshold values, corresponding to patient bed and clothing surfaces, were found to be between -970 and -950 HU. The algorithm was constrained by the 45 cm CT field-of-view (FOV), which limited the detected radii to < or = 22.5 cm and led to occasional radius underestimation in the case of object truncation by CT. Two methods incorporating the algorithm were implemented: physical model (PM) and best fit (BF). The PM method computed an offset that produced maximum overlap of calculated and true radii for the phantom scans, and applied that offset as a calculated-to-true radius transformation. For the BF method, the calculated-to-true radius transformation was based upon a linear regression between calculated and true radii. For the PM method, a fixed offset of +2.75 cm provided maximum calculated-to-true radius overlap for the phantom study, which accounted for the camera system's object contour detect sensor surface-to-detector face distance. For the BF method, a linear regression of true versus calculated radius from a reference patient scan was used as a calculated-to-true radius transform. Both methods were applied to ten patient scans. For -970 and -950 HU thresholds, the combined overall average root-mean-square (rms) error in radial position for eight patient scans without truncation were 3.37 cm (12.9%) for PM and 1.99 cm (8.6%) for BF, indicating BF is superior to PM in the absence of truncation. For two patient scans with truncation, the rms error was 3.24 cm (12.2%) for PM and 4.10 cm (18.2%) for BF. The slightly better performance of PM in the case of truncation is anomalous, due to FOV edge truncation artifacts in the CT reconstruction, and thus is suspect. The calculated NCO contour for a patient SPECT/CT scan was used with an iterative reconstruction algorithm that incorporated compensation for system resolution. The resulting image was qualitatively superior to the image obtained by reconstructing the data using the fixed radius stored by the scanner. The result was also superior to the image reconstructed using the iterative algorithm provided with the system, which does not incorporate resolution modeling. These results suggest that, under conditions of no or only mild lateral truncation of the CT scan, the algorithm is capable of providing radius estimates suitable for iterative SPECT reconstruction collimator geometric resolution modeling.

Production of taxadiene by engineering of mevalonate pathway in Escherichia coli and endophytic fungus Alternaria alternata TPF6.

PubMed

Bian, Guangkai; Yuan, Yujie; Tao, Hui; Shi, Xiaofei; Zhong, Xiaofang; Han, Yichao; Fu, Shuai; Fang, Chengxiang; Deng, Zixin; Liu, Tiangang

2017-04-01

Taxol (paclitaxel) is a diterpenoid compound with significant and extensive applications in the treatment of cancer. The production of Taxol and relevant intermediates by engineered microbes is an attractive alternative to the semichemical synthesis of Taxol. In this study, based on a previously developed platform, the authors first established taxadiene production in mutant E. coli T2 and T4 by engineering of the mevalonate (MVA) pathway. The authors then developed an Agrobacterium tumefaciens-mediated transformation (ATMT) method and verified the strength of heterologous promoters in Alternaria alternata TPF6. The authors next transformed the taxadiene-producing platform into A. alternata TPF6, and the MVA pathway was engineered, with introduction of the plant taxadiene-forming gene. Notably, by co-overexpression of isopentenyl diphosphate isomerase (Idi), a truncated version of 3-hydroxy-3-methylglutaryl-CoA reductase (tHMG1), and taxadiene synthase (TS), the authors could detect 61.9 ± 6.3 μg/L taxadiene in the engineered strain GB127. This is the first demonstration of taxadiene production in filamentous fungi, and the approach presented in this study provides a new method for microbial production of Taxol. The well-established ATMT method and the known promoter strengths facilitated further engineering of taxaenes in this fungus. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modulation of spectral intensity, polarization and coherence of a stochastic electromagnetic beam.

PubMed

Wu, Gaofeng; Cai, Yangjian

2011-04-25

Analytical formula for the cross-spectral density matrix of a stochastic electromagnetic Gaussian Schell-model (EGSM) beam truncated by a circular phase aperture propagating in free space is derived with the help of a tensor method, which provides a reliable and fast way for studying the propagation and transformation of a truncated EGSM beam. Statistics properties, such as the spectral intensity, the degree of coherence, the degree of polarization and the polarization ellipse of a truncated EGSM beam in free space are studied numerically. The propagation factor of a truncated EGSM beam is also analyzed. Our numerical results show that we can modulate the spectral intensity, the polarization, the coherence and the propagation factor of an EGSM beam by a circular phase aperture. It is found that the phase aperture can be used to shape the beam profile of an EGSM beam and generate electromagnetic partially coherent dark hollow or flat-topped beam, which is useful in some applications, such as optical trapping, material processing, free-space optical communications.

A proportional hazards regression model for the subdistribution with right-censored and left-truncated competing risks data

PubMed Central

Zhang, Xu; Zhang, Mei-Jie; Fine, Jason

2012-01-01

With competing risks failure time data, one often needs to assess the covariate effects on the cumulative incidence probabilities. Fine and Gray proposed a proportional hazards regression model to directly model the subdistribution of a competing risk. They developed the estimating procedure for right-censored competing risks data, based on the inverse probability of censoring weighting. Right-censored and left-truncated competing risks data sometimes occur in biomedical researches. In this paper, we study the proportional hazards regression model for the subdistribution of a competing risk with right-censored and left-truncated data. We adopt a new weighting technique to estimate the parameters in this model. We have derived the large sample properties of the proposed estimators. To illustrate the application of the new method, we analyze the failure time data for children with acute leukemia. In this example, the failure times for children who had bone marrow transplants were left truncated. PMID:21557288

Spectroscopic constraints on the form of the stellar cluster mass function

NASA Astrophysics Data System (ADS)

Bastian, N.; Konstantopoulos, I. S.; Trancho, G.; Weisz, D. R.; Larsen, S. S.; Fouesneau, M.; Kaschinski, C. B.; Gieles, M.

2012-05-01

This contribution addresses the question of whether the initial cluster mass function (ICMF) has a fundamental limit (or truncation) at high masses. The shape of the ICMF at high masses can be studied using the most massive young (<10 Myr) clusters, however this has proven difficult due to low-number statistics. In this contribution we use an alternative method based on the luminosities of the brightest clusters, combined with their ages. The advantages are that more clusters can be used and that the ICMF leaves a distinct pattern on the global relation between the cluster luminosity and median age within a population. If a truncation is present, a generic prediction (nearly independent of the cluster disruption law adopted) is that the median age of bright clusters should be younger than that of fainter clusters. In the case of an non-truncated ICMF, the median age should be independent of cluster luminosity. Here, we present optical spectroscopy of twelve young stellar clusters in the face-on spiral galaxy NGC 2997. The spectra are used to estimate the age of each cluster, and the brightness of the clusters is taken from the literature. The observations are compared with the model expectations of Larsen (2009, A&A, 494, 539) for various ICMF forms and both mass dependent and mass independent cluster disruption. While there exists some degeneracy between the truncation mass and the amount of mass independent disruption, the observations favour a truncated ICMF. For low or modest amounts of mass independent disruption, a truncation mass of 5-6 × 105 M⊙ is estimated, consistent with previous determinations. Additionally, we investigate possible truncations in the ICMF in the spiral galaxy M 83, the interacting Antennae galaxies, and the collection of spiral and dwarf galaxies present in Larsen (2009, A&A, 494, 539) based on photometric catalogues taken from the literature, and find that all catalogues are consistent with having a truncation in the cluster mass functions. However for the case of the Antennae, we find a truncation mass of a few × 106M⊙ , suggesting a dependence on the environment, as has been previously suggested.

Effect of Truncating AUC at 12, 24 and 48 hr When Evaluating the Bioequivalence of Drugs with a Long Half-Life.

PubMed

Moreno, Isabel; Ochoa, Dolores; Román, Manuel; Cabaleiro, Teresa; Abad-Santos, Francisco

2016-01-01

Bioequivalence studies of drugs with a long half-life require long periods of time for pharmacokinetic sampling. The latest update of the European guideline allows the area under the curve (AUC) truncated at 72 hr to be used as an alternative to AUC0-t as the primary parameter. The objective of this study was to evaluate the effect of truncating the AUC at 48, 24 and 12 hr on the acceptance of the bioequivalence criterion as compared with truncation at 72 hr in bioequivalence trials. The effect of truncated AUC on the within-individual coefficient of variation (CVw) and on the ratio of the formulations was also analysed. Twenty-eight drugs were selected from bioequivalence trials. Pharmacokinetic data were analysed using WinNonLin 2.0 based on the trapezoidal method. Analysis of variance (ANOVA) was performed to obtain the ratios and 90% confidence intervals for AUC at different time-points. The degree of agreement of AUC0-72 in relation to AUC0-48 and AUC0-24, according to the Landis and Koch classification, was 'almost perfect'. Statistically significant differences were observed when the CVw of AUC truncated at 72, 48 and 24 hr was compared with the CVw of AUC0-12. There were no statistically significant differences in the AUC ratio at any time-point. Compared to AUC0-72, Pearson's correlation coefficient for mean AUC, AUC ratio and AUC CVw was worse for AUC0-12 than AUC0-24 or AUC0-48. These preliminary results could suggest that AUC truncation at 24 or 48 hr is adequate to determine whether two formulations are bioequivalent. © 2015 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy.

PubMed

Norton, Nadine; Li, Duanxiang; Rampersaud, Evadnie; Morales, Ana; Martin, Eden R; Zuchner, Stephan; Guo, Shengru; Gonzalez, Michael; Hedges, Dale J; Robertson, Peggy D; Krumm, Niklas; Nickerson, Deborah A; Hershberger, Ray E

2013-04-01

BACKGROUND- Familial dilated cardiomyopathy (DCM) is a genetically heterogeneous disease with >30 known genes. TTN truncating variants were recently implicated in a candidate gene study to cause 25% of familial and 18% of sporadic DCM cases. METHODS AND RESULTS- We used an unbiased genome-wide approach using both linkage analysis and variant filtering across the exome sequences of 48 individuals affected with DCM from 17 families to identify genetic cause. Linkage analysis ranked the TTN region as falling under the second highest genome-wide multipoint linkage peak, multipoint logarithm of odds, 1.59. We identified 6 TTN truncating variants carried by individuals affected with DCM in 7 of 17 DCM families (logarithm of odds, 2.99); 2 of these 7 families also had novel missense variants that segregated with disease. Two additional novel truncating TTN variants did not segregate with DCM. Nucleotide diversity at the TTN locus, including missense variants, was comparable with 5 other known DCM genes. The average number of missense variants in the exome sequences from the DCM cases or the ≈5400 cases from the Exome Sequencing Project was ≈23 per individual. The average number of TTN truncating variants in the Exome Sequencing Project was 0.014 per individual. We also identified a region (chr9q21.11-q22.31) with no known DCM genes with a maximum heterogeneity logarithm of odds score of 1.74. CONCLUSIONS- These data suggest that TTN truncating variants contribute to DCM cause. However, the lack of segregation of all identified TTN truncating variants illustrates the challenge of determining variant pathogenicity even with full exome sequencing.

Shaping the beam profile of a partially coherent beam by a phase aperture

NASA Astrophysics Data System (ADS)

Wu, Gaofeng; Cai, Yangjian; Chen, Jun

2011-08-01

By use of a tensor method, an analytical formula for a partially coherent Gaussian Schell-model (GSM) beam truncated by a circular phase aperture propagating through a paraxial ABCD optical system is derived. The propagation properties of a GSM beam truncated by a circular phase aperture in free space are studied numerically. It is found that the circular phase aperture can be used to shape the beam profile of a GSM beam and generate partially coherent dark hollow or flat-topped beam, which is useful in many applications, e.g., optical trapping, free-space optical communication, and material thermal processing. The propagation factor of a GSM beam truncated by a circular phase aperture is also analyzed.

Efficient Implementations of the Quadrature-Free Discontinuous Galerkin Method

NASA Technical Reports Server (NTRS)

Lockard, David P.; Atkins, Harold L.

1999-01-01

The efficiency of the quadrature-free form of the dis- continuous Galerkin method in two dimensions, and briefly in three dimensions, is examined. Most of the work for constant-coefficient, linear problems involves the volume and edge integrations, and the transformation of information from the volume to the edges. These operations can be viewed as matrix-vector multiplications. Many of the matrices are sparse as a result of symmetry, and blocking and specialized multiplication routines are used to account for the sparsity. By optimizing these operations, a 35% reduction in total CPU time is achieved. For nonlinear problems, the calculation of the flux becomes dominant because of the cost associated with polynomial products and inversion. This component of the work can be reduced by up to 75% when the products are approximated by truncating terms. Because the cost is high for nonlinear problems on general elements, it is suggested that simplified physics and the most efficient element types be used over most of the domain.

Fluorescence in-situ hybridization method reveals that carboxyl-terminal fragments of transactive response DNA-binding protein-43 truncated at the amino acid residue 218 reduce poly(A)+ RNA expression.

PubMed

Higashi, Shinji; Watanabe, Ryohei; Arai, Tetsuaki

2018-07-04

Transactive response (TAR) DNA-binding protein 43 (TDP-43) has emerged as an important contributor to amyotrophic lateral sclerosis and frontotemporal lobar degeneration. To understand the association of TDP-43 with complex RNA processing in disease pathogenesis, we performed fluorescence in-situ hybridization using HeLa cells transfected with a series of deleted TDP-43 constructs and investigated the effect of truncation of TDP-43 on the expression of poly(A) RNA. Endogenous and overexpressed full-length TDP-43 localized to the perichromatin region and interchromatin space adjacent to poly(A) RNA. Deleted variants of TDP-43 containing RNA recognition motif 1 and truncating N-terminal region induced cytoplasmic inclusions in which poly(A) RNA was recruited. Carboxyl-terminal TDP-43 truncated at residue 202 or 218 was distributed in the cytoplasm as punctate structures. Carboxyl-terminal TDP-43 truncated at residue 218, but not at 202, significantly decreased poly(A) RNA expression by ∼24% compared with the level in control cells. Our results suggest that the disturbance of RNA metabolism induced by pathogenic fragments plays central roles in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration.

A Bayesian approach to truncated data sets: An application to Malmquist bias in Supernova Cosmology

NASA Astrophysics Data System (ADS)

March, Marisa Cristina

2018-01-01

A problem commonly encountered in statistical analysis of data is that of truncated data sets. A truncated data set is one in which a number of data points are completely missing from a sample, this is in contrast to a censored sample in which partial information is missing from some data points. In astrophysics this problem is commonly seen in a magnitude limited survey such that the survey is incomplete at fainter magnitudes, that is, certain faint objects are simply not observed. The effect of this `missing data' is manifested as Malmquist bias and can result in biases in parameter inference if it is not accounted for. In Frequentist methodologies the Malmquist bias is often corrected for by analysing many simulations and computing the appropriate correction factors. One problem with this methodology is that the corrections are model dependent. In this poster we derive a Bayesian methodology for accounting for truncated data sets in problems of parameter inference and model selection. We first show the methodology for a simple Gaussian linear model and then go on to show the method for accounting for a truncated data set in the case for cosmological parameter inference with a magnitude limited supernova Ia survey.

Engineering of GlcNAc-1-Phosphotransferase for Production of Highly Phosphorylated Lysosomal Enzymes for Enzyme Replacement Therapy.

PubMed

Liu, Lin; Lee, Wang-Sik; Doray, Balraj; Kornfeld, Stuart

2017-06-16

Several lysosomal enzymes currently used for enzyme replacement therapy in patients with lysosomal storage diseases contain very low levels of mannose 6-phosphate, limiting their uptake via mannose 6-phosphate receptors on the surface of the deficient cells. These enzymes are produced at high levels by mammalian cells and depend on endogenous GlcNAc-1-phosphotransferase α/β precursor to phosphorylate the mannose residues on their glycan chains. We show that co-expression of an engineered truncated GlcNAc-1-phosphotransferase α/β precursor and the lysosomal enzyme of interest in the producing cells resulted in markedly increased phosphorylation and cellular uptake of the secreted lysosomal enzyme. This method also results in the production of highly phosphorylated acid β-glucocerebrosidase, a lysosomal enzyme that normally has just trace amounts of this modification.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

NASA Astrophysics Data System (ADS)

Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

2017-10-01

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces.

PubMed

Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

2017-10-28

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

Comparison of Two Methods Used to Model Shape Parameters of Pareto Distributions

USGS Publications Warehouse

Liu, C.; Charpentier, R.R.; Su, J.

2011-01-01

Two methods are compared for estimating the shape parameters of Pareto field-size (or pool-size) distributions for petroleum resource assessment. Both methods assume mature exploration in which most of the larger fields have been discovered. Both methods use the sizes of larger discovered fields to estimate the numbers and sizes of smaller fields: (1) the tail-truncated method uses a plot of field size versus size rank, and (2) the log-geometric method uses data binned in field-size classes and the ratios of adjacent bin counts. Simulation experiments were conducted using discovered oil and gas pool-size distributions from four petroleum systems in Alberta, Canada and using Pareto distributions generated by Monte Carlo simulation. The estimates of the shape parameters of the Pareto distributions, calculated by both the tail-truncated and log-geometric methods, generally stabilize where discovered pool numbers are greater than 100. However, with fewer than 100 discoveries, these estimates can vary greatly with each new discovery. The estimated shape parameters of the tail-truncated method are more stable and larger than those of the log-geometric method where the number of discovered pools is more than 100. Both methods, however, tend to underestimate the shape parameter. Monte Carlo simulation was also used to create sequences of discovered pool sizes by sampling from a Pareto distribution with a discovery process model using a defined exploration efficiency (in order to show how biased the sampling was in favor of larger fields being discovered first). A higher (more biased) exploration efficiency gives better estimates of the Pareto shape parameters. ?? 2011 International Association for Mathematical Geosciences.

Reconstruction of truncated TCT and SPECT data from a right-angle dual-camera system for myocardial SPECT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsui, B.M.W.; Frey, E.C.; Lalush, D.S.

1996-12-31

We investigated methods to accurately reconstruct 180{degrees} truncated TCT and SPECT projection data obtained from a right-angle dual-camera SPECT system for myocardial SPECT with attenuation compensation. The 180{degrees} data reconstruction methods would permit substantial savings in transmission data acquisition time. Simulation data from the 3D MCAT phantom and clinical data from large patients were used in the evaluation study. Different transmission reconstruction methods including the FBP, transmission ML-EM, transmission ML-SA, and BIT algorithms with and without using the body contour as support, were used in the TCT image reconstructions. The accuracy of both the TCT and attenuation compensated SPECT imagesmore » were evaluated for different degrees of truncation and noise levels. We found that using the FBP reconstructed TCT images resulted in higher count density in the left ventricular (LV) wall of the attenuation compensated SPECT images. The LV wall count density obtained using the iteratively reconstructed TCT images with and without support were similar to each other and were more accurate than that using the FBP. However, the TCT images obtained with support show fewer image artifacts than without support. Among the iterative reconstruction algorithms, the ML-SA algorithm provides the most accurate reconstruction but is the slowest. The BIT algorithm is the fastest but shows the most image artifacts. We conclude that accurate attenuation compensated images can be obtained with truncated 180{degrees} data from large patients using a right-angle dual-camera SPECT system.« less

Chromomycin SA analogs from a marine-derived Streptomyces sp.

PubMed Central

Hu, Youcai; Espindola, Ana Paula D. M; Stewart, Nathan A.; Wei, Shuguang; Posner, Bruce A.; MacMillan, John B.

2011-01-01

Two chromomycin SA analogs, chromomycin SA3 and chromomycin SA2, along with deacetylchromomycin A3 and five previously reported chromomycin analogs were isolated from a marine-derived Streptomyces sp. The structures of the new compounds were determined by spectroscopic methods including 1D and 2D NMR techniques, HRMS and chemical methods. Chromomycin SA3 and chromomycin SA2 are the first naturally occuring chromomycin analogs with truncated side-chains. Biological evaluation of chromomycin analogs for cytotoxicity against two non-small cell lung cancer (NSCLC) cell-lines, A549 and HCC44, demonstrated a decrease in cytotoxicity for the truncated sides chain chromomycin analogs. PMID:21807523

Large scale exact quantum dynamics calculations: Ten thousand quantum states of acetonitrile

NASA Astrophysics Data System (ADS)

Halverson, Thomas; Poirier, Bill

2015-03-01

'Exact' quantum dynamics (EQD) calculations of the vibrational spectrum of acetonitrile (CH3CN) are performed, using two different methods: (1) phase-space-truncated momentum-symmetrized Gaussian basis and (2) correlated truncated harmonic oscillator basis. In both cases, a simple classical phase space picture is used to optimize the selection of individual basis functions-leading to drastic reductions in basis size, in comparison with existing methods. Massive parallelization is also employed. Together, these tools-implemented into a single, easy-to-use computer code-enable a calculation of tens of thousands of vibrational states of CH3CN to an accuracy of 0.001-10 cm-1.

A nonperturbative light-front coupled-cluster method

NASA Astrophysics Data System (ADS)

Hiller, J. R.

2012-10-01

The nonperturbative Hamiltonian eigenvalue problem for bound states of a quantum field theory is formulated in terms of Dirac's light-front coordinates and then approximated by the exponential-operator technique of the many-body coupled-cluster method. This approximation eliminates any need for the usual approximation of Fock-space truncation. Instead, the exponentiated operator is truncated, and the terms retained are determined by a set of nonlinear integral equations. These equations are solved simultaneously with an effective eigenvalue problem in the valence sector, where the number of constituents is small. Matrix elements can be calculated, with extensions of techniques from standard coupled-cluster theory, to obtain form factors and other observables.

Why do people reject unintended inequity? Responders' rejection in a truncated ultimatum game.

PubMed

Ohmura, Yu; Yamagishi, Toshio

2005-04-01

Rejection of an inequitable and yet unintended outcome in a truncated ultimatum game was examined in an experiment with 46 undergraduate students (27 men and 19 women) from a large national university in Japan. In an ultimatum game, one of two players, the proposer, makes an offer to divide a fixed-sum of money. The other player, the responder, decides whether to accept or reject the offer. When the responder rejects the proposer's offer, neither of the two players receives a reward. Previous work examining the behavior of participants in the truncated ultimatum game employed strategy method in their experimental design. We examined whether these previous findings would be replicated in an experimental design that did not use the strategy method and instead used the standard one-shot game. Seven out of 46 responders given an inequitable offer rejected it, replicating prior results with the strategy method. We further found that subjects who rejected an offer that was involuntary and yet inequitable did not over-attribute intentions to the proposer's involuntary behavior more strongly than did acceptors. These findings strongly suggest that aversion to inequity is the explanation for the subjects' rejection of the inequitable offer.

A five-residue sequence near the carboxyl terminus of the polytopic membrane protein lac permease is required for stability within the membrane.

PubMed Central

Roepe, P D; Zbar, R I; Sarkar, H K; Kaback, H R

1989-01-01

The lac permease (lacY gene product) of Escherichia coli contains 417 amino acid residues and is predicted to have a short hydrophilic amino terminus on the inner surface of the cytoplasmic membrane, multiple transmembrane hydrophobic segments in alpha-helical conformation, and a 17-amino acid residue hydrophilic carboxyl-terminal tail on the inner surface of the membrane. To assess the importance of the carboxyl terminus, the properties of several truncation mutants were studied. The mutants were constructed by site-directed mutagenesis such that stop codons were placed at specified positions, and the altered lacY genes were expressed at a relatively low rate from plasmid pACYC184. Permease truncated at position 407 or 401 retains full activity, and a normal complement of molecules is present in the membrane, as judged by immunoblot analyses. Thus, it is apparent that the carboxyl-terminal tail plays no direct role in membrane insertion of the permease, its stability, or in the mechanism of lactose/H+ symport. In marked contrast, when truncations are made at residues 396 (i.e., 4 amino acid residues from the carboxyl terminus of putative helix XII), 389, 372, or 346, the permease is no longer found in the membrane. Remarkably, however, when each of the mutated lacY genes is expressed at a high rate by means of the T7 RNA polymerase system [Tabor, S. & Richardson, C. C. (1985) Proc. Natl. Acad. Sci. USA 82, 1074-1079], all of the truncated permeases are present in the membrane, as indicated by [35S]methionine incorporation studies; however, permease truncated at residue 396, 389, 372, or 346 is defective with respect to lactose/H+ symport. Finally, pulse-chase experiments indicate that wild-type permease or permease truncated at residue 401 is stable, whereas permease truncated at or prior to residue 396 is degraded at a significant rate. The results are consistent with the notion that residues 396-401 in putative helix XII are important for protection against proteolytic degradation and suggest that this region of the permease may be necessary for proper folding. Images PMID:2657733

Acoustic plane wave diffraction from a truncated semi-infinite cone in axial irradiation

NASA Astrophysics Data System (ADS)

Kuryliak, Dozyslav; Lysechko, Victor

2017-11-01

The diffraction problem of the plane acoustic wave on the semi-infinite truncated soft and rigid cones in the case of axial incidence is solved. The problem is formulated as a boundary-value problem in terms of Helmholtz equation, with Dirichlet and Neumann boundary conditions, for scattered velocity potential. The incident field is taken to be the total field of semi-infinite cone, the expression of which is obtained by solving the auxiliary diffraction problem by the use of Kontorovich-Lebedev integral transformation. The diffracted field is sought via the expansion in series of the eigenfunctions for subdomains of the Helmholtz equation taking into account the edge condition. The corresponding diffraction problem is reduced to infinite system of linear algebraic equations (ISLAE) making use of mode matching technique and orthogonality properties of the Legendre functions. The method of analytical regularization is applied in order to extract the singular part in ISLAE, invert it exactly and reduce the problem to ISLAE of the second kind, which is readily amenable to calculation. The numerical solution of this system relies on the reduction method; and its accuracy depends on the truncation order. The case of degeneration of the truncated semi-infinite cone into an aperture in infinite plane is considered. Characteristic features of diffracted field in near and far fields as functions of cone's parameters are examined.

Capturing of the monoterpene olefin limonene produced in Saccharomyces cerevisiae.

PubMed

Jongedijk, Esmer; Cankar, Katarina; Ranzijn, Jorn; van der Krol, Sander; Bouwmeester, Harro; Beekwilder, Jules

2015-01-01

Monoterpene olefins such as limonene are plant compounds with applications as flavouring and fragrance agents, as solvents and potentially also in polymer and fuel chemistry. We engineered baker's yeast Saccharomyces cerevisiae to express a (-)-limonene synthase from Perilla frutescens and a (+)-limonene synthase from Citrus limon. Both proteins were expressed either with their native plastid targeting signal or in a truncated form in which the plastidial sorting signal was removed. The yeast host strain for expression was AE9 K197G, which expresses a mutant Erg20 enzyme. This enzyme catalyses the formation of geranyl diphosphate, which is the precursor for monoterpenes. Several methods were tested to capture limonene produced by the yeast. Extraction from the culture medium by pentane, or by the addition of CaCl2 followed by solid-phase micro-extraction, did not lead to detectable limonene, indicating that limonene is rapidly lost from the culture medium. Volatile terpenes such as limonene may also be trapped in a dodecane phase added to the medium during fermentation. This method resulted in recovery of 0.028 mg/l (+)-limonene and 0.060 mg/l (-)-limonene in strains using the truncated Citrus and Perilla synthases, respectively. Trapping the headspace during culture of the limonene synthase-expressing strains resulted in higher titres, at 0.12 mg/l (+)-limonene and 0.49 mg/l (-)-limonene. These results show that the volatile properties of the olefins produced require specific methods for efficient recovery of these molecules from biotechnological production systems. Copyright © 2014 John Wiley & Sons, Ltd.

Trading Land: A Review of Approaches to Accounting for Upstream Land Requirements of Traded Products

PubMed Central

Haberl, Helmut; Kastner, Thomas; Wiedenhofer, Dominik; Eisenmenger, Nina; Erb, Karl‐Heinz

2015-01-01

Summary Land use is recognized as a pervasive driver of environmental impacts, including climate change and biodiversity loss. Global trade leads to “telecoupling” between the land use of production and the consumption of biomass‐based goods and services. Telecoupling is captured by accounts of the upstream land requirements associated with traded products, also commonly referred to as land footprints. These accounts face challenges in two main areas: (1) the allocation of land to products traded and consumed and (2) the metrics to account for differences in land quality and land‐use intensity. For two main families of accounting approaches (biophysical, factor‐based and environmentally extended input‐output analysis), this review discusses conceptual differences and compares results for land footprints. Biophysical approaches are able to capture a large number of products and different land uses, but suffer from a truncation problem. Economic approaches solve the truncation problem, but are hampered by the limited disaggregation of sectors and products. In light of the conceptual differences, the overall similarity of results generated by both types of approaches is remarkable. Diametrically opposed results for some of the world's largest producers and consumers of biomass‐based products, however, make interpretation difficult. This review aims to provide clarity on some of the underlying conceptual issues of accounting for land footprints. PMID:27547028

The Extended Erlang-Truncated Exponential distribution: Properties and application to rainfall data.

PubMed

Okorie, I E; Akpanta, A C; Ohakwe, J; Chikezie, D C

2017-06-01

The Erlang-Truncated Exponential ETE distribution is modified and the new lifetime distribution is called the Extended Erlang-Truncated Exponential EETE distribution. Some statistical and reliability properties of the new distribution are given and the method of maximum likelihood estimate was proposed for estimating the model parameters. The usefulness and flexibility of the EETE distribution was illustrated with an uncensored data set and its fit was compared with that of the ETE and three other three-parameter distributions. Results based on the minimized log-likelihood ([Formula: see text]), Akaike information criterion (AIC), Bayesian information criterion (BIC) and the generalized Cramér-von Mises [Formula: see text] statistics shows that the EETE distribution provides a more reasonable fit than the one based on the other competing distributions.

Stereospecific Synthesis of threo- and erythro-β-Hydroxyglutamic Acid During Kutzneride Biosynthesis

PubMed Central

Strieker, Matthias; Nolan, Elizabeth M.; Walsh, Christopher T.; Marahiel, Mohamed A.

2009-01-01

The antifungal and antimicrobial kutznerides, hexadepsipeptides comprised of one α-hydroxy acid and five non-proteinogenic amino acids, are remarkable examples of the structural diversity found in nonribosomally-produced natural products. They contain D-3-hydroxyglutamic acid, which is found in the threo and erythro isomers in mature kutznerides. In this study, two putative non-heme iron oxygenase enzymes, KtzO and KtzP, were recombinantly expressed, characterized biochemically in vitro, and found to stereospecifically hydroxylate the β-position of glutamic acid. KtzO generates threo-L-hydroxyglutamic acid and KtzP catalyzes the formation of the erythro-isomer bound to the peptidyl carrier protein of the third module of the nonribosomal peptide synthetase KtzH. This module has a truncated adenylation domain and is unable to activate and incorporate glutamic acid. The lack of a functional adenylation domain in the third KtzH module is compensated in trans by the stand-alone adenylation domain KtzN, which activates and transfers glutamic acid onto the carrier of KtzH in the presence of the truncated adenylation domain and either KtzO or KtzP. A method that employs non-hydrolyzable coenzyme A analogs was developed and used to determine the kinetic parameters for KtzO- and KtzP-catalyzed hydroxylation of glutamic acid bound to the carrier protein. A detailed mechanism for the in trans compensation of the truncated adenylation domain and the stereospecific hydroxyglutamic acid generation and incorporation is presented. These insights may guide the use of KtzO/KtzP and KtzN or other in trans modification/restoration tools in biocombinatorial engineering approaches. PMID:19722489

Neurophysiological modification of CA1 pyramidal neurons in a transgenic mouse expressing a truncated form of disrupted-in-schizophrenia 1

PubMed Central

Booth, Clair A; Brown, Jonathan T; Randall, Andrew D

2014-01-01

A t(1;11) balanced chromosomal translocation transects the Disc1 gene in a large Scottish family and produces genome-wide linkage to schizophrenia and recurrent major depressive disorder. This study describes our in vitro investigations into neurophysiological function in hippocampal area CA1 of a transgenic mouse (DISC1tr) that expresses a truncated version of DISC1 designed to reproduce aspects of the genetic situation in the Scottish t(1;11) pedigree. We employed both patch-clamp and extracellular recording methods in vitro to compare intrinsic properties and synaptic function and plasticity between DISC1tr animals and wild-type littermates. Patch-clamp analysis of CA1 pyramidal neurons (CA1-PNs) revealed no genotype dependence in multiple subthreshold parameters, including resting potential, input resistance, hyperpolarization-activated ‘sag’ and resonance properties. Suprathreshold stimuli revealed no alteration to action potential (AP) waveform, although the initial rate of AP production was higher in DISC1tr mice. No difference was observed in afterhyperpolarizing potentials following trains of 5–25 APs at 50 Hz. Patch-clamp analysis of synaptic responses in the Schaffer collateral commissural (SC) pathway indicated no genotype-dependence of paired pulse facilitation, excitatory postsynaptic potential summation or AMPA/NMDA ratio. Extracellular recordings also revealed an absence of changes to SC synaptic responses and indicated input–output and short-term plasticity were also unaltered in the temporoammonic (TA) input. However, in DISC1tr mice theta burst-induced long-term potentiation was enhanced in the SC pathway but completely lost in the TA pathway. These data demonstrate that expressing a truncated form of DISC1 affects intrinsic properties of CA1-PNs and produces pathway-specific effects on long-term synaptic plasticity. PMID:24712988

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

PubMed

Easton, Douglas F; Lesueur, Fabienne; Decker, Brennan; Michailidou, Kyriaki; Li, Jun; Allen, Jamie; Luccarini, Craig; Pooley, Karen A; Shah, Mitul; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Ahmad, Jamil; Thompson, Ella R; Damiola, Francesca; Pertesi, Maroulio; Voegele, Catherine; Mebirouk, Noura; Robinot, Nivonirina; Durand, Geoffroy; Forey, Nathalie; Luben, Robert N; Ahmed, Shahana; Aittomäki, Kristiina; Anton-Culver, Hoda; Arndt, Volker; Baynes, Caroline; Beckman, Matthias W; Benitez, Javier; Van Den Berg, David; Blot, William J; Bogdanova, Natalia V; Bojesen, Stig E; Brenner, Hermann; Chang-Claude, Jenny; Chia, Kee Seng; Choi, Ji-Yeob; Conroy, Don M; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Eriksson, Mikael; Fasching, Peter A; Figueroa, Jonine; Flyger, Henrik; Fostira, Florentia; García-Closas, Montserrat; Giles, Graham G; Glendon, Gord; González-Neira, Anna; Guénel, Pascal; Haiman, Christopher A; Hall, Per; Hart, Steven N; Hartman, Mikael; Hooning, Maartje J; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; James, Paul A; John, Esther M; Johnson, Nichola; Jones, Michael; Kabisch, Maria; Kang, Daehee; Kosma, Veli-Matti; Kristensen, Vessela; Lambrechts, Diether; Li, Na; Lindblom, Annika; Long, Jirong; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Matsuo, Keitaro; Meindl, Alfons; Mitchell, Gillian; Muir, Kenneth; Nevelsteen, Ines; van den Ouweland, Ans; Peterlongo, Paolo; Phuah, Sze Yee; Pylkäs, Katri; Rowley, Simone M; Sangrajrang, Suleeporn; Schmutzler, Rita K; Shen, Chen-Yang; Shu, Xiao-Ou; Southey, Melissa C; Surowy, Harald; Swerdlow, Anthony; Teo, Soo H; Tollenaar, Rob A E M; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; Vachon, Celine; Verhoef, Senno; Wong-Brown, Michelle; Zheng, Wei; Zheng, Ying; Nevanlinna, Heli; Scott, Rodney J; Andrulis, Irene L; Wu, Anna H; Hopper, John L; Couch, Fergus J; Winqvist, Robert; Burwinkel, Barbara; Sawyer, Elinor J; Schmidt, Marjanka K; Rudolph, Anja; Dörk, Thilo; Brauch, Hiltrud; Hamann, Ute; Neuhausen, Susan L; Milne, Roger L; Fletcher, Olivia; Pharoah, Paul D P; Campbell, Ian G; Dunning, Alison M; Le Calvez-Kelm, Florence; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia

2016-05-01

BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Photosynthetic antenna engineering to improve crop yields.

PubMed

Kirst, Henning; Gabilly, Stéphane T; Niyogi, Krishna K; Lemaux, Peggy G; Melis, Anastasios

2017-05-01

Evidence shows that decreasing the light-harvesting antenna size of the photosystems in tobacco helps to increase the photosynthetic productivity and plant canopy biomass accumulation under high-density cultivation conditions. Decreasing, or truncating, the chlorophyll antenna size of the photosystems can theoretically improve photosynthetic solar energy conversion efficiency and productivity in mass cultures of algae or plants by up to threefold. A Truncated Light-harvesting chlorophyll Antenna size (TLA), in all classes of photosynthetic organisms, would help to alleviate excess absorption of sunlight and the ensuing wasteful non-photochemical dissipation of excitation energy. Thus, solar-to-biomass energy conversion efficiency and photosynthetic productivity in high-density cultures can be increased. Applicability of the TLA concept was previously shown in green microalgae and cyanobacteria, but it has not yet been demonstrated in crop plants. In this work, the TLA concept was applied in high-density tobacco canopies. The work showed a 25% improvement in stem and leaf biomass accumulation for the TLA tobacco canopies over that measured with their wild-type counterparts grown under the same ambient conditions. Distinct canopy appearance differences are described between the TLA and wild type tobacco plants. Findings are discussed in terms of concept application to crop plants, leading to significant improvements in agronomy, agricultural productivity, and application of photosynthesis for the generation of commodity products in crop leaves.

Constrained Kalman Filtering Via Density Function Truncation for Turbofan Engine Health Estimation

NASA Technical Reports Server (NTRS)

Simon, Dan; Simon, Donald L.

2006-01-01

Kalman filters are often used to estimate the state variables of a dynamic system. However, in the application of Kalman filters some known signal information is often either ignored or dealt with heuristically. For instance, state variable constraints (which may be based on physical considerations) are often neglected because they do not fit easily into the structure of the Kalman filter. This paper develops an analytic method of incorporating state variable inequality constraints in the Kalman filter. The resultant filter truncates the PDF (probability density function) of the Kalman filter estimate at the known constraints and then computes the constrained filter estimate as the mean of the truncated PDF. The incorporation of state variable constraints increases the computational effort of the filter but significantly improves its estimation accuracy. The improvement is demonstrated via simulation results obtained from a turbofan engine model. The turbofan engine model contains 3 state variables, 11 measurements, and 10 component health parameters. It is also shown that the truncated Kalman filter may be a more accurate way of incorporating inequality constraints than other constrained filters (e.g., the projection approach to constrained filtering).

A comparison of methods for computing the sigma-coordinate pressure gradient force for flow over sloped terrain in a hybrid theta-sigma model

NASA Technical Reports Server (NTRS)

Johnson, D. R.; Uccellini, L. W.

1983-01-01

In connection with the employment of the sigma coordinates introduced by Phillips (1957), problems can arise regarding an accurate finite-difference computation of the pressure gradient force. Over steeply sloped terrain, the calculation of the sigma-coordinate pressure gradient force involves computing the difference between two large terms of opposite sign which results in large truncation error. To reduce the truncation error, several finite-difference methods have been designed and implemented. The present investigation has the objective to provide another method of computing the sigma-coordinate pressure gradient force. Phillips' method is applied for the elimination of a hydrostatic component to a flux formulation. The new technique is compared with four other methods for computing the pressure gradient force. The work is motivated by the desire to use an isentropic and sigma-coordinate hybrid model for experiments designed to study flow near mountainous terrain.

Series approximation to probability densities

NASA Astrophysics Data System (ADS)

Cohen, L.

2018-04-01

One of the historical and fundamental uses of the Edgeworth and Gram-Charlier series is to "correct" a Gaussian density when it is determined that the probability density under consideration has moments that do not correspond to the Gaussian [5, 6]. There is a fundamental difficulty with these methods in that if the series are truncated, then the resulting approximate density is not manifestly positive. The aim of this paper is to attempt to expand a probability density so that if it is truncated it will still be manifestly positive.

Estimating inverse-probability weights for longitudinal data with dropout or truncation: The xtrccipw command.

PubMed

Daza, Eric J; Hudgens, Michael G; Herring, Amy H

Individuals may drop out of a longitudinal study, rendering their outcomes unobserved but still well defined. However, they may also undergo truncation (for example, death), beyond which their outcomes are no longer meaningful. Kurland and Heagerty (2005, Biostatistics 6: 241-258) developed a method to conduct regression conditioning on nontruncation, that is, regression conditioning on continuation (RCC), for longitudinal outcomes that are monotonically missing at random (for example, because of dropout). This method first estimates the probability of dropout among continuing individuals to construct inverse-probability weights (IPWs), then fits generalized estimating equations (GEE) with these IPWs. In this article, we present the xtrccipw command, which can both estimate the IPWs required by RCC and then use these IPWs in a GEE estimator by calling the glm command from within xtrccipw. In the absence of truncation, the xtrccipw command can also be used to run a weighted GEE analysis. We demonstrate the xtrccipw command by analyzing an example dataset and the original Kurland and Heagerty (2005) data. We also use xtrccipw to illustrate some empirical properties of RCC through a simulation study.

A truncated generalized singular value decomposition algorithm for moving force identification with ill-posed problems

NASA Astrophysics Data System (ADS)

Chen, Zhen; Chan, Tommy H. T.

2017-08-01

This paper proposes a new methodology for moving force identification (MFI) from the responses of bridge deck. Based on the existing time domain method (TDM), the MFI problem eventually becomes solving the linear algebraic equation in the form Ax = b . The vector b is usually contaminated by an unknown error e generating from measurement error, which often called the vector e as ''noise''. With the ill-posed problems that exist in the inverse problem, the identification force would be sensitive to the noise e . The proposed truncated generalized singular value decomposition method (TGSVD) aims at obtaining an acceptable solution and making the noise to be less sensitive to perturbations with the ill-posed problems. The illustrated results show that the TGSVD has many advantages such as higher precision, better adaptability and noise immunity compared with TDM. In addition, choosing a proper regularization matrix L and a truncation parameter k are very useful to improve the identification accuracy and to solve ill-posed problems when it is used to identify the moving force on bridge.

Effectively-truncated large-scale shell-model calculations and nuclei around 100Sn

NASA Astrophysics Data System (ADS)

Gargano, A.; Coraggio, L.; Itaco, N.

2017-09-01

This paper presents a short overview of a procedure we have recently introduced, dubbed the double-step truncation method, which is aimed to reduce the computational complexity of large-scale shell-model calculations. Within this procedure, one starts with a realistic shell-model Hamiltonian defined in a large model space, and then, by analyzing the effective single particle energies of this Hamiltonian as a function of the number of valence protons and/or neutrons, reduced model spaces are identified containing only the single-particle orbitals relevant to the description of the spectroscopic properties of a certain class of nuclei. As a final step, new effective shell-model Hamiltonians defined within the reduced model spaces are derived by way of a unitary transformation of the original large-scale Hamiltonian. A detailed account of this transformation is given and the merit of the double-step truncation method is illustrated by discussing few selected results for 96Mo, described as four protons and four neutrons outside 88Sr. Some new preliminary results for light odd-tin isotopes from A = 101 to 107 are also reported.

Estimating inverse-probability weights for longitudinal data with dropout or truncation: The xtrccipw command

PubMed Central

Hudgens, Michael G.; Herring, Amy H.

2017-01-01

Individuals may drop out of a longitudinal study, rendering their outcomes unobserved but still well defined. However, they may also undergo truncation (for example, death), beyond which their outcomes are no longer meaningful. Kurland and Heagerty (2005, Biostatistics 6: 241–258) developed a method to conduct regression conditioning on nontruncation, that is, regression conditioning on continuation (RCC), for longitudinal outcomes that are monotonically missing at random (for example, because of dropout). This method first estimates the probability of dropout among continuing individuals to construct inverse-probability weights (IPWs), then fits generalized estimating equations (GEE) with these IPWs. In this article, we present the xtrccipw command, which can both estimate the IPWs required by RCC and then use these IPWs in a GEE estimator by calling the glm command from within xtrccipw. In the absence of truncation, the xtrccipw command can also be used to run a weighted GEE analysis. We demonstrate the xtrccipw command by analyzing an example dataset and the original Kurland and Heagerty (2005) data. We also use xtrccipw to illustrate some empirical properties of RCC through a simulation study. PMID:29755297

Miraxanthin-V, Liriodenin and Chitranone are Hepcidin Antagonist In silico for Iron Deficiency Anemia

NASA Astrophysics Data System (ADS)

Yotriana, S.; Suselo, YH; Muthmainah; Indarto, D.

2018-03-01

Anemia is one of the greatest nutrition problem in the world that is commonly found in children, pregnant women and reproductive women. This disorder is predominantly caused by iron deficiency. Hepcidin, a hepatic hormone, regulates iron metabolism and high serum levels of this hormone are detected in patients with iron deficiency anemia (IDA). Anticalin is a sintetic compound which is able to interacts with hepcidin leading to inhibition of ferroportin-hepcidin binding complexes but its therapeutic effects are still under investigation. Indonesia has various herbal plants which are potentially developed to treat some human diseases. Therefore, the purpose of this study was to identify phytochemicals derived from Indonesian plants that is able to inhibit hepcidin-ferroportin interaction. A bioinformatics study with molecular docking method was used in this study. Three-dimensional structures of human hepcidin and anticalin were obtained from the Protein Data Bank (ID: 1M4F and 4QAE respectively). Because their molecular size was big, each molecule was cut into 2 parts of its binding sites. All phytochemicals structures were obtained from HerbalDB and PubChem NCBI database. Truncated anticalin/phytochemicals were molecularly docked with truncated hepcidin by using AutoDock Vina 1.1.2. and their interactions were visualized using PyMol 1.3. Truncated Anticalin had -4.6 and -4.2 kcal/mol binding affinity to truncated human hepcidin. Truncated anticalin 1 was bound to Cys13, Cys14, Arg16 and Ser17 residues in truncated hepcidin 1 while truncated anticalin 2 was at Cy23 and Lys24 residues in truncated hepcidin 2. Miraxanthine-V, Liriodenin and Chitranone had lower binding affinity (-4.8±0.77, -4.7±0.33 and -5.01±0.30 kcal/mol respectively) than that of anticalin and occupied binding sites as same as anticalin did. There are three phytochemicals that potentially become hepcidin antagonists in silico. In vitro assays are required for verification of the antagonist effect of these phytochemicals on iron metabolism.

An efficient and near linear scaling pair natural orbital based local coupled cluster method.

PubMed

Riplinger, Christoph; Neese, Frank

2013-01-21

In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 10(5)-10(6) relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy estimate based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calculations reported here featured >8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.

Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method.

PubMed

He, Xiaowei; Liang, Jimin; Wang, Xiaorui; Yu, Jingjing; Qu, Xiaochao; Wang, Xiaodong; Hou, Yanbin; Chen, Duofang; Liu, Fang; Tian, Jie

2010-11-22

In this paper, we present an incomplete variables truncated conjugate gradient (IVTCG) method for bioluminescence tomography (BLT). Considering the sparse characteristic of the light source and insufficient surface measurement in the BLT scenarios, we combine a sparseness-inducing (ℓ1 norm) regularization term with a quadratic error term in the IVTCG-based framework for solving the inverse problem. By limiting the number of variables updated at each iterative and combining a variable splitting strategy to find the search direction more efficiently, it obtains fast and stable source reconstruction, even without a priori information of the permissible source region and multispectral measurements. Numerical experiments on a mouse atlas validate the effectiveness of the method. In vivo mouse experimental results further indicate its potential for a practical BLT system.

Quantitative Evaluation of E1 Endoglucanase Recovery from Tobacco Leaves Using the Vacuum Infiltration-Centrifugation Method

PubMed Central

Kingsbury, Nathaniel J.; McDonald, Karen A.

2014-01-01

As a production platform for recombinant proteins, plant leaf tissue has many advantages, but commercialization of this technology has been hindered by high recovery and purification costs. Vacuum infiltration-centrifugation (VI-C) is a technique to obtain extracellularly-targeted products from the apoplast wash fluid (AWF). Because of its selective recovery of secreted proteins without homogenizing the whole tissue, VI-C can potentially reduce downstream production costs. Lab scale experiments were conducted to quantitatively evaluate the VI-C method and compared to homogenization techniques in terms of product purity, concentration, and other desirable characteristics. From agroinfiltrated Nicotiana benthamiana leaves, up to 81% of a truncated version of E1 endoglucanase from Acidothermus cellulolyticus was recovered with VI-C versus homogenate extraction, and average purity and concentration increases of 4.2-fold and 3.1-fold, respectively, were observed. Formulas were developed to predict recovery yields of secreted protein obtained by performing multiple rounds of VI-C on the same leaf tissue. From this, it was determined that three rounds of VI-C recovered 97% of the total active recombinant protein accessible to the VI-C procedure. The results suggest that AWF recovery is an efficient process that could reduce downstream processing steps and costs for plant-made recombinant proteins. PMID:24971334

Stochastic static fault slip inversion from geodetic data with non-negativity and bounds constraints

NASA Astrophysics Data System (ADS)

Nocquet, J.-M.

