Complexity of parallel implementation of domain decomposition techniques for elliptic partial differential equations

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

Gropp, W.D.; Keyes, D.E.

1988-03-01

The authors discuss the parallel implementation of preconditioned conjugate gradient (PCG)-based domain decomposition techniques for self-adjoint elliptic partial differential equations in two dimensions on several architectures. The complexity of these methods is described on a variety of message-passing parallel computers as a function of the size of the problem, number of processors and relative communication speeds of the processors. They show that communication startups are very important, and that even the small amount of global communication in these methods can significantly reduce the performance of many message-passing architectures.

Canopy carbon budget of Siebold's beech (Fagus crenata) sapling under free air ozone exposure.

PubMed

Watanabe, Makoto; Hoshika, Yasutomo; Inada, Naoki; Koike, Takayoshi

2014-01-01

To determine the effects of ozone (O3) on the canopy carbon budget, we investigated photosynthesis and respiration of leaves of Siebold's beech saplings under free air O3 exposure (60 nmol mol(-1), during daytime) in relation to the within-canopy light gradient; we then calculated the canopy-level photosynthetic carbon gain (PCG) and respiratory carbon loss (RCL) using a canopy photosynthesis model. Susceptibilities of photosynthesis and respiration to O3 were greater in leaves of upper canopy than in the lower canopy. The canopy net carbon gain (NCG) was reduced by O3 by 12.4% during one growing season. The increased RCL was the main factor for the O3-induced reduction in NCG in late summer, while contributions of the reduced PCG and the increased RCL to the NCG were almost the same in autumn. These results indicate contributions of changes in PCG and RCL under O3 to NCG were different between seasons. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fast divide-and-conquer algorithm for evaluating polarization in classical force fields

NASA Astrophysics Data System (ADS)

Nocito, Dominique; Beran, Gregory J. O.

2017-03-01

Evaluation of the self-consistent polarization energy forms a major computational bottleneck in polarizable force fields. In large systems, the linear polarization equations are typically solved iteratively with techniques based on Jacobi iterations (JI) or preconditioned conjugate gradients (PCG). Two new variants of JI are proposed here that exploit domain decomposition to accelerate the convergence of the induced dipoles. The first, divide-and-conquer JI (DC-JI), is a block Jacobi algorithm which solves the polarization equations within non-overlapping sub-clusters of atoms directly via Cholesky decomposition, and iterates to capture interactions between sub-clusters. The second, fuzzy DC-JI, achieves further acceleration by employing overlapping blocks. Fuzzy DC-JI is analogous to an additive Schwarz method, but with distance-based weighting when averaging the fuzzy dipoles from different blocks. Key to the success of these algorithms is the use of K-means clustering to identify natural atomic sub-clusters automatically for both algorithms and to determine the appropriate weights in fuzzy DC-JI. The algorithm employs knowledge of the 3-D spatial interactions to group important elements in the 2-D polarization matrix. When coupled with direct inversion in the iterative subspace (DIIS) extrapolation, fuzzy DC-JI/DIIS in particular converges in a comparable number of iterations as PCG, but with lower computational cost per iteration. In the end, the new algorithms demonstrated here accelerate the evaluation of the polarization energy by 2-3 fold compared to existing implementations of PCG or JI/DIIS.

Optimal and fast E/B separation with a dual messenger field

NASA Astrophysics Data System (ADS)

Kodi Ramanah, Doogesh; Lavaux, Guilhem; Wandelt, Benjamin D.

2018-05-01

We adapt our recently proposed dual messenger algorithm for spin field reconstruction and showcase its efficiency and effectiveness in Wiener filtering polarized cosmic microwave background (CMB) maps. Unlike conventional preconditioned conjugate gradient (PCG) solvers, our preconditioner-free technique can deal with high-resolution joint temperature and polarization maps with inhomogeneous noise distributions and arbitrary mask geometries with relative ease. Various convergence diagnostics illustrate the high quality of the dual messenger reconstruction. In contrast, the PCG implementation fails to converge to a reasonable solution for the specific problem considered. The implementation of the dual messenger method is straightforward and guarantees numerical stability and convergence. We show how the algorithm can be modified to generate fluctuation maps, which, combined with the Wiener filter solution, yield unbiased constrained signal realizations, consistent with observed data. This algorithm presents a pathway to exact global analyses of high-resolution and high-sensitivity CMB data for a statistically optimal separation of E and B modes. It is therefore relevant for current and next-generation CMB experiments, in the quest for the elusive primordial B-mode signal.

A Microfluidic, High Throughput Protein Crystal Growth Method for Microgravity

PubMed Central

Carruthers Jr, Carl W.; Gerdts, Cory; Johnson, Michael D.; Webb, Paul

2013-01-01

The attenuation of sedimentation and convection in microgravity can sometimes decrease irregularities formed during macromolecular crystal growth. Current terrestrial protein crystal growth (PCG) capabilities are very different than those used during the Shuttle era and that are currently on the International Space Station (ISS). The focus of this experiment was to demonstrate the use of a commercial off-the-shelf, high throughput, PCG method in microgravity. Using Protein BioSolutions’ microfluidic Plug Maker™/CrystalCard™ system, we tested the ability to grow crystals of the regulator of glucose metabolism and adipogenesis: peroxisome proliferator-activated receptor gamma (apo-hPPAR-γ LBD), as well as several PCG standards. Overall, we sent 25 CrystalCards™ to the ISS, containing ~10,000 individual microgravity PCG experiments in a 3U NanoRacks NanoLab (1U = 103 cm.). After 70 days on the ISS, our samples were returned with 16 of 25 (64%) microgravity cards having crystals, compared to 12 of 25 (48%) of the ground controls. Encouragingly, there were more apo-hPPAR-γ LBD crystals in the microgravity PCG cards than the 1g controls. These positive results hope to introduce the use of the PCG standard of low sample volume and large experimental density to the microgravity environment and provide new opportunities for macromolecular samples that may crystallize poorly in standard laboratories. PMID:24278480

The Human Polycomb Group Complex Associates with Pericentromeric Heterochromatin to Form a Novel Nuclear Domain

PubMed Central

Saurin, Andrew J.; Shiels, Carol; Williamson, Jill; Satijn, David P.E.; Otte, Arie P.; Sheer, Denise; Freemont, Paul S.

1998-01-01

The Polycomb group (PcG) complex is a chromatin-associated multiprotein complex, involved in the stable repression of homeotic gene activity in Drosophila. Recently, a mammalian PcG complex has been identified with several PcG proteins implicated in the regulation of Hox gene expression. Although the mammalian PcG complex appears analogous to the complex in Drosophila, the molecular mechanisms and functions for the mammalian PcG complex remain unknown. Here we describe a detailed characterization of the human PcG complex in terms of cellular localization and chromosomal association. By using antibodies that specifically recognize three human PcG proteins— RING1, BMI1, and hPc2—we demonstrate in a number of human cell lines that the PcG complex forms a unique discrete nuclear structure that we term PcG bodies. PcG bodies are prominent novel nuclear structures with the larger PcG foci generally localized near the centromeres, as visualized with a kinetochore antibody marker. In both normal fetal and adult fibroblasts, PcG bodies are not randomly dispersed, but appear clustered into defined areas within the nucleus. We show in three different human cell lines that the PcG complex can tightly associate with large pericentromeric heterochromatin regions (1q12) on chromosome 1, and with related pericentromeric sequences on different chromosomes, providing evidence for a mammalian PcG–heterochromatin association. Furthermore, these heterochromatin-bound PcG complexes remain stably associated throughout mitosis, thereby allowing the potential inheritance of the PcG complex through successive cell divisions. We discuss these results in terms of the known function of the PcG complex as a transcriptional repression complex. PMID:9722603

An interior-point method for total variation regularized positron emission tomography image reconstruction

NASA Astrophysics Data System (ADS)

Bai, Bing

2012-03-01

There has been a lot of work on total variation (TV) regularized tomographic image reconstruction recently. Many of them use gradient-based optimization algorithms with a differentiable approximation of the TV functional. In this paper we apply TV regularization in Positron Emission Tomography (PET) image reconstruction. We reconstruct the PET image in a Bayesian framework, using Poisson noise model and TV prior functional. The original optimization problem is transformed to an equivalent problem with inequality constraints by adding auxiliary variables. Then we use an interior point method with logarithmic barrier functions to solve the constrained optimization problem. In this method, a series of points approaching the solution from inside the feasible region are found by solving a sequence of subproblems characterized by an increasing positive parameter. We use preconditioned conjugate gradient (PCG) algorithm to solve the subproblems directly. The nonnegativity constraint is enforced by bend line search. The exact expression of the TV functional is used in our calculations. Simulation results show that the algorithm converges fast and the convergence is insensitive to the values of the regularization and reconstruction parameters.

Discrete wavelet-aided delineation of PCG signal events via analysis of an area curve length-based decision statistic.

PubMed

Homaeinezhad, M R; Atyabi, S A; Daneshvar, E; Ghaffari, A; Tahmasebi, M

2010-12-01

The aim of this study is to describe a robust unified framework for segmentation of the phonocardiogram (PCG) signal sounds based on the false-alarm probability (FAP) bounded segmentation of a properly calculated detection measure. To this end, first the original PCG signal is appropriately pre-processed and then, a fixed sample size sliding window is moved on the pre-processed signal. In each slid, the area under the excerpted segment is multiplied by its curve-length to generate the Area Curve Length (ACL) metric to be used as the segmentation decision statistic (DS). Afterwards, histogram parameters of the nonlinearly enhanced DS metric are used for regulation of the α-level Neyman-Pearson classifier for FAP-bounded delineation of the PCG events. The proposed method was applied to all 85 records of Nursing Student Heart Sounds database (NSHSDB) including stenosis, insufficiency, regurgitation, gallop, septal defect, split sound, rumble, murmur, clicks, friction rub and snap disorders with different sampling frequencies. Also, the method was applied to the records obtained from an electronic stethoscope board designed for fulfillment of this study in the presence of high-level power-line noise and external disturbing sounds and as the results, no false positive (FP) or false negative (FN) errors were detected. High noise robustness, acceptable detection-segmentation accuracy of PCG events in various cardiac system conditions, and having no parameters dependency to the acquisition sampling frequency can be mentioned as the principal virtues and abilities of the proposed ACL-based PCG events detection-segmentation algorithm.

A comparative evaluation of subepithelial connective tissue graft (SCTG) versus platelet concentrate graft (PCG) in the treatment of gingival recession using coronally advanced flap technique: A 12-month study

PubMed Central

Kumar, G. Naveen Vital; Murthy, K. Raja Venkatesh

2013-01-01

Objective: The objective of this study was to clinically evaluate and compare the efficacy of platelet concentrate graft (PCG) with that of subepithelial connective tissue graft (SCTG) using a coronally advanced flap technique in the treatment of gingival recession. Materials and Methods: Twelve patients with a total of 24 gingival recession defects were selected and randomly assigned either to experimental site-A (SCTG) or experimental site-B (PCG). The clinical parameters were recorded at baseline up to 12 months post-operatively and compared. Results: The mean vertical recession depth (VRD) statistically significantly decreased from 2.50 ± 0.48 mm to 0.54 ± 0.50 mm with PCG and from 2.75 ± 0.58 mm to 0.54 ± 0.45 mm with SCTG at 12 months. No statistically significant differences between the treatments were found for VRD and clinical attachment level (CAL), while keratinized tissue width (KTW) gain was statistically significant. Conclusion: Both the SCTG and the PCG group resulted in a significant amount of root coverage. The PCG technique was less invasive and required minimal time and clinical maneuver. It resulted in superior aesthetic outcome and lower post-surgical discomfort at the 12 months follow-up. PMID:24554889

Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications

PubMed Central

Wang, Wei; Qin, Jiang-Jiang; Voruganti, Sukesh; Nag, Subhasree; Zhou, Jianwei; Zhang, Ruiwen

2016-01-01

Polycomb group (PcG) proteins are transcriptional repressors that regulate several crucial developmental and physiological processes in the cell. More recently, they have been found to play important roles in human carcinogenesis and cancer development and progression. The deregulation and dysfunction of PcG proteins often lead to blocking or inappropriate activation of developmental pathways, enhancing cellular proliferation, inhibiting apoptosis, and increasing the cancer stem cell population. Genetic and molecular investigations of PcG proteins have long been focused on their PcG functions. However, PcG proteins have recently been shown to exert non-polycomb functions, contributing to the regulation of diverse cellular functions. We and others have demonstrated that PcG proteins regulate the expression and function of several oncogenes and tumor suppressor genes in a PcG-independent manner, and PcG proteins are associated with the survival of patients with cancer. In this review, we summarize the recent advances in the research on PcG proteins, including both the polycomb-repressive and non-polycomb functions. We specifically focus on the mechanisms by which PcG proteins play roles in cancer initiation, development, and progression. Finally, we discuss the potential value of PcG proteins as molecular biomarkers for the diagnosis and prognosis of cancer, and as molecular targets for cancer therapy. PMID:26227500

Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications.

PubMed

Wang, Wei; Qin, Jiang-Jiang; Voruganti, Sukesh; Nag, Subhasree; Zhou, Jianwei; Zhang, Ruiwen

2015-11-01

Polycomb group (PcG) proteins are transcriptional repressors that regulate several crucial developmental and physiological processes in the cell. More recently, they have been found to play important roles in human carcinogenesis and cancer development and progression. The deregulation and dysfunction of PcG proteins often lead to blocking or inappropriate activation of developmental pathways, enhancing cellular proliferation, inhibiting apoptosis, and increasing the cancer stem cell population. Genetic and molecular investigations of PcG proteins have long been focused on their PcG functions. However, PcG proteins have recently been shown to exert non-classical-Pc-functions, contributing to the regulation of diverse cellular functions. We and others have demonstrated that PcG proteins regulate the expression and function of several oncogenes and tumor suppressor genes in a PcG-independent manner, and PcG proteins are associated with the survival of patients with cancer. In this review, we summarize the recent advances in the research on PcG proteins, including both the Pc-repressive and non-classical-Pc-functions. We specifically focus on the mechanisms by which PcG proteins play roles in cancer initiation, development, and progression. Finally, we discuss the potential value of PcG proteins as molecular biomarkers for the diagnosis and prognosis of cancer, and as molecular targets for cancer therapy. © 2015 Wiley Periodicals, Inc.

Genome-wide analysis of Polycomb targets in Drosophila

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

Schwartz, Yuri B.; Kahn, Tatyana G.; Nix, David A.

2006-04-01

Polycomb Group (PcG) complexes are multiprotein assemblages that bind to chromatin and establish chromatin states leading to epigenetic silencing. PcG proteins regulate homeotic genes in flies and vertebrates but little is known about other PcG targets and the role of the PcG in development, differentiation and disease. We have determined the distribution of the PcG proteins PC, E(Z) and PSC and of histone H3K27 trimethylation in the Drosophila genome. At more than 200 PcG target genes, binding sites for the three PcG proteins colocalize to presumptive Polycomb Response Elements (PREs). In contrast, H3 me3K27 forms broad domains including the entiremore » transcription unit and regulatory regions. PcG targets are highly enriched in genes encoding transcription factors but receptors, signaling proteins, morphogens and regulators representing all major developmental pathways are also included.« less

Regulation of gene transcription by Polycomb proteins

PubMed Central

Aranda, Sergi; Mas, Gloria; Di Croce, Luciano

2015-01-01

The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation. PMID:26665172

Extemporaneously preparative biodegradable injectable polymer systems exhibiting temperature-responsive irreversible gelation.

PubMed

Yoshida, Yasuyuki; Takata, Kazuyuki; Takai, Hiroki; Kawahara, Keisuke; Kuzuya, Akinori; Ohya, Yuichi

2017-10-01

On clinical application of biodegradable injectable polymer (IP) systems, quick extemporaneous preparation of IP formulations and longer duration time gel state after injection into the body are the important targets to be developed. Previously, we had reported temperature-responsive covalent gelation systems via bio-orthogonal thiol-ene reaction by 'mixing strategy' of amphiphilic biodegradable tri-block copolymer (tri-PCG) attaching acryloyl groups on both termini (tri-PCG-Acryl) with reactive polythiol. In other previous works, we found 'freeze-dry with PEG/dispersion' method as quick extemporaneous preparation method of biodegradable IP formulations. In this study, we applied this quick preparative method to the temperature-triggered covalent gelation system. The instant formulation (D-sample) could be prepared by 'freeze-dry with PEG/dispersion' just mixing of tri-PCG-Acryl micelle dispersion and tri-PCG/DPMP micelle dispersion with PEG, that can be prepared in 30 s from the dried samples. The obtained D-sample showed irreversible gelation and long duration time of gel state, which was basically the same as the formulations prepared by the usual heating dissolution method (S-sample). Interestingly, the D-sample could maintain its sol state for a longer time (24 h) after preparing the formulation at r.t. compared with the S-sample, which became a gel in 3 h after preparing. The IP system showed good biocompatibility and long duration time of the gel state after subcutaneous implantation. These characteristics of D-samples, quick extemporaneous preparation and high stability in the sol state before injection, would be very convenient in a clinical setting.

Parametric modelling of cardiac system multiple measurement signals: an open-source computer framework for performance evaluation of ECG, PCG and ABP event detectors.

PubMed

Homaeinezhad, M R; Sabetian, P; Feizollahi, A; Ghaffari, A; Rahmani, R

2012-02-01

The major focus of this study is to present a performance accuracy assessment framework based on mathematical modelling of cardiac system multiple measurement signals. Three mathematical algebraic subroutines with simple structural functions for synthetic generation of the synchronously triggered electrocardiogram (ECG), phonocardiogram (PCG) and arterial blood pressure (ABP) signals are described. In the case of ECG signals, normal and abnormal PQRST cycles in complicated conditions such as fascicular ventricular tachycardia, rate dependent conduction block and acute Q-wave infarctions of inferior and anterolateral walls can be simulated. Also, continuous ABP waveform with corresponding individual events such as systolic, diastolic and dicrotic pressures with normal or abnormal morphologies can be generated by another part of the model. In addition, the mathematical synthetic PCG framework is able to generate the S4-S1-S2-S3 cycles in normal and in cardiac disorder conditions such as stenosis, insufficiency, regurgitation and gallop. In the PCG model, the amplitude and frequency content (5-700 Hz) of each sound and variation patterns can be specified. The three proposed models were implemented to generate artificial signals with varies abnormality types and signal-to-noise ratios (SNR), for quantitative detection-delineation performance assessment of several ECG, PCG and ABP individual event detectors designed based on the Hilbert transform, discrete wavelet transform, geometric features such as area curve length (ACLM), the multiple higher order moments (MHOM) metric, and the principal components analysed geometric index (PCAGI). For each method the detection-delineation operating characteristics were obtained automatically in terms of sensitivity, positive predictivity and delineation (segmentation) error rms and checked by the cardiologist. The Matlab m-file script of the synthetic ECG, ABP and PCG signal generators are available in the Appendix.

Exclusion of primary congenital glaucoma (PCG) from two candidate regions of chromosomes 1 and 6

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

Sarfarazi, M.; Akarsu, A.N.; Barsoum-Homsy, M.

1994-09-01

PCG is a genetically heterogeneous condition in which a significant proportion of families inherit in an autosomally recessive fashion. Although association of PCG with chromosomal abnormalities has been repeatedly reported in the literature, the chromosomal location of this condition is still unknown. Therefore, this study is designed to identify the chromosomal location of the PCG locus by positional mapping. We have identified 80 PCG families with a total of 261 potential informative meiosis. A group of 19 pedigrees with a minimum of 2 affected children in each pedigree and consanguinity in most of the parental generation were selected as ourmore » initial screening panel. This panel consists of a total of 44 affected and 93 unaffected individuals giving a total of 99 informative meiosis, including 5 phase-known. We used polymerase chain reaction (PCR), denaturing polyacrylamide gels and silver staining to genotype our families. We first screened for markers on 1q21-q31, the reported location for juvenile primary open-angle glaucoma and excluded a region of 30 cM as the likely site for the PCG locus. Association of PCG with both ring chromosome 6 and HLA-B8 has also been reported. Therefore, we genotyped our PCG panel with PCR applicable markers from 6p21. Significant negative lod scores were obtained for D6S105 (Z = -18.70) and D6S306 (Z = -5.99) at {theta}=0.001. HLA class 1 region has also contained one of the tubulin genes (TUBB) which is an obvious candidate for PCG. Study of this gene revealed a significant negative lod score with PCG (Z = -16.74, {theta}=0.001). A multipoint linkage analysis of markers in this and other regions containing the candidate genes will be presented.« less

Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2

PubMed Central

Perera, Pumi; Mora-García, Santiago; de Leau, Erica; Thornton, Harry; de Alves, Flavia Lima; Rapsilber, Juri; Yang, Suxin; James, Geo Velikkakam; Schneeberger, Korbinian; Finnegan, E. Jean; Turck, Franziska; Goodrich, Justin

2015-01-01

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity. PMID:26642436

Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Li, Xiaoye; Husbands, Parry; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2002-01-01

The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. For systems that are ill-conditioned, it is often necessary to use a preconditioning technique. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and ILU(O) preconditioned CG (PCG) using different programming paradigms and architectures. Results show that for this class of applications: ordering significantly improves overall performance on both distributed and distributed shared-memory systems, that cache reuse may be more important than reducing communication, that it is possible to achieve message-passing performance using shared-memory constructs through careful data ordering and distribution, and that a hybrid MPI+OpenMP paradigm increases programming complexity with little performance gains. A implementation of CG on the Cray MTA does not require special ordering or partitioning to obtain high efficiency and scalability, giving it a distinct advantage for adaptive applications; however, it shows limited scalability for PCG due to a lack of thread level parallelism.

Nucleotide substitutions revealing specific functions of Polycomb group genes.

PubMed

Bajusz, Izabella; Sipos, László; Pirity, Melinda K

2015-04-01

POLYCOMB group (PCG) proteins belong to the family of epigenetic regulators of genes playing important roles in differentiation and development. Mutants of PcG genes were isolated first in the fruit fly, Drosophila melanogaster, resulting in spectacular segmental transformations due to the ectopic expression of homeotic genes. Homologs of Drosophila PcG genes were also identified in plants and in vertebrates and subsequent experiments revealed the general role of PCG proteins in the maintenance of the repressed state of chromatin through cell divisions. The past decades of gene targeting experiments have allowed us to make significant strides towards understanding how the network of PCG proteins influences multiple aspects of cellular fate determination during development. Being involved in the transmission of specific expression profiles of different cell lineages, PCG proteins were found to control wide spectra of unrelated epigenetic processes in vertebrates, such as stem cell plasticity and renewal, genomic imprinting and inactivation of X-chromosome. PCG proteins also affect regulation of metabolic genes being important for switching programs between pluripotency and differentiation. Insight into the precise roles of PCG proteins in normal physiological processes has emerged from studies employing cell culture-based systems and genetically modified animals. Here we summarize the findings obtained from PcG mutant fruit flies and mice generated to date with a focus on PRC1 and PRC2 members altered by nucleotide substitutions resulting in specific alleles. We also include a compilation of lessons learned from these models about the in vivo functions of this complex protein family. With multiple knockout lines, sophisticated approaches to study the consequences of peculiar missense point mutations, and insights from complementary gain-of-function systems in hand, we are now in a unique position to significantly advance our understanding of the molecular basis of in vivo functions of PcG proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Tolerability and Outcomes of First-Line Pemetrexed-Cisplatin Followed by Gefitinib Maintenance Therapy Versus Gefitinib Monotherapy in Korean Patients with Advanced Nonsquamous Non-small Cell Lung Cancer: A Post Hoc Descriptive Subgroup Analysis of a Randomized, Phase 3 Trial.

PubMed

Kang, Jin Hyoung; Ahn, Myung-Ju; Kim, Dong-Wan; Cho, Eun Kyung; Kim, Joo-Hang; Shin, Sang Won; Wang, Xin; Kim, Jong Seok; Orlando, Mauro; Park, Keunchil

2016-04-01

We recently reported on a randomized, open-label, phase 3 trial comparing pemetrexed-cisplatin chemotherapy followed by gefitinib maintenance therapy (PC/G) with gefitinib monotherapy in patients with non-small cell lung cancer (NSCLC). Here, we report on a post hoc subgroup analysis of that study assessing the demographics and disposition of the Korean patient subgroup, and comparing the tolerability of PC/G and gefitinib monotherapy and the tumor response with respect to epidermal growth factor receptor (EGFR) status. Patients, who were ≥ 18 years, chemonaïve, Korean, light ex-smokers/never-smokers with advanced NSCLC, were randomly assigned (1:1) to PC/G or gefitinib monotherapy. Treatment-emergent adverse events (TEAEs) were graded, and tumor response was measured as change in lesion sum from baseline at best response. The study was registered with ClinicalTrials. gov, NCT01017874. Overall, 111 Korean patients were treated (PC/G, 51; gefitinib, 60). Between-arm characteristics were balanced and similar to those of the overall population. Treatment discontinuations due to adverse events were low (PC/G: 1, 2.0%; gefitinib: 7, 11.7%). Overall, 92 patients (82.9%) reported ≥ 1 TEAE (PC/G, 44; gefitinib, 48); few patients (PC/G, 16; gefitinib, 7) reported severe TEAEs; the most frequent was neutropenia (PC/G arm) and elevated alanine aminotransferase (gefitinib arm). The lesion sum was decreased by PC/G treatment in most patients, regardless of EGFR mutation status, while gefitinib monotherapy reduced the lesion sum in EGFR-positive patients but had no effect in EGFR-negative patients. Our results confirm that both PC/G and gefitinib were well tolerated in Korean patients, regardless of EGFR status; however, patients with EGFR wild-type NSCLC may not benefit from gefitinib monotherapy.

Documentation of a numerical code for the simulation of variable density ground-water flow in three dimensions

USGS Publications Warehouse

Kuiper, L.K.

1985-01-01

A numerical code is documented for the simulation of variable density time dependent groundwater flow in three dimensions. The groundwater density, although variable with distance, is assumed to be constant in time. The Integrated Finite Difference grid elements in the code follow the geologic strata in the modeled area. If appropriate, the determination of hydraulic head in confining beds can be deleted to decrease computation time. The strongly implicit procedure (SIP), successive over-relaxation (SOR), and eight different preconditioned conjugate gradient (PCG) methods are used to solve the approximating equations. The use of the computer program that performs the calculations in the numerical code is emphasized. Detailed instructions are given for using the computer program, including input data formats. An example simulation and the Fortran listing of the program are included. (USGS)

Comparison of an algebraic multigrid algorithm to two iterative solvers used for modeling ground water flow and transport

USGS Publications Warehouse

Detwiler, R.L.; Mehl, S.; Rajaram, H.; Cheung, W.W.

2002-01-01

Numerical solution of large-scale ground water flow and transport problems is often constrained by the convergence behavior of the iterative solvers used to solve the resulting systems of equations. We demonstrate the ability of an algebraic multigrid algorithm (AMG) to efficiently solve the large, sparse systems of equations that result from computational models of ground water flow and transport in large and complex domains. Unlike geometric multigrid methods, this algorithm is applicable to problems in complex flow geometries, such as those encountered in pore-scale modeling of two-phase flow and transport. We integrated AMG into MODFLOW 2000 to compare two- and three-dimensional flow simulations using AMG to simulations using PCG2, a preconditioned conjugate gradient solver that uses the modified incomplete Cholesky preconditioner and is included with MODFLOW 2000. CPU times required for convergence with AMG were up to 140 times faster than those for PCG2. The cost of this increased speed was up to a nine-fold increase in required random access memory (RAM) for the three-dimensional problems and up to a four-fold increase in required RAM for the two-dimensional problems. We also compared two-dimensional numerical simulations of steady-state transport using AMG and the generalized minimum residual method with an incomplete LU-decomposition preconditioner. For these transport simulations, AMG yielded increased speeds of up to 17 times with only a 20% increase in required RAM. The ability of AMG to solve flow and transport problems in large, complex flow systems and its ready availability make it an ideal solver for use in both field-scale and pore-scale modeling.

Roles of inner blood-retinal barrier organic anion transporter 3 in the vitreous/retina-to-blood efflux transport of p-aminohippuric acid, benzylpenicillin, and 6-mercaptopurine.

PubMed

Hosoya, Ken-ichi; Makihara, Akihide; Tsujikawa, Yuki; Yoneyama, Daisuke; Mori, Shinobu; Terasaki, Tetsuya; Akanuma, Shin-ichi; Tomi, Masatoshi; Tachikawa, Masanori

2009-04-01

The purpose of the present study was to characterize rat organic anion transporter (Oat) 3 (Oat3, Slc22a8) in the efflux transport at the inner blood-retinal barrier (BRB). Reverse transcription-polymerase chain reaction analysis showed that rat (r) Oat3 mRNA is expressed in retinal vascular endothelial cells (RVECs), but not rOat1 and rOat2 mRNA. The expression of Oat3 in the retina and human cultured retinal endothelial cells was further confirmed by Western blot analysis. Immunohistochemical staining in RVECs showed that rOat3 is colocalized with glucose transporter 1, but not P-glycoprotein, suggesting that rOat3 is possibly located at the abluminal membrane of the RVEC. The contribution of rOat3 to the efflux of [(3)H]p-aminohippuric acid ([(3)H]PAH), [(3)H]benzylpenicillin ([(3)H]PCG), and [(14)C]6-mercaptopurine ([(14)C]6-MP), substrates of rOat3, from the vitreous humor/retina to the circulating blood across the inner BRB was evaluated using the microdialysis method. [(3)H]PAH, [(3)H]PCG, [(14)C]6-MP, and [(14)C] or [(3)H]d-mannitol, a bulk flow marker, were biexponentially eliminated from the vitreous humor after vitreous bolus injection. The elimination rate constant of [(3)H]PAH, [(3)H]PCG, and [(14)C]6-MP during the terminal phase was approximately 2-fold greater than that of d-mannitol. This efflux transport was reduced in the retinal presence of probenecid, PAH, and PCG, whereas it was not inhibited by digoxin. In conclusion, rOat3 is expressed at the inner BRB and involved in the vitreous humor/retina-to-blood transport of PAH, PCG, and 6-MP. This transport system is one mechanism to limit the retinal distribution of PAH, PCG, and 6-MP.

G-Jitter Effects in Protein Crystal Growth - A Numerical Study

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Baugher, C. R.