2018-04-01

Despite surface displacements observed by geodesy are linear combinations of slip at faults in an elastic medium, determining the spatial distribution of fault slip remains a ill-posed inverse problem. A widely used approach to circumvent the illness of the inversion is to add regularization constraints in terms of smoothing and/or damping so that the linear system becomes invertible. However, the choice of regularization parameters is often arbitrary, and sometimes leads to significantly different results. Furthermore, the resolution analysis is usually empirical and cannot be made independently of the regularization. The stochastic approach of inverse problems (Tarantola & Valette 1982; Tarantola 2005) provides a rigorous framework where the a priori information about the searched parameters is combined with the observations in order to derive posterior probabilities of the unkown parameters. Here, I investigate an approach where the prior probability density function (pdf) is a multivariate Gaussian function, with single truncation to impose positivity of slip or double truncation to impose positivity and upper bounds on slip for interseismic modeling. I show that the joint posterior pdf is similar to the linear untruncated Gaussian case and can be expressed as a Truncated Multi-Variate Normal (TMVN) distribution. The TMVN form can then be used to obtain semi-analytical formulas for the single, two-dimensional or n-dimensional marginal pdf. The semi-analytical formula involves the product of a Gaussian by an integral term that can be evaluated using recent developments in TMVN probabilities calculations (e.g. Genz & Bretz 2009). Posterior mean and covariance can also be efficiently derived. I show that the Maximum Posterior (MAP) can be obtained using a Non-Negative Least-Squares algorithm (Lawson & Hanson 1974) for the single truncated case or using the Bounded-Variable Least-Squares algorithm (Stark & Parker 1995) for the double truncated case. I show that the case of independent uniform priors can be approximated using TMVN. The numerical equivalence to Bayesian inversions using Monte Carlo Markov Chain (MCMC) sampling is shown for a synthetic example and a real case for interseismic modeling in Central Peru. The TMVN method overcomes several limitations of the Bayesian approach using MCMC sampling. First, the need of computer power is largely reduced. Second, unlike Bayesian MCMC based approach, marginal pdf, mean, variance or covariance are obtained independently one from each other. Third, the probability and cumulative density functions can be obtained with any density of points. Finally, determining the Maximum Posterior (MAP) is extremely fast.

Cortical dipole imaging using truncated total least squares considering transfer matrix error.

PubMed

Hori, Junichi; Takeuchi, Kosuke

2013-01-01

Cortical dipole imaging has been proposed as a method to visualize electroencephalogram in high spatial resolution. We investigated the inverse technique of cortical dipole imaging using a truncated total least squares (TTLS). The TTLS is a regularization technique to reduce the influence from both the measurement noise and the transfer matrix error caused by the head model distortion. The estimation of the regularization parameter was also investigated based on L-curve. The computer simulation suggested that the estimation accuracy was improved by the TTLS compared with Tikhonov regularization. The proposed method was applied to human experimental data of visual evoked potentials. We confirmed the TTLS provided the high spatial resolution of cortical dipole imaging.

Non-homologous end joining-mediated functional marker selection for DNA cloning in the yeast Kluyveromyces marxianus.

PubMed

Hoshida, Hisashi; Murakami, Nobutada; Suzuki, Ayako; Tamura, Ryoko; Asakawa, Jun; Abdel-Banat, Babiker M A; Nonklang, Sanom; Nakamura, Mikiko; Akada, Rinji

2014-01-01

The cloning of DNA fragments into vectors or host genomes has traditionally been performed using Escherichia coli with restriction enzymes and DNA ligase or homologous recombination-based reactions. We report here a novel DNA cloning method that does not require DNA end processing or homologous recombination, but that ensures highly accurate cloning. The method exploits the efficient non-homologous end-joining (NHEJ) activity of the yeast Kluyveromyces marxianus and consists of a novel functional marker selection system. First, to demonstrate the applicability of NHEJ to DNA cloning, a C-terminal-truncated non-functional ura3 selection marker and the truncated region were PCR-amplified separately, mixed and directly used for the transformation. URA3(+) transformants appeared on the selection plates, indicating that the two DNA fragments were correctly joined by NHEJ to generate a functional URA3 gene that had inserted into the yeast chromosome. To develop the cloning system, the shortest URA3 C-terminal encoding sequence that could restore the function of a truncated non-functional ura3 was determined by deletion analysis, and was included in the primers to amplify target DNAs for cloning. Transformation with PCR-amplified target DNAs and C-terminal truncated ura3 produced numerous transformant colonies, in which a functional URA3 gene was generated and was integrated into the chromosome with the target DNAs. Several K. marxianus circular plasmids with different selection markers were also developed for NHEJ-based cloning and recombinant DNA construction. The one-step DNA cloning method developed here is a relatively simple and reliable procedure among the DNA cloning systems developed to date. Copyright © 2013 John Wiley & Sons, Ltd.

Zero-truncated negative binomial - Erlang distribution

NASA Astrophysics Data System (ADS)

Bodhisuwan, Winai; Pudprommarat, Chookait; Bodhisuwan, Rujira; Saothayanun, Luckhana

2017-11-01

The zero-truncated negative binomial-Erlang distribution is introduced. It is developed from negative binomial-Erlang distribution. In this work, the probability mass function is derived and some properties are included. The parameters of the zero-truncated negative binomial-Erlang distribution are estimated by using the maximum likelihood estimation. Finally, the proposed distribution is applied to real data, the number of methamphetamine in the Bangkok, Thailand. Based on the results, it shows that the zero-truncated negative binomial-Erlang distribution provided a better fit than the zero-truncated Poisson, zero-truncated negative binomial, zero-truncated generalized negative-binomial and zero-truncated Poisson-Lindley distributions for this data.

A Short Isoform of Human Cytomegalovirus US3 Functions as a Dominant Negative Inhibitor of the Full-Length Form

PubMed Central

Shin, Jinwook; Park, Boyoun; Lee, Sungwook; Kim, Youngkyun; Biegalke, Bonita J.; Kang, Seongman; Ahn, Kwangseog

2006-01-01

Human cytomegalovirus encodes four unique short (US) region proteins, each of which is independently sufficient for causing the down-regulation of major histocompatibility complex (MHC) class I molecules on the cell surface. This down-regulation enables infected cells to evade recognition by cytotoxic T lymphocytes (CTLs) but makes them vulnerable to lysis by natural killer (NK) cells, which lyse those cells that lack MHC class I molecules. The 22-kDa US3 glycoprotein is able to down-regulate the surface expression of MHC class I molecules by dual mechanisms: direct endoplasmic reticulum retention by physical association and/or tapasin inhibition. The alternative splicing of the US3 gene generates two additional products, including 17-kDa and 3.5-kDa truncated isoforms; however, the functional significance of these isoforms during viral infection is unknown. Here, we describe a novel mode of self-regulation of US3 function that uses the endogenously produced truncated isoform. The truncated isoform itself neither binds to MHC class I molecules nor prevents the full-length US3 from interacting with MHC class I molecules. Instead, the truncated isoform associates with tapasin and competes with full-length US3 for binding to tapasin; thus, it suppresses the action of US3 that causes the disruption of the function of tapasin. Our results indicate that the truncated isoform of the US3 locus acts as a dominant negative regulator of full-length US3 activity. These data reflect the manner in which the virus has developed temporal survival strategies during viral infection against immune surveillance involving both CTLs and NK cells. PMID:16699020

A short isoform of human cytomegalovirus US3 functions as a dominant negative inhibitor of the full-length form.

PubMed

Shin, Jinwook; Park, Boyoun; Lee, Sungwook; Kim, Youngkyun; Biegalke, Bonita J; Kang, Seongman; Ahn, Kwangseog

2006-06-01

Human cytomegalovirus encodes four unique short (US) region proteins, each of which is independently sufficient for causing the down-regulation of major histocompatibility complex (MHC) class I molecules on the cell surface. This down-regulation enables infected cells to evade recognition by cytotoxic T lymphocytes (CTLs) but makes them vulnerable to lysis by natural killer (NK) cells, which lyse those cells that lack MHC class I molecules. The 22-kDa US3 glycoprotein is able to down-regulate the surface expression of MHC class I molecules by dual mechanisms: direct endoplasmic reticulum retention by physical association and/or tapasin inhibition. The alternative splicing of the US3 gene generates two additional products, including 17-kDa and 3.5-kDa truncated isoforms; however, the functional significance of these isoforms during viral infection is unknown. Here, we describe a novel mode of self-regulation of US3 function that uses the endogenously produced truncated isoform. The truncated isoform itself neither binds to MHC class I molecules nor prevents the full-length US3 from interacting with MHC class I molecules. Instead, the truncated isoform associates with tapasin and competes with full-length US3 for binding to tapasin; thus, it suppresses the action of US3 that causes the disruption of the function of tapasin. Our results indicate that the truncated isoform of the US3 locus acts as a dominant negative regulator of full-length US3 activity. These data reflect the manner in which the virus has developed temporal survival strategies during viral infection against immune surveillance involving both CTLs and NK cells.

The bZIP Transcription Factor Fgap1 Mediates Oxidative Stress Response and Trichothecene Biosynthesis But Not Virulence in Fusarium graminearum

PubMed Central

Montibus, Mathilde; Ducos, Christine; Bonnin-Verdal, Marie-Noelle; Bormann, Jorg; Ponts, Nadia; Richard-Forget, Florence; Barreau, Christian

2013-01-01

Redox sensing is of primary importance for fungi to cope with oxidant compounds found in their environment. Plant pathogens are particularly subject to the oxidative burst during the primary steps of infection. In the budding yeast Saccharomyces cerevisiae, it is the transcription factor Yap1 that mediates the response to oxidative stress via activation of genes coding for detoxification enzymes. In the cereal pathogen Fusarium graminearum, Fgap1 a homologue of Yap1 was identified and its role was investigated. During infection, this pathogen produces mycotoxins belonging to the trichothecenes family that accumulate in the grains. The global regulation of toxin biosynthesis is not completely understood. However, it is now clearly established that an oxidative stress activates the production of toxins by F. graminearum. The involvement of Fgap1 in this activation was investigated. A deleted mutant and a strain expressing a truncated constitutive form of Fgap1 were constructed. None of the mutants was affected in pathogenicity. The deleted mutant showed higher level of trichothecenes production associated with overexpression of Tri genes. Moreover activation of toxin accumulation in response to oxidative stress was no longer observed. Regarding the mutant with the truncated constitutive form of Fgap1, toxin production was strongly reduced. Expression of oxidative stress response genes was not activated in the deleted mutant and expression of the gene encoding the mitochondrial superoxide dismutase MnSOD1 was up-regulated in the mutant with the truncated constitutive form of Fgap1. Our results demonstrate that Fgap1 plays a key role in the link between oxidative stress response and F. graminearum secondary metabolism. PMID:24349499

Patchwork sampling of stochastic differential equations

NASA Astrophysics Data System (ADS)

Kürsten, Rüdiger; Behn, Ulrich

2016-03-01

We propose a method to sample stationary properties of solutions of stochastic differential equations, which is accurate and efficient if there are rarely visited regions or rare transitions between distinct regions of the state space. The method is based on a complete, nonoverlapping partition of the state space into patches on which the stochastic process is ergodic. On each of these patches we run simulations of the process strictly truncated to the corresponding patch, which allows effective simulations also in rarely visited regions. The correct weight for each patch is obtained by counting the attempted transitions between all different patches. The results are patchworked to cover the whole state space. We extend the concept of truncated Markov chains which is originally formulated for processes which obey detailed balance to processes not fulfilling detailed balance. The method is illustrated by three examples, describing the one-dimensional diffusion of an overdamped particle in a double-well potential, a system of many globally coupled overdamped particles in double-well potentials subject to additive Gaussian white noise, and the overdamped motion of a particle on the circle in a periodic potential subject to a deterministic drift and additive noise. In an appendix we explain how other well-known Markov chain Monte Carlo algorithms can be related to truncated Markov chains.

Effects of modal truncation and condensation methods on the Frequency Response Function of a stage reducer connected by rigid coupling to a planetary gear system

NASA Astrophysics Data System (ADS)

Bouslema, Marwa; Frikha, Ahmed; Abdennadhar, Moez; Fakhfakh, Tahar; Nasri, Rachid; Haddar, Mohamed

2017-12-01

The present paper is aimed at the application of a substructure methodology, based on the Frequency Response Function (FRF) simulation technique, to analyze the vibration of a stage reducer connected by a rigid coupling to a planetary gear system. The computation of the vibration response was achieved using the FRF-based substructuring method. First of all, the two subsystems were analyzed separately and their FRF were obtained. Then the coupled model was analyzed indirectly using the substructuring technique. A comparison between the full system response and the coupled model response using the FRF substructuring was investigated to validate the coupling method. Furthermore, a parametric study of the effect of the shaft coupling stiffness on the FRF was discussed and the effects of modal truncation and condensation methods on the FRF of subsystems were analyzed.

Multibody model reduction by component mode synthesis and component cost analysis

NASA Technical Reports Server (NTRS)

Spanos, J. T.; Mingori, D. L.

1990-01-01

The classical assumed-modes method is widely used in modeling the dynamics of flexible multibody systems. According to the method, the elastic deformation of each component in the system is expanded in a series of spatial and temporal functions known as modes and modal coordinates, respectively. This paper focuses on the selection of component modes used in the assumed-modes expansion. A two-stage component modal reduction method is proposed combining Component Mode Synthesis (CMS) with Component Cost Analysis (CCA). First, each component model is truncated such that the contribution of the high frequency subsystem to the static response is preserved. Second, a new CMS procedure is employed to assemble the system model and CCA is used to further truncate component modes in accordance with their contribution to a quadratic cost function of the system output. The proposed method is demonstrated with a simple example of a flexible two-body system.

Comparison of the iterated equation of motion approach and the density matrix formalism for the quantum Rabi model

NASA Astrophysics Data System (ADS)

Kalthoff, Mona; Keim, Frederik; Krull, Holger; Uhrig, Götz S.

2017-05-01

The density matrix formalism and the equation of motion approach are two semi-analytical methods that can be used to compute the non-equilibrium dynamics of correlated systems. While for a bilinear Hamiltonian both formalisms yield the exact result, for any non-bilinear Hamiltonian a truncation is necessary. Due to the fact that the commonly used truncation schemes differ for these two methods, the accuracy of the obtained results depends significantly on the chosen approach. In this paper, both formalisms are applied to the quantum Rabi model. This allows us to compare the approximate results and the exact dynamics of the system and enables us to discuss the accuracy of the approximations as well as the advantages and the disadvantages of both methods. It is shown to which extent the results fulfill physical requirements for the observables and which properties of the methods lead to unphysical results.

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

PubMed Central

Easton, Douglas F; Lesueur, Fabienne; Decker, Brennan; Michailidou, Kyriaki; Li, Jun; Allen, Jamie; Luccarini, Craig; Pooley, Karen A; Shah, Mitul; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Ahmad, Jamil; Thompson, Ella R; Damiola, Francesca; Pertesi, Maroulio; Voegele, Catherine; Mebirouk, Noura; Robinot, Nivonirina; Durand, Geoffroy; Forey, Nathalie; Luben, Robert N; Ahmed, Shahana; Aittomäki, Kristiina; Anton-Culver, Hoda; Arndt, Volker; Baynes, Caroline; Beckman, Matthias W; Benitez, Javier; Van Den Berg, David; Blot, William J; Bogdanova, Natalia V; Bojesen, Stig E; Brenner, Hermann; Chang-Claude, Jenny; Chia, Kee Seng; Choi, Ji-Yeob; Conroy, Don M; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Eriksson, Mikael; Fasching, Peter A; Figueroa, Jonine; Flyger, Henrik; Fostira, Florentia; García-Closas, Montserrat; Giles, Graham G; Glendon, Gord; González-Neira, Anna; Guénel, Pascal; Haiman, Christopher A; Hall, Per; Hart, Steven N; Hartman, Mikael; Hooning, Maartje J; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; James, Paul A; John, Esther M; Johnson, Nichola; Jones, Michael; Kabisch, Maria; Kang, Daehee; Kosma, Veli-Matti; Kristensen, Vessela; Lambrechts, Diether; Li, Na; Lindblom, Annika; Long, Jirong; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Matsuo, Keitaro; Meindl, Alfons; Mitchell, Gillian; Muir, Kenneth; Nevelsteen, Ines; van den Ouweland, Ans; Peterlongo, Paolo; Phuah, Sze Yee; Pylkäs, Katri; Rowley, Simone M; Sangrajrang, Suleeporn; Schmutzler, Rita K; Shen, Chen-Yang; Shu, Xiao-Ou; Southey, Melissa C; Surowy, Harald; Swerdlow, Anthony; Teo, Soo H; Tollenaar, Rob A E M; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; Vachon, Celine; Verhoef, Senno; Wong-Brown, Michelle; Zheng, Wei; Zheng, Ying; Nevanlinna, Heli; Scott, Rodney J; Andrulis, Irene L; Wu, Anna H; Hopper, John L; Couch, Fergus J; Winqvist, Robert; Burwinkel, Barbara; Sawyer, Elinor J; Schmidt, Marjanka K; Rudolph, Anja; Dörk, Thilo; Brauch, Hiltrud; Hamann, Ute; Neuhausen, Susan L; Milne, Roger L; Fletcher, Olivia; Pharoah, Paul D P; Campbell, Ian G; Dunning, Alison M; Le Calvez-Kelm, Florence; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia

2016-01-01

Background BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. Methods We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. Results The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). Conclusions These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels. PMID:26921362

N-terminus of Cardiac Myosin Essential Light Chain Modulates Myosin Step-Size

PubMed Central

Wang, Yihua; Ajtai, Katalin; Kazmierczak, Katarzyna; Szczesna-Cordary, Danuta; Burghardt, Thomas P.

2016-01-01

Muscle myosin cyclically hydrolyzes ATP to translate actin. Ventricular cardiac myosin (βmys) moves actin with three distinct unitary step-sizes resulting from its lever-arm rotation and with step-frequencies that are modulated in a myosin regulation mechanism. The lever-arm associated essential light chain (vELC) binds actin by its 43 residue N-terminal extension. Unitary steps were proposed to involve the vELC N-terminal extension with the 8 nm step engaging the vELC/actin bond facilitating an extra ~19 degrees of lever-arm rotation while the predominant 5 nm step forgoes vELC/actin binding. A minor 3 nm step is the unlikely conversion of the completed 5 to the 8 nm step. This hypothesis was tested using a 17 residue N-terminal truncated vELC in porcine βmys (Δ17βmys) and a 43 residue N-terminal truncated human vELC expressed in transgenic mouse heart (Δ43αmys). Step-size and step-frequency were measured using the Qdot motility assay. Both Δ17βmys and Δ43αmys had significantly increased 5 nm step-frequency and coincident loss in the 8 nm step-frequency compared to native proteins suggesting the vELC/actin interaction drives step-size preference. Step-size and step-frequency probability densities depend on the relative fraction of truncated vELC and relate linearly to pure myosin species concentrations in a mixture containing native vELC homodimer, two truncated vELCs in the modified homodimer, and one native and one truncated vELC in the heterodimer. Step-size and step-frequency, measured for native homodimer and at two or more known relative fractions of truncated vELC, are surmised for each pure species by using a new analytical method. PMID:26671638

Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks

PubMed Central

Decker, Brennan; Allen, Jamie; Luccarini, Craig; Pooley, Karen A; Shah, Mitul; Bolla, Manjeet K; Wang, Qin; Ahmed, Shahana; Baynes, Caroline; Conroy, Don M; Brown, Judith; Luben, Robert; Ostrander, Elaine A; Pharoah, Paul DP; Dunning, Alison M; Easton, Douglas F

2017-01-01

Background Breast cancer (BC) is the most common malignancy in women and has a major heritable component. The risks associated with most rare susceptibility variants are not well estimated. To better characterise the contribution of variants in ATM, CHEK2, PALB2 and XRCC2, we sequenced their coding regions in 13 087 BC cases and 5488 controls from East Anglia, UK. Methods Gene coding regions were enriched via PCR, sequenced, variant called and filtered for quality. ORs for BC risk were estimated separately for carriers of truncating variants and of rare missense variants, which were further subdivided by functional domain and pathogenicity as predicted by four in silico algorithms. Results Truncating variants in PALB2 (OR=4.69, 95% CI 2.27 to 9.68), ATM (OR=3.26; 95% CI 1.82 to 6.46) and CHEK2 (OR=3.11; 95% CI 2.15 to 4.69), but not XRCC2 (OR=0.94; 95% CI 0.26 to 4.19) were associated with increased BC risk. Truncating variants in ATM and CHEK2 were more strongly associated with risk of oestrogen receptor (ER)-positive than ER-negative disease, while those in PALB2 were associated with similar risks for both subtypes. There was also some evidence that missense variants in ATM, CHEK2 and PALB2 may contribute to BC risk, but larger studies are necessary to quantify the magnitude of this effect. Conclusions Truncating variants in PALB2 are associated with a higher risk of BC than those in ATM or CHEK2. A substantial risk of BC due to truncating XRCC2 variants can be excluded. PMID:28779002

Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome.

PubMed

Gripp, Karen W; Robbins, Katherine M; Sobreira, Nara L; Witmer, P Dane; Bird, Lynne M; Avela, Kristiina; Makitie, Outi; Alves, Daniela; Hogue, Jacob S; Zackai, Elaine H; Doheny, Kimberly F; Stabley, Deborah L; Sol-Church, Katia

2015-02-01

Lateral meningocele syndrome (LMS, OMIM%130720), also known as Lehman syndrome, is a very rare skeletal disorder with facial anomalies, hypotonia and meningocele-related neurologic dysfunction. The characteristic lateral meningoceles represent the severe end of the dural ectasia spectrum and are typically most severe in the lower spine. Facial features of LMS include hypertelorism and telecanthus, high arched eyebrows, ptosis, midfacial hypoplasia, micrognathia, high and narrow palate, low-set ears and a hypotonic appearance. Hyperextensibility, hernias and scoliosis reflect a connective tissue abnormality, and aortic dilation, a high-pitched nasal voice, wormian bones and osteolysis may be present. Lateral meningocele syndrome has phenotypic overlap with Hajdu-Cheney syndrome. We performed exome resequencing in five unrelated individuals with LMS and identified heterozygous truncating NOTCH3 mutations. In an additional unrelated individual Sanger sequencing revealed a deleterious variant in the same exon 33. In total, five novel de novo NOTCH3 mutations were identified in six unrelated patients. One had a 26 bp deletion (c.6461_6486del, p.G2154fsTer78), two carried the same single base pair insertion (c.6692_93insC, p.P2231fsTer11), and three individuals had a nonsense point mutation at c.6247A > T (pK2083*), c.6663C > G (p.Y2221*) or c.6732C > A, (p.Y2244*). All mutations cluster into the last coding exon, resulting in premature termination of the protein and truncation of the negative regulatory proline-glutamate-serine-threonine rich PEST domain. Our results suggest that mutant mRNA products escape nonsense mediated decay. The truncated NOTCH3 may cause gain-of-function through decreased clearance of the active intracellular product, resembling NOTCH2 mutations in the clinically related Hajdu-Cheney syndrome and contrasting the NOTCH3 missense mutations causing CADASIL. © 2014 Wiley Periodicals, Inc.

A new CZE method for profiling human serum albumin and its related forms to assess the quality of biopharmaceuticals.

PubMed

Alahmad, Youssef; Tran, Nguyet Thuy; Le Potier, Isabelle; Forest, Eric; Jorieux, Sylvie; Taverna, Myriam

2011-01-01

We present a new CZE method, which uses a polyethylene oxide-coated capillary to separate native HSA from more than five of its structural variants. These variants include oxidized, truncated, and cysteinylated forms of HSA which can all be found in biopharmaceutical products. Both CE and MS confirmed the high degree of heterogeneity of HSA preparations. Recovery studies demonstrated that adsorption of HSA on the capillary was significantly reduced under the conditions we developed, which led to a satisfactory repeatability (RSD for migration times and relative peak areas were less than 0.2 and 7.0%, respectively). Assignment of the main peaks was attempted using in vitro degraded/stressed HSA. We used our method to test batch-to-batch comparability and detected slight quantitative differences in the proportion of native HSA in batches produced from different fractionation methods. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

FAST TRACK COMMUNICATION: Ground-state fidelity and entanglement entropy for the quantum three-state Potts model in one spatial dimension

NASA Astrophysics Data System (ADS)

Dai, Yan-Wei; Hu, Bing-Quan; Zhao, Jian-Hui; Zhou, Huan-Qiang

2010-09-01

The ground-state fidelity per lattice site is computed for the quantum three-state Potts model in a transverse magnetic field on an infinite-size lattice in one spatial dimension in terms of the infinite matrix product state algorithm. It is found that, on the one hand, a pinch point is identified on the fidelity surface around the critical point, and on the other hand, the ground-state fidelity per lattice site exhibits bifurcations at pseudo critical points for different values of the truncation dimension, which in turn approach the critical point as the truncation dimension becomes large. This implies that the ground-state fidelity per lattice site enables us to capture spontaneous symmetry breaking when the control parameter crosses the critical value. In addition, a finite-entanglement scaling of the von Neumann entropy is performed with respect to the truncation dimension, resulting in a precise determination of the central charge at the critical point. Finally, we compute the transverse magnetization, from which the critical exponent β is extracted from the numerical data.

Tree Tensor Network State with Variable Tensor Order: An Efficient Multireference Method for Strongly Correlated Systems

PubMed Central

2015-01-01

We study the tree-tensor-network-state (TTNS) method with variable tensor orders for quantum chemistry. TTNS is a variational method to efficiently approximate complete active space (CAS) configuration interaction (CI) wave functions in a tensor product form. TTNS can be considered as a higher order generalization of the matrix product state (MPS) method. The MPS wave function is formulated as products of matrices in a multiparticle basis spanning a truncated Hilbert space of the original CAS-CI problem. These matrices belong to active orbitals organized in a one-dimensional array, while tensors in TTNS are defined upon a tree-like arrangement of the same orbitals. The tree-structure is advantageous since the distance between two arbitrary orbitals in the tree scales only logarithmically with the number of orbitals N, whereas the scaling is linear in the MPS array. It is found to be beneficial from the computational costs point of view to keep strongly correlated orbitals in close vicinity in both arrangements; therefore, the TTNS ansatz is better suited for multireference problems with numerous highly correlated orbitals. To exploit the advantages of TTNS a novel algorithm is designed to optimize the tree tensor network topology based on quantum information theory and entanglement. The superior performance of the TTNS method is illustrated on the ionic-neutral avoided crossing of LiF. It is also shown that the avoided crossing of LiF can be localized using only ground state properties, namely one-orbital entanglement. PMID:25844072

Patient-bounded extrapolation using low-dose priors for volume-of-interest imaging in C-arm CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Y.; Maier, A.; Berger, M.

2015-04-15

Purpose: Three-dimensional (3D) volume-of-interest (VOI) imaging with C-arm systems provides anatomical information in a predefined 3D target region at a considerably low x-ray dose. However, VOI imaging involves laterally truncated projections from which conventional reconstruction algorithms generally yield images with severe truncation artifacts. Heuristic based extrapolation methods, e.g., water cylinder extrapolation, typically rely on techniques that complete the truncated data by means of a continuity assumption and thus appear to be ad-hoc. It is our goal to improve the image quality of VOI imaging by exploiting existing patient-specific prior information in the workflow. Methods: A necessary initial step prior tomore » a 3D acquisition is to isocenter the patient with respect to the target to be scanned. To this end, low-dose fluoroscopic x-ray acquisitions are usually applied from anterior–posterior (AP) and medio-lateral (ML) views. Based on this, the patient is isocentered by repositioning the table. In this work, we present a patient-bounded extrapolation method that makes use of these noncollimated fluoroscopic images to improve image quality in 3D VOI reconstruction. The algorithm first extracts the 2D patient contours from the noncollimated AP and ML fluoroscopic images. These 2D contours are then combined to estimate a volumetric model of the patient. Forward-projecting the shape of the model at the eventually acquired C-arm rotation views gives the patient boundary information in the projection domain. In this manner, we are in the position to substantially improve image quality by enforcing the extrapolated line profiles to end at the known patient boundaries, derived from the 3D shape model estimate. Results: The proposed method was evaluated on eight clinical datasets with different degrees of truncation. The proposed algorithm achieved a relative root mean square error (rRMSE) of about 1.0% with respect to the reference reconstruction on nontruncated data, even in the presence of severe truncation, compared to a rRMSE of 8.0% when applying a state-of-the-art heuristic extrapolation technique. Conclusions: The method we proposed in this paper leads to a major improvement in image quality for 3D C-arm based VOI imaging. It involves no additional radiation when using fluoroscopic images that are acquired during the patient isocentering process. The model estimation can be readily integrated into the existing interventional workflow without additional hardware.« less

Phenylalanine 445 within oxidosqualene-lanosterol cyclase from Saccharomyces cerevisiae influences C-Ring cyclization and deprotonation reactions.

PubMed

Wu, Tung-Kung; Liu, Yuan-Ting; Chiu, Feng-Hsuan; Chang, Cheng-Hsiang

2006-10-12

[reaction: see text] We describe the Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase Phe445 site-saturated mutants that generate truncated tricyclic and altered deprotonation product profiles. Among these mutants, only polar side-chain group substitutions genetically complemented yeast viability and produced spatially related product diversity, supporting the Johnson model that cation-pi interactions between a carbocationic intermediate and an enzyme can be replaced by an electrostatic or polar side chain to stabilize the cationic intermediate, but with product differentiation.

Improving the precision of our ecosystem calipers: a modified morphometric technique for estimating marine mammal mass and body composition.

PubMed

Shero, Michelle R; Pearson, Linnea E; Costa, Daniel P; Burns, Jennifer M

2014-01-01

Mass and body composition are indices of overall animal health and energetic balance and are often used as indicators of resource availability in the environment. This study used morphometric models and isotopic dilution techniques, two commonly used methods in the marine mammal field, to assess body composition of Weddell seals (Leptonychotes weddellii, N = 111). Findings indicated that traditional morphometric models that use a series of circular, truncated cones to calculate marine mammal blubber volume and mass overestimated the animal's measured body mass by 26.9±1.5% SE. However, we developed a new morphometric model that uses elliptical truncated cones, and estimates mass with only -2.8±1.7% error (N = 10). Because this elliptical truncated cone model can estimate body mass without the need for additional correction factors, it has the potential to be a broadly applicable method in marine mammal species. While using elliptical truncated cones yielded significantly smaller blubber mass estimates than circular cones (10.2±0.8% difference; or 3.5±0.3% total body mass), both truncated cone models significantly underestimated total body lipid content as compared to isotopic dilution results, suggesting that animals have substantial internal lipid stores (N = 76). Multiple linear regressions were used to determine the minimum number of morphometric measurements needed to reliably estimate animal mass and body composition so that future animal handling times could be reduced. Reduced models estimated body mass and lipid mass with reasonable accuracy using fewer than five morphometric measurements (root-mean-square-error: 4.91% for body mass, 10.90% for lipid mass, and 10.43% for % lipid). This indicates that when test datasets are available to create calibration coefficients, regression models also offer a way to improve body mass and condition estimates in situations where animal handling times must be short and efficient.

Ectopic expression of syncollin in INS-1 beta-cells sorts it into granules and impairs regulated secretion.

PubMed

Li, Jingsong; Luo, Ruihua; Hooi, Shing Chuan; Ruga, Pilar; Zhang, Jiping; Meda, Paolo; Li, GuoDong

2005-03-22

Syncollin was first demonstrated to be a protein capable of affecting granule fusion in a cell-free system, but later studies revealed its luminal localization in zymogen granules. To determine its possible role in exocytosis in the intact cell, syncollin and a truncated form of the protein (lacking the N-terminal hydrophobic domain) were stably transfected in insulin-secreting INS-1 cells since these well-studied exocytotic cells appear not to express the protein per se. Studies by subcellular fractionation analysis, double immunofluorescence staining, and electron microscopy examination revealed that transfection of syncollin produced strong signals in the insulin secretory granules, whereas the product from transfecting the truncated syncollin was predominantly associated with the Golgi apparatus and to a lesser degree with the endoplasmic reticulum. The expressed products were associated with membranes and not the soluble fractions in either cytoplasm or the lumens of organelles. Importantly, insulin release stimulated by various secretagogues was severely impaired in cells expressing syncollin, but not affected by expressing truncated syncollin. Transfection of syncollin appeared not to impede insulin biosynthesis and processing, since cellular contents of proinsulin and insulin and the number of secretory granules were not altered. In addition, the early signals (membrane depolarization and Ca(2+) responses) for regulated insulin secretion were unaffected. These findings indicate that syncollin may be targeted to insulin secretory granules specifically and impair regulated secretion at a distal stage.

A new biotype of Fusarium oxysporum f. sp. lycopersici race 2 emerged by a transposon-driven mutation of avirulence gene AVR1.

PubMed

Kashiwa, Takeshi; Suzuki, Tatsuya; Sato, Akira; Akai, Kotaro; Teraoka, Tohru; Komatsu, Ken; Arie, Tsutomu

2016-07-01

Emergence of races in Fusarium oxysporum f. sp. lycopersici (Fol) is caused by loss or mutation of at least one avirulence (AVR) gene. The product of AVR1 is a small protein (Avr1) secreted by Fol in tomato xylem sap during infection. This protein triggers Fol race 1 specific resistance (I) in tomato, indicating that AVR1 is an AVR gene. Deletion of AVR1 in race 1 resulted in the emergence of race 2, and an additional mutation in AVR2 generated race 3. Previously, we reported a new biotype of race 3, KoChi-1, in which AVR1 was truncated by a transposon Hormin, which suggested a new route to evolution of races in Fol However, to date no race 2 isolate carrying Hormin-truncated AVR1 has been reported. In this report, we describe such isolates, represented by Chiba-5, in which Hormin insertion occurred in AVR1 at a position different from that in KoChi-1. AVR1 truncation in both isolates resulted in production of defective Avr1 proteins. Chiba-5 and KoChi-1 belong to different phylogenetic clades, A1 and A2, respectively, suggesting that insertion of Hormin in AVR1 in Chiba-5 and KoChi-1 occurred as independent evolutionary events. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Renormalization group contraction of tensor networks in three dimensions

NASA Astrophysics Data System (ADS)

García-Sáez, Artur; Latorre, José I.

2013-02-01

We present a new strategy for contracting tensor networks in arbitrary geometries. This method is designed to follow as strictly as possible the renormalization group philosophy, by first contracting tensors in an exact way and, then, performing a controlled truncation of the resulting tensor. We benchmark this approximation procedure in two dimensions against an exact contraction. We then apply the same idea to a three-dimensional quantum system. The underlying rational for emphasizing the exact coarse graining renormalization group step prior to truncation is related to monogamy of entanglement.

Compensating for velocity truncation during subaperture polishing by controllable and time-variant tool influence functions.

PubMed

Dong, Zhichao; Cheng, Haobo; Tam, Hon-Yuen

2015-02-10

The velocity-varying regime used in deterministic subaperture polishing employs a time-invariant tool influence function (TIF) to figure localized surface errors by varying the transverse velocities of polishing tools. Desired transverse velocities have to be truncated if they exceed the maximal velocity of computer numerical control (CNC) machines, which induces excessive material removal and reduces figuring efficiency (FE). A time-variant (TV) TIF regime is presented, in which a TIF serves as a variable to compensate for excessive material removal when the transverse velocities are truncated. Compared with other methods, the TV-TIF regime exhibits better performance in terms of convergence rate, FE, and versatility; its operability can also be strengthened by a TIF library. Comparative experiments were conducted on a magnetorheological finishing machine to validate the effectiveness of the TV-TIF regime. Without a TV-TIF, the tool made an unwished dent (depth of 76 nm) at the center because of the velocity truncation problem. Through compensation with a TV-TIF, the dent was completely removed by the second figuring process, and a TV-TIF improved the FE from 0.029 to 0.066  mm(3)/h.

Tuning TiO2 nanoparticle morphology in graphene-TiO2 hybrids by graphene surface modification

NASA Astrophysics Data System (ADS)

Sordello, Fabrizio; Zeb, Gul; Hu, Kaiwen; Calza, Paola; Minero, Claudio; Szkopek, Thomas; Cerruti, Marta

2014-05-01

We report the hydrothermal synthesis of graphene (GNP)-TiO2 nanoparticle (NP) hybrids using COOH and NH2 functionalized GNP as a shape controller. Anatase was the only TiO2 crystalline phase nucleated on the functionalized GNP, whereas traces of rutile were detected on unfunctionalized GNP. X-Ray Photoelectron spectroscopy (XPS) showed C-Ti bonds on all hybrids, thus confirming heterogeneous nucleation. GNP functionalization induced the nucleation of TiO2 NPs with specific shapes and crystalline facets exposed. COOH functionalization directed the synthesis of anatase truncated bipyramids, bonded to graphene sheets via the {101} facets, while NH2 functionalization induced the formation of belted truncated bipyramids, bonded to graphene via the {100} facets. Belted truncated bipyramids formed on unfunctionalized GNP too, however the NPs were more irregular and rounded. These effects were ascribed to pH variations in the proximity of the functionalized GNP sheets, due to the high density of COOH or NH2 groups. Because of the different reactivity of anatase {100} and {101} crystalline facets, we hypothesize that the hybrid materials will behave differently as photocatalysts, and that the COOH-GNP-TiO2 hybrids will be better photocatalysts for water splitting and H2 production.We report the hydrothermal synthesis of graphene (GNP)-TiO2 nanoparticle (NP) hybrids using COOH and NH2 functionalized GNP as a shape controller. Anatase was the only TiO2 crystalline phase nucleated on the functionalized GNP, whereas traces of rutile were detected on unfunctionalized GNP. X-Ray Photoelectron spectroscopy (XPS) showed C-Ti bonds on all hybrids, thus confirming heterogeneous nucleation. GNP functionalization induced the nucleation of TiO2 NPs with specific shapes and crystalline facets exposed. COOH functionalization directed the synthesis of anatase truncated bipyramids, bonded to graphene sheets via the {101} facets, while NH2 functionalization induced the formation of belted truncated bipyramids, bonded to graphene via the {100} facets. Belted truncated bipyramids formed on unfunctionalized GNP too, however the NPs were more irregular and rounded. These effects were ascribed to pH variations in the proximity of the functionalized GNP sheets, due to the high density of COOH or NH2 groups. Because of the different reactivity of anatase {100} and {101} crystalline facets, we hypothesize that the hybrid materials will behave differently as photocatalysts, and that the COOH-GNP-TiO2 hybrids will be better photocatalysts for water splitting and H2 production. Electronic supplementary information (ESI) available: Statistical analysis of the D : G intensity ratio, additional XPS analysis and TEM micrographs. See DOI: 10.1039/c4nr01322k

An improved method for purification of recombinant truncated heme oxygenase-1 by expanded bed adsorption and gel filtration.

PubMed

Hu, Hong-Bo; Wang, Wei; Han, Ling; Zhou, Wen-Pu; Zhang, Xue-Hong

2007-03-01

Recombinant truncated human heme oxygenase-1 (hHO-1) expressed in Escherichia coli was efficiently separated and purified from feedstock by DEAE-ion exchange expanded bed adsorption. Protocol optimization of hHO-1 on DEAE adsorbent resulted in adsorption in 0 M NaCl and elution in 150 mM NaCl at a pH of 8.5. The active enzyme fractions separated from the expanded bed column were further purified by a Superdex 75 gel filtration step. The specific hHO-1 activity increased from 0.82 +/- 0.05 to 24.8 +/- 1.8 U/mg during the whole purification steps. The recovery and purification factor of truncated hHO-1 of the whole purification were 72.7 +/- 4.7 and 30.2 +/- 2.3%, respectively. This purification process can decrease the demand on the preparation of feedstock and simplify the purification process.

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.

PubMed

Beck, David A C; Armen, Roger S; Daggett, Valerie

2005-01-18

The correct treatment of van der Waals and electrostatic nonbonded interactions in molecular force fields is essential for performing realistic molecular dynamics (MD) simulations of solvated polypeptides. The most computationally tractable treatment of nonbonded interactions in MD utilizes a spherical distance cutoff (typically, 8-12 A) to reduce the number of pairwise interactions. In this work, we assess three spherical atom-based cutoff approaches for use with all-atom explicit solvent MD: abrupt truncation, a CHARMM-style electrostatic shift truncation, and our own force-shifted truncation. The chosen system for this study is an end-capped 17-residue alanine-based alpha-helical peptide, selected because of its use in previous computational and experimental studies. We compare the time-averaged helical content calculated from these MD trajectories with experiment. We also examine the effect of varying the cutoff treatment and distance on energy conservation. We find that the abrupt truncation approach is pathological in its inability to conserve energy. The CHARMM-style shift truncation performs quite well but suffers from energetic instability. On the other hand, the force-shifted spherical cutoff method conserves energy, correctly predicts the experimental helical content, and shows convergence in simulation statistics as the cutoff is increased. This work demonstrates that by using proper and rigorous techniques, it is possible to correctly model polypeptide dynamics in solution with a spherical cutoff. The inherent computational advantage of spherical cutoffs over Ewald summation (and related) techniques is essential in accessing longer MD time scales.

Genetic and phenotypic analysis of daily Israeli Holstein milk, fat, and protein production as determined by a real-time milk analyzer.

PubMed

Weller, J I; Ezra, E

2016-12-01

The objective was to test the hypothesis that more frequent but less accurately analyzed milk components may give a more representative measure of a cow's total lactation production. Daily records for milk production and fat and protein concentration collected by the AfiLab recording system (Afimilk, Kibbutz Afikim, Israel) from January 2014 to January 2016 from 47 large kibbutz (communal) herds distributed throughout Israel with a total of 37,486 Israeli Holstein cows were compared with the same statistics derived from monthly test day records derived by Bentley and Foss milk analyzers at the central laboratory of the Israel Cattle Breeders Association. The lactation means for all traits were quite similar for the 2 methods in both parities, except for fat production, which was lower for the daily records. This finding corresponded to fat lactation curves, which showed that daily results were lower with low days in milk (DIM) but almost equal to the monthly results after 125 DIM. Relative to monthly records, daily records overestimated protein percentage before 150 DIM and underestimated protein percentage in the second half of the lactation. The standard deviation for first- and second-parity daily records scored by the monthly and daily system were least similar for fat percentage, but even for this trait the difference was no more than 0.1 percentage points. The standard deviations for complete lactation production were slightly lower for the daily results for all traits but protein production. First-parity heritabilities were higher for lactations computed from daily records for all traits except for protein percentage, but differences were not significant. For daily records, coefficients of determination to predict future milk, fat, and protein lactation production from truncated lactations were greatest and root mean squared errors were least if the mean production from the last 2 weeks before the truncation date was used to estimate future production. Daily first-parity partial lactations for milk, fat, and protein production with <150 DIM predicted future lactation more accurately than corresponding monthly partial lactations. With only 30 DIM, genetic correlations between predicted and actual lactations ranged from 0.73 to 0.79 for milk, fat, and protein production. Real-time daily recording of fat and protein concentration by the daily recording system may be preferable to monthly analysis for herd-management decisions and genetic evaluation. Further study is required to compare the results of individual cows in multiple lactations. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Scout-view Assisted Interior Micro-CT

PubMed Central

Sen Sharma, Kriti; Holzner, Christian; Vasilescu, Dragoş M.; Jin, Xin; Narayanan, Shree; Agah, Masoud; Hoffman, Eric A.; Yu, Hengyong; Wang, Ge

2013-01-01

Micro computed tomography (micro-CT) is a widely-used imaging technique. A challenge of micro-CT is to quantitatively reconstruct a sample larger than the field-of-view (FOV) of the detector. This scenario is characterized by truncated projections and associated image artifacts. However, for such truncated scans, a low resolution scout scan with an increased FOV is frequently acquired so as to position the sample properly. This study shows that the otherwise discarded scout scans can provide sufficient additional information to uniquely and stably reconstruct the interior region of interest. Two interior reconstruction methods are designed to utilize the multi-resolution data without a significant computational overhead. While most previous studies used numerically truncated global projections as interior data, this study uses truly hybrid scans where global and interior scans were carried out at different resolutions. Additionally, owing to the lack of standard interior micro-CT phantoms, we designed and fabricated novel interior micro-CT phantoms for this study to provide means of validation for our algorithms. Finally, two characteristic samples from separate studies were scanned to show the effect of our reconstructions. The presented methods show significant improvements over existing reconstruction algorithms. PMID:23732478

Phase retrieval via incremental truncated amplitude flow algorithm

NASA Astrophysics Data System (ADS)

Zhang, Quanbing; Wang, Zhifa; Wang, Linjie; Cheng, Shichao

2017-10-01

This paper considers the phase retrieval problem of recovering the unknown signal from the given quadratic measurements. A phase retrieval algorithm based on Incremental Truncated Amplitude Flow (ITAF) which combines the ITWF algorithm and the TAF algorithm is proposed. The proposed ITAF algorithm enhances the initialization by performing both of the truncation methods used in ITWF and TAF respectively, and improves the performance in the gradient stage by applying the incremental method proposed in ITWF to the loop stage of TAF. Moreover, the original sampling vector and measurements are preprocessed before initialization according to the variance of the sensing matrix. Simulation experiments verified the feasibility and validity of the proposed ITAF algorithm. The experimental results show that it can obtain higher success rate and faster convergence speed compared with other algorithms. Especially, for the noiseless random Gaussian signals, ITAF can recover any real-valued signal accurately from the magnitude measurements whose number is about 2.5 times of the signal length, which is close to the theoretic limit (about 2 times of the signal length). And it usually converges to the optimal solution within 20 iterations which is much less than the state-of-the-art algorithms.

Mechanism of the CO-sensing heme protein CooA: new insights from the truncated heme domain and UVRR spectroscopy

PubMed Central

Ibrahim, Mohammed; Kuchinskas, Michael; Youn, Hwan; Kerby, Robert L.; Roberts, Gary P.; Poulos, Thomas L.; Spiro, Thomas G.

2007-01-01

The bacterial CO-sensing heme protein CooA activates expression of genes whose products perform CO-metabolism by binding its target DNA in response to CO binding. The required conformational change has been proposed to result from CO-induced displacement of the heme and of the adjacent C-helix, which connects the sensory and DNA-binding domains. Support for this proposal comes from UV Resonance Raman (UVRR) spectroscopy, which reveals a more hydrophobic environment for the C-helix residue Trp110 when CO binds. In addition, we find a tyrosine UVRR response, which is attributable to weakening of a Tyr55-Glu83 H-bond that anchors the proximal side of the heme. Both Trp and Tyr responses are augmented in the heme domain when the DNA-binding domain has been removed, apparently reflecting loss of the inter-domain restraint. This augmentation is abolished by a Glu83Gln substitution, which weakens the anchoring H-bond. The CO recombination rate following photolysis of the CO adduct is similar for truncated and full-length protein, though truncation does increase the rate of CO association in the absence of photolysis; together these data indicate that truncation causes a faster dissociation of the endogenous Pro2 ligand. These findings are discussed in the light of structural evidence that the N-terminal tail, once released from the heme, selects the proper orientation of the DNA-binding domain, via docking interactions. PMID:17720248

Truncation Without Shape Constraints: The Latter Stages of Prosodic Acquisition.

ERIC Educational Resources Information Center

Kehoe, Margaret M.

2000-01-01

Evaluates the claim of uniform size and shape restrictions in prosodic development using a cross-sectional database of English-speaking children's multisyllabic word productions. Suggests children's increasing faithfulness to unstressed syllables can be explained by different constraint rankings that relate to edge alignment, syllable structure,…

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory.

PubMed

Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2017-04-28

The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N 6 ) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory

NASA Astrophysics Data System (ADS)

Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F.; Neese, Frank

2017-04-01

The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.

Equivalence of truncated count mixture distributions and mixtures of truncated count distributions.

PubMed

Böhning, Dankmar; Kuhnert, Ronny

2006-12-01

This article is about modeling count data with zero truncation. A parametric count density family is considered. The truncated mixture of densities from this family is different from the mixture of truncated densities from the same family. Whereas the former model is more natural to formulate and to interpret, the latter model is theoretically easier to treat. It is shown that for any mixing distribution leading to a truncated mixture, a (usually different) mixing distribution can be found so that the associated mixture of truncated densities equals the truncated mixture, and vice versa. This implies that the likelihood surfaces for both situations agree, and in this sense both models are equivalent. Zero-truncated count data models are used frequently in the capture-recapture setting to estimate population size, and it can be shown that the two Horvitz-Thompson estimators, associated with the two models, agree. In particular, it is possible to achieve strong results for mixtures of truncated Poisson densities, including reliable, global construction of the unique NPMLE (nonparametric maximum likelihood estimator) of the mixing distribution, implying a unique estimator for the population size. The benefit of these results lies in the fact that it is valid to work with the mixture of truncated count densities, which is less appealing for the practitioner but theoretically easier. Mixtures of truncated count densities form a convex linear model, for which a developed theory exists, including global maximum likelihood theory as well as algorithmic approaches. Once the problem has been solved in this class, it might readily be transformed back to the original problem by means of an explicitly given mapping. Applications of these ideas are given, particularly in the case of the truncated Poisson family.