1995-01-01

The impact of spacecraft acceleration environment on Protein Crystal Growth (PCG) is studied. A brief overview of the Space Shuttle acceleration environment is provided followed by a simple scaling procedure used to obtain estimates of the flow and concentration field characteristics in PCG. A detailed two-dimensional numerical model is then used to simulate the PCG system response to different disturbance scenarios; viz. residual g effects, impulse type disturbances and oscillatory inputs. The results show that PCG is susceptible to g-jitter and is a good candidate for vibration isolation.

RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor.

PubMed

Satijn, D P; Gunster, M J; van der Vlag, J; Hamer, K M; Schul, W; Alkema, M J; Saurin, A J; Freemont, P S; van Driel, R; Otte, A P

1997-07-01

The Polycomb (Pc) protein is a component of a multimeric, chromatin-associated Polycomb group (PcG) protein complex, which is involved in stable repression of gene activity. The identities of components of the PcG protein complex are largely unknown. In a two-hybrid screen with a vertebrate Pc homolog as a target, we identify the human RING1 protein as interacting with Pc. RING1 is a protein that contains the RING finger motif, a specific zinc-binding domain, which is found in many regulatory proteins. So far, the function of the RING1 protein has remained enigmatic. Here, we show that RING1 coimmunoprecipitates with a human Pc homolog, the vertebrate PcG protein BMI1, and HPH1, a human homolog of the PcG protein Polyhomeotic (Ph). Also, RING1 colocalizes with these vertebrate PcG proteins in nuclear domains of SW480 human colorectal adenocarcinoma and Saos-2 human osteosarcoma cells. Finally, we show that RING1, like Pc, is able to repress gene activity when targeted to a reporter gene. Our findings indicate that RING1 is associated with the human PcG protein complex and that RING1, like PcG proteins, can act as a transcriptional repressor.

Oxidative/Nitrosative Stress and Protein Damages in Aqueous Humor of Hyperglycemic Rabbits: Effects of Two Oral Antidiabetics, Pioglitazone and Repaglinide

PubMed Central

Gumieniczek, Anna; Owczarek, Beata; Pawlikowska, Bernadeta

2012-01-01

The present study was undertaken to determine oxidative/nitrosative stress in aqueous humor of alloxan-induced hyperglycemic rabbits and to investigate the effects of two oral antidiabetic drugs, pioglitazone from peroxisome proliferator-activated receptor gamma (PPARγ) agonists and repaglinide from nonsulfonylurea KATP channel blockers. Ascorbic acid (AA), glutathione (GSH), total antioxidant status (TAS), lipid peroxidation products (LPO), total nitrites (NO2), advanced oxidized protein products (AOPP), and protein carbonyl groups (PCG) were determined using respective colorimetric and ELISA methods. In our hyperglycemic animals, AA decreased by 77%, GSH by 45%, and TAS by 66% as compared to control animals. Simultaneously, LPO increased by 78%, PCG by 60%, AOPP by 84%, and NO2 by 70%. In pioglitazone-treated animals, AA and TAS increased above control values while GSH and PCG were normalized. In turn, LPO was reduced by 54%, AOPP by 84%, and NO2 by 24%, in relation to hyperglycemic rabbits. With repaglinide, AA and TAS were normalized, GSH increased by 20%, while LPO decreased by 45%. Our results show that pioglitazone and repaglinide differ significantly in their ability to ameliorate the parameters like NO2, PCG, and AOPP. In this area, the multimodal action of pioglitazone as PPARγ agonist is probably essential. PMID:22474428

Time-frequency analysis of phonocardiogram signals using wavelet transform: a comparative study.

PubMed

Ergen, Burhan; Tatar, Yetkin; Gulcur, Halil Ozcan

2012-01-01

Analysis of phonocardiogram (PCG) signals provides a non-invasive means to determine the abnormalities caused by cardiovascular system pathology. In general, time-frequency representation (TFR) methods are used to study the PCG signal because it is one of the non-stationary bio-signals. The continuous wavelet transform (CWT) is especially suitable for the analysis of non-stationary signals and to obtain the TFR, due to its high resolution, both in time and in frequency and has recently become a favourite tool. It decomposes a signal in terms of elementary contributions called wavelets, which are shifted and dilated copies of a fixed mother wavelet function, and yields a joint TFR. Although the basic characteristics of the wavelets are similar, each type of the wavelets produces a different TFR. In this study, eight real types of the most known wavelets are examined on typical PCG signals indicating heart abnormalities in order to determine the best wavelet to obtain a reliable TFR. For this purpose, the wavelet energy and frequency spectrum estimations based on the CWT and the spectra of the chosen wavelets were compared with the energy distribution and the autoregressive frequency spectra in order to determine the most suitable wavelet. The results show that Morlet wavelet is the most reliable wavelet for the time-frequency analysis of PCG signals.

An extended basis inexact shift-invert Lanczos for the efficient solution of large-scale generalized eigenproblems

NASA Astrophysics Data System (ADS)

Rewieński, M.; Lamecki, A.; Mrozowski, M.

2013-09-01

This paper proposes a technique, based on the Inexact Shift-Invert Lanczos (ISIL) method with Inexact Jacobi Orthogonal Component Correction (IJOCC) refinement, and a preconditioned conjugate-gradient (PCG) linear solver with multilevel preconditioner, for finding several eigenvalues for generalized symmetric eigenproblems. Several eigenvalues are found by constructing (with the ISIL process) an extended projection basis. Presented results of numerical experiments confirm the technique can be effectively applied to challenging, large-scale problems characterized by very dense spectra, such as resonant cavities with spatial dimensions which are large with respect to wavelengths of the resonating electromagnetic fields. It is also shown that the proposed scheme based on inexact linear solves delivers superior performance, as compared to methods which rely on exact linear solves, indicating tremendous potential of the 'inexact solve' concept. Finally, the scheme which generates an extended projection basis is found to provide a cost-efficient alternative to classical deflation schemes when several eigenvalues are computed.

Plots, Calculations and Graphics Tools (PCG2). Software Transfer Request Presentation

NASA Technical Reports Server (NTRS)

Richardson, Marilou R.

2010-01-01

This slide presentation reviews the development of the Plots, Calculations and Graphics Tools (PCG2) system. PCG2 is an easy to use tool that provides a single user interface to view data in a pictorial, tabular or graphical format. It allows the user to view the same display and data in the Control Room, engineering office area, or remote sites. PCG2 supports extensive and regular engineering needs that are both planned and unplanned and it supports the ability to compare, contrast and perform ad hoc data mining over the entire domain of a program's test data.

Parallel conjugate gradient algorithms for manipulator dynamic simulation

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheld, Robert E.

1989-01-01

Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).

PcG and trxG in plants - friends or foes.

PubMed

Pu, Li; Sung, Zinmay Renee

2015-05-01

The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals. Copyright © 2015 Elsevier Ltd. All rights reserved.

A review of intelligent systems for heart sound signal analysis.

PubMed

Nabih-Ali, Mohammed; El-Dahshan, El-Sayed A; Yahia, Ashraf S

2017-10-01

Intelligent computer-aided diagnosis (CAD) systems can enhance the diagnostic capabilities of physicians and reduce the time required for accurate diagnosis. CAD systems could provide physicians with a suggestion about the diagnostic of heart diseases. The objective of this paper is to review the recent published preprocessing, feature extraction and classification techniques and their state of the art of phonocardiogram (PCG) signal analysis. Published literature reviewed in this paper shows the potential of machine learning techniques as a design tool in PCG CAD systems and reveals that the CAD systems for PCG signal analysis are still an open problem. Related studies are compared to their datasets, feature extraction techniques and the classifiers they used. Current achievements and limitations in developing CAD systems for PCG signal analysis using machine learning techniques are presented and discussed. In the light of this review, a number of future research directions for PCG signal analysis are provided.

Determination of the binding properties of p-cresyl glucuronide to human serum albumin.

PubMed

Yi, Dan; Monteiro, Elisa Bernardes; Chambert, Stéphane; Soula, Hédi A; Daleprane, Julio B; Soulage, Christophe O

2018-04-26

p-Cresyl glucuronide (p-CG) is a by-product of tyrosine metabolism that accumulates in patients with end-stage renal disease. p-CG binding to human serum albumin in physiological conditions (37°C, pH 7.40) was studied by ultrafiltration (MWCO 10 kDa) and data were analyzed assuming one binding site. The estimated value of the association constant was 2.77×10 3  M -1 and a maximal stoichiometry of 3.80 mol per mole. At a concentration relevant for end-stage renal patients, p-CG was 23% bound to albumin. Competition experiments, using fluorescent probes, demonstrated that p-CG did not bind to Sudlow's site I or site II. The p-CG did not interfere with the binding of p-cresyl-sulfate or indoxyl sulfate to serum albumin. Copyright © 2018. Published by Elsevier B.V.

Comparison of automatic denoising methods for phonocardiograms with extraction of signal parameters via the Hilbert Transform

NASA Astrophysics Data System (ADS)

Messer, Sheila R.; Agzarian, John; Abbott, Derek

2001-05-01

Phonocardiograms (PCGs) have many advantages over traditional auscultation (listening to the heart) because they may be replayed, may be analyzed for spectral and frequency content, and frequencies inaudible to the human ear may be recorded. However, various sources of noise may pollute a PCG including lung sounds, environmental noise and noise generated from contact between the recording device and the skin. Because PCG signals are known to be nonlinear and it is often not possible to determine their noise content, traditional de-noising methods may not be effectively applied. However, other methods including wavelet de-noising, wavelet packet de-noising and averaging can be employed to de-noise the PCG. This study examines and compares these de-noising methods. This study answers such questions as to which de-noising method gives a better SNR, the magnitude of signal information that is lost as a result of the de-noising process, the appropriate uses of the different methods down to such specifics as to which wavelets and decomposition levels give best results in wavelet and wavelet packet de-noising. In general, the wavelet and wavelet packet de-noising performed roughly equally with optimal de-noising occurring at 3-5 levels of decomposition. Averaging also proved a highly useful de- noising technique; however, in some cases averaging is not appropriate. The Hilbert Transform is used to illustrate the results of the de-noising process and to extract instantaneous features including instantaneous amplitude, frequency, and phase.

Mobile Phonocardiogram Diagnosis in Newborns Using Support Vector Machine

PubMed Central

Amiri, Amir Mohammad; Abtahi, Mohammadreza; Constant, Nick; Mankodiya, Kunal

2017-01-01

Phonocardiogram (PCG) monitoring on newborns is one of the most important and challenging tasks in the heart assessment in the early ages of life. In this paper, we present a novel approach for cardiac monitoring applied in PCG data. This basic system coupled with denoising, segmentation, cardiac cycle selection and classification of heart sound can be used widely for a large number of the data. This paper describes the problems and additional advantages of the PCG method including the possibility of recording heart sound at home, removing unwanted noises and data reduction on a mobile device, and an intelligent system to diagnose heart diseases on the cloud server. A wide range of physiological features from various analysis domains, including modeling, time/frequency domain analysis, an algorithm, etc., is proposed in order to extract features which will be considered as inputs for the classifier. In order to record the PCG data set from multiple subjects over one year, an electronic stethoscope was used for collecting data that was connected to a mobile device. In this study, we used different types of classifiers in order to distinguish between healthy and pathological heart sounds, and a comparison on the performances revealed that support vector machine (SVM) provides 92.2% accuracy and AUC = 0.98 in a time of 1.14 seconds for training, on a dataset of 116 samples. PMID:28335471

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.

PubMed

Tolhuis, Bas; de Wit, Elzo; Muijrers, Inhua; Teunissen, Hans; Talhout, Wendy; van Steensel, Bas; van Lohuizen, Maarten

2006-06-01

Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila melanogaster Kc cells. We found that Pc associates with large genomic regions of up to approximately 150 kb in size, hereafter referred to as 'Pc domains'. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 Lys27 and is generally transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains.

The Neurochemical and Microstructural Changes in the Brain of Systemic Lupus Erythematosus Patients: A Multimodal MRI Study

PubMed Central

Zhang, Zhiyan; Wang, Yukai; Shen, Zhiwei; Yang, Zhongxian; Li, Li; Chen, Dongxiao; Yan, Gen; Cheng, Xiaofang; Shen, Yuanyu; Tang, Xiangyong; Hu, Wei; Wu, Renhua

2016-01-01

The diagnosis and pathology of neuropsychiatric systemic lupus erythematosus (NPSLE) remains challenging. Herein, we used multimodal imaging to assess anatomical and functional changes in brains of SLE patients instead of a single MRI approach generally used in previous studies. Twenty-two NPSLE patients, 21 non-NPSLE patients and 20 healthy controls (HCs) underwent 3.0 T MRI with multivoxel magnetic resonance spectroscopy, T1-weighted volumetric images for voxel based morphometry (VBM) and diffusional kurtosis imaging (DKI) scans. While there were findings in other basal ganglia regions, the most consistent findings were observed in the posterior cingulate gyrus (PCG). The reduction of multiple metabolite concentration was observed in the PCG in the two patient groups, and the NPSLE patients were more prominent. The two patient groups displayed lower diffusional kurtosis (MK) values in the bilateral PCG compared with HCs (p < 0.01) as assessed by DKI. Grey matter reduction in the PCG was observed in the NPSLE group using VBM. Positive correlations among cognitive function scores and imaging metrics in bilateral PCG were detected. Multimodal imaging is useful for evaluating SLE subjects and potentially determining disease pathology. Impairments of cognitive function in SLE patients may be interpreted by metabolic and microstructural changes in the PCG. PMID:26758023

Recycling of paint-contaminated grit.

PubMed

Taha, R; al-Alawi, D; al-Nabhani, M; Pillay, A E; al-Hamdi, A

2001-08-01

The impact on the environment of using paint-contaminated grit (PCG) as a partial or full replacement for sand in Portland cement mortar and asphalt concrete mixtures was investigated. The grit waste material originated from abrasive blasting of offshore steel structures. There is a major environmental concern regarding the safe disposal of the spent blasting abrasives that contain paint chips or paint particles and other debris removed from the surface of the steel structures. This work investigated the potential reuse of PCG in Portland cement concrete (PCC) and hot mix asphalt concrete. Several studies were conducted to establish the integrity of the materials containing the recycled grit. These included the chemical and physical characterization of natural sand and PCG, the assay of leaches associated with the grit material for hazardous metal contaminants, such as Cr, Cd and Pb, and the assessment of the mechanical properties of the PCG-substituted mortars by applying special tests (such as Marshall stability and determination of the flow properties) to the PCG-substituted asphalt concrete mixtures. The overall results demonstrated that the potential reuse of PCG in PCC and asphalt concrete mixtures would not pose any environmental threat and could produce several benefits, such as reduced disposal costs, protection of water sources from improper disposal practices and reduced costs in the production of natural aggregates and asphalt cement.

Geomorphology of comet 67P/Churyumov–Gerasimenko

USGS Publications Warehouse

Birch, Samuel P. D.; Tang, Y.; Hayes, A. G.; Kirk, Randolph L.; Bodewitz, D.; Campins, H.; Fernandez, Y.; de Freitas Bart, R.; Kutsop, N. W.; Sierks, H.; Soderblom, J. M.; Squyres, S. W.; Vincent, J.-B.

2017-01-01

We present a global geomorphological map of comet 67P/Churyumov–Gerasimenko (67P/C-G) using data acquired by the Rosetta Orbiter’s OSIRIS Narrow Angle Camera. The images used in our study were acquired between 2014 August and 2015 May, before 67P/C-G passed through perihelion. Imagery of the Southern hemisphere was included in our study, allowing us to compare the contrasting hemispheres of 67P/C-G in a single study. Our work also puts into greater context the morphologies studied in previous works, and also the morphologies observed on previously visited cometary nuclei. Relative to other nuclei, 67P/C-G appears most similar to 81P/Wild 2, with a topographically heterogeneous surface dominated by smooth-floored pits. Our mapping describes the landscapes of 67P/C-G when they were first observed by Rosetta, and our map can be used to detect changes in surface morphologies after its perihelion passage. Our mapping reveals strong latitudinal dependences for emplaced units and a highly heterogeneous surface. Layered bedrock units that represent the exposed nucleus of 67P/C-G are dominant at southern latitudes, while topographically smooth, dust covered regions dominate the Northern hemisphere. Equatorial latitudes are dominated by smooth terrain units that show evidence for flow structures. We observe no obvious differences between the comet’s two lobes, with the only longitudinal variations being the Imhotep and Hatmehit basins. These correlations suggest a strong seasonal forcing on the surface evolution of 67P/C-G, where materials are transported from the Southern hemisphere to Northern hemisphere basins over multiple orbital time-scales.

The Role of Genetic Ancestry in Brazilian Patients With Primary Congenital Glaucoma.

PubMed

Rolim, Hévila; Cronemberger, Sebastião; Rangel, Hayana; Batista, Wagner D; Bastos-Rodrigues, Luciana; De Marco, Luiz

2016-01-01

The relationship between clinical data and genetic ancestry in Brazilian patients with primary congenital glaucoma (PCG) was studied. Thirty patients with PCG and 60 unrelated controls underwent a complete ophthalmological examination. The PCG inclusion criterion was prior surgery with a minimum follow-up of 6 months after the last surgical procedure. Clinical data were recorded and DNA from each individual was extracted and genotyped for a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms (indels). Eighteen (60%) children had bilateral disease and 16 (53.3%) were male. The mean age at diagnosis was 6.3 months and surgical follow-up time varied from 8 to 85 months. For the PCG group, the proportion of Europeans, Africans, and Amerindians was 0.784±0.044 (mean±SEM), 0.149±0.035, and 0.067±0.023, respectively, whereas for the control group was 0.730±0.048, 0.132±0.034, and 0.138±0.032, respectively. An increased proportion of African indels was associated with worse surgical prognosis (P=0.036). There was also a statistically significant (P<0.05) positive correlation between axial length and African component (initial: R=0.625; final: R=0.567). An increased proportion of African indels was associated with worse prognosis for PCG in a mixed population. Genetic ancestry markers may be helpful in assessing risk factors for surgical outcomes in PCG. Further studies are needed to unveil the role of ancestry in heterogeneous populations such as Brazilians with PCG.

Microgravity

NASA Image and Video Library

1988-10-24

Mission Specialist George (Pinky) D. Nelson uses a 35 mm camera to photograph a protein crystal grown during the STS-26 Protein Crystal Growth (PCG-II-01) experiment. The protein crystal growth (PCG) carrier is shown deployed from the PCG Refrigerator/Incubator Mocule (R/IM) located in the middeck forward locker. The R/IM contained three Vapor Diffusion Apparatus (VDS) trays (one of which is shown). A total of sixty protein crystal samples were processed during the STS-26 mission.

Molecular architecture of polycomb repressive complexes

PubMed Central

Chittock, Emily C.; Latwiel, Sebastian; Miller, Thomas C.R.

2017-01-01

The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle. Here, we discuss some highlights of recent PcG structures and the insights they have given us into how these complexes regulate transcription through chromatin. PMID:28202673

Ex vivo localization and permeation of cisplatin from novel topical formulations through excised pig, goat, and mice skin and in vitro characterization for effective management of skin-cited malignancies.

PubMed

Gupta, Vandana; Trivedi, Piyush

2015-01-01

It would be advantageous to administer cisplatin topically for treatment of cutaneous malignancies. Present work focuses on ex vivo and in vitro characterization of proultraflexible topical formulations. Permeation of cisplatin through the excised pig, goat, and mice skin was quantitatively determined. Data indicate that protransfersome carbopol gel (pcg) formulation clearly delayed drug permeation through skin. Permeation of cisplatin from protransfersome system (ps) formulation was enhanced by approximately 1.5 fold compared with pcg for pig and goat skin. Localization of drug from pcg was higher and showed less permeation. Cisplatin-loaded pcg formulation is better to treat cutaneous malignancies.

Processing of fetal heart rate through non-invasive adaptive system based on recursive least squares algorithm

NASA Astrophysics Data System (ADS)

Fajkus, Marcel; Nedoma, Jan; Martinek, Radek; Vasinek, Vladimir

2017-10-01

In this article, we describe an innovative non-invasive method of Fetal Phonocardiography (fPCG) using fiber-optic sensors and adaptive algorithm for the measurement of fetal heart rate (fHR). Conventional PCG is based on a noninvasive scanning of acoustic signals by means of a microphone placed on the thorax. As for fPCG, the microphone is placed on the maternal abdomen. Our solution is based on patent pending non-invasive scanning of acoustic signals by means of a fiber-optic interferometer. Fiber-optic sensors are resistant to technical artifacts such as electromagnetic interferences (EMI), thus they can be used in situations where it is impossible to use conventional EFM methods, e.g. during Magnetic Resonance Imaging (MRI) examination or in case of delivery in water. The adaptive evaluation system is based on Recursive least squares (RLS) algorithm. Based on real measurements provided on five volunteers with their written consent, we created a simplified dynamic signal model of a distribution of heartbeat sounds (HS) through the human body. Our created model allows us to verification of the proposed adaptive system RLS algorithm. The functionality of the proposed non-invasive adaptive system was verified by objective parameters such as Sensitivity (S+) and Signal to Noise Ratio (SNR).

Lineage specific expression of Polycomb Group Proteins in human embryonic stem cells in vitro.

PubMed

Pethe, Prasad; Pursani, Varsha; Bhartiya, Deepa

2015-05-01

Human embryonic (hES) stem cells are an excellent model to study lineage specification and differentiation into various cell types. Differentiation necessitates repression of specific genes not required for a particular lineage. Polycomb Group (PcG) proteins are key histone modifiers, whose primary function is gene repression. PcG proteins form complexes called Polycomb Repressive Complexes (PRCs), which catalyze histone modifications such as H2AK119ub1, H3K27me3, and H3K9me3. PcG proteins play a crucial role during differentiation of stem cells. The expression of PcG transcripts during differentiation of hES cells into endoderm, mesoderm, and ectoderm lineage is yet to be shown. In-house derived hES cell line KIND1 was differentiated into endoderm, mesoderm, and ectoderm lineages; followed by characterization using RT-PCR for HNF4A, CDX2, MEF2C, TBX5, SOX1, and MAP2. qRT-PCR and western blotting was performed to compare expression of PcG transcripts and proteins across all the three lineages. We observed that cells differentiated into endoderm showed upregulation of RING1B, BMI1, EZH2, and EED transcripts. Mesoderm differentiation was characterized by significant downregulation of all PcG transcripts during later stages. BMI1 and RING1B were upregulated while EZH2, SUZ12, and EED remained low during ectoderm differentiation. Western blotting also showed distinct expression of BMI1 and EZH2 during differentiation into three germ layers. Our study shows that hES cells differentiating into endoderm, mesoderm, and ectoderm lineages show distinct PcG expression profile at transcript and protein level. © 2015 International Federation for Cell Biology.

A Comparative Study on Fetal Heart Rates Estimated from Fetal Phonography and Cardiotocography

PubMed Central

Ibrahim, Emad A.; Al Awar, Shamsa; Balayah, Zuhur H.; Hadjileontiadis, Leontios J.; Khandoker, Ahsan H.

2017-01-01

The aim of this study is to investigate that fetal heart rates (fHR) extracted from fetal phonocardiography (fPCG) could convey similar information of fHR from cardiotocography (CTG). Four-channel fPCG sensors made of low cost (<$1) ceramic piezo vibration sensor within 3D-printed casings were used to collect abdominal phonogram signals from 20 pregnant mothers (>34 weeks of gestation). A novel multi-lag covariance matrix-based eigenvalue decomposition technique was used to separate maternal breathing, fetal heart sounds (fHS) and maternal heart sounds (mHS) from abdominal phonogram signals. Prior to the fHR estimation, the fPCG signals were denoised using a multi-resolution wavelet-based filter. The proposed source separation technique was first tested in separating sources from synthetically mixed signals and then on raw abdominal phonogram signals. fHR signals extracted from fPCG signals were validated using simultaneous recorded CTG-based fHR recordings.The experimental results have shown that the fHR derived from the acquired fPCG can be used to detect periods of acceleration and deceleration, which are critical indication of the fetus' well-being. Moreover, a comparative analysis demonstrated that fHRs from CTG and fPCG signals were in good agreement (Bland Altman plot has mean = −0.21 BPM and ±2 SD = ±3) with statistical significance (p < 0.001 and Spearman correlation coefficient ρ = 0.95). The study findings show that fHR estimated from fPCG could be a reliable substitute for fHR from the CTG, opening up the possibility of a low cost monitoring tool for fetal well-being. PMID:29089896

Cell Cycle-Dependent Recruitment of Polycomb Proteins to the ASNS Promoter Counteracts C/ebp-Mediated Transcriptional Activation in Bombyx mori

PubMed Central

Li, Zhiqing; Cheng, Daojun; Mon, Hiroaki; Zhu, Li; Xu, Jian; Tatsuke, Tsuneyuki; Lee, Jae Man; Xia, Qingyou; Kusakabe, Takahiro

2013-01-01

Epigenetic modifiers and transcription factors contribute to developmentally programmed gene expression. Here, we establish a functional link between epigenetic regulation by Polycomb group (PcG) proteins and transcriptional regulation by C/ebp that orchestrates the correct expression of Bombyx mori asparagine synthetase (BmASNS), a gene involved in the biosynthesis of asparagine. We show that the cis-regulatory elements of YY1-binding motifs and the CpG island present on the BmASNS promoter are required for the recruitment of PcG proteins and the subsequent deposition of the epigenetic repression mark H3K27me3. RNAi-mediated knockdown of PcG genes leads to derepression of the BmASNS gene via the recruitment of activators, including BmC/ebp, to the promoter. Intriguingly, we find that PcG proteins and BmC/ebp can dynamically modulate the transcriptional output of the BmASNS target in a cell cycle-dependent manner. It will be essential to suppress BmASNS expression by PcG proteins at the G2/M phase of the cell cycle in the presence of BmC/ebp activator. Thus, our results provide a novel insight into the molecular mechanism underlying the recruitment and regulation of the PcG system at a discrete gene locus in Bombyx mori. PMID:23382816

Site-Specific Expression of Polycomb-Group Genes Encoding the HPC-HPH/PRC1 Complex in Clinically Defined Primary Nodal and Cutaneous Large B-Cell Lymphomas

PubMed Central

Raaphorst, Frank M.; Vermeer, Maarten; Fieret, Elly; Blokzijl, Tjasso; Dukers, Danny; Sewalt, Richard G.A.B.; Otte, Arie P.; Willemze, Rein; Meijer, Chris J.L.M.

2004-01-01

Polycomb-group (PcG) genes preserve cell identity by gene silencing, and contribute to regulation of lymphopoiesis and malignant transformation. We show that primary nodal large B-cell lymphomas (LBCLs), and secondary cutaneous deposits from such lymphomas, abnormally express the BMI-1, RING1, and HPH1 PcG genes in cycling neoplastic cells. By contrast, tumor cells in primary cutaneous LBCLs lacked BMI-1 expression, whereas RING1 was variably detected. Lack of BMI-1 expression was characteristic for primary cutaneous LBCLs, because other primary extranodal LBCLs originating from brain, testes, and stomach were BMI-1-positive. Expression of HPH1 was rarely detected in primary cutaneous LBCLs of the head or trunk and abundant in primary cutaneous LBCLs of the legs, which fits well with its earlier recognition as a distinct clinical pathological entity with different clinical behavior. We conclude that clinically defined subclasses of primary LBCLs display site-specific abnormal expression patterns of PcG genes of the HPC-HPH/PRC1 PcG complex. Some of these patterns (such as the expression profile of BMI-1) may be diagnostically relevant. We propose that distinct expression profiles of PcG genes results in abnormal formation of HPC-HPH/PRC1 PcG complexes, and that this contributes to lymphomagenesis and different clinical behavior of clinically defined LBCLs. PMID:14742259

The heart sound preprocessor

NASA Technical Reports Server (NTRS)

Chen, W. T.

1972-01-01

Technology developed for signal and data processing was applied to diagnostic techniques in the area of phonocardiography (pcg), the graphic recording of the sounds of the heart generated by the functioning of the aortic and ventricular valves. The relatively broad bandwidth of the PCG signal (20 to 2000 Hz) was reduced to less than 100 Hz by the use of a heart sound envelope. The process involves full-wave rectification of the PCG signal, envelope detection of the rectified wave, and low pass filtering of the resultant envelope.

CASIS PCG 6

NASA Image and Video Library

2017-06-06

iss052e000508 (June 6, 2017) --- View of astronaut Jack Fischer working with the Neutron Crystallographic Studies of Human Acetylcholinesterase for the Design of Accelerated Reactivators (CASIS PCG 6) experiment in the Japanese Experiment Module

An Automatic Segmentation Method Combining an Active Contour Model and a Classification Technique for Detecting Polycomb-group Proteinsin High-Throughput Microscopy Images.

PubMed

Gregoretti, Francesco; Cesarini, Elisa; Lanzuolo, Chiara; Oliva, Gennaro; Antonelli, Laura

2016-01-01

The large amount of data generated in biological experiments that rely on advanced microscopy can be handled only with automated image analysis. Most analyses require a reliable cell image segmentation eventually capable of detecting subcellular structures.We present an automatic segmentation method to detect Polycomb group (PcG) proteins areas isolated from nuclei regions in high-resolution fluorescent cell image stacks. It combines two segmentation algorithms that use an active contour model and a classification technique serving as a tool to better understand the subcellular three-dimensional distribution of PcG proteins in live cell image sequences. We obtained accurate results throughout several cell image datasets, coming from different cell types and corresponding to different fluorescent labels, without requiring elaborate adjustments to each dataset.

A periplasmic D-alanyl-D-alanine dipeptidase in the gram-negative bacterium Salmonella enterica.

PubMed

Hilbert, F; García-del Portillo, F; Groisman, E A

1999-04-01

The VanX protein is a D-alanyl-D-alanine (D-Ala-D-Ala) dipeptidase essential for resistance to the glycopeptide antibiotic vancomycin. While this enzymatic activity has been typically associated with vancomycin- and teicoplainin-resistant enterococci, we now report the identification of a D-Ala-D-Ala dipeptidase in the gram-negative species Salmonella enterica. The Salmonella enzyme is only 36% identical to VanX but exhibits a similar substrate specificity: it hydrolyzes D-Ala-D-Ala, DL-Ala-DL-Phe, and D-Ala-Gly but not the tripeptides D-Ala-D-Ala-D-Ala and DL-Ala-DL-Lys-Gly or the dipeptides L-Ala-L-Ala, N-acetyl-D-Ala-D-Ala, and L-Leu-Pro. The Salmonella dipeptidase gene, designated pcgL, appears to have been acquired by horizontal gene transfer because pcgL-hybridizing sequences were not detected in related bacterial species and the G+C content of the pcgL-containing region (41%) is much lower than the overall G+C content of the Salmonella chromosome (52%). In contrast to wild-type Salmonella, a pcgL mutant was unable to use D-Ala-D-Ala as a sole carbon source. The pcgL gene conferred D-Ala-D-Ala dipeptidase activity upon Escherichia coli K-12 but did not allow growth on D-Ala-D-Ala. The PcgL protein localizes to the periplasmic space of Salmonella, suggesting that this dipeptidase participates in peptidoglycan metabolism.