Expression, purification and in vitro refolding of the recombinant truncated Saposin-like protein 2 antigen for development of diagnosis of human fascioliasis.

PubMed

Mirzadeh, Abolfazl; Valadkhani, Zarrintaj; Yoosefy, Asiyeh; Babaie, Jalal; Golkar, Majid; Esmaeili Rastaghi, Ahmad Reza; Kazemi-Rad, Elham; Ashrafi, Keyhan

2017-07-01

Early diagnosis of fascioliasis is critical in prevention of injury to the liver and bile ducts. Saposin-like protein (FhSAP-2) is probably the most ideal antigen of Fasciola hepatica for development of ELISA kits. SAP-2 has a conserved tertiary structure containing three disulfide bonds and conformational epitopes. Therefore, antigenicity of SAP-2 is greatly depends on disulfide bond formation and proper folding. We produced the recombinant truncated SAP-2 (rtSAP-2) in the SHuffle ® T7 and Rosetta strain of Escherichia coli, in soluble and insoluble forms, respectively and purified by immobilized metal affinity chromatography (IMAC). The refolding process of denatured rtSAP-2 was performed using dialysis and dilution methods in the presence of chemical additives, along with reduced/oxidized glutathione (in vitro). Physicochemical studies, including non-reducing gel electrophoresis, Ellman's assay, Western blotting and ELISA showed the most antigenicity and likely correct folding of rtSAP-2, which was obtained by dialysis method. An IgG ELISA test was developed using rtSAP-2 refolded by dialysis and compared with excretory/secretory products of parasite with 52 positive fascioliasis samples, 79 other parasitic samples and 70 negative controls samples. The results exhibited 100% sensitivity and 98% specificity for rtSAP-2, also, 100% and 95.3% for excretory/secretory (E/S) antigen, respectively. In conclusion, it is suggested that rtSAP-2 with the correct folding could be used as a candidate antigen for detection of human fascioliasis. Copyright © 2017 Elsevier B.V. All rights reserved.

Discovering graphical Granger causality using the truncating lasso penalty

PubMed Central

Shojaie, Ali; Michailidis, George

2010-01-01

Motivation: Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes. Results: In this article, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large p, small n setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples. Availability: The proposed truncating lasso method is implemented in the R-package ‘grangerTlasso’ and is freely available at http://www.stat.lsa.umich.edu/∼shojaie/ Contact: shojaie@umich.edu PMID:20823316

Bayesian Methods for Effective Field Theories

NASA Astrophysics Data System (ADS)

Wesolowski, Sarah

Microscopic predictions of the properties of atomic nuclei have reached a high level of precision in the past decade. This progress mandates improved uncertainty quantification (UQ) for a robust comparison of experiment with theory. With the uncertainty from many-body methods under control, calculations are now sensitive to the input inter-nucleon interactions. These interactions include parameters that must be fit to experiment, inducing both uncertainty from the fit and from missing physics in the operator structure of the Hamiltonian. Furthermore, the implementation of the inter-nucleon interactions is not unique, which presents the additional problem of assessing results using different interactions. Effective field theories (EFTs) take advantage of a separation of high- and low-energy scales in the problem to form a power-counting scheme that allows the organization of terms in the Hamiltonian based on their expected contribution to observable predictions. This scheme gives a natural framework for quantification of uncertainty due to missing physics. The free parameters of the EFT, called the low-energy constants (LECs), must be fit to data, but in a properly constructed EFT these constants will be natural-sized, i.e., of order unity. The constraints provided by the EFT, namely the size of the systematic uncertainty from truncation of the theory and the natural size of the LECs, are assumed information even before a calculation is performed or a fit is done. Bayesian statistical methods provide a framework for treating uncertainties that naturally incorporates prior information as well as putting stochastic and systematic uncertainties on an equal footing. For EFT UQ Bayesian methods allow the relevant EFT properties to be incorporated quantitatively as prior probability distribution functions (pdfs). Following the logic of probability theory, observable quantities and underlying physical parameters such as the EFT breakdown scale may be expressed as pdfs that incorporate the prior pdfs. Problems of model selection, such as distinguishing between competing EFT implementations, are also natural in a Bayesian framework. In this thesis we focus on two complementary topics for EFT UQ using Bayesian methods--quantifying EFT truncation uncertainty and parameter estimation for LECs. Using the order-by-order calculations and underlying EFT constraints as prior information, we show how to estimate EFT truncation uncertainties. We then apply the result to calculating truncation uncertainties on predictions of nucleon-nucleon scattering in chiral effective field theory. We apply model-checking diagnostics to our calculations to ensure that the statistical model of truncation uncertainty produces consistent results. A framework for EFT parameter estimation based on EFT convergence properties and naturalness is developed which includes a series of diagnostics to ensure the extraction of the maximum amount of available information from data to estimate LECs with minimal bias. We develop this framework using model EFTs and apply it to the problem of extrapolating lattice quantum chromodynamics results for the nucleon mass. We then apply aspects of the parameter estimation framework to perform case studies in chiral EFT parameter estimation, investigating a possible operator redundancy at fourth order in the chiral expansion and the appropriate inclusion of truncation uncertainty in estimating LECs.

Enhancement of low visibility aerial images using histogram truncation and an explicit Retinex representation for balancing contrast and color consistency

NASA Astrophysics Data System (ADS)

Liu, Changjiang; Cheng, Irene; Zhang, Yi; Basu, Anup

2017-06-01

This paper presents an improved multi-scale Retinex (MSR) based enhancement for ariel images under low visibility. For traditional multi-scale Retinex, three scales are commonly employed, which limits its application scenarios. We extend our research to a general purpose enhanced method, and design an MSR with more than three scales. Based on the mathematical analysis and deductions, an explicit multi-scale representation is proposed that balances image contrast and color consistency. In addition, a histogram truncation technique is introduced as a post-processing strategy to remap the multi-scale Retinex output to the dynamic range of the display. Analysis of experimental results and comparisons with existing algorithms demonstrate the effectiveness and generality of the proposed method. Results on image quality assessment proves the accuracy of the proposed method with respect to both objective and subjective criteria.

Adaptive eigenspace method for inverse scattering problems in the frequency domain

NASA Astrophysics Data System (ADS)

Grote, Marcus J.; Kray, Marie; Nahum, Uri

2017-02-01

A nonlinear optimization method is proposed for the solution of inverse scattering problems in the frequency domain, when the scattered field is governed by the Helmholtz equation. The time-harmonic inverse medium problem is formulated as a PDE-constrained optimization problem and solved by an inexact truncated Newton-type iteration. Instead of a grid-based discrete representation, the unknown wave speed is projected to a particular finite-dimensional basis of eigenfunctions, which is iteratively adapted during the optimization. Truncating the adaptive eigenspace (AE) basis at a (small and slowly increasing) finite number of eigenfunctions effectively introduces regularization into the inversion and thus avoids the need for standard Tikhonov-type regularization. Both analytical and numerical evidence underpins the accuracy of the AE representation. Numerical experiments demonstrate the efficiency and robustness to missing or noisy data of the resulting adaptive eigenspace inversion method.

Comparison of two methods based on photoplethysmography for the diagnosis of peripheral arterial disease.

PubMed

Høyer, Christian; Nielsen, Nikolaj Schandorph; Jordansen, Malene Kragh Overvad; Zacho, Helle Damgaard

2017-12-01

To examine the interchangeability of two methods for distal pressure measurement based on photoplethysmography using a truncated or full display of the arterial inflow curve, respectively. Toe and ankle pressures were obtained from 69 patients suspected of peripheral arterial disease (PAD). Observer reproducibility of the curve readings was examined by blinded reassessment of the pressure curves in a randomly selected subgroup (60 limbs). There were no significant differences in mean pressures between the two methods (p for all > .455). The limits of agreement for the differences were -15.0-15.4 mmHg for right toe pressures, -16.3-16.2 mmHg for left toe pressures, -14.2-15.7 mmHg for right ankle pressures, and -18.3-17.7 mmHg for left ankle pressures. Correlation analysis revealed intraclass correlation coefficients ≥0.960 for all measuring sites. Cohen's Kappa showed excellent agreement in diagnostic classification, with κ = 0.930 for the diagnosis of PAD and perfect agreement in the diagnosis of critical limb ischemia (κ = 1.000). The analysis of intra-observer variation for curve reading showed limits of agreement of -3.9-4.0 for toe pressures and -7.6-7.7 for ankle pressures for the method involving truncated display and -3.1-3.2 for toe pressures and -6.3-8.6 for ankle pressures for the method involving full display of the signal. The present study shows minimal differences in diagnostic classification, as well as in ankle and toe pressures, between the full display and the truncated display of the photoplethysmographic pulse signal. Furthermore, the inter-observer variation was low for both of the photoplethysmographic methods investigated.

Infinite occupation number basis of bosons: Solving a numerical challenge

NASA Astrophysics Data System (ADS)

Geißler, Andreas; Hofstetter, Walter

2017-06-01

In any bosonic lattice system, which is not dominated by local interactions and thus "frozen" in a Mott-type state, numerical methods have to cope with the infinite size of the corresponding Hilbert space even for finite lattice sizes. While it is common practice to restrict the local occupation number basis to Nc lowest occupied states, the presence of a finite condensate fraction requires the complete number basis for an exact representation of the many-body ground state. In this work we present a truncation scheme to account for contributions from higher number states. By simply adding a single coherent-tail state to this common truncation, we demonstrate increased numerical accuracy and the possible increase in numerical efficiency of this method for the Gutzwiller variational wave function and within dynamical mean-field theory.

Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we proposemore » specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.« less

Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

DOE PAGES

Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

2016-01-01

This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we proposemore » specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.« less

The status of the strong coupling from tau decays in 2016

NASA Astrophysics Data System (ADS)

Boito, Diogo; Golterman, Maarten; Maltman, Kim; Peris, Santiago

2017-06-01

While the idea of using the operator product expansion (OPE) to extract the strong coupling from hadronic τ decay data is not new, there is an ongoing controversy over how to include quark-hadron ;duality violations; (i.e., resonance effects) which are not described by the OPE. One approach attempts to suppress duality violations enough that they might become negligible, but pays the price of an uncontrolled OPE truncation. We critically examine a recent analysis using this approach and show that it fails to properly account for non-perturbative effects, making the resulting determination of the strong coupling unreliable. In a different approach duality violations are taken into account with a model, avoiding the OPE truncation. This second approach provides a self-consistent determination of the strong coupling from τ decays.

Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Zhen; Horton, John R.; Cheng, Xiadong

2009-11-02

Circular permutation of Candida antarctica lipase B yields several enzyme variants with substantially increased catalytic activity. To better understand the structural and functional consequences of protein termini reorganization, we have applied protein engineering and x-ray crystallography to cp283, one of the most active hydrolase variants. Our initial investigation has focused on the role of an extended surface loop, created by linking the native N- and C-termini, on protein integrity. Incremental truncation of the loop partially compensates for observed losses in secondary structure and the permutants temperature of unfolding. Unexpectedly, the improvements are accompanied by quaternary-structure changes from monomer to dimer.more » The crystal structures of one truncated variant (cp283{Delta}7) in the apo-form determined at 1.49 {angstrom} resolution and with a bound phosphonate inhibitor at 1.69 {angstrom} resolution confirmed the formation of a homodimer by swapping of the enzyme's 35-residue N-terminal region. Separately, the new protein termini at amino acid positions 282/283 convert the narrow access tunnel to the catalytic triad into a broad crevice for accelerated substrate entry and product exit while preserving the native active-site topology for optimal catalytic turnover.« less

Development of a competitive ELISA using a truncated E2 recombinant protein as antigen for detection of antibodies to classical swine fever virus.

PubMed

Clavijo, A; Lin, M; Riva, J; Mallory, M; Lin, F; Zhou, E M

2001-02-01

The sequence encoding a truncated E2 glycoprotein of the Alfort/187 strain of classical swine fever virus (CSFV) was expressed in Escherichia coli using the pET expression system and the recombinant product purified by Ni-NTA agarose affinity chromatography. The antigenicity of this recombinant protein was demonstrated by immunoblot using anti- CSFV-specific antibodies. A monoclonal antibody was produced against the truncated E2 protein and used as competitor in an ELISA for the detection of antibodies to CSFV. Specific antibodies were demonstrated by competitive ELISA (C-ELISA) as early as 21 days post-infection (dpi) in experimentally infected pigs. Seroconversion was demonstrated by C-ELISA and neutralising peroxidase-linked assay (NPLA) in all infected animals by 4 weeks. No cross-reaction with antibodies to bovine viral diarrhoea virus (BVDV) was seen in the C-ELISA using sera from experimentally infected pigs. The C-ELISA is not intended as a substitute for the NPLA. However, it is expected it will be useful for monitoring and prevalence studies. It will also assist in testing a large number of samples in the event of an outbreak. Copyright 2001 Harcourt Publishers Ltd.

Novel germline PALB2 truncating mutations in African-American breast cancer patients

PubMed Central

Zheng, Yonglan; Zhang, Jing; Niu, Qun; Huo, Dezheng; Olopade, Olufunmilayo I.

2011-01-01

Background It has been demonstrated that PALB2 acts as a bridging molecule between the BRCA1 and BRCA2 proteins and is responsible for facilitating BRCA2-mediated DNA repair. Truncating mutations in the PALB2 gene have been reported to be enriched in Fanconi anemia and breast cancer patients in various populations. Methods We evaluated the contribution of PALB2 germline mutations in 279 African-American breast cancer patients including 29 patients with a strong family history, 29 patients with a moderate family history, 75 patients with a weak family history, and 146 non-familial or sporadic breast cancer cases. Results After direct sequencing of all the coding exons, exon/intron boundaries, 5′UTR and 3′UTR of PALB2, three (1.08%; 3 in 279) novel monoallelic truncating mutations were identified: c.758dupT (exon4), c.1479delC (exon4) and c.3048delT (exon 10); together with 50 sequence variants, 27 of which are novel. None of the truncating mutations were found in 262 controls from the same population. Conclusions PALB2 mutations are present in both familial and non-familial breast cancer among African-Americans. Rare PALB2 mutations account for a small but substantial proportion of breast cancer patients. PMID:21932393

Environmental and genetic factors affecting cow survival of Israeli Holsteins.

PubMed

Weller, J I; Ezra, E

2015-01-01

The objectives were to investigate the effects of various environmental factors that may affect herd-life of Israeli Holsteins, including first-calving age and season, calving ease, number of progeny born, and service sire for first calving in complete and truncated records; and to estimate heritabilities and genetic correlations between herd-life and the other traits included in the Israeli breeding index. The basic data set consisted of 590,869 cows in milk recording herds with first freshening day between 1985 and at least 8 yr before the cut-off date of September 15, 2013. Herd-life was measured as days from first calving to culling. The phenotypic and genetic trends for herd-life were 5.7 and 16.8d/yr. The genetic trend was almost linear, whereas the phenotypic trend showed 4 peaks and 3 valleys. Cows born in February and March had the shortest herd-life, whereas cows born in September had the longest herd-life. Herd-life was maximal with calving age of 23mo, which is 1mo less than the mean calving age, and minimal at 19 and 31mo of calving age. Dystocia and twinning on first-parity calving reduced herd-life by approximately180 and 120d, but the interaction effect increased herd-life by 140d. Heritability for herd-life was 0.14. Despite the fact that the service sire effect was significant in the fixed model analysis, service sire effect accounted for <0.05% of the total variance. In the analysis of 1,431,938 truncated records, the effects of dystocia and twinning rate were very similar but less than 50% of the effects found in the analysis of complete records. Pregnancy at the truncation date increased expected herd-life by 432d. The correlation between actual herd-life and predicted herd-life based on truncated records was 0.44. Genetic correlations between the truncated records and actual herd-life were 0.75 for records truncated after 6mo but approached unity for records truncated after 3 yr. The genetic correlations of herd-life with first-parity milk, fat, and protein production, somatic cell score (SCS), and female fertility were all positive, except for SCS, in which negative values are economically favorable. The highest correlations with herd-life in absolute value were with female fertility and SCS. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

WE-EF-207-06: Dedicated Cone-Beam Breast CT with Laterally-Shifted Detector: Monte Carlo Evaluation of X-Ray Scatter Distribution and Scatter-To-Primary Ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, L; Vedantham, S; Karellas, A

2015-06-15

Purpose: To determine the spatial distribution of x-ray scatter and scatter-to-primary ratio (SPR) in projections during cone-beam breast CT (CBBCT) with laterally-shifted detector that results in coronal (fan-angle) truncation. Methods: We hypothesized that CBBCT with coronal truncation would lower SPR due to reduction in irradiated breast volume, and that the location of maximum x-ray scatter fluence (scatter-peak) in the detector plane can be determined from the ratio of irradiated-to-total breast volume, breast dimensions and system geometry. Monte Carlo simulations (GEANT4) reflecting a prototype CBBCT system were used to record the position-dependent primary and scatter x-ray photon fluence incident on themore » detector without coronal truncation (full fan-angle, 2f=24-degrees) and with coronal truncation (fan-angle, f+ f=12+2.7-degrees). Semi-ellipsoidal breasts (10/14/18-cm diameter, chest-wall to nipple length: 0.75xdiameter, 2%/14%/100% fibroglandular content) aligned with the axis-of-rotation (AOR) were modeled. Mono-energy photons were simulated and weighted for 2 spectra (49kVp, 1.4-mm Al HVL; 60kVp, 3.76-mm Al HVL). In addition to SPR, the scatter maps were analyzed to identify the location of the scatter-peak. Results: For CBBCT without fan-angle truncation, the scatter-peaks were aligned with the projection of the AOR onto the detector for all breasts. With truncated fan-beam, the scatter-peaks were laterally-shifted from the projection of the AOR along the fan-angle direction by 14/38/70-pixels for 10/14/18-cm diameter breasts. The corresponding theoretical shifts were 14.8/39.7/68-pixels (p=0.47, 2-tailed paired-ratio t-test). Along the cone-angle, the shift in scatter-peaks between truncated and full-fan angle CBBCT were 2/2/4 -pixels for 10/14/18-cm diameter breasts. CBBCT with fan-angle truncation reduced SPR by 14/22/28% for 10/14/18-cm diameter breasts. 60kVp reduced SPR by 21–25% compared to 49kVp. Peak SPR for CBBCT with fan-angle truncation (60kVp) were 0.09/0.25/0.73 for 10/14/18-cm diameter breasts. Conclusion: CBBCT with laterally-shifted detector geometry and with appropriate kVp/beam quality reduces SPR. If residual scatter needs correction, the location corresponding to scatter-peak can be analytically computed. This work was supported in part by NIH R01 CA128906. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or NCI.« less

Increased ethanol accumulation from glucose via reduction of ATP level in a recombinant strain of Saccharomyces cerevisiae overexpressing alkaline phosphatase.

PubMed

Semkiv, Marta V; Dmytruk, Kostyantyn V; Abbas, Charles A; Sibirny, Andriy A

2014-05-15

The production of ethyl alcohol by fermentation represents the largest scale application of Saccharomyces cerevisiae in industrial biotechnology. Increased worldwide demand for fuel bioethanol is anticipated over the next decade and will exceed 200 billion liters from further expansions. Our working hypothesis was that the drop in ATP level in S. cerevisiae cells during alcoholic fermentation should lead to an increase in ethanol production (yield and productivity) with a greater amount of the utilized glucose converted to ethanol. Our approach to achieve this goal is to decrease the intracellular ATP level via increasing the unspecific alkaline phosphatase activity. Intact and truncated versions of the S. cerevisiae PHO8 gene coding for vacuolar or cytosolic forms of alkaline phosphatase were fused with the alcohol dehydrogenase gene (ADH1) promoter. The constructed expression cassettes used for transformation vectors also contained the dominant selective marker kanMX4 and S. cerevisiae δ-sequence to facilitate multicopy integration to the genome. Laboratory and industrial ethanol producing strains BY4742 and AS400 overexpressing vacuolar form of alkaline phosphatase were characterized by a slightly lowered intracellular ATP level and biomass accumulation and by an increase in ethanol productivity (13% and 7%) when compared to the parental strains. The strains expressing truncated cytosolic form of alkaline phosphatase showed a prolonged lag-phase, reduced biomass accumulation and a strong defect in ethanol production. Overexpression of vacuolar alkaline phosphatase leads to an increased ethanol yield in S. cerevisiae.

Abscisic Acid Antagonizes Ethylene Production through the ABI4-Mediated Transcriptional Repression of ACS4 and ACS8 in Arabidopsis.

PubMed

Dong, Zhijun; Yu, Yanwen; Li, Shenghui; Wang, Juan; Tang, Saijun; Huang, Rongfeng

2016-01-04

Increasing evidence has revealed that abscisic acid (ABA) negatively modulates ethylene biosynthesis, although the underlying mechanism remains unclear. To identify the factors involved, we conducted a screen for ABA-insensitive mutants with altered ethylene production in Arabidopsis. A dominant allele of ABI4, abi4-152, which produces a putative protein with a 16-amino-acid truncation at the C-terminus of ABI4, reduces ethylene production. By contrast, two recessive knockout alleles of ABI4, abi4-102 and abi4-103, result in increased ethylene evolution, indicating that ABI4 negatively regulates ethylene production. Further analyses showed that expression of the ethylene biosynthesis genes ACS4, ACS8, and ACO2 was significantly decreased in abi4-152 but increased in the knockout mutants, with partial dependence on ABA. Chromatin immunoprecipitation-quantitative PCR assays showed that ABI4 directly binds the promoters of these ethylene biosynthesis genes and that ABA enhances this interaction. A fusion protein containing the truncated ABI4-152 peptide accumulated to higher levels than its full-length counterpart in transgenic plants, suggesting that ABI4 is destabilized by its C terminus. Therefore, our results demonstrate that ABA negatively regulates ethylene production through ABI4-mediated transcriptional repression of the ethylene biosynthesis genes ACS4 and ACS8 in Arabidopsis. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

A novel proteolytic processing of prolysyl oxidase.

PubMed

Atsawasuwan, Phimon; Mochida, Yoshiyuki; Katafuchi, Michitsuna; Tokutomi, Kentaro; Mocanu, Viorel; Parker, Carol E; Yamauchi, Mitsuo

2011-01-01

Lysyl oxidase (LOX) is an amine oxidase that is critical for the stability of connective tissues. The secreted proLOX is enzymatically quiescent and is activated through proteolytic cleavage between residues Gly(162) and Asp(163) (residue numbers according to the mouse LOX) by bone morphogenetic protein (BMP)-1 gene products. Here we report a novel processing of proLOX identified in vitro and in vivo. Two forms of mature LOX were identified and characterized by their immunoreactivity to specific antibodies, amine oxidase activity, and mass spectrometry. One form was identified as a well-characterized BMP-1 processed LOX protein. Another was found to be a truncated form of LOX resulting from the cleavage at the carboxy terminus of Arg(192). The truncated form of LOX still appeared to retain amine oxidase activity. The results from the proLOX gene deletion and mutation experiments indicated that the processing occurs independent of the cleavage of proLOX by BMP-1 gene products and likely requires the presence of LOX propeptide. These results indicate that proLOX could be processed by two different mechanisms producing two forms of active LOX.

Genetic analysis of Chinese families reveals a novel truncation allele of the retinitis pigmentosa GTPase regulator gene

PubMed Central

Hu, Fang; Zeng, Xiang-Yun; Liu, Lin-Lin; Luo, Yao-Ling; Jiang, Yi-Ping; Wang, Hui; Xie, Jing; Hu, Cheng-Quan; Gan, Lin; Huang, Liang

2014-01-01

AIM To make comprehensive molecular diagnosis for retinitis pigmentosa (RP) patients in a consanguineous Han Chinese family using next generation sequencing based Capture-NGS screen technology. METHODS A five-generation Han Chinese family diagnosed as non-syndromic X-linked recessive RP (XLRP) was recruited, including four affected males, four obligate female carriers and eleven unaffected family members. Capture-NGS was performed using a custom designed capture panel covers 163 known retinal disease genes including 47 RP genes, followed by the validation of detected mutation using Sanger sequencing in all recruited family members. RESULTS Capture-NGS in one affected 47-year-old male reveals a novel mutation, c.2417_2418insG:p.E806fs, in exon ORF15 of RP GTPase regulator (RPGR) gene results in a frameshift change that results in a premature stop codon and a truncated protein product. The mutation was further validated in three of four affected males and two of four female carriers but not in the other unaffected family members. CONCLUSION We have identified a novel mutation, c.2417_2418insG:p.E806fs, in a Han Chinese family with XLRP. Our findings expand the mutation spectrum of RPGR and the phenotypic spectrum of XLRP in Han Chinese families, and confirms Capture-NGS could be an effective and economic approach for the comprehensive molecular diagnosis of RP. PMID:25349787

Dissolution of fine particle fraction from truncated Anderson cascade impactor with an enhancer cell.

PubMed

Tay, Justin Yong Soon; Liew, Celine Valeria; Heng, Paul Wan Sia

2018-04-22

Dissolution testing for inhalers were previously conducted either on unfractionated drug-carrier powders or drug of specific aerodynamic particle size. In this study, the collection of the full fine particle fraction (FPF) was attempted on a single stage. Capsules containing 30 mg of 2% salbutamol sulfate (SS) was tested to have a FPF of 9 ± 1% using the full set of Andersen cascade impactor (ACI) and a modified Rotahaler® capable of achieving 4.0 kPa pressure drop at 60 L/min air flow rate. A truncated ACI comprising the USP throat, pre-separator, stage 0, stage 4, stage F, polytetrafluoroethylene funnel (TF) and small collection plate (sCP) was found to be capable of achieving a FPF of 9% collected on TF and sCP. An adhesive tape was used to collect the FPF from the TF and sCP and held in place by an enhancer cell in a 200 mL round bottom vessel containing 50 mL Gamble's solution with 0.2 v/v, % Tween 80. Dissolution testing of SS and Seretide® showed burst release of SS and salmeterol while sustained release of fluticasone. This study demonstrated a reproducible method which may be used for evaluation of the full FPF of orally inhaled products. Copyright © 2018 Elsevier B.V. All rights reserved.

Optimization and validation of indirect ELISA using truncated TssB protein for the serodiagnosis of glanders amongst equines.

PubMed

Singha, Harisankar; Malik, Praveen; Goyal, Sachin K; Khurana, Sandip K; Mukhopadhyay, Chiranjay; Eshwara, Vandana K; Singh, Raj K

2014-01-01

To express truncated TssB protein of Burkholderia mallei and to evaluate its diagnostic efficacy for serological detection of glanders among equines. In an attempt to develop recombinant protein based enzyme-linked immunosorbent assay (ELISA), N-terminal 200 amino acid sequences of B. mallei TssB protein-a type 6 secretory effector protein--were expressed in prokaryotic expression system. Diagnostic potential of recombinant TssB protein was evaluated in indirect ELISA using a panel of glanders positive (n = 49), negative (n = 30), and field serum samples (n = 1811). Cross-reactivity of the assay was assessed with equine disease control serum and human melioidosis positive serum. In comparison to CFT, diagnostic sensitivity and specificity of ELISA were 99.7% and 100%, respectively. The indirect ELISA method using the truncated TssB offered safer and more rapid and efficient means of serodiagnosis of glanders in equines. These data highlight the use of TssB as potential diagnostic antigen for serological diagnosis of glanders.

Scintillation analysis of truncated Bessel beams via numerical turbulence propagation simulation.

PubMed

Eyyuboğlu, Halil T; Voelz, David; Xiao, Xifeng

2013-11-20

Scintillation aspects of truncated Bessel beams propagated through atmospheric turbulence are investigated using a numerical wave optics random phase screen simulation method. On-axis, aperture averaged scintillation and scintillation relative to a classical Gaussian beam of equal source power and scintillation per unit received power are evaluated. It is found that in almost all circumstances studied, the zeroth-order Bessel beam will deliver the lowest scintillation. Low aperture averaged scintillation levels are also observed for the fourth-order Bessel beam truncated by a narrower source window. When assessed relative to the scintillation of a Gaussian beam of equal source power, Bessel beams generally have less scintillation, particularly at small receiver aperture sizes and small beam orders. Upon including in this relative performance measure the criteria of per unit received power, this advantageous position of Bessel beams mostly disappears, but zeroth- and first-order Bessel beams continue to offer some advantage for relatively smaller aperture sizes, larger source powers, larger source plane dimensions, and intermediate propagation lengths.

A feature refinement approach for statistical interior CT reconstruction

NASA Astrophysics Data System (ADS)

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-01

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)—minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

A feature refinement approach for statistical interior CT reconstruction.

PubMed

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-21

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)-minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

Furin is a chemokine-modifying enzyme: in vitro and in vivo processing of CXCL10 generates a C-terminally truncated chemokine retaining full activity.

PubMed

Hensbergen, Paul J; Verzijl, Dennis; Balog, Crina I A; Dijkman, Remco; van der Schors, Roel C; van der Raaij-Helmer, Elizabeth M H; van der Plas, Mariena J A; Leurs, Rob; Deelder, André M; Smit, Martine J; Tensen, Cornelis P

2004-04-02

Chemokines comprise a class of structurally related proteins that are involved in many aspects of leukocyte migration under basal and inflammatory conditions. In addition to the large number of genes, limited processing of these proteins by a variety of enzymes enhances the complexity of the total spectrum of chemokine variants. We have recently shown that the native chemokine CXCL10 is processed at the C terminus, thereby shedding the last four amino acids. The present study was performed to elucidate the mechanism in vivo and in vitro and to study the biological activity of this novel isoform of CXCL10. Using a combination of protein purification and mass spectrometric techniques, we show that the production of C-terminally truncated CXCL10 by primary keratinocytes is inhibited in vivo by a specific inhibitor of pro-protein convertases (e.g. furin) but not by inhibition of matrix metalloproteinases. Moreover, CXCL10 is processed by furin in vitro, which is abrogated by a mutation in the furin recognition site. Using GTPgammaS binding, Ca(2+) mobilization, and chemotaxis assays, we demonstrate that the C-terminally truncated CXCL10 variant is a potent ligand for CXCR3. Moreover, the inverse agonist activity on the virally encoded receptor ORF74 and the direct antibacterial activity of CXCL10 are fully retained. Hence, we have identified furin as a novel chemokine-modifying enzyme in vitro and most probably also in vivo, generating a C-terminally truncated CXCL10, which fully retains its (inverse) agonistic properties.

[Effect of N-terminal truncation of Bacillus acidopullulyticus pullulanase on enzyme properties and functions].

PubMed

Chen, A'na; Liu, Xiuxia; Dai, Xiaofeng; Zhan, Jinling; Peng, Feng; Li, Lu; Wang, Fen; Li, Song; Yang, Yankun; Bai, Zhonghu

2016-03-01

We constructed different N-terminal truncated variants based on Bacillus acidopullulyticus pullulanase 3D structure (PDB code 2WAN), and studied the effects of truncated mutation on soluble expression, enzymatic properties, and application in saccharification. Upon expression, the variants of X45 domain deletion existed as inclusion bodies, whereas deletion of CBM41 domain had an effective effect on soluble expression level. The variants that lack of CBM41 (M1), lack of X25 (M3), and lack both of CBM41 and X25 (M5) had the same optimal pH (5.0) and optimal temperature (60 degrees C) with the wild-type pullulanase (WT). The K(m) of M1 and M5 were 1.42 mg/mL and 1.85 mg/mL, respectively, 2.4- and 3.1-fold higher than that of the WT. k(cat)/K(m) value of M5 was 40% lower than that of the WT. Substrate specificity results show that the enzymes exhibited greater activity with the low-molecular-weight dextrin than with high-molecular-weight soluble starch. When pullulanases were added to the saccharification reaction system, the dextrose equivalent of the WT, M1, M3, and M5 were 93.6%, 94.7%, 94.5%, and93.1%, respectively. These results indicate that the deletion of CBM41 domain and/or X25 domain did not affect the practical application in starch saccharification process. Furthermore, low-molecular-weight variants facilitate the heterologous expression. Truncated variants may be more suitable for industrial production than the WT.

Analytic assessment of Laplacian estimates via novel variable interring distances concentric ring electrodes.

PubMed

Makeyev, Oleksandr; Besio, Walter G

2016-08-01

Noninvasive concentric ring electrodes are a promising alternative to conventional disc electrodes. Currently, superiority of tripolar concentric ring electrodes over disc electrodes, in particular, in accuracy of Laplacian estimation has been demonstrated in a range of applications. In our recent work we have shown that accuracy of Laplacian estimation can be improved with multipolar concentric ring electrodes using a general approach to estimation of the Laplacian for an (n + 1)-polar electrode with n rings using the (4n + 1)-point method for n ≥ 2. This paper takes the next step toward further improving the Laplacian estimate by proposing novel variable inter-ring distances concentric ring electrodes. Derived using a modified (4n + 1)-point method, linearly increasing inter-ring distances tripolar (n = 2) and quadripolar (n = 3) electrode configurations are analytically compared to their constant inter-ring distances counterparts using coefficients of the Taylor series truncation terms. Obtained results suggest that increasing inter-ring distances electrode configurations may decrease the truncation error of the Laplacian estimation resulting in more accurate Laplacian estimates compared to respective constant inter-ring distances configurations. For currently used tripolar electrode configuration the truncation error may be decreased more than two-fold while for the quadripolar more than seven-fold decrease is expected.

Theoretical study of hydrogen storage in a truncated triangular pyramid molecule consisting of pyridine and benzene rings bridged by vinylene groups

NASA Astrophysics Data System (ADS)

Ishikawa, Shigeru; Nemoto, Tetsushi; Yamabe, Tokio

2018-06-01

Hydrogen storage in a truncated triangular pyramid molecule C33H21N3, which consists of three pyridine rings and one benzene ring bridged by six vinylene groups, is studied by quantum chemical methods. The molecule is derived by substituting three benzene rings in a truncated tetrahedron hydrocarbon C36H24 with pyridine rings. The optimized molecular structure under C 3v symmetry shows no imaginary vibrational modes at the B3LYP/cc-pVTZ level of theory. The hydrogen storage process is investigated based on the MP2/cc-pVTZ method. Like the structure before substitution, the C33H21N3 molecule has a cavity that stores a hydrogen molecule with a binding energy of - 140 meV. The Langmuir isotherm shows that this cavity can store hydrogen at higher temperatures and lower pressures than usual physisorption materials. The C33H21N3 molecule has a kinetic advantage over the C36H24 molecule because the former molecule has a lower barrier (+ 560 meV) for the hydrogen molecule entering the cavity compared with the latter molecule (+ 730 meV) owing to the lack of hydrogen atoms narrowing the opening.

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

DOE PAGES

Hao, Yue; Blair, Patricia M.; Sharma, Abhishek; ...

2015-01-30

Peptide antibiotics represent a class of conformationally-constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here in this paper, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide amore » rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).« less

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Yue; Blair, Patricia M.; Sharma, Abhishek

Peptide antibiotics represent a class of conformationally-constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here in this paper, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide amore » rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).« less

Constitutively expressing cell lines that secrete a truncated bovine herpes virus-1 glycoprotein (gpI) stimulate T-lymphocyte responsiveness.

PubMed

Leary, T P; Gao, Y; Splitter, G A

1992-07-01

The desire to obtain authentically glycosylated viral protein products in sufficient quantity for immunological study has led to the use of eucaryotic expression vectors for protein production. An additional advantage is that these protein products can be studied individually in the absence of their native viral environment. We have cloned a complementary DNA (cDNA) encoding bovine herpes virus-1 (BHV-1) glycoprotein 1 (gpI) into the eucaryotic expression vector, pZipNeo SVX1. Since this protein is normally embedded within the membrane of BHV-1 infected cells, we removed sequences encoding the transmembrane domain of the native protein. After transfection of the plasmid construct into the canine osteosarcoma cell line, D17, or Madin-Darby bovine kidney (MDBK) cells, a truncated BHV-1 (gpI) was secreted into the culture medium as demonstrated by radioimmunoprecipitation and SDS-PAGE. Both a CD4+ T-lymphocyte line specific for BHV-1 and freshly isolated T lymphocytes could recognize and respond to the secreted recombinant gpI. Further, recombinant gpI could elicit both antibody and cellular responses in cattle when used as an immunogen. Having established constitutively glycoprotein producing cell lines, future studies in vaccine evaluation of gpI will be facilitated.

Truncation of the TAR DNA-binding protein 43 is not a prerequisite for cytoplasmic relocalization, and is suppressed by caspase inhibition and by introduction of the A90V sequence variant

PubMed Central

Brandon, Nicholas J.; Moss, Stephen J.

2017-01-01

The RNA-binding and -processing protein TAR DNA-binding protein 43 (TDP-43) is heavily linked to the underlying causes and pathology of neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. In these diseases, TDP-43 is mislocalized, hyperphosphorylated, ubiquitinated, aggregated and cleaved. The importance of TDP-43 cleavage in the disease pathogenesis is still poorly understood. Here we detail the use of D-sorbitol as an exogenous stressor that causes TDP-43 cleavage in HeLa cells, resulting in a 35 kDa truncated product that accumulates in the cytoplasm within one hour of treatment. We confirm that the formation of this 35 kDa cleavage product is mediated by the activation of caspases. Inhibition of caspases blocks the cleavage of TDP-43, but does not prevent the accumulation of full-length protein in the cytoplasm. Using D-sorbitol as a stressor and caspase activator, we also demonstrate that the A90V variant of TDP-43, which lies adjacent to the caspase cleavage site within the nuclear localization sequence of TDP-43, confers partial resistance against caspase-mediated generation of the 35 kDa cleavage product. PMID:28510586

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

PubMed

Kietrys, Anna M; Velema, Willem A; Kool, Eric T

2017-11-29

Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

National Centers for Environmental Prediction

Science.gov Websites

resolution at T574 becomes ~ 23 km T382 Spectral truncation equivalent to horizontal resolution ~37 km T254 Spectral truncation equivalent to horizontal resolution ~50-55 km T190 Spectral truncation equivalent to horizontal resolution ~70 km T126 Spectral truncation equivalent to horizontal resolution ~100 km UM Unified

Impact of degree truncation on the spread of a contagious process on networks.

PubMed

Harling, Guy; Onnela, Jukka-Pekka

2018-03-01

Understanding how person-to-person contagious processes spread through a population requires accurate information on connections between population members. However, such connectivity data, when collected via interview, is often incomplete due to partial recall, respondent fatigue or study design, e.g., fixed choice designs (FCD) truncate out-degree by limiting the number of contacts each respondent can report. Past research has shown how FCD truncation affects network properties, but its implications for predicted speed and size of spreading processes remain largely unexplored. To study the impact of degree truncation on predictions of spreading process outcomes, we generated collections of synthetic networks containing specific properties (degree distribution, degree-assortativity, clustering), and also used empirical social network data from 75 villages in Karnataka, India. We simulated FCD using various truncation thresholds and ran a susceptible-infectious-recovered (SIR) process on each network. We found that spreading processes propagated on truncated networks resulted in slower and smaller epidemics, with a sudden decrease in prediction accuracy at a level of truncation that varied by network type. Our results have implications beyond FCD to truncation due to any limited sampling from a larger network. We conclude that knowledge of network structure is important for understanding the accuracy of predictions of process spread on degree truncated networks.

Modifications Of Discrete Ordinate Method For Computations With High Scattering Anisotropy: Comparative Analysis

NASA Technical Reports Server (NTRS)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2012-01-01

A numerical accuracy analysis of the radiative transfer equation (RTE) solution based on separation of the diffuse light field into anisotropic and smooth parts is presented. The analysis uses three different algorithms based on the discrete ordinate method (DOM). Two methods, DOMAS and DOM2+, that do not use the truncation of the phase function, are compared against the TMS-method. DOMAS and DOM2+ use the Small-Angle Modification of RTE and the single scattering term, respectively, as an anisotropic part. The TMS method uses Delta-M method for truncation of the phase function along with the single scattering correction. For reference, a standard discrete ordinate method, DOM, is also included in analysis. The obtained results for cases with high scattering anisotropy show that at low number of streams (16, 32) only DOMAS provides an accurate solution in the aureole area. Outside of the aureole, the convergence and accuracy of DOMAS, and TMS is found to be approximately similar: DOMAS was found more accurate in cases with coarse aerosol and liquid water cloud models, except low optical depth, while the TMS showed better results in case of ice cloud.

Analytical Investigation of Elastic Thin-Walled Cylinder and Truncated Cone Shell Intersection Under Internal Pressure.

PubMed

Zamani, J; Soltani, B; Aghaei, M

2014-10-01

An elastic solution of cylinder-truncated cone shell intersection under internal pressure is presented. The edge solution theory that has been used in this study takes bending moments and shearing forces into account in the thin-walled shell of revolution element. The general solution of the cone equations is based on power series method. The effect of cone apex angle on the stress distribution in conical and cylindrical parts of structure is investigated. In addition, the effect of the intersection and boundary locations on the circumferential and longitudinal stresses is evaluated and it is shown that how quantitatively they are essential.

An iterative truncation method for unbounded electromagnetic problems using varying order finite elements

NASA Astrophysics Data System (ADS)

Paul, Prakash

2009-12-01

The finite element method (FEM) is used to solve three-dimensional electromagnetic scattering and radiation problems. Finite element (FE) solutions of this kind contain two main types of error: discretization error and boundary error. Discretization error depends on the number of free parameters used to model the problem, and on how effectively these parameters are distributed throughout the problem space. To reduce the discretization error, the polynomial order of the finite elements is increased, either uniformly over the problem domain or selectively in those areas with the poorest solution quality. Boundary error arises from the condition applied to the boundary that is used to truncate the computational domain. To reduce the boundary error, an iterative absorbing boundary condition (IABC) is implemented. The IABC starts with an inexpensive boundary condition and gradually improves the quality of the boundary condition as the iteration continues. An automatic error control (AEC) is implemented to balance the two types of error. With the AEC, the boundary condition is improved when the discretization error has fallen to a low enough level to make this worth doing. The AEC has these characteristics: (i) it uses a very inexpensive truncation method initially; (ii) it allows the truncation boundary to be very close to the scatterer/radiator; (iii) it puts more computational effort on the parts of the problem domain where it is most needed; and (iv) it can provide as accurate a solution as needed depending on the computational price one is willing to pay. To further reduce the computational cost, disjoint scatterers and radiators that are relatively far from each other are bounded separately and solved using a multi-region method (MRM), which leads to savings in computational cost. A simple analytical way to decide whether the MRM or the single region method will be computationally cheaper is also described. To validate the accuracy and savings in computation time, different shaped metallic and dielectric obstacles (spheres, ogives, cube, flat plate, multi-layer slab etc.) are used for the scattering problems. For the radiation problems, waveguide excited antennas (horn antenna, waveguide with flange, microstrip patch antenna) are used. Using the AEC the peak reduction in computation time during the iteration is typically a factor of 2, compared to the IABC using the same element orders throughout. In some cases, it can be as high as a factor of 4.

Evolution of the anti-truncated stellar profiles of S0 galaxies since z = 0.6 in the SHARDS survey. I. Sample and methods

NASA Astrophysics Data System (ADS)

Borlaff, Alejandro; Eliche-Moral, M. Carmen; Beckman, John E.; Ciambur, Bogdan C.; Pérez-González, Pablo G.; Barro, Guillermo; Cava, Antonio; Cardiel, Nicolas

2017-08-01

Context. The controversy about the origin of the structure of early-type S0-E/S0 galaxies may be due to the difficulty of comparing surface brightness profiles with different depths, photometric corrections and point spread function (PSF) effects (which are almost always ignored). Aims: We aim to quantify the properties of Type-III (anti-truncated) discs in a sample of S0 galaxies at 0.2

Advanced proteomic liquid chromatography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Fang; Smith, Richard D.; Shen, Yufeng

2012-10-26

Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.

One-sided truncated sequential t-test: application to natural resource sampling

Treesearch

Gary W. Fowler; William G. O' Regan

1974-01-01

A new procedure for constructing one-sided truncated sequential t-tests and its application to natural resource sampling are described. Monte Carlo procedures were used to develop a series of one-sided truncated sequential t-tests and the associated approximations to the operating characteristic and average sample number functions. Different truncation points and...

Beam hardening correction for interior tomography based on exponential formed model and radon inversion transform

NASA Astrophysics Data System (ADS)

Chen, Siyu; Zhang, Hanming; Li, Lei; Xi, Xiaoqi; Han, Yu; Yan, Bin

2016-10-01

X-ray computed tomography (CT) has been extensively applied in industrial non-destructive testing (NDT). However, in practical applications, the X-ray beam polychromaticity often results in beam hardening problems for image reconstruction. The beam hardening artifacts, which manifested as cupping, streaks and flares, not only debase the image quality, but also disturb the subsequent analyses. Unfortunately, conventional CT scanning requires that the scanned object is completely covered by the field of view (FOV), the state-of-art beam hardening correction methods only consider the ideal scanning configuration, and often suffer problems for interior tomography due to the projection truncation. Aiming at this problem, this paper proposed a beam hardening correction method based on radon inversion transform for interior tomography. Experimental results show that, compared to the conventional correction algorithms, the proposed approach has achieved excellent performance in both beam hardening artifacts reduction and truncation artifacts suppression. Therefore, the presented method has vitally theoretic and practicable meaning in artifacts correction of industrial CT.

Deletion of a non-catalytic region increases the enzymatic activity of a β-agarase from Flammeovirga sp. MY04

NASA Astrophysics Data System (ADS)

Han, Wenjun; Gu, Jingyan; Liu, Huihui; Li, Fuchuan; Wu, Zhihong; Li, Yuezhong

2015-10-01

A Glycoside hydrolase (GH) typically contains one catalytic module and varied non-catalytic regions (NCRs). However, effects of the NCRs to the catalytic modules remain mostly unclear except the carbohydrate-binding modules (CBMs). AgaG4 is a GH16 endo- β-agarase of the agarolytic marine bacterium Flammeovirga sp. MY04. The enzyme consists of an extra sugar-binding peptide within the catalytic module, with no predictable CBMs but function-unknown sequences in the NCR, which is a new characteristic of agarase sequences. In this study, we deleted the NCR sequence, a 140-amino acid peptide at the C-terminus and expressed the truncated gene, agaG4-T140, in Escherichia coli. After purification and refolding, the truncated agarase rAgaG4-T140 retained the same catalytic temperature and pH value as rAgaG4. Using combined fluorescent labeling, HPLC and MS/MS techniques, we identified the end-products of agarose degradation by rAgaG4-T140 as neoagarotetraose and neoagarohexaose, with a final molar ratio of 1.53:1 and a conversion ratio of approximately 70%, which were similar to those of rAgaG4. However, the truncated agarase rAgaG4-T140 markedly decreased in protein solubility by 15 times and increased in enzymatic activities by 35 times. The oligosaccharide production of rAgaG4-T140 was approximately 25 times the weight of that produced by equimolar rAgaG4. This study provides some insights into the influences of NCR on the biochemical characteristics of agarase AgaG4 and implies some new strategies to improve the properties of a GH enzyme.

Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product*

PubMed Central

Dunne, Matthew; Leicht, Stefan; Krichel, Boris; Thompson, Andrew; Gómez-Torres, Natalia; Garde, Sonia; Narbad, Arjan; Mayer, Melinda J.

2016-01-01

Bacteriophages produce endolysins, which lyse the bacterial host cell to release newly produced virions. The timing of lysis is regulated and is thought to involve the activation of a molecular switch. We present a crystal structure of the activated endolysin CTP1L that targets Clostridium tyrobutyricum, consisting of a complex between the full-length protein and an N-terminally truncated C-terminal cell wall binding domain (CBD). The truncated CBD is produced through an internal translation start site within the endolysin gene. Mutants affecting the internal translation site change the oligomeric state of the endolysin and reduce lytic activity. The activity can be modulated by reconstitution of the full-length endolysin-CBD complex with free CBD. The same oligomerization mechanism applies to the CD27L endolysin that targets Clostridium difficile and the CS74L endolysin that targets Clostridium sporogenes. When the CTP1L endolysin gene is introduced into the commensal bacterium Lactococcus lactis, the truncated CBD is also produced, showing that the alternative start codon can be used in other bacterial species. The identification of a translational switch affecting oligomerization presented here has implications for the design of effective endolysins for the treatment of bacterial infections. PMID:26683375

Parametric instability analysis of truncated conical shells using the Haar wavelet method

NASA Astrophysics Data System (ADS)

Dai, Qiyi; Cao, Qingjie

2018-05-01

In this paper, the Haar wavelet method is employed to analyze the parametric instability of truncated conical shells under static and time dependent periodic axial loads. The present work is based on the Love first-approximation theory for classical thin shells. The displacement field is expressed as the Haar wavelet series in the axial direction and trigonometric functions in the circumferential direction. Then the partial differential equations are reduced into a system of coupled Mathieu-type ordinary differential equations describing dynamic instability behavior of the shell. Using Bolotin's method, the first-order and second-order approximations of principal instability regions are determined. The correctness of present method is examined by comparing the results with those in the literature and very good agreement is observed. The difference between the first-order and second-order approximations of principal instability regions for tensile and compressive loads is also investigated. Finally, numerical results are presented to bring out the influences of various parameters like static load factors, boundary conditions and shell geometrical characteristics on the domains of parametric instability of conical shells.

Model predictive control based on reduced order models applied to belt conveyor system.

PubMed

Chen, Wei; Li, Xin

2016-11-01

In the paper, a model predictive controller based on reduced order model is proposed to control belt conveyor system, which is an electro-mechanics complex system with long visco-elastic body. Firstly, in order to design low-degree controller, the balanced truncation method is used for belt conveyor model reduction. Secondly, MPC algorithm based on reduced order model for belt conveyor system is presented. Because of the error bound between the full-order model and reduced order model, two Kalman state estimators are applied in the control scheme to achieve better system performance. Finally, the simulation experiments are shown that balanced truncation method can significantly reduce the model order with high-accuracy and model predictive control based on reduced-model performs well in controlling the belt conveyor system. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Empirical estimation of a distribution function with truncated and doubly interval-censored data and its application to AIDS studies.

PubMed

Sun, J

1995-09-01

In this paper we discuss the non-parametric estimation of a distribution function based on incomplete data for which the measurement origin of a survival time or the date of enrollment in a study is known only to belong to an interval. Also the survival time of interest itself is observed from a truncated distribution and is known only to lie in an interval. To estimate the distribution function, a simple self-consistency algorithm, a generalization of Turnbull's (1976, Journal of the Royal Statistical Association, Series B 38, 290-295) self-consistency algorithm, is proposed. This method is then used to analyze two AIDS cohort studies, for which direct use of the EM algorithm (Dempster, Laird and Rubin, 1976, Journal of the Royal Statistical Association, Series B 39, 1-38), which is computationally complicated, has previously been the usual method of the analysis.

Robust Stimulation of W1282X-CFTR Channel Activity by a Combination of Allosteric Modulators

PubMed Central

Wang, Wei; Hong, Jeong S.; Rab, Andras; Sorscher, Eric J.; Kirk, Kevin L.

2016-01-01

W1282X is a common nonsense mutation among cystic fibrosis patients that results in the production of a truncated Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) channel. Here we show that the channel activity of the W1282X-CFTR polypeptide is exceptionally low in excised membrane patches at normally saturating doses of ATP and PKA (single channel open probability (PO) < 0.01). However, W1282X-CFTR channels were stimulated by two CFTR modulators, the FDA-approved VX-770 and the dietary compound curcumin. Each of these compounds is an allosteric modulator of CFTR gating that promotes channel activity in the absence of the native ligand, ATP. Although W1282X-CFTR channels were stimulated by VX-770 in the absence of ATP their activities remained dependent on PKA phosphorylation. Thus, activated W1282X-CFTR channels should remain under physiologic control by cyclic nucleotide signaling pathways in vivo. VX-770 and curcumin exerted additive effects on W1282X-CFTR channel gating (opening/closing) in excised patches such that the Po of the truncated channel approached unity (> 0.9) when treated with both modulators. VX-770 and curcumin also additively stimulated W1282X-CFTR mediated currents in polarized FRT epithelial monolayers. In this setting, however, the stimulated W1282X-CFTR currents were smaller than those mediated by wild type CFTR (3–5%) due presumably to lower expression levels or cell surface targeting of the truncated protein. Combining allosteric modulators of different mechanistic classes is worth considering as a treatment option for W1282X CF patients perhaps when coupled with maneuvers to increase expression of the truncated protein. PMID:27007499

Recombinant Protein Truncation Strategy for Inducing Bactericidal Antibodies to the Macrophage Infectivity Potentiator Protein of Neisseria meningitidis and Circumventing Potential Cross-Reactivity with Human FK506-Binding Proteins

PubMed Central

Bielecka, Magdalena K.; Devos, Nathalie; Gilbert, Mélanie; Hung, Miao-Chiu; Weynants, Vincent; Heckels, John E.

2014-01-01

A recombinant macrophage infectivity potentiator (rMIP) protein of Neisseria meningitidis induces significant serum bactericidal antibody production in mice and is a candidate meningococcal vaccine antigen. However, bioinformatics analysis of MIP showed some amino acid sequence similarity to human FK506-binding proteins (FKBPs) in residues 166 to 252 located in the globular domain of the protein. To circumvent the potential concern over generating antibodies that could recognize human proteins, we immunized mice with recombinant truncated type I rMIP proteins that lacked the globular domain and the signal leader peptide (LP) signal sequence (amino acids 1 to 22) and contained the His purification tag at either the N or C terminus (C-term). The immunogenicity of truncated rMIP proteins was compared to that of full (i.e., full-length) rMIP proteins (containing the globular domain) with either an N- or C-terminal His tag and with or without the LP sequence. By comparing the functional murine antibody responses to these various constructs, we determined that C-term His truncated rMIP (−LP) delivered in liposomes induced high levels of antibodies that bound to the surface of wild-type but not Δmip mutant meningococci and showed bactericidal activity against homologous type I MIP (median titers of 128 to 256) and heterologous type II and III (median titers of 256 to 512) strains, thereby providing at least 82% serogroup B strain coverage. In contrast, in constructs lacking the LP, placement of the His tag at the N terminus appeared to abrogate bactericidal activity. The strategy used in this study would obviate any potential concerns regarding the use of MIP antigens for inclusion in bacterial vaccines. PMID:25452551

Variability of Currents in Great South Channel and Over Georges Bank: Observation and Modeling

DTIC Science & Technology

1992-06-01

Rizzoli motivated me to study the driv:,: mechanism of stratified tidal rectification using diagnostic analysis methods . Conversations with Glen...drifter trajectories in the 1988 and 1989 surveys give further encouragement that the analysis method yields an accurate picture of the nontidal flow...harmonic truncation method . Scaling analysis argues that this method is not appropriate for a step topography because it is valid only when the

Incorporating Truncating Variants in PALB2, CHEK2 and ATM into the BOADICEA Breast Cancer Risk Model

PubMed Central

Lee, Andrew J.; Cunningham, Alex P.; Tischkowitz, Marc; Simard, Jacques; Pharoah, Paul D.; Easton, Douglas F.; Antoniou, Antonis C.

2016-01-01

Purpose The proliferation of gene-panel testing precipitates the need for a breast cancer (BC) risk model that incorporates the effects of mutations in several genes and family history (FH). We extended the BOADICEA model to incorporate the effects of truncating variants in PALB2, CHEK2 and ATM. Methods The BC incidence was modelled via the explicit effects of truncating variants in BRCA1/2, PALB2, CHEK2 and ATM and other unobserved genetic effects using segregation analysis methods. Results The predicted average BC risk by age 80 for an ATM mutation carrier is 28%, 30% for CHEK2, 50% for PALB2, 74% for BRCA1 and BRCA2. However, the BC risks are predicted to increase with FH-burden. In families with mutations, predicted risks for mutation-negative members depend on both FH and the specific mutation. The reduction in BC risk after negative predictive-testing is greatest when a BRCA1 mutation is identified in the family, but for women whose relatives carry a CHEK2 or ATM mutation, the risks decrease slightly. Conclusions The model may be a valuable tool for counselling women who have undergone gene-panel testing for providing consistent risks and harmonizing their clinical management. A web-application can be used to obtain BC- risks in clinical practice (http://ccge.medschl.cam.ac.uk/boadicea/). PMID:27464310

Reduced-rank approximations to the far-field transform in the gridded fast multipole method

NASA Astrophysics Data System (ADS)

Hesford, Andrew J.; Waag, Robert C.

2011-05-01

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly.

Reduced-Rank Approximations to the Far-Field Transform in the Gridded Fast Multipole Method.

PubMed

Hesford, Andrew J; Waag, Robert C

2011-05-10

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly.

Reduced-Rank Approximations to the Far-Field Transform in the Gridded Fast Multipole Method

PubMed Central

Hesford, Andrew J.; Waag, Robert C.

2011-01-01

The fast multipole method (FMM) has been shown to have a reduced computational dependence on the size of finest-level groups of elements when the elements are positioned on a regular grid and FFT convolution is used to represent neighboring interactions. However, transformations between plane-wave expansions used for FMM interactions and pressure distributions used for neighboring interactions remain significant contributors to the cost of FMM computations when finest-level groups are large. The transformation operators, which are forward and inverse Fourier transforms with the wave space confined to the unit sphere, are smooth and well approximated using reduced-rank decompositions that further reduce the computational dependence of the FMM on finest-level group size. The adaptive cross approximation (ACA) is selected to represent the forward and adjoint far-field transformation operators required by the FMM. However, the actual error of the ACA is found to be greater than that predicted using traditional estimates, and the ACA generally performs worse than the approximation resulting from a truncated singular-value decomposition (SVD). To overcome these issues while avoiding the cost of a full-scale SVD, the ACA is employed with more stringent accuracy demands and recompressed using a reduced, truncated SVD. The results show a greatly reduced approximation error that performs comparably to the full-scale truncated SVD without degrading the asymptotic computational efficiency associated with ACA matrix assembly. PMID:21552350

Advanced proteomic liquid chromatography

PubMed Central

Xie, Fang; Smith, Richard D.; Shen, Yufeng

2012-01-01

Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput. PMID:22840822

The genetic and economic effect of preliminary culling in the seedling orchard

Treesearch

Don E. Riemenschneider

1977-01-01

The genetic and economic effects of two stages of truncation selection in a white spruce seedling orchard were investigated by computer simulation. Genetic effects were computed by assuming a bivariate distribution of juvenile and mature traits and volume was used as the selection criterion. Seed production was assumed to rise in a linear fashion to maturity and then...

Comparative Characterization of Complete and Truncated Forms of Lactobacillus amylovorus α-Amylase and Role of the C-Terminal Direct Repeats in Raw-Starch Binding

PubMed Central

Rodriguez Sanoja, R.; Morlon-Guyot, J.; Jore, J.; Pintado, J.; Juge, N.; Guyot, J. P.

2000-01-01

Two constructs derived from the α-amylase gene (amyA) of Lactobacillus amylovorus were expressed in Lactobacillus plantarum, and their expression products were purified, characterized, and compared. These products correspond to the complete (AmyA) and truncated (AmyAΔ) forms of α-amylase; AmyAΔ lacks the 66-kDa carboxyl-terminal direct-repeating-unit region. AmyA and AmyAΔ exhibit similar amylase activities towards a range of soluble substrates (amylose, amylopectin and α-cyclodextrin, and soluble starch). The specific activities of the enzymes towards soluble starch are similar, but the KM and Vmax values of AmyAΔ were slightly higher than those of AmyA, whereas the thermal stability of AmyAΔ was lower than that of AmyA. In contrast to AmyA, AmyAΔ is unable to bind to β-cyclodextrin and is only weakly active towards glycogen. More striking is the fact that AmyAΔ cannot bind or hydrolyze raw starch, demonstrating that the carboxyl-terminal repeating-unit domain of AmyA is required for raw-starch binding activity. PMID:10919790

Truncated Painlevé expansion: Tanh-traveling wave solutions and reduction of sine-Poisson equation to a quadrature for stationary and nonstationary three-dimensional collisionless cold plasma

NASA Astrophysics Data System (ADS)

Ibrahim, R. S.; El-Kalaawy, O. H.

2006-10-01

The relativistic nonlinear self-consistent equations for a collisionless cold plasma with stationary ions [R. S. Ibrahim, IMA J. Appl. Math. 68, 523 (2003)] are extended to 3 and 3+1 dimensions. The resulting system of equations is reduced to the sine-Poisson equation. The truncated Painlevé expansion and reduction of the partial differential equation to a quadrature problem (RQ method) are described and applied to obtain the traveling wave solutions of the sine-Poisson equation for stationary and nonstationary equations in 3 and 3+1 dimensions describing the charge-density equilibrium configuration model.

Modern CACSD using the Robust-Control Toolbox

NASA Technical Reports Server (NTRS)

Chiang, Richard Y.; Safonov, Michael G.

1989-01-01

The Robust-Control Toolbox is a collection of 40 M-files which extend the capability of PC/PRO-MATLAB to do modern multivariable robust control system design. Included are robust analysis tools like singular values and structured singular values, robust synthesis tools like continuous/discrete H(exp 2)/H infinity synthesis and Linear Quadratic Gaussian Loop Transfer Recovery methods and a variety of robust model reduction tools such as Hankel approximation, balanced truncation and balanced stochastic truncation, etc. The capabilities of the toolbox are described and illustated with examples to show how easily they can be used in practice. Examples include structured singular value analysis, H infinity loop-shaping and large space structure model reduction.

Discrete conservation properties for shallow water flows using mixed mimetic spectral elements

NASA Astrophysics Data System (ADS)

Lee, D.; Palha, A.; Gerritsma, M.

2018-03-01

A mixed mimetic spectral element method is applied to solve the rotating shallow water equations. The mixed method uses the recently developed spectral element histopolation functions, which exactly satisfy the fundamental theorem of calculus with respect to the standard Lagrange basis functions in one dimension. These are used to construct tensor product solution spaces which satisfy the generalized Stokes theorem, as well as the annihilation of the gradient operator by the curl and the curl by the divergence. This allows for the exact conservation of first order moments (mass, vorticity), as well as higher moments (energy, potential enstrophy), subject to the truncation error of the time stepping scheme. The continuity equation is solved in the strong form, such that mass conservation holds point wise, while the momentum equation is solved in the weak form such that vorticity is globally conserved. While mass, vorticity and energy conservation hold for any quadrature rule, potential enstrophy conservation is dependent on exact spatial integration. The method possesses a weak form statement of geostrophic balance due to the compatible nature of the solution spaces and arbitrarily high order spatial error convergence.

Symplectic Propagation of the Map, Tangent Map and Tangent Map Derivative through Quadrupole and Combined-Function Dipole Magnets without Truncation

NASA Astrophysics Data System (ADS)

Bruhwiler, D. L.; Cary, J. R.; Shasharina, S.

1998-04-01

The MAPA accelerator modeling code symplectically advances the full nonlinear map, tangent map and tangent map derivative through all accelerator elements. The tangent map and its derivative are nonlinear generalizations of Browns first- and second-order matrices(K. Brown, SLAC-75, Rev. 4 (1982), pp. 107-118.), and they are valid even near the edges of the dynamic aperture, which may be beyond the radius of convergence for a truncated Taylor series. In order to avoid truncation of the map and its derivatives, the Hamiltonian is split into pieces for which the map can be obtained analytically. Yoshidas method(H. Yoshida, Phys. Lett. A 150 (1990), pp. 262-268.) is then used to obtain a symplectic approximation to the map, while the tangent map and its derivative are appropriately composed at each step to obtain them with equal accuracy. We discuss our splitting of the quadrupole and combined-function dipole Hamiltonians and show that typically few steps are required for a high-energy accelerator.

“Smooth” Semiparametric Regression Analysis for Arbitrarily Censored Time-to-Event Data

PubMed Central

Zhang, Min; Davidian, Marie

2008-01-01

Summary A general framework for regression analysis of time-to-event data subject to arbitrary patterns of censoring is proposed. The approach is relevant when the analyst is willing to assume that distributions governing model components that are ordinarily left unspecified in popular semiparametric regression models, such as the baseline hazard function in the proportional hazards model, have densities satisfying mild “smoothness” conditions. Densities are approximated by a truncated series expansion that, for fixed degree of truncation, results in a “parametric” representation, which makes likelihood-based inference coupled with adaptive choice of the degree of truncation, and hence flexibility of the model, computationally and conceptually straightforward with data subject to any pattern of censoring. The formulation allows popular models, such as the proportional hazards, proportional odds, and accelerated failure time models, to be placed in a common framework; provides a principled basis for choosing among them; and renders useful extensions of the models straightforward. The utility and performance of the methods are demonstrated via simulations and by application to data from time-to-event studies. PMID:17970813

Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation

PubMed Central

Nguyen, Houbi; Jäger, Marcus; Moretto, Alessandro; Gruebele, Martin; Kelly, Jeffery W.

2003-01-01

The equilibrium unfolding of the Formin binding protein 28 (FBP) WW domain, a stable three-stranded β-sheet protein, can be described as reversible apparent two-state folding. Kinetics studied by laser temperature jump reveal a third state at temperatures below the midpoint of unfolding. The FBP free-energy surface can be tuned between three-state and two-state kinetics by changing the temperature, by truncation of the C terminus, or by selected point mutations. FBP WW domain is the smallest three-state folder studied to date and the only one that can be freely tuned between three-state and apparent two-state folding by several methods (temperature, truncation, and mutation). Its small size (28–37 residues), the availability of a quantitative reaction coordinate (φT), the fast folding time scale (10s of μs), and the tunability of the folding routes by small temperature or sequence changes make this system the ideal prototype for studying more subtle features of the folding free-energy landscape by simulations or analytical theory. PMID:12651955

A conformal truncation framework for infinite-volume dynamics

DOE PAGES

Katz, Emanuel; Khandker, Zuhair U.; Walters, Matthew T.

2016-07-28

Here, we present a new framework for studying conformal field theories deformed by one or more relevant operators. The original CFT is described in infinite volume using a basis of states with definite momentum, P, and conformal Casimir, C. The relevant deformation is then considered using lightcone quantization, with the resulting Hamiltonian expressed in terms of this CFT basis. Truncating to states with C ≤ C max, one can numerically find the resulting spectrum, as well as other dynamical quantities, such as spectral densities of operators. This method requires the introduction of an appropriate regulator, which can be chosen tomore » preserve the conformal structure of the basis. We check this framework in three dimensions for various perturbative deformations of a free scalar CFT, and for the case of a free O(N) CFT deformed by a mass term and a non-perturbative quartic interaction at large- N. In all cases, the truncation scheme correctly reproduces known analytic results. As a result, we also discuss a general procedure for generating a basis of Casimir eigenstates for a free CFT in any number of dimensions.« less

Strategies for Characterization of Low-Abundant Intact or Truncated Low-Molecular-Weight Proteins From Human Plasma.

PubMed

Cai, Tanxi; Yang, Fuquan

2017-01-01

Low-molecular-weight region (LMW, MW≤30kDa) of human serum/plasma proteins, including small intact proteins, truncated fragments of larger proteins, along with some other small components, has been associated with the ongoing physiological and pathological events, and thereby represent a treasure trove of diagnostic molecules. Great progress in the mining of novel biomarkers from this diagnostic treasure trove for disease diagnosis and health monitoring has been achieved based on serum samples from healthy individuals and patients and powerful new approaches in biochemistry and systems biology. However, cumulative evidence indicates that many potential LMW protein biomarkers might still have escaped from detection due to their low abundance, the dynamic complexity of serum/plasma, and the limited efficiency of characterization approaches. Here, we provide an overview of the current state of knowledge with respect to strategies for the characterization of low-abundant LMW proteins (small intact or truncated proteins) from human serum/plasma, involving prefractionation or enrichment methods to reduce dynamic range and mass spectrometry-based characterization of low-abundant LMW proteins. © 2017 Elsevier Inc. All rights reserved.

Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation.

PubMed

Nguyen, Houbi; Jager, Marcus; Moretto, Alessandro; Gruebele, Martin; Kelly, Jeffery W

2003-04-01

The equilibrium unfolding of the Formin binding protein 28 (FBP) WW domain, a stable three-stranded beta-sheet protein, can be described as reversible apparent two-state folding. Kinetics studied by laser temperature jump reveal a third state at temperatures below the midpoint of unfolding. The FBP free-energy surface can be tuned between three-state and two-state kinetics by changing the temperature, by truncation of the C terminus, or by selected point mutations. FBP WW domain is the smallest three-state folder studied to date and the only one that can be freely tuned between three-state and apparent two-state folding by several methods (temperature, truncation, and mutation). Its small size (28-37 residues), the availability of a quantitative reaction coordinate (phi(T)), the fast folding time scale (10s of micros), and the tunability of the folding routes by small temperature or sequence changes make this system the ideal prototype for studying more subtle features of the folding free-energy landscape by simulations or analytical theory.

Statistical methods of fracture characterization using acoustic borehole televiewer log interpretation

NASA Astrophysics Data System (ADS)

Massiot, Cécile; Townend, John; Nicol, Andrew; McNamara, David D.

2017-08-01

Acoustic borehole televiewer (BHTV) logs provide measurements of fracture attributes (orientations, thickness, and spacing) at depth. Orientation, censoring, and truncation sampling biases similar to those described for one-dimensional outcrop scanlines, and other logging or drilling artifacts specific to BHTV logs, can affect the interpretation of fracture attributes from BHTV logs. K-means, fuzzy K-means, and agglomerative clustering methods provide transparent means of separating fracture groups on the basis of their orientation. Fracture spacing is calculated for each of these fracture sets. Maximum likelihood estimation using truncated distributions permits the fitting of several probability distributions to the fracture attribute data sets within truncation limits, which can then be extrapolated over the entire range where they naturally occur. Akaike Information Criterion (AIC) and Schwartz Bayesian Criterion (SBC) statistical information criteria rank the distributions by how well they fit the data. We demonstrate these attribute analysis methods with a data set derived from three BHTV logs acquired from the high-temperature Rotokawa geothermal field, New Zealand. Varying BHTV log quality reduces the number of input data points, but careful selection of the quality levels where fractures are deemed fully sampled increases the reliability of the analysis. Spacing data analysis comprising up to 300 data points and spanning three orders of magnitude can be approximated similarly well (similar AIC rankings) with several distributions. Several clustering configurations and probability distributions can often characterize the data at similar levels of statistical criteria. Thus, several scenarios should be considered when using BHTV log data to constrain numerical fracture models.

Truncation of C-terminal 20 amino acids in PA-X contributes to adaptation of swine influenza virus in pigs.

PubMed

Xu, Guanlong; Zhang, Xuxiao; Sun, Yipeng; Liu, Qinfang; Sun, Honglei; Xiong, Xin; Jiang, Ming; He, Qiming; Wang, Yu; Pu, Juan; Guo, Xin; Yang, Hanchun; Liu, Jinhua

2016-02-25

The PA-X protein is a fusion protein incorporating the N-terminal 191 amino acids of the PA protein with a short C-terminal sequence encoded by an overlapping ORF (X-ORF) in segment 3 that is accessed by + 1 ribosomal frameshifting, and this X-ORF exists in either full length or a truncated form (either 61-or 41-condons). Genetic evolution analysis indicates that all swine influenza viruses (SIVs) possessed full-length PA-X prior to 1985, but since then SIVs with truncated PA-X have gradually increased and become dominant, implying that truncation of this protein may contribute to the adaptation of influenza virus in pigs. To verify this hypothesis, we constructed PA-X extended viruses in the background of a "triple-reassortment" H1N2 SIV with truncated PA-X, and evaluated their biological characteristics in vitro and in vivo. Compared with full-length PA-X, SIV with truncated PA-X had increased viral replication in porcine cells and swine respiratory tissues, along with enhanced pathogenicity, replication and transmissibility in pigs. Furthermore, we found that truncation of PA-X improved the inhibition of IFN-I mRNA expression. Hereby, our results imply that truncation of PA-X may contribute to the adaptation of SIV in pigs.

The combination of i-leader truncation and gemcitabine improves oncolytic adenovirus efficacy in an immunocompetent model.

PubMed

Puig-Saus, C; Laborda, E; Rodríguez-García, A; Cascalló, M; Moreno, R; Alemany, R

2014-02-01

Adenovirus (Ad) i-leader protein is a small protein of unknown function. The C-terminus truncation of the i-leader protein increases Ad release from infected cells and cytotoxicity. In the current study, we use the i-leader truncation to enhance the potency of an oncolytic Ad. In vitro, an i-leader truncated oncolytic Ad is released faster to the supernatant of infected cells, generates larger plaques, and is more cytotoxic in both human and Syrian hamster cell lines. In mice bearing human tumor xenografts, the i-leader truncation enhances oncolytic efficacy. However, in a Syrian hamster pancreatic tumor model, which is immunocompetent and less permissive to human Ad, antitumor efficacy is only observed when the i-leader truncated oncolytic Ad, but not the non-truncated version, is combined with gemcitabine. This synergistic effect observed in the Syrian hamster model was not seen in vitro or in immunodeficient mice bearing the same pancreatic hamster tumors, suggesting a role of the immune system in this synergism. These results highlight the interest of the i-leader C-terminus truncation because it enhances the antitumor potency of an oncolytic Ad and provides synergistic effects with gemcitabine in the presence of an immune competent system.

Computer modeling of multiple-channel input signals and intermodulation losses caused by nonlinear traveling wave tube amplifiers

NASA Technical Reports Server (NTRS)

Stankiewicz, N.

1982-01-01

The multiple channel input signal to a soft limiter amplifier as a traveling wave tube is represented as a finite, linear sum of Gaussian functions in the frequency domain. Linear regression is used to fit the channel shapes to a least squares residual error. Distortions in output signal, namely intermodulation products, are produced by the nonlinear gain characteristic of the amplifier and constitute the principal noise analyzed in this study. The signal to noise ratios are calculated for various input powers from saturation to 10 dB below saturation for two specific distributions of channels. A criterion for the truncation of the series expansion of the nonlinear transfer characteristic is given. It is found that he signal to noise ratios are very sensitive to the coefficients used in this expansion. Improper or incorrect truncation of the series leads to ambiguous results in the signal to noise ratios.

Construction and application of novel feedback-resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthases by engineering the N-terminal domain for L-phenylalanine synthesis.

PubMed

Zhang, Chuanzhi; Kang, Zhen; Zhang, Junli; Du, Guocheng; Chen, Jian; Yu, Xiaobin

2014-04-01

3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHP synthase) encoded by aroF is the first enzyme of the shikimate pathway. In the present study, an AroF variant with a deficiency in residue Ile11 (named AroF*) was shown to be insensitive to l-tyrosine. According to three-dimensional structure analysis, nine AroF variants were constructed with truncation of different N-terminal fragments, and overexpression of the variants AroF(Δ(1-9)) , AroF(Δ(1-10)) , AroF(Δ(1-12)) and, in particular, AroF(Δ(1-11)) significantly increased the accumulation of l-phenylalanine (l-Phe). However, the AroG and AroH variants with similar truncations of the N-terminal fragments decreased the production of l-Phe. By co-overexpressing AroF(Δ(1-11)) and PheA(fbr) , the production of l-Phe was increased from 2.36 ± 0.07 g L(-1) (co-overexpression of the wild-type AroF and PheA(fbr) ) to 4.29 ± 0.06 g L(-1) . The novel variant AroF(Δ(1-11)) showed great potential for the production of aromatic amino acids and their derivatives. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models

NASA Astrophysics Data System (ADS)

Rodgers, Jocelyn M.; Weeks, John D.

2009-12-01

Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular, results for the simple point charge/extended (SPC/E) water model treated with spherically truncated Coulomb interactions suggested by local molecular field theory [J. M. Rodgers and J. D. Weeks, Proc. Natl. Acad. Sci. U.S.A. 105, 19136 (2008)] are presented. We extend the results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically truncated bulk species.

Consumer vinegar test for determining calcium disintegration.

PubMed

Mason, N A; Patel, J D; Dressman, J B; Shimp, L A

1992-09-01

A consumer test and standardized methods were compared for measuring the disintegration of calcium tablets, and the disintegration results were compared with results of dissolution testing to determine the ability of the consumer test of disintegration to predict bioavailability of calcium. Disintegration of 17 calcium supplement products, in tablet form, was studied in Simulated Gastric Fluid Test Solution, USP, without pepsin (GF), in distilled water, and in white distilled vinegar. For disintegration testing with GF and with distilled water, six tablets of each product were placed in an apparatus and immersed in the solution at 37 degrees C for 60 minutes. Six tablets of each product were tested in 200 mL of vinegar at room temperature for 30 minutes. Disintegration was determined by visual observation. Seven products were tested for dissolution in GF or water. Three samples of each product were tested at intervals over 120 minutes for calcium content. Results of testing with an ion-selective electrode were converted to milligrams and compared with the calcium content of the tablets (as claimed on the package label). The mean disintegration times of various calcium products in vinegar ranged from 1.8 to greater than 30 minutes. The mean time in distilled water and GF ranged from 1.6 to greater than 60 minutes and from 1.0 to greater than 60 minutes, respectively. Results were in agreement in 87% to 93% of cases between the consumer vinegar test and the standardized disintegration test methods, a significant correlation. No correlation was found between disintegration time and the extent of dissolution. The disintegration and dissolution of commercially available calcium tablets was highly variable.(ABSTRACT TRUNCATED AT 250 WORDS)

Stable expression and purification of a functional processed Fab' fragment from a single nascent polypeptide in CHO cells expressing the mCAT-1 retroviral receptor.

PubMed

Camper, Nicolas; Byrne, Teresa; Burden, Roberta E; Lowry, Jenny; Gray, Breena; Johnston, James A; Migaud, Marie E; Olwill, Shane A; Buick, Richard J; Scott, Christopher J

2011-09-30

Monoclonal antibodies and derivative formats such as Fab' fragments are used in a broad range of therapeutic, diagnostic and research applications. New systems and methodologies that can improve the production of these proteins are consequently of much interest. Here we present a novel approach for the rapid production of processed Fab' fragments in a CHO cell line that has been engineered to express the mouse cationic amino acid transporter receptor 1 (mCAT-1). This facilitated the introduction of the target antibody gene through retroviral transfection, rapidly producing stable expression. Using this system, we designed a single retroviral vector construct for the expression of a target Fab' fragment as a single polypeptide with a furin cleavage site and a FMDV 2A self-cleaving peptide introduced to bridge the light and truncated heavy chain regions. The introduction of these cleavage motifs ensured equimolar expression and processing of the heavy and light domains as exemplified by the production of an active chimeric Fab' fragment against the Fas receptor, routinely expressed in 1-2mg/L yield in spinner-flask cell cultures. These results demonstrate that this method could have application in the facile production of bioactive Fab' fragments. Copyright © 2011 Elsevier B.V. All rights reserved.

Video Extrapolation Method Based on Time-Varying Energy Optimization and CIP.

PubMed

Sakaino, Hidetomo

2016-09-01

Video extrapolation/prediction methods are often used to synthesize new videos from images. For fluid-like images and dynamic textures as well as moving rigid objects, most state-of-the-art video extrapolation methods use non-physics-based models that learn orthogonal bases from a number of images but at high computation cost. Unfortunately, data truncation can cause image degradation, i.e., blur, artifact, and insufficient motion changes. To extrapolate videos that more strictly follow physical rules, this paper proposes a physics-based method that needs only a few images and is truncation-free. We utilize physics-based equations with image intensity and velocity: optical flow, Navier-Stokes, continuity, and advection equations. These allow us to use partial difference equations to deal with the local image feature changes. Image degradation during extrapolation is minimized by updating model parameters, where a novel time-varying energy balancer model that uses energy based image features, i.e., texture, velocity, and edge. Moreover, the advection equation is discretized by high-order constrained interpolation profile for lower quantization error than can be achieved by the previous finite difference method in long-term videos. Experiments show that the proposed energy based video extrapolation method outperforms the state-of-the-art video extrapolation methods in terms of image quality and computation cost.

Construction of energy-stable Galerkin reduced order models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalashnikova, Irina; Barone, Matthew Franklin; Arunajatesan, Srinivasan

2013-05-01

This report aims to unify several approaches for building stable projection-based reduced order models (ROMs). Attention is focused on linear time-invariant (LTI) systems. The model reduction procedure consists of two steps: the computation of a reduced basis, and the projection of the governing partial differential equations (PDEs) onto this reduced basis. Two kinds of reduced bases are considered: the proper orthogonal decomposition (POD) basis and the balanced truncation basis. The projection step of the model reduction can be done in two ways: via continuous projection or via discrete projection. First, an approach for building energy-stable Galerkin ROMs for linear hyperbolicmore » or incompletely parabolic systems of PDEs using continuous projection is proposed. The idea is to apply to the set of PDEs a transformation induced by the Lyapunov function for the system, and to build the ROM in the transformed variables. The resulting ROM will be energy-stable for any choice of reduced basis. It is shown that, for many PDE systems, the desired transformation is induced by a special weighted L2 inner product, termed the %E2%80%9Csymmetry inner product%E2%80%9D. Attention is then turned to building energy-stable ROMs via discrete projection. A discrete counterpart of the continuous symmetry inner product, a weighted L2 inner product termed the %E2%80%9CLyapunov inner product%E2%80%9D, is derived. The weighting matrix that defines the Lyapunov inner product can be computed in a black-box fashion for a stable LTI system arising from the discretization of a system of PDEs in space. It is shown that a ROM constructed via discrete projection using the Lyapunov inner product will be energy-stable for any choice of reduced basis. Connections between the Lyapunov inner product and the inner product induced by the balanced truncation algorithm are made. Comparisons are also made between the symmetry inner product and the Lyapunov inner product. The performance of ROMs constructed using these inner products is evaluated on several benchmark test cases.« less

Generation and application of the equations of condition for high order Runge-Kutta methods

NASA Technical Reports Server (NTRS)

Haley, D. C.

1972-01-01

This thesis develops the equations of condition necessary for determining the coefficients for Runge-Kutta methods used in the solution of ordinary differential equations. The equations of condition are developed for Runge-Kutta methods of order four through order nine. Once developed, these equations are used in a comparison of the local truncation errors for several sets of Runge-Kutta coefficients for methods of order three up through methods of order eight.

Errors in finite-difference computations on curvilinear coordinate systems

NASA Technical Reports Server (NTRS)

Mastin, C. W.; Thompson, J. F.

1980-01-01

Curvilinear coordinate systems were used extensively to solve partial differential equations on arbitrary regions. An analysis of truncation error in the computation of derivatives revealed why numerical results may be erroneous. A more accurate method of computing derivatives is presented.

Truncation of C-terminal 20 amino acids in PA-X contributes to adaptation of swine influenza virus in pigs

PubMed Central

Xu, Guanlong; Zhang, Xuxiao; Sun, Yipeng; Liu, Qinfang; Sun, Honglei; Xiong, Xin; Jiang, Ming; He, Qiming; Wang, Yu; Pu, Juan; Guo, Xin; Yang, Hanchun; Liu, Jinhua

2016-01-01

The PA-X protein is a fusion protein incorporating the N-terminal 191 amino acids of the PA protein with a short C-terminal sequence encoded by an overlapping ORF (X-ORF) in segment 3 that is accessed by + 1 ribosomal frameshifting, and this X-ORF exists in either full length or a truncated form (either 61-or 41-condons). Genetic evolution analysis indicates that all swine influenza viruses (SIVs) possessed full-length PA-X prior to 1985, but since then SIVs with truncated PA-X have gradually increased and become dominant, implying that truncation of this protein may contribute to the adaptation of influenza virus in pigs. To verify this hypothesis, we constructed PA-X extended viruses in the background of a “triple-reassortment” H1N2 SIV with truncated PA-X, and evaluated their biological characteristics in vitro and in vivo. Compared with full-length PA-X, SIV with truncated PA-X had increased viral replication in porcine cells and swine respiratory tissues, along with enhanced pathogenicity, replication and transmissibility in pigs. Furthermore, we found that truncation of PA-X improved the inhibition of IFN-I mRNA expression. Hereby, our results imply that truncation of PA-X may contribute to the adaptation of SIV in pigs. PMID:26912401

Designing fire safe interiors.

PubMed

Belles, D W

1992-01-01

Any product that causes a fire to grow large is deficient in fire safety performance. A large fire in any building represents a serious hazard. Multiple-death fires almost always are linked to fires that grow quickly to a large size. Interior finishes have large, continuous surfaces over which fire can spread. They are regulated to slow initial fire growth, and must be qualified for use on the basis of fire tests. To obtain meaningful results, specimens must be representative of actual installation. Variables--such as the substrate, the adhesive, and product thickness and density--can affect product performance. The tunnel test may not adequately evaluate some products, such as foam plastics or textile wall coverings, thermoplastic materials, or materials of minimal mass. Where questions exist, products should be evaluated on a full-scale basis. Curtains and draperies are examples of products that ignite easily and spread flames readily. The present method for testing curtains and draperies evaluates one fabric at a time. Although a fabric tested alone may perform well, fabrics that meet test standards individually sometimes perform poorly when tested in combination. Contents and furnishings constitute the major fuels in many fires. Contents may involve paper products and other lightweight materials that are easily ignited and capable of fast fire growth. Similarly, a small source may ignite many items of furniture that are capable of sustained fire growth. Upholstered furniture can reach peak burning rates in less than 5 minutes. Furnishings have been associated with many multiple-death fires.(ABSTRACT TRUNCATED AT 250 WORDS)

Sediment diffusion method improves wastewater nitrogen removal in the receiving lake sediments.

PubMed

Aalto, Sanni L; Saarenheimo, Jatta; Ropponen, Janne; Juntunen, Janne; Rissanen, Antti J; Tiirola, Marja

2018-07-01

Sediment microbes have a great potential to transform reactive N to harmless N 2 , thus decreasing wastewater nitrogen load into aquatic ecosystems. Here, we examined if spatial allocation of the wastewater discharge by a specially constructed sediment diffuser pipe system enhanced the microbial nitrate reduction processes. Full-scale experiments were set on two Finnish lake sites, Keuruu and Petäjävesi, and effects on the nitrate removal processes were studied using the stable isotope pairing technique. All nitrate reduction rates followed nitrate concentrations, being highest at the wastewater-influenced sampling points. Complete denitrification with N 2 as an end-product was the main nitrate reduction process, indicating that the high nitrate and organic matter concentrations of wastewater did not promote nitrous oxide (N 2 O) production (truncated denitrification) or ammonification (dissimilatory nitrate reduction to ammonium; DNRA). Using 3D simulation, we demonstrated that the sediment diffusion method enhanced the contact time and amount of wastewater near the sediment surface especially in spring and in autumn, altering organic matter concentration and oxygen levels, and increasing the denitrification capacity of the sediment. We estimated that natural denitrification potentially removed 3-10% of discharged wastewater nitrate in the 33 ha study area of Keuruu, and the sediment diffusion method increased this areal denitrification capacity on average 45%. Overall, our results indicate that sediment diffusion method can supplement wastewater treatment plant (WWTP) nitrate removal without enhancing alternative harmful processes. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Prior-based artifact correction (PBAC) in computed tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heußer, Thorsten, E-mail: thorsten.heusser@dkfz-heidelberg.de; Brehm, Marcus; Ritschl, Ludwig

2014-02-15

Purpose: Image quality in computed tomography (CT) often suffers from artifacts which may reduce the diagnostic value of the image. In many cases, these artifacts result from missing or corrupt regions in the projection data, e.g., in the case of metal, truncation, and limited angle artifacts. The authors propose a generalized correction method for different kinds of artifacts resulting from missing or corrupt data by making use of available prior knowledge to perform data completion. Methods: The proposed prior-based artifact correction (PBAC) method requires prior knowledge in form of a planning CT of the same patient or in form ofmore » a CT scan of a different patient showing the same body region. In both cases, the prior image is registered to the patient image using a deformable transformation. The registered prior is forward projected and data completion of the patient projections is performed using smooth sinogram inpainting. The obtained projection data are used to reconstruct the corrected image. Results: The authors investigate metal and truncation artifacts in patient data sets acquired with a clinical CT and limited angle artifacts in an anthropomorphic head phantom data set acquired with a gantry-based flat detector CT device. In all cases, the corrected images obtained by PBAC are nearly artifact-free. Compared to conventional correction methods, PBAC achieves better artifact suppression while preserving the patient-specific anatomy at the same time. Further, the authors show that prominent anatomical details in the prior image seem to have only minor impact on the correction result. Conclusions: The results show that PBAC has the potential to effectively correct for metal, truncation, and limited angle artifacts if adequate prior data are available. Since the proposed method makes use of a generalized algorithm, PBAC may also be applicable to other artifacts resulting from missing or corrupt data.« less

Manipulation of GES and ERG20 for geraniol overproduction in Saccharomyces cerevisiae.

PubMed

Jiang, Guo-Zhen; Yao, Ming-Dong; Wang, Ying; Zhou, Liang; Song, Tian-Qing; Liu, Hong; Xiao, Wen-Hai; Yuan, Ying-Jin

2017-05-01

Manipulation of monoterpene synthases to maximize flux towards targeted products from GPP (geranyl diphosphate) is the main challenge for heterologous monoterpene overproduction, in addition to cell toxicity from compounds themselves. In our study, by manipulation of the key enzymes geraniol synthase (GES) and farnesyl diphosphate synthase (Erg20), geraniol (a valuable acyclic monoterpene alcohol) overproduction was achieved in Saccharomyces cerevisiae with truncated 3-hydroxy-3-methylglutaryl-coenzyme reductase (tHMGR) and isopentenyl diphosphate isomerase (IDI1) overexpressed. The expressions of all above engineered genes were under the control of Gal promoter for alleviating product toxicity. Geraniol production varied from trace amount to 43.19mg/L (CrGES, GES from Catharanthus roseus) by screening of nine GESs from diverse species. Further through protein structure analysis and site-directed mutation in CrGES, it was firstly demonstrated that among the high-conserved amino acid residues located in active pocket, Y436 and D501 with strong affinity to diphosphate function group, were critical for the dephosphorylation (the core step for geraniol formation). Moreover, the truncation position of the transit peptide from the N-terminus of CrGES was found to influence protein expression and activity significantly, obtaining a titer of 191.61mg/L geraniol in strain with CrGES truncated at S43 (t3CrGES). Furthermore, directed by surface electrostatics distribution of t3CrGES and Erg20 WW (Erg20 F96W-N127W ), co-expression of the reverse fusion of Erg20 ww /t3CrGES and another copy of Erg20 WW promoted the geraniol titer to 523.96mg/L at shakes flask level, due to enhancing GPP accessibility led by protein interaction of t3CrGES-Erg20 WW and the free Erg20 WW . Eventually, a highest reported titer of 1.68g/L geraniol in eukaryote cells was achieved in 2.0L fed-batch fermentation under carbon restriction strategy. Our research opens large opportunities for other microbial production of monoterpenes. It also sets a good reference for desired compounds overproduction in microorganisms in terms of manipulation of key enzymes by protein engineering and metabolic engineering. Copyright © 2017. Published by Elsevier Inc.

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells

PubMed Central

Barua, Dipak; Hlavacek, William S.

2013-01-01

In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β—catenin, which is regulated by a multiprotein complex called the destruction complex. The destruction complex comprises APC, Axin, β—catenin, serine/threonine kinases, and other proteins. The kinases and , which are recruited by Axin, mediate phosphorylation of β—catenin, which initiates its ubiquitination and proteosomal degradation. The mechanism of regulation of β—catenin degradation by the destruction complex and the role of truncation of APC in colorectal cancer are not entirely understood. Through formulation and analysis of a rule-based computational model, we investigated the regulation of β—catenin phosphorylation and degradation by APC and the effect of APC truncation on function of the destruction complex. The model integrates available mechanistic knowledge about site-specific interactions and phosphorylation of destruction complex components and is consistent with an array of published data. We find that the phosphorylated truncated form of APC can outcompete Axin for binding to β—catenin, provided that Axin is limiting, and thereby sequester β—catenin away from Axin and the Axin-recruited kinases and . Full-length APC also competes with Axin for binding to β—catenin; however, full-length APC is able, through its SAMP repeats, which bind Axin and which are missing in truncated oncogenic forms of APC, to bring β—catenin into indirect association with Axin and Axin-recruited kinases. Because our model indicates that the positive effects of truncated APC on β—catenin levels depend on phosphorylation of APC, at the first 20-amino acid repeat, and because phosphorylation of this site is mediated by , we suggest that is a potential target for therapeutic intervention in colorectal cancer. Specific inhibition of is predicted to limit binding of β—catenin to truncated APC and thereby to reverse the effect of APC truncation. PMID:24086117

Correction to: Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells.

PubMed

Pietrosemoli, Natalia; Mella, Sébastien; Yennek, Siham; Baghdadi, Meryem B; Sakai, Hiroshi; Sambasivan, Ramkumar; Pala, Francesca; Di Girolamo, Daniela; Tajbakhsh, Shahragim

2018-06-06

After publication of this article [1], the authors noted that the legends for supplementary files Figures S3 and S4 were truncated in the production process, therefore lacking some information concerning these Figures. The complete legends are included in this Correction. The authors apologize for any inconvenience that this might have caused.

Truncated Hormone Inhibits Breast Tumor Blood Vessel Formation, Not Tumor Growth | Center for Cancer Research

Cancer.gov

The hormone prolactin (PRL) plays a critical role in normal breast development by stimulating the proliferation of mammary cells, the production of milk proteins, and the formation of new mammary blood vessels. Unfortunately, the same cell and vessel growth pathways controlled by PRL in normal cells also operate in breast cancer cells, and elevated plasma PRL is a risk factor

Balancing Performance and Sustainability in Next-Generation PMR Technologies for OMC Structures

DTIC Science & Technology

2016-05-26

Additionally, the reactive intermediates can form an elimination product that conjugates with glutathione, thereby depleting the concentration of...thermomechanical properties of polyimides, but due to its truncated molecular weight, is processable, thus enabling the fabrication of fiber reinforced polymer ...degradation of the remaining polymer . The oligomers possessing anilines with a higher degree of aliphatic character (PMR-1, -6, and -7), exhibit significant

Soluble γ-secretase modulators selectively inhibit the production of the 42-amino acid amyloid β peptide variant and augment the production of multiple carboxy-truncated amyloid β species.

PubMed

Wagner, Steven L; Zhang, Can; Cheng, Soan; Nguyen, Phuong; Zhang, Xulun; Rynearson, Kevin D; Wang, Rong; Li, Yueming; Sisodia, Sangram S; Mobley, William C; Tanzi, Rudolph E

2014-02-04

Alzheimer's disease (AD) is characterized pathologically by an abundance of extracellular neuritic plaques composed primarily of the 42-amino acid amyloid β peptide variant (Aβ42). In the majority of familial AD (FAD) cases, e.g., those harboring mutations in presenilin 1 (PS1), there is a relative increase in the levels of Aβ42 compared to the levels of Aβ40. We previously reported the characterization of a series of aminothiazole-bridged aromates termed aryl aminothiazole γ-secretase modulators or AGSMs [Kounnas, M. Z., et al. (2010) Neuron 67, 769-780] and showed their potential for use in the treatment of FAD [Wagner, S. L., et al. (2012) Arch. Neurol. 69, 1255-1258]. Here we describe a series of GSMs with physicochemical properties improved compared to those of AGSMs. Specific heterocycle replacements of the phenyl rings in AGSMs provided potent molecules with improved aqueous solubilities. A number of these soluble γ-secretase modulators (SGSMs) potently lowered Aβ42 levels without inhibiting proteolysis of Notch or causing accumulation of amyloid precursor protein carboxy-terminal fragments, even at concentrations approximately 1000-fold greater than their IC50 values for reducing Aβ42 levels. The effects of one potent SGSM on Aβ peptide production were verified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry, showing enhanced production of a number of carboxy-truncated Aβ species. This SGSM also inhibited Aβ42 peptide production in a highly purified reconstituted γ-secretase in vitro assay system and retained the ability to modulate γ-secretase-mediated proteolysis in a stably transfected cell culture model overexpressing a human PS1 mutation validating the potential for use in FAD.

Volume-of-interest reconstruction from severely truncated data in dental cone-beam CT

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Kusnoto, Budi; Han, Xiao; Sidky, E. Y.; Pan, Xiaochuan

2015-03-01

As cone-beam computed tomography (CBCT) has gained popularity rapidly in dental imaging applications in the past two decades, radiation dose in CBCT imaging remains a potential, health concern to the patients. It is a common practice in dental CBCT imaging that only a small volume of interest (VOI) containing the teeth of interest is illuminated, thus substantially lowering imaging radiation dose. However, this would yield data with severe truncations along both transverse and longitudinal directions. Although images within the VOI reconstructed from truncated data can be of some practical utility, they often are compromised significantly by truncation artifacts. In this work, we investigate optimization-based reconstruction algorithms for VOI image reconstruction from CBCT data of dental patients containing severe truncations. In an attempt to further reduce imaging dose, we also investigate optimization-based image reconstruction from severely truncated data collected at projection views substantially fewer than those used in clinical dental applications. Results of our study show that appropriately designed optimization-based reconstruction can yield VOI images with reduced truncation artifacts, and that, when reconstructing from only one half, or even one quarter, of clinical data, it can also produce VOI images comparable to that of clinical images.