Implementing clinical governance in English primary care groups/trusts: reconciling quality improvement and quality assurance.

PubMed

Campbell, S M; Sheaff, R; Sibbald, B; Marshall, M N; Pickard, S; Gask, L; Halliwell, S; Rogers, A; Roland, M O

2002-03-01

To investigate the concept of clinical governance being advocated by primary care groups/trusts (PCG/Ts), approaches being used to implement clinical governance, and potential barriers to its successful implementation in primary care. Qualitative case studies using semi-structured interviews and documentation review. Twelve purposively sampled PCG/Ts in England. Fifty senior staff including chief executives, clinical governance leads, mental health leads, and lay board members. Participants' perceptions of the role of clinical governance in PCG/Ts. PCG/Ts recognise that the successful implementation of clinical governance in general practice will require cultural as well as organisational changes, and the support of practices. They are focusing their energies on supporting practices and getting them involved in quality improvement activities. These activities include, but move beyond, conventional approaches to quality assessment (audit, incentives) to incorporate approaches which emphasise corporate and shared learning. PCG/Ts are also engaged in setting up systems for monitoring quality and for dealing with poor performance. Barriers include structural barriers (weak contractual levers to influence general practices), resource barriers (perceived lack of staff or money), and cultural barriers (suspicion by practice staff or problems overcoming the perceived blame culture associated with quality assessment). PCG/Ts are focusing on setting up systems for implementing clinical governance which seek to emphasise developmental and supportive approaches which will engage health professionals. Progress is intentionally incremental but formidable challenges lie ahead, not least reconciling the dual role of supporting practices while monitoring (and dealing with poor) performance.

CYP1B1 and MYOC Mutations in Vietnamese Primary Congenital Glaucoma Patients.

PubMed

Do, Tan; Shei, William; Chau, Pham Thi Minh; Trang, Doan Le; Yong, Victor H K; Ng, Xiao Yu; Chen, Yue Ming; Aung, Tin; Vithana, Eranga N

2016-05-01

Primary congenital glaucoma (PCG, OMIM 231300), the most common glaucoma in infancy, is caused by developmental defects in the anterior chamber angle. The 3 implicated genes are cytochrome P450 family I subfamily B polypeptide 1 (CYP1B1), latent transforming growth factor β-binding protein 2 (LTBP2), and myocilin (MYOC). In this study, we sought to determine CYP1B1 and MYOC sequence variations in a Vietnamese cohort of index cases with PCG and their families. Thirty Vietnamese subjects with PCG and 120 normal Vietnamese subjects were recruited. PCG was defined by the presence of at least 2 of the following clinical manifestations: increased corneal diameter (>10 mm at birth), corneal edema, Haab's striae, optic disc changes, and absence of other ocular or systemic diseases associated with childhood glaucoma. The coding exons, intron and exon boundaries, and untranslated regions of CYP1B1 and MYOC genes were PCR amplified and subjected to bidirectional sequencing in all subjects. We identified 2 homozygous and 3 heterozygous CYP1B1 sequence alterations in our study subjects. Among the 5 mutations identified, 2 (p.H279L and p.L283F) were novel mutations, whereas 3 (p.A121_S122insDRPAFA, p.L107V, and p.V320L) had been previously reported in PCG cases. None of these mutations was observed in any of the 120 controls. Haplotypes generated with 6 non-disease-causing intragenic single nucleotide polymorphisms detected in CYP1B1 indicated that the most common haplotype in Vietnamese population is similar to that found in Chinese and Japanese. The genotype-phenotype correlation showed no significant difference between mutation and no-mutation groups for quantitative clinical features (presenting intraocular pressure, corneal diameter, number of surgeries performed, the cup-to-disc ratio) as well as for qualitative factors (bilateral cases, phenotype severity, and the prognosis) (P>0.05). Five out of 30 families with PCG (16.7%) had disease attributable to CYP1B1 alterations suggesting that CYP1B1 is not the major gene causing PCG in Vietnamese unlike in the case of Arab or Romany patients. This percentage is similar to that detected in studies of Japanese and Chinese patients with sporadic PCG. PCG has proven to be an ocular disease of genetic heterogeneity, calling for further studies to identify novel genes causing this disease.

Effects of a psychological intervention on the quality of life of obese adolescents under a multidisciplinary treatment.

PubMed

Freitas, Camila R M; Gunnarsdottir, Thrudur; Fidelix, Yara L; Tenório, Thiago R S; Lofrano-Prado, Mara C; Hill, James O; Prado, Wagner L

To investigate the effects of multidisciplinary treatment with and without psychological counseling on obese adolescents' self-reported quality of life. Seventy-six obese adolescents (15.87±1.53 y) were allocated into psychological counseling group (PCG; n=36) or control group (CG; n=40) for 12 weeks. All participants received the same supervised exercise training, nutritional and clinical counseling. Participants in PCG also received psychological counseling. QOL was measured before and after 12 weeks of intervention by Generic Questionnaire for the Evaluation of Quality of Life (SF-36). The dropout rate was higher in GC (22.5%) when compared with PCG (0.0%) (p<0.001). After 12 weeks, participants from PCG presents lower body weight, relative fat mass and higher free fat mass (p<0.001 for all) compared to GC. QOL improved among adolescents from both groups (p<0.05), however, a better QOL was reported from those adolescents enrolled in PCG. The inclusion of a psychological counseling component in multidisciplinary treatment for adolescent obesity appears to provide benefits observed for improved QOL as compared with treatment without psychological counseling. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Implementing clinical governance in English primary care groups/trusts: reconciling quality improvement and quality assurance

PubMed Central

Campbell, S; Sheaff, R; Sibbald, B; Marshall, M; Pickard, S; Gask, L; Halliwell, S; Rogers, A; Roland, M

2002-01-01

Objectives: To investigate the concept of clinical governance being advocated by primary care groups/trusts (PCG/Ts), approaches being used to implement clinical governance, and potential barriers to its successful implementation in primary care. Design: Qualitative case studies using semi-structured interviews and documentation review. Setting: Twelve purposively sampled PCG/Ts in England. Participants: Fifty senior staff including chief executives, clinical governance leads, mental health leads, and lay board members. Main outcome measures: Participants' perceptions of the role of clinical governance in PCG/Ts. Results: PCG/Ts recognise that the successful implementation of clinical governance in general practice will require cultural as well as organisational changes, and the support of practices. They are focusing their energies on supporting practices and getting them involved in quality improvement activities. These activities include, but move beyond, conventional approaches to quality assessment (audit, incentives) to incorporate approaches which emphasise corporate and shared learning. PCG/Ts are also engaged in setting up systems for monitoring quality and for dealing with poor performance. Barriers include structural barriers (weak contractual levers to influence general practices), resource barriers (perceived lack of staff or money), and cultural barriers (suspicion by practice staff or problems overcoming the perceived blame culture associated with quality assessment). Conclusion: PCG/Ts are focusing on setting up systems for implementing clinical governance which seek to emphasise developmental and supportive approaches which will engage health professionals. Progress is intentionally incremental but formidable challenges lie ahead, not least reconciling the dual role of supporting practices while monitoring (and dealing with poor) performance. PMID:12078380

[Laser therapy and famotidine in complex restorative treatment of primary chronic gastroduodenitis].

PubMed

Filimonov, R M; Musaeva, O M

2003-01-01

Primary chronic gastroduodenitis (PCG) is one of the most frequent diseases of the gastrointestinal tract. Timely and efficient treatment of patients with PCG promotes ulcer prevention. In this connection, an urgent problem of restorative medicine is to develop medical programs with active introduction of pharmacophysiotherapeutic complexes, in particular, laser therapy and anti-secretory preparation (famotidine) that increase therapeutic efficacy of treatment of this disease. To this end, we give results of treatment of 50 patients with primary chronic gastroduodenitis (26 having undergone laser therapy only, and 24 having had a combination of laser therapy and famotidine), which demonstrated that the complex action method has a more adequate effect on pathogenetic components in this disease than monotherapy.

Repeatability and Reliability Characterization of Phonocardiograph Systems Using Wavelet and Backpropagation Neural Network

NASA Astrophysics Data System (ADS)

Sumarna; Astono, J.; Purwanto, A.; Agustika, D. K.

2018-04-01

Phonocardiograph (PCG) system consisting of an electronic stethoscope, mic condenser, mic preamp, and the battery has been developed. PCG system is used to detect heart abnormalities. Although PCG is not popular because of many things that affect its performance, in this research we try to reduce the factors that affecting its consistency To find out whether the system is repeatable and reliable the system have to be characterized first. This research aims to see whether the PCG system can provide the same results for measurements of the same patient. Characterization of the system is done by analyzing whether the PCG system can recognize the S1 and S2 part of the same person. From the recording result, S1 and S2 then transformed by using Discrete Wavelet Transform of Haar mother wavelet of level 1 and extracted the feature by using data range of approximation coefficients. The result was analyzed by using pattern recognition system of backpropagation neural network. Partially obtained data used as training data and partly used as test data. From the results of the pattern recognition system, it can be concluded that the system accuracy in recognizing S1 reach 87.5% and S2 only hit 67%.

Effect of Prenatal Counseling on Breastfeeding Rates in Mothers of Twins.

PubMed

Mikami, Fernanda Cristina Ferreira; de Lourdes Brizot, Maria; Tase, Terezinha Hideco; Saccuman, Elizabeth; Vieira Francisco, Rossana Pulcineli; Zugaib, Marcelo

To investigate the effect of antenatal breastfeeding counseling on the breastfeeding rates for women who give birth to twins. Prospective randomized trial. Multiple Pregnancy Unit, Obstetrics Department, University of São Paulo, Brazil. A total of 171 mothers of twins and their 342 infants. The participants were randomized into the prenatal counseling group (PCG) or control group (CG). Breastfeeding data were collected through personal interviews at three times after birth: 30 to 40 days (Time 1), 90 days (Time 2), and 180 days (Time 3). The primary endpoint was a comparison of the mothers' breastfeeding rates between PCG and CG in each analyzed period. The secondary endpoint was the comparison of the overall rates of twin infant breastfeeding between PCG and CG until 180 days after birth. The final analysis included 68 women pregnant with twins in the PCG and 60 in the CG. There was no significant difference in the breastfeeding rates between PCG and CG in the analyzed periods: Time 1 (odds ratio [OR] = 1.87, 95% confidence interval [CI] [0.71, 4.95]), Time 2 (OR = 1.50, 95% CI [0.72, 3.10]), and Time 3 (OR = 1.06, 95% CI [0.51, 2.19]). Also, no difference existed in the overall rates of breastfeeding between PCG and CG at 180 days. In women pregnant with twins, antenatal breastfeeding counseling did not significantly affect the breastfeeding rates. Further research about the best moment to counsel mothers of twins is needed to improve breastfeeding rates. Copyright © 2017 AWHONN, the Association of Women’s Health, Obstetric and Neonatal Nurses. Published by Elsevier Inc. All rights reserved.

BLISTER Regulates Polycomb-Target Genes, Represses Stress-Regulated Genes and Promotes Stress Responses in Arabidopsis thaliana.

PubMed

Kleinmanns, Julia A; Schatlowski, Nicole; Heckmann, David; Schubert, Daniel

2017-01-01

HIGHLIGHTS The PRC2 interacting protein BLISTER likely acts downstream of PRC2 to silence Polycomb target genes and is a key regulator of specific stress responses in Arabidopsis . Polycomb group (PcG) proteins are key epigenetic regulators of development. The highly conserved Polycomb repressive complex 2 (PRC2) represses thousands of target genes by trimethylating H3K27 (H3K27me3). Plant specific PcG components and functions are largely unknown, however, we previously identified the plant-specific protein BLISTER (BLI) as a PRC2 interactor. BLI regulates PcG target genes and promotes cold stress resistance. To further understand the function of BLI , we analyzed the transcriptional profile of bli-1 mutants. Approximately 40% of the up-regulated genes in bli are PcG target genes, however, bli-1 mutants did not show changes in H3K27me3 levels at all tested genes, indicating that BLI regulates PcG target genes downstream of or in parallel to PRC2. Interestingly, a significant number of BLI regulated H3K27me3 target genes is regulated by the stress hormone absciscic acid (ABA). We further reveal an overrepresentation of genes responding to abiotic stresses such as drought, high salinity, or heat stress among the up-regulated genes in bli mutants. Consistently, bli mutants showed reduced desiccation stress tolerance. We conclude that the PRC2 associated protein BLI is a key regulator of stress-responsive genes in Arabidopsis : it represses ABA-responsive PcG target genes, likely downstream of PRC2, and promotes resistance to several stresses such as cold and drought.

Stuxnet Facilitates the Degradation of Polycomb Protein during Development.

PubMed

Du, Juan; Zhang, Junzheng; He, Tao; Li, Yajuan; Su, Ying; Tie, Feng; Liu, Min; Harte, Peter J; Zhu, Alan Jian

2016-06-20

Polycomb-group (PcG) proteins function to ensure correct deployment of developmental programs by epigenetically repressing target gene expression. Despite the importance, few studies have been focused on the regulation of PcG activity itself. Here, we report a Drosophila gene, stuxnet (stx), that controls Pc protein stability. We find that heightened stx activity leads to homeotic transformation, reduced Pc activity, and de-repression of PcG targets. Conversely, stx mutants, which can be rescued by decreased Pc expression, display developmental defects resembling hyperactivation of Pc. Our biochemical analyses provide a mechanistic basis for the interaction between stx and Pc; Stx facilitates Pc degradation in the proteasome, independent of ubiquitin modification. Furthermore, this mode of regulation is conserved in vertebrates. Mouse stx promotes degradation of Cbx4, an orthologous Pc protein, in vertebrate cells and induces homeotic transformation in Drosophila. Our results highlight an evolutionarily conserved mechanism of regulated protein degradation on PcG homeostasis and epigenetic activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Modeling of PCG fluid dynamics: Salient results

NASA Technical Reports Server (NTRS)

Ramachandran, N.

1993-01-01

Materials processing in space-based laboratories has already yielded higher quality crystals during previous space flights, and opportunities for several fluids experiments are anticipated during the extended duration missions planned for the future. Crystal growth in space benefits not only from its reduced gravity environment but also from the absence of the hydrostatic pressure which assists certain crystal growth and refinement methods. Gravity-driven phenomena are thus reduced in strength, and a purely diffusive fluid's behavior can be attained. In addition, past materials science experiments have shown that microgravity can also help produce larger crystals. While gravity-related effects are definitely curtailed in space, they are nevertheless present to some degree due to the acceleration environment onboard the spacecraft. This residual acceleration level is comprised of quasi-steady, oscillatory, and transient components, and is caused by a variety of mechanisms. For example, gravity gradient forces produce low frequency disturbances, and the operation of machinery, control thrusters, solar panels, human activity, etc. contribute to higher frequency accelerations. These disturbances are collectively referred to as g-jitter, and they can be deleterious to certain experiments where the minimization of the acceleration level is important. Advanced vibration isolation techniques can be utilized to actively filter out some of the detrimental frequencies and help in obtaining optimum results. However, the successful application of this technology requires the detailed analysis of candidate fluids experiments to gauge their response to g-jitter and to determine their acceleration sensitivities. Several crystal growth experiments in the Protein Crystal Growth (PCG) area, besides others, are expected to be carried out on future shuttle flights and on Space Station Freedom. The need for vibration isolation systems or components for microgravity science experiments can be expected to grow as experiments and available hardware becomes more complex. This technology will also find increased application as the science community develops an awareness of their specific needs relative to the environment available in manned space missions. Vibration isolation research strives to develop a microgravity environment requirement that defines tolerance limits on the allowable g-level, and provides the required technology to achieve it. This effort will assist in establishing the tolerable acceleration levels for specific fluids experiments. The primary effort is directed towards modeling PCG and the approach undertaken for this investigation is outlined. The objectives of this research are: (1) to computationally determine vibration sensitivity of protein crystal growth experiments; (2) determine if these experiments can benefit from vibration isolation techniques; and (3) provide realistic requirements for vibration isolation technology.

The ULT trxG Fatcors play a role in Arabidopsis Fertilization

USDA-ARS?s Scientific Manuscript database

Trithorax group (trxG) and Polycomb group (PcG) proteins are epigenetic modifiers that play key roles in eukaryotic development by promoting active or repressive gene expression states, respectively. Although PcG proteins have well-defined roles in controlling developmental transitions, cell fate de...

Astronaut Scott Parazynski works with PCG experiment on middeck

NASA Image and Video Library

1994-11-14

STS066-13-029 (3-14 Nov 1994) --- On the Space Shuttle Atlantis' mid-deck, astronaut Scott E. Parazynski, mission specialist, works at one of two areas onboard the Shuttle which support the Protein Crystal Growth (PCG) experiment. This particular section is called the Vapor Diffusion Apparatus (VDA), housed in a Single Locker Thermal Enclosure (STES). Together with the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES) the VDA represents the continuing research into the structures of proteins and other macromolecules such as viruses. In addition to using the microgravity of space to grow high-quality protein crystals for structural analyses, the experiments are expected to help develop technologies and methods to improve the protein crystallization process on Earth as well as in space.

40 CFR 80.340 - What standards and requirements apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2011 CFR

2011-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG)? 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention... gasoline by blending blendstocks into previously certified gasoline (PCG)? (a) Any refiner who produces...

40 CFR 80.340 - What standards and requirements apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2010 CFR

2010-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG)? 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention... gasoline by blending blendstocks into previously certified gasoline (PCG)? (a) Any refiner who produces...

40 CFR 80.340 - What standards and requirements apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2013 CFR

2013-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG)? 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention... gasoline by blending blendstocks into previously certified gasoline (PCG)? (a) Any refiner who produces...

40 CFR 80.340 - What standards and requirements apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2012 CFR

2012-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG)? 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention... gasoline by blending blendstocks into previously certified gasoline (PCG)? (a) Any refiner who produces...

40 CFR 80.340 - What standards and requirements apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2014 CFR

2014-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG)? 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention... gasoline by blending blendstocks into previously certified gasoline (PCG)? (a) Any refiner who produces...

40 CFR 80.1640 - Standards and requirements that apply to refiners producing gasoline by blending blendstocks into...

Code of Federal Regulations, 2014 CFR

2014-07-01

... to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG). 80... (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur § 80.1640 Standards and requirements that apply to refiners producing gasoline by blending blendstocks into previously certified gasoline (PCG...

The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants

USDA-ARS?s Scientific Manuscript database

During development, trithorax group (trxG) chromatin remodeling complexes counteract repression by Polycomb group (PcG) complexes to sustain active expression of key regulatory genes. Although PcG complexes are well characterized in plants, little is known about trxG activities. Here we demonstrate ...

Polycomb group (PcG) proteins and Pax6 cooperate to inhibit in vivo reprogramming of the developing Drosophila eye.

PubMed

Zhu, Jinjin; Ordway, Alison J; Weber, Lena; Buddika, Kasun; Kumar, Justin P

2018-04-04

How different cells and tissues commit to and determine their fates has been a central question in developmental biology since the seminal embryological experiments conducted by Wilhelm Roux and Hans Driesch in sea urchins and frogs. Here, we demonstrate that Polycomb group (PcG) proteins maintain Drosophila eye specification by suppressing the activation of alternative fate choices. The loss of PcG in the developing eye results in a cellular reprogramming event in which the eye is redirected to a wing fate. This fate transformation occurs with either the individual loss of Polycomb proteins or the simultaneous reduction of the Pleiohomeotic repressive complex and Pax6. Interestingly, the requirement for retinal selector genes is limited to Pax6, as the removal of more downstream members does not lead to the eye-wing transformation. We also show that distinct PcG complexes are required during different developmental windows throughout eye formation. These findings build on earlier observations that the eye can be reprogrammed to initiate head epidermis, antennal and leg development. © 2018. Published by The Company of Biologists Ltd.

Charting the functional relevance of Broca's area for visual word recognition and picture naming in Dutch using fMRI-guided TMS.

PubMed

Wheat, Katherine L; Cornelissen, Piers L; Sack, Alexander T; Schuhmann, Teresa; Goebel, Rainer; Blomert, Leo

2013-05-01

Magnetoencephalography (MEG) has shown pseudohomophone priming effects at Broca's area (specifically pars opercularis of left inferior frontal gyrus and precentral gyrus; LIFGpo/PCG) within ∼100ms of viewing a word. This is consistent with Broca's area involvement in fast phonological access during visual word recognition. Here we used online transcranial magnetic stimulation (TMS) to investigate whether LIFGpo/PCG is necessary for (not just correlated with) visual word recognition by ∼100ms. Pulses were delivered to individually fMRI-defined LIFGpo/PCG in Dutch speakers 75-500ms after stimulus onset during reading and picture naming. Reading and picture naming reactions times were significantly slower following pulses at 225-300ms. Contrary to predictions, there was no disruption to reading for pulses before 225ms. This does not provide evidence in favour of a functional role for LIFGpo/PCG in reading before 225ms in this case, but does extend previous findings in picture stimuli to written Dutch words. Copyright © 2012 Elsevier Inc. All rights reserved.

40 CFR 80.1235 - What gasoline is subject to the benzene requirements of this subpart?

Code of Federal Regulations, 2014 CFR

2014-07-01

... blendstock or finished gasoline to produce gasoline. (2) Oxygenate added to PCG downstream of the refinery... downstream of the refinery or importer that produced or imported PCG adds oxygenate to such product, it shall... credit generation under this subpart. (3) Butane added to finished gasoline, RBOB, CBOB downstream of the...

(PCG) Protein Crystal Growth Gamma-Interferon

NASA Technical Reports Server (NTRS)

1989-01-01

(PCG) Protein Crystal Growth Gamma-Interferon. Stimulates the body's immune system and is used clinically in the treatment of cancer. Potential as an anti-tumor agent against solid tumors as well as leukemia's and lymphomas. It has additional utility as an anti-ineffective agent, including antiviral, anti-bacterial, and anti-parasitic activities. Principal Investigator on STS-26 was Charles Bugg.

(PCG) Protein Crystal Growth Canavalin

NASA Technical Reports Server (NTRS)

1989-01-01

(PCG) Protein Crystal Growth Canavalin. The major storage protein of leguminous plants and a major source of dietary protein for humans and domestic animals. It is studied in efforts to enhance nutritional value of proteins through protein engineerings. It is isolated from Jack Bean because of it's potential as a nutritional substance. Principal Investigator on STS-26 was Alex McPherson.

Survey of familial glaucoma shows a high incidence of cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in non-consanguineous congenital forms in a Spanish population

PubMed Central

Millá, Elena; Mañé, Begoña; Duch, Susana; Hernan, Imma; Borràs, Emma; Planas, Ester; Dias, Miguel de Sousa; Carballo, Miguel

2013-01-01

Purpose To identify myocilin (MYOC) and cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in a Spanish population with different clinical forms of familial glaucoma or ocular hypertension (OHT). Methods Index patients from 226 families participated in this study. Patients were diagnosed with familial glaucoma or OHT by complete ophthalmologic examination. Screening for MYOC mutations was performed in 207 index patients: 96 with adult-onset primary open-angle glaucoma (POAG), 21 with primary congenital glaucoma (PCG), 18 with juvenile-onset open-angle glaucoma (JOAG), five with Axenfeld-Rieger syndrome (ARS), and 67 with other types of glaucoma. One hundred two of the families (including all those in whom a MYOC mutation was detected) were also screened for CYP1B1 mutations: 45 POAG, 25 PCG, 21 JOAG, four ARS, and seven others. Results We examined 292 individuals (patients and relatives) with a positive family history of glaucoma or OHT. We identified two novel MYOC variants, p.Lys39Arg and p.Glu218Lys, in two families with POAG, and six previously reported MYOC mutations in seven families with POAG (four), JOAG (one), PCG (one), and normotensive glaucoma (one). CYP1B1 mutations were found in 16 index patients with PCG (nine), POAG (three), JOAG (two), and ARS (two). Conclusions The high percentage (9/25=36%) of mutations in CYP1B1 found in non-consanguineous patients with congenital glaucoma mandates genetic testing. However, the percentage of mutations (9/207=4.4%) in MYOC associated with glaucoma is relatively low in our population. The variable phenotype expression of glaucoma, even in families, cannot be explained with a digenic mechanism between MYOC and CYP1B1. PMID:23922489

Polycomb group protein bodybuilding: working out the routines.

PubMed

Sievers, Cem; Paro, Renato

2013-09-30

Polycomb group (PcG) proteins regulate gene expression by modifying chemical and structural properties of chromatin. Isono et al. (2013) now report in Developmental Cell a polymerization-dependent mechanism used by PcG proteins to form higher-order chromatin structures, referred to as Polycomb bodies, and demonstrate its necessity for gene silencing. Copyright © 2013 Elsevier Inc. All rights reserved.

Pho dynamically interacts with Spt5 to facilitate transcriptional switches at the hsp70 locus.

PubMed

Pereira, Allwyn; Paro, Renato

2017-12-06

Numerous target genes of the Polycomb group (PcG) are transiently activated by a stimulus and subsequently repressed. However, mechanisms by which PcG proteins regulate such target genes remain elusive. We employed the heat shock-responsive hsp70 locus in Drosophila to study the chromatin dynamics of PRC1 and its interplay with known regulators of the locus before, during and after heat shock. We detected mutually exclusive binding patterns for HSF and PRC1 at the hsp70 locus. We found that Pleiohomeotic (Pho), a DNA-binding PcG member, dynamically interacts with Spt5, an elongation factor. The dynamic interaction switch between Pho and Spt5 is triggered by the recruitment of HSF to chromatin. Mutation in the protein-protein interaction domain (REPO domain) of Pho interferes with the dynamics of its interaction with Spt5. The transcriptional kinetics of the heat shock response is negatively affected by a mutation in the REPO domain of Pho. We propose that a dynamic interaction switch between PcG proteins and an elongation factor enables stress-inducible genes to efficiently switch between ON/OFF states in the presence/absence of the activating stimulus.

Imaging of heart acoustic based on the sub-space methods using a microphone array.

PubMed

Moghaddasi, Hanie; Almasganj, Farshad; Zoroufian, Arezoo

2017-07-01

Heart disease is one of the leading causes of death around the world. Phonocardiogram (PCG) is an important bio-signal which represents the acoustic activity of heart, typically without any spatiotemporal information of the involved acoustic sources. The aim of this study is to analyze the PCG by employing a microphone array by which the heart internal sound sources could be localized, too. In this paper, it is intended to propose a modality by which the locations of the active sources in the heart could also be investigated, during a cardiac cycle. In this way, a microphone array with six microphones is employed as the recording set up to be put on the human chest. In the following, the Group Delay MUSIC algorithm which is a sub-space based localization method is used to estimate the location of the heart sources in different phases of the PCG. We achieved to 0.14cm mean error for the sources of first heart sound (S 1 ) simulator and 0.21cm mean error for the sources of second heart sound (S 2 ) simulator with Group Delay MUSIC algorithm. The acoustical diagrams created for human subjects show distinct patterns in various phases of the cardiac cycles such as the first and second heart sounds. Moreover, the evaluated source locations for the heart valves are matched with the ones that are obtained via the 4-dimensional (4D) echocardiography applied, to a real human case. Imaging of heart acoustic map presents a new outlook to indicate the acoustic properties of cardiovascular system and disorders of valves and thereby, in the future, could be used as a new diagnostic tool. Copyright © 2017. Published by Elsevier B.V.

Short germ insects utilize both the ancestral and derived mode of Polycomb group-mediated epigenetic silencing of Hox genes

PubMed Central

Matsuoka, Yuji; Bando, Tetsuya; Watanabe, Takahito; Ishimaru, Yoshiyasu; Noji, Sumihare; Popadić, Aleksandar; Mito, Taro

2015-01-01

In insect species that undergo long germ segmentation, such as Drosophila, all segments are specified simultaneously at the early blastoderm stage. As embryogenesis progresses, the expression boundaries of Hox genes are established by repression of gap genes, which is subsequently replaced by Polycomb group (PcG) silencing. At present, however, it is not known whether patterning occurs this way in a more ancestral (short germ) mode of embryogenesis, where segments are added gradually during posterior elongation. In this study, two members of the PcG family, Enhancer of zeste (E(z)) and Suppressor of zeste 12 (Su(z)12), were analyzed in the short germ cricket, Gryllus bimaculatus. Results suggest that although stepwise negative regulation by gap and PcG genes is present in anterior members of the Hox cluster, it does not account for regulation of two posterior Hox genes, abdominal-A (abd-A) and Abdominal-B (Abd-B). Instead, abd-A and Abd-B are predominantly regulated by PcG genes, which is the mode present in vertebrates. These findings suggest that an intriguing transition of the PcG-mediated silencing of Hox genes may have occurred during animal evolution. The ancestral bilaterian state may have resembled the current vertebrate mode of regulation, where PcG-mediated silencing of Hox genes occurs before their expression is initiated and is responsible for the establishment of individual expression domains. Then, during insect evolution, the repression by transcription factors may have been acquired in anterior Hox genes of short germ insects, while PcG silencing was maintained in posterior Hox genes. PMID:25948756

CYP1B1 copy number variation is not a major contributor to primary congenital glaucoma.

PubMed

Souzeau, Emmanuelle; Hayes, Melanie; Ruddle, Jonathan B; Elder, James E; Staffieri, Sandra E; Kearns, Lisa S; Mackey, David A; Zhou, Tiger; Ridge, Bronwyn; Burdon, Kathryn P; Dubowsky, Andrew; Craig, Jamie E

2015-01-01

To evaluate the prevalence and the diagnostic utility of testing for CYP1B1 copy number variation (CNV) in primary congenital glaucoma (PCG) cases unexplained by CYP1B1 point mutations in The Australian and New Zealand Registry of Advanced Glaucoma. In total, 50 PCG cases either heterozygous for disease-causing variants or with no CYP1B1 sequence variants were included in the study. CYP1B1 CNV was analyzed by Multiplex Ligation-dependent Probe Amplification (MLPA). No deletions or duplications were found in any of the cases. This is the first study to report on CYP1B1 CNV in PCG cases. Our findings show that this mechanism is not a major contributor to the phenotype and is of limited diagnostic utility.

Solar-insolation-induced changes in the coma morphology of comet 67P/Churyumov-Gerasimenko. Optical monitoring with the Nordic Optical Telescope

NASA Astrophysics Data System (ADS)

Zaprudin, B.; Lehto, H. J.; Nilsson, K.; Somero, A.; Pursimo, T.; Snodgrass, C.; Schulz, R.

2017-07-01

Context. 67P/Churyumov-Gerasimenko (67P/C-G) is a short-period Jupiter family comet with an orbital period of 6.55 yr. Being the target comet of ESA's Rosetta mission, 67P/C-G has become one of the most intensively studied minor bodies of the solar system. The Rosetta Orbiter and the Philae Lander have brought us unique information about the structure and activity of the comet nucleus, as well as its activity along the orbit, composition of gas, and dust particles emitted into the coma. However, as Rosetta stayed in very close proximity to the cometary nucleus (less than 500 km with a few short excursions reaching up to 1500 km), it could not see the global picture of a coma at the scales reachable by telescopic observations (103 - 105 km). Aims: In this work we aim to connect in-situ observations made by Rosetta with the morphological evolution of the coma structures monitored by the ground-based observations. In particular, we concentrate on causal relationships between the coma morphology and evolution observed with the Nordic Optical Telescope (NOT) in the Canary Islands, and the seasonal changes of the insolation and the activity of the comet observed by the Rosetta instruments. Methods: Comet 67P/C-G was monitored with the NOT in imaging mode in two colors. Imaging optical observations were performed roughly on a weekly basis, which provides good coverage of short- and long-term variability. With the three dimensional modeling of the coma produced by active regions on the southern hemisphere, we aim to qualify the observed morphology by connecting it to the activity observed by Rosetta. Results: During our monitoring program, we detected major changes in the coma morphology of comet 67P/C-G. These were long-term and long-lasting changes. They do not represent any sudden outburst or short transient event, but are connected to seasonal changes of the surface insolation and the emergence of new active regions on the irregular shaped comet nucleus. We have also found significant deviations in morphological changes from the prediction models based on previous apparitions of 67P/C-G, like the time delay of the morphology changes and the reduced activity in the northern hemisphere. According to our modeling of coma structures and geometry of observations, the changes are clearly connected with the activity in the southern hemisphere observed by the Rosetta spacecraft.

Preliminary results seen with Rosetta/ROSINA: early cometary activity of 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Gasc, Sebastien; Altwegg, Kathrin; Jäckel, Annette; Rubin, Martin; Tzou, Chia-Yu; Wurz, Peter; Fiethe, Björn; Korth, Axel; Rème, Henri

2014-11-01

On 1 August 2014, the ROSETTA spacecraft approached the comet 67P/Churyumov-Gerasimenko (67P/CG) close enough to start its detailed characterisation. In this phase, the distance between Rosetta and 67P/CG is below 1’000 km, at a heliocentric distance of less than 3.6 AU. The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) [1] measures the composition of 67P/CG’s atmosphere and ionosphere, and additionally derives the bulk velocity of gas. ROSINA consists of the COmetary Pressure Sensor (COPS) and two mass spectrometers for the analysis of neutral gas and cometary ions in the coma of the comet: the Double Focusing Mass Spectrometer (DFMS) and the Reflectron Time Of Flight mass spectrometer (RTOF). Since beginning of August, the ROSINA sensors are continuously monitoring the density and chemical composition of the coma of 67P/CG. The goal of this work is not only to determine the abundance of major species like CO2, CO, and H2O, but also to analyse the development of the composition as a function of the heliocentric distance. We will present the first mass spectra of RTOF as well as the total density and the molecular composition measurements obtained at 67P/CG.

Goal Reconstruction: How Teton Blends Situated Action and Planned Action

DTIC Science & Technology

1989-11-03

DTIC FILE COPY CV), Goal reconstruction: How Teton blends N situated action and planned action N Tec~jcal Report PCG- 16 Kurt VanLehn I William Bali...situated action and planned action Technical Report PCG- 16 Kurt VanLehn William Bail Departments of Psychology and Computer Science Carnegie-Mellon...Research, under contract N00014-88-K-0086 and by the Information Sciences Division, Office of Naval Research, under contract N00014-K-0678

IODINE-131 IN POST-MORTEM HUMAN THYROIDS

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

Visalli, F.I.; Goldin, A.S.

1964-03-01

Fifty-seven thyroid samples were made available by three New England hospitals during the period May 14, 1962, through January 10, 1963. Up to the middle of September, /sup 131/I was detected in three out of 37 samples (range 47 to 51 pC/g). Positive values for /sup 131/I were found in 6 out of 15 post- mortem thyroids from September 15 through October 26 (range 41 to 58 pC/g). From November 4 through January 10, 1963, one positive value (29 pC/g) of /sup 131/I was noted among five samples collected. The highest individual thyroid burden noted represented about one-sixth of themore » RP0 of 1.5 rem/yr, and the average of 20 samples after September 15, 1962, represented about one-eighth of the RPG of 0.5 rem/yr. (auth)« less

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

NASA Technical Reports Server (NTRS)

Herren, B.

1992-01-01

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Inter-Fullerene Electronic Coupling Controls the Efficiency of Photoinduced Charge Generation in Organic Bulk Heterojunctions

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

Larson, Bryon W.; Reid, Obadiah G.; Coffey, David C.

2016-09-26

Photoinduced charge generation (PCG) dynamics are notoriously difficult to correlate with specific molecular properties in device relevant polymer:fullerene organic photovoltaic blend films due to the highly complex nature of the solid state blend morphology. Here, this study uses six judiciously selected trifluoromethylfullerenes blended with the prototypical polymer poly(3-hexylthiophene) and measure the PCG dynamics in 50 fs-500 ns time scales with time-resolved microwave conductivity and femtosecond transient absorption spectroscopy. The isomeric purity and thorough chemical characterization of the fullerenes used in this study allow for a detailed correlation between molecular properties, driving force, local intermolecular electronic coupling and, ultimately, the efficiencymore » of PCG yield. The findings show that the molecular design of the fullerene not only determines inter-fullerene electronic coupling, but also influences the decay dynamics of free holes in the donor phase even when the polymer microstructure remains unchanged.« less

Angiopoietin-1 is required for Schlemm’s canal development in mice and humans

PubMed Central

Thomson, Benjamin R.; Tompson, Stuart W.; Kizhatil, Krishnakumar; Yanovitch, Tammy L.; Kalaydjieva, Luba; Azmanov, Dimitar N.; Finzi, Simone; Tanna, Christine E.; Mackey, David A.; Bradfield, Yasmin S.; Javadiyan, Shari; Wiggs, Janey L.; Pasutto, Francesca; John, Simon W.M.; Craig, Jamie E.; Jin, Jing; Young, Terri L.

2017-01-01

Primary congenital glaucoma (PCG) is a leading cause of blindness in children worldwide and is caused by developmental defects in 2 aqueous humor outflow structures, Schlemm’s canal (SC) and the trabecular meshwork. We previously identified loss-of-function mutations in the angiopoietin (ANGPT) receptor TEK in families with PCG and showed that ANGPT/TEK signaling is essential for SC development. Here, we describe roles for the major ANGPT ligands in the development of the aqueous outflow pathway. We determined that ANGPT1 is essential for SC development, and that Angpt1-knockout mice form a severely hypomorphic canal with elevated intraocular pressure. By contrast, ANGPT2 was dispensable, although mice deficient in both Angpt1 and Angpt2 completely lacked SC, indicating that ANGPT2 compensates for the loss of ANGPT1. In addition, we identified 3 human subjects with rare ANGPT1 variants within an international cohort of 284 PCG patients. Loss of function in 2 of the 3 patient alleles was observed by functional analysis of ANGPT1 variants in a combined in silico, in vitro, and in vivo approach, supporting a causative role for ANGPT1 in disease. By linking ANGPT1 with PCG, these results highlight the importance of ANGPT/TEK signaling in glaucoma pathogenesis and identify a candidate target for therapeutic development. PMID:29106382

Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners

PubMed Central

Strübbe, Gero; Popp, Christian; Schmidt, Alexander; Pauli, Andrea; Ringrose, Leonie; Beisel, Christian; Paro, Renato

2011-01-01

The maintenance of specific gene expression patterns during cellular proliferation is crucial for the identity of every cell type and the development of tissues in multicellular organisms. Such a cellular memory function is conveyed by the complex interplay of the Polycomb and Trithorax groups of proteins (PcG/TrxG). These proteins exert their function at the level of chromatin by establishing and maintaining repressed (PcG) and active (TrxG) chromatin domains. Past studies indicated that a core PcG protein complex is potentially associated with cell type or even cell stage-specific sets of accessory proteins. In order to better understand the dynamic aspects underlying PcG composition and function we have established an inducible version of the biotinylation tagging approach to purify Polycomb and associated factors from Drosophila embryos. This system enabled fast and efficient isolation of Polycomb containing complexes under near physiological conditions, thereby preserving substoichiometric interactions. Novel interacting proteins were identified by highly sensitive mass spectrometric analysis. We found many TrxG related proteins, suggesting a previously unrecognized extent of molecular interaction of the two counteracting chromatin regulatory protein groups. Furthermore, our analysis revealed an association of PcG protein complexes with the cohesin complex and showed that Polycomb-dependent silencing of a transgenic reporter depends on cohesin function. PMID:21415365

Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements.

PubMed

Kahn, Tatyana G; Dorafshan, Eshagh; Schultheis, Dorothea; Zare, Aman; Stenberg, Per; Reim, Ingolf; Pirrotta, Vincenzo; Schwartz, Yuri B

2016-12-01

Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and was proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). Here, we present a strict test of this hypothesis using the Drosophila model. We discover that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). We find that PRC1 can bind PREs in the absence of PRC2 but at many PREs PRC2 requires PRC1 to be targeted. We show that one role of H3K27me3 is to allow PcG complexes anchored at PREs to interact with surrounding chromatin. In contrast, the bulk of H2AK118ub is unrelated to PcG repression. These findings radically change our view of how PcG repression is targeted and suggest that PRC1 and PRC2 can communicate independently of histone modifications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Primary Congenital Glaucoma Versus Glaucoma Following Congenital Cataract Surgery: Comparative Clinical Features and Long-term Outcomes.

PubMed

Neustein, Rebecca F; Bruce, Beau B; Beck, Allen D

2016-10-01

To report and compare visual and glaucoma outcomes in primary congenital glaucoma (PCG) vs glaucoma following congenital cataract surgery (GFCS). Retrospective, observational, comparative case series. Setting: Emory Eye Center, Atlanta, Georgia. Pediatric glaucoma patients (age 0-18 years) treated at Emory by 1 clinician with ≥2-year follow-up. Glaucoma was defined according to the 9th Consensus Report of the World Glaucoma Association. Snellen-equivalent logMAR visual acuity (VA) and glaucoma control (IOP ≤21, no devastating complications, no recommendation for further glaucoma surgery). Asymptotic Wilcoxon-Mann-Whitney rank sum tests were employed to compare glaucoma subgroups. Included were 72 PCG and 56 GFCS cases, with mean follow-up time of 7.4 ± 4.1 and 8.0 ± 3.8 years, respectively. At last follow-up, PCG showed better median VA than GFCS in worse-seeing eyes (20/60 [interquartile range (IQR) 20/30-20/200] vs 20/400 [IQR 20/70-hand motion], respectively, P < .0001) and in better-seeing eyes of bilaterally-affected children (20/30 [IQR 20/20-20/60] vs 20/70 [IQR 20/35-20/100], respectively, P = .024).The following variables characterized the PCG and GFCS groups' glaucoma status, respectively: mean age at diagnosis (years), 0.70 ± 1.3 vs 3.3 ± 3.5 (P < .0001); median IOP (mm Hg), 15.50 [IQR 12.1-19.4] vs 17.50 [IQR 14.9-22], P = .037; median number of glaucoma medications at last follow-up, 1.49 [IQR 0-2] vs 2.54 [IQR 1-4], P < .0001; median number of glaucoma surgeries, 1.0 [IQR 1-2] vs 1.25 [IQR 0.5-2.0], P = .09. Children with PCG (vs those with GFCS) presented earlier, had better vision, required fewer medications to control disease, and had lower IOP at last follow-up. Copyright © 2016 Elsevier Inc. All rights reserved.

Brain network dynamics in the human articulatory loop.

PubMed

Nishida, Masaaki; Korzeniewska, Anna; Crone, Nathan E; Toyoda, Goichiro; Nakai, Yasuo; Ofen, Noa; Brown, Erik C; Asano, Eishi

2017-08-01

The articulatory loop is a fundamental component of language function, involved in the short-term buffer of auditory information followed by its vocal reproduction. We characterized the network dynamics of the human articulatory loop, using invasive recording and stimulation. We measured high-gamma activity 70-110 Hz recorded intracranially when patients with epilepsy either only listened to, or listened to and then reproduced two successive tones by humming. We also conducted network analyses, and analyzed behavioral responses to cortical stimulation. Presentation of the initial tone elicited high-gamma augmentation bilaterally in the superior-temporal gyrus (STG) within 40ms, and in the precentral and inferior-frontal gyri (PCG and IFG) within 160ms after sound onset. During presentation of the second tone, high-gamma augmentation was reduced in STG but enhanced in IFG. The task requiring tone reproduction further enhanced high-gamma augmentation in PCG during and after sound presentation. Event-related causality (ERC) analysis revealed dominant flows within STG immediately after sound onset, followed by reciprocal interactions involving PCG and IFG. Measurement of cortico-cortical evoked-potentials (CCEPs) confirmed connectivity between distant high-gamma sites in the articulatory loop. High-frequency stimulation of precentral high-gamma sites in either hemisphere induced speech arrest, inability to control vocalization, or forced vocalization. Vocalization of tones was accompanied by high-gamma augmentation over larger extents of PCG. Bilateral PCG rapidly and directly receives feed-forward signals from STG, and may promptly initiate motor planning including sub-vocal rehearsal for short-term buffering of auditory stimuli. Enhanced high-gamma augmentation in IFG during presentation of the second tone may reflect high-order processing of the tone sequence. The articulatory loop employs sustained reciprocal propagation of neural activity across a network of cortical sites with strong neurophysiological connectivity. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Trichloroethylene-induced alterations in DNA methylation were enriched in polycomb protein binding sites in effector/memory CD4+ T cells

PubMed Central

Gilbert, Kathleen M.; Blossom, Sarah J.; Reisfeld, Brad; Erickson, Stephen W.; Vyas, Kanan; Maher, Mary; Broadfoot, Brannon; West, Kirk; Bai, Shasha; Cooney, Craig A.; Bhattacharyya, Sudeepa

2017-01-01

Abstract Exposure to industrial solvent and water pollutant trichloroethylene (TCE) can promote autoimmunity, and expand effector/memory (CD62L) CD4+ T cells. In order to better understand etiology reduced representation bisulfite sequencing was used to study how a 40-week exposure to TCE in drinking water altered methylation of ∼337 770 CpG sites across the entire genome of effector/memory CD4+ T cells from MRL+/+ mice. Regardless of TCE exposure, 62% of CpG sites in autosomal chromosomes were hypomethylated (0–15% methylation), and 25% were hypermethylated (85–100% methylation). In contrast, only 6% of the CpGs on the X chromosome were hypomethylated, and 51% had mid-range methylation levels. In terms of TCE impact, TCE altered (≥ 10%) the methylation of 233 CpG sites in effector/memory CD4+ T cells. Approximately 31.7% of these differentially methylated sites occurred in regions known to bind one or more Polycomb group (PcG) proteins, namely Ezh2, Suz12, Mtf2 or Jarid2. In comparison, only 23.3% of CpG sites not differentially methylated by TCE were found in PcG protein binding regions. Transcriptomics revealed that TCE altered the expression of ∼560 genes in the same effector/memory CD4+ T cells. At least 80% of the immune genes altered by TCE had binding sites for PcG proteins flanking their transcription start site, or were regulated by other transcription factors that were in turn ordered by PcG proteins at their own transcription start site. Thus, PcG proteins, and the differential methylation of their binding sites, may represent a new mechanism by which TCE could alter the function of effector/memory CD4+ T cells. PMID:29129997

Dopamine Signaling Leads to Loss of Polycomb Repression and Aberrant Gene Activation in Experimental Parkinsonism

PubMed Central

Lerdrup, Mads; Gomes, Ana-Luisa; Kryh, Hanna; Spigolon, Giada; Caboche, Jocelyne; Fisone, Gilberto; Hansen, Klaus

2014-01-01

Polycomb group (PcG) proteins bind to and repress genes in embryonic stem cells through lineage commitment to the terminal differentiated state. PcG repressed genes are commonly characterized by the presence of the epigenetic histone mark H3K27me3, catalyzed by the Polycomb repressive complex 2. Here, we present in vivo evidence for a previously unrecognized plasticity of PcG-repressed genes in terminally differentiated brain neurons of parkisonian mice. We show that acute administration of the dopamine precursor, L-DOPA, induces a remarkable increase in H3K27me3S28 phosphorylation. The induction of the H3K27me3S28p histone mark specifically occurs in medium spiny neurons expressing dopamine D1 receptors and is dependent on Msk1 kinase activity and DARPP-32-mediated inhibition of protein phosphatase-1. Chromatin immunoprecipitation (ChIP) experiments showed that increased H3K27me3S28p was accompanied by reduced PcG binding to regulatory regions of genes. An analysis of the genome wide distribution of L-DOPA-induced H3K27me3S28 phosphorylation by ChIP sequencing (ChIP-seq) in combination with expression analysis by RNA-sequencing (RNA-seq) showed that the induction of H3K27me3S28p correlated with increased expression of a subset of PcG repressed genes. We found that induction of H3K27me3S28p persisted during chronic L-DOPA administration to parkisonian mice and correlated with aberrant gene expression. We propose that dopaminergic transmission can activate PcG repressed genes in the adult brain and thereby contribute to long-term maladaptive responses including the motor complications, or dyskinesia, caused by prolonged administration of L-DOPA in Parkinson's disease. PMID:25254549

Protein Crystal Growth (PCG) experiment aboard mission STS-66

NASA Technical Reports Server (NTRS)

2000-01-01

On the Space Shuttle Orbiter Atlantis' middeck, Astronaut Joseph R. Tarner, mission specialist, works at an area amidst several lockers which support the Protein Crystal Growth (PCG) experiment during the STS-66 mission. This particular section is called the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES). Together with the Vapor Diffusion Apparatus (VDA), housed in Single Locker Thermal Enclosure (SLTES), the COS/TES represents the continuing research into the structure of proteins and other macromolecules such as viruses.

Astronaut Joseph R. Tanner works with PCG experiment on middeck

NASA Image and Video Library

1994-11-14

On the Space Shuttle Atlantis' mid-deck, astronaut Joseph R. Tanner, mission specialist, works at area amidst several lockers onboard the Shuttle which support the Protein Crystal Growth (PCG) experiment. This particular section is called the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES). Together with the Vapor Diffusion Apparatus (VDA), housed in a Single Locker Thermal Enclosure (SLTES) which is out of frame, the Cos/TES represents the continuing research into the structures of proteins and other macromolecules such as viruses.

Versioned distributed arrays for resilience in scientific applications: Global view resilience

DOE PAGES

Chien, A.; Balaji, P.; Beckman, P.; ...

2015-06-01

Exascale studies project reliability challenges for future high-performance computing (HPC) systems. We propose the Global View Resilience (GVR) system, a library that enables applications to add resilience in a portable, application-controlled fashion using versioned distributed arrays. We describe GVR’s interfaces to distributed arrays, versioning, and cross-layer error recovery. Using several large applications (OpenMC, the preconditioned conjugate gradient solver PCG, ddcMD, and Chombo), we evaluate the programmer effort to add resilience. The required changes are small (<2% LOC), localized, and machine-independent, requiring no software architecture changes. We also measure the overhead of adding GVR versioning and show that generally overheads <2%more » are achieved. We conclude that GVR’s interfaces and implementation are flexible and portable and create a gentle-slope path to tolerate growing error rates in future systems.« less

[Three-dimensional genome organization: a lesson from the Polycomb-Group proteins].

PubMed

Bantignies, Frédéric

2013-01-01

As more and more genomes are being explored and annotated, important features of three-dimensional (3D) genome organization are just being uncovered. In the light of what we know about Polycomb group (PcG) proteins, we will present the latest findings on this topic. The PcG proteins are well-conserved chromatin factors that repress transcription of numerous target genes. They bind the genome at specific sites, forming chromatin domains of associated histone modifications as well as higher-order chromatin structures. These 3D chromatin structures involve the interactions between PcG-bound regulatory regions at short- and long-range distances, and may significantly contribute to PcG function. Recent high throughput "Chromosome Conformation Capture" (3C) analyses have revealed many other higher order structures along the chromatin fiber, partitioning the genomes into well demarcated topological domains. This revealed an unprecedented link between linear epigenetic domains and chromosome architecture, which might be intimately connected to genome function. © Société de Biologie, 2013.

The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia.

PubMed

Di Costanzo, Antonella; Del Gaudio, Nunzio; Conte, Lidio; Dell'Aversana, Carmela; Vermeulen, Michiel; de Thé, Hugues; Migliaccio, Antimo; Nebbioso, Angela; Altucci, Lucia

2018-05-01

Polycomb group (PcG) proteins regulate transcription, playing a key role in stemness and differentiation. Deregulation of PcG members is known to be involved in cancer pathogenesis. Emerging evidence suggests that CBX2, a member of the PcG protein family, is overexpressed in several human tumors, correlating with lower overall survival. Unraveling the mechanisms regulating CBX2 expression may thus provide a promising new target for anticancer strategies. Here we show that the HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia. We identify CBX4 and RNF4 as the E3 SUMO and E3 ubiquitin ligase, respectively, and describe the specific molecular mechanism regulating CBX2 protein stability. Finally, we show that CBX2-depleted leukemic cells display impaired proliferation, underscoring its critical role in regulating leukemia cell tumorogenicity. Our results show that SAHA affects CBX2 stability, revealing a potential SAHA-mediated anti-leukemic activity though SUMO2/3 pathway.

Diamagnetic region(s): structure of the unmagnetized plasma around Comet 67P/CG

NASA Astrophysics Data System (ADS)

Henri, P.; Vallières, X.; Hajra, R.; Goetz, C.; Richter, I.; Glassmeier, K.-H.; Galand, M.; Rubin, M.; Eriksson, A. I.; Nemeth, Z.; Vigren, E.; Beth, A.; Burch, J. L.; Carr, C.; Nilsson, H.; Tsurutani, B.; Wattieaux, G.

2017-07-01

The ESA's comet chaser Rosetta has monitored the evolution of the ionized atmosphere of comet 67P/Churyumov-Gerasimenko (67P/CG) and its interaction with the solar wind, during more than 2 yr. Around perihelion, while the cometary outgassing rate was highest, Rosetta crossed hundreds of unmagnetized regions, but did not seem to have crossed a large-scale diamagnetic cavity as anticipated. Using in situ Rosetta observations, we characterize the structure of the unmagnetized plasma found around comet 67P/CG. Plasma density measurements from RPC-MIP are analysed in the unmagnetized regions identified with RPC-MAG. The plasma observations are discussed in the context of the cometary escaping neutral atmosphere, observed by ROSINA/COPS. The plasma density in the different diamagnetic regions crossed by Rosetta ranges from ˜100 to ˜1500 cm-3. They exhibit a remarkably systematic behaviour that essentially depends on the comet activity and the cometary ionosphere expansion. An effective total ionization frequency is obtained from in situ observations during the high outgassing activity phase of comet 67P/CG. Although several diamagnetic regions have been crossed over a large range of distances to the comet nucleus (from 50 to 400 km) and to the Sun (1.25-2.4 au), in situ observations give strong evidence for a single diamagnetic region, located close to the electron exobase. Moreover, the observations are consistent with an unstable contact surface that can locally extend up to about 10 times the electron exobase.

Efficient, high-power, and radially polarized fiber laser

PubMed Central

Lin, Di; Xia, Kegui; Li, Jianlang; Li, Ruxin; Ueda, Ken-ichi; Li, Guoqiang; Li, Xiaojun

2017-01-01

We demonstrate an ytterbium-doped fiber laser that emits high-power radially polarized light efficiently. In this study, a photonic crystal grating (PCG) was used as a polarization-selective output coupler, and the power of the radially polarized laser reached 2.42 W with a slope efficiency of 45.9% and a polarization purity of 96%. The results reveal that the inclusion of the PCG mirror into the fiber laser are particularly promising for generating high-power radially polarized light efficiently in view of its many important applications. PMID:20596223

Distributed Memory Parallel Computing with SEAWAT

NASA Astrophysics Data System (ADS)

Verkaik, J.; Huizer, S.; van Engelen, J.; Oude Essink, G.; Ram, R.; Vuik, K.

2017-12-01

Fresh groundwater reserves in coastal aquifers are threatened by sea-level rise, extreme weather conditions, increasing urbanization and associated groundwater extraction rates. To counteract these threats, accurate high-resolution numerical models are required to optimize the management of these precious reserves. The major model drawbacks are long run times and large memory requirements, limiting the predictive power of these models. Distributed memory parallel computing is an efficient technique for reducing run times and memory requirements, where the problem is divided over multiple processor cores. A new Parallel Krylov Solver (PKS) for SEAWAT is presented. PKS has recently been applied to MODFLOW and includes Conjugate Gradient (CG) and Biconjugate Gradient Stabilized (BiCGSTAB) linear accelerators. Both accelerators are preconditioned by an overlapping additive Schwarz preconditioner in a way that: a) subdomains are partitioned using Recursive Coordinate Bisection (RCB) load balancing, b) each subdomain uses local memory only and communicates with other subdomains by Message Passing Interface (MPI) within the linear accelerator, c) it is fully integrated in SEAWAT. Within SEAWAT, the PKS-CG solver replaces the Preconditioned Conjugate Gradient (PCG) solver for solving the variable-density groundwater flow equation and the PKS-BiCGSTAB solver replaces the Generalized Conjugate Gradient (GCG) solver for solving the advection-diffusion equation. PKS supports the third-order Total Variation Diminishing (TVD) scheme for computing advection. Benchmarks were performed on the Dutch national supercomputer (https://userinfo.surfsara.nl/systems/cartesius) using up to 128 cores, for a synthetic 3D Henry model (100 million cells) and the real-life Sand Engine model ( 10 million cells). The Sand Engine model was used to investigate the potential effect of the long-term morphological evolution of a large sand replenishment and climate change on fresh groundwater resources. Speed-ups up to 40 were obtained with the new PKS solver.

Complex wet-environments in electronic-structure calculations

NASA Astrophysics Data System (ADS)

Fisicaro, Giuseppe; Genovese, Luigi; Andreussi, Oliviero; Marzari, Nicola; Goedecker, Stefan

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of an applied electrochemical potentials, including complex electrostatic screening coming from the solvent. In the present work we present a solver to handle both the Generalized Poisson and the Poisson-Boltzmann equation. A preconditioned conjugate gradient (PCG) method has been implemented for the Generalized Poisson and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations. On the other hand, a self-consistent procedure enables us to solve the Poisson-Boltzmann problem. The algorithms take advantage of a preconditioning procedure based on the BigDFT Poisson solver for the standard Poisson equation. They exhibit very high accuracy and parallel efficiency, and allow different boundary conditions, including surfaces. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and it will be released as a independent program, suitable for integration in other codes. We present test calculations for large proteins to demonstrate efficiency and performances. This work was done within the PASC and NCCR MARVEL projects. Computer resources were provided by the Swiss National Supercomputing Centre (CSCS) under Project ID s499. LG acknowledges also support from the EXTMOS EU project.

Structure and dynamics of the umagnetized plasma around comet 67P/CG

NASA Astrophysics Data System (ADS)

Henri, P.; Vallières, X.; Gilet, N.; Hajra, R.; Moré, J.; Goetz, C.; Richter, I.; Glassmeier, K. H.; Galand, M. F.; Heritier, K. L.; Eriksson, A. I.; Nemeth, Z.; Tsurutani, B.; Rubin, M.; Altwegg, K.

2016-12-01

At distances close enough to the Sun, when comets are characterised by a significant outgassing, the cometary neutral density may become large enough for both the cometary plasma and the cometary gas to be coupled, through ion-neutral and electron-neutral collisions. This coupling enables the formation of an unmagnetised expanding cometary ionosphere around the comet nucleus, also called diamagnetic cavity, within which the solar wind magnetic field cannot penetrate. The instruments of the Rosetta Plasma Consortium (RPC), onboard the Rosetta Orbiter, enable us to better constrain the structure, dynamics and stability of the plasma around comet 67P/CG. Recently, magnetic field measurements (RPC-MAG) have shown the existence of such a diamagnetic region around comet 67P/CG [Götz et al., 2016]. Contrary to a single, large scale, diamagnetic cavity such as what was observed around comet Halley, Rosetta have crossed several diamagnetic structures along its trajectory around comet 67P/CG. Using electron density measurements from the Mutual Impedance Probe (RPC-MIP) during the different diamagnetic cavity crossings, identified by the flux gate magnetometer (RPC-MAG), we map the unmagnetised plasma density around comet 67P/CG. Our aims is to better constrain the structure, dynamics and stability of this inner cometary plasma layer characterised by cold electrons (as witnessed by the Langmuir Probes RPC-LAP). The ionisation ratio in these unmagnetised region(s) is computed from the measured electron (RPC-MIP) and neutral gas (ROSINA/COPS) densities. In order to assess the importance of solar EUV radiation as a source of ionisation, the observed electron density will be compared to a the density expected from an ionospheric model taking into account solar radiation absorption. The crossings of diamagnetic region(s) by Rosetta show that the unmagnetised cometary plasma is particularly homogeneous, compared to the highly dynamical magnetised plasma observed in adjacent magnetised regions. Moreover, during the crossings of multiple, successive diamagnetic region(s) over time scales of tens of minutes or hours, the plasma density is almost identical in the different unmagnetised regions, suggesting that these unmagnetised regions may be a single diamagnetic structure crossed several times by Rosetta.

O-GlcNAc cycling: Emerging Roles in Development and Epigenetics

PubMed Central

Love, Dona C.; Krause, Michael W.; Hanover, John A.