Matrix product state description of Halperin states

NASA Astrophysics Data System (ADS)

Crépel, V.; Estienne, B.; Bernevig, B. A.; Lecheminant, P.; Regnault, N.

2018-04-01

Many fractional quantum Hall states can be expressed as a correlator of a given conformal field theory used to describe their edge physics. As a consequence, these states admit an economical representation as an exact matrix product state (MPS) that was extensively studied for the systems without any spin or any other internal degrees of freedom. In that case, the correlators are built from a single electronic operator, which is primary with respect to the underlying conformal field theory. We generalize this construction to the archetype of Abelian multicomponent fractional quantum Hall wave functions, the Halperin states. These can be written as conformal blocks involving multiple electronic operators and we explicitly derive their exact MPS representation. In particular, we deal with the caveat of the full wave-function symmetry and show that any additional SU(2) symmetry is preserved by the natural MPS truncation scheme provided by the conformal dimension. We use our method to characterize the topological order of the Halperin states by extracting the topological entanglement entropy. We also evaluate their bulk correlation lengths, which are compared to plasma analogy arguments.

Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics.

PubMed

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S; Overall, Christopher M

2010-05-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases.

Production of an aminoterminally truncated, stable type of bioactive mouse fibroblast growth factor 4 in Escherichia coli.

PubMed

Sugawara, Saiko; Ito, Toshihiko; Sato, Shiori; Sato, Yuki; Kasuga, Kano; Kojima, Ikuo; Kobayashi, Masayuki

2014-05-01

In mice, fibroblast growth factor 4 (Fgf4) is a crucial gene for the generation of trophectoderm, progenitor cells of the placenta. Therefore, exogenous FGF4 promotes the isolation and maintenance of trophoblast stem cells from preimplantation embryos. We previously produced a 6× histidine (His)-tagged, mouse FGF4 (Pro(31)-Leu(202)) without a secretory signal peptide at the amino-terminus, referred to as HismFGF4, in Escherichia coli. Here, we found that HismFGF4 was unstable, such as in phosphate-buffered saline. In these conditions, site-specific cleavage between Ser(50) and Leu(51) was identified. In order to generate stable mouse FGF4 derivatives, a 6× His-tagged mouse FGF4 (Leu(51)-Leu(202)), termed HismFGF4L, was expressed in E. coli. HismFGF4L could be purified from the supernatant of cell lysates by heparin column chromatography. In phosphate-buffered saline, HismFGF4L was relatively stable. HismFGF4L exerted significant mitogenic activities at concentrations as low as 0.01 nM (P < 0.01) in mouse embryonic fibroblast Balb/c 3T3 cells expressing FGF receptor 2. In the presence of PD173074, an FGF receptor inhibitor, the growth-promoting activity of HismFGF4L was abolished. Taken together, we suggest that aminoterminally truncated HismFGF4L is capable of promoting the proliferation of mouse-derived cells via an authentic FGF signaling pathway. We consider that HismFGF4L is useful as a derivative of mouse FGF4 protein for analyzing the effects of mouse FGF4 and for stimulating cell growth of mouse-derived cells, such as trophoblast stem cells. Our study provides a simple method for the production of a bioactive, stable mouse FGF4 derivative in E. coli. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics*

PubMed Central

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S.; Overall, Christopher M.

2010-01-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases. PMID:20305284

Interference of a speB 5' untranslated region partial deletion with mRNA degradation in Streptococcus pyogenes.

PubMed

Chen, Z; Mashburn-Warren, L; Merritt, J; Federle, M J; Kreth, J

2017-10-01

The 5' untranslated region (5' UTR) of an mRNA molecule embeds important determinants that modify its stability and translation efficiency. In Streptococcus pyogenes, a strict human pathogen, a gene encoding a secreted protease (speB) has a large 5' UTR with unknown functions. Here we describe that a partial deletion of the speB 5' UTR caused a general accumulation of mRNA in the stationary phase, and that the mRNA accumulation was due to retarded mRNA degradation. The phenotype was observed in several M serotypes harboring the partial deletion of the speB 5' UTR. The phenotype was triggered by the production of the truncated speB 5' UTR, but not by the disruption of the intact speB 5' UTR. RNase Y, a major endoribonuclease, was previously shown to play a central role in bulk mRNA turnover in stationary phase. However, in contrast to our expectations, we observed a weaker interaction between the truncated speB 5' UTR and RNase Y compared with the wild-type, which suggests that other unidentified RNA degrading components are required for the pleiotropic effects observed from the speB UTR truncation. Our study demonstrates how S. pyogenes uses distinct mRNA degradation schemes in exponential and stationary growth phases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A novel homozygous truncating GNAT1 mutation implicated in retinal degeneration.

PubMed

Carrigan, Matthew; Duignan, Emma; Humphries, Pete; Palfi, Arpad; Kenna, Paul F; Farrar, G Jane

2016-04-01

The GNAT1 gene encodes the α subunit of the rod transducin protein, a key element in the rod phototransduction cascade. Variants in GNAT1 have been implicated in stationary night-blindness in the past, but unlike other proteins in the same pathway, it has not previously been implicated in retinitis pigmentosa. A panel of 182 retinopathy-associated genes was sequenced to locate disease-causing mutations in patients with inherited retinopathies. Sequencing revealed a novel homozygous truncating mutation in the GNAT1 gene in a patient with significant pigmentary disturbance and constriction of visual fields, a presentation consistent with retinitis pigmentosa. This is the first report of a patient homozygous for a complete loss-of-function GNAT1 mutation. The clinical data from this patient provide definitive evidence of retinitis pigmentosa with late onset in addition to the lifelong night-blindness that would be expected from a lack of transducin function. These data suggest that some truncating GNAT1 variants can indeed cause a recessive, mild, late-onset retinal degeneration in human beings rather than just stationary night-blindness as reported previously, with notable similarities to the phenotype of the Gnat1 knockout mouse. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Very high order discontinuous Galerkin method in elliptic problems

NASA Astrophysics Data System (ADS)

Jaśkowiec, Jan

2017-09-01

The paper deals with high-order discontinuous Galerkin (DG) method with the approximation order that exceeds 20 and reaches 100 and even 1000 with respect to one-dimensional case. To achieve such a high order solution, the DG method with finite difference method has to be applied. The basis functions of this method are high-order orthogonal Legendre or Chebyshev polynomials. These polynomials are defined in one-dimensional space (1D), but they can be easily adapted to two-dimensional space (2D) by cross products. There are no nodes in the elements and the degrees of freedom are coefficients of linear combination of basis functions. In this sort of analysis the reference elements are needed, so the transformations of the reference element into the real one are needed as well as the transformations connected with the mesh skeleton. Due to orthogonality of the basis functions, the obtained matrices are sparse even for finite elements with more than thousands degrees of freedom. In consequence, the truncation errors are limited and very high-order analysis can be performed. The paper is illustrated with a set of benchmark examples of 1D and 2D for the elliptic problems. The example presents the great effectiveness of the method that can shorten the length of calculation over hundreds times.

Very high order discontinuous Galerkin method in elliptic problems

NASA Astrophysics Data System (ADS)

Jaśkowiec, Jan

2018-07-01

The paper deals with high-order discontinuous Galerkin (DG) method with the approximation order that exceeds 20 and reaches 100 and even 1000 with respect to one-dimensional case. To achieve such a high order solution, the DG method with finite difference method has to be applied. The basis functions of this method are high-order orthogonal Legendre or Chebyshev polynomials. These polynomials are defined in one-dimensional space (1D), but they can be easily adapted to two-dimensional space (2D) by cross products. There are no nodes in the elements and the degrees of freedom are coefficients of linear combination of basis functions. In this sort of analysis the reference elements are needed, so the transformations of the reference element into the real one are needed as well as the transformations connected with the mesh skeleton. Due to orthogonality of the basis functions, the obtained matrices are sparse even for finite elements with more than thousands degrees of freedom. In consequence, the truncation errors are limited and very high-order analysis can be performed. The paper is illustrated with a set of benchmark examples of 1D and 2D for the elliptic problems. The example presents the great effectiveness of the method that can shorten the length of calculation over hundreds times.

Investigation of propagation dynamics of truncated vector vortex beams.

PubMed

Srinivas, P; Perumangatt, C; Lal, Nijil; Singh, R P; Srinivasan, B

2018-06-01

In this Letter, we experimentally investigate the propagation dynamics of truncated vector vortex beams generated using a Sagnac interferometer. Upon focusing, the truncated vector vortex beam is found to regain its original intensity structure within the Rayleigh range. In order to explain such behavior, the propagation dynamics of a truncated vector vortex beam is simulated by decomposing it into the sum of integral charge beams with associated complex weights. We also show that the polarization of the truncated composite vector vortex beam is preserved all along the propagation axis. The experimental observations are consistent with theoretical predictions based on previous literature and are in good agreement with our simulation results. The results hold importance as vector vortex modes are eigenmodes of the optical fiber.

Discovery of Super-Thin Disks in Nearby Edge-on Spiral Galaxies

NASA Astrophysics Data System (ADS)

Schechtman-Rook, A.; Bershady, M. A.

2014-03-01

We report the identification of a super-thin disk (hz˜ 60 pc) in the edge-on spiral galaxy NGC 891. This component is only apparent after we perform a physically motivated attenuation correction, based on detailed radiation transfer models, to our sub-arcsecond resolution near-infrared imaging. In addition to the super-thin disk, we also find several structural features near the center of NGC 891, including an inner disk truncation at ˜3 kpc. Inner disk truncations may be commonplace among massive spiral galaxies, possibly due to the effects of instabilities, such as bars. Having successfully demonstrated our methods, we are poised to apply them to a small sample of nearby edge-on galaxies, consisting both of massive and low-mass spirals.

Construction of energy-stable projection-based reduced order models

DOE PAGES

Kalashnikova, Irina; Barone, Matthew F.; Arunajatesan, Srinivasan; ...

2014-12-15

Our paper aims to unify and extend several approaches for building stable projection-based reduced order models (ROMs) using the energy method and the concept of “energy-stability”. Attention is focused on linear time-invariant (LTI) systems. First, an approach for building energy stable Galerkin ROMs for linear hyperbolic or incompletely parabolic systems of partial differential equations (PDEs) using continuous projection is proposed. The key idea is to apply to the system a transformation induced by the Lyapunov function for the system, and to build the ROM in the transformed variables. The result of this procedure will be a ROM that is energy-stablemore » for any choice of reduced basis. It is shown that, for many PDE systems, the desired transformation is induced by a special inner product, termed the “symmetry inner product”. Next, attention is turned to building energy-stable ROMs via discrete projection. A discrete counterpart of the continuous symmetry inner product, termed the “Lyapunov inner product”, is derived. Moreover, it is shown that the Lyapunov inner product can be computed in a black-box fashion for a stable LTI system ari sing from the discretization of a system of PDEs in space. Projection in this inner product guarantees a ROM that is energy-stable, again for any choice of reduced basis. Connections between the Lyapunov inner product and the inner product induced by the balanced truncation algorithm are made. We also made comparisons between the symmetry inner product and the Lyapunov inner product. Performance of ROMs constructed using these inner products is evaluated on several benchmark test cases.« less

A structure adapted multipole method for electrostatic interactions in protein dynamics

NASA Astrophysics Data System (ADS)

Niedermeier, Christoph; Tavan, Paul

1994-07-01

We present an algorithm for rapid approximate evaluation of electrostatic interactions in molecular dynamics simulations of proteins. Traditional algorithms require computational work of the order O(N2) for a system of N particles. Truncation methods which try to avoid that effort entail untolerably large errors in forces, energies and other observables. Hierarchical multipole expansion algorithms, which can account for the electrostatics to numerical accuracy, scale with O(N log N) or even with O(N) if they become augmented by a sophisticated scheme for summing up forces. To further reduce the computational effort we propose an algorithm that also uses a hierarchical multipole scheme but considers only the first two multipole moments (i.e., charges and dipoles). Our strategy is based on the consideration that numerical accuracy may not be necessary to reproduce protein dynamics with sufficient correctness. As opposed to previous methods, our scheme for hierarchical decomposition is adjusted to structural and dynamical features of the particular protein considered rather than chosen rigidly as a cubic grid. As compared to truncation methods we manage to reduce errors in the computation of electrostatic forces by a factor of 10 with only marginal additional effort.

Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set

NASA Astrophysics Data System (ADS)

Bennie, Simon J.; Stella, Martina; Miller, Thomas F.; Manby, Frederick R.

2015-07-01

Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O ( N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.

The roles played by highly truncated splice variants of G protein-coupled receptors

PubMed Central

2012-01-01

Alternative splicing of G protein-coupled receptor (GPCR) genes greatly increases the total number of receptor isoforms which may be expressed in a cell-dependent and time-dependent manner. This increased diversity of cell signaling options caused by the generation of splice variants is further enhanced by receptor dimerization. When alternative splicing generates highly truncated GPCRs with less than seven transmembrane (TM) domains, the predominant effect in vitro is that of a dominant-negative mutation associated with the retention of the wild-type receptor in the endoplasmic reticulum (ER). For constitutively active (agonist-independent) GPCRs, their attenuated expression on the cell surface, and consequent decreased basal activity due to the dominant-negative effect of truncated splice variants, has pathological consequences. Truncated splice variants may conversely offer protection from disease when expression of co-receptors for binding of infectious agents to cells is attenuated due to ER retention of the wild-type co-receptor. In this review, we will see that GPCRs retained in the ER can still be functionally active but also that highly truncated GPCRs may also be functionally active. Although rare, some truncated splice variants still bind ligand and activate cell signaling responses. More importantly, by forming heterodimers with full-length GPCRs, some truncated splice variants also provide opportunities to generate receptor complexes with unique pharmacological properties. So, instead of assuming that highly truncated GPCRs are associated with faulty transcription processes, it is time to reassess their potential benefit to the host organism. PMID:22938630

Fast and accurate matrix completion via truncated nuclear norm regularization.

PubMed

Hu, Yao; Zhang, Debing; Ye, Jieping; Li, Xuelong; He, Xiaofei

2013-09-01

Recovering a large matrix from a small subset of its entries is a challenging problem arising in many real applications, such as image inpainting and recommender systems. Many existing approaches formulate this problem as a general low-rank matrix approximation problem. Since the rank operator is nonconvex and discontinuous, most of the recent theoretical studies use the nuclear norm as a convex relaxation. One major limitation of the existing approaches based on nuclear norm minimization is that all the singular values are simultaneously minimized, and thus the rank may not be well approximated in practice. In this paper, we propose to achieve a better approximation to the rank of matrix by truncated nuclear norm, which is given by the nuclear norm subtracted by the sum of the largest few singular values. In addition, we develop a novel matrix completion algorithm by minimizing the Truncated Nuclear Norm. We further develop three efficient iterative procedures, TNNR-ADMM, TNNR-APGL, and TNNR-ADMMAP, to solve the optimization problem. TNNR-ADMM utilizes the alternating direction method of multipliers (ADMM), while TNNR-AGPL applies the accelerated proximal gradient line search method (APGL) for the final optimization. For TNNR-ADMMAP, we make use of an adaptive penalty according to a novel update rule for ADMM to achieve a faster convergence rate. Our empirical study shows encouraging results of the proposed algorithms in comparison to the state-of-the-art matrix completion algorithms on both synthetic and real visual datasets.

High Order Numerical Methods for the Investigation of the Two Dimensional Richtmyer-Meshkov Instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Don, W-S; Gotllieb, D; Shu, C-W

2001-11-26

For flows that contain significant structure, high order schemes offer large advantages over low order schemes. Fundamentally, the reason comes from the truncation error of the differencing operators. If one examines carefully the expression for the truncation error, one will see that for a fixed computational cost that the error can be made much smaller by increasing the numerical order than by increasing the number of grid points. One can readily derive the following expression which holds for systems dominated by hyperbolic effects and advanced explicitly in time: flops = const * p{sup 2} * k{sup (d+1)(p+1)/p}/E{sup (d+1)/p} where flopsmore » denotes floating point operations, p denotes numerical order, d denotes spatial dimension, where E denotes the truncation error of the difference operator, and where k denotes the Fourier wavenumber. For flows that contain structure, such as turbulent flows or any calculation where, say, vortices are present, there will be significant energy in the high values of k. Thus, one can see that the rate of growth of the flops is very different for different values of p. Further, the constant in front of the expression is also very different. With a low order scheme, one quickly reaches the limit of the computer. With the high order scheme, one can obtain far more modes before the limit of the computer is reached. Here we examine the application of spectral methods and the Weighted Essentially Non-Oscillatory (WENO) scheme to the Richtmyer-Meshkov Instability. We show the intricate structure that these high order schemes can calculate and we show that the two methods, though very different, converge to the same numerical solution indicating that the numerical solution is very likely physically correct.« less

A homomeric geranyl diphosphate synthase-encoding gene from Camptotheca acuminata and its combinatorial optimization for production of geraniol in Escherichia coli.

PubMed

Yang, Lixia; Jiang, Liangzhen; Li, Wei; Yang, Yun; Zhang, Guolin; Luo, Yinggang

2017-10-01

Geranyl diphosphate (GPP), the unique precursor for all monoterpenoids, is biosynthesized from isopentenyl diphosphate and dimethylallyl diphosphate via the head-to-tail condensation reaction catalyzed by GPP synthase (GPPS). Herein a homomeric GPPS from Camptotheca acuminata, a camptothecin-producing plant, was obtained from 5'- and 3'-rapid amplification of cDNA ends and subsequent overlap extension and convenient PCR amplifications. The truncate CaGPPS was introduced to replace ispA of pBbA5c-MevT(CO)-MBIS(CO, ispA), a de novo biosynthetic construct for farnesyl diphosphate generation, and overexpressed in Escherichia coli, together with the truncate geraniol synthase-encoding gene from C. acuminata (tCaGES), to confirm CaGPPS-catalyzed reaction in vivo. A 24.0 ± 1.3 mg L -1 of geraniol was produced in the recombinant E. coli. The production of GPP was also validated by the direct UPLC-HRMS E analyses. The tCaGPPS and tCaGES genes with different copy numbers were introduced into E. coli to balance their catalytic potential for high-yield geraniol production. A 1.6-fold increase of geraniol production was obtained when four copies of tCaGPPS and one copy of tCaGES were introduced into E. coli. The following fermentation conditions optimization, including removal of organic layers and addition of new n-decane, led to a 74.6 ± 6.5 mg L -1 of geraniol production. The present study suggested that the gene copy number optimization, i.e., the ratio of tCaGPPS and tCaGES, plays an important role in geraniol production in the recombinant E. coli. The removal and addition of organic solvent are very useful for sustainable high-yield production of geraniol in the recombinant E. coli in view of that the solubility of geraniol is limited in the fermentation broth and/or n-decane.

Application of a truncated normal failure distribution in reliability testing

NASA Technical Reports Server (NTRS)

Groves, C., Jr.

1968-01-01

Statistical truncated normal distribution function is applied as a time-to-failure distribution function in equipment reliability estimations. Age-dependent characteristics of the truncated function provide a basis for formulating a system of high-reliability testing that effectively merges statistical, engineering, and cost considerations.

A Truncated Cauchy Distribution

ERIC Educational Resources Information Center

Nadarajah, Saralees; Kotz, Samuel

2006-01-01

A truncated version of the Cauchy distribution is introduced. Unlike the Cauchy distribution, this possesses finite moments of all orders and could therefore be a better model for certain practical situations. One such situation in finance is discussed. Explicit expressions for the moments of the truncated distribution are also derived.

Metabolic Engineering of the Regulators in Nitrogen Catabolite Repression To Reduce the Production of Ethyl Carbamate in a Model Rice Wine System

PubMed Central

Zhao, Xinrui; Zou, Huijun; Fu, Jianwei; Chen, Jian

2014-01-01

Rice wine has been one of the most popular traditional alcoholic drinks in China. However, the presence of potentially carcinogenic ethyl carbamate (EC) in rice wine has raised a series of food safety issues. During rice wine production, the key reason for EC formation is urea accumulation, which occurs because of nitrogen catabolite repression (NCR) in Saccharomyces cerevisiae. NCR represses urea utilization by retaining Gln3p in the cytoplasm when preferred nitrogen sources are present. In order to increase the nuclear localization of Gln3p, some possible phosphorylation sites on the nuclear localization signal were mutated and the nuclear localization regulation signal was truncated, and the disruption of URE2 provided an additional method of reducing urea accumulation. By combining these strategies, the genes involved in urea utilization (DUR1,2 and DUR3) could be significantly activated in the presence of glutamine. During shake flask fermentations of the genetically modified strains, very little urea accumulated in the medium. Furthermore, the concentrations of urea and EC were reduced by 63% and 72%, respectively, in a model rice wine system. Examination of the normal nutrients in rice wine indicated that there were few differences in fermentation characteristics between the wild-type strain and the genetically modified strain. These results show that metabolic engineering of the NCR regulators has great potential as a method for eliminating EC during rice wine production. PMID:24185848

Characterization of cytidylyltransferase enzyme activity through high performance liquid chromatography.

PubMed

Brault, James P; Friesen, Jon A

2016-10-01

The cytidylyltransferases are a family of enzymes that utilize cytidine 5'-triphosphate (CTP) to synthesize molecules that are typically precursors to membrane phospholipids. The most extensively studied cytidylyltransferase is CTP:phosphocholine cytidylyltransferase (CCT), which catalyzes conversion of phosphocholine and CTP to cytidine diphosphocholine (CDP-choline), a step critical for synthesis of the membrane phospholipid phosphatidylcholine (PC). The current method used to determine catalytic activity of CCT measures production of radiolabeled CDP-choline from (14)C-labeled phosphocholine. The goal of this research was to develop a CCT enzyme assay that employed separation of non-radioactive CDP-choline from CTP. A C18 reverse phase column with a mobile phase of 0.1 M ammonium bicarbonate (98%) and acetonitrile (2%) (pH 7.4) resulted in separation of solutions of the substrate CTP from the product CDP-choline. A previously characterized truncated version of rat CCTα (denoted CCTα236) was used to test the HPLC enzyme assay by measuring CDP-choline product formation. The Vmax for CCTα236 was 3850 nmol/min/mg and K0.5 values for CTP and phosphocholine were 4.07 mM and 2.49 mM, respectively. The HPLC method was applied to glycerol 3-phosphate cytidylyltransferase (GCT) and CTP:2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), members of the cytidylyltransferase family that produce CDP-glycerol and CDP-methylerythritol, respectively. Copyright © 2016 Elsevier Inc. All rights reserved.

Metabolic engineering of the regulators in nitrogen catabolite repression to reduce the production of ethyl carbamate in a model rice wine system.

PubMed

Zhao, Xinrui; Zou, Huijun; Fu, Jianwei; Zhou, Jingwen; Du, Guocheng; Chen, Jian

2014-01-01

Rice wine has been one of the most popular traditional alcoholic drinks in China. However, the presence of potentially carcinogenic ethyl carbamate (EC) in rice wine has raised a series of food safety issues. During rice wine production, the key reason for EC formation is urea accumulation, which occurs because of nitrogen catabolite repression (NCR) in Saccharomyces cerevisiae. NCR represses urea utilization by retaining Gln3p in the cytoplasm when preferred nitrogen sources are present. In order to increase the nuclear localization of Gln3p, some possible phosphorylation sites on the nuclear localization signal were mutated and the nuclear localization regulation signal was truncated, and the disruption of URE2 provided an additional method of reducing urea accumulation. By combining these strategies, the genes involved in urea utilization (DUR1,2 and DUR3) could be significantly activated in the presence of glutamine. During shake flask fermentations of the genetically modified strains, very little urea accumulated in the medium. Furthermore, the concentrations of urea and EC were reduced by 63% and 72%, respectively, in a model rice wine system. Examination of the normal nutrients in rice wine indicated that there were few differences in fermentation characteristics between the wild-type strain and the genetically modified strain. These results show that metabolic engineering of the NCR regulators has great potential as a method for eliminating EC during rice wine production.

Truncation of CPC solar collectors and its effect on energy collection

NASA Astrophysics Data System (ADS)

Carvalho, M. J.; Collares-Pereira, M.; Gordon, J. M.; Rabl, A.

1985-01-01

Analytic expressions are derived for the angular acceptance function of two-dimensional compound parabolic concentrator solar collectors (CPC's) of arbitrary degree of truncation. Taking into account the effect of truncation on both optical and thermal losses in real collectors, the increase in monthly and yearly collectible energy is also evaluated. Prior analyses that have ignored the correct behavior of the angular acceptance function at large angles for truncated collectors are shown to be in error by 0-2 percent in calculations of yearly collectible energy for stationary collectors.

Hardware Design and Implementation of Fixed-Width Standard and Truncated 4×4, 6×6, 8×8 and 12×12-BIT Multipliers Using Fpga

NASA Astrophysics Data System (ADS)

Rais, Muhammad H.

2010-06-01

This paper presents Field Programmable Gate Array (FPGA) implementation of standard and truncated multipliers using Very High Speed Integrated Circuit Hardware Description Language (VHDL). Truncated multiplier is a good candidate for digital signal processing (DSP) applications such as finite impulse response (FIR) and discrete cosine transform (DCT). Remarkable reduction in FPGA resources, delay, and power can be achieved using truncated multipliers instead of standard parallel multipliers when the full precision of the standard multiplier is not required. The truncated multipliers show significant improvement as compared to standard multipliers. Results show that the anomaly in Spartan-3 AN average connection and maximum pin delay have been efficiently reduced in Virtex-4 device.

A generalized right truncated bivariate Poisson regression model with applications to health data.

PubMed

Islam, M Ataharul; Chowdhury, Rafiqul I

2017-01-01

A generalized right truncated bivariate Poisson regression model is proposed in this paper. Estimation and tests for goodness of fit and over or under dispersion are illustrated for both untruncated and right truncated bivariate Poisson regression models using marginal-conditional approach. Estimation and test procedures are illustrated for bivariate Poisson regression models with applications to Health and Retirement Study data on number of health conditions and the number of health care services utilized. The proposed test statistics are easy to compute and it is evident from the results that the models fit the data very well. A comparison between the right truncated and untruncated bivariate Poisson regression models using the test for nonnested models clearly shows that the truncated model performs significantly better than the untruncated model.

A generalized right truncated bivariate Poisson regression model with applications to health data

PubMed Central

Islam, M. Ataharul; Chowdhury, Rafiqul I.

2017-01-01

A generalized right truncated bivariate Poisson regression model is proposed in this paper. Estimation and tests for goodness of fit and over or under dispersion are illustrated for both untruncated and right truncated bivariate Poisson regression models using marginal-conditional approach. Estimation and test procedures are illustrated for bivariate Poisson regression models with applications to Health and Retirement Study data on number of health conditions and the number of health care services utilized. The proposed test statistics are easy to compute and it is evident from the results that the models fit the data very well. A comparison between the right truncated and untruncated bivariate Poisson regression models using the test for nonnested models clearly shows that the truncated model performs significantly better than the untruncated model. PMID:28586344

Measuring a Truncated Disk in Aquila X-1

NASA Technical Reports Server (NTRS)

King, Ashley L.; Tomsick, John A.; Miller, Jon M.; Chenevez, Jerome; Barret, Didier; Boggs, Steven E.; Chakrabarty, Deepto; Christensen, Finn E.; Craig, William W.; Feurst, Felix;

Optical colour image watermarking based on phase-truncated linear canonical transform and image decomposition

NASA Astrophysics Data System (ADS)

Su, Yonggang; Tang, Chen; Li, Biyuan; Lei, Zhenkun

2018-05-01

This paper presents a novel optical colour image watermarking scheme based on phase-truncated linear canonical transform (PT-LCT) and image decomposition (ID). In this proposed scheme, a PT-LCT-based asymmetric cryptography is designed to encode the colour watermark into a noise-like pattern, and an ID-based multilevel embedding method is constructed to embed the encoded colour watermark into a colour host image. The PT-LCT-based asymmetric cryptography, which can be optically implemented by double random phase encoding with a quadratic phase system, can provide a higher security to resist various common cryptographic attacks. And the ID-based multilevel embedding method, which can be digitally implemented by a computer, can make the information of the colour watermark disperse better in the colour host image. The proposed colour image watermarking scheme possesses high security and can achieve a higher robustness while preserving the watermark’s invisibility. The good performance of the proposed scheme has been demonstrated by extensive experiments and comparison with other relevant schemes.

Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Xiaolu; Steele, Ryan P., E-mail: ryan.steele@utah.edu

This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behavedmore » spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.« less

Prevalence of PALB2 Mutations in Breast Cancer Patients in Multi-Ethnic Asian Population in Malaysia and Singapore

PubMed Central

Phuah, Sze Yee; Lee, Sheau Yee; Kang, Peter; Kang, In Nee; Yoon, Sook-Yee; Thong, Meow Keong; Hartman, Mikael; Sng, Jen-Hwei; Yip, Cheng Har; Taib, Nur Aishah Mohd; Teo, Soo-Hwang

2013-01-01

Background The partner and localizer of breast cancer 2 (PALB2) is responsible for facilitating BRCA2-mediated DNA repair by serving as a bridging molecule, acting as the physical and functional link between the breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) proteins. Truncating mutations in the PALB2 gene are rare but are thought to be associated with increased risks of developing breast cancer in various populations. Methods We evaluated the contribution of PALB2 germline mutations in 122 Asian women with breast cancer, all of whom had significant family history of breast and other cancers. Further screening for nine PALB2 mutations was conducted in 874 Malaysian and 532 Singaporean breast cancer patients, and in 1342 unaffected Malaysian and 541 unaffected Singaporean women. Results By analyzing the entire coding region of PALB2, we found two novel truncating mutations and ten missense mutations in families tested negative for BRCA1/2-mutations. One additional novel truncating PALB2 mutation was identified in one patient through genotyping analysis. Our results indicate a low prevalence of deleterious PALB2 mutations and a specific mutation profile within the Malaysian and Singaporean populations. PMID:23977390

Study on Effects of The Shape of Cavitator on Supercavitation Flow Field Characteristics

NASA Astrophysics Data System (ADS)

Wang, Rui; Dang, Jianjun; Yao, Zhong

2018-03-01

The cavitator is the key part of the nose of the vehicle to induce the formation of supercavity, which has an important influence in the cavity formation rate, cavity shape and cavity stability. To study the influence of the shape on the supercavitation flew field characteristics, the cavity characteristics and the resistance characteristics of different shapes of cavitator under different working conditions are obtained by combining technical methods of numerical simulation and experimental research in water tunnel. The simulation results are contrast and analyzed with the test results. The analysis results show that : in terms of the cavity size, the inverted-conic cavitator can form the biggest cavity size, followed by the disk cavitator, and the truncated-conic cavitator is the least; in terms of the cavity formation speed, the inverted-conic cavitator has the fastest cavity formation speed, then is the truncated-conic cavitator, and the disk cavitator is the least; in terms of the drag characteristic, the truncated-conic cavitator has the maximum coefficient, disk cavitator is the next, the inverted-conic cavitator is the minimal. The research conclusion can provide reference and basis for the head shape design of supercavitating underwater ordnance and the design of hydrodynamic layout.

Optimization of finite difference forward modeling for elastic waves based on optimum combined window functions

NASA Astrophysics Data System (ADS)

Jian, Wang; Xiaohong, Meng; Hong, Liu; Wanqiu, Zheng; Yaning, Liu; Sheng, Gui; Zhiyang, Wang

2017-03-01

Full waveform inversion and reverse time migration are active research areas for seismic exploration. Forward modeling in the time domain determines the precision of the results, and numerical solutions of finite difference have been widely adopted as an important mathematical tool for forward modeling. In this article, the optimum combined of window functions was designed based on the finite difference operator using a truncated approximation of the spatial convolution series in pseudo-spectrum space, to normalize the outcomes of existing window functions for different orders. The proposed combined window functions not only inherit the characteristics of the various window functions, to provide better truncation results, but also control the truncation error of the finite difference operator manually and visually by adjusting the combinations and analyzing the characteristics of the main and side lobes of the amplitude response. Error level and elastic forward modeling under the proposed combined system were compared with outcomes from conventional window functions and modified binomial windows. Numerical dispersion is significantly suppressed, which is compared with modified binomial window function finite-difference and conventional finite-difference. Numerical simulation verifies the reliability of the proposed method.

Geology and structure of the Malpaso caldera and El Ocote ignimbrite, Aguascalientes, Mexico

NASA Astrophysics Data System (ADS)

Nieto-Obregón, Jorge; Aguirre-Díaz, Gerardo

2008-10-01

A new caldera, named Malpaso, is reported west of the city of Aguascalientes, Mexico. The Malpaso caldera is a volcano-tectonic depression, highly fractured and faulted, and was filled by voluminous pyroclastic products related to the caldera collapse. Due to these characteristics it as a graben caldera. It is truncated by younger normal faults of the Calvillo and Aguascalientes grabens. In this work we present a summary of the geologic and structural observations on this caldera, as well as a description of the main caldera product, the high-grade El Ocote ignimbrite.

Comparison of Resource Requirements for a Wind Tunnel Test Designed with Conventional vs. Modern Design of Experiments Methods

NASA Technical Reports Server (NTRS)

DeLoach, Richard; Micol, John R.

2011-01-01

The factors that determine data volume requirements in a typical wind tunnel test are identified. It is suggested that productivity in wind tunnel testing can be enhanced by managing the inference error risk associated with evaluating residuals in a response surface modeling experiment. The relationship between minimum data volume requirements and the factors upon which they depend is described and certain simplifications to this relationship are realized when specific model adequacy criteria are adopted. The question of response model residual evaluation is treated and certain practical aspects of response surface modeling are considered, including inference subspace truncation. A wind tunnel test plan developed by using the Modern Design of Experiments illustrates the advantages of an early estimate of data volume requirements. Comparisons are made with a representative One Factor At a Time (OFAT) wind tunnel test matrix developed to evaluate a surface to air missile.

Current-horn suppression for reduced coherent-synchrotron-radiation-induced emittance growth in strong bunch compression

NASA Astrophysics Data System (ADS)

Charles, T. K.; Paganin, D. M.; Latina, A.; Boland, M. J.; Dowd, R. T.

2017-03-01

Control of coherent synchrotron radiation (CSR)-induced emittance growth is essential in linear accelerators designed to deliver very high brightness electron beams. Extreme current values at the head and tail of the electron bunch, resulting from strong bunch compression, are responsible for large CSR production leading to significant transverse projected emittance growth. The Linac Coherent Light Source (LCLS) truncates the head and tail current spikes which greatly improves free electron laser (FEL) performance. Here we consider the underlying dynamics that lead to formation of current spikes (also referred to as current horns), which has been identified as caustics forming in electron trajectories. We present a method to analytically determine conditions required to avoid the caustic formation and therefore prevent the current spikes from forming. These required conditions can be easily met, without increasing the transverse slice emittance, through inclusion of an octupole magnet in the middle of a bunch compressor.

Entanglement Holographic Mapping of Many-Body Localized System by Spectrum Bifurcation Renormalization Group

NASA Astrophysics Data System (ADS)

You, Yi-Zhuang; Qi, Xiao-Liang; Xu, Cenke

We introduce the spectrum bifurcation renormalization group (SBRG) as a generalization of the real-space renormalization group for the many-body localized (MBL) system without truncating the Hilbert space. Starting from a disordered many-body Hamiltonian in the full MBL phase, the SBRG flows to the MBL fixed-point Hamiltonian, and generates the local conserved quantities and the matrix product state representations for all eigenstates. The method is applicable to both spin and fermion models with arbitrary interaction strength on any lattice in all dimensions, as long as the models are in the MBL phase. In particular, we focus on the 1 d interacting Majorana chain with strong disorder, and map out its phase diagram using the entanglement entropy. The SBRG flow also generates an entanglement holographic mapping, which duals the MBL state to a fragmented holographic space decorated with small blackholes.

The 2000 revision of the joint UK/US geomagnetic field models and an IGRF 2000 candidate model

USGS Publications Warehouse

Macmillan, S.; Quinn, J.M.

2000-01-01

The method of derivation of the joint UK/US spherical harmonic geomagnetic main-field and secular-variation models is presented. Early versions of these models, with the main field truncated at degree 10, are the UK/US candidates for the IGRF 2000 model. The main-field model describes the Earth's magnetic field at the 2000.0 epoch, while the secular-variation model predicts the evolution of this field between 2000.0 and 2005.0. A revised 1995.0 main-field model was also generated. Regional models for the continental US, Alaska and Hawaii were also produced as a by-product of the UK/US global modelling effort. Copy right?? The Society of Geomagnetism and Earth, Planetary and Space Sciences (SGEPSS); The Seismological Society of Japan; The Volcanological Society of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sciences.

Truncating SLC5A7 mutations underlie a spectrum of dominant hereditary motor neuropathies

PubMed Central

Salter, Claire G.; Beijer, Danique; Hardy, Holly; Barwick, Katy E.S.; Bower, Matthew; Mademan, Ines; De Jonghe, Peter; Deconinck, Tine; Russell, Mark A.; McEntagart, Meriel M.; Chioza, Barry A.; Blakely, Randy D.; Chilton, John K.; De Bleecker, Jan; Baets, Jonathan; Baple, Emma L.

2018-01-01

Objective To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs). Methods The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family. Variants were annotated and filtered, initially focusing on genes associated with neuropathy. Candidate variants were further investigated and confirmed by dideoxy sequence analysis and cosegregation studies. Thorough patient phenotyping was completed, comprising clinical history, examination, and neurologic investigation. Results dHMNs are a heterogeneous group of peripheral motor neuron disorders characterized by length-dependent neuropathy and progressive distal limb muscle weakness and wasting. We previously reported a dominant-negative frameshift mutation located in the concluding exon of the SLC5A7 gene encoding the choline transporter (CHT), leading to protein truncation, as the likely cause of dominantly-inherited dHMN-VII in an extended UK family. In this study, our genetic studies identified distinct heterozygous frameshift mutations located in the last coding exon of SLC5A7, predicted to result in the truncation of the CHT C-terminus, as the likely cause of the condition in each family. Conclusions This study corroborates C-terminal CHT truncation as a cause of autosomal dominant dHMN, confirming upper limb predominating over lower limb involvement, and broadening the clinical spectrum arising from CHT malfunction. PMID:29582019

Cystathionine β-Synthase Inhibition Is a Potential Therapeutic Approach to Treatment of Ischemic Injury

PubMed Central

Chan, Su Jing; Chai, Chou; Lim, Tze Wei; Yamamoto, Mie; Lo, Eng H; Lai, Mitchell Kim Peng

2015-01-01

Hydrogen sulfide (H2S) has been reported to exacerbate stroke outcome in experimental models. Cystathionine β-synthase (CBS) has been implicated as the predominant H2S-producing enzyme in central nervous system. When SH-SY5Y cells were transfected to overexpress CBS, these cells were able to synthesize H2S when exposed to high levels of enzyme substrates but not substrate concentrations that may reflect normal physiological conditions. At the same time, these cells demonstrated exacerbated cell death when subjected to oxygen and glucose deprivation (OGD) together with high substrate concentrations, indicating that H2S production has a detrimental effect on cell survival. This effect could be abolished by CBS inhibition. The same effect was observed with primary astrocytes exposed to OGD and high substrates or sodium hydrosulfide. In addition, CBS was upregulated and activated by truncation in primary astrocytes subjected to OGD. When rats were subjected to permanent middle cerebral artery occlusion, CBS activation was also observed. These results imply that in acute ischemic conditions, CBS is upregulated and activated by truncation causing an increased production of H2S, which exacerbate the ischemic injuries. Therefore, CBS inhibition may be a viable approach to stroke treatment. PMID:25873304

Stochastic Frontier Model Approach for Measuring Stock Market Efficiency with Different Distributions

PubMed Central

Hasan, Md. Zobaer; Kamil, Anton Abdulbasah; Mustafa, Adli; Baten, Md. Azizul

2012-01-01

The stock market is considered essential for economic growth and expected to contribute to improved productivity. An efficient pricing mechanism of the stock market can be a driving force for channeling savings into profitable investments and thus facilitating optimal allocation of capital. This study investigated the technical efficiency of selected groups of companies of Bangladesh Stock Market that is the Dhaka Stock Exchange (DSE) market, using the stochastic frontier production function approach. For this, the authors considered the Cobb-Douglas Stochastic frontier in which the technical inefficiency effects are defined by a model with two distributional assumptions. Truncated normal and half-normal distributions were used in the model and both time-variant and time-invariant inefficiency effects were estimated. The results reveal that technical efficiency decreased gradually over the reference period and that truncated normal distribution is preferable to half-normal distribution for technical inefficiency effects. The value of technical efficiency was high for the investment group and low for the bank group, as compared with other groups in the DSE market for both distributions in time- varying environment whereas it was high for the investment group but low for the ceramic group as compared with other groups in the DSE market for both distributions in time-invariant situation. PMID:22629352

Termination and read-through proteins encoded by genome segment 9 of Colorado tick fever virus.

PubMed

Mohd Jaafar, Fauziah; Attoui, Houssam; De Micco, Philippe; De Lamballerie, Xavier

2004-08-01

Genome segment 9 (Seg-9) of Colorado tick fever virus (CTFV) is 1884 bp long and contains a large open reading frame (ORF; 1845 nt in length overall), although a single in-frame stop codon (at nt 1052-1054) reduces the ORF coding capacity by approximately 40 %. However, analyses of highly conserved RNA sequences in the vicinity of the stop codon indicate that it belongs to a class of 'leaky terminators'. The third nucleotide positions in codons situated both before and after the stop codon, shows the highest variability, suggesting that both regions are translated during virus replication. This also suggests that the stop signal is functionally leaky, allowing read-through translation to occur. Indeed, both the truncated 'termination' protein and the full-length 'read-through' protein (VP9 and VP9', respectively) were detected in CTFV-infected cells, in cells transfected with a plasmid expressing only Seg-9 protein products, and in the in vitro translation products from undenatured Seg-9 ssRNA. The ratios of full-length and truncated proteins generated suggest that read-through may be down-regulated by other viral proteins. Western blot analysis of infected cells and purified CTFV showed that VP9 is a structural component of the virion, while VP9' is a non-structural protein.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaboud, M.; Aad, G.; Abbott, B.

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum with the ATLAS experiment at the Large Hadron Collider are reported. The data were collected in proton-proton collisions at a centre-of-mass energy of 13 TeV and correspond to an integrated luminosity of 3.2 fb -1. The observed data are in agreement with the Standard Model expectations. Exclusion limits are presented in models of new phenomena including pair production of dark matter candidates or large extra spatial dimensions. In a simplified model of dark matter and an axial-vector mediator, the search excludes mediatormore » masses below 710 GeV for dark matter candidate masses below 150 GeV. In an effective theory of dark matter production, values of the suppression scale M * up to 570 GeV are excluded and the effect of truncation for various coupling values is reported. Finally, for the ADD large extra spatial dimension model the search places more stringent limits than earlier searches in the same event topology, excluding M D up to about 2.3 (2.8) TeV for two (six) additional spatial dimensions; the limits are reduced by 20-40% depending on the number of additional spatial dimensions when applying a truncation procedure.« less

Genome sequence of the lager brewing yeast, an interspecies hybrid.

PubMed

Nakao, Yoshihiro; Kanamori, Takeshi; Itoh, Takehiko; Kodama, Yukiko; Rainieri, Sandra; Nakamura, Norihisa; Shimonaga, Tomoko; Hattori, Masahira; Ashikari, Toshihiko

2009-04-01

This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production.

Stochastic frontier model approach for measuring stock market efficiency with different distributions.

PubMed

Hasan, Md Zobaer; Kamil, Anton Abdulbasah; Mustafa, Adli; Baten, Md Azizul

2012-01-01

The stock market is considered essential for economic growth and expected to contribute to improved productivity. An efficient pricing mechanism of the stock market can be a driving force for channeling savings into profitable investments and thus facilitating optimal allocation of capital. This study investigated the technical efficiency of selected groups of companies of Bangladesh Stock Market that is the Dhaka Stock Exchange (DSE) market, using the stochastic frontier production function approach. For this, the authors considered the Cobb-Douglas Stochastic frontier in which the technical inefficiency effects are defined by a model with two distributional assumptions. Truncated normal and half-normal distributions were used in the model and both time-variant and time-invariant inefficiency effects were estimated. The results reveal that technical efficiency decreased gradually over the reference period and that truncated normal distribution is preferable to half-normal distribution for technical inefficiency effects. The value of technical efficiency was high for the investment group and low for the bank group, as compared with other groups in the DSE market for both distributions in time-varying environment whereas it was high for the investment group but low for the ceramic group as compared with other groups in the DSE market for both distributions in time-invariant situation.

Genome Sequence of the Lager Brewing Yeast, an Interspecies Hybrid

PubMed Central

Nakao, Yoshihiro; Kanamori, Takeshi; Itoh, Takehiko; Kodama, Yukiko; Rainieri, Sandra; Nakamura, Norihisa; Shimonaga, Tomoko; Hattori, Masahira; Ashikari, Toshihiko

2009-01-01

This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production. PMID:19261625

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells

DOE PAGES

Barua, Dipak; Hlavacek, William S.

2013-09-26

In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β—catenin, which is regulated by a multiprotein complex called the destruction complex. The destruction complex comprises APC, Axin, β—catenin, serine/threonine kinases, and other proteins. The kinases CK1α and GSK–3β, which are recruited by Axin, mediate phosphorylation of β—catenin, which initiates its ubiquitination and proteosomal degradation. The mechanism of regulation of β—catenin degradation by the destruction complex and the role of truncation of APC in colorectal cancer are not entirely understood. Through formulation and analysis of amore » rule-based computational model, we investigated the regulation of β—catenin phosphorylation and degradation by APC and the effect of APC truncation on function of the destruction complex. The model integrates available mechanistic knowledge about site-specific interactions and phosphorylation of destruction complex components and is consistent with an array of published data. In this paper, we find that the phosphorylated truncated form of APC can outcompete Axin for binding to β—catenin, provided that Axin is limiting, and thereby sequester β—catenin away from Axin and the Axin-recruited kinases CK1α and GSK–3β. Full-length APC also competes with Axin for binding to β—catenin; however, full-length APC is able, through its SAMP repeats, which bind Axin and which are missing in truncated oncogenic forms of APC, to bring β—catenin into indirect association with Axin and Axin-recruited kinases. Because our model indicates that the positive effects of truncated APC on β—catenin levels depend on phosphorylation of APC, at the first 20-amino acid repeat, and because phosphorylation of this site is mediated by CK1ϵ, we suggest that CK1ϵ is a potential target for therapeutic intervention in colorectal cancer. Finally, specific inhibition of CK1ϵ is predicted to limit binding of β—catenin to truncated APC and thereby to reverse the effect of APC truncation.« less

Pulmonary MRA: differentiation of pulmonary embolism from truncation artefact.

PubMed

Bannas, Peter; Schiebler, Mark L; Motosugi, Utaroh; François, Christopher J; Reeder, Scott B; Nagle, Scott K

2014-08-01

Truncation artefact (Gibbs ringing) causes central signal drop within vessels in pulmonary magnetic resonance angiography (MRA) that can be mistaken for emboli, reducing diagnostic accuracy for pulmonary embolism (PE). We propose a quantitative approach to differentiate truncation artefact from PE. Twenty-eight patients who underwent pulmonary computed tomography angiography (CTA) for suspected PE were recruited for pulmonary MRA. Signal intensity drops within pulmonary arteries that persisted on both arterial-phase and delayed-phase MRA were identified. The percent signal loss between the vessel lumen and central drop was measured. CTA served as the reference standard for presence of pulmonary emboli. A total of 65 signal intensity drops were identified on MRA. Of these, 48 (74%) were artefacts and 17 (26%) were PE, as confirmed by CTA. Truncation artefacts had a significantly lower median signal drop than PE on both arterial-phase (26% [range 12-58%] vs. 85% [range 53-91%]) and delayed-phase MRA (26% [range 11-55%] vs. 77% [range 47-89%]), p < 0.0001 for both. Receiver operating characteristic (ROC) analyses revealed a threshold value of 51% (arterial phase) and 47% signal drop (delayed phase) to differentiate between truncation artefact and PE with 100% sensitivity and greater than 90% specificity. Quantitative signal drop is an objective tool to help differentiate truncation artefact and pulmonary embolism in pulmonary MRA. • Inexperienced readers may mistake truncation artefacts for emboli on pulmonary MRA • Pulmonary emboli have non-uniform signal drop • 51% (arterial phase) and 47% (delayed phase) cut-off differentiates truncation artefact from PE • Quantitative signal drop measurement enables more accurate pulmonary embolism diagnosis with MRA.

Gene expression of galectin-9/ecalectin, a potent eosinophil chemoattractant, and/or the insertional isoform in human colorectal carcinoma cell lines and detection of frame-shift mutations for protein sequence truncations in the second functional lectin domain.