2010-01-01

The nutrient-sensing hexosamine signaling pathway modulates the levels of O-linked N-acetylglucosamine (O-GlcNAc) on key targets impacting cellular signaling, protein turnover and gene expression. O-GlcNAc cycling may be deregulated in neurodegenerative disease, cancer, and diabetes. Studies in model organisms demonstrate that the O-GlcNAc transferase (OGT/Sxc) is essential for Polycomb group (PcG) repression of the homeotic genes, clusters of genes responsible for the adult body plan. Surprisingly, from flies to man, the O-GlcNAcase (OGA, MGEA5) gene is embedded within the NK cluster, the most evolutionarily ancient of three homeobox gene clusters regulated by PcG repression. PcG repression also plays a key role in maintaining stem cell identity, recruiting the DNA methyltransferase machinery for imprinting, and in X-chromosome inactivation. Intriguingly, the Ogt gene resides near the Xist locus in vertebrates and is subject to regulation by PcG-dependent X-inactivation. OGT is also an enzymatic component of the human dosage compensation complex. These ‘evo-devo’ relationships linking O-GlcNAc cycling to higher order chromatin structure provide insights into how nutrient availability may influence the epigenetic regulation of gene expression. O-GlcNAc cycling at promoters and PcG repression represent concrete mechanisms by which nutritional information may be transmitted across generations in the intra-uterine environment. Thus, the nutrient-sensing hexosamine signaling pathway may be a key contributor to the metabolic deregulation resulting from prenatal exposure to famine, or the ‘vicious cycle’ observed in children of mothers with type-2 diabetes and metabolic disease. PMID:20488252

SAMS Acceleration Measurements on Mir from June to November 1995

NASA Technical Reports Server (NTRS)

DeLombard, Richard; Hrovat, Ken; Moskowitz, Milton; McPherson, Kevin

1996-01-01

The NASA Microgravity Science and Applications Division (MSAD) sponsors science experiments on a variety of microgravity carriers, including sounding rockets, drop towers, parabolic aircraft, and Orbiter missions. The MSAD sponsors the Space Acceleration Measurement System (SAMS) to support microgravity science experiments with acceleration measurements to characterize the microgravity environment to which the experiments were exposed. The Principal Investigator Microgravity Services project at the NASA Lewis Research Center supports principal investigators of microgravity experiments as they evaluate the effects of varying acceleration levels on their experiments. In 1993, a cooperative effort was started between the United States and Russia involving science utilization of the Russian Mir space station by scientists from the United States and Russia. MSAD is currently sponsoring science experiments participating in the Shuttle-Mir Science Program in cooperation with the Russians on the Mir space station. Included in the complement of MSAD experiments and equipment is a SAMS unit In a manner similar to Orbiter mission support, the SAMS unit supports science experiments from the U.S. and Russia by measuring the microgravity environment during experiment operations. The initial SAMS supported experiment was a Protein Crystal Growth (PCG) experiment from June to November 1995. SAMS data were obtained during the PCG operations on Mir in accordance with the PCG Principal Investigator's requirements. This report presents an overview of the SAMS data recorded to support this PCG experiment. The report contains plots of the SAMS 100 Hz sensor head data as an overview of the microgravity environment, including the STS-74 Shuttle-Mir docking.

Design Considerations for Aural Vital Signs Using PZT Piezoelectric Ceramics Sensor Based on the Computerization Method.

PubMed

Noimanee, Suranan; Tunkasiri, Tawee; Siriwitayakorn, Kingkeo; Tantrakoon, Jerapong

2007-11-11

The purpose was to illustrate how system developed for measurement of the aural vital signs such as patient's heart and lung sounds in the hospital. For heart sounds measurement must operate the frequency response between 20 - 800 Hz, and lung sounds measurement must operate the frequency response between 160 - 4,000 Hz. The method was designed PZT piezoelectric ceramics for both frequency response in the same PZT sensor. It converts a signal from aural vital sign form to voltage signal. The signal is suitably amplified and re-filtered in band pass frequency band. It is converted to digital signal by an analog to digital conversion circuitry developed for the purpose. The results were that all signals can fed to personal computer through the sound card port. With the supporting software for drawing of graphic on the screen, the signal for a specific duration is accessed and stored in the computer's memory in term of each patient's data. In conclusion, the data of each patient call dot pcg (.pcg) for drawing graph and dot wave (.wave) for sound listening or automatic sending via electronic mail to the physician for later analysis of interpreting the sounds on the basis of their time domain and frequency domain representation to diagnose heart disorders.

Combined trabeculotomy-trabeculectomy versus Ahmed valve implantation for refractory primary congenital glaucoma in Egyptian patients: a long-term follow-up

PubMed Central

Helmy, Hazem

2016-01-01

Introduction Primary congenital glaucoma (PCG) is the most common type of glaucoma in pediatric patients. The aim of this study was to compare the effectiveness of combined trabeculotomy-trabeculectomy versus Ahmed valve implantation for cases of PCG refractory to traditional incisional angle surgery (goniotomy and trabeculotomy) in the Egyptian population. Methods The study was conducted in the Glaucoma Clinic of the Research Institute of Ophthalmology (Egypt). The study included 66 eyes of 66 patients (in two groups) with advanced PCG who had previous failed goniotomy, trabeculotomy, or both. Group 1 included 33 patients who underwent trabeculotomy-trabeculectomy procedures; group 2 included 33 patients who underwent FP 8 Ahmed valve implantation. The main outcome measures were intraocular pressure (IOP) reduction, corneal diameter, and axial length stability in both groups. Secondary outcome measures included detection of complications in both groups. Results The average ages of the patients were 13.5 ± 3.9 months and 15.3 ± 5.8 months in groups 1 and 2, respectively. Ten patients (30.3%) in group 1 and 9 patients (27.3%) in group 2 had family histories of PCG. Positive consanguinity was present in 26 patients (78.8%) in group 1 and in 27 patients (81.8%) in group 2. In group 1, the mean intraocular pressure (IOP) value decreased from 33.6 ± 3.4 mmHg preoperatively to 13.8 ± 0.6, 16.9 ± 1.5, 18.2 ± 2.5, 19.8 ± 3.6, and 20.2 ± 3.1 mmHg in the first postoperative month and after years 1, 2, 3, and 4, respectively (p < 0.001). In group 2, the mean IOP value decreased from 33.4 ± 4.5 mmHg preoperatively to 13.3 ± 1.1, 16.3 ± 1.6, 18.1 ± 1.0, 19.1 ± 3.5, and 19.9 ± 3.7 mmHg in the first postoperative month and after years 1, 2, 3, and 4, respectively (p < 0.001). The average number of medications decreased from 2.2 ± 0.4 preoperatively to 1.8 ± 0.4 postoperatively in group 1, while it decreased from 2.1 ± 0.4 preoperatively to 1.9 ± 0.3 postoperatively in group 2. The success rate in group 1 was 97, 91, 76, and 61% in years 1, 2, 3, and 4, respectively, whereas the success rate in group 2 was 97, 93, 81, and 66% in years 1, 2, 3, and 4, respectively. Conclusion Both procedures, i.e., combined trabeculotomy-trabeculectomy and Ahmed valve implantation are suitable options in advanced PCG with failed trabeculotomy and goniotomy. Ahmed valve implanation has a better long-term survival, but trabeculotomy-trabeculectomy provides a second chance for surgical intervention. PMID:27053995

Altered Expression of Polycomb Group Genes in Glioblastoma Multiforme

PubMed Central

Li, Gang; Warden, Charles; Zou, Zhaoxia; Neman, Josh; Krueger, Joseph S.; Jain, Alisha; Jandial, Rahul; Chen, Mike

2013-01-01

The Polycomb group (PcG) proteins play a critical role in histone mediated epigenetics which has been implicated in the malignant evolution of glioblastoma multiforme (GBM). By systematically interrogating The Cancer Genome Atlas (TCGA), we discovered widespread aberrant expression of the PcG members in GBM samples compared to normal brain. The most striking differences were upregulation of EZH2, PHF19, CBX8 and PHC2 and downregulation of CBX7, CBX6, EZH1 and RYBP. Interestingly, changes in EZH2, PHF19, CBX7, CBX6 and EZH1 occurred progressively as astrocytoma grade increased. We validated the aberrant expression of CBX6, CBX7, CBX8 and EZH2 in GBM cell lines by Western blotting and qRT-PCR, and further the aberrant expression of CBX6 in GBM tissue samples by immunohistochemical staining. To determine if there was functional significance to the diminished CBX6 levels in GBM, CBX6 was overexpressed in GBM cells resulting in decreased proliferative capacity. In conclusion, aberrant expression of PcG proteins in GBMs may play a role in the development or maintenance of the malignancy. PMID:24260522

Altered expression of polycomb group genes in glioblastoma multiforme.

PubMed

Li, Gang; Warden, Charles; Zou, Zhaoxia; Neman, Josh; Krueger, Joseph S; Jain, Alisha; Jandial, Rahul; Chen, Mike

2013-01-01

The Polycomb group (PcG) proteins play a critical role in histone mediated epigenetics which has been implicated in the malignant evolution of glioblastoma multiforme (GBM). By systematically interrogating The Cancer Genome Atlas (TCGA), we discovered widespread aberrant expression of the PcG members in GBM samples compared to normal brain. The most striking differences were upregulation of EZH2, PHF19, CBX8 and PHC2 and downregulation of CBX7, CBX6, EZH1 and RYBP. Interestingly, changes in EZH2, PHF19, CBX7, CBX6 and EZH1 occurred progressively as astrocytoma grade increased. We validated the aberrant expression of CBX6, CBX7, CBX8 and EZH2 in GBM cell lines by Western blotting and qRT-PCR, and further the aberrant expression of CBX6 in GBM tissue samples by immunohistochemical staining. To determine if there was functional significance to the diminished CBX6 levels in GBM, CBX6 was overexpressed in GBM cells resulting in decreased proliferative capacity. In conclusion, aberrant expression of PcG proteins in GBMs may play a role in the development or maintenance of the malignancy.

Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution.

PubMed

Mosquna, Assaf; Katz, Aviva; Decker, Eva L; Rensing, Stefan A; Reski, Ralf; Ohad, Nir

2009-07-01

The Polycomb group (PcG) complex is involved in the epigenetic control of gene expression profiles. In flowering plants, PcG proteins regulate vegetative and reproductive programs. Epigenetically inherited states established in the gametophyte generation are maintained after fertilization in the sporophyte generation, having a profound influence on seed development. The gametophyte size and phase dominance were dramatically reduced during angiosperm evolution, and have specialized in flowering plants to support the reproductive process. The moss Physcomitrella patens is an ideal organism in which to study epigenetic processes during the gametophyte stage, as it possesses a dominant photosynthetic gametophytic haploid phase and efficient homologous recombination, allowing targeted gene replacement. We show that P. patens PcG protein FIE (PpFIE) accumulates in haploid meristematic cells and in cells that undergo fate transition during dedifferentiation programs in the gametophyte. In the absence of PpFIE, meristems overproliferate and are unable to develop leafy gametophytes or reach the reproductive phase. This aberrant phenotype might result from failure of the PcG complex to repress proliferation and differentiation of three-faced apical stem cells, which are designated to become lateral shoots. The PpFIE phenotype can be partially rescued by FIE of Arabidopsis thaliana, a flowering plant that diverged >450 million years ago from bryophytes. PpFIE can partially complement the A. thaliana fie mutant, illustrating functional conservation of the protein during evolution in regulating the differentiation of meristematic cells in gametophyte development, both in bryophytes and angiosperms. This mechanism was harnessed at the onset of the evolution of alternating generations, facilitating the establishment of sporophytic developmental programs.

Identification of a single ancestral CYP1B1 mutation in Slovak Gypsies (Roms) affected with primary congenital glaucoma.

PubMed

Plásilová, M; Stoilov, I; Sarfarazi, M; Kádasi, L; Feráková, E; Ferák, V

1999-04-01

Primary congenital glaucoma (PCG) is an autosomal recessive eye disease that occurs at an unusually high frequency in the ethnic isolate of Roms (Gypsies) in Slovakia. Recently, we linked the disease in this population to the GLC3A locus on 2p21. At this locus, mutations in the cytochrome P4501B1 (CYP1B1) gene have been identified as a molecular basis for this condition. Here, we report the results of CYP1B1 mutation screening of 43 PCG patients from 26 Slovak Rom families. A homozygous G-->A transition at nucleotide 1505 in the highly conserved region of exon 3 was detected in all families. This mutation results in the E387K substitution, which affects the conserved K helix region of the cytochrome P450 molecule. Determination of the CYP1B1 polymorphic background showed a common DNA haplotype in all patients, thus indicating that the E387K mutation in Roms has originated from a single ancestral mutational event. The Slovak Roms represent the first population in which PCG is found to result from a single mutation in the CYP1B1 gene, so that a founder effect is the most plausible explanation of its increased incidence. An ARMS-PCR assay has been developed for fast detection of this mutation, thus allowing direct DNA based prenatal diagnosis as well as gene carrier detection in this particular population. Screening of 158 healthy Roms identified 17 (10.8%) mutation carriers, indicating that the frequency of PCG in this population may be even higher than originally estimated.

Genetic heterogeneity and minor CYP1B1 involvement in the molecular basis of primary congenital glaucoma in Gypsies.

PubMed

Sivadorai, P; Cherninkova, S; Bouwer, S; Kamenarova, K; Angelicheva, D; Seeman, P; Hollingsworth, K; Mihaylova, V; Oscar, A; Dimitrova, G; Kaneva, R; Tournev, I; Kalaydjieva, L

2008-07-01

Primary congenital glaucoma (PCG) is a genetically heterogeneous disorder of autosomal recessive inheritance, with mutations in the cytochrome P450 1B1 (CYP1B1) gene detected in an average of approximately 50% of cases worldwide. The Roma/Gypsies are considered to be a rare example of a single founder CYP1B1 mutation, E387K (identified in the Slovak Roma), accounting for 100% of disease alleles. Contrary to this concept, unusual genetic heterogeneity was revealed in this study of 21 Gypsy PCG patients from Bulgaria and 715 controls from the general Gypsy population. In our small sample of affected subjects, we identified five different CYP1B1 mutations - four known (E229K, R368H, E387K and R390C) and one novel and potentially pathogenic (F445I), which together accounted for approximately 30% of disease alleles. E387K was rare in both the patient and the control group, indicating that its high frequency in the Slovak Roma is the product of local founder effect not representative of the overall molecular pattern of PCG in the Gypsy population. Data on other Mendelian disorders and on the population genetics of the Gypsies suggest that a true founder mutation is likely to exist and has remained undetected. Our analysis of another candidate gene, MYOC, and the GLC3B and GLC3C loci did not provide support for their involvement. The molecular basis of PCG in the Gypsies is thus unresolved, and diagnostic analyses should be extended beyond the E387K mutation.

Increased Expression of PcG Protein YY1 Negatively Regulates B Cell Development while Allowing Accumulation of Myeloid Cells and LT-HSC Cells

PubMed Central

Pan, Xuan; Jones, Morgan; Jiang, Jie; Zaprazna, Kristina; Yu, Duonan; Pear, Warren; Maillard, Ivan; Atchison, Michael L.

2012-01-01

Ying Yang 1 (YY1) is a multifunctional Polycomb Group (PcG) transcription factor that binds to multiple enhancer binding sites in the immunoglobulin (Ig) loci and plays vital roles in early B cell development. PcG proteins have important functions in hematopoietic stem cell renewal and YY1 is the only mammalian PcG protein with DNA binding specificity. Conditional knock-out of YY1 in the mouse B cell lineage results in arrest at the pro-B cell stage, and dosage effects have been observed at various YY1 expression levels. To investigate the impact of elevated YY1 expression on hematopoetic development, we utilized a mouse in vivo bone marrow reconstitution system. We found that mouse bone marrow cells expressing elevated levels of YY1 exhibited a selective disadvantage as they progressed from hematopoietic stem/progenitor cells to pro-B, pre-B, immature B and re-circulating B cell stages, but no disadvantage of YY1 over-expression was observed in myeloid lineage cells. Furthermore, mouse bone marrow cells expressing elevated levels of YY1 displayed enrichment for cells with surface markers characteristic of long-term hematopoietic stem cells (HSC). YY1 expression induced apoptosis in mouse B cell lines in vitro, and resulted in down-regulated expression of anti-apoptotic genes Bcl-xl and NFκB2, while no impact was observed in a mouse myeloid line. B cell apoptosis and LT-HSC enrichment induced by YY1 suggest that novel strategies to induce YY1 expression could have beneficial effects in the treatment of B lineage malignancies while preserving normal HSCs. PMID:22292011

Protective effect of D-002, a mixture of beeswax alcohols, against indomethacin-induced gastric ulcers and mechanism of action.

PubMed

Pérez, Yohani; Oyárzabal, Ambar; Mas, Rosa; Molina, Vivian; Jiménez, Sonia

2013-01-01

D-002, a mixture of higher aliphatic beeswax alcohols, produces gastroprotective and antioxidant effects. To investigate the gastroprotective effect of D-002 against indomethacin-induced ulcers, oxidative variables and myeloperoxidase (MPO) activity in the rat gastric mucosa were examined. Rats were randomized into six groups: a negative vehicle control and five indomethacin (50 mg/kg) treated groups, comprising a positive control, three groups treated orally with D-002 (5, 25 and 100 mg/kg) and one group with omeprazole 20 mg/kg intraperitoneally (ip). The contents of malondialdehyde (MDA), protein carbonyl groups (PCG), hydroxyl radical generation and catalase (CAT), glutathione peroxidase (GSH-PX), superoxide dismutase (SOD) and MPO enzyme activities in the rat gastric mucosa were assessed. Indomethacin increased the content of MDA and PCG, the generation of *OH radical and MPO enzyme activity, while it decreased the CAT, GSH-PX and SOD activities as compared to the negative controls. D-002 (5-100 mg/kg) significantly and dose-dependently reduced indomethacin-induced ulceration to 75 %. Also, D-002 decreased the content of MDA and PCG, the generation of hydroxyl radicals and MPO activity as compared to the positive controls. The highest dose of D-002 (100 mg/kg) increased significantly GSH-PX and SOD activities, while all doses used increased CAT activities. Omeprazole 20 mg/kg, the reference drug, reduced significantly the ulcers (93 %), MDA and PCG, the generation of hydroxyl radicals and MPO activity, and increased the CAT, GSH-PX and SOD activities. D-002 treatment produced gastroprotective effects against indomethacin-induced gastric ulceration, which can be related to the reduction of hydroxyl radical generation, lipid peroxidation, protein oxidation and MPO activity, and to the increase of the antioxidant enzymes activities in the rat gastric mucosa.

The prevalence, population structure and screening test specificity of penicillin-susceptible Staphylococcus aureus bacteremia isolates in Malmö, Sweden.

PubMed

Resman, Fredrik; Thegerström, John; Månsson, Fredrik; Ahl, Jonas; Tham, Johan; Riesbeck, Kristian

2016-08-01

The objectives of this study were to examine the prevalence of penicillin-susceptible bacteremic Staphylococcus aureus in the Malmö area in 2014, to re-evaluate the phenotypic methods of penicillinase detection on these isolates, and to investigate the clonal distribution of penicillin-susceptible isolates. All non-redundant S. aureus from blood in the Malmö catchment area in southern Sweden 2014 were screened for penicillin susceptibility using PcG 1U disk diffusion, E-test PcG and the nitrocefin test. All isolates screened as likely susceptible were subjected to PCR for detection of penicillinase (blaZ) and spa-typing. Almost one out of three bacteremic isolates (80/257; 31.1%) were susceptible to penicillin. All screening methods except for the nitrocefin test alone had a low proportion of isolates falsely tested as susceptible, but no method used in the study had perfect specificity compared with PCR. Penicillin-susceptible isolates had a distinct phylogenetic distribution, and two clonal complexes (CC5 and CC45) constituted half of the isolates. Almost one third of S. aureus isolated from blood in southern Sweden in 2014 was susceptible to penicillin. Considering that intravenous penicillin has theoretical advantages compared with the standard treatment in the study area, we argue that routine testing of penicillin susceptibility should be reconsidered. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes

PubMed Central

Rose, Nathan R; King, Hamish W; Blackledge, Neil P; Fursova, Nadezda A; Ember, Katherine JI; Fischer, Roman; Kessler, Benedikt M; Klose, Robert J

2016-01-01

Polycomb group (PcG) proteins function as chromatin-based transcriptional repressors that are essential for normal gene regulation during development. However, how these systems function to achieve transcriptional regulation remains very poorly understood. Here, we discover that the histone H2AK119 E3 ubiquitin ligase activity of Polycomb repressive complex 1 (PRC1) is defined by the composition of its catalytic subunits and is highly regulated by RYBP/YAF2-dependent stimulation. In mouse embryonic stem cells, RYBP plays a central role in shaping H2AK119 mono-ubiquitylation at PcG targets and underpins an activity-based communication between PRC1 and Polycomb repressive complex 2 (PRC2) which is required for normal histone H3 lysine 27 trimethylation (H3K27me3). Without normal histone modification-dependent communication between PRC1 and PRC2, repressive Polycomb chromatin domains can erode, rendering target genes susceptible to inappropriate gene expression signals. This suggests that activity-based communication and histone modification-dependent thresholds create a localized form of epigenetic memory required for normal PcG chromatin domain function in gene regulation. DOI: http://dx.doi.org/10.7554/eLife.18591.001 PMID:27705745

Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer.

PubMed

Clermont, Pier-Luc; Crea, Francesco; Chiang, Yan Ting; Lin, Dong; Zhang, Amy; Wang, James Z L; Parolia, Abhijit; Wu, Rebecca; Xue, Hui; Wang, Yuwei; Ding, Jiarui; Thu, Kelsie L; Lam, Wan L; Shah, Sohrab P; Collins, Colin C; Wang, Yuzhuo; Helgason, Cheryl D

2016-01-01

While localized prostate cancer (PCa) can be effectively cured, metastatic disease inevitably progresses to a lethal state called castration-resistant prostate cancer (CRPC). Emerging evidence suggests that aberrant epigenetic repression by the polycomb group (PcG) complexes fuels PCa progression, providing novel therapeutic opportunities. In the search for potential epigenetic drivers of CRPC, we analyzed the molecular profile of PcG members in patient-derived xenografts and clinical samples. Overall, our results identify the PcG protein and methyl-lysine reader CBX2 as a potential therapeutic target in advanced PCa. We report that CBX2 was recurrently up-regulated in metastatic CRPC and that elevated CBX2 expression was correlated with poor clinical outcome in PCa cohorts. Furthermore, CBX2 depletion abrogated cell viability and induced caspase 3-mediated apoptosis in metastatic PCa cell lines. Mechanistically explaining this phenotype, microarray analysis in CBX2-depleted cells revealed that CBX2 controls the expression of many key regulators of cell proliferation and metastasis. Taken together, this study provides the first evidence that CBX2 inhibition induces cancer cell death, positioning CBX2 as an attractive drug target in lethal CRPC.

Cosmochemical implications of CONSERT permittivity characterization of 67P/C-G

NASA Astrophysics Data System (ADS)

Levasseur-Regourd, A.; Hérique, Alain; Kofman, Wlodek; Beck, Pierre; Bonal, Lydie; Buttarazzi, Ilaria; Heggy, Essam; Lasue, Jeremie; Quirico, Eric; Zine, Sonia

2016-10-01

Unique information about the internal structure of the nucleus of comet 67P/C-G was provided by the CONSERT bistatic radar on-board Rosetta and Philae [1]. Analysis of the propagation of its signal throughout the small lobe indicated that the real part of the permittivity at 90 MHz is of (1.27±0.05). The first interpretation of this value using dielectric properties of mixtures of dust and ices (H2O, CO2), led to the conclusion that the comet porosity ranges between 75-85%. In addition, the dust/ice ratio was found to range between 0.4-2.6 and the permittivity of dust (including 30% of porosity) was determined to be lower than 2.9.The dust permittivity estimate is now reduced by taking into account the updated values of nucleus density and of dust/ice ratio, in order of providing further insights into the nature of the constituents of comet 67P/C-G [2]. We adopt a systematic approach: i) determination of the dust permittivity as a function of the ice (I) to dust (D) and vacuum (V) volume fraction; ii) comparison with the permittivity of meteoritic, mineral and organic materials from literature and laboratory measurements; iii) test of several composition models of the nucleus, corresponding to cosmochemical end members of 67P/C-G. For each of these models the location in the ternary I/D/V diagram is calculated based on available dielectric measurements, and confronted to the locus of 67P/C-G. The number of compliant models is small and the cosmochemical implications of each are discussed [2]. An important fraction of carbonaceous material is required in the dust in order to match CONSERT permittivity observations, establishing that comets represent a massive carbon reservoir.Support from Centre National d'Études Spatiales (CNES, France) for this work, based on observations with CONSERT on board Rosetta, is acknowledged. The CONSERT instrument was designed, built and operated by IPAG, LATMOS and MPS and was financially supported by CNES, CNRS, UJF/UGA, DLR and MPS. Rosetta is an ESA mission with contributions from its member states and NASA.[1] Kofman et al., Science, 349, 6247, aaa0639, 2015. [2] Herique et al., MNRAS, submitted, 2016.

How primordial is the structure of comet 67P/C-G (and of comets in general)?

NASA Astrophysics Data System (ADS)

Morbidelli, Alessandro; Jutzi, Martin; Benz, Willy; Toliou, Anastasia; Rickman, Hans; Bottke, William; Brasser, Ramon

2016-10-01

Several properties of the comet 67P-CG suggest that it is a primordial planetesimal. On the other hand, the size-frequency distribution (SFD) of the craters detected by the New Horizons missions at the surface of Pluto and Charon reveal that the SFD of trans-Neptunian objects smaller than 100km in diameter is very similar to that of the asteroid belt. Because the asteroid belt SFD is at collisional equilibrium, this observation suggests that the SFD of the trans-Neptunian population is at collisional equilibrium as well, implying that comet-size bodies should be the product of collisional fragmentation and not primordial objects. To test whether comet 67P-CG could be a (possibly lucky) survivor of the original population, we conducted a series of numerical impact experiments, where an object with the shape and the density of 67P-CG, and material strength varying from 10 to 1,000 Pa, is hit on the "head" by a 100m projectile at different speeds. From these experiments we derive the impact energy required to disrupt the body catastrophically, or destroy its bi-lobed shape, as a function of impact speed. Next, we consider a dynamical model where the original trans-Neptunian disk is dispersed during a phase of temporary dynamical instability of the giant planets, which successfully reproduces the scattered disk and Oort cloud populations inferred from the current fluxes of Jupiter-family and long period comets. We find that, if the dynamical dispersal of the disk occurs late, as in the Late Heavy Bombardment hypothesis, a 67P-CG-like body has a negligible probability to avoid all catastrophic collisions. During this phase, however, the collisional equilibrium SFD measured by the New Horizons mission can be established. Instead, if the dispersal of the disk occurred as soon as gas was removed, a 67P-CG-like body has about a 20% chance to avoid catastrophic collisions. Nevertheless it would still undergo 10s of reshaping collisions. We estimate that, statistically, the last reshaping collision should have happened 250My-1Gy ago, implying that the actual morphology of 67P-CG should be younger than this age.

Minimum Error Bounded Efficient L1 Tracker with Occlusion Detection (PREPRINT)

DTIC Science & Technology

2011-01-01

Minimum Error Bounded Efficient `1 Tracker with Occlusion Detection Xue Mei\\ ∗ Haibin Ling† Yi Wu†[ Erik Blasch‡ Li Bai] \\Assembly Test Technology...proposed BPR-L1 tracker is tested on several challenging benchmark sequences involving chal- lenges such as occlusion and illumination changes. In all...point method de - pends on the value of the regularization parameter λ. In the experiments, we found that the total number of PCG is a few hundred. The

Circumferential Trabeculotomy Versus Conventional Angle Surgery: Comparing Long-term Surgical Success and Clinical Outcomes in Children With Primary Congenital Glaucoma.

PubMed

Neustein, Rebecca F; Beck, Allen D

2017-11-01

This study compares the long-term efficacy of circumferential trabeculotomy to that of conventional angle surgeries in primary congenital glaucoma (PCG), as judged by glaucoma and visual outcomes. Retrospective observational case series. Setting: Emory Eye Center, Atlanta, Georgia. This was a single-institution retrospective study involving children with PCG who underwent circumferential trabeculotomy, standard trabeculotomy, or goniotomy with ≥2-year follow-up. Postoperative success (intraocular pressure [IOP] < 22 mm Hg ± glaucoma medications, without glaucoma progression/additional IOP-lowering surgery), Snellen-equivalent visual acuity (VA), and IOP at last follow-up. Kaplan-Meier method estimated the probability of glaucoma control vs time postoperatively, and values were compared between angle surgery cohorts using Wilcoxon signed rank tests, Mann-Whitney U tests, and Fisher exact tests. Included were 58 eyes (33 children) after circumferential trabeculotomy and 42 eyes (27 children) after standard trabeculotomy/goniotomy, with mean follow-up of 7.2 ± 4.0 and 8.2 ± 4.5 years, respectively. Postoperative success at last follow-up in the circumferential vs conventional cohorts was 81% (47 of 58 eyes) vs 31% (13 of 42 eyes) (P < .0001). At last follow-up, the circumferential cohort had better median VA than the conventional cohort (20/30 (interquartile range [IQR] 20/25 to 20/70) vs 20/70 (IQR 20/40 to 20/200), P = .009), required fewer glaucoma medications (0.55 ± 1.2 vs 1.61 ± 1.51, P < .0001), had lower IOP in first operated eye (15.2 ± 3.6 vs 18.2 ± 7.0, P = .048), and had comparable incidence of devastating complications (P = .065). In this retrospective study, circumferential trabeculotomy afforded better long-term success and visual outcomes than conventional angle surgery for children with PCG. Copyright © 2017 Elsevier Inc. All rights reserved.

Increased Gray Matter Volume and Resting-State Functional Connectivity in Somatosensory Cortex and their Relationship with Autistic Symptoms in Young Boys with Autism Spectrum Disorder.

PubMed

Wang, Jia; Fu, Kuang; Chen, Lei; Duan, Xujun; Guo, Xiaonan; Chen, Heng; Wu, Qiong; Xia, Wei; Wu, Lijie; Chen, Huafu

2017-01-01

Autism spectrum disorder (ASD) has been widely recognized as a complex neurodevelopmental disorder. A large number of neuroimaging studies suggest abnormalities in brain structure and function of patients with ASD, but there is still no consistent conclusion. We sought to investigate both of the structural and functional brain changes in 3-7-year-old children with ASD compared with typically developing controls (TDs), and to assess whether these alterations are associated with autistic behavioral symptoms. Firstly, we applied an optimized method of voxel-based morphometry (VBM) analysis on structural magnetic resonance imaging (sMRI) data to assess the differences of gray matter volume (GMV) between 31 autistic boys aged 3-7 and 31 age- and handness-matched male TDs. Secondly, we used clusters with between-group differences as seed regions to generate intrinsic functional connectivity maps based on resting-state functional connectivity magnetic resonance imaging (rs-fcMRI) in order to evaluate the functional impairments induced by structural alterations. Brain-behavior correlations were assessed among GMV, functional connectivity and symptom severity in children with ASD. VBM analyses revealed increased GMV in left superior temporal gyrus (STG) and left postcentral gyrus (PCG) in ASD children, comparing with TDs. Using left PCG as a seed region, ASD children displayed significantly higher positive connectivity with right angular gyrus (AG) and greater negative connectivity with right superior parietal gyrus (SPG) and right superior occipital gyrus (SOG), which were associated with the severity of symptoms in social interaction, communication and self-care ability. We suggest that stronger functional connectivity between left PCG and right AG, SPG, and SOG detected in young boys with ASD may serve as important indicators of disease severity. Our study provided preliminary functional evidence that may underlie impaired higher-order multisensory integration in ASD children.

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

Rana, S; Park, S; Zheng, Y

Purpose: The purpose of this study is to investigate the dosimetric feasibility of hypo-fractionated intensity modulated proton therapy (IMPT) for unilateral metallic prosthesis prostate cancer patients based on proton collaborative group (PCG)-GU002-10 (NCT01230866) protocol criteria. Methods: A total of five unilateral metallic prosthesis prostate cancer cases were included in this retrospective study. For each case, IMPT plans were generated for treatment to be delivered with 7.6 Gy[RBE] per fraction in 5 fractions per week for a total dose of 38 Gy(RBE). Each plan was generated using two anterior-oblique beams and one lateral beam. Treatment plans were optimized with an objectivemore » meeting PCG-GU002-10 (NCT01230866) protocol criteria: (i) planning target volume (PTV): D99.5% > 36.1 Gy[RBE], (ii) rectum: V24 < 35%, V33.6 < 10%, (iii) bladder: V39 < 8 cc, and (iv) femoral head: V23 < 1cc. Results: All five cases satisfied PTV D99.5% (average=36.82 Gy[RBE]; range, 36.36–37.13 Gy[RBE]). PTV D95% ranged from 36.66 Gy[RBE] to 38.65 Gy[RBE] and PTV V100 ranged from 95.47% to 97.95%. For the rectum, V24 was less than 35% (average=14.07 Gy[RBE]; range, 6.22–18.42%, whereas V33.6 Gy[RBE] was less than 10% (average=6.83; range, 3.06 – 9.15%). Rectal mean dose ranged from 4.22 Gy[RBE] to 9.97 Gy[RBE]. For the bladder, V39 was found to be less than 8 cc (average=3.69 cc; range, 0.19–7.68 cc). Bladder mean dose ranged from 4.22 Gy[RBE] to 18.83 Gy[RBE]. For the femoral head, V23 was 0 in all five cases. Conclusion: All five unilateral metallic prosthesis prostate cancer IMPT plans generated with one lateral and two anterior-oblique beams satisfied the dosimetric criteria of PCG-GU002-10 (NCT01230866) protocol.« less

Some Aspects of Parallel Implementation of the Finite Element Method on Message Passing Architectures

DTIC Science & Technology

1988-05-01

for Advanced Computer Studies and Department of Computer Science University of Maryland College Park, MD 20742 4, ABSTRACT We discuss some aspects of...Computer Studies and Technology & Dept. of Compute. Scienc II. CONTROLLING OFFICE NAME AND ADDRESS Viyriyf~ 12. REPORT DATE Department of the Navy uo...number)-1/ 2.) We study the performance of CG and PCG by examining its performance for u E (0,1), for solving the two model problems with an accuracy

Long-term surgical outcome of conventional trabeculotomy for childhood glaucoma.

PubMed

Ozawa, Hiroko; Yamane, Mio; Inoue, Eisuke; Yoshida-Uemura, Tomoyo; Katagiri, Satoshi; Yokoi, Tadashi; Nishina, Sachiko; Azuma, Noriyuki

2017-05-01

To investigate the long-term surgical outcomes of conventional trabeculotomy in eyes with childhood glaucoma in a Japanese population. In this retrospective observational study, we enrolled Japanese patients with childhood glaucoma who underwent a conventional trabeculotomy at least once before age 3 years from 1986 to 2014 in our hospital. One hundred seven eyes of 64 patients (24 girls, 40 boys; mean age, 2.8 ± 5.1 months) were included. Sixty-eight (64%) eyes had primary childhood glaucoma (PCG) and 39 (36%) eyes had secondary childhood glaucoma (SCG). The average numbers of surgical operations performed to treat the two glaucoma types that resulted in significantly (p < 0.001) different surgical success rates were 1.4 ± 0.7 and 2.1 ± 0.8. Statistical analysis showed that eyes with PCG, compared with those with SCG, were successfully treated by one trabeculotomy and up to three trabeculotomies (hazard ratios 6.66 and 4.02, respectively). Age, gender, systemic complications, corneal diameter, corneal edema, and preoperative intraocular pressure did not significantly affect the surgical outcomes. Most eyes with PCG are treatable with a maximum of three trabeculotomies. However, SCG usually is refractory to trabeculotomy, and a more promising surgery must be designed.

The Emerging Role of Epigenetics in the Regulation of Female Puberty.

PubMed

Lomniczi, Alejandro; Ojeda, Sergio R

2016-01-01

In recent years the pace of discovering the molecular and genetic underpinnings of the pubertal process has accelerated considerably. Genes required for human puberty to occur have been identified and evidence has been provided suggesting that the initiation of puberty requires coordinated changes in the output of a multiplicity of genes organized into functional networks. Recent evidence suggests that a dual mechanism of epigenetic regulation affecting the transcriptional activity of neurons involved in stimulating gonadotropin-releasing hormone release plays a fundamental role in the timing of puberty. The Polycomb group (PcG) of transcriptional silencers appears to be a major component of the repressive arm of this mechanism. PcG proteins prevent the premature initiation of female puberty by silencing the Kiss1 gene in kisspeptin neurons of the arcuate nucleus (ARC) of the hypothalamus. Because the abundance of histone marks either catalyzed by--or associated with--the Trithorax group (TrxG) of transcriptional activators increases at the time when PcG control subsides, it appears that the TrxG complex is the counteracting partner of PcG-mediated gene silencing. In this chapter, we discuss the concept that a switch from epigenetic repression to activation within ARC kisspeptin neurons is a core mechanism underlying the initiation of female puberty. © 2016 S. Karger AG, Basel.

The Emerging Role of Epigenetics in the Regulation of Female Puberty

PubMed Central

Lomniczi, Alejandro; Ojeda, Sergio R.

2016-01-01

In recent years the pace of discovering the molecular and genetic underpinnings of the pubertal process has accelerated considerably. Genes required for human puberty to occur have been identified and evidence has been provided suggesting that the initiation of puberty requires coordinated changes in the output of a multiplicity of genes organized into functional networks. Recent evidence suggests that a dual mechanism of epigenetic regulation affecting the transcriptional activity of neurons involved in stimulating gonadotropin-releasing hormone release plays a fundamental role in the timing of puberty. The Polycomb group (PcG) of transcriptional silencers appears to be a major component of the repressive arm of this mechanism. PcG proteins prevent the premature initiation of female puberty by silencing the Kiss1 gene in kisspeptin neurons of the arcuate nucleus (ARC) of the hypothalamus. Because the abundance of histone marks either catalyzed by – or associated with – the Trithorax group (TrxG) of transcriptional activators increases at the time when PcG control subsides, it appears that the TrxG complex is the counteracting partner of PcG-mediated gene silencing. In this chapter, we discuss the concept that a switch from epigenetic repression to activation within ARC kisspeptin neurons is a core mechanism underlying the initiation of female puberty. PMID:26680569

The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity.

PubMed

de la Paz Sanchez, Maria; Aceves-García, Pamela; Petrone, Emilio; Steckenborn, Stefan; Vega-León, Rosario; Álvarez-Buylla, Elena R; Garay-Arroyo, Adriana; García-Ponce, Berenice

2015-11-01

Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations. The epigenetic factors Polycomb group (PcG) and Trithorax group (TrxG) are involved in developmental processes that respond to environmental signals, playing important roles in plant plasticity. In this review, we discuss current knowledge of TrxG and PcG functions in different developmental processes in response to internal and environmental cues and we also integrate the emerging evidence concerning their function in plant plasticity. Many such plastic responses rely on meristematic cell behavior, including stem cell niche maintenance, cellular reprogramming, flowering and dormancy as well as stress memory. This information will help to determine how to integrate the role of epigenetic regulation into models of gene regulatory networks, which have mostly included transcriptional interactions underlying various aspects of plant development and its plastic response to environmental conditions. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Polycomb group protein complexes exchange rapidly in living Drosophila.

PubMed

Ficz, Gabriella; Heintzmann, Rainer; Arndt-Jovin, Donna J

2005-09-01

Fluorescence recovery after photobleaching (FRAP) microscopy was used to determine the kinetic properties of Polycomb group (PcG) proteins in whole living Drosophila organisms (embryos) and tissues (wing imaginal discs and salivary glands). PcG genes are essential genes in higher eukaryotes responsible for the maintenance of the spatially distinct repression of developmentally important regulators such as the homeotic genes. Their absence, as well as overexpression, causes transformations in the axial organization of the body. Although protein complexes have been isolated in vitro, little is known about their stability or exact mechanism of repression in vivo. We determined the translational diffusion constants of PcG proteins, dissociation constants and residence times for complexes in vivo at different developmental stages. In polytene nuclei, the rate constants suggest heterogeneity of the complexes. Computer simulations with new models for spatially distributed protein complexes were performed in systems showing both diffusion and binding equilibria, and the results compared with our experimental data. We were able to determine forward and reverse rate constants for complex formation. Complexes exchanged within a period of 1-10 minutes, more than an order of magnitude faster than the cell cycle time, ruling out models of repression in which access of transcription activators to the chromatin is limited and demonstrating that long-term repression primarily reflects mass-action chemical equilibria.

Expanding the clinical spectrum of COL1A1 mutations in different forms of glaucoma.

PubMed

Mauri, Lucia; Uebe, Steffen; Sticht, Heinrich; Vossmerbaeumer, Urs; Weisschuh, Nicole; Manfredini, Emanuela; Maselli, Edoardo; Patrosso, Mariacristina; Weinreb, Robert N; Penco, Silvana; Reis, André; Pasutto, Francesca

2016-08-02

Primary congenital glaucoma (PCG) and early onset glaucomas are one of the major causes of children and young adult blindness worldwide. Both autosomal recessive and dominant inheritance have been described with involvement of several genes including CYP1B1, FOXC1, PITX2, MYOC and PAX6. However, mutations in these genes explain only a small fraction of cases suggesting the presence of further candidate genes. To elucidate further genetic causes of these conditions whole exome sequencing (WES) was performed in an Italian patient, diagnosed with PCG and retinal detachment, and his unaffected parents. Sanger sequencing of the complete coding region of COL1A1 was performed in a total of 26 further patients diagnosed with PCG or early onset glaucoma. Exclusion of pathogenic variations in known glaucoma genes as CYP1B1, MYOC, FOXC1, PITX2 and PAX6 was additionally done per Sanger sequencing and Multiple Ligation-dependent Probe Amplification (MLPA) analysis. In the patient diagnosed with PCG and retinal detachment, analysis of WES data identified compound heterozygous variants in COL1A1 (p.Met264Leu; p.Ala1083Thr). Targeted COL1A1 screening of 26 additional patients detected three further heterozygous variants (p.Arg253*, p.Gly767Ser and p.Gly154Val) in three distinct subjects: two of them diagnosed with early onset glaucoma and mild form of osteogenesis imperfecta (OI), one patient with a diagnosis of PCG at age 4 years. All five variants affected evolutionary, highly conserved amino acids indicating important functional restrictions. Molecular modeling predicted that the heterozygous variants are dominant in effect and affect protein stability and thus the amount of available protein, while the compound heterozygous variants act as recessive alleles and impair binding affinity to two main COL1A1 binding proteins: Hsp47 and fibronectin. Dominant inherited mutations in COL1A1 are known causes of connective tissues disorders such as OI. These disorders are also associated with different ocular abnormalities, although recognition of the common pathology for both features is seldom being recognized. Our results expand the role of COL1A1 mutations in different forms of early-onset glaucoma with and without signs of OI. Thus, we suggest including COL1A1 mutation screening in the genetic work-up of glaucoma cases and detailed ophthalmic examinations with fundus analysis in patients with OI.

Applications of the second virial coefficient: protein crystallization and solubility

PubMed Central

Wilson, William W.; DeLucas, Lawrence J.

2014-01-01

This article begins by highlighting some of the ground-based studies emanating from NASA’s Microgravity Protein Crystal Growth (PCG) program. This is followed by a more detailed discussion of the history of and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (B values) as a diagnostic indicator of solution conditions conducive to protein crystallization. A second application of measured B values involves the determination of solution conditions that improve or maximize the solubility of aqueous and membrane proteins. These two important applications have led to several technological improvements that simplify the experimental expertise required, enable the measurement of membrane proteins and improve the diagnostic capability and measurement throughput. PMID:24817708

Large scale morphological changes in the Hapi region on comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Davidsson, Bjorn; Lee, Seungwon; von Allmen, Paul; Schloerb, Peter; Hofstadter, Mark; Sierks, Holger; Barbieri, Cesare; Gulkis, Samuel; Keller, Horst Uwe; Koschny, Detlef; Lamy, Philippe; Rickman, Hans; Rodrigo, Rafa; MIRO Team; OSIRIS Team

2017-10-01

The Hapi region is located on the northern hemisphere of comet 67P/C-G at the neck that joins the two lobes of the nucleus. It primarily consists of granular material that is unresolved at 0.35 m/pixel resolution and that forms a smooth surface with small slopes with respect to local gravity. The OSIRIS cameras on the ESA spacecraft Rosetta observed Hapi regularly since its rendezvous with the comet in August 2014. No changes were seen during the first five months in orbit but on December 30, 2014, two spots appeared in Hapi. Over the course of two months they grew gradually into a 110 by 70 meter shallow depression with a depth of about 0.5 meters. We use OSIRIS observations to characterize the morphology and spectrophotometry of the region. We use measurements of the thermal emission of the comet by the MIRO millimeter and submillimeter radiometer in combination with thermophysical modeling to characterize the surface temperature, near surface temperature gradient, and thermal inertia of the region. The formation mechanism of the depression is discussed in view of these empirical data.

Global and Spatially Resolved Photometric Properties of the Nucleus of Comet 67P/C-G from OSIRIS Images

NASA Astrophysics Data System (ADS)

Lamy, P.

2014-04-01

Following the successful wake-up of the ROSETTA spacecraft on 20 January 2014, the OSIRIS imaging system was fully re-commissioned at the end of March 2014 confirming its initial excellent performances. The OSIRIS instrument includes two cameras: the Narrow Angle Camera (NAC) and the Wide Angle Camera (WAC) with respective fieldsofview of 2.2° and 12°, both equipped with 2K by 2K CCD detectors and dual filter wheels. The NAC filters allow a spectral coverage of 270 to 990 nm tailored to the investigation of the mineralogical composition of the nucleus of comet P/Churyumov- Gerasimenko whereas those of the WAC (245-632 nm) aim at characterizing its coma [1]. The NAC has already secured a set of four complete light curves of the nucleus of 67P/C-G between 3 March and 24 April 2014 with a primary purpose of characterizing its rotational state. A preliminary spin period of 12.4 hours has been obtained, similar to its very first determination from a light curve obtained in 2003 with the Hubble space telescope [2]. The NAC and WAC will be recalibrated in the forthcoming weeks using the same stellar calibrators VEGA and the solar analog 16 Cyg B as for past inflight calibration campaigns in support of the flybys of asteroids Steins and Lutetia. This will allow comparing the pre- and post-hibernation performances of the cameras and correct the quantum efficiency response of the two CCD and the throughput for all channels (i.e., filters) if required. The accurate photometric analysis of the images requires utmost care due to several instrumental problems, the most severe and complex to handle being the presence of optical ghosts which result from multiple reflections on the two filters inserted in the optical beam and on the thick window which protects the CCD detector from cosmic ray impacts. These ghosts prominently appear as either slightly defocused images offset from the primary images or large round or elliptical halos. We will first present results on the global photometric properties of the nucleus of comet 67P/C-G, albedo, phase function and spectral reflectivity and compare with previous results obtained with the Hubble and Spitzer space telescopes [2, 3, 4]. Then observations during the approach and first bound orbits in July-August 2014 will allow mapping the surface of the nucleus with OSIRIS at a scale of up to 1 meter per pixel. The images will be used to reconstruct the 3D surface of the nucleus at highresolution allowing separating true photometric variations from topographic effects. We will present results on the spatially resolved photometric properties of the nucleus based on a novel method developed in the space of the facets representing the three-dimensional shape of the body. This method successfully implemented in the cases of the nucleus of comet 9P/Tempel 2 and of asteroid (2867) Steins [5] has the advantage of automatically tracking the same local surface element on a series of images. The analysis will then proceed with the determination of the global Hapke and other standard photometric parameters as well as their two-dimensional variations across the surface. This allows defining, in the body-fixed reference frame, ``high residual regions'' (HRRs) which correspond to significant relative differences between the observed and modeled photometric parameters such as the singlescattering albedo (SSA), the mean roughness slope angle, and the reflectivity gradient. Of particular interest will be the search for ice patches and possible mineralogical differences resulting from the past activity of the comet.

High expression of Polycomb group protein EZH2 predicts poor survival in salivary gland adenoid cystic carcinoma.

PubMed

Vékony, H; Raaphorst, F M; Otte, A P; van Lohuizen, M; Leemans, C R; van der Waal, I; Bloemena, E

2008-06-01

The prognosis of adenoid cystic carcinoma (ACC), a malignant salivary gland tumour, depends on clinicopathological parameters. To decipher the biological behaviour of ACC, and to identify patients at risk of developing metastases, additional markers are needed. Expression of the cell cycle proteins p53, cyclin D1, p16(INK4a), E2F1 and Ki-67, together with the Polycomb group (PcG) proteins BMI-1, MEL-18, EZH2 and EED was investigated immunohistochemically 21 formalin-fixed, paraffin-embedded primary ACCs in relation to tumour characteristics. ACC revealed significantly increased expression of the cell cycle proteins compared to normal salivary tissue (n = 17). Members of the two PcG complexes displayed mutually exclusive expression in normal salivary gland tissue, with BMI-1 and MEL-18 being abundantly present. In ACC, this expression pattern was disturbed, with EZH2 and EED showing significantly increased expression levels. In univariate analysis, presence of recurrence, poor differentiation and high EZH2 levels (>25% immunopositivity) significantly correlated with unfavourable outcome. ACCs with high proliferative rate (>25% Ki-67 immunopositivity) significantly correlated with high levels of EZH2 and p16. Only the development of recurrence was an independent prognostic factor of survival in multivariate analysis. Expression of PcG complexes and of essential cell cycle proteins is highly deregulated in ACC. Also, EZH2 expression has prognostic relevance in this malignancy.

Professional oral hygiene as a therapeutic option for pediatric patients with plasma cell gingivitis: preliminary results of a prospective case series.

PubMed

Arduino, Paolo G; D'Aiuto, Francesco; Cavallito, Claudio; Carcieri, Paola; Carbone, Mario; Conrotto, Davide; Defabianis, Patrizia; Broccoletti, Roberto

2011-12-01

Plasma cell gingivitis (PCG) is a rare, benign inflammatory condition of unclear etiology with no definitive standard of care ever reported to our knowledge. The aim of this case series is to ascertain the clinical efficacy of professional oral hygiene and periodontal therapy in younger individuals with a histologically confirmed diagnosis of PCG. All patients received non-surgical periodontal therapy, including oral hygiene instructions, and thorough supragingival scaling and polishing with the removal of all deposits and staining combined with the use of antimicrobials in a 9-week cohort study. Clinical outcome variables were recorded at baseline and 4 weeks after the intervention and included, as periodontal parameters, full-mouth plaque scores (FMPS), full-mouth bleeding scores (FMBS), the clinical extension of gingival involvement, and patient-related outcomes (visual analog score of pain). A total of 11 patients (six males and five females; mean age: 11 ± 0.86 years) were recruited. Four weeks after finishing the oral hygiene and periodontal therapy protocol, a statistically significant reduction was observed for FMPS (P = 0.000), FMBS (P = 0.000), reported pain (P = 0.003) and clinical gingival involvement (P = 0.003). Standard, professional oral hygiene procedures and non-surgical periodontal therapy including antimicrobials were associated with a marked improvement of clinical and patient-related outcomes in pediatric cases of PCG.

Protein Crystal Growth (PCG)Insulin Crystals

NASA Technical Reports Server (NTRS)

1991-01-01

Facilitates the incorporation of glucose into cells. In diabetics, there is either a decrease in or complete lack of insulin, therby leading to several harmful complications. Principal Investigator was Charles Bugg.

Coarse graining for synchronization in directed networks

NASA Astrophysics Data System (ADS)

Zeng, An; Lü, Linyuan

2011-05-01

Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.

Intraocular pressure and biomechanical corneal properties measure by ocular response analyser in patients with primary congenital glaucoma.

PubMed

Perucho-González, Lucía; Martínez de la Casa, Jose María; Morales-Fernández, Laura; Bañeros-Rojas, Paula; Saenz-Francés, Federico; García-Feijoó, Julían

2016-08-01

To measure the differences in corneal hysteresis (CH) and corneal resistance factor (CRF) in primary congenital glaucoma (PCG) and in control subjects using ocular response analyser (ORA) and also to compare intraocular pressure (IOP) measurements given by ORA against IOP given by Perkins tonometer, a handheld version of Goldman applanation tonometer (GAT), to determine correlation. One hundred and eighteen eyes of 78 patients with PCG (group I) and 103 eyes of 53 controls (group II) were evaluated using ORA. In all participants, IOP was measured using the Perkins tonometer. The ORA device uses applanation pressure peaks to generate the corneal-compensated IOP (IOPcc), which is reportedly independent of corneal thickness, and the measurement of Goldman-correlated IOP (IOPg), which is influenced by corneal thickness. The measures in group I were as follows: IOPcc 20.92 ± 5.33; IOPg 18.87 ± 6.67; CH 8.51 ± 2.25; CRF 9.85 ± 3.03; and IOP measured by Goldman 18.32 ± 5.13. The measures in group II were as follows: IOPcc 14.33 ± 2.91; IOPg 14.77 ± 3.00; CH 11.37 ± 1.61; CRF 11.02 ± 1.74; and IOP measured by Goldman 13.74 ± 2.42. The differences of all parameters compared between both groups were statistically significant (p < 0.001 for CH and for all IOP measures and p = 0.001 for CRF). The values of IOPcc, IOPg and IOP measured with Goldman were higher in group I than the values in group II. However, CH and CRF values were lower in group I. A decrease in CH and CRF has been observed in patients with PCG compared to controls. Future research should assess how these parameters are modified in PCG and whether they could provide more information about progression. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

On a model of three-dimensional bursting and its parallel implementation

NASA Astrophysics Data System (ADS)

Tabik, S.; Romero, L. F.; Garzón, E. M.; Ramos, J. I.

2008-04-01

A mathematical model for the simulation of three-dimensional bursting phenomena and its parallel implementation are presented. The model consists of four nonlinearly coupled partial differential equations that include fast and slow variables, and exhibits bursting in the absence of diffusion. The differential equations have been discretized by means of a second-order accurate in both space and time, linearly-implicit finite difference method in equally-spaced grids. The resulting system of linear algebraic equations at each time level has been solved by means of the Preconditioned Conjugate Gradient (PCG) method. Three different parallel implementations of the proposed mathematical model have been developed; two of these implementations, i.e., the MPI and the PETSc codes, are based on a message passing paradigm, while the third one, i.e., the OpenMP code, is based on a shared space address paradigm. These three implementations are evaluated on two current high performance parallel architectures, i.e., a dual-processor cluster and a Shared Distributed Memory (SDM) system. A novel representation of the results that emphasizes the most relevant factors that affect the performance of the paralled implementations, is proposed. The comparative analysis of the computational results shows that the MPI and the OpenMP implementations are about twice more efficient than the PETSc code on the SDM system. It is also shown that, for the conditions reported here, the nonlinear dynamics of the three-dimensional bursting phenomena exhibits three stages characterized by asynchronous, synchronous and then asynchronous oscillations, before a quiescent state is reached. It is also shown that the fast system reaches steady state in much less time than the slow variables.

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Porcine Elastase. This enzyme is associated with the degradation of lung tissue in people suffering from emphysema. It is useful in studying causes of this disease. Principal Investigator on STS-26 was Charles Bugg.

Microgravity

NASA Image and Video Library

1995-10-20

Onboard Space Shuttle Columbia (STS-73) Mission Specialists Catherine Cady Coleman works at the glovebox facility in support of the Protein Crystal Growth Glovebox (PCG-GBX) experiment in the United States Microgravity Laboratory 2 (USML-2) Spacelab science module.

PCG: A prototype incremental compilation facility for the SAGA environment, appendix F

NASA Technical Reports Server (NTRS)

Kimball, Joseph John

1985-01-01

A programming environment supports the activity of developing and maintaining software. New environments provide language-oriented tools such as syntax-directed editors, whose usefulness is enhanced because they embody language-specific knowledge. When syntactic and semantic analysis occur early in the cycle of program production, that is, during editing, the use of a standard compiler is inefficient, for it must re-analyze the program before generating code. Likewise, it is inefficient to recompile an entire file, when the editor can determine that only portions of it need updating. The pcg, or Pascal code generation, facility described here generates code directly from the syntax trees produced by the SAGA syntax directed Pascal editor. By preserving the intermediate code used in the previous compilation, it can limit recompilation to the routines actually modified by editing.

Identification of novel diagnostic biomarkers for thyroid carcinoma.

PubMed

Wang, Xiliang; Zhang, Qing; Cai, Zhiming; Dai, Yifan; Mou, Lisha

2017-12-19

Thyroid carcinoma (THCA) is the most universal endocrine malignancy worldwide. Unfortunately, a limited number of large-scale analyses have been performed to identify biomarkers for THCA. Here, we conducted a meta-analysis using 505 THCA patients and 59 normal controls from The Cancer Genome Atlas. After identifying differentially expressed long non-coding RNA (lncRNA) and protein coding genes (PCG), we found vast difference in various lncRNA-PCG co-expressed pairs in THCA. A dysregulation network with scale-free topology was constructed. Four molecules (LA16c-380H5.2, RP11-203J24.8, MLF1 and SDC4) could potentially serve as diagnostic biomarkers of THCA with high sensitivity and specificity. We further represent a diagnostic panel with expression cutoff values. Our results demonstrate the potential application of those four molecules as novel independent biomarkers for THCA diagnosis.

Deciphering the Role of POLYCOMB REPRESSIVE COMPLEX1 Variants in Regulating the Acquisition of Flowering Competence in Arabidopsis1

PubMed Central

Picó, Sara; Merini, Wiam

2015-01-01

Polycomb group (PcG) proteins play important roles in regulating developmental phase transitions in plants; however, little is known about the role of the PcG machinery in regulating the transition from juvenile to adult phase. Here, we show that Arabidopsis (Arabidopsis thaliana) B lymphoma Moloney murine leukemia virus insertion region1 homolog (BMI1) POLYCOMB REPRESSIVE COMPLEX1 (PRC1) components participate in the repression of microRNA156 (miR156). Loss of AtBMI1 function leads to the up-regulation of the primary transcript of MIR156A and MIR156C at the time the levels of miR156 should decline, resulting in an extended juvenile phase and delayed flowering. Conversely, the PRC1 component EMBRYONIC FLOWER (EMF1) participates in the regulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE and MIR172 genes. Accordingly, plants impaired in EMF1 function displayed misexpression of these genes early in development, which contributes to a CONSTANS-independent up-regulation of FLOWERING LOCUS T (FT) leading to the earliest flowering phenotype described in Arabidopsis. Our findings show how the different regulatory roles of two functional PRC1 variants coordinate the acquisition of flowering competence and help to reach the threshold of FT necessary to flower. Furthermore, we show how two central regulatory mechanisms, such as PcG and microRNA, assemble to achieve a developmental outcome. PMID:25897002

Deciphering the Role of POLYCOMB REPRESSIVE COMPLEX1 Variants in Regulating the Acquisition of Flowering Competence in Arabidopsis.

PubMed

Picó, Sara; Ortiz-Marchena, M Isabel; Merini, Wiam; Calonje, Myriam

2015-08-01

Polycomb group (PcG) proteins play important roles in regulating developmental phase transitions in plants; however, little is known about the role of the PcG machinery in regulating the transition from juvenile to adult phase. Here, we show that Arabidopsis (Arabidopsis thaliana) B lymphoma Moloney murine leukemia virus insertion region1 homolog (BMI1) POLYCOMB REPRESSIVE COMPLEX1 (PRC1) components participate in the repression of microRNA156 (miR156). Loss of AtBMI1 function leads to the up-regulation of the primary transcript of MIR156A and MIR156C at the time the levels of miR156 should decline, resulting in an extended juvenile phase and delayed flowering. Conversely, the PRC1 component EMBRYONIC FLOWER (EMF1) participates in the regulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE and MIR172 genes. Accordingly, plants impaired in EMF1 function displayed misexpression of these genes early in development, which contributes to a CONSTANS-independent up-regulation of FLOWERING LOCUS T (FT) leading to the earliest flowering phenotype described in Arabidopsis. Our findings show how the different regulatory roles of two functional PRC1 variants coordinate the acquisition of flowering competence and help to reach the threshold of FT necessary to flower. Furthermore, we show how two central regulatory mechanisms, such as PcG and microRNA, assemble to achieve a developmental outcome. © 2015 American Society of Plant Biologists. All Rights Reserved.

Optimal wavelet denoising for smart biomonitor systems

NASA Astrophysics Data System (ADS)

Messer, Sheila R.; Agzarian, John; Abbott, Derek

2001-03-01

Future smart-systems promise many benefits for biomedical diagnostics. The ideal is for simple portable systems that display and interpret information from smart integrated probes or MEMS-based devices. In this paper, we will discuss a step towards this vision with a heart bio-monitor case study. An electronic stethoscope is used to record heart sounds and the problem of extracting noise from the signal is addressed via the use of wavelets and averaging. In our example of heartbeat analysis, phonocardiograms (PCGs) have many advantages in that they may be replayed and analysed for spectral and frequency information. Many sources of noise may pollute a PCG including foetal breath sounds if the subject is pregnant, lung and breath sounds, environmental noise and noise from contact between the recording device and the skin. Wavelets can be employed to denoise the PCG. The signal is decomposed by a discrete wavelet transform. Due to the efficient decomposition of heart signals, their wavelet coefficients tend to be much larger than those due to noise. Thus, coefficients below a certain level are regarded as noise and are thresholded out. The signal can then be reconstructed without significant loss of information in the signal. The questions that this study attempts to answer are which wavelet families, levels of decomposition, and thresholding techniques best remove the noise in a PCG. The use of averaging in combination with wavelet denoising is also addressed. Possible applications of the Hilbert Transform to heart sound analysis are discussed.