PubMed

Lahm, H; Hoeflich, A; Andre, S; Sordat, B; Kaltner, H; Wolf, E; Gabius, H J

2000-09-01

The family of Ca2+-independent galactoside-binding lectins with the beta-strand topology of the jelly-roll, referred to as galectins, is known to mediate and modulate a variety of cellular activities. Their functional versatility explains the current interest in monitoring their expression in cancer research, so far primarily focused on galectin-1 and -3. Tandem-repeat-type galectin-9 and its (most probably) allelic variant ecalectin, a potent eosinophil chemoattractant, are known to be human leukocyte products. We show by RT-PCR with primers specific for both that their mRNA is expressed in 17 of 21 human colorectal cancer lines. As also indicated by restriction analysis, in addition to the expected transcript of 571 bp an otherwise identical isoform coding for a 32-amino acid extension of the link peptide was detected. Positive cell lines differentially expressed either one (7 lines) or both transcripts (10 lines). Sequence analysis of RT-PCR products, performed in four cases, allowed to assign the standard transcript to ecalectin in the case of SW480 cells and detected two point mutations in the insert of the link peptide-coding sequence in WiDr and Colo205. Furthermore, this analysis identified the insertion of a single nucleotide into the coding sequence generating a frame-shift mutation, an event which has so far not been reported for any galectin. This alteration encountered in both transcripts of the WiDr line and the isoform transcript of Colo205 cells will most likely truncate the protein part within the second (C-terminal) carbohydrate recognition domain. Our results thus reveal the presence of mRNA for a galectin-9-isoform or a potent eosinophil chemoattractant (ecalectin) or a truncated version thereof with preserved N-terminal carbohydrate recognition domain in established human colon cancer cell lines.

Fast multipole method using Cartesian tensor in beam dynamic simulation

DOE PAGES

Zhang, He; Huang, He; Li, Rui; ...

2017-03-06

Here, the fast multipole method (FMM) using traceless totally symmetric Cartesian tensor to calculate the Coulomb interaction between charged particles will be presented. The Cartesian tensor-based FMM can be generalized to treat other non-oscillating interactions with the help of the differential algebra or the truncated power series algebra. Issues on implementation of the FMM in beam dynamic simulations are also discussed.

Perspective on rainbow-ladder truncation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eichmann, G.; Institut fuer Physik, Karl-Franzens-Universitaet Graz, A-8010 Graz; Alkofer, R.

2008-04-15

Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light.

Perspective on rainbow-ladder truncation

NASA Astrophysics Data System (ADS)

Eichmann, G.; Alkofer, R.; Cloët, I. C.; Krassnigg, A.; Roberts, C. D.

2008-04-01

Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light.

Model and controller reduction of large-scale structures based on projection methods

NASA Astrophysics Data System (ADS)

Gildin, Eduardo

The design of low-order controllers for high-order plants is a challenging problem theoretically as well as from a computational point of view. Frequently, robust controller design techniques result in high-order controllers. It is then interesting to achieve reduced-order models and controllers while maintaining robustness properties. Controller designed for large structures based on models obtained by finite element techniques yield large state-space dimensions. In this case, problems related to storage, accuracy and computational speed may arise. Thus, model reduction methods capable of addressing controller reduction problems are of primary importance to allow the practical applicability of advanced controller design methods for high-order systems. A challenging large-scale control problem that has emerged recently is the protection of civil structures, such as high-rise buildings and long-span bridges, from dynamic loadings such as earthquakes, high wind, heavy traffic, and deliberate attacks. Even though significant effort has been spent in the application of control theory to the design of civil structures in order increase their safety and reliability, several challenging issues are open problems for real-time implementation. This dissertation addresses with the development of methodologies for controller reduction for real-time implementation in seismic protection of civil structures using projection methods. Three classes of schemes are analyzed for model and controller reduction: nodal truncation, singular value decomposition methods and Krylov-based methods. A family of benchmark problems for structural control are used as a framework for a comparative study of model and controller reduction techniques. It is shown that classical model and controller reduction techniques, such as balanced truncation, modal truncation and moment matching by Krylov techniques, yield reduced-order controllers that do not guarantee stability of the closed-loop system, that is, the reduced-order controller implemented with the full-order plant. A controller reduction approach is proposed such that to guarantee closed-loop stability. It is based on the concept of dissipativity (or positivity) of linear dynamical systems. Utilizing passivity preserving model reduction together with dissipative-LQG controllers, effective low-order optimal controllers are obtained. Results are shown through simulations.

Integrated analysis of germline and somatic variants in ovarian cancer.

PubMed

Kanchi, Krishna L; Johnson, Kimberly J; Lu, Charles; McLellan, Michael D; Leiserson, Mark D M; Wendl, Michael C; Zhang, Qunyuan; Koboldt, Daniel C; Xie, Mingchao; Kandoth, Cyriac; McMichael, Joshua F; Wyczalkowski, Matthew A; Larson, David E; Schmidt, Heather K; Miller, Christopher A; Fulton, Robert S; Spellman, Paul T; Mardis, Elaine R; Druley, Todd E; Graubert, Timothy A; Goodfellow, Paul J; Raphael, Benjamin J; Wilson, Richard K; Ding, Li

2014-01-01

We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyse germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2 and PALB2. In addition, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B and MLL3). Evidence for loss of heterozygosity was found in 100 and 76% of cases with germline BRCA1 and BRCA2 truncations, respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 222 candidate functional germline truncation and missense variants, including two pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK and MLL pathways.

Effect of data truncation in an implementation of pixel clustering on a custom computing machine

NASA Astrophysics Data System (ADS)

Leeser, Miriam E.; Theiler, James P.; Estlick, Michael; Kitaryeva, Natalya V.; Szymanski, John J.

2000-10-01

We investigate the effect of truncating the precision of hyperspectral image data for the purpose of more efficiently segmenting the image using a variant of k-means clustering. We describe the implementation of the algorithm on field-programmable gate array (FPGA) hardware. Truncating the data to only a few bits per pixel in each spectral channel permits a more compact hardware design, enabling greater parallelism, and ultimately a more rapid execution. It also enables the storage of larger images in the onboard memory. In exchange for faster clustering, however, one trades off the quality of the produced segmentation. We find, however, that the clustering algorithm can tolerate considerable data truncation with little degradation in cluster quality. This robustness to truncated data can be extended by computing the cluster centers to a few more bits of precision than the data. Since there are so many more pixels than centers, the more aggressive data truncation leads to significant gains in the number of pixels that can be stored in memory and processed in hardware concurrently.

Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice.

PubMed

Wein, Nicolas; Vulin, Adeline; Falzarano, Maria S; Szigyarto, Christina Al-Khalili; Maiti, Baijayanta; Findlay, Andrew; Heller, Kristin N; Uhlén, Mathias; Bakthavachalu, Baskar; Messina, Sonia; Vita, Giuseppe; Passarelli, Chiara; Brioschi, Simona; Bovolenta, Matteo; Neri, Marcella; Gualandi, Francesca; Wilton, Steve D; Rodino-Klapac, Louise R; Yang, Lin; Dunn, Diane M; Schoenberg, Daniel R; Weiss, Robert B; Howard, Michael T; Ferlini, Alessandra; Flanigan, Kevin M

2014-09-01

Most mutations that truncate the reading frame of the DMD gene cause loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity has been shown to result from alternative translation initiation beginning in DMD exon 6 that leads to expression of a highly functional N-truncated dystrophin. Here we demonstrate that this isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid inducible. We confirmed IRES activity by both peptide sequencing and ribosome profiling in muscle from individuals with minimal symptoms despite the presence of truncating mutations. We generated a truncated reading frame upstream of the IRES by exon skipping, which led to synthesis of a functional N-truncated isoform in both human subject-derived cell lines and in a new DMD mouse model, where expression of the truncated isoform protected muscle from contraction-induced injury and corrected muscle force to the same level as that observed in control mice. These results support a potential therapeutic approach for patients with mutations within the 5' exons of DMD.

Familial Prion Disease with Alzheimer Disease-Like Tau Pathology and Clinical Phenotype

PubMed Central

Jayadev, Suman; Nochlin, David; Poorkaj, Parvoneh; Steinbart, Ellen J.; Mastrianni, James A.; Montine, Thomas J.; Ghetti, Bernardino; Schellenberg, Gerard D.; Bird, Thomas D.; Leverenz, James B.

2011-01-01

Objective To describe the Alzheimer disease (AD)-like clinical and pathological features, including marked neurofibrillary tangle (NFT) pathology, of a familial prion disease due to a rare nonsense mutation of the prion gene (PRNP). Methods Longitudinal clinical assessments were available for the proband and her mother. After death, both underwent neuropathological evaluation. PRNP was sequenced after failure to find immunopositive Aβ deposits in the proband and the documentation of prion protein (PrP) immunopositive pathology. Results The proband presented at age 42 years with a 3-year history of progressive short-term memory impairment and depression. Neuropsychological testing found impaired memory performance, with relatively preserved attention and construction. She was diagnosed with AD and died at age 47 years. Neuropathologic evaluation revealed extensive limbic and neocortical NFT formation and neuritic plaques consistent with a Braak stage of VI. The NFTs were immunopositive, with multiple tau antibodies, and electron microscopy revealed paired helical filaments. However, the neuritic plaques were immunonegative for Aβ, whereas immunostaining for PrP was positive. The mother of the proband had a similar presentation, including depression, and had been diagnosed clinically and pathologically as AD. Reevaluation of her brain tissue confirmed similar tau and PrP immunostaining findings. Genetic analysis revealed that both the proband and her mother had a rare PRNP mutation (Q160X) that resulted in the production of truncated PrP. Interpretation We suggest that PRNP mutations that result in a truncation of PrP lead to a prolonged clinical course consistent with a clinical diagnosis of AD and severe AD-like NFTs. PMID:21416485

Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study.

PubMed

Le Calvez-Kelm, Florence; Lesueur, Fabienne; Damiola, Francesca; Vallée, Maxime; Voegele, Catherine; Babikyan, Davit; Durand, Geoffroy; Forey, Nathalie; McKay-Chopin, Sandrine; Robinot, Nivonirina; Nguyen-Dumont, Tù; Thomas, Alun; Byrnes, Graham B; Hopper, John L; Southey, Melissa C; Andrulis, Irene L; John, Esther M; Tavtigian, Sean V

2011-01-18

Both protein-truncating variants and some missense substitutions in CHEK2 confer increased risk of breast cancer. However, no large-scale study has used full open reading frame mutation screening to assess the contribution of rare missense substitutions in CHEK2 to breast cancer risk. This absence has been due in part to a lack of validated statistical methods for summarizing risk attributable to large numbers of individually rare missense substitutions. Previously, we adapted an in silico assessment of missense substitutions used for analysis of unclassified missense substitutions in BRCA1 and BRCA2 to the problem of assessing candidate genes using rare missense substitution data observed in case-control mutation-screening studies. The method involves stratifying rare missense substitutions observed in cases and/or controls into a series of grades ordered a priori from least to most likely to be evolutionarily deleterious, followed by a logistic regression test for trends to compare the frequency distributions of the graded missense substitutions in cases versus controls. Here we used this approach to analyze CHEK2 mutation-screening data from a population-based series of 1,303 female breast cancer patients and 1,109 unaffected female controls. We found evidence of risk associated with rare, evolutionarily unlikely CHEK2 missense substitutions. Additional findings were that (1) the risk estimate for the most severe grade of CHEK2 missense substitutions (denoted C65) is approximately equivalent to that of CHEK2 protein-truncating variants; (2) the population attributable fraction and the familial relative risk explained by the pool of rare missense substitutions were similar to those explained by the pool of protein-truncating variants; and (3) post hoc power calculations implied that scaling up case-control mutation screening to examine entire biochemical pathways would require roughly 2,000 cases and controls to achieve acceptable statistical power. This study shows that CHEK2 harbors many rare sequence variants that confer increased risk of breast cancer and that a substantial proportion of these are missense substitutions. The study validates our analytic approach to rare missense substitutions and provides a method to combine data from protein-truncating variants and rare missense substitutions into a one degree of freedom per gene test.

Comparative performance of modified full-length and truncated Bacillus thuringiensis-cry1Ac genes in transgenic tomato.

PubMed

Koul, Bhupendra; Yadav, Reena; Sanyal, Indraneel; Amla, Devindra Vijay

2015-01-01

Bt-cry1Ac gene has been reputedly effective against Helicoverpa armigera a notorious lepidopteran pest. Reports on the expression of full-length and truncated cry1Ac genes in plants for effective resistance against Helicoverpa sp. have been documented however, their performance is still ambiguous. Moreover, the question remains to be addressed that truncation of 3' end of the native gene was documented and suggested for active insecticidal toxin production while the most successful transgenic event(s) of commercialized-cotton are based on full-length of the cry gene. Therefore, we performed a comparative study on the efficacy of the two versions of cry1Ac genes (full-length: 3,510 bp and truncated: 1,845 bp) in T0 and T1 transgenic tomato plants and analyzed the extent of protection against H. armigera and also compared the results with our previous findings related to a successful transgenic tomato line Ab25E, expressing cry1Ab gene. The integration of cry1Ac gene(s) in T0 transgenic plants and its inheritance in T1 progeny was observed by PCR, RT-PCR and Southern blot hybridization analysis while, the toxin integrity, expression and toxicity was monitored by Western immunoassay, DAS-ELISA and insect bioassay respectively. An average transformation frequency and Bt-Cry protein content of 16.93 ± 2.10 and 0.0020-0.0128% of total soluble protein (TSP) was obtained with pRD400 vector (Trcry1Ac) while, a much lower value of 9.30 ± 2.041 and 0.0001 - 0.0026% of TSP was observed with pNBRI-1 vector (Flcry1Ac), respectively. The promising Trcry1Ac T0 transgenic plants and their T1 progeny gave full protection from H. armigera. Although Flcry1Ac gene showed lower transformation frequency and lower expression, it showed higher toxicity to H. armigera when compared with truncated Trcry1Ac gene. The full-length cry1Ac gene can be redesigned for higher expression and performance in dicots or a hybrid gene could be designed having a blend of strong receptor binding and stable expression characteristics for enhanced efficacy and toxicity to the susceptible insects.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

Sensitivity studies and a simple ozone perturbation experiment with a truncated two-dimensional model of the stratosphere

NASA Technical Reports Server (NTRS)

Stordal, Frode; Garcia, Rolando R.

1987-01-01

The 1-1/2-D model of Holton (1986), which is actually a highly truncated two-dimensional model, describes latitudinal variations of tracer mixing ratios in terms of their projections onto second-order Legendre polynomials. The present study extends the work of Holton by including tracers with photochemical production in the stratosphere (O3 and NOy). It also includes latitudinal variations in the photochemical sources and sinks, improving slightly the calculated global mean profiles for the long-lived tracers studied by Holton and improving substantially the latitudinal behavior of ozone. Sensitivity tests of the dynamical parameters in the model are performed, showing that the response of the model to changes in vertical residual meridional winds and horizontal diffusion coefficients is similar to that of a full two-dimensional model. A simple ozone perturbation experiment shows the model's ability to reproduce large-scale latitudinal variations in total ozone column depletions as well as ozone changes in the chemically controlled upper stratosphere.

[Integrated quality assurance].

PubMed

Bögel, K; Stöhr, K

1994-07-01

The definition of terms and connotation of "Quality", "Quality Assurance" and "Integration" lead to an analysis and understanding of inhibiting and fostering factors of the "Health Triad" of people, animals and environment. Although "Quality" is largely or ultimately determined by the consumer, there are considerable differences as this term is applied by (a) the individual consumer, (b) the dynamic producer defending or gaining markets, (c) those engaged in traditional product manufacturing, or (d) governments setting (minimum) requirements for the sake of free trade. "Quality Assurance" offers cooperation of partners all along the food chain from "pasture to table". The managerial process turned into a continuum of responsibility and agreement on processes and product characteristics. This overcomes the disadvantages of strategies stressing distinct defense barriers. In practice this philosophy of a predominant role of defence barriers proved largely partnership destructive, in that it permitted to shift responsibilities for failures and to claim administrative competence according to momentary situations and interests. "Integrated Quality Assurance" means mutual agreement of two or more partners along the food chain (e. g. feed producers, farmers, animal health industry, veterinarians and food processors) on product characteristics and production methods. It involves essential system elements including facilities, materials, manpower, information, transport, management etc. Different principles and procedures of quality assurance have been introduced in practice, including agriculture and food processing. These different approaches are not mutually exclusive but largely of complementary nature.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans.

PubMed

Ambigapathy, Ganesh; Zheng, Zhaoqing; Li, Wei; Keifer, Joyce

2013-01-01

Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF) are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.

Identification of a Functionally Distinct Truncated BDNF mRNA Splice Variant and Protein in Trachemys scripta elegans

PubMed Central

Ambigapathy, Ganesh; Zheng, Zhaoqing; Li, Wei; Keifer, Joyce

2013-01-01

Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF) are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein. PMID:23825634

Abundance of truncated and full-length ChitA and ChitB chitinases in healthy and diseased maize tissues

USDA-ARS?s Scientific Manuscript database

Chitinase modifying proteins, cmps, are secreted fungal proteases that combat plant defenses by truncating plant class IV chitinases. We initially discovered that ChitA and ChitB, two plant class IV chitinases that are abundant in developing and mature kernels of corn, are truncated by cmps during e...

Overexpression of a type-I isopentenyl pyrophosphate isomerase of Artemisia annua in the cytosol leads to high arteannuin B production and artemisinin increase.

PubMed

Ma, Dongming; Li, Gui; Alejos-Gonzalez, Fatima; Zhu, Yue; Xue, Zhen; Wang, Aimin; Zhang, Hui; Li, Xing; Ye, Hechun; Wang, Hong; Liu, Benye; Xie, De-Yu

2017-08-01

We recently characterized a gene-terpene network that is associated with artemisinin biosynthesis in self-pollinated (SP) Artemisia annua, an effective antimalarial plant. We hypothesize that an alteration of gene expression in the network may improve the production of artemisinin and its precursors. In this study, we cloned an isopentenyl pyrophosphate isomerase (IPPI) cDNA, AaIPPI1, from Artemisia annua (Aa). The full-length cDNA encodes a type-I IPPI containing a plastid transit peptide (PTP) at its amino terminus. After the removal of the PTP, the recombinant truncated AaIPPI1 isomerized isopentenyl pyrophosphate (IPP) to dimethyl allyl pyrophosphate (DMAPP) and vice versa. The steady-state equilibrium ratio of IPP/DMAPP in the enzymatic reactions was approximately 1:7. The truncated AaIPPI1 was overexpressed in the cytosol of the SP A. annua variety. The leaves of transgenic plants produced approximately 4% arteannuin B (g g -1 , dry weight, dw) and 0.17-0.25% artemisinin (g g -1 , dw), the levels of which were significantly higher than those in the leaves of wild-type plants. In addition, transgenic plants showed an increase in artemisinic acid production of more than 1% (g g -1 , dw). In contrast, isoprene formation was significantly reduced in transgenic plants. These results provide evidence that overexpression of AaIPPI1 in the cytosol can lead to metabolic alterations of terpenoid biosynthesis, and show that these transgenic plants have the potential to yield high production levels of arteannuin B as a new precursor source for artemisinin. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Role of the Carboxy Terminus of SecA in Iron Acquisition, Protein Translocation, and Virulence of the Bacterial Pathogen Acinetobacter baumannii

PubMed Central

Fiester, Steven E.; Nwugo, Chika C.; Penwell, William F.; Neary, John M.; Beckett, Amber C.; Arivett, Brock A.; Schmidt, Robert E.; Geiger, Sarah C.; Connerly, Pamela L.; Menke, Sharon M.; Tomaras, Andrew P.

2015-01-01

Acinetobacter baumannii is a Gram-negative opportunistic nosocomial pathogen that causes pneumonia and soft tissue and systemic infections. Screening of a transposon insertion library of A. baumannii ATCC 19606T resulted in the identification of the 2010 derivative, which, although capable of growing well in iron-rich media, failed to prosper under iron chelation. Genetic, molecular, and functional assays showed that 2010's iron utilization-deficient phenotype is due to an insertion within the 3′ end of secA, which results in the production of a C-terminally truncated derivative of SecA. SecA plays a critical role in protein translocation through the SecYEG membrane channel. Accordingly, the secA mutation resulted in undetectable amounts of the ferric acinetobactin outer membrane receptor protein BauA while not affecting the production of other acinetobactin membrane protein transport components, such as BauB and BauE, or the secretion of acinetobactin by 2010 cells cultured in the presence of subinhibitory concentrations of the synthetic iron chelator 2,2′-dipyridyl. Outer membrane proteins involved in nutrient transport, adherence, and biofilm formation were also reduced in 2010. The SecA truncation also increased production of 30 different proteins, including proteins involved in adaptation/tolerance responses. Although some of these protein changes could negatively affect the pathobiology of the 2010 derivative, its virulence defect is mainly due to its inability to acquire iron via the acinetobactin-mediated system. These results together indicate that although the C terminus of the A. baumannii ATCC 19606T SecA is not essential for viability, it plays a critical role in the production and translocation of different proteins and virulence. PMID:25605767

High truncated-O-glycan score predicts adverse clinical outcome in patients with localized clear-cell renal cell carcinoma after surgery.

PubMed

NguyenHoang, SonTung; Liu, Yidong; Xu, Le; Zhou, Lin; Chang, Yuan; Fu, Qiang; Liu, Zheng; Lin, Zongming; Xu, Jiejie

2017-10-03

Truncated O-glycans, including Tn-antigen, sTn-antigen, T-antigen, sT-antigen, are incomplete glycosylated structures and their expression occur frequently in tumor tissue. The study aims to evaluate the abundance of each truncated O-glycans and its clinical significance in postoperative patients with localized clear-cell renal cell carcinoma (ccRCC). We used immunohistochemical testing to analyze the expression of truncated O-glycans in tumor specimens from 401 patients with localized ccRCC. Truncated-O-glycan score was built by integrating the expression level of Tn-, sTn- and sT-antigen. Kaplan-Meier survival and Cox regression analysis were done to compare clinical outcomes in subgroups. Receiver operating characteristic (ROC) was applied to assess the impact of prognostic factors on overall survival (OS) and recurrence-free survival (RFS). The results identified Tn-, sTn-, sT-antigen as independent prognosticators. The OS and RFS were shortened among the 198 (49.4%) patients with high Truncated-O-glycan score than among the 203 (50.6%) patients with low score (hazard ratio for OS, 7.060; 95% confidence interval [CI]: 2.765 to 18.027; p <0.001; for RFS, 4.612; 95% CI: 2.141 to 9.931; p <0.001). There is no difference between low-risk patients and high-risk patients in low score group ( p = 0.987). High-risk patients with low score showed a better prognosis than low-risk patient with high score ( p = 0.029). The Truncated-O-glycan score showed better prognostic value for OS (AUC: 0.739, p = 0.003) and RFS (AUC: 0.719, p = 0.003) than TNM stage. In summary, the high Truncated-O-glycan score could predict adverse clinical outcome in localized ccRCC patients after surgery.

The F(N) method for the one-angle radiative transfer equation applied to plant canopies

NASA Technical Reports Server (NTRS)

Ganapol, B. D.; Myneni, R. B.

1992-01-01

The paper presents a semianalytical solution method, called the F(N) method, for the one-angle radiative transfer equation in slab geometry. The F(N) method is based on two integral equations specifying the intensities exiting the boundaries of the vegetation canopy; the solution is obtained through an expansion in a set of basis functions with expansion coefficients to be determined. The advantage of this method is that it avoids spatial truncation error entirely because it requires discretization only in the angular variable.

Detection of oxidative stress in heart by estimating the dinitrophenylhydrazine derivative of malonaldehyde.

PubMed

Cordis, G A; Maulik, N; Das, D K

1995-08-01

Accurate estimation of the oxidative stress in heart is necessary because the pathogenesis of many heart diseases are believed to be mediated at least in part from the development of oxidative stress resulting from the generation of oxygen free radicals and reduced antioxidant defense system. The most widely used method for this purpose has been the estimation of malonaldehyde (MDA), a lipid peroxidation product, by the thiobarbituric acid (TBA) reaction method. However, because of the nonspecificity of this method, the results are often erroneous. The present report describes a method using high-performance liquid chromatography (HPLC) to estimate MDA. To develop the oxidative stress, two different models were used: ischaemic-reperfused heart and perfusing the heart with a hydroxyl radical (OH+) generating system. The coronary effluents obtained from the isolated rat heart before ischaemia and during the reperfusion of ischaemic heart, as well as during the perfusion of the heart with the OH+ generating system were collected, derivatized with 2,4-dinitrophenylhydrazine (DNPH) and extracted with pentane. Aliquots of 25 microliters in acetonitrile were injected onto a Beckman Ultrasphere C18 (3 microns) column. The products were eluted isocratically with a mobile phase containing acetonitrile-water-acetic acid (40:60:0.1, v/v/v), measured at 307 nm using a Waters M-490 multichannel UV detector and collected for gas chromatography-mass spectrometry (GC-MS). The peaks were identified by co-chromatography with DNPH derivatives of authentic standards, peak addition, and by GC-MS. The retention time for MDA-DNPH was 5.3 min.(ABSTRACT TRUNCATED AT 250 WORDS)

The Shock and Vibration Digest. Volume 18, Number 6

DTIC Science & Technology

1986-06-01

linear, quadratic, or cubic. Bessel function Reed [124] reported a method for computing solutions were obtained for a truncated pyramid amplitudes of a...86-1198 A. Ragab, Chung C. Fu Seismic Analysis of a Large LMFBR with Flu- Cairo Univ., Giza , Egypt . . *. id-Structure Imteractions Computers Struc

Propagation of a general-type beam through a truncated fractional Fourier transform optical system.

PubMed

Zhao, Chengliang; Cai, Yangjian

2010-03-01

Paraxial propagation of a general-type beam through a truncated fractional Fourier transform (FRT) optical system is investigated. Analytical formulas for the electric field and effective beam width of a general-type beam in the FRT plane are derived based on the Collins formula. Our formulas can be used to study the propagation of a variety of laser beams--such as Gaussian, cos-Gaussian, cosh-Gaussian, sine-Gaussian, sinh-Gaussian, flat-topped, Hermite-cosh-Gaussian, Hermite-sine-Gaussian, higher-order annular Gaussian, Hermite-sinh-Gaussian and Hermite-cos-Gaussian beams--through a FRT optical system with or without truncation. The propagation properties of a Hermite-cos-Gaussian beam passing through a rectangularly truncated FRT optical system are studied as a numerical example. Our results clearly show that the truncated FRT optical system provides a convenient way for laser beam shaping.

Truncation Depth Rule-of-Thumb for Convolutional Codes

NASA Technical Reports Server (NTRS)

Moision, Bruce

2009-01-01

In this innovation, it is shown that a commonly used rule of thumb (that the truncation depth of a convolutional code should be five times the memory length, m, of the code) is accurate only for rate 1/2 codes. In fact, the truncation depth should be 2.5 m/(1 - r), where r is the code rate. The accuracy of this new rule is demonstrated by tabulating the distance properties of a large set of known codes. This new rule was derived by bounding the losses due to truncation as a function of the code rate. With regard to particular codes, a good indicator of the required truncation depth is the path length at which all paths that diverge from a particular path have accumulated the minimum distance of the code. It is shown that the new rule of thumb provides an accurate prediction of this depth for codes of varying rates.

Invariance of Topological Indices Under Hilbert Space Truncation

DOE PAGES

Huang, Zhoushen; Zhu, Wei; Arovas, Daniel P.; ...

2018-01-05

Here, we show that the topological index of a wave function, computed in the space of twisted boundary phases, is preserved under Hilbert space truncation, provided the truncated state remains normalizable. If truncation affects the boundary condition of the resulting state, the invariant index may acquire a different physical interpretation. If the index is symmetry protected, the truncation should preserve the protecting symmetry. We discuss implications of this invariance using paradigmatic integer and fractional Chern insulators, Z 2 topological insulators, and spin-1 Affleck-Kennedy-Lieb-Tasaki and Heisenberg chains, as well as its relation with the notion of bulk entanglement. As a possiblemore » application, we propose a partial quantum tomography scheme from which the topological index of a generic multicomponent wave function can be extracted by measuring only a small subset of wave function components, equivalent to the measurement of a bulk entanglement topological index.« less

Variation in shape of the lingula in the adult human mandible

PubMed Central

TULI, A.; CHOUDHRY, R.; CHOUDHRY, S.; RAHEJA, S.; AGARWAL, S.

2000-01-01

The lingulae of both sides of 165 dry adult human mandibles, 131 males and 34 females of Indian origin, were classified by their shape into 4 types: 1, triangular; 2, truncated; 3, nodular; and 4, assimilated. Triangular lingulae were found in 226 (68.5%) sides, truncated in 52 (15.8%), nodular in 36 (10.9%) and assimilated in 16 (4.8%) sides. Triangular lingulae were found bilaterally in 110, truncated in 23, nodular in 17 and assimilated in 7 mandibles. Of the remaining 8 mandibles with different appearances on the 2 sides, 6 had a combination of triangular and truncated and 2 had nodular and assimilated. The incidence of triangular and assimilated types in the male and female mandibles are almost equal. In the truncated type it was double in the male mandibles while the nodular type was a little less than double in the female mandibles. PMID:11005723

Invariance of Topological Indices Under Hilbert Space Truncation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Zhoushen; Zhu, Wei; Arovas, Daniel P.

Here, we show that the topological index of a wave function, computed in the space of twisted boundary phases, is preserved under Hilbert space truncation, provided the truncated state remains normalizable. If truncation affects the boundary condition of the resulting state, the invariant index may acquire a different physical interpretation. If the index is symmetry protected, the truncation should preserve the protecting symmetry. We discuss implications of this invariance using paradigmatic integer and fractional Chern insulators, Z 2 topological insulators, and spin-1 Affleck-Kennedy-Lieb-Tasaki and Heisenberg chains, as well as its relation with the notion of bulk entanglement. As a possiblemore » application, we propose a partial quantum tomography scheme from which the topological index of a generic multicomponent wave function can be extracted by measuring only a small subset of wave function components, equivalent to the measurement of a bulk entanglement topological index.« less

Implication of observed cloud variability for parameterizations of microphysical and radiative transfer processes in climate models

NASA Astrophysics Data System (ADS)

Huang, D.; Liu, Y.

2014-12-01

The effects of subgrid cloud variability on grid-average microphysical rates and radiative fluxes are examined by use of long-term retrieval products at the Tropical West Pacific (TWP), Southern Great Plains (SGP), and North Slope of Alaska (NSA) sites of the Department of Energy's Atmospheric Radiation Measurement (ARM) Program. Four commonly used distribution functions, the truncated Gaussian, Gamma, lognormal, and Weibull distributions, are constrained to have the same mean and standard deviation as observed cloud liquid water content. The PDFs are then used to upscale relevant physical processes to obtain grid-average process rates. It is found that the truncated Gaussian representation results in up to 30% mean bias in autoconversion rate whereas the mean bias for the lognormal representation is about 10%. The Gamma and Weibull distribution function performs the best for the grid-average autoconversion rate with the mean relative bias less than 5%. For radiative fluxes, the lognormal and truncated Gaussian representations perform better than the Gamma and Weibull representations. The results show that the optimal choice of subgrid cloud distribution function depends on the nonlinearity of the process of interest and thus there is no single distribution function that works best for all parameterizations. Examination of the scale (window size) dependence of the mean bias indicates that the bias in grid-average process rates monotonically increases with increasing window sizes, suggesting the increasing importance of subgrid variability with increasing grid sizes.

Protective Immunity and Safety of a Genetically Modified Influenza Virus Vaccine

PubMed Central

Garcia, Cristiana Couto; Filho, Bruno Galvão; Gonçalves, Ana Paula de Faria; Lima, Braulio Henrique Freire; Lopes, Gabriel Augusto Oliveira; Rachid, Milene Alvarenga; Peixoto, Andiara Cristina Cardoso; de Oliveira, Danilo Bretas; Ataíde, Marco Antônio; Zirke, Carla Aparecida; Cotrim, Tatiane Marques; Costa, Érica Azevedo; Almeida, Gabriel Magno de Freitas; Russo, Remo Castro; Gazzinelli, Ricardo Tostes; Machado, Alexandre de Magalhães Vieira

2014-01-01

Recombinant influenza viruses are promising viral platforms to be used as antigen delivery vectors. To this aim, one of the most promising approaches consists of generating recombinant viruses harboring partially truncated neuraminidase (NA) segments. To date, all studies have pointed to safety and usefulness of this viral platform. However, some aspects of the inflammatory and immune responses triggered by those recombinant viruses and their safety to immunocompromised hosts remained to be elucidated. In the present study, we generated a recombinant influenza virus harboring a truncated NA segment (vNA-Δ) and evaluated the innate and inflammatory responses and the safety of this recombinant virus in wild type or knock-out (KO) mice with impaired innate (Myd88 -/-) or acquired (RAG -/-) immune responses. Infection using truncated neuraminidase influenza virus was harmless regarding lung and systemic inflammatory response in wild type mice and was highly attenuated in KO mice. We also demonstrated that vNA-Δ infection does not induce unbalanced cytokine production that strongly contributes to lung damage in infected mice. In addition, the recombinant influenza virus was able to trigger both local and systemic virus-specific humoral and CD8+ T cellular immune responses which protected immunized mice against the challenge with a lethal dose of homologous A/PR8/34 influenza virus. Taken together, our findings suggest and reinforce the safety of using NA deleted influenza viruses as antigen delivery vectors against human or veterinary pathogens. PMID:24927156

Clinical and Functional Analyses of p73R1 Mutations in Prostate Cancer

DTIC Science & Technology

2005-02-01

mutations in several genes (BRCA 1, BRCA2, and CHEK2) whose products are involved in this pathway have been associated with increased risk for this...screened this gene for mutations in prostate cancer. Two germline truncating mutations were identified. Genotyping of 403 men with sporadic prostate...based on mutation screening of candidate genes involved in the DNA damage- signaling pathway. Genomic instability is a common feature of all human

Truncated Hormone Inhibits Breast Tumor Blood Vessel Formation, Not Tumor Growth | Center for Cancer Research

Cancer.gov

The hormone prolactin (PRL) plays a critical role in normal breast development by stimulating the proliferation of mammary cells, the production of milk proteins, and the formation of new mammary blood vessels. Unfortunately, the same cell and vessel growth pathways controlled by PRL in normal cells also operate in breast cancer cells, and elevated plasma PRL is a risk factor for breast cancer, especially in post-menopausal women.

Gibbs sampling on large lattice with GMRF

NASA Astrophysics Data System (ADS)

Marcotte, Denis; Allard, Denis

2018-02-01

Gibbs sampling is routinely used to sample truncated Gaussian distributions. These distributions naturally occur when associating latent Gaussian fields to category fields obtained by discrete simulation methods like multipoint, sequential indicator simulation and object-based simulation. The latent Gaussians are often used in data assimilation and history matching algorithms. When the Gibbs sampling is applied on a large lattice, the computing cost can become prohibitive. The usual practice of using local neighborhoods is unsatisfying as it can diverge and it does not reproduce exactly the desired covariance. A better approach is to use Gaussian Markov Random Fields (GMRF) which enables to compute the conditional distributions at any point without having to compute and invert the full covariance matrix. As the GMRF is locally defined, it allows simultaneous updating of all points that do not share neighbors (coding sets). We propose a new simultaneous Gibbs updating strategy on coding sets that can be efficiently computed by convolution and applied with an acceptance/rejection method in the truncated case. We study empirically the speed of convergence, the effect of choice of boundary conditions, of the correlation range and of GMRF smoothness. We show that the convergence is slower in the Gaussian case on the torus than for the finite case studied in the literature. However, in the truncated Gaussian case, we show that short scale correlation is quickly restored and the conditioning categories at each lattice point imprint the long scale correlation. Hence our approach enables to realistically apply Gibbs sampling on large 2D or 3D lattice with the desired GMRF covariance.

Functional analysis of truncated and site-directed mutagenesis dextransucrases to produce different type dextrans.

PubMed

Wang, Chao; Zhang, Hong-Bin; Li, Meng-Qi; Hu, Xue-Qin; Li, Yao

2017-07-01

Dextrans with distinct molecular size and structure are increasingly being used in the food and pharmaceutical industries. Dextran is produced by dextransucrase (DSR, EC2.4.5.1), which is produced by Leuconostoc mesenteroides. DSR belongs to glycosyl hydrolase family (GH70) and synthesizes branched α-glucan (dextran) with both 5% α(1-3) and 95% α(1-6) glycosidic linkages. The DSR gene dex-YG (Genebank, Accession No. DQ345760) was cloned from the wild strain Leuconostoc mesenteroides 0326. This study generated a series of C-terminally truncated variants of dextransucrase and substituting the amino-acid residues in the active site of DSR. With shorter length of DSR, its polysaccharide-synthesizing capability was impaired heavily, whereas oligosaccharide (acting as prebiotics)-synthesizing capability increased significantly, efficiently producing special sizes of dextran. All truncated mutant enzymes were active. Results demonstrated that the catalytic domain dextransucrase was likely in 800 aa or less. Based on the three-dimensional structure model of dextransucrase built through homology modeling methods, the DSR and its mutants with the acceptor substrate of maltose and donor substrate of sucrose were studied by molecular-docking method. Substituting these amino-acid residues significantly affected enzyme activities. Compared with the wild-type dextran, mutant enzymes catalyzed the synthesis of a-glucan with 1-9% α(1-3) and 90-98% α(1-6) branching linkages. Some mutants introduced a small amount of α(1-4) linkages and α(1-2) linkages. This strategy can be effectively used for the rational protein design of dextransucrase. Copyright © 2017 Elsevier Inc. All rights reserved.

Prognostic and predictive value of TP53 mutations in node-positive breast cancer patients treated with anthracycline- or anthracycline/taxane-based adjuvant therapy: results from the BIG 02-98 phase III trial

PubMed Central

2012-01-01

Abstract Introduction Pre-clinical data suggest p53-dependent anthracycline-induced apoptosis and p53-independent taxane activity. However, dedicated clinical research has not defined a predictive role for TP53 gene mutations. The aim of the current study was to retrospectively explore the prognosis and predictive values of TP53 somatic mutations in the BIG 02-98 randomized phase III trial in which women with node-positive breast cancer were treated with adjuvant doxorubicin-based chemotherapy with or without docetaxel. Methods The prognostic and predictive values of TP53 were analyzed in tumor samples by gene sequencing within exons 5 to 8. Patients were classified according to p53 protein status predicted from TP53 gene sequence, as wild-type (no TP53 variation or TP53 variations which are predicted not to modify p53 protein sequence) or mutant (p53 nonsynonymous mutations). Mutations were subcategorized according to missense or truncating mutations. Survival analyses were performed using the Kaplan-Meier method and log-rank test. Cox-regression analysis was used to identify independent predictors of outcome. Results TP53 gene status was determined for 18% (520 of 2887) of the women enrolled in BIG 02-98. TP53 gene variations were found in 17% (90 of 520). Nonsynonymous p53 mutations, found in 16.3% (85 of 520), were associated with older age, ductal morphology, higher grade and hormone-receptor negativity. Of the nonsynonymous mutations, 12.3% (64 of 520) were missense and 3.6% were truncating (19 of 520). Only truncating mutations showed significant independent prognostic value, with an increased recurrence risk compared to patients with non-modified p53 protein (hazard ratio = 3.21, 95% confidence interval = 1.740 to 5.935, P = 0.0002). p53 status had no significant predictive value for response to docetaxel. Conclusions p53 truncating mutations were uncommon but associated with poor prognosis. No significant predictive role for p53 status was detected. Trial registration ClinicalTrials.gov NCT00174655 PMID:22551440

On the Old Saw That Dialogue Is a Socratic but Not an Aristotelian Method of Moral Education

ERIC Educational Resources Information Center

Kristjánsson, Kristján

2014-01-01

Kristján Kristjánsson's aim in this article is to bury the old saw that dialogue is exclusively a Socratic but not an Aristotelian method of education for moral character. Although the truncated discussion in Aristotle's "Nicomachean Ethics" of the character development of the young may indicate that it is merely the result of…

Fast Multiscale Algorithms for Wave Propagation in Heterogeneous Environments

DTIC Science & Technology

2016-01-07

methods for waves’’, Nonlinear solvers for high- intensity focused ultrasound with application to cancer treatment, AIMS, Palo Alto, 2012. ``Hermite...formulation but different parametrizations. . . . . . . . . . . . 6 4 Density µ(t) at mode 0 for scattering of a plane Gaussian pulse from a sphere. On the...spatiotemporal scales. Two crucial components of the highly-efficient, general-purpose wave simulator we envision are • Reliable, low -cost methods for truncating

Guide on the Effective Block Approach for the Fatigue Life Assessment of Metallic Structures

DTIC Science & Technology

2013-01-01

Load Interpretation Truncation Validation coupon test program NDI Non-Destructive Inspection QF Quantitative Fractography RAAF Royal Australian...even more-so with the advent of quantitative fractography . 3 LEFM forms the basis of most state-of-art CG models. UNCLASSIFIED 1 UNCLASSIFIED DSTO...preferred method for obtaining the CGR data is by quantitative fractography (QF). This method is well suited to small cracks where other measurement

Accuracy of Course Placement Validity Statistics under Various Soft Truncation Conditions. ACT Research Report Series 99-2.

ERIC Educational Resources Information Center

Schiel, Jeff L.; King, Jason E.

Analyses of data from operational course placement systems are subject to the effects of truncation; students with low placement test scores may enroll in a remedial course, rather than a standard-level course, and therefore will not have outcome data from the standard course. In "soft" truncation, some (but not all) students who score…

Generalized M-factor of hollow Gaussian beams through a hard-edge circular aperture

NASA Astrophysics Data System (ADS)

Deng, Dongmei

2005-06-01

Based on the generalized truncated second-order moments, the generalized M-factor (MG2-factor) of three-dimensional hollow Gaussian beams (HGBs) through a hard-edge circular aperture is studied in cylindrical coordinate system analytically and numerically. The closed-form expression for the MG2-factor of the truncated HGBs, which is dependent on the truncation parameter β and the beam order n, can be simplified to that of the truncated, the untruncated Gaussian beams and the untruncated HGBs. Also, the power fraction is demonstrated analytically and numerically, which shows that the area of the dark region across the HGBs increases as n increasing.

Expression Templates for Truncated Power Series

NASA Astrophysics Data System (ADS)

Cary, John R.; Shasharina, Svetlana G.

1997-05-01

Truncated power series are used extensively in accelerator transport modeling for rapid tracking and analysis of nonlinearity. Such mathematical objects are naturally represented computationally as objects in C++. This is more intuitive and produces more transparent code through operator overloading. However, C++ object use often comes with a computational speed loss due, e.g., to the creation of temporaries. We have developed a subset of truncated power series expression templates(http://monet.uwaterloo.ca/blitz/). Such expression templates use the powerful template processing facility of C++ to combine complicated expressions into series operations that exectute more rapidly. We compare computational speeds with existing truncated power series libraries.

Sensitivity of selected geomagnetic properties to truncation level of spherical harmonic expansions

NASA Technical Reports Server (NTRS)

Benton, E. R.; Estes, R. H.; Langel, R. A.; Muth, L. A.

1982-01-01

The model dependence of Gauss coefficients associated with a lack of spherical harmonic orthogonality on a nonuniform Magsat data grid is shown to be minor, where the fitting level exceeds the harmonic order by a value of approximately four. The shape of the magnetic energy spectrum outside the core, and the sensitivity to truncation level of magnetic contour location and the number of their intersections on the core-mantle boundary, suggest that spherical harmonic expansions of the main geomagnetic field should be truncated at a truncation level value of not more than eight if they are to be extrapolated to the core.

You’re Cut Off: HD and MHD Simulations of Truncated Accretion Disks

NASA Astrophysics Data System (ADS)

Hogg, J. Drew; Reynolds, Christopher S.

2017-01-01

Truncated accretion disks are commonly invoked to explain the spectro-temporal variability from accreting black holes in both small systems, i.e. state transitions in galactic black hole binaries (GBHBs), and large systems, i.e. low-luminosity active galactic nuclei (LLAGNs). In the canonical truncated disk model of moderately low accretion rate systems, gas in the inner region of the accretion disk occupies a hot, radiatively inefficient phase, which leads to a geometrically thick disk, while the gas in the outer region occupies a cooler, radiatively efficient phase that resides in the standard geometrically thin disk. Observationally, there is strong empirical evidence to support this phenomenological model, but a detailed understanding of the disk behavior is lacking. We present well-resolved hydrodynamic (HD) and magnetohydrodynamic (MHD) numerical models that use a toy cooling prescription to produce the first sustained truncated accretion disks. Using these simulations, we study the dynamics, angular momentum transport, and energetics of a truncated disk in the two different regimes. We compare the behaviors of the HD and MHD disks and emphasize the need to incorporate a full MHD treatment in any discussion of truncated accretion disk evolution.

SU-E-J-167: Improvement of Time-Ordered Four Dimensional Cone-Beam CT; Image Mosaicing with Real and Virtual Projections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakano, M; Kida, S; Masutani, Y

2014-06-01

Purpose: In the previous study, we developed time-ordered fourdimensional (4D) cone-beam CT (CBCT) technique to visualize nonperiodic organ motion, such as peristaltic motion of gastrointestinal organs and adjacent area, using half-scan reconstruction method. One important obstacle was that truncation of projection was caused by asymmetric location of flat-panel detector (FPD) in order to cover whole abdomen or pelvis in one rotation. In this study, we propose image mosaicing to extend projection data to make possible to reconstruct full field-of-view (FOV) image using half-scan reconstruction. Methods: The projections of prostate cancer patients were acquired using the X-ray Volume Imaging system (XVI,more » version 4.5) on Synergy linear accelerator system (Elekta, UK). The XVI system has three options of FOV, S, M and L, and M FOV was chosen for pelvic CBCT acquisition, with a FPD panel 11.5 cm offset. The method to produce extended projections consists of three main steps: First, normal three-dimensional (3D) reconstruction which contains whole pelvis was implemented using real projections. Second, virtual projections were produced by reprojection process of the reconstructed 3D image. Third, real and virtual projections in each angle were combined into one extended mosaic projection. Then, 4D CBCT images were reconstructed using our inhouse reconstruction software based on Feldkamp, Davis and Kress algorithm. The angular range of each reconstruction phase in the 4D reconstruction was 180 degrees, and the range moved as time progressed. Results: Projection data were successfully extended without discontinuous boundary between real and virtual projections. Using mosaic projections, 4D CBCT image sets were reconstructed without artifacts caused by the truncation, and thus, whole pelvis was clearly visible. Conclusion: The present method provides extended projections which contain whole pelvis. The presented reconstruction method also enables time-ordered 4D CBCT reconstruction of organs with non-periodic motion with full FOV without projection-truncation artifacts. This work was partly supported by the JSPS Core-to-Core Program(No. 23003). This work was partly supported by JSPS KAKENHI 24234567.« less

Scaffold Library for Tissue Engineering: A Geometric Evaluation

PubMed Central

Chantarapanich, Nattapon; Puttawibul, Puttisak; Sucharitpwatskul, Sedthawatt; Jeamwatthanachai, Pongnarin; Inglam, Samroeng; Sitthiseripratip, Kriskrai

2012-01-01

Tissue engineering scaffold is a biological substitute that aims to restore, to maintain, or to improve tissue functions. Currently available manufacturing technology, that is, additive manufacturing is essentially applied to fabricate the scaffold according to the predefined computer aided design (CAD) model. To develop scaffold CAD libraries, the polyhedrons could be used in the scaffold libraries development. In this present study, one hundred and nineteen polyhedron models were evaluated according to the established criteria. The proposed criteria included considerations on geometry, manufacturing feasibility, and mechanical strength of these polyhedrons. CAD and finite element (FE) method were employed as tools in evaluation. The result of evaluation revealed that the close-cellular scaffold included truncated octahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. In addition, the suitable polyhedrons for using as open-cellular scaffold libraries included hexahedron, truncated octahedron, truncated hexahedron, cuboctahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. However, not all pore size to beam thickness ratios (PO : BT) were good for making the open-cellular scaffold. The PO : BT ratio of each library, generating the enclosed pore inside the scaffold, was excluded to avoid the impossibility of material removal after the fabrication. The close-cellular libraries presented the constant porosity which is irrespective to the different pore sizes. The relationship between PO : BT ratio and porosity of open-cellular scaffold libraries was displayed in the form of Logistic Power function. The possibility of merging two different types of libraries to produce the composite structure was geometrically evaluated in terms of the intersection index and was mechanically evaluated by means of FE analysis to observe the stress level. The couples of polyhedrons presenting low intersection index and high stress level were excluded. Good couples for producing the reinforced scaffold were hexahedron-truncated hexahedron and cuboctahedron-rhombitruncated cuboctahedron. PMID:23056147

General relaxation schemes in multigrid algorithms for higher order singularity methods

NASA Technical Reports Server (NTRS)

Oskam, B.; Fray, J. M. J.