Neurobiological evidence for attention bias to food, emotional dysregulation, disinhibition and deficient somatosensory awareness in obesity with binge eating disorder.

PubMed

Aviram-Friedman, Roni; Astbury, Nerys; Ochner, Christopher N; Contento, Isobel; Geliebter, Allan

2018-02-01

To refine the biobehavioral markers of binge eating disorder (BED). We conducted fMRI brain scans using images of high energy processed food (HEPF), low energy unprocessed food (LEUF), or non-foods (NF) in 42 adults (obese with BED [obese -BED; n=13] and obese with no BED [obese non-BED; n=29]) selected via ads. Two blood oxygenated level dependent (BOLD) signal contrast maps were examined: food versus nonfood, and HEPF versus LEUF. In addition, score differences on the disinhibition scale were correlated with BOLD signals. food versus nonfood showed greater BOLD activity for BED in emotional, motivational and somatosensory brain areas: insula, anterior cingulate cortex (ACC), Brodmann areas (BA) 19 & 32, inferior parietal lobule (IPL), posterior cingulate cortex (PCC), and lingual, postcentral, middle temporal and cuneate gyri (p≤0.005; k≥88). HEPF versus LEUF showed greater BOLD activity for BED in inhibitory brain regions: BA 6, middle and superior frontal gyri (p<0.01; k≥119). The groups also differed in the relationships between disinhibition and BOLD activity in the postcentral gyrus (PCG; p=0.04) and ACC-BA 32 (p=0.02). For all participants jointly, PCG BOLD amplitude predicted greater disinhibition (p=0.04). Food images elicited neural activity indicating attention bias (cuneate & PCG), emotion dysregulation (BA 19 & 32), and disinhibition (MFG, BA6 & SFG) in obese with BED. These may help tailor a treatment for the obesity with BED phenotype. Copyright © 2017. Published by Elsevier Inc.

Use of general purpose graphics processing units with MODFLOW

USGS Publications Warehouse

Hughes, Joseph D.; White, Jeremy T.

2013-01-01

To evaluate the use of general-purpose graphics processing units (GPGPUs) to improve the performance of MODFLOW, an unstructured preconditioned conjugate gradient (UPCG) solver has been developed. The UPCG solver uses a compressed sparse row storage scheme and includes Jacobi, zero fill-in incomplete, and modified-incomplete lower-upper (LU) factorization, and generalized least-squares polynomial preconditioners. The UPCG solver also includes options for sequential and parallel solution on the central processing unit (CPU) using OpenMP. For simulations utilizing the GPGPU, all basic linear algebra operations are performed on the GPGPU; memory copies between the central processing unit CPU and GPCPU occur prior to the first iteration of the UPCG solver and after satisfying head and flow criteria or exceeding a maximum number of iterations. The efficiency of the UPCG solver for GPGPU and CPU solutions is benchmarked using simulations of a synthetic, heterogeneous unconfined aquifer with tens of thousands to millions of active grid cells. Testing indicates GPGPU speedups on the order of 2 to 8, relative to the standard MODFLOW preconditioned conjugate gradient (PCG) solver, can be achieved when (1) memory copies between the CPU and GPGPU are optimized, (2) the percentage of time performing memory copies between the CPU and GPGPU is small relative to the calculation time, (3) high-performance GPGPU cards are utilized, and (4) CPU-GPGPU combinations are used to execute sequential operations that are difficult to parallelize. Furthermore, UPCG solver testing indicates GPGPU speedups exceed parallel CPU speedups achieved using OpenMP on multicore CPUs for preconditioners that can be easily parallelized.

Expanded resources through utilization of a primary care giver extracorporeal membrane oxygenation model.

PubMed

Freeman, Regi; Nault, Chrissy; Mowry, Jole'; Baldridge, Paula

2012-01-01

Extracorporeal membrane oxygenation (ECMO) is a long-term extracorporeal support for critically ill patients with life-threatening compromises in cardiac and/or respiratory function. The unpredictability of ECMO resources for a large pediatric and adult population prompted a need for the ability to respond to significant fluctuations in the volume of patients on ECMO. Through multidisciplinary collaboration, the Primary Care Giver (PCG) ECMO Staffing Model was developed to accommodate unpredictable fluctuations in ECMO activity and to maintain flexibility and fiscal responsibility in turbulent economic times. Advancements in extracorporeal technology supported the opportunity to develop a safe and extended staffing model for ECMO. Combining the use of a centrifugal pump system with specialized and experienced cardiovascular intensive care nurses and the ECMO specialist team provided a milieu for education and training to support the new staffing model. The PCG ECMO model provides a safe, flexible, and fiscally responsible staffing model for variable ECMO activity.

JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals

PubMed Central

Takahashi, Sachiko; Ohta, Kazunori; Furubayashi, Naoki; Yan, Bin; Koga, Misako; Wada, Yoshio; Yamada, Mitsugu; Inaka, Koji; Tanaka, Hiroaki; Miyoshi, Hiroshi; Kobayashi, Tomoyuki; Kamigaichi, Shigeki

2013-01-01

The Japan Aerospace Exploration Agency (JAXA) started a high-quality protein crystal growth project, now called JAXA PCG, on the International Space Station (ISS) in 2002. Using the counter-diffusion technique, 14 sessions of experiments have been performed as of 2012 with 580 proteins crystallized in total. Over the course of these experiments, a user-friendly interface framework for high accessibility has been constructed and crystallization techniques improved; devices to maximize the use of the microgravity environment have been designed, resulting in some high-resolution crystal growth. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the ISS, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed. In this article, the current status of JAXA PCG is discussed, and a rational approach to high-quality protein crystal growth in microgravity based on numerical analyses is explained. PMID:24121350

Identification of novel diagnostic biomarkers for thyroid carcinoma

PubMed Central

Wang, Xiliang; Zhang, Qing; Cai, Zhiming; Dai, Yifan; Mou, Lisha

2017-01-01

Thyroid carcinoma (THCA) is the most universal endocrine malignancy worldwide. Unfortunately, a limited number of large-scale analyses have been performed to identify biomarkers for THCA. Here, we conducted a meta-analysis using 505 THCA patients and 59 normal controls from The Cancer Genome Atlas. After identifying differentially expressed long non-coding RNA (lncRNA) and protein coding genes (PCG), we found vast difference in various lncRNA-PCG co-expressed pairs in THCA. A dysregulation network with scale-free topology was constructed. Four molecules (LA16c-380H5.2, RP11-203J24.8, MLF1 and SDC4) could potentially serve as diagnostic biomarkers of THCA with high sensitivity and specificity. We further represent a diagnostic panel with expression cutoff values. Our results demonstrate the potential application of those four molecules as novel independent biomarkers for THCA diagnosis. PMID:29340074

From Phonomecanocardiography to Phonocardiography computer aided

NASA Astrophysics Data System (ADS)

Granados, J.; Tavera, F.; López, G.; Velázquez, J. M.; Hernández, R. T.; López, G. A.

2017-01-01

Due to lack of training doctors to identify many of the disorders in the heart by conventional listening, it is necessary to add an objective and methodological analysis to support this technique. In order to obtain information of the performance of the heart to be able to diagnose heart disease through a simple, cost-effective procedure by means of a data acquisition system, we have obtained Phonocardiograms (PCG), which are images of the sounds emitted by the heart. A program of acoustic, visual and artificial vision recognition was elaborated to interpret them. Based on the results of previous research of cardiologists a code of interpretation of PCG and associated diseases was elaborated. Also a site, within the university campus, of experimental sampling of cardiac data was created. Phonocardiography computer-aided is a viable and low cost procedure which provides additional medical information to make a diagnosis of complex heart diseases. We show some previous results.

A robust dataset-agnostic heart disease classifier from Phonocardiogram.

PubMed

Banerjee, Rohan; Dutta Choudhury, Anirban; Deshpande, Parijat; Bhattacharya, Sakyajit; Pal, Arpan; Mandana, K M

2017-07-01

Automatic classification of normal and abnormal heart sounds is a popular area of research. However, building a robust algorithm unaffected by signal quality and patient demography is a challenge. In this paper we have analysed a wide list of Phonocardiogram (PCG) features in time and frequency domain along with morphological and statistical features to construct a robust and discriminative feature set for dataset-agnostic classification of normal and cardiac patients. The large and open access database, made available in Physionet 2016 challenge was used for feature selection, internal validation and creation of training models. A second dataset of 41 PCG segments, collected using our in-house smart phone based digital stethoscope from an Indian hospital was used for performance evaluation. Our proposed methodology yielded sensitivity and specificity scores of 0.76 and 0.75 respectively on the test dataset in classifying cardiovascular diseases. The methodology also outperformed three popular prior art approaches, when applied on the same dataset.

Design and evaluation of a parametric model for cardiac sounds.

PubMed

Ibarra-Hernández, Roilhi F; Alonso-Arévalo, Miguel A; Cruz-Gutiérrez, Alejandro; Licona-Chávez, Ana L; Villarreal-Reyes, Salvador

2017-10-01

Heart sound analysis plays an important role in the auscultative diagnosis process to detect the presence of cardiovascular diseases. In this paper we propose a novel parametric heart sound model that accurately represents normal and pathological cardiac audio signals, also known as phonocardiograms (PCG). The proposed model considers that the PCG signal is formed by the sum of two parts: one of them is deterministic and the other one is stochastic. The first part contains most of the acoustic energy. This part is modeled by the Matching Pursuit (MP) algorithm, which performs an analysis-synthesis procedure to represent the PCG signal as a linear combination of elementary waveforms. The second part, also called residual, is obtained after subtracting the deterministic signal from the original heart sound recording and can be accurately represented as an autoregressive process using the Linear Predictive Coding (LPC) technique. We evaluate the proposed heart sound model by performing subjective and objective tests using signals corresponding to different pathological cardiac sounds. The results of the objective evaluation show an average Percentage of Root-Mean-Square Difference of approximately 5% between the original heart sound and the reconstructed signal. For the subjective test we conducted a formal methodology for perceptual evaluation of audio quality with the assistance of medical experts. Statistical results of the subjective evaluation show that our model provides a highly accurate approximation of real heart sound signals. We are not aware of any previous heart sound model rigorously evaluated as our proposal. Copyright © 2017 Elsevier Ltd. All rights reserved.

The NUCLEAR FACTOR-CONSTANS complex antagonizes Polycomb repression to de-repress FLOWERING LOCUS T expression in response to inductive long days in Arabidopsis.

PubMed

Luo, Xiao; Gao, Zheng; Wang, Yizhong; Chen, Zhijuan; Zhang, Wenju; Huang, Jirong; Yu, Hao; He, Yuehui

2018-07-01

Many plants sense the seasonal cues, day length or photoperiod changes, to align the timing of the developmental transition to flowering with changing seasons for reproductive success. Inductive day lengths through the photoperiod pathway induce the expression of FLOWERING LOCUS T (FT) or FT relatives that encode a major mobile florigen to promote flowering. In Arabidopsis thaliana, under inductive long days the photoperiod pathway output CONSTANS (CO) accumulates toward the end of the day, and associates with the B and C subunits of Nuclear Factor Y (NF-Y) to form the NF-CO complex that acts to promote FT expression near dusk, whereas Polycomb group (PcG) proteins function to silence FT expression. How NF-CO acts to antagonize the function of PcG proteins to regulate FT expression remains unclear. Here, we show that the NF-CO complex bound to the proximal FT promoter, through chromatin looping, acts in concert with an NF-Y complex bound to a distal enhancer to reduce the levels of PcG proteins, including both Polycomb repressive complex 1 (PRC1) and PRC2 at the FT promoter, leading to a relieving of Polycomb silencing and thus FT de-repression near dusk. Thus, our study provides molecular insights on how the 'active' photoperiod pathway and the 'repressive' Polycomb silencing system interact to control temporal FT expression, conferring the long-day induction of flowering in Arabidopsis. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Change in fasting plasma glucose and incident type 2 diabetes mellitus: results from a prospective cohort study.

PubMed

Mozaffary, Amirhossein; Asgari, Samaneh; Tohidi, Maryam; Kazempour-Ardebili, Sara; Azizi, Fereidoun; Hadaegh, Farzad

2016-05-23

To investigate the association between changes in fasting plasma glucose (FPG) values and incident type 2 diabetes (T2D) in a cohort of the Iranian population. Prospective cohort study. This study was conducted within the framework of the Tehran Lipid and Glucose Study (TLGS) to investigate the association between change in FPG between baseline examination (1999-2001) and the second visit (2002-2005) with incident T2D. A total of 3981 non-diabetic participants aged ≥20 years. T2D was defined if the participant was using antidiabetic drugs or if FPG was ≥7 mmol/L or if the 2 h post-challenge plasma glucose (2-hPCG) was ≥11.1 mmol/L. During a median follow-up of 6.17 years, after the second examination, 288 new cases of T2D were identified. In a multivariate Cox proportional hazard analysis using age as timescale, we presented a simple model including FPG change (HR 1.19, 95% CI 1.07 to 1.33) and baseline waist circumference (WC) (HR 1.004, 95% CI 1.001 to 1.008) with a discriminative power (C-index) of 72%. Furthermore, we showed that the highest quartile of FPG change enhanced the T2D risk to 1.65 (95% CI 1.2 to 2.27) compared with the lowest quartile (p for trend=0.004).The independent risk of FPG change resisted further adjustment with 2-hPCG change. Adding the 2-hPCG change only slightly increased the discriminative power of the model including FPG change and baseline value of WC (0.73% vs 0.72%). After the study population had been limited to those with normal fasting glucose/normal glucose tolerance, FPG change remained an independent predictor (HR 1.57, 95% CI 1.31 to 1.88). Two measurements of FPG obtained about 3 years apart can help to identify populations at risk of incident T2D independently of important traditional risk factors and their changes, including 2-hPCG change. 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/

Scattering Mechanisms and Nature of the Indirect Propagation Paths Measured by the CONSERT Instrument during the Late Phase of Philae's Descent onto 67P/Churyumov-Gerasimenko's Surface

NASA Astrophysics Data System (ADS)

Plettemeier, D.; Statz, C.; Herique, A.; Rogez, Y.; Zine, S.; Ciarletti, V.; Kofman, W. W.

2017-12-01

Bi-static electromagnetic wave propagation measurements performed by the Comet Nucleus Sounding Experiment by Radiowave Transmission (CONSERT) during the descent of Philae onto comet 67P/Churyumov-Gerasimenko's surface (SDL) complement the data obtained during the first science sequence (FSS). These SDL measurements allow analyses of the comet's surface and near subsurface dielectric and roughness properties - especially in vicinity of the designated Agilkia landing site - during the late phase of the descent and support the main scientific objective of CONSERT, the dielectric characterization of the comet's nucleus. In order to perform the propagation measurements, the CONSERT instrument unit aboard the lander received and processed the radio signal emitted by the orbiter's CONSERT counterpart. The lander's CONSERT unit then transmitted a signal back to the orbiter. This happened at a time scale of milliseconds for each measurement and a temporal resolution of the signal below 30m. Multiple measurements were performed throughout the descent and the first science sequence. The signal received by the CONSERT unit aboard Rosetta consists of the direct propagation path between Rosetta and lander Philae as well as indirect propagation paths. These measured paths consist of reflections from 67P/C-G's surface and near subsurface. Due to the large footprint of CONSERT's receiving and transmitting antenna's in the bi-static context and the complex surface geometry of 67P/C-G, the measured signatures are likely to originate from a region with approximately 1,5 km diameter subsequently covering a large portion of the head and resulting in a scattering angle between orbiter, surface and lander dependent on the measurement position. With the direct propagation path between lander and orbiter as a calibration reference and a varying scattering angle (up to approximately 40°), bounds on the likely scattering mechanisms can be imposed and localized. The information on the scattering mechanisms is crucial for the creation of a surface permittivity map of 67P/C-G and the contextualization of the permittivity estimation based on CONSERT's FSS measurements. From the localized permittivity and roughness distributions based on the SDL measurements further properties with regard to 67P/C-G's composition can be derived.

Tunicate cytostatic factor TC14-3 induces a polycomb group gene and histone modification through Ca2+ binding and protein dimerization

PubMed Central

2012-01-01

Background As many invertebrate species have multipotent cells that undergo cell growth and differentiation during regeneration and budding, many unique and interesting homeostatic factors are expected to exist in those animals. However, our understanding of such factors and global mechanisms remains very poor. Single zooids of the tunicate, Polyandrocarpa misakiensis, can give off as many as 40 buds during the life span. Bud development proceeds by means of transdifferentiation of very limited number of cells and tissues. TC14-3 is one of several different but closely related polypeptides isolated from P. misakiensis. It acts as a cytostatic factor that regulates proliferation, adhesion, and differentiation of multipotent cells, although the molecular mechanism remains uncertain. The Polycomb group (PcG) genes are involved in epigenetic control of genomic activity in mammals. In invertebrates except Drosophila, PcG and histone methylation have not been studied so extensively, and genome-wide gene regulation is poorly understood. Results When Phe65 of TC14-3 was mutated to an acidic amino acid, the resultant mutant protein failed to dimerize. The replacement of Thr69 with Arg69 made dimers unstable. When Glu106 was changed to Gly106, the resultant mutant protein completely lost Ca2+ binding. All these mutant proteins lacked cytostatic activity, indicating the requirement of protein dimerization and calcium for the activity. Polyandrocarpa Eed, a component of PcG, is highly expressed during budding, like TC14-3. When wild-type and mutant TC14-3s were applied in vivo and in vitro to Polyandrocarpa cells, only wild-type TC14-3 could induce Eed without affecting histone methyltransferase gene expression. Eed-expressing cells underwent trimethylation of histone H3 lysine27. PmEed knockdown by RNA interference rescued cultured cells from the growth-inhibitory effects of TC14-3. Conclusion These results show that in P. misakiensis, the cytostatic activity of TC14-3 is mediated by PmEed and resultant histone modification, and that the gene expression requires both the protein dimerization and Ca2+-binding of TC14-3. This system consisting of a humoral factor, PcG, and histone methylation would contribute to the homeostatic regulation of cell growth and terminal differentiation of invertebrate multipotent cells. PMID:22296827

Formation of bi-lobed 67P/C-G-like shapes by sub-catastrophic collisions

NASA Astrophysics Data System (ADS)

Jutzi, Martin; Benz, Willy

2016-10-01

Small bodies with a bi-lobe shape such as comet 67P/C-G have been argued to form as the result of low velocity (v ≈ vesc) collisional mergers of similar-sized bodies very early on in the history of the solar system [1]. However, the recent analysis of the subsequent collisional survival of the global structure and shape of comet 67P/C-G strongly suggests that such a structure will not survive until today [2]. Hence, the comet must have acquired its present characteristics as a result of a collision occurring at later time when the relative velocities between small bodies are much higher (v >> vesc).One possible scenario would be that 67P/C-G-like bi-lobe structures form as the result of collisional disruptions of larger parent bodies [3]. Whether the internal properties of such larger parent bodies, the timing of such a collision, and the subsequent survival of the shape produced is compatible with observations will remain to be seen.Here, we propose a scenario in which the final bi-lobe shapes result from low-energy, sub-catastrophic impacts. We start with bodies of about the same mass as comet 67P/C-G, which are rotating and are slightly elongated (i.e., with properties which are consistent with the outcome of the disruptions of larger bodies). We use a SPH shock physics code to model the impacts, the subsequent re-accumulation of material and the reconfiguration into a stable final shape. Our modelling results suggest that these kind of collisions result in "splitting" events which frequently lead to formation of bi-lobe 67P/C-G-like shapes.The frequency of such small-scale impact events is consistent with a young (less than 1 Gy) age of the shape of comet 67P/C-G [2]. Equally important, the probability for such a shape-forming event to take place without a subsequent shape-destroying event occurring until today is reasonably high.Although the collisions considered in this work can alter the global shape, their respective energy is small enough not to lead to any substantial global-scale heating or compaction, consistent with the observed primordial characteristics of comets.[1] Jutzi&Asphaug, 2015, Science 348. [2] Jutzi et al., submitted. [3] Schwartz et al., in prep.

Cognitive behaviour therapy for older adults experiencing insomnia and depression in a community mental health setting: Study protocol for a randomised controlled trial.

PubMed

Sadler, Paul; McLaren, Suzanne; Klein, Britt; Jenkins, Megan; Harvey, Jack

2015-11-27

Cognitive behaviour therapy for insomnia (CBT-I) is a well-established treatment; however, the evidence is largely limited to homogenous samples. Although emerging research has indicated that CBT-I is also effective for comorbid insomnia, CBT-I has not been tested among a complex sample of older adults with comorbid insomnia and depression. Furthermore, no study has explored whether modifying CBT-I to target associated depressive symptoms could potentially enhance sleep and mood outcomes. Therefore, this study aims to report a protocol designed to test whether an advanced form of CBT for insomnia and depression (CBT-I-D) is more effective at reducing insomnia and depressive symptoms compared to a standard CBT-I and psychoeducation control group (PCG) for older adults in a community mental health setting. We aim to recruit 150 older adults with comorbid insomnia who have presented to community mental health services for depression. Eligible participants will be randomly allocated via block/cluster randomisation to one of three group therapy conditions: CBT-I, CBT-I-D, or PCG. Participants who receive CBT-I will only practice strategies designed to improve their sleep, whereas participants who receive CBT-I-D will practice additional strategies designed to also improve their mood. This trial will implement a mixed-methods design involving quantitative outcome measures and qualitative focus groups. The primary outcome measures are insomnia and depression severity, and secondary outcomes are anxiety, hopelessness, beliefs about sleep, comorbid sleep conditions, and health. Outcomes will be assessed at pre-intervention (week 0), post-intervention (week 8), and 3-month follow-up (week 20). This CBT study protocol has been designed to address comorbid insomnia and depression for older adults receiving community mental health services. The proposed trial will determine whether CBT-I is more effective for older adults with comorbid insomnia and depression compared to a PCG. It will also establish whether an advanced form of CBT-I-D generates greater reductions in insomnia and depression severity compared to standard CBT-I. The results from the proposed trial are anticipated to have important clinical implications for older adults, researchers, therapists, and community mental health services. Australian and New Zealand Clinical Trials Registry (ANZCTR): ACTRN: 12615000067572 , Date Registered 12 December 2014.

Performance evaluation of OpenFOAM on many-core architectures

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

Brzobohatý, Tomáš; Říha, Lubomír; Karásek, Tomáš, E-mail: tomas.karasek@vsb.cz

In this article application of Open Source Field Operation and Manipulation (OpenFOAM) C++ libraries for solving engineering problems on many-core architectures is presented. Objective of this article is to present scalability of OpenFOAM on parallel platforms solving real engineering problems of fluid dynamics. Scalability test of OpenFOAM is performed using various hardware and different implementation of standard PCG and PBiCG Krylov iterative methods. Speed up of various implementations of linear solvers using GPU and MIC accelerators are presented in this paper. Numerical experiments of 3D lid-driven cavity flow for several cases with various number of cells are presented.

The global surface composition of 67P/CG nucleus by Rosetta/VIRTIS. (I) Prelanding mission phase

NASA Astrophysics Data System (ADS)

Filacchione, Gianrico; Capaccioni, Fabrizio; Ciarniello, Mauro; Raponi, Andrea; Tosi, Federico; De Sanctis, Maria Cristina; Erard, Stéphane; Morvan, Dominique Bockelée; Leyrat, Cedric; Arnold, Gabriele; Schmitt, Bernard; Quirico, Eric; Piccioni, Giuseppe; Migliorini, Alessandra; Capria, Maria Teresa; Palomba, Ernesto; Cerroni, Priscilla; Longobardo, Andrea; Barucci, Antonella; Fornasier, Sonia; Carlson, Robert W.; Jaumann, Ralf; Stephan, Katrin; Moroz, Lyuba V.; Kappel, David; Rousseau, Batiste; Fonti, Sergio; Mancarella, Francesca; Despan, Daniela; Faure, Mathilde

2016-08-01

From August to November 2014 the Rosetta orbiter has performed an extensive observation campaign aimed at the characterization of 67P/CG nucleus properties and to the selection of the Philae landing site. The campaign led to the production of a global map of the illuminated portion of 67P/CG nucleus. During this prelanding phase the comet's heliocentric distance decreased from 3.62 to 2.93 AU while Rosetta was orbiting around the nucleus at distances between 100 to 10 km. VIRTIS-M, the Visible and InfraRed Thermal Imaging Spectrometer - Mapping channel (Coradini et al., [2007] Space Sci. Rev., 128, 529-559) onboard the orbiter, has acquired 0.25-5.1 μm hyperspectral data of the entire illuminated surface, e.g. the north hemisphere and the equatorial regions, with spatial resolution between 2.5 and 25 m/pixel. I/F spectra have been corrected for thermal emission removal in the 3.5-5.1 μm range and for surface's photometric response. The resulting reflectance spectra have been used to compute several Cometary Spectral Indicators (CSI): single scattering albedo at 0.55 μm, 0.5-0.8 μm and 1.0-2.5 μm spectral slopes, 3.2 μm organic material and 2.0 μm water ice band parameters (center, depth) with the aim to map their spatial distribution on the surface and to study their temporal variability as the nucleus moved towards the Sun. Indeed, throughout the investigated period, the nucleus surface shows a significant increase of the single scattering albedo along with a decrease of the 0.5-0.8 and 1.0-2.5 μm spectral slopes, indicating a flattening of the reflectance. We attribute the origin of this effect to the partial removal of the dust layer caused by the increased contribution of water sublimation to the gaseous activity as comet crossed the frost-line. The regions more active at the time of these observations, like Hapi in the neck/north pole area, appear brighter, bluer and richer in organic material than the rest of the large and small lobe of the nucleus. The parallel coordinates method (Inselberg [1985] Vis. Comput., 1, 69-91) has been used to identify associations between average values of the spectral indicators and the properties of the geomorphological units as defined by (Thomas et al., [2015] Science, 347, 6220) and (El-Maarr et al., [2015] Astron. Astrophys., 583, A26). Three classes have been identified (smooth/active areas, dust covered areas and depressions), which can be clustered on the basis of the 3.2 μm organic material's band depth, while consolidated terrains show a high variability of the spectral properties resulting being distributed across all three classes. These results show how the spectral variability of the nucleus surface is more variegated than the morphological classes and that 67P/CG surface properties are dynamical, changing with the heliocentric distance and with activity processes.

Extreme 3D reconstruction of the final ROSETTA/PHILAE landing site

NASA Astrophysics Data System (ADS)

Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquiere, Gilles; Delmas, Cédric; Durand, Joelle; Garmier, Romain; Gaudon, Philippe; Jurado, Eric

2016-04-01

The Philae lander aboard the Rosetta spacecraft successfully landed at the surface of comet 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) after two rebounds on November 12, 2014. The final landing site, now known as « Abydos », has been identified on images acquired by the OSIRIS imaging system onboard the Rosetta orbiter[1]. The available images of Abydos are very limited in number and reveal a very extreme topography containing cliffs and overhangs. Furthermore, the surface is only observed under very high incidence angles of 60° on average, which implies that the images also exhibit lots of cast shadows. This makes it very difficult to reconstruct the 3D topography with standard methods such as photogrammetry or standard clinometry. We apply a new method called ''Multiresolution PhotoClinometry by Deformation'' (MPCD, [2]) to retrieve the 3D topography of the area around Abydos. The method works in two main steps: (i) a DTM of this region is extracted from a low resolution MPCD global shape model of comet 67P/C-G, and (ii) the resulting triangular mesh is progressively deformed at increasing spatial sampling down to 0.25 m in order to match a set of 14 images of Abydos with projected pixel scales between 1 and 8 m. The method used to perform the image matching is a quasi-Newton non-linear optimization method called L-BFGS-b[3] especially suited to large-scale problems. Finally, we also checked the compatibility of the final MPCD digital terrain model with a set of five panoramic images obtained by the CIVA-P instrument aboard Philae[4]. [1] Lamy et al., 2016, submitted. [2] Capanna et al., Three dimensional reconstruction using multiresoluton photoclinometry by deformation, The visual Computer, v. 29(6-8) pp. 825-835, 2013. [3] Morales et al., Remark on "Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization", v.38(1) pp.1-4, ACM Trans. Math. Softw., 2011 [4] Bibring et al., 67P/Churyumov-Gerasimenko surface properties as derived from CIVA panoramic images, Science, v. 349(6247), 2015

Marginal adaptation, fracture load and macroscopic failure mode of adhesively luted PMMA-based CAD/CAM inlays.