1981-01-01

Relaxation schemes based on approximate and incomplete factorization technique (AF) are described. The AF schemes allow construction of a fast multigrid method for solving integral equations of the second and first kind. The smoothing factors for integral equations of the first kind, and comparison with similar results from the second kind of equations are a novel item. Application of the MD algorithm shows convergence to the level of truncation error of a second order accurate panel method.

The convolutional differentiator method for numerical modelling of acoustic and elastic wavefields

NASA Astrophysics Data System (ADS)

Zhang, Zhong-Jie; Teng, Ji-Wen; Yang, Ding-Hui

1996-02-01

Based on the techniques of forward and inverse Fourier transformation, the authors discussed the design scheme of ordinary differentiator used and applied in the simulation of acoustic and elastic wavefields in isotropic media respectively. To compress Gibbs effects by truncation effectively, Hanning window is introduced in. The model computation shows that, the convolutional differentiator method has the advantages of rapidity, low requirements of computer’s inner storage and high precision, which is a potential method of numerical simulation.

Expression of truncated Int6/eIF3e in mammary alveolar epithelium leads to persistent hyperplasia and tumorigenesis

PubMed Central

Mack, David L; Boulanger, Corinne A; Callahan, Robert; Smith, Gilbert H

2007-01-01

Introduction Int6 has been shown to be an interactive participant with the protein translation initiation complex eIF3, the COP9 signalosome and the regulatory lid of the 26S proteasome. Insertion of mouse mammary tumor virus into the Int6 locus creates a C-terminally truncated form of the protein. Expression of the truncated form of Int6 (Int6sh) in stably transfected human and mouse mammary epithelial cell lines leads to cellular transformation. In addition, decreased expression of Int6/eIF3e is observed in approximately one third of all human breast carcinomas. Methods To validate that Int6sh has transforming activity in vivo, a transgenic mouse model was designed using the whey acidic protein (Wap) promoter to target expression of truncated Int6 to differentiating alveolar epithelial cells in the mammary gland. Microarray analyses were performed on normal, premalignant and malignant WapInt6sh expressing tissues. Results Mammary tumors developed in 42% of WapInt6sh heterozygous parous females at an average age of 18 months. In WapInt6sh mice, the contralateral mammary glands from both tumorous and non-tumorous tissues contained widespread focal alveolar hyperplasia. Only 4% of WapInt6sh non-breeding females developed tumors by 2 years of age. The Wap promoter is active only during estrus in the mammary tissue of cycling non-pregnant mice. Microarray analyses of mammary tissues demonstrated that Int6sh expression in the alveolar tissue altered the mammary transcriptome in a specific manner that was detectable even in the first pregnancy. This Int6sh-specific transcriptome pattern subsequently persisted in both the Int6sh-expressing alveolar hyperplasia and mammary tumors. These observations are consistent with the conclusion that WapInt6sh-expressing alveolar cells survive involution following the cessation of lactation, and subsequently give rise to the mammary tumors that arise in aging multiparous females. Conclusion These observations provide direct in vivo evidence that mammary-specific expression of the Int6sh truncation leads to persistence of alveolar hyperplasia with the accompanying increased predisposition to mammary tumorigenesis. PMID:17626637

Radiographic evaluation of BFX acetabular component position in dogs.

PubMed

Renwick, Alasdair; Gemmill, Toby; Pink, Jonathan; Brodbelt, David; McKee, Malcolm

2011-07-01

To assess the reliability of radiographic measurement of angle of lateral opening (ALO) and angle of version of BFX acetabular cups. In vitro radiographic study. BFX cups (24, 28, and 32 mm). Total hip replacement constructs (cups, 17 mm femoral head and a #7 CFX stem) were mounted on an inclinometer. Ventrodorsal radiographs were obtained with ALO varying between 21° and 70° and inclination set at 0°, 10°, 20°, and 30°. Radiographs were randomized using a random sequence generator. Three observers blinded to the radiograph order assessed ALO using 3 methods: (1) an ellipse method based on trigonometry; (2) using a measurement from the center of the femoral head to the truncated surface of the cup; (3) by visual estimation using a reference chart. Version was measured by assessing the ventral edge of the truncated surface. ALO methods 2 and 3 were accurate and precise to within 10° and were significantly more accurate and precise than method 1 (P < .001). All methods were significantly less accurate with increasing inclination. Version measurement was accurate and precise to within 7° with 0-20° of inclination, but significantly less accurate with 30° of inclination. Methods 2 and 3, but not method 1, were sufficiently accurate and precise to be clinically useful. Version measurement was clinically useful when inclination was ≤ 20°. © Copyright 2011 by The American College of Veterinary Surgeons.

Exclusive J / Ψ vector-meson production in high-energy nuclear collisions

NASA Astrophysics Data System (ADS)

Ramnath, A.; Weigert, H.; Hamilton, A.

2014-12-01

We illustrate the first steps in a cross-section determination for exclusive J / Ψ production in ultra-peripheral heavy ion collisions from two viewpoints. First, the setup for a theoretical calculation is done in the context of the Colour Glass Condensate effective field theory, using the Gaussian truncation to parametrise rapidity-averaged n-point correlators. Secondly, a feasibility study is carried out using STARlight Monte Carlo simulations to predict how many exclusive J / Ψ vector-mesons might be expected in ATLAS at the LHC. In a data set corresponding to 160 μb-1 of total integrated luminosity, about 150 candidate events are expected.

Transient Dynamics Simulation of Airflow in a CT-Scanned Human Airway Tree: More or Fewer Terminal Bronchi?

PubMed Central

Zhang, Baihua; Li, Jianhua; Yue, Yong; Qian, Wei

2017-01-01

Using computational fluid dynamics (CFD) method, the feasibility of simulating transient airflow in a CT-based airway tree with more than 100 outlets for a whole respiratory period is studied, and the influence of truncations of terminal bronchi on CFD characteristics is investigated. After an airway model with 122 outlets is extracted from CT images, the transient airflow is simulated. Spatial and temporal variations of flow velocity, wall pressure, and wall shear stress are presented; the flow pattern and lobar distribution of air are gotten as well. All results are compared with those of a truncated model with 22 outlets. It is found that the flow pattern shows lobar heterogeneity that the near-wall air in the trachea is inhaled into the upper lobe while the center flow enters the other lobes, and the lobar distribution of air is significantly correlated with the outlet area ratio. The truncation decreases airflow to right and left upper lobes and increases the deviation of airflow distributions between inspiration and expiration. Simulating the transient airflow in an airway tree model with 122 bronchi using CFD is feasible. The model with more terminal bronchi decreases the difference between the lobar distributions at inspiration and at expiration. PMID:29333194

Use of T7 RNA polymerase to direct expression of outer Surface Protein A (OspA) from the Lyme disease Spirochete, Borrelia burgdorferi

NASA Technical Reports Server (NTRS)

Dunn, John J.; Lade, Barbara N.

1991-01-01

The OspA gene from a North American strain of the Lyme disease Spirochete, Borrelia burgdorferi, was cloned under the control of transciption and translation signals from bacteriophage T7. Full-length OspA protein, a 273 amino acid (31kD) lipoprotein, is expressed poorly in Escherichia coli and is associated with the insoluble membrane fraction. In contrast, a truncated form of OspA lacking the amino-terminal signal sequence which normally would direct localization of the protein to the outer membrane is expressed at very high levels (less than or equal to 100 mg/liter) and is soluble. The truncated protein was purified to homogeneity and is being tested to see if it will be useful as an immunogen in a vaccine against Lyme disease. Circular dichroism and fluorescence spectroscopy was used to characterize the secondary structure and study conformational changes in the protein. Studies underway with other surface proteins from B burgdorferi and a related spirochete, B. hermsii, which causes relapsing fever, leads us to conclude that a strategy similar to that used to express the truncated OspA can provide a facile method for producing variations of Borrelia lipoproteins which are highly expressed in E. coli and soluble without exposure to detergents.

Expression and Secretion of Cyan Fluorescent Protein (CFP) in B. subtilis using the Chitinase Promoter from Bacillus pumilus SG2

PubMed Central

Shali, Abbas; Rigi, Garshasb; Pornour, Majid; Ahmadian, Gholamreza

2017-01-01

Background: Improved cyan fluorescent protein (ICFP) is a monochromic, green fluorescent protein (GFP) derivative produced by Aequorea macrodactyla in a process similar to GFP. This protein has strong absorption spectra at wavelengths 426-446 nm. ICFP can be used in cell, organelle or intracellular protein labeling, investigating the protein-protein interactions as well as assessing the promoter activities. Methods: In our previous study, the promoters of two chitinases (ChiS and ChiL) from Bacillus pumilus SG2 were assessed in B. subtilis and their regulatory elements were characterized. In the present study, icfp was cloned downstream of several truncated promoters obtained in the former study, and ICFP expression was evaluated in B. subtilis. Results: Extracellular expression and secretion of ICFP were analyzed under the control of different truncated versions of ChiSL promoters grown on different media. Results from SDS-PAGE and fluorimetric analyses showed that there were different expression rates of CFP; however, the UPChi-ICFP3 construct exhibited a higher level of expression and secretion in the culture medium. Conclusion: Our presented results revealed that inserting this truncated form of Chi promoter upstream of the ICFP, as a reporter gene, in B. subtilis led to an approximately ten fold increase in ICFP expression. PMID:28088132

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

PubMed

Chen, Wei; Shen, Jana K

2014-10-15

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

PubMed Central

Chen, Wei; Shen, Jana K.

2014-01-01

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

A new titinopathy

PubMed Central

De Cid, Rafael; Ben Yaou, Rabah; Roudaut, Carinne; Charton, Karine; Baulande, Sylvain; Leturcq, France; Romero, Norma Beatriz; Malfatti, Edoardo; Beuvin, Maud; Vihola, Anna; Criqui, Audrey; Nelson, Isabelle; Nectoux, Juliette; Ben Aim, Laurène; Caloustian, Christophe; Olaso, Robert; Udd, Bjarne; Bonne, Gisèle; Eymard, Bruno

2015-01-01

Objective: To identify the genetic defects present in 3 families with muscular dystrophy, contractures, and calpain 3 deficiency. Methods: We performed targeted exome sequencing on one patient presenting a deficiency in calpain 3 on Western blot but for which mutations in the gene had been excluded. The identification of a homozygous truncating mutation in the M-line part of titin prompted us to sequence this region in 2 additional patients presenting similar clinical and biochemical characteristics. Results: The 3 patients shared similar features: coexistence of limb-girdle weakness and early-onset diffuse joint contractures without cardiomyopathy. The biopsies showed rimmed vacuoles, a dystrophic pattern, and secondary reduction in calpain 3. We identified a novel homozygous mutation in the exon Mex3 of the TTN gene in the first patient. At protein level, this mutation introduces a stop codon at the level of Mex3. Interestingly, we identified truncating mutations in both alleles in the same region of the TTN gene in patients from 2 additional families. Molecular protein analyses confirm loss of the C-ter part of titin. Conclusions: Our study broadens the phenotype of titinopathies with the report of a new clinical entity with prominent contractures and no cardiac abnormality and where the recessive mutations lead to truncation of the M-line titin and secondary calpain 3 deficiency. PMID:26581302

Local equilibrium solutions in simple anisotropic cosmological models, as described by relativistic fluid dynamics

NASA Astrophysics Data System (ADS)

Shogin, Dmitry; Amund Amundsen, Per

2016-10-01

We test the physical relevance of the full and the truncated versions of the Israel-Stewart (IS) theory of irreversible thermodynamics in a cosmological setting. Using a dynamical systems method, we determine the asymptotic future of plane symmetric Bianchi type I spacetimes with a viscous mathematical fluid, keeping track of the magnitude of the relative dissipative fluxes, which determines the applicability of the IS theory. We consider the situations where the dissipative mechanisms of shear and bulk viscosity are involved separately and simultaneously. It is demonstrated that the only case in the given model when the fluid asymptotically approaches local thermal equilibrium, and the underlying assumptions of the IS theory are therefore not violated, is that of a dissipative fluid with vanishing bulk viscosity. The truncated IS equations for shear viscosity are found to produce solutions which manifest pathological dynamical features and, in addition, to be strongly sensitive to the choice of initial conditions. Since these features are observed already in the case of an oversimplified mathematical fluid model, we have no reason to assume that the truncation of the IS transport equations will produce relevant results for physically more realistic fluids. The possible role of bulk and shear viscosity in cosmological evolution is also discussed.

A Fourier Method for Sidelobe Reduction in Equally Spaced Linear Arrays

NASA Astrophysics Data System (ADS)

Safaai-Jazi, Ahmad; Stutzman, Warren L.

2018-04-01

Uniformly excited, equally spaced linear arrays have a sidelobe level larger than -13.3 dB, which is too high for many applications. This limitation can be remedied by nonuniform excitation of array elements. We present an efficient method for sidelobe reduction in equally spaced linear arrays with low penalty on the directivity. The method involves the following steps: construction of a periodic function containing only the sidelobes of the uniformly excited array, calculation of the Fourier series of this periodic function, subtracting the series from the array factor of the original uniformly excited array after it is truncated, and finally mitigating the truncation effects which yields significant increase in sidelobe level reduction. A sidelobe reduction factor is incorporated into element currents that makes much larger sidelobe reductions possible and also allows varying the sidelobe level incrementally. It is shown that such newly formed arrays can provide sidelobe levels that are at least 22.7 dB below those of the uniformly excited arrays with the same size and number of elements. Analytical expressions for element currents are presented. Radiation characteristics of the sidelobe-reduced arrays introduced here are examined, and numerical results for directivity, sidelobe level, and half-power beam width are presented for example cases. Performance improvements over popular conventional array synthesis methods, such as Chebyshev and linear current tapered arrays, are obtained with the new method.

Lactobacillus bulgaricus Proteinase Expressed in Lactococcus lactis Is a Powerful Carrier for Cell Wall-Associated and Secreted Bovine β-Lactoglobulin Fusion Proteins

PubMed Central

Bernasconi, Eric; Germond, Jacques-Edouard; Delley, Michèle; Fritsché, Rodolphe; Corthésy, Blaise

2002-01-01

Lactic acid bacteria have a good potential as agents for the delivery of heterologous proteins to the gastrointestinal mucosa and thus for the reequilibration of inappropriate immune responses to food antigens. Bovine β-lactoglobulin (BLG) is considered a major allergen in cow's milk allergy. We have designed recombinant Lactococcus lactis expressing either full-length BLG or BLG-derived octapeptide T6 (IDALNENK) as fusions with Lactobacillus bulgaricus extracellular proteinase (PrtB). In addition to constructs encoding full-length PrtB for the targeting of heterologous proteins to the cell surface, we generated vectors aiming at the release into the medium of truncated PrtB derivatives lacking 100 (PrtB∂, PrtB∂-BLG, and PrtB∂-T6) or 807 (PrtBΔ) C-terminal amino acids. Expression of recombinant products was confirmed using either anti-PrtB, anti-BLG, or anti-peptide T6 antiserum. All forms of the full-length and truncated recombinant products were efficiently translocated, irrespective of the presence of eucaryotic BLG sequences in the fusion proteins. L. lactis expressing PrtB∂-BLG yielded up to 170 μg per 109 CFU in the culture supernatant and 9 μg per 109 CFU at the bacterial cell surface within 14 h. Therefore, protein fusions relying on the use of PrtB gene products are adequate for concomitant cell surface display and secretion by recombinant L. lactis and thus may ensure maximal bioavailability of the eucaryotic antigen in the gut-associated lymphoid tissue. PMID:12039750

RG flow from Φ 4 theory to the 2D Ising model

DOE PAGES

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel; ...

2017-08-16

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

The orderly nano array of truncated octahedra Cu2O nanocrystals with the enhancement of visible light photocatalytic activity

NASA Astrophysics Data System (ADS)

Wei, Xiaofeng; Pan, Jiaqi; Mei, Jie; Zheng, Yingying; Cui, Can; Li, Chaorong

2018-07-01

The orderly nano array is able to improve the light utilization efficiency and has been thought to be a promising way for advancing photocatalysis. The orderly nano array of truncated octahedra Cu2O nanocrystals have been successfully fabricated by the facile solution-based one-step reduction and self-assembly method. The results of XRD, SEM and TEM indicate that the Cu2O nano array is successfully assembled on the Si substrate. The photocatalytic activity of the Cu2O orderly nano array is investigated under visible light irradiation, and it is demonstrated to be significantly enhanced after the Cu2O is self-assembled orderly. Furthermore, the surface orderly structure of the nano array is considered as the main reason for the enhancement.

Notes on Accuracy of Finite-Volume Discretization Schemes on Irregular Grids

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.

2011-01-01

Truncation-error analysis is a reliable tool in predicting convergence rates of discretization errors on regular smooth grids. However, it is often misleading in application to finite-volume discretization schemes on irregular (e.g., unstructured) grids. Convergence of truncation errors severely degrades on general irregular grids; a design-order convergence can be achieved only on grids with a certain degree of geometric regularity. Such degradation of truncation-error convergence does not necessarily imply a lower-order convergence of discretization errors. In these notes, irregular-grid computations demonstrate that the design-order discretization-error convergence can be achieved even when truncation errors exhibit a lower-order convergence or, in some cases, do not converge at all.

Toward a Value for Guided Rafting on Southern Rivers

Treesearch

J. Michael Bowker; Donald B.K. English; Jason A. Donovan

1996-01-01

This study examines per trip consumer surplus associated with guided whitewater rafting on two southern rivers. First, household recreation demand functions are estimated based on the individual travel cost model using truncated count data regression methods and alternative price specifications. Findings show mean per trip consumer surplus point estimates between $89...

Truncated RAP-MUSIC (TRAP-MUSIC) for MEG and EEG source localization.

PubMed

Mäkelä, Niko; Stenroos, Matti; Sarvas, Jukka; Ilmoniemi, Risto J

2018-02-15

Electrically active brain regions can be located applying MUltiple SIgnal Classification (MUSIC) on magneto- or electroencephalographic (MEG; EEG) data. We introduce a new MUSIC method, called truncated recursively-applied-and-projected MUSIC (TRAP-MUSIC). It corrects a hidden deficiency of the conventional RAP-MUSIC algorithm, which prevents estimation of the true number of brain-signal sources accurately. The correction is done by applying a sequential dimension reduction to the signal-subspace projection. We show that TRAP-MUSIC significantly improves the performance of MUSIC-type localization; in particular, it successfully and robustly locates active brain regions and estimates their number. We compare TRAP-MUSIC and RAP-MUSIC in simulations with varying key parameters, e.g., signal-to-noise ratio, correlation between source time-courses, and initial estimate for the dimension of the signal space. In addition, we validate TRAP-MUSIC with measured MEG data. We suggest that with the proposed TRAP-MUSIC method, MUSIC-type localization could become more reliable and suitable for various online and offline MEG and EEG applications. Copyright © 2017 Elsevier Inc. All rights reserved.

A Simple Method to Avoid Nonspecific Signal When Using Monoclonal Anti-Tau Antibodies in Western Blotting of Mouse Brain Proteins.

PubMed

Petry, Franck R; Nicholls, Samantha B; Hébert, Sébastien S; Planel, Emmanuel

2017-01-01

In Alzheimer's disease and other tauopathies, tau displays several abnormal post-translation modifications such as hyperphosphorylation, truncation, conformation, and oligomerization. Mouse monoclonal antibodies have been raised against such tau modifications for research, diagnostic, and therapeutic purposes. However, many of these primary antibodies are at risk of giving nonspecific signals in common Western blotting procedures. Not because they are unspecific, but because the secondary antibodies used to detect them will also detect the heavy chain of endogenous mouse immunoglobulins (Igs), and give a nonspecific signal at the same molecular weight than tau protein (around 50 kDa). Here, we propose the use of anti-light chain secondary antibodies as a simple and efficient technique to prevent nonspecific Igs signals at around 50 kDa. We demonstrate the efficacy of this method by removing artifactual signals when using monoclonal antibodies directed at tau phosphorylation (AT100, 12E8, AT270), tau truncation (TauC3), tau oligomerization (TOMA), or tau abnormal conformation (Alz50), in wild-type, 3×Tg-AD, and tau knockout mice.

Search for new phenomena in events with a photon and missing transverse momentum in pp collisions at $$ \\sqrt{s}=13 $$ TeV with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2016-06-09

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum with the ATLAS experiment at the Large Hadron Collider are reported. The data were collected in proton-proton collisions at a centre-of-mass energy of 13 TeV and correspond to an integrated luminosity of 3.2 fb -1. The observed data are in agreement with the Standard Model expectations. Exclusion limits are presented in models of new phenomena including pair production of dark matter candidates or large extra spatial dimensions. In a simplified model of dark matter and an axial-vector mediator, the search excludes mediatormore » masses below 710 GeV for dark matter candidate masses below 150 GeV. In an effective theory of dark matter production, values of the suppression scale M * up to 570 GeV are excluded and the effect of truncation for various coupling values is reported. Finally, for the ADD large extra spatial dimension model the search places more stringent limits than earlier searches in the same event topology, excluding M D up to about 2.3 (2.8) TeV for two (six) additional spatial dimensions; the limits are reduced by 20-40% depending on the number of additional spatial dimensions when applying a truncation procedure.« less

Immunomodulatory and Anti-Inflammatory Activities of Chicken Cathelicidin-2 Derived Peptides

PubMed Central

van Dijk, Albert; van Eldik, Mandy; Veldhuizen, Edwin J. A.; Tjeerdsma-van Bokhoven, Hanne L. M.; de Zoete, Marcel R.; Bikker, Floris J.; Haagsman, Henk P.

2016-01-01

Host Defence Peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. For this purpose we examined whether chicken cathelicidin-2 (CATH-2)-derived peptides modulate the function and inflammatory response of avian immune cells. Using a chicken macrophage cell line (HD11) we found that full-length CATH-2 dose-dependently induced transcription of chemokines CXCLi2/IL-8, MCP-3 and CCLi4/RANTES, but not of pro-inflammatory cytokine IL-1β. In addition, CATH-2 efficiently inhibited IL-1β and nitric oxide production by HD11 cells induced by different sources of lipopolysaccharides (LPS). N-terminal truncated CATH-2 derived peptides maintained the capacity to selectively induce chemokine transcription, but despite their high LPS affinity several analogs lacked LPS-neutralizing capacity. Substitution of phenylalanine residues by tryptophan introduced endotoxin neutralization capacity in inactive truncated CATH-2 derived peptides. In contrast, amino acid substitution of phenylalanine by tyrosine abrogated endotoxin neutralization activity of CATH-2 analogs. These findings support a pivotal role for aromatic residues in peptide-mediated endotoxin neutralization by CATH-2 analogs and were shown to be independent of LPS affinity. The capacity to modulate chemokine production and dampen endotoxin-induced pro-inflammatory responses in chicken immune cells implicates that small CATH-2 based peptides could serve as leads for the design of CATH-2 based immunomodulatory anti-infectives. PMID:26848845

Immunomodulatory and Anti-Inflammatory Activities of Chicken Cathelicidin-2 Derived Peptides.

PubMed

van Dijk, Albert; van Eldik, Mandy; Veldhuizen, Edwin J A; Tjeerdsma-van Bokhoven, Hanne L M; de Zoete, Marcel R; Bikker, Floris J; Haagsman, Henk P

2016-01-01

Host Defence Peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. For this purpose we examined whether chicken cathelicidin-2 (CATH-2)-derived peptides modulate the function and inflammatory response of avian immune cells. Using a chicken macrophage cell line (HD11) we found that full-length CATH-2 dose-dependently induced transcription of chemokines CXCLi2/IL-8, MCP-3 and CCLi4/RANTES, but not of pro-inflammatory cytokine IL-1β. In addition, CATH-2 efficiently inhibited IL-1β and nitric oxide production by HD11 cells induced by different sources of lipopolysaccharides (LPS). N-terminal truncated CATH-2 derived peptides maintained the capacity to selectively induce chemokine transcription, but despite their high LPS affinity several analogs lacked LPS-neutralizing capacity. Substitution of phenylalanine residues by tryptophan introduced endotoxin neutralization capacity in inactive truncated CATH-2 derived peptides. In contrast, amino acid substitution of phenylalanine by tyrosine abrogated endotoxin neutralization activity of CATH-2 analogs. These findings support a pivotal role for aromatic residues in peptide-mediated endotoxin neutralization by CATH-2 analogs and were shown to be independent of LPS affinity. The capacity to modulate chemokine production and dampen endotoxin-induced pro-inflammatory responses in chicken immune cells implicates that small CATH-2 based peptides could serve as leads for the design of CATH-2 based immunomodulatory anti-infectives.

A simplification of the fractional Hartley transform applied to image security system in phase

NASA Astrophysics Data System (ADS)

Jimenez, Carlos J.; Vilardy, Juan M.; Perez, Ronal

2017-01-01

In this work we develop a new encryption system for encoded image in phase using the fractional Hartley transform (FrHT), truncation operations and random phase masks (RPMs). We introduce a simplification of the FrHT with the purpose of computing this transform in an efficient and fast way. The security of the encryption system is increased by using nonlinear operations, such as the phase encoding and the truncation operations. The image to encrypt (original image) is encoded in phase and the truncation operations applied in the encryption-decryption system are the amplitude and phase truncations. The encrypted image is protected by six keys, which are the two fractional orders of the FrHTs, the two RPMs and the two pseudorandom code images generated by the amplitude and phase truncation operations. All these keys have to be correct for a proper recovery of the original image in the decryption system. We present digital results that confirm our approach.

Maximum nondiffracting propagation distance of aperture-truncated Airy beams

NASA Astrophysics Data System (ADS)

Chu, Xingchun; Zhao, Shanghong; Fang, Yingwu

2018-05-01

Airy beams have called attention of many researchers due to their non-diffracting, self-healing and transverse accelerating properties. A key issue in research of Airy beams and its applications is how to evaluate their nondiffracting propagation distance. In this paper, the critical transverse extent of physically realizable Airy beams is analyzed under the local spatial frequency methodology. The maximum nondiffracting propagation distance of aperture-truncated Airy beams is formulated and analyzed based on their local spatial frequency. The validity of the formula is verified by comparing the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam, aperture-truncated exponentially decaying Airy beam and exponentially decaying Airy beam. Results show that the formula can be used to evaluate accurately the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam. Therefore, it can guide us to select appropriate parameters to generate Airy beams with long nondiffracting propagation distance that have potential application in the fields of laser weapons or optical communications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Arriaga, G.; Hada, T.; Nariyuki, Y.

The triple-degenerate derivative nonlinear Schroedinger (TDNLS) system modified with resistive wave damping and growth is truncated to study the coherent coupling of four waves, three Alfven and one acoustic, near resonance. In the conservative case, the truncation equations derive from a time independent Hamiltonian function with two degrees of freedom. Using a Poincare map analysis, two parameters regimes are explored. In the first regime we check how the modulational instability of the TDNLS system affects to the dynamics of the truncation model, while in the second one the exact triple degenerated case is discussed. In the dissipative case, the truncationmore » model gives rise to a six dimensional flow with five free parameters. Computing some bifurcation diagrams the dependence with the sound to Alfven velocity ratio as well as the Alfven modes involved in the truncation is analyzed. The system exhibits a wealth of dynamics including chaotic attractor, several kinds of bifurcations, and crises. The truncation model was compared to numerical integrations of the TDNLS system.« less

Characterization of the native form and the carboxy-terminally truncated halotolerant form of α-amylases from Bacillus subtilis strain FP-133.

PubMed

Takenaka, Shinji; Miyatake, Ayaka; Tanaka, Kosei; Kuntiya, Ampin; Techapun, Charin; Leksawasdi, Noppol; Seesuriyachan, Phisit; Chaiyaso, Thanongsak; Watanabe, Masanori; Yoshida, Ken-ichi

2015-06-01

Two amylases, amylase I and amylase II from Bacillus subtilis strain FP-133, were purified to homogeneity and characterized. Their stabilities toward temperature, pH, and organic solvents, and their substrate specificities toward polysaccharides and oligosaccharides were similar. Under moderately high salt conditions, both amylases were more stable than commercial B. licheniformis amylase, and amylase I retained higher amylase activity than amylase II. The N-terminal amino acid sequence, genomic southern blot analysis, and MALDI-TOFF-MS analysis indicated that the halotolerant amylase I was produced by limited carboxy-terminal truncation of the amylase II peptide. The deduced amino acid sequence of amylase II was >95% identical to that of previously reported B. subtilis α-amylases, but their carboxy-terminal truncation points differed. Three recombinant amylases--full-length amylase corresponding to amylase II, an artificially truncated amylase corresponding to amylase I, and an amylase with a larger artificial C-terminal truncation--were expressed in B. subtilis. The artificially truncated recombinant amylases had the same high amylase activity as amylase I under moderately high salt conditions. Sequence comparisons indicated that an increased ratio of Asp/Glu residues in the enzyme may be one factor responsible for increasing halotolerance. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteolytic cleavage of polymeric tau protein by caspase-3: implications for Alzheimer disease.

PubMed

Jarero-Basulto, Jose J; Luna-Muñoz, Jose; Mena, Raul; Kristofikova, Zdena; Ripova, Daniela; Perry, George; Binder, Lester I; Garcia-Sierra, Francisco

2013-12-01

Truncated tau protein at Asp(421) is associated with neurofibrillary pathology in Alzheimer disease (AD); however, little is known about its presence in the form of nonfibrillary aggregates. Here, we report immunohistochemical staining of the Tau-C3 antibody, which recognizes Asp(421)-truncated tau, in a group of AD cases with different extents of cognitive impairment. In the hippocampus, we found distinct nonfibrillary aggregates of Asp(421)-truncated tau. Unlike Asp(421)-composed neurofibrillary tangles, however, these nonfibrillary pathologies did not increase significantly with respect to the Braak staging and, therefore, make no significant contribution to cognitive impairment. On the other hand, despite in vitro evidence that caspase-3 cleaves monomeric tau at Asp(421), to date, this truncation has not been demonstrated to be executed by this protease in polymeric tau entities. We determined that Asp(421) truncation can be produced by caspase-3 in oligomeric and multimeric complexes of recombinant full-length tau in isolated native tau filaments in vitro and in situ in neurofibrillary tangles analyzed in fresh brain slices from AD cases. Our data suggest that generation of this pathologic Asp(421) truncation of tau in long-lasting fibrillary structures may produce further permanent toxicity for neurons in the brains of patients with AD.

Comparison of Cliff-Lorimer-Based Methods of Scanning Transmission Electron Microscopy (STEM) Quantitative X-Ray Microanalysis for Application to Silicon Oxycarbides Thin Films.

PubMed

Parisini, Andrea; Frabboni, Stefano; Gazzadi, Gian Carlo; Rosa, Rodolfo; Armigliato, Aldo

2018-06-01

In this work, we compare the results of different Cliff-Lorimer (Cliff & Lorimer 1975) based methods in the case of a quantitative energy dispersive spectrometry investigation of light elements in ternary C-O-Si thin films. To determine the Cliff-Lorimer (C-L) k-factors, we fabricated, by focused ion beam, a standard consisting of a wedge lamella with a truncated tip, composed of two parallel SiO2 and 4H-SiC stripes. In 4H-SiC, it was not possible to obtain reliable k-factors from standard extrapolation methods owing to the strong CK-photon absorption. To overcome this problem, an extrapolation method exploiting the shape of the truncated tip of the lamella is proposed herein. The k-factors thus determined, were then used in an application of the C-L quantification procedure to a defect found at the SiO2/4H-SiC interface in the channel region of a metal-oxide field-effect-transistor device. As in this procedure, the sample thickness is required, a method to determine this quantity from the averaged and normalized scanning transmission electron microscopy intensity is also detailed. Monte Carlo simulations were used to investigate the discrepancy between experimental and theoretical k-factors and to bridge the gap between the k-factor and the Watanabe and Williams ζ-factor methods (Watanabe & Williams, 2006).

Distinct spatiotemporal accumulation of N-truncated and full-length amyloid-β42 in Alzheimer's disease.

PubMed

Shinohara, Mitsuru; Koga, Shunsuke; Konno, Takuya; Nix, Jeremy; Shinohara, Motoko; Aoki, Naoya; Das, Pritam; Parisi, Joseph E; Petersen, Ronald C; Rosenberry, Terrone L; Dickson, Dennis W; Bu, Guojun

2017-12-01

Accumulation of amyloid-β peptides is a dominant feature in the pathogenesis of Alzheimer's disease; however, it is not clear how individual amyloid-β species accumulate and affect other neuropathological and clinical features in the disease. Thus, we compared the accumulation of N-terminally truncated amyloid-β and full-length amyloid-β, depending on disease stage as well as brain area, and determined how these amyloid-β species respectively correlate with clinicopathological features of Alzheimer's disease. To this end, the amounts of amyloid-β species and other proteins related to amyloid-β metabolism or Alzheimer's disease were quantified by enzyme-linked immunosorbent assays (ELISA) or theoretically calculated in 12 brain regions, including neocortical, limbic and subcortical areas from Alzheimer's disease cases (n = 19), neurologically normal elderly without amyloid-β accumulation (normal ageing, n = 13), and neurologically normal elderly with cortical amyloid-β accumulation (pathological ageing, n = 15). We observed that N-terminally truncated amyloid-β42 and full-length amyloid-β42 accumulations distributed differently across disease stages and brain areas, while N-terminally truncated amyloid-β40 and full-length amyloid-β40 accumulation showed an almost identical distribution pattern. Cortical N-terminally truncated amyloid-β42 accumulation was increased in Alzheimer's disease compared to pathological ageing, whereas cortical full-length amyloid-β42 accumulation was comparable between Alzheimer's disease and pathological ageing. Moreover, N-terminally truncated amyloid-β42 were more likely to accumulate more in specific brain areas, especially some limbic areas, while full-length amyloid-β42 tended to accumulate more in several neocortical areas, including frontal cortices. Immunoprecipitation followed by mass spectrometry analysis showed that several N-terminally truncated amyloid-β42 species, represented by pyroglutamylated amyloid-β11-42, were enriched in these areas, consistent with ELISA results. N-terminally truncated amyloid-β42 accumulation showed significant regional association with BACE1 and neprilysin, but not PSD95 that regionally associated with full-length amyloid-β42 accumulation. Interestingly, accumulations of tau and to a greater extent apolipoprotein E (apoE, encoded by APOE) were more strongly correlated with N-terminally truncated amyloid-β42 accumulation than those of other amyloid-β species across brain areas and disease stages. Consistently, immunohistochemical staining and in vitro binding assays showed that apoE co-localized and bound more strongly with pyroglutamylated amyloid-β11-x fibrils than full-length amyloid-β fibrils. Retrospective review of clinical records showed that accumulation of N-terminally truncated amyloid-β42 in cortical areas was associated with disease onset, duration and cognitive scores. Collectively, N-terminally truncated amyloid-β42 species have spatiotemporal accumulation patterns distinct from full-length amyloid-β42, likely due to different mechanisms governing their accumulations in the brain. These truncated amyloid-β species could play critical roles in the disease by linking other clinicopathological features of Alzheimer's disease. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Excluding Noise from Short Krylov Subspace Approximations to the Truncated Singular Value Decomposition (SVD)

DTIC Science & Technology

2017-09-27

ARL-TR-8161•SEP 2017 US Army Research Laboratory Excluding Noise from Short Krylov Subspace Approximations to the Truncated Singular Value...originator. ARL-TR-8161•SEP 2017 US Army Research Laboratory Excluding Noise from Short Krylov Subspace Approximations to the Truncated Singular Value...unlimited. October 2015–January 2016 US Army Research Laboratory ATTN: RDRL-CIH-C Aberdeen Proving Ground, MD 21005-5066 primary author’s email

Probabilistic Sensitivity Analysis with Respect to Bounds of Truncated Distributions (PREPRINT)

DTIC Science & Technology

2010-04-01

AFRL-RX-WP-TP-2010-4147 PROBABILISTIC SENSITIVITY ANALYSIS WITH RESPECT TO BOUNDS OF TRUNCATED DISTRIBUTIONS (PREPRINT) H. Millwater and...5a. CONTRACT NUMBER In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62102F 6. AUTHOR(S) H. Millwater and Y. Feng 5d. PROJECT...Z39-18 1 Probabilistic Sensitivity Analysis with respect to Bounds of Truncated Distributions H. Millwater and Y. Feng Department of Mechanical

Hairy black holes and duality in an extended supergravity model

NASA Astrophysics Data System (ADS)

Anabalón, Andrés; Astefanesei, Dumitru; Gallerati, Antonio; Trigiante, Mario

2018-04-01

We consider a D = 4, N=2 gauged supergravity with an electromagnetic Fayet-Iliopoulos term. We restrict to the uncharged, single dilaton consistent truncation and point out that the bulk Lagrangian is self-dual under electromagnetic duality. Within this truncation, we construct two families of exact hairy black hole solutions, which are asymptotically AdS 4. When a duality transformation is applied on these solutions, they are mapped to two other inequivalent families of hairy black hole solutions. The mixed boundary conditions of the scalar field correspond to adding a triple-trace operator to the dual field theory action. We also show that this truncation contains all the consistent single dilaton truncations of gauged N=8 supergravity with a possible ω-deformation.

Autocorrelation as a source of truncated Lévy flights in foreign exchange rates

NASA Astrophysics Data System (ADS)

Figueiredo, Annibal; Gleria, Iram; Matsushita, Raul; Da Silva, Sergio

2003-05-01

We suggest that the ultraslow speed of convergence associated with truncated Lévy flights (Phys. Rev. Lett. 73 (1994) 2946) may well be explained by autocorrelations in data. We show how a particular type of autocorrelation generates power laws consistent with a truncated Lévy flight. Stock exchanges have been suggested to be modeled by a truncated Lévy flight (Nature 376 (1995) 46; Physica A 297 (2001) 509; Econom. Bull. 7 (2002) 1). Here foreign exchange rate data are taken instead. Scaling power laws in the “probability of return to the origin” are shown to emerge for most currencies. A novel approach to measure how distant a process is from a Gaussian regime is presented.

A finite state projection algorithm for the stationary solution of the chemical master equation.

PubMed

Gupta, Ankit; Mikelson, Jan; Khammash, Mustafa

2017-10-21

The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash [J. Chem. Phys. 124(4), 044104 (2006)], to provide approximate solutions to the CME by truncating the state-space. The FSP works well for finite time-periods but it cannot be used for estimating the stationary solutions of CMEs, which are often of interest in systems biology. The aim of this paper is to develop a version of FSP which we refer to as the stationary FSP (sFSP) that allows one to obtain accurate approximations of the stationary solutions of a CME by solving a finite linear-algebraic system that yields the stationary distribution of a continuous-time Markov chain over the truncated state-space. We derive bounds for the approximation error incurred by sFSP and we establish that under certain stability conditions, these errors can be made arbitrarily small by appropriately expanding the truncated state-space. We provide several examples to illustrate our sFSP method and demonstrate its efficiency in estimating the stationary distributions. In particular, we show that using a quantized tensor-train implementation of our sFSP method, problems admitting more than 100 × 10 6 states can be efficiently solved.

A finite state projection algorithm for the stationary solution of the chemical master equation

NASA Astrophysics Data System (ADS)

Gupta, Ankit; Mikelson, Jan; Khammash, Mustafa

2017-10-01

The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash [J. Chem. Phys. 124(4), 044104 (2006)], to provide approximate solutions to the CME by truncating the state-space. The FSP works well for finite time-periods but it cannot be used for estimating the stationary solutions of CMEs, which are often of interest in systems biology. The aim of this paper is to develop a version of FSP which we refer to as the stationary FSP (sFSP) that allows one to obtain accurate approximations of the stationary solutions of a CME by solving a finite linear-algebraic system that yields the stationary distribution of a continuous-time Markov chain over the truncated state-space. We derive bounds for the approximation error incurred by sFSP and we establish that under certain stability conditions, these errors can be made arbitrarily small by appropriately expanding the truncated state-space. We provide several examples to illustrate our sFSP method and demonstrate its efficiency in estimating the stationary distributions. In particular, we show that using a quantized tensor-train implementation of our sFSP method, problems admitting more than 100 × 106 states can be efficiently solved.

Automated Fmoc-based solid-phase synthesis of peptide thioesters with self-purification effect and application in the construction of immobilized SH3 domains.

PubMed

Mende, Franziska; Beisswenger, Michael; Seitz, Oliver

2010-08-18

Peptide thioesters are important building blocks in the total synthesis of proteins and protein domains via fragment ligation. However, synthetic access of peptide thioesters still is a bottleneck of this powerful ligation chemistry. The commonly used methods for the Fmoc-based synthesis of peptide thioesters involve nonautomated solution steps that have to be performed after the solid-phase assembly of the peptide. Usually, HPLC purification is required. Herein, a method that enables crude peptides to be used in divergent native chemical ligations reactions is described. We present an Fmoc-based solid-phase synthesis of peptide thioesters with self-purification which facilitates access to these important building blocks, since the often cumbersome HPLC purification can be avoided. Fmoc-protected amino acids are coupled on a safety catch sulfonamide resin. The self-purifying effect is achieved through the combination of (a) N-terminal coupling of a cleavable cyclization linker and subsequent backbone-to-side chain cyclization, (b) activation of the sulfonamide linkage by alkylation, (c) thiolysis for the selective detachment of truncation products, and (d) TFA cleavage for the liberation of the desired peptide thioester in unprotected form. We have previously shown a method wherein cyclization was performed after carboxymethylation of the sulfonamide. However, the automation of this method was difficult and side reactions at methionine residues hampered the general applicability. The new design involves peptide synthesis on a modified carboxy-functionalized sulfonamide linker, a substantially milder activation of the sulfonamide bond and the use of monomethoxytrityl as well as 2-phenyl-isopropyl protecting groups. This approach solved the problems with methionine containing peptides and enabled the complete automation of the self-purifying synthesis of peptide thioesters. The study also addressed problems in the synthesis of difficult peptides. Aggregated truncation products can resist extraction and contaminate full-length thioesters obtained after TFA cleavage. It is shown that significant enhancements of the purity were achieved when mild acidic extractions were included in the wash protocols after thiolysis. The potential of the method was demonstrated in the parallel synthesis of 20-40 amino acid long peptide thioesters, which were obtained in excellent purities. The thioesters and cysteinyl peptides were used without purification in the assembly of immobilized SH3 protein domains of SHO1 in yeast. A cysteine scan by native chemical ligation suggested single amino acid to cysteine substitutions that (a) confer useful ligation yields, (b) support correct folding, and (c) sustain the function of the folded protein domain. The chemical synthesis of the SH3-domain of SHO1 succeeded in highest yields when cysteine placements at positions S23, F24, and E36 were avoided. The synthetic SH3 mutants were examined in a binding assay, which indicated that N27C, L30C, and D34C mutations provide functional SH3-domain.

Quantification of angiotensin-converting-enzyme-mediated degradation of human chemerin 145-154 in plasma by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.

PubMed

John, Harald; Hierer, Jessica; Haas, Olga; Forssmann, Wolf-Georg

2007-03-01

Chemerin is a chemoattractive protein acting as a ligand for the G-protein-coupled receptor ChemR23/CMKLR1 and plays an important role in the innate and adaptive immunity. Proteolytic processing of its C terminus is essential for receptor binding and physiological activity. Therefore, we investigated the plasma stability of the decapeptide chemerin 145-154 (P(145)-F(154)) corresponding to the C terminus of the physiologically active chemerin variant E(21)-F(154) from human hemofiltrate. For monitoring concentration-time profiles and degradation products we developed a novel matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry procedure using an internal peptide standard (hemorphin LVV-H7) for quantification. The linear range covers 2.5 orders of magnitude in the lower micromolar concentration range (lower limit of quantification 0.312 microg/ml, 0.25 microM) characterized by satisfactory reproducibility (CV < or =9%), accuracy (< or =10%), ruggedness, and recovery (98%). We found that chemerin 145-154 is C-terminally truncated in human citrate plasma by the cleavage of the penultimate dipeptidyl residue. N-terminal truncation was not observed. In contrast to citrate plasma, no degradation was detected in ethylenediammetetraacetate (EDTA) plasma. We identified angiotensin-converting-enzyme (ACE) to be responsible for C-terminal truncation, which could be completely inhibited by EDTA and captopril. These results are relevant to clarify the natural processing of chemerin and the potential involvement of ACE in mediating the immune response.

Functional and structural characterization of domain truncated violaxanthin de-epoxidase.

PubMed

Hallin, Erik Ingmar; Guo, Kuo; Åkerlund, Hans-Erik

2016-08-01

Photosynthetic organisms need protection against excessive light. By using non-photochemical quenching, where the excess light is converted into heat, the organism can survive at higher light intensities. This process is partly initiated by the formation of zeaxanthin, which is achieved by the de-epoxidation of violaxanthin and antheraxanthin to zeaxanthin. This reaction is catalyzed by violaxanthin de-epoxidase (VDE). VDE consists of three domains of which the central lipocalin-like domain has been the most characterized. By truncating the domains surrounding the lipocalin-like domain, we show that VDE activity is possible without the C-terminal domain but not without the N-terminal domain. The N-terminal domain shows no VDE activity by itself but when separately expressed domains are mixed, VDE activity is possible. This shows that these domains can be folded separately and could therefore be studied separately. An increase of the hydrodynamic radius of wild-type VDE was observed when pH was lowered toward the pH required for activity, consistent with a pH-dependent oligomerization. The C-terminally truncated VDE did not show such an oligomerization, was relatively more active at higher pH but did not alter the KM for ascorbate. Circular dichroism measurements revealed the presence of α-helical structure in both the N- and C-terminal domains. By measuring the initial formation of the product, VDE was found to convert a large number of violaxanthin molecules to antheraxanthin before producing any zeaxanthin, favoring a model where violaxanthin is bound non-symmetrically in VDE. © 2016 Scandinavian Plant Physiology Society.

BRCA1 sequence variations in 160 individuals referred to a breast/ovarian family cancer clinic. Institut Curie Breast Cancer Group.

PubMed Central

Stoppa-Lyonnet, D; Laurent-Puig, P; Essioux, L; Pagès, S; Ithier, G; Ligot, L; Fourquet, A; Salmon, R J; Clough, K B; Pouillart, P; Bonaïti-Pellié, C; Thomas, G

1997-01-01

An account of familial aggregation in breast/ovarian cancer has become possible with the identification of BRCA1 germ-line mutations. We evaluated, for 249 individuals registered with the Institut Curie in Paris, the prior probability that an individual carried a mutation that predisposes to these diseases. We chose 160 women for BRCA1 analysis: 103 with a family history of breast cancer and 57 with a family history of breast-ovarian cancer. To detect small mutations, we generated and analyzed 35 overlapping genomic PCR products that cover the coding portion of the gene, by using denaturing gradient gel electrophoresis. Thirty-eight truncating mutations (32 frameshifts, 4 nonsense mutations, and 2 splice variants) were observed in 15% of women with a family history of breast cancer only and in 40% of those with a history of breast-ovarian cancer. Twelve of 25 distinct truncating mutations identified were novel and unique. Most BRCA1 mutations that had been reported more than five times in the Breast Cancer Information Core were present in our series. One mutation (5149del4) observed in two apparently unrelated families most likely originates from a common ancestor. The position of truncating mutations did not significantly affect the ratio of the risk of breast cancer to that of ovarian cancer. In addition, 15 DNA variants (14 missense mutations and 1 neutral mutation) were identified, 9 of which were novel. Indirect evidence suggests that seven of these mutations are deleterious. Images Figure 2 Figure 3 PMID:9150149

A Recombinant Raccoon Poxvirus Vaccine Expressing both Yersinia pestis F1 and Truncated V Antigens Protects Animals against Lethal Plague

PubMed Central

Rocke, Tonie E.; Kingstad-Bakke, Brock; Berlier, Willy; Osorio, Jorge E.

2014-01-01

In previous studies, we demonstrated in mice and prairie dogs that simultaneous administration of two recombinant raccoon poxviruses (rRCN) expressing Yersinia pestis antigens (F1 and V307—a truncated version of the V protein) provided superior protection against plague challenge compared to individual single antigen constructs. To reduce costs of vaccine production and facilitate implementation of a sylvatic plague vaccine (SPV) control program for prairie dogs, a dual antigen construct is more desirable. Here we report the construction and characterization of a novel RCN-vectored vaccine that simultaneously expresses both F1 and V307 antigens. This dual antigen vaccine provided similar levels of protection against plague in both mice and prairie dogs as compared to simultaneous administration of the two single antigen constructs and was also shown to protect mice against an F1 negative strain of Y. pestis. The equivalent safety, immunogenicity and efficacy profile of the dual RCN-F1/V307 construct warrants further evaluation in field efficacy studies in sylvatic plague endemic areas. PMID:26344891

Truncated variants of apolipoprotein B cause hypobetalipoproteinaemia.

PubMed Central

Collins, D R; Knott, T J; Pease, R J; Powell, L M; Wallis, S C; Robertson, S; Pullinger, C R; Milne, R W; Marcel, Y L; Humphries, S E

1988-01-01

Familial hypobetalipoproteinaemia is a rare autosomal dominant disorder in which levels of apo-B-containing plasma lipoproteins are approximately half-normal in heterozygotes and virtually absent in homozygotes. Here we describe mutations of the apo-B gene that cause two different truncated variants of apo-B in unrelated individuals with hypobetalipoproteinaemia. One variant, apo-B(His1795----Met-Trp-Leu-Val-Thr-Term) is predicted to be 1799 amino acids long and arises from deletion of a single nucleotide (G) from leucine codon 1794. This protein was found at low levels in very low density and low density lipoprotein fractions in the blood. The second, shorter variant, apo-B(Arg1306----Term), is caused by mutation of a CpG dinucleotide in arginine codon 1306 converting it to a stop codon and predicting a protein of 1305 residues. The product of this allele could not be detected in the circulation. The differences in size and behaviour of these two variants compared to apo-B100 or apo-B48 point to domains that may be important for the assembly, secretion or stability of apo-B-containing lipoproteins. Images PMID:2843815

A recombinant raccoon poxvirus vaccine expressing both Yersinia pestis F1 and truncated V antigens protects animals against lethal plague.

USGS Publications Warehouse

Rocke, Tonie E.; Kingstad-Bakke, B; Berlier, W; Osorio, J.E.

2014-01-01

In previous studies, we demonstrated in mice and prairie dogs that simultaneous administration of two recombinant raccoon poxviruses (rRCN) expressing Yersinia pestis antigens (F1 and V307-a truncated version of the V protein) provided superior protection against plague challenge compared to individual single antigen constructs. To reduce costs of vaccine production and facilitate implementation of a sylvatic plague vaccine (SPV) control program for prairie dogs, a dual antigen construct is more desirable. Here we report the construction and characterization of a novel RCN-vectored vaccine that simultaneously expresses both F1 and V307 antigens. This dual antigen vaccine provided similar levels of protection against plague in both mice and prairie dogs as compared to simultaneous administration of the two single antigen constructs and was also shown to protect mice against an F1 negative strain of Y. pestis.. The equivalent safety, immunogenicity and efficacy profile of the dual RCN-F1/V307 construct warrants further evaluation in field efficacy studies in sylvatic plague endemic areas.

Truncated Hexa-Octahedral Magnetite Crystals in Martian Meteorite ALH84001: Evidence of Biogenic Activity on Early Mars

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K.; Clemett, S. J.; Schwartz, C.; McIntosh, J. R.; Bazylinski, D. A.; Kirschvink, J.; McKay, D. S.; Gibson, E. K.; Vali, H.; Romanek, C. S.

2004-01-01

The landmark paper by McKay et al. [1] cited four lines of evidence associated with the Martian meteorite ALH84001 to support the hypothesis that life existed on Mars approximately 4 Ga ago. Now, more than five years later, attention has focused on the ALH84001 magnetite grains embedded within carbonate globules in the ALH84001 meteorite. We have suggested that up to approx.25% of the ALH84001 magnetite crystals are products of biological activity [e.g., 2]. The remaining magnetites lack sufficient characteristics to constrain their origin. The papers of Thomas Keprta et al. were criticized arguing that the three dimensional structure of ALH84001 magnetite crystals can only be unambiguously determined using electron tomographic techniques. Clemett et al. [3] confirmed that magnetites produced by magnetotactic bacteria strain MV-I display a truncated hexa-octahedral geometry using electron tomography and validated the use of the multi-tilt classical transmission microscopy technique used by [2]. Recently the geometry of the purported martian biogenic magnetites was shown be identical to that for MV-1 magnetites using electron tomography [6].

SU-E-J-114: A Practical Hybrid Method for Improving the Quality of CT-CBCT Deformable Image Registration for Head and Neck Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, C; Kumarasiri, A; Chetvertkov, M

2015-06-15

Purpose: Accurate deformable image registration (DIR) between CT and CBCT in H&N is challenging. In this study, we propose a practical hybrid method that uses not only the pixel intensities but also organ physical properties, structure volume of interest (VOI), and interactive local registrations. Methods: Five oropharyngeal cancer patients were selected retrospectively. For each patient, the planning CT was registered to the last fraction CBCT, where the anatomy difference was largest. A three step registration strategy was tested; Step1) DIR using pixel intensity only, Step2) DIR with additional use of structure VOI and rigidity penalty, and Step3) interactive local correction.more » For Step1, a public-domain open-source DIR algorithm was used (cubic B-spline, mutual information, steepest gradient optimization, and 4-level multi-resolution). For Step2, rigidity penalty was applied on bony anatomies and brain, and a structure VOI was used to handle the body truncation such as the shoulder cut-off on CBCT. Finally, in Step3, the registrations were reviewed on our in-house developed software and the erroneous areas were corrected via a local registration using level-set motion algorithm. Results: After Step1, there were considerable amount of registration errors in soft tissues and unrealistic stretching in the posterior to the neck and near the shoulder due to body truncation. The brain was also found deformed to a measurable extent near the superior border of CBCT. Such errors could be effectively removed by using a structure VOI and rigidity penalty. The rest of the local soft tissue error could be corrected using the interactive software tool. The estimated interactive correction time was approximately 5 minutes. Conclusion: The DIR using only the image pixel intensity was vulnerable to noise and body truncation. A corrective action was inevitable to achieve good quality of registrations. We found the proposed three-step hybrid method efficient and practical for CT/CBCT registrations in H&N. My department receives grant support from Industrial partners: (a) Varian Medical Systems, Palo Alto, CA, and (b) Philips HealthCare, Best, Netherlands.« less

Multi-scale Methods in Quantum Field Theory

NASA Astrophysics Data System (ADS)

Polyzou, W. N.; Michlin, Tracie; Bulut, Fatih

2018-05-01

Daubechies wavelets are used to make an exact multi-scale decomposition of quantum fields. For reactions that involve a finite energy that take place in a finite volume, the number of relevant quantum mechanical degrees of freedom is finite. The wavelet decomposition has natural resolution and volume truncations that can be used to isolate the relevant degrees of freedom. The application of flow equation methods to construct effective theories that decouple coarse and fine scale degrees of freedom is examined.

The Dynamics of Truncated Black Hole Accretion Disks. I. Viscous Hydrodynamic Case

NASA Astrophysics Data System (ADS)

Hogg, J. Drew; Reynolds, Christopher S.

2017-07-01

Truncated accretion disks are commonly invoked to explain the spectro-temporal variability in accreting black holes in both small systems, I.e., state transitions in galactic black hole binaries (GBHBs), and large systems, I.e., low-luminosity active galactic nuclei (LLAGNs). In the canonical truncated disk model of moderately low accretion rate systems, gas in the inner region of the accretion disk occupies a hot, radiatively inefficient phase, which leads to a geometrically thick disk, while the gas in the outer region occupies a cooler, radiatively efficient phase that resides in the standard geometrically thin disk. Observationally, there is strong empirical evidence to support this phenomenological model, but a detailed understanding of the dynamics of truncated disks is lacking. We present a well-resolved viscous, hydrodynamic simulation that uses an ad hoc cooling prescription to drive a thermal instability and, hence, produce the first sustained truncated accretion disk. With this simulation, we perform a study of the dynamics, angular momentum transport, and energetics of a truncated disk. We find that the time variability introduced by the quasi-periodic transition of gas from efficient cooling to inefficient cooling impacts the evolution of the simulated disk. A consequence of the thermal instability is that an outflow is launched from the hot/cold gas interface, which drives large, sub-Keplerian convective cells into the disk atmosphere. The convective cells introduce a viscous θ - ϕ stress that is less than the generic r - ϕ viscous stress component, but greatly influences the evolution of the disk. In the truncated disk, we find that the bulk of the accreted gas is in the hot phase.

The Dynamics of Truncated Black Hole Accretion Disks. I. Viscous Hydrodynamic Case

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hogg, J. Drew; Reynolds, Christopher S.

Truncated accretion disks are commonly invoked to explain the spectro-temporal variability in accreting black holes in both small systems, i.e., state transitions in galactic black hole binaries (GBHBs), and large systems, i.e., low-luminosity active galactic nuclei (LLAGNs). In the canonical truncated disk model of moderately low accretion rate systems, gas in the inner region of the accretion disk occupies a hot, radiatively inefficient phase, which leads to a geometrically thick disk, while the gas in the outer region occupies a cooler, radiatively efficient phase that resides in the standard geometrically thin disk. Observationally, there is strong empirical evidence to supportmore » this phenomenological model, but a detailed understanding of the dynamics of truncated disks is lacking. We present a well-resolved viscous, hydrodynamic simulation that uses an ad hoc cooling prescription to drive a thermal instability and, hence, produce the first sustained truncated accretion disk. With this simulation, we perform a study of the dynamics, angular momentum transport, and energetics of a truncated disk. We find that the time variability introduced by the quasi-periodic transition of gas from efficient cooling to inefficient cooling impacts the evolution of the simulated disk. A consequence of the thermal instability is that an outflow is launched from the hot/cold gas interface, which drives large, sub-Keplerian convective cells into the disk atmosphere. The convective cells introduce a viscous θ − ϕ stress that is less than the generic r − ϕ viscous stress component, but greatly influences the evolution of the disk. In the truncated disk, we find that the bulk of the accreted gas is in the hot phase.« less

Differences in the length of the carboxyl terminus mediate functional properties of neurokinin-1 receptor

PubMed Central

Lai, Jian-Ping; Lai, Saien; Tuluc, Florin; Tansky, Morris F.; Kilpatrick, Laurie E.; Leeman, Susan E.; Douglas, Steven D.

2008-01-01

The neurokinin-1 receptor (NK1R) has two naturally occurring forms that differ in the length of the carboxyl terminus: a full-length receptor consisting of 407 aa and a truncated receptor consisting of 311 aa. We examined whether there are differential signaling properties attributable to the carboxyl terminus of this receptor by using stably transfected human embryonic kidney (HEK293) cell lines that express either full-length or truncated NK1R. Substance P (SP) specifically triggered intracellular calcium increase in HEK293 cells expressing full-length NK1R but had no effect in the cells expressing the truncated NK1R. In addition, in cells expressing full-length NK1R, SP activated NF-κB and IL-8 mRNA expression, but in cells expressing the truncated NK1R, SP did not activate NF-κB, and it decreased IL-8 mRNA expression. In cells expressing full-length NK1R, SP stimulated phosphorylation of PKCδ but inhibited phosphorylation of PKCδ in cells expressing truncated NK1R. There are also differences in the timing of SP-induced ERK activation in cells expressing the two different forms of the receptor. Full-length NK1R activation of ERK was rapid (peak within 1–2 min), whereas truncated NK1R-mediated activation was slower (peak at 20–30 min). Thus, the carboxyl terminus of NK1R is the structural basis for differences in the functional properties of the full-length and truncated NK1R. These differences may provide important information toward the design of new NK1R receptor antagonists. PMID:18713853

Evidence for new C-terminally truncated variants of α- and β-tubulins

PubMed Central

Aillaud, Chrystelle; Bosc, Christophe; Saoudi, Yasmina; Denarier, Eric; Peris, Leticia; Sago, Laila; Taulet, Nicolas; Cieren, Adeline; Tort, Olivia; Magiera, Maria M.; Janke, Carsten; Redeker, Virginie; Andrieux, Annie; Moutin, Marie-Jo

2016-01-01

Cellular α-tubulin can bear various carboxy-terminal sequences: full-length tubulin arising from gene neosynthesis is tyrosinated, and two truncated variants, corresponding to detyrosinated and Δ2 α‑tubulin, result from the sequential cleavage of one or two C-terminal residues, respectively. Here, by using a novel antibody named 3EG that is highly specific to the –EEEG C-terminal sequence, we demonstrate the occurrence in neuronal tissues of a new αΔ3‑tubulin variant corresponding to α1A/B‑tubulin deleted of its last three residues (EEY). αΔ3‑tubulin has a specific distribution pattern: its quantity in the brain is similar to that of αΔ2-tubulin around birth but is much lower in adult tissue. This truncated α1A/B-tubulin variant can be generated from αΔ2-tubulin by the deglutamylases CCP1, CCP4, CCP5, and CCP6 but not by CCP2 and CCP3. Moreover, using 3EG antibody, we identify a C‑terminally truncated β-tubulin form with the same –EEEG C-terminal sequence. Using mass spectrometry, we demonstrate that β2A/B-tubulin is modified by truncation of the four C-terminal residues (EDEA). We show that this newly identified βΔ4-tubulin is ubiquitously present in cells and tissues and that its level is constant throughout the cell cycle. These new C-terminally truncated α- and β-tubulin variants, both ending with –EEEG sequence, are expected to regulate microtubule physiology. Of interest, the αΔ3-tubulin seems to be related to dynamic microtubules, resembling tyrosinated-tubulin rather than the other truncated variants, and may have critical function(s) in neuronal development. PMID:26739754

Automatic method for estimation of in situ effective contact angle from X-ray micro tomography images of two-phase flow in porous media.

PubMed

Scanziani, Alessio; Singh, Kamaljit; Blunt, Martin J; Guadagnini, Alberto

2017-06-15

Multiphase flow in porous media is strongly influenced by the wettability of the system, which affects the arrangement of the interfaces of different phases residing in the pores. We present a method for estimating the effective contact angle, which quantifies the wettability and controls the local capillary pressure within the complex pore space of natural rock samples, based on the physical constraint of constant curvature of the interface between two fluids. This algorithm is able to extract a large number of measurements from a single rock core, resulting in a characteristic distribution of effective in situ contact angle for the system, that is modelled as a truncated Gaussian probability density distribution. The method is first validated on synthetic images, where the exact angle is known analytically; then the results obtained from measurements within the pore space of rock samples imaged at a resolution of a few microns are compared to direct manual assessment. Finally the method is applied to X-ray micro computed tomography (micro-CT) scans of two Ketton cores after waterflooding, that display water-wet and mixed-wet behaviour. The resulting distribution of in situ contact angles is characterized in terms of a mixture of truncated Gaussian densities. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Pulse reflectometry as an acoustical inverse problem: Regularization of the bore reconstruction

NASA Astrophysics Data System (ADS)

Forbes, Barbara J.; Sharp, David B.; Kemp, Jonathan A.

2002-11-01

The theoretical basis of acoustic pulse reflectometry, a noninvasive method for the reconstruction of an acoustical duct from the reflections measured in response to an input pulse, is reviewed in terms of the inversion of the central Fredholm equation. It is known that this is an ill-posed problem in the context of finite-bandwidth experimental signals. Recent work by the authors has proposed the truncated singular value decomposition (TSVD) in the regularization of the transient input impulse response, a non-measurable quantity from which the spatial bore reconstruction is derived. In the present paper we further emphasize the relevance of the singular system framework to reflectometry applications, examining for the first time the transient bases of the system. In particular, by varying the truncation point for increasing condition numbers of the system matrix, it is found that the effects of out-of-bandwidth singular functions on the bore reconstruction can be systematically studied.

Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

DOE PAGES

Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; ...

2015-03-01

Within contemporary hadron physics there are two common methods for determining the momentum- dependence of the interaction between quarks: the top-down approach, which works toward an ab initiocomputation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD’s gauge sector coincides with that required in order to describe ground-state hadron observables usingmore » a nonperturbative truncation of QCD’s Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.« less

Classification With Truncated Distance Kernel.

PubMed

Huang, Xiaolin; Suykens, Johan A K; Wang, Shuning; Hornegger, Joachim; Maier, Andreas

2018-05-01

This brief proposes a truncated distance (TL1) kernel, which results in a classifier that is nonlinear in the global region but is linear in each subregion. With this kernel, the subregion structure can be trained using all the training data and local linear classifiers can be established simultaneously. The TL1 kernel has good adaptiveness to nonlinearity and is suitable for problems which require different nonlinearities in different areas. Though the TL1 kernel is not positive semidefinite, some classical kernel learning methods are still applicable which means that the TL1 kernel can be directly used in standard toolboxes by replacing the kernel evaluation. In numerical experiments, the TL1 kernel with a pregiven parameter achieves similar or better performance than the radial basis function kernel with the parameter tuned by cross validation, implying the TL1 kernel a promising nonlinear kernel for classification tasks.

Exact first order scattering correction for vector radiative transfer in coupled atmosphere and ocean systems

NASA Astrophysics Data System (ADS)

Zhai, Peng-Wang; Hu, Yongxiang; Josset, Damien B.; Trepte, Charles R.; Lucker, Patricia L.; Lin, Bing

2012-06-01

We have developed a Vector Radiative Transfer (VRT) code for coupled atmosphere and ocean systems based on the successive order of scattering (SOS) method. In order to achieve efficiency and maintain accuracy, the scattering matrix is expanded in terms of the Wigner d functions and the delta fit or delta-M technique is used to truncate the commonly-present large forward scattering peak. To further improve the accuracy of the SOS code, we have implemented the analytical first order scattering treatment using the exact scattering matrix of the medium in the SOS code. The expansion and truncation techniques are kept for higher order scattering. The exact first order scattering correction was originally published by Nakajima and Takana.1 A new contribution of this work is to account for the exact secondary light scattering caused by the light reflected by and transmitted through the rough air-sea interface.

Characterization of mTOR-Responsive Truncated mRNAs in Cell Proliferation

DTIC Science & Technology

2017-07-01

AWARD NUMBER: W81XWH-16-1-0135 TITLE: Characterization of mTOR-Responsive Truncated mRNAs in Cell Proliferation PRINCIPAL INVESTIGATOR...TITLE AND SUBTITLE 5a. CONTRACT NUMBER Characterization of mTOR-Responsive Truncated mRNAs in Cell Proliferation 5b. GRANT NUMBER 8W1XWH-16-1...Sclerosis Complex (TSC) 1 or 2 gene leads to deregulated mTOR activation and consequent cell proliferation/growth. Thus, studying the mTOR pathway

Exact and approximate Fourier rebinning algorithms for the solution of the data truncation problem in 3-D PET.

PubMed

Bouallègue, Fayçal Ben; Crouzet, Jean-François; Comtat, Claude; Fourcade, Marjolaine; Mohammadi, Bijan; Mariano-Goulart, Denis

2007-07-01

This paper presents an extended 3-D exact rebinning formula in the Fourier space that leads to an iterative reprojection algorithm (iterative FOREPROJ), which enables the estimation of unmeasured oblique projection data on the basis of the whole set of measured data. In first approximation, this analytical formula also leads to an extended Fourier rebinning equation that is the basis for an approximate reprojection algorithm (extended FORE). These algorithms were evaluated on numerically simulated 3-D positron emission tomography (PET) data for the solution of the truncation problem, i.e., the estimation of the missing portions in the oblique projection data, before the application of algorithms that require complete projection data such as some rebinning methods (FOREX) or 3-D reconstruction algorithms (3DRP or direct Fourier methods). By taking advantage of all the 3-D data statistics, the iterative FOREPROJ reprojection provides a reliable alternative to the classical FOREPROJ method, which only exploits the low-statistics nonoblique data. It significantly improves the quality of the external reconstructed slices without loss of spatial resolution. As for the approximate extended FORE algorithm, it clearly exhibits limitations due to axial interpolations, but will require clinical studies with more realistic measured data in order to decide on its pertinence.

Truncation-based energy weighting string method for efficiently resolving small energy barriers

NASA Astrophysics Data System (ADS)

Carilli, Michael F.; Delaney, Kris T.; Fredrickson, Glenn H.

2015-08-01

The string method is a useful numerical technique for resolving minimum energy paths in rare-event barrier-crossing problems. However, when applied to systems with relatively small energy barriers, the string method becomes inconvenient since many images trace out physically uninteresting regions where the barrier has already been crossed and recrossing is unlikely. Energy weighting alleviates this difficulty to an extent, but typical implementations still require the string's endpoints to evolve to stable states that may be far from the barrier, and deciding upon a suitable energy weighting scheme can be an iterative process dependent on both the application and the number of images used. A second difficulty arises when treating nucleation problems: for later images along the string, the nucleus grows to fill the computational domain. These later images are unphysical due to confinement effects and must be discarded. In both cases, computational resources associated with unphysical or uninteresting images are wasted. We present a new energy weighting scheme that eliminates all of the above difficulties by actively truncating the string as it evolves and forcing all images, including the endpoints, to remain within and cover uniformly a desired barrier region. The calculation can proceed in one step without iterating on strategy, requiring only an estimate of an energy value below which images become uninteresting.

Two-body potential model based on cosine series expansion for ionic materials

DOE PAGES

Oda, Takuji; Weber, William J.; Tanigawa, Hisashi

2015-09-23

There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potentialmore » model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.« less

Large-scale exact diagonalizations reveal low-momentum scales of nuclei

NASA Astrophysics Data System (ADS)

Forssén, C.; Carlsson, B. D.; Johansson, H. T.; Sääf, D.; Bansal, A.; Hagen, G.; Papenbrock, T.

2018-03-01

Ab initio methods aim to solve the nuclear many-body problem with controlled approximations. Virtually exact numerical solutions for realistic interactions can only be obtained for certain special cases such as few-nucleon systems. Here we extend the reach of exact diagonalization methods to handle model spaces with dimension exceeding 1010 on a single compute node. This allows us to perform no-core shell model (NCSM) calculations for 6Li in model spaces up to Nmax=22 and to reveal the 4He+d halo structure of this nucleus. Still, the use of a finite harmonic-oscillator basis implies truncations in both infrared (IR) and ultraviolet (UV) length scales. These truncations impose finite-size corrections on observables computed in this basis. We perform IR extrapolations of energies and radii computed in the NCSM and with the coupled-cluster method at several fixed UV cutoffs. It is shown that this strategy enables information gain also from data that is not fully UV converged. IR extrapolations improve the accuracy of relevant bound-state observables for a range of UV cutoffs, thus making them profitable tools. We relate the momentum scale that governs the exponential IR convergence to the threshold energy for the first open decay channel. Using large-scale NCSM calculations we numerically verify this small-momentum scale of finite nuclei.

Improving the Accuracy of Laplacian Estimation with Novel Variable Inter-Ring Distances Concentric Ring Electrodes

PubMed Central

Makeyev, Oleksandr; Besio, Walter G.

2016-01-01

Noninvasive concentric ring electrodes are a promising alternative to conventional disc electrodes. Currently, the superiority of tripolar concentric ring electrodes over disc electrodes, in particular, in accuracy of Laplacian estimation, has been demonstrated in a range of applications. In our recent work, we have shown that accuracy of Laplacian estimation can be improved with multipolar concentric ring electrodes using a general approach to estimation of the Laplacian for an (n + 1)-polar electrode with n rings using the (4n + 1)-point method for n ≥ 2. This paper takes the next step toward further improving the Laplacian estimate by proposing novel variable inter-ring distances concentric ring electrodes. Derived using a modified (4n + 1)-point method, linearly increasing and decreasing inter-ring distances tripolar (n = 2) and quadripolar (n = 3) electrode configurations are compared to their constant inter-ring distances counterparts. Finite element method modeling and analytic results are consistent and suggest that increasing inter-ring distances electrode configurations may decrease the truncation error resulting in more accurate Laplacian estimates compared to respective constant inter-ring distances configurations. For currently used tripolar electrode configuration, the truncation error may be decreased more than two-fold, while for the quadripolar configuration more than a six-fold decrease is expected. PMID:27294933

Improving the Accuracy of Laplacian Estimation with Novel Variable Inter-Ring Distances Concentric Ring Electrodes.

PubMed

Makeyev, Oleksandr; Besio, Walter G

2016-06-10

Noninvasive concentric ring electrodes are a promising alternative to conventional disc electrodes. Currently, the superiority of tripolar concentric ring electrodes over disc electrodes, in particular, in accuracy of Laplacian estimation, has been demonstrated in a range of applications. In our recent work, we have shown that accuracy of Laplacian estimation can be improved with multipolar concentric ring electrodes using a general approach to estimation of the Laplacian for an (n + 1)-polar electrode with n rings using the (4n + 1)-point method for n ≥ 2. This paper takes the next step toward further improving the Laplacian estimate by proposing novel variable inter-ring distances concentric ring electrodes. Derived using a modified (4n + 1)-point method, linearly increasing and decreasing inter-ring distances tripolar (n = 2) and quadripolar (n = 3) electrode configurations are compared to their constant inter-ring distances counterparts. Finite element method modeling and analytic results are consistent and suggest that increasing inter-ring distances electrode configurations may decrease the truncation error resulting in more accurate Laplacian estimates compared to respective constant inter-ring distances configurations. For currently used tripolar electrode configuration, the truncation error may be decreased more than two-fold, while for the quadripolar configuration more than a six-fold decrease is expected.

Acute γ-secretase Inhibition of Nonhuman Primate CNS Shifts Amyloid Precursor Protein (APP) Metabolism from Amyloid-β Production to Alternative APP Fragments without Amyloid-β Rebound

PubMed Central

Cook, Jacquelynn J.; Wildsmith, Kristin R.; Gilberto, David B.; Holahan, Marie A.; Kinney, Gene G.; Mathers, Parker D.; Michener, Maria S.; Price, Eric A.; Shearman, Mark S.; Simon, Adam J.; Wang, Jennifer X.; Wu, Guoxin; Yarasheski, Kevin E.; Bateman, Randall J.

2010-01-01

The accumulation of amyloid beta (Aβ) in Alzheimer’s disease is caused by an imbalance of production and clearance, which leads to increased soluble Aβ species and extracellular plaque formation in the brain. Multiple Aβ-lowering therapies are currently in development: an important goal is to characterize the molecular mechanisms of action and effects on physiological processing of Aβ, as well as other amyloid precursor protein (APP) metabolites, in models which approximate human Aβ physiology. To this end, we report the translation of the human in vivo stable-isotope-labeling kinetics (SILK) method to a rhesus monkey cisterna magna ported (CMP) nonhuman primate model, and use the model to test the mechanisms of action of a γ-secretase inhibitor (GSI). A major concern of inhibiting the enzymes which produce Aβ (β- and γ-secretase) is that precursors of Aβ may accumulate and cause a rapid increase in Aβ production when enzyme inhibition discontinues. In this study, the GSI MK-0752 was administered to conscious CMP rhesus monkeys in conjunction with in vivo stable isotope labeling, and dose-dependently reduced newly generated CNS Aβ. In contrast to systemic Aβ metabolism, CNS Aβ production was not increased after the GSI was cleared. These results indicate that most of the CNS APP was metabolized to products other than Aβ, including C-terminal truncated forms of Aβ: 1–14, 1–15 and 1–16; this demonstrates an alternative degradation pathway for CNS amyloid precursor protein during γ-secretase inhibition. PMID:20463236

Truncated hemoglobins in actinorhizal nodules of Datisca glomerata.

PubMed

Pawlowski, K; Jacobsen, K R; Alloisio, N; Ford Denison, R; Klein, M; Tjepkema, J D; Winzer, T; Sirrenberg, A; Guan, C; Berry, A M

2007-11-01

Three types of hemoglobins exist in higher plants, symbiotic, non-symbiotic, and truncated hemoglobins. Symbiotic (class II) hemoglobins play a role in oxygen supply to intracellular nitrogen-fixing symbionts in legume root nodules, and in one case ( Parasponia Sp.), a non-symbiotic (class I) hemoglobin has been recruited for this function. Here we report the induction of a host gene, dgtrHB1, encoding a truncated hemoglobin in Frankia-induced nodules of the actinorhizal plant Datisca glomerata. Induction takes place specifically in cells infected by the microsymbiont, prior to the onset of bacterial nitrogen fixation. A bacterial gene (Frankia trHBO) encoding a truncated hemoglobin with O (2)-binding kinetics suitable for the facilitation of O (2) diffusion ( ) is also expressed in symbiosis. Nodule oximetry confirms the presence of a molecule that binds oxygen reversibly in D. glomerata nodules, but indicates a low overall hemoglobin concentration suggesting a local function. Frankia trHbO is likely to be responsible for this activity. The function of the D. glomerata truncated hemoglobin is unknown; a possible role in nitric oxide detoxification is suggested.

Tidal truncation and barotropic convergence in a channel network tidally driven from opposing entrances

USGS Publications Warehouse

Warner, J.C.; Schoellhamer, D.; Schladow, G.

2003-01-01

Residual circulation patterns in a channel network that is tidally driven from entrances on opposite sides are controlled by the temporal phasing and spatial asymmetry of the two forcing tides. The Napa/Sonoma Marsh Complex in San Francisco Bay, CA, is such a system. A sill on the west entrance to the system prevents a complete tidal range at spring tides that results in tidal truncation of water levels. Tidal truncation does not occur on the east side but asymmetries develop due to friction and off-channel wetland storage. The east and west asymmetric tides meet in the middle to produce a barotropic convergence zone that controls the transport of water and sediment. During spring tides, tidally averaged water-surface elevations are higher on the truncated west side. This creates tidally averaged fluxes of water and sediment to the east. During neap tides, the water levels are not truncated and the propagation speed of the tides controls residual circulation, creating a tidally averaged flux in the opposite direction. ?? 2003 Elsevier Science B.V. All rights reserved.

Approximated maximum likelihood estimation in multifractal random walks

NASA Astrophysics Data System (ADS)

Løvsletten, O.; Rypdal, M.

2012-04-01

We present an approximated maximum likelihood method for the multifractal random walk processes of [E. Bacry , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.64.026103 64, 026103 (2001)]. The likelihood is computed using a Laplace approximation and a truncation in the dependency structure for the latent volatility. The procedure is implemented as a package in the r computer language. Its performance is tested on synthetic data and compared to an inference approach based on the generalized method of moments. The method is applied to estimate parameters for various financial stock indices.

An efficient computer based wavelets approximation method to solve Fuzzy boundary value differential equations

NASA Astrophysics Data System (ADS)

Alam Khan, Najeeb; Razzaq, Oyoon Abdul

2016-03-01

In the present work a wavelets approximation method is employed to solve fuzzy boundary value differential equations (FBVDEs). Essentially, a truncated Legendre wavelets series together with the Legendre wavelets operational matrix of derivative are utilized to convert FB- VDE into a simple computational problem by reducing it into a system of fuzzy algebraic linear equations. The capability of scheme is investigated on second order FB- VDE considered under generalized H-differentiability. Solutions are represented graphically showing competency and accuracy of this method.

Application of a Threshold Method to Airborne-Spaceborne Attenuating-Wavelength Radars for the Estimation of Space-Time Rain-Rate Statistics.

NASA Astrophysics Data System (ADS)

Meneghini, Robert

1998-09-01

A method is proposed for estimating the area-average rain-rate distribution from attenuating-wavelength spaceborne or airborne radar data. Because highly attenuated radar returns yield unreliable estimates of the rain rate, these are eliminated by means of a proxy variable, Q, derived from the apparent radar reflectivity factors and a power law relating the attenuation coefficient and the reflectivity factor. In determining the probability distribution function of areawide rain rates, the elimination of attenuated measurements at high rain rates and the loss of data at light rain rates, because of low signal-to-noise ratios, leads to truncation of the distribution at the low and high ends. To estimate it over all rain rates, a lognormal distribution is assumed, the parameters of which are obtained from a nonlinear least squares fit to the truncated distribution. Implementation of this type of threshold method depends on the method used in estimating the high-resolution rain-rate estimates (e.g., either the standard Z-R or the Hitschfeld-Bordan estimate) and on the type of rain-rate estimate (either point or path averaged). To test the method, measured drop size distributions are used to characterize the rain along the radar beam. Comparisons with the standard single-threshold method or with the sample mean, taken over the high-resolution estimates, show that the present method usually provides more accurate determinations of the area-averaged rain rate if the values of the threshold parameter, QT, are chosen in the range from 0.2 to 0.4.

An ectromelia virus profilin homolog interacts with cellular tropomyosin and viral A-type inclusion protein.

PubMed

Butler-Cole, Christine; Wagner, Mary J; Da Silva, Melissa; Brown, Gordon D; Burke, Robert D; Upton, Chris

2007-07-24

Profilins are critical to cytoskeletal dynamics in eukaryotes; however, little is known about their viral counterparts. In this study, a poxviral profilin homolog, ectromelia virus strain Moscow gene 141 (ECTV-PH), was investigated by a variety of experimental and bioinformatics techniques to characterize its interactions with cellular and viral proteins. Profilin-like proteins are encoded by all orthopoxviruses sequenced to date, and share over 90% amino acid (aa) identity. Sequence comparisons show highest similarity to mammalian type 1 profilins; however, a conserved 3 aa deletion in mammalian type 3 and poxviral profilins suggests that these homologs may be more closely related. Structural analysis shows that ECTV-PH can be successfully modelled onto both the profilin 1 crystal structure and profilin 3 homology model, though few of the surface residues thought to be required for binding actin, poly(L-proline), and PIP2 are conserved. Immunoprecipitation and mass spectrometry identified two proteins that interact with ECTV-PH within infected cells: alpha-tropomyosin, a 38 kDa cellular actin-binding protein, and the 84 kDa product of vaccinia virus strain Western Reserve (VACV-WR) 148, which is the truncated VACV counterpart of the orthopoxvirus A-type inclusion (ATI) protein. Western and far-western blots demonstrated that the interaction with alpha-tropomyosin is direct, and immunofluorescence experiments suggest that ECTV-PH and alpha-tropomyosin may colocalize to structures that resemble actin tails and cellular protrusions. Sequence comparisons of the poxviral ATI proteins show that although full-length orthologs are only present in cowpox and ectromelia viruses, an ~ 700 aa truncated ATI protein is conserved in over 90% of sequenced orthopoxviruses. Immunofluorescence studies indicate that ECTV-PH localizes to cytoplasmic inclusion bodies formed by both truncated and full-length versions of the viral ATI protein. Furthermore, colocalization of ECTV-PH and truncated ATI protein to protrusions from the cell surface was observed. These results suggest a role for ECTV-PH in intracellular transport of viral proteins or intercellular spread of the virus. Broader implications include better understanding of the virus-host relationship and mechanisms by which cells organize and control the actin cytoskeleton.

Site-specific Phosphorylation Protects Glycogen Synthase Kinase-3β from Calpain-mediated Truncation of Its N and C Termini*

PubMed Central

Ma, Shanshan; Liu, Shaojun; Huang, Qiaoying; Xie, Bo; Lai, Bingquan; Wang, Chong; Song, Bin; Li, Mingtao

2012-01-01

Glycogen synthase kinase-3β (GSK-3β), a key regulator of neuronal apoptosis, is inhibited by the phosphorylation of Ser-9/Ser-389 and was recently shown to be cleaved by calpain at the N terminus, leading to its subsequent activation. In this study calpain was found to cleave GSK-3β not only at the N terminus but also at the C terminus, and cleavage sites were identified at residues Thr-38–Thr-39 and Ile-384–Gln-385. Furthermore, the cleavage of GSK-3β occurred in tandem with Ser-9 dephosphorylation during cerebellar granule neuron apoptosis. Increasing Ser-9 phosphorylation of GSK-3β by inhibiting phosphatase 1/2A or pretreating with purified active Akt inhibited calpain-mediated cleavage of GSK-3β at both N and C termini, whereas non-phosphorylatable mutant GSK-3β S9A facilitated its cleavage. In contrast, Ser-389 phosphorylation selectively inhibited the cleavage of GSK-3β at the C terminus but not the N terminus. Calpain-mediated cleavage resulted in three truncated products, all of which contained an intact kinase domain: ΔN-GSK-3β (amino acids 39–420), ΔC-GSK-3β (amino acids 1–384), and ΔN/ΔC-GSK-3β (amino acids 39–384). All three truncated products showed increased kinase and pro-apoptotic activity, with ΔN/ΔC-GSK-3β being the most active form. This observation suggests that the GSK-3β C terminus acts as an autoinhibitory domain similar to the N terminus. Taken together, these findings demonstrate that calpain-mediated cleavage activates GSK-3β by removing its N- and C-terminal autoinhibitory domains and that Ser-9 phosphorylation inhibits the cleavage of GSK-3β at both termini. In contrast, Ser-389 phosphorylation inhibits only C-terminal cleavage but not N-terminal cleavage. These findings also identify a mechanism by which site-specific phosphorylation and calpain-mediated cleavage operate in concert to regulate GSK-3β activity. PMID:22496446

Site-specific phosphorylation protects glycogen synthase kinase-3β from calpain-mediated truncation of its N and C termini.

PubMed

Ma, Shanshan; Liu, Shaojun; Huang, Qiaoying; Xie, Bo; Lai, Bingquan; Wang, Chong; Song, Bin; Li, Mingtao

2012-06-29

Glycogen synthase kinase-3β (GSK-3β), a key regulator of neuronal apoptosis, is inhibited by the phosphorylation of Ser-9/Ser-389 and was recently shown to be cleaved by calpain at the N terminus, leading to its subsequent activation. In this study calpain was found to cleave GSK-3β not only at the N terminus but also at the C terminus, and cleavage sites were identified at residues Thr-38-Thr-39 and Ile-384-Gln-385. Furthermore, the cleavage of GSK-3β occurred in tandem with Ser-9 dephosphorylation during cerebellar granule neuron apoptosis. Increasing Ser-9 phosphorylation of GSK-3β by inhibiting phosphatase 1/2A or pretreating with purified active Akt inhibited calpain-mediated cleavage of GSK-3β at both N and C termini, whereas non-phosphorylatable mutant GSK-3β S9A facilitated its cleavage. In contrast, Ser-389 phosphorylation selectively inhibited the cleavage of GSK-3β at the C terminus but not the N terminus. Calpain-mediated cleavage resulted in three truncated products, all of which contained an intact kinase domain: ΔN-GSK-3β (amino acids 39-420), ΔC-GSK-3β (amino acids 1-384), and ΔN/ΔC-GSK-3β (amino acids 39-384). All three truncated products showed increased kinase and pro-apoptotic activity, with ΔN/ΔC-GSK-3β being the most active form. This observation suggests that the GSK-3β C terminus acts as an autoinhibitory domain similar to the N terminus. Taken together, these findings demonstrate that calpain-mediated cleavage activates GSK-3β by removing its N- and C-terminal autoinhibitory domains and that Ser-9 phosphorylation inhibits the cleavage of GSK-3β at both termini. In contrast, Ser-389 phosphorylation inhibits only C-terminal cleavage but not N-terminal cleavage. These findings also identify a mechanism by which site-specific phosphorylation and calpain-mediated cleavage operate in concert to regulate GSK-3β activity.

Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichius, Alexander; Bidard, Frédérique; Buchholz, Franziska

2015-04-20

Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.

Ultra-sensitive detection of kanamycin for food safety using a reduced graphene oxide-based fluorescent aptasensor

NASA Astrophysics Data System (ADS)

Ha, Na-Reum; Jung, In-Pil; La, Im-Joung; Jung, Ho-Sup; Yoon, Moon-Young

2017-01-01

Overuse of antibiotics has caused serious problems, such as appearance of super bacteria, whose accumulation in the human body through the food chain is a concern. Kanamycin is a common antibiotic used to treat diverse infections; however, residual kanamycin can cause many side effects in humans. Thus, development of an ultra-sensitive, precise, and simple detection system for residual kanamycin in food products is urgently needed for food safety. In this study, we identified kanamycin-binding aptamers via a new screening method, and truncated variants were analyzed for optimization of the minimal sequence required for target binding. We found various aptamers with high binding affinity from 34.7 to 669 nanomolar Kdapp values with good specificity against kanamycin. Furthermore, we developed a reduced graphene oxide (RGO)-based fluorescent aptasensor for kanamycin detection. In this system, kanamycin was detected at a concentration as low as 1 pM (582.6 fg/mL). In addition, this method could detect kanamycin accurately in kanamycin-spiked blood serum and milk samples. Consequently, this simple, rapid, and sensitive kanamycin detection system with newly structural and functional analysis aptamer exhibits outstanding detection compared to previous methods and provides a new possibility for point of care testing and food safety.

Producing aglycons of ginsenosides in bakers' yeast

PubMed Central

Dai, Zhubo; Wang, Beibei; Liu, Yi; Shi, Mingyu; Wang, Dong; Zhang, Xianan; Liu, Tao; Huang, Luqi; Zhang, Xueli

2014-01-01

Ginsenosides are the primary bioactive components of ginseng, which is a popular medicinal plant that exhibits diverse pharmacological activities. Protopanaxadiol, protopanaxatriol and oleanolic acid are three basic aglycons of ginsenosides. Producing aglycons of ginsenosides in Saccharomyces cerevisiae was realized in this work and provides an alternative route compared to traditional extraction methods. Synthetic pathways of these three aglycons were constructed in S. cerevisiae by introducing β-amyrin synthase, oleanolic acid synthase, dammarenediol-II synthase, protopanaxadiol synthase, protopanaxatriol synthase and NADPH-cytochrome P450 reductase from different plants. In addition, a truncated 3-hydroxy-3-methylglutaryl-CoA reductase, squalene synthase and 2,3-oxidosqualene synthase genes were overexpressed to increase the precursor supply for improving aglycon production. Strain GY-1 was obtained, which produced 17.2 mg/L protopanaxadiol, 15.9 mg/L protopanaxatriol and 21.4 mg/L oleanolic acid. The yeast strains engineered in this work can serve as the basis for creating an alternative way for producing ginsenosides in place of extractions from plant sources. PMID:24424342

Fabrication of 2-inch nano patterned sapphire substrate with high uniformity by two-beam laser interference lithography

NASA Astrophysics Data System (ADS)

Dai, LongGui; Yang, Fan; Yue, Gen; Jiang, Yang; Jia, Haiqiang; Wang, Wenxin; Chen, Hong

2014-11-01

Generally, nano-scale patterned sapphire substrate (NPSS) has better performance than micro-scale patterned sapphire substrate (MPSS) in improving the light extraction efficiency of LEDs. Laser interference lithography (LIL) is one of the powerful fabrication methods for periodic nanostructures without photo-masks for different designs. However, Lloyd's mirror LIL system has the disadvantage that fabricated patterns are inevitably distorted, especially for large-area twodimensional (2D) periodic nanostructures. Herein, we introduce two-beam LIL system to fabricate consistent large-area NPSS. Quantitative analysis and characterization indicate that the high uniformity of the photoresist arrays is achieved. Through the combination of dry etching and wet etching techniques, the well-defined NPSS with period of 460 nm were prepared on the whole sapphire substrate. The deviation is 4.34% for the bottom width of the triangle truncated pyramid arrays on the whole 2-inch sapphire substrate, which is suitable for the application in industrial production of NPSS.

The finite state projection algorithm for the solution of the chemical master equation.

PubMed

Munsky, Brian; Khammash, Mustafa

2006-01-28

This article introduces the finite state projection (FSP) method for use in the stochastic analysis of chemically reacting systems. One can describe the chemical populations of such systems with probability density vectors that evolve according to a set of linear ordinary differential equations known as the chemical master equation (CME). Unlike Monte Carlo methods such as the stochastic simulation algorithm (SSA) or tau leaping, the FSP directly solves or approximates the solution of the CME. If the CME describes a system that has a finite number of distinct population vectors, the FSP method provides an exact analytical solution. When an infinite or extremely large number of population variations is possible, the state space can be truncated, and the FSP method provides a certificate of accuracy for how closely the truncated space approximation matches the true solution. The proposed FSP algorithm systematically increases the projection space in order to meet prespecified tolerance in the total probability density error. For any system in which a sufficiently accurate FSP exists, the FSP algorithm is shown to converge in a finite number of steps. The FSP is utilized to solve two examples taken from the field of systems biology, and comparisons are made between the FSP, the SSA, and tau leaping algorithms. In both examples, the FSP outperforms the SSA in terms of accuracy as well as computational efficiency. Furthermore, due to very small molecular counts in these particular examples, the FSP also performs far more effectively than tau leaping methods.

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data.

PubMed

Reisetter, Anna C; Muehlbauer, Michael J; Bain, James R; Nodzenski, Michael; Stevens, Robert D; Ilkayeva, Olga; Metzger, Boyd E; Newgard, Christopher B; Lowe, William L; Scholtens, Denise M

2017-02-02

Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based or large-scale clinical studies demands large numbers of subjects and therefore sample batching for gas-chromatography/mass spectrometry (GC/MS) non-targeted assays. When run over weeks or months, technical noise due to batch and run-order threatens data interpretability. Application of existing normalization methods to metabolomics is challenged by unsatisfied modeling assumptions and, notably, failure to address batch-specific truncation of low abundance compounds. To curtail technical noise and make GC/MS metabolomics data amenable to analyses describing biologically relevant variability, we propose mixture model normalization (mixnorm) that accommodates truncated data and estimates per-metabolite batch and run-order effects using quality control samples. Mixnorm outperforms other approaches across many metrics, including improved correlation of non-targeted and targeted measurements and superior performance when metabolite detectability varies according to batch. For some metrics, particularly when truncation is less frequent for a metabolite, mean centering and median scaling demonstrate comparable performance to mixnorm. When quality control samples are systematically included in batches, mixnorm is uniquely suited to normalizing non-targeted GC/MS metabolomics data due to explicit accommodation of batch effects, run order and varying thresholds of detectability. Especially in large-scale studies, normalization is crucial for drawing accurate conclusions from non-targeted GC/MS metabolomics data.

3D spherical-cap fitting procedure for (truncated) sessile nano- and micro-droplets & -bubbles.

PubMed

Tan, Huanshu; Peng, Shuhua; Sun, Chao; Zhang, Xuehua; Lohse, Detlef

2016-11-01

In the study of nanobubbles, nanodroplets or nanolenses immobilised on a substrate, a cross-section of a spherical cap is widely applied to extract geometrical information from atomic force microscopy (AFM) topographic images. In this paper, we have developed a comprehensive 3D spherical-cap fitting procedure (3D-SCFP) to extract morphologic characteristics of complete or truncated spherical caps from AFM images. Our procedure integrates several advanced digital image analysis techniques to construct a 3D spherical-cap model, from which the geometrical parameters of the nanostructures are extracted automatically by a simple algorithm. The procedure takes into account all valid data points in the construction of the 3D spherical-cap model to achieve high fidelity in morphology analysis. We compare our 3D fitting procedure with the commonly used 2D cross-sectional profile fitting method to determine the contact angle of a complete spherical cap and a truncated spherical cap. The results from 3D-SCFP are consistent and accurate, while 2D fitting is unavoidably arbitrary in the selection of the cross-section and has a much lower number of data points on which the fitting can be based, which in addition is biased to the top of the spherical cap. We expect that the developed 3D spherical-cap fitting procedure will find many applications in imaging analysis.

Incorporating truncating variants in PALB2, CHEK2, and ATM into the BOADICEA breast cancer risk model.

PubMed

Lee, Andrew J; Cunningham, Alex P; Tischkowitz, Marc; Simard, Jacques; Pharoah, Paul D; Easton, Douglas F; Antoniou, Antonis C

2016-12-01

The proliferation of gene panel testing precipitates the need for a breast cancer (BC) risk model that incorporates the effects of mutations in several genes and family history (FH). We extended the BOADICEA model to incorporate the effects of truncating variants in PALB2, CHEK2, and ATM. The BC incidence was modeled via the explicit effects of truncating variants in BRCA1/2, PALB2, CHEK2, and ATM and other unobserved genetic effects using segregation analysis methods. The predicted average BC risk by age 80 for an ATM mutation carrier is 28%, 30% for CHEK2, 50% for PALB2, and 74% for BRCA1 and BRCA2. However, the BC risks are predicted to increase with FH burden. In families with mutations, predicted risks for mutation-negative members depend on both FH and the specific mutation. The reduction in BC risk after negative predictive testing is greatest when a BRCA1 mutation is identified in the family, but for women whose relatives carry a CHEK2 or ATM mutation, the risks decrease slightly. The model may be a valuable tool for counseling women who have undergone gene panel testing for providing consistent risks and harmonizing their clinical management. A Web application can be used to obtain BC risks in clinical practice (http://ccge.medschl.cam.ac.uk/boadicea/).Genet Med 18 12, 1190-1198.

Statistical analysis tables for truncated or censored samples

NASA Technical Reports Server (NTRS)

Cohen, A. C.; Cooley, C. G.

1971-01-01

Compilation describes characteristics of truncated and censored samples, and presents six illustrations of practical use of tables in computing mean and variance estimates for normal distribution using selected samples.

Validation of APF as a Urinary Biomarker for Interstitial Cystitis

DTIC Science & Technology

2014-10-01

its C-terminus—in order to determine whether FL-CKAP4 could improve APF binding response over the truncated rCKAP4 used in our preliminary studies...recognized by a CKAP4 antibody, indicating high activity. However, when tested by SPR, FL-CKAP4 did not improve APF binding response over the truncated ...rCKAP4 (Figure 2). We then concentrated our efforts on optimization of the truncated rCKAP4 to generate stronger binding . Using the extracellular domain