PubMed

Ender, Andreas; Bienz, Stefan; Mörmann, Werner; Mehl, Albert; Attin, Thomas; Stawarczyk, Bogna

2016-02-01

To evaluate marginal adaptation, fracture load and failure types of CAD/CAM polymeric inlays. Standardized prepared human molars (48) were divided into four groups (n=12): (A) PCG (positive control group); adhesively luted glass-ceramic inlays, (B) TRX; CAD/CAM polymeric inlays luted using a self-adhesive resin cement, (C) TAC; CAD/CAM polymeric inlays luted using a conventional resin cement, and (D) NCG (negative control group); direct-filled resin-based composite restorations. All specimens were subjected to a chewing simulator. Before and after chewing fatigue, marginal adaptation was assessed at two interfaces: (1) between dental hard tissues and luting cement and (2) between luting cement and restoration. Thereafter, the specimens were loaded and the fracture loads, as well as the failure types, were determined. The data were analysed using three- and one-way ANOVA with post hoc Scheffé test, two sample Student's t-test (p<0.05). Before and after chewing fatigue, marginal adaptation for interface 1 showed significantly better results for TRX and PCG than for TAC (p=0.001-0.02) and NCG (p=0.001-0.047). For interface 2, marginal adaptation for TAC was significantly inferior to TRX (p<0.001) and PCG (p<0.001). Chewing fatigue had a negative impact on the marginal adaptation of TAC and NCG. No significant differences in fracture load were found between all tested groups. Self-adhesive luted polymeric CAD/CAM inlays showed similar marginal adaptation and fracture load values compared to adhesively luted glass-ceramic inlays. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Evolution of the coma composition at 67P/Churyumov-Gerasimenko as seen by ROSINA/Rosetta from November 2014 to April 2015

NASA Astrophysics Data System (ADS)

Gasc, Sébastien; Altwegg, Kathrin; Balsiger, Hans; Calmonte, Ursina; Galli, André; Jäckel, Annette; Le Roy, Léna; Rubin, Martin; Tzou, Chia-Yu; Wurz, Peter; Berthelier, Jean-Jacques; Fiethe, Björn; Fuselier, Stephen; Gombosi, Tamas; De Keyser, Johan; Mall, Urs; Rème, Henri

2015-04-01

The European Space Agency's Rosetta spacecraft, with the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) onboard [1], has been following and observing comet 67P/Churyumov-Gerasimenko (67P/C-G) since August 2014. ROSINA has provided new information on the molecular, elemental, and isotopic composition of 67P/C-G's coma [2,3]. ROSINA consists of a pressure sensor (COPS) and two mass spectrometers, the Double Focusing Mass Spectrometer (DFMS) and the Reflectron Time Of Flight mass spectrometer (RTOF). DFMS has a high mass resolution (ca. 3'000 at 1%) and a high sensitivity, whereas RTOF has a wide mass range (from 1 amu/e to >300 amu/e) and a high temporal resolution. Both mass spectrometers are designed to measure cometary neutral gas as well as cometary ions. In this work, we present the first results and discuss the evolution of the composition of the coma measured by ROSINA from November 2014 until the end of March 2015. During this period, Rosetta delivered the lander, then stayed in bound orbits at distances of 20-30 km away from the comet center, and finally performed comet flybys from 10 km up to 250 km away from 67P/C-G. [1] Balsiger, H. et al.: ROSINA-Rosetta Orbiter Spectrometer for Ion and Neutral Analysis, Space Science Reviews, Vol. 128, 745-801, 2007 [2] Altwegg, K. et al.: Comet 67P/Churyumov-Gerasimenko, a true Kuiper belt comet as judged from its D/H in water, Science Express, 2014 [3] Hässig, M. et al.: Time variability and heterogeneity in the coma of 67P/Churyumov-Gerasimenko, Science, in press, 2015

Gonioscopy assisted transluminal trabeculotomy: an ab interno circumferential trabeculotomy for the treatment of primary congenital glaucoma and juvenile open angle glaucoma.

PubMed

Grover, Davinder S; Smith, Oluwatosin; Fellman, Ronald L; Godfrey, David G; Butler, Michelle R; Montes de Oca, Ildamaris; Feuer, William J

2015-08-01

To introduce a novel ab interno 360° trabeculotomy for treating primary congenital glaucoma (PCG) and juvenile open angle glaucoma (JOAG) and report preliminary results. A retrospective chart review of patients who underwent a gonioscopy assisted transluminal trabeculotomy (GATT) procedure by four of the authors (DSG, OS, RLF and DGG) between October 2011 and October 2013. The surgery was performed in patients ≤30 years old with a dysgenic anterior segment angle and uncontrolled PCG and JOAG. Fourteen eyes of 10 patients underwent GATT with follow-up >12 months (12-33 months; mean 20.4). Patients ranged in age from 17 months to 30 years (mean=18.4 years), and five (50%) were female patients. No complications occurred during or following surgery except for early postoperative hyphema in five (36%) of eyes, all cleared by 1 month. The mean intraocular pressure (IOP) decreased from 27.3 to 14.8 mm Hg and the mean number of medications required decreased from 2.6 to 0.86. Five eyes had a drop in IOP ≥15 mm Hg (range 15-39). The preliminary results and safety for GATT, a minimally invasive conjunctival sparing circumferential trabeculotomy, are promising and at least equivalent to previous results for ab externo trabeculotomy for the treatment of PCG and JOAG. All eyes in the study were considered a clinical success. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Does photobiomodulation therapy is better than cryotherapy in muscle recovery after a high-intensity exercise? A randomized, double-blind, placebo-controlled clinical trial.

PubMed

De Marchi, Thiago; Schmitt, Vinicius Mazzochi; Machado, Guilherme Pinheiro; de Sene, Juliane Souza; de Col, Camila Dallavechia; Tairova, Olga; Salvador, Mirian; Leal-Junior, Ernesto Cesar Pinto

2017-02-01

This study aimed to determine the effectiveness of photobiomodulation therapy (PBMT) and cryotherapy, in isolated and combined forms, as muscle recovery techniques after muscle fatigue-inducing protocol. Forty volunteers were randomly divided into five groups: a placebo group (PG); a PBMT group (PBMT); a cryotherapy group (CG); a cryotherapy-PBMT group (CPG); and a PBMT-cryotherapy group (PCG). All subjects performed four sessions at 24-h intervals, during which they submitted to isometric assessment (MVC) and blood collection in the pre-exercise period, and 5 and 60 min post-exercise, while the muscle fatigue induction protocol occurred after the pre-exercise collections. In the remaining sessions performed 24, 48, and 72 h later, only blood collections and MVCs were performed. A single treatment with PBMT and/or cryotherapy was applied after only 2 min of completing the post-5-min MVC test at the first session. In the intragroup comparison, it was found that exercise led to a significant decrease (p < 0.05) in the production of MVC in all groups. Comparing the results of MVCs between groups, we observed significant increases in the MVC capacity of the PBMT, CPG, and PCG volunteers in comparison with both PG and CG (p < 0.05). We observed a significant decrease in the concentrations of the biochemical markers of oxidative damage (TBARS and PC) in all groups and muscle damage (creatine kinase-CK) in the PBMT, PCG, and CPG compared with the PG (p < 0.01). The clinical impact of these findings is clear because they demonstrate that the use of phototherapy is more effective than the use of cryotherapy for muscle recovery, additionally cryotherapy decreases PBMT efficacy.

Polycomb (PcG) Proteins, BMI1 and SUZ12, Regulate Arsenic-induced Cell Transformation*

PubMed Central

Kim, Hong-Gyum; Kim, Dong Joon; Li, Shengqing; Lee, Kun Yeong; Li, Xiang; Bode, Ann M.; Dong, Zigang

2012-01-01

Inorganic arsenic is a well-documented human carcinogen associated with cancers of the skin, lung, liver, and bladder. However, the underlying mechanisms explaining the tumorigenic role of arsenic are not well understood. The present study explored a potential mechanism of cell transformation induced by arsenic exposure. Exposure to a low dose (0.5 μm) of arsenic trioxide (As2O3) caused transformation of BALB/c 3T3 cells. In addition, in a xenograft mouse model, tumor growth of the arsenic-induced transformed cells was dramatically increased. In arsenic-induced transformed cells, polycomb group (PcG) proteins, including BMI1 and SUZ12, were activated resulting in enhanced histone H3K27 tri-methylation levels. On the other hand, tumor suppressor p16INK4a and p19ARF mRNA and protein expression were dramatically suppressed. Introduction of small hairpin (sh) RNA-BMI1 or -SUZ12 into BALB/c 3T3 cells resulted in suppression of arsenic-induced transformation. Histone H3K27 tri-methylation returned to normal in BMI1- or SUZ12-knockdown BALB/c 3T3 cells compared with BMI1- or SUZ12-wildtype cells after arsenic exposure. As a consequence, the expression of p16INK4a and p19ARF was recovered in arsenic-treated BMI1- or SUZ12-knockdown cells. Thus, arsenic-induced cell transformation was blocked by inhibition of PcG function. Taken together, these results strongly suggest that the polycomb proteins, BMI1 and SUZ12 are required for cell transformation induced by organic arsenic exposure. PMID:22843710

The early Pleistocene deciduous hominid molar FS-72 from the Sangiran Dome of Java, Indonesia: A taxonomic reappraisal based on its comparative endostructural characterization.

PubMed

Zanolli, Clément; Grine, Frederick E; Kullmer, Ottmar; Schrenk, Friedemann; Macchiarelli, Roberto

2015-08-01

Among the ten fossil hominid deciduous teeth reported so far from the Pleistocene sediments of the Sangiran Dome of Java are two isolated lower second molars: specimens PCG.2 from the Kabuh Formation and FS-72 from the Pucangan Formation. While PCG.2 appears to be certainly attributable to Homo erectus, FS-72 is somewhat more problematic, even though it is commonly listed within the Indonesian H. erectus hypodigm. Largely because of its large size, it was originally attributed to Meganthropus paleojavanicus. Subsequent study highlighted a set of metric and nonmetric crown features also found in Australopith and African early Homo (notably H. habilis) homologues. An additional problem with the taxonomic assignment of isolated teeth from the Pleistocene of Java is the presence of Pongo in these same deposits. To assess the taxonomic affinity of FS-72, we investigated its inner structure (tissue proportions and enamel-dentine junction morphology) by using techniques of 2-3D virtual imaging coupled with geometric morphometric analyses. The results show that FS-72 has thinner enamel compared to fossil and recent humans and that its topographic repartition more closely follows the pongine pattern. It also exhibits a Pongo-like elongated morphology of the enamel-dentine junction, with proportionally lower and mesiodistally spaced dentine horns. Given the morphological and metric similarities between fossil orangutan and H. erectus molars, we tested the hypothesis that its internal morphology more closely resembles the patterns evinced by PCG.2 and modern humans than Pongo. Accordingly, we consider that FS-72 more likely represents a dm2 of Pongo rather than Homo. © 2015 Wiley Periodicals, Inc.

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Isocitrate Lyase. Target enzyme for fungicides. A better understanding of this enzyme should lead to the discovery of more potent fungicides to treat serious crop diseases such as rice blast. It regulates the flow of metabolic intermediates required for cell growth. Principal Investigator for STS-26 was Charles Bugg.

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Isocitrate Lysase. Target enzyme for fungicides. A better understanding of this enzyme should lead to the discovery of more potent fungicides to treat serious crop diseases such as rice blast. It regulates the flow of metabolic intermediates required for cell growth. Principal Investigator on STS-26 was Charles Bugg.

Association between depression in carers and malnutrition in children aged 6 months to 5 years

PubMed Central

Ganiyu, Adewale B.; Firth, Jacqueline A.

2017-01-01

Background Childhood malnutrition is an important risk factor for child mortality and underlies close to 50% of child deaths worldwide. Previous studies have found an association between maternal depression and child malnutrition, but it is not known whether this association exists in Botswana. In addition, previous studies excluded non-maternal primary caregivers (PCGs). It is unclear whether the association between primary caregiver depression and child malnutrition remains when non-maternal PCGs are included. Aim The aim of this study was to determine if there is an association between PCG depression and malnutrition in children aged between 6 months and 5 years in Mahalapye, Botswana. Setting The study was conducted in the child welfare clinics of Xhosa and Airstrip clinics, two primary health care facilities in Mahalapye, Botswana. Methods This was a case control study. Cases were malnourished children aged between 6 months and 5 years, and controls were non-malnourished children matched for age and gender. The outcome of interest was depression in the PCGs of the cases and controls, which was assessed using the Patient Health Questionnaire 9 (PHQ 9), a depression screening tool. Results From a sample of 171 children, 84 of whom were malnourished, we found that the malnourished children were significantly more likely to have depressed PCGs (odds ratio = 4.33; 95% CI: 1.89, 9.89) than non-malnourished children in the 6-month to 5-year age group; the PCGs of malnourished children also had lower educational status. Conclusion This study found a significant association between PCG depression and child malnutrition. PMID:28155288

Two variants of minimum discarded fill ordering

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

D'Azevedo, E.F.; Forsyth, P.A.; Tang, Wei-Pai

1991-01-01

It is well known that the ordering of the unknowns can have a significant effect on the convergence of Preconditioned Conjugate Gradient (PCG) methods. There has been considerable experimental work on the effects of ordering for regular finite difference problems. In many cases, good results have been obtained with preconditioners based on diagonal, spiral or natural row orderings. However, for finite element problems having unstructured grids or grids generated by a local refinement approach, it is difficult to define many of the orderings for more regular problems. A recently proposed Minimum Discarded Fill (MDF) ordering technique is effective in findingmore » high quality Incomplete LU (ILU) preconditioners, especially for problems arising from unstructured finite element grids. Testing indicates this algorithm can identify a rather complicated physical structure in an anisotropic problem and orders the unknowns in the preferred'' direction. The MDF technique may be viewed as the numerical analogue of the minimum deficiency algorithm in sparse matrix technology. At any stage of the partial elimination, the MDF technique chooses the next pivot node so as to minimize the amount of discarded fill. In this work, two efficient variants of the MDF technique are explored to produce cost-effective high-order ILU preconditioners. The Threshold MDF orderings combine MDF ideas with drop tolerance techniques to identify the sparsity pattern in the ILU preconditioners. These techniques identify an ordering that encourages fast decay of the entries in the ILU factorization. The Minimum Update Matrix (MUM) ordering technique is a simplification of the MDF ordering and is closely related to the minimum degree algorithm. The MUM ordering is especially for large problems arising from Navier-Stokes problems. Some interesting pictures of the orderings are presented using a visualization tool. 22 refs., 4 figs., 7 tabs.« less

A mechanism for comet surface collapse as observed by Rosetta on 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Prialnik, D.; Sierks, H.

2017-07-01

We explore a possible mechanism that may explain sudden depressions of surface areas on a comet nucleus, as suggested by observations of the Rosetta mission on comet 67P/Churyumov-Gerasimenko (hereafter, 67P/C-G). Assuming the area is covered by a thin, compact dust layer of low permeability to gas flow compared to deeper, porous layers, gas can accumulate below the surface when a surge of gas release from amorphous ice occurs upon crystallization. The gas pressure is found to exceed the hydrostatic pressure down to a depth of a few metres. The rapid build-up of pressure may weaken the already fragile, highly porous structure. Eventually, the high pressure gradient that arises drives the gas out and the pressure falls well below the hydrostatic pressure. The rapid pressure drop may result in collapse. Since the crystallization front lies at some depth below the surface, the location on the orbit when this phenomenon occurs is determined by the thermal lag, which, in turn, depends on the thermal conductivity. Numerical simulations show that mostly such activity occurs post-perihelion, but it may also occur pre-perihelion. When permeability is uniform, crystallization still causes increased gas production, but the gas pressure inside the nucleus remains below hydrostatic pressure.

Microgravity

NASA Image and Video Library

1995-03-02

Astronaut Wendy B. Lawrence, flight engineer and mission specialist for STS-67, scribbles notes on the margin of a checklist while monitoring an experiment on the Space Shuttle Endeavour's mid-deck. The experiment is the Protein Crystal Growth (PCG), which takes up locker space near the Commercial Materials Dispersion Apparatus Instruments Technology Associates Experiment (CMIX).

Amélioration des performances d'une implantation parallélovectorielle du gradient conjugué par extension du schéma de stockage matriciel

NASA Astrophysics Data System (ADS)

Magnin, H.; Coulomb, J. L.

1993-03-01

Electromagnetic field computation with the Finite Element (FE) method implies solving of large linear systems of equations. Performances and memory capacities of today computers allow to achieve three-dimensional FE discretizations of electromagnetic problems, but the number of unknowns grows high. So, to improve time to the numerical solution of the linear system(s) thus arising, the use of parallel and/or vector computers has to be envisaged. In this paper, the main constitutive steps of the Pre-conditioned Conjugate Gradient algorithm (PCG) are analysed. After a short recall of our previous work concerning their improvement by use of vector and parallel computations, we show some speedup limitations due to the sparse row-wise matrix storage scheme employed. Then, an extension of this matrix representation is proposed, leading to introduce redundant storage of non-zero coefficients. In spite of the “memory waste” thus implied, it is shown how this extension can be successfully employed to increase the speedup due to parallelism and vectorization on the whole algorithm, and in particular to derive a parallel preconditioner. La résolution par la méthode des éléments finis des équations de l'électromagnétisme conduit à résoudre de grands systèmes d'équations linéaires. Les capacités mémoire et les performances actuelles des systèmes informatiques permettent de traiter les problèmes électromagnétiques par discrétisation tridimensionnelle, mais alors le nombre d'inconnues devient très élevé. Ainsi, la résolution en un temps raisonnable des équations linéaires associées à de telles discrétisations conduit à envisager l'emploi d'ordinateurs à architecture parallèle. Dans cet article, les différentes étapes constitutives de l'algorithme du gradient conjugué préconditionné (GCP) sont analysées. Après un court rappel de nos travaux antérieurs concemant leur amélioration par utilisation de traitements parallèles et vectoriels, nous montrons les limitations du gain de temps dues au mode de stockage matriciel utilisé : la représentation creuse dite “Morse”. Nous proposons alors une extension de ce mode de stockage, conduisant à l'introduction de redondance au niveau du rangement des termes matriciels en mémoire. Malgré le “gaspillage” mémoire ainsi occasionné, il apparait que cette extension peut être mise à profit pour augmenter sensiblement les gains par parallélisation et vectorisation de l'ensemble de l'algorithme du gradient conjugué, et notamment pour la réalisation d'un pré-conditionnement parallèle.

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Canavalin. The major storage protein of leguminous plants and a major source of dietary protein for humans and domestic animals. It is studied in efforts to enhance nutritional value of proteins through protein engineerings. It is isolated from Jack Bean because of it's potential as a nutritional substance. Principal Investigator on STS-26 was Alex McPherson.

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Gamma-Interferon. Stimulates the body's immune system and is used clinically in the treatment of cancer. Potential as an anti-tumor agent against solid tumors as well as leukemia's and lymphomas. It has additional utility as an anti-ineffective agent, including antiviral, anti-bacterial, and anti-parasitic activities. Principal Investigator on STS-26 was Charles Bugg.

STS-66 Space Shuttle mission report

NASA Technical Reports Server (NTRS)

Fricke, Robert W., Jr.

1995-01-01

The primary objective of this flight was to accomplish complementary science objectives by operating the Atmospheric Laboratory for Applications and Science-3 (ATLAS-3) and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere-Shuttle Pallet Satellite (CRISTA-SPAS). The secondary objectives of this flight were to perform the operations of the Shuttle Solar Backscatter Ultraviolet/A (SSBUV/A) payload, the Experiment of the Sun Complementing the Atlas Payload and Education-II (ESCAPE-II) payload, the Physiological and Anatomical Rodent Experiment/National Institutes of Health Rodents (PARE/NIH-R) payload, the Protein Crystal Growth-Thermal Enclosure System (PCG-TES) payload, the Protein Crystal Growth-Single Locker Thermal Enclosure System (PCG-STES), the Space Tissue/National Institutes of Health Cells STL/N -A payload, the Space Acceleration Measurement Systems (SAMS) Experiment, and Heat Pipe Performance Experiment (HPPE) payload. The 11-day plus 2 contingency day STS-66 mission was flown as planned, with no contingency days used for weather avoidance or Orbiter contingency operations. Appendix A lists the sources of data from which this report was prepared, and Appendix B defines all acronyms and abbreviations used in the report.

Trithorax dependent changes in chromatin landscape at enhancer and promoter regions drive female puberty.

PubMed

Toro, Carlos A; Wright, Hollis; Aylwin, Carlos F; Ojeda, Sergio R; Lomniczi, Alejandro

2018-01-04

Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. Here we identify two members of the Trithorax group (TrxG) of modifiers, mixed-lineage leukemia 1 (MLL1), and 3 (MLL3), as central components of an activating epigenetic machinery that dynamically counteracts PcG repression. Preceding puberty, MLL1 changes the chromatin configuration at the promoters of Kiss1 and Tac3, two genes required for puberty to occur, from repressive to permissive. Concomitantly, MLL3 institutes a chromatin structure that changes the functional status of a Kiss1 enhancer from poised to active. RNAi-mediated, ARC-specific Mll1 knockdown reduced Kiss1 and Tac3 expression, whereas CRISPR-Cas9-directed epigenome silencing of the Kiss1 enhancer selectively reduced Kiss1 activity. Both interventions delay puberty and disrupt reproductive cyclicity. Our results demonstrate that an epigenetic switch from transcriptional repression to activation is crucial to the regulatory mechanism controlling the timing of mammalian puberty.

GSK126 (EZH2 inhibitor) interferes with ultraviolet A radiation-induced photoaging of human skin fibroblast cells

PubMed Central

Qin, Haiyan; Zhang, Guang; Zhang, Lianbo

2018-01-01

Polycomb group genes (PcG) encode chromatin modification proteins that are involved in the epigenetic regulation of cell differentiation, proliferation and the aging processes. The key subunit of the PcG complex, enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), has a central role in a variety of mechanisms, such as the formation of chromatin structure, gene expression regulation and DNA damage. In the present study, ultraviolet A (UVA) was used to radiate human dermal fibroblasts in order to construct a photo-aged cell model. Subsequently, the cell viability assay, Hoechst staining, apoptosis detection using flow cytometry, senescence-associated β-galactosidase (SA-β-gal) staining and erythrocyte exclusion experiments were performed. GSK126, a histone methylation enzyme inhibitor of EZH2, was used as an experimental factor. Results suggested that GSK126 downregulated the mRNA expression levels of EZH2 and upregulated the mRNA expression levels of BMI-1. Notably, GSK126 affected the transcription of various photoaging-related genes and thus protected against photoaging induced by UVA radiation. PMID:29545866

STS-66 Space Shuttle mission report

NASA Astrophysics Data System (ADS)

Fricke, Robert W., Jr.

1995-02-01

The primary objective of this flight was to accomplish complementary science objectives by operating the Atmospheric Laboratory for Applications and Science-3 (ATLAS-3) and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere-Shuttle Pallet Satellite (CRISTA-SPAS). The secondary objectives of this flight were to perform the operations of the Shuttle Solar Backscatter Ultraviolet/A (SSBUV/A) payload, the Experiment of the Sun Complementing the Atlas Payload and Education-II (ESCAPE-II) payload, the Physiological and Anatomical Rodent Experiment/National Institutes of Health Rodents (PARE/NIH-R) payload, the Protein Crystal Growth-Thermal Enclosure System (PCG-TES) payload, the Protein Crystal Growth-Single Locker Thermal Enclosure System (PCG-STES), the Space Tissue/National Institutes of Health Cells STL/N -A payload, the Space Acceleration Measurement Systems (SAMS) Experiment, and Heat Pipe Performance Experiment (HPPE) payload. The 11-day plus 2 contingency day STS-66 mission was flown as planned, with no contingency days used for weather avoidance or Orbiter contingency operations. Appendix A lists the sources of data from which this report was prepared, and Appendix B defines all acronyms and abbreviations used in the report.

Polycomb-like 2 Associates with PRC2 and Regulates Transcriptional Networks during Mouse Embryonic Stem Cell Self-Renewal and Differentiation

PubMed Central

Walker, Emily; Chang, Wing Y.; Hunkapiller, Julie; Cagney, Gerard; Garcha, Kamal; Torchia, Joseph; Krogan, Nevan J.; Reiter, Jeremy F.; Stanford, William L.

2010-01-01

Summary Polycomb group (PcG) proteins are conserved epigenetic transcriptional repressors that control numerous developmental gene expression programs and have recently been implicated in modulating embryonic stem cell (ESC) fate. We identified the PcG protein PCL2 (polycomb-like 2) in a genome-wide screen for regulators of self-renewal and pluripotency and predicted that it would play an important role in mouse ESC fate determination. Using multiple biochemical strategies, we provide evidence that PCL2 is a Polycomb Repressive Complex 2 (PRC2)-associated protein in mouse ESCs. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics, defects in differentiation and altered patterns of histone methylation. Integration of global gene expression and promoter occupancy analyses allowed us to identify PCL2 and PRC2 transcriptional targets and draft regulatory networks. We describe the role of PCL2 in both modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation. PMID:20144788

How Polycomb-Mediated Cell Memory Deals With a Changing Environment: Variations in PcG complexes and proteins assortment convey plasticity to epigenetic regulation as a response to environment.

PubMed

Marasca, Federica; Bodega, Beatrice; Orlando, Valerio

2018-04-01

Cells and tissues are continuously exposed to a changing microenvironment, hence the necessity of a flexible modulation of gene expression that in complex organism have been achieved through specialized chromatin mechanisms. Chromatin-based cell memory enables cells to maintain their identity by fixing lineage specific transcriptional programs, ensuring their faithful transmission through cell division; in particular PcG-based memory system evolved to maintain the silenced state of developmental and cell cycle genes. In evolution the complexity of this system have increased, particularly in vertebrates, indicating combinatorial and dynamic properties of Polycomb proteins, in some cases even overflowing outside the cell nucleus. Therefore, their function may not be limited to the imposition of rigid states of genetic programs, but on the ability to recognize signals and allow plastic transcriptional changes in response to different stimuli. Here, we discuss the most novel PcG mediated memory functions in facing and responding to the challenges posed by a fluctuating environment. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Structure and Formation of Comets: Updates from Post-Rosetta Solid Fraction Analyses

NASA Astrophysics Data System (ADS)

Levasseur-Regourd, A. C.; Bentley, M. S.; Kofman, W. W.; Brouet, Y.; Ciarletti, V.; Hadamcik, E.; Herique, A.; Lasue, J.; Mannel, T.; Schmied, R.

2016-12-01

The combination of investigations of 67P/C-G by Rosetta, theoretical and experimental studies, and remote observations allowed unprecedented insight into the structure and formation of comets. Rosetta mission has provided ground-truth for the low-density and high porosity of the nucleus, without heterogeneities larger than a few meters in its small lobe [1,2]. Further studies related to CONSERT experiment now suggest that the porosity increases inside the nucleus [3,4]. Rosetta has also provided ground-truth for the aggregated structure of dust particles within a wide range of sizes in the inner coma [e.g. 5-7]. Such discoveries confirm previous interpretations of remote observations of solar light scattered by dust in cometary comae. Differences in structure between the two parts of the nucleus, strongly suspected from previous high-resolution images of the surface [8] and possibly suggested from some remote observations in fragmenting sub-nuclei [9], might be pointed out from data obtained shortly before Rosetta controlled descent in September 2016. Further analyses by MIDAS of dust particles morphology at submicron-sizes [7,10], as well as compilations of remote observations of solar light scattered by 67P/C-G [11], are presently taking place. We will discuss how such results could lead to a better understanding of dust growth processes during the formation, specifically of 67P/C-G, and more generally, thanks to the link now provided between structural properties of dust and remote polarimetric observations, of comet's nuclei in the early Solar System. References. 1 Kofman et al. Science 2015. 2 Pätzold et al. Nature 2016. 3 Ciarletti et al. A&A 2015. 4 Brouet et al. MNRAS 2016 (under revision). 5. Rotundi et al. Science 2015. 6 Langevin et al. Icarus 2016. 7 Bentley et al. Nature 2016. 8 Massironi et al. Nature 2016. 9 Hadamcik et al. A&A 2016. 10. Mannel et al. Leiden symposium 2016. 11 Hadamcik et al. Leiden symposium 2016.

[Epidemiology and clinical characteristics of primary congenital glaucoma].

PubMed

Aziz, A; Fakhoury, O; Matonti, F; Pieri, E; Denis, D

2015-12-01

Primary congenital glaucoma (PCG) is a rare and sight threatening condition. Few large epidemiological studies are available in the literature concerning this condition. The purpose of the study was to evaluate the epidemiological and clinical characteristics of children affected by PCG. Children affected by PCG, from 1 day to 3 years old at the time of diagnosis were retrospectively included between 1999 and 2014. The analysis concerned the pregnancy, family history, initial referral, clinical presentation with description of the classic findings in this condition, mean age at first consultation, duration of follow-up and presence of a delay in treatment, defined as a delay of over one month from the appearance of clinical signs until diagnosis. Two groups were defined according to age at appearance of the clinical signs: "early" group prior to 2 months old and "late" group beyond 2 months up until 3 years old. One hundred and forty-one eyes of 71 children were included, with 49.3% girls (n=35 children) and 50.7% boys (n=36 children) for a male:female ratio of 1.02. The "early" group included 50 children i.e. 70.3% of the population; the "late" group 21 children or 29.7% of the population. A first-degree family history of congenital glaucoma existed in 28% of cases (n=19). The average age at first consultation was 13.1 months for the entire population, and the mean duration of follow-up was 56.6 months. Involvement was bilateral in 99.3% of cases (n=70 children) and the most frequent clinical sign was buphthalmos in 64.5% of eyes (n=91 eyes). Treatment was delayed in 35.3% of cases (n=25 children). This study is of particular relevance because it was performed over a long period and on a large population, considering the rare prevalence of the pathology, and has found epidemiological and clinical data comparable with those available in the literature for similar populations. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Cupping reversal in pediatric glaucoma--evaluation of the retinal nerve fiber layer and visual field.

PubMed

Ely, Amanda L; El-Dairi, Mays A; Freedman, Sharon F

2014-11-01

To identify optic nerve head (ONH) cupping reversal and associated optical coherence tomography (OCT) and Humphrey visual field changes in pediatric glaucoma. Retrospective observational case series. Sequential surgical cases of juvenile open-angle glaucoma (OAG) or primary congenital glaucoma (PCG) with sustained postoperative intraocular pressure (IOP) reduction. Group 1 had preoperative and postoperative ONH photographs and OCT; Group 2 had preoperative clinical ONH assessment and postoperative imaging. Cupping evaluation was confirmed by masked glaucoma and neuro-ophthalmology specialists. Of 80 cases, 9 eyes (9 children) met criteria for Group 1; 24 eyes (19 children) met criteria for Group 2. Group 1: Five of 9 eyes (56%) demonstrated cupping reversal, with preoperative vs postoperative mean IOP 34.2 ± 6.6 mm Hg vs 10.6 ± 4.1 mm Hg (P < .00001) and mean average retinal nerve fiber layer (RNFL) 71.0 ± 30 μm vs 62.8 ± 24 μm (P = .4), respectively. RNFL was stable in 4 of 5 eyes (all juvenile OAG), but thinned (Δ = -41 μm) in 1 eye with PCG. Humphrey visual fields (reliable in 2 of 3 eyes) showed no significant change. Group 2: Fourteen of 24 PCG eyes (58%) demonstrated cupping reversal, with preoperative vs postoperative mean IOP 36.1 ± 8.9 mm Hg vs 13.3 ± 2.1 mm Hg (P < .00001). Two eyes had thin RNFL postoperatively despite healthy-appearing ONH. Postoperative RNFL showed statistically significant linear correlation with preoperative (but not postoperative) cup-to-disc ratio. Limitations include small numbers, few reliable Humphrey visual fields, and absent preoperative imaging (Group 2). Some eyes with IOP reduction and ONH cupping reversal show continued RNFL thinning postoperatively. The preoperative ONH cup-to-disc ratio predicted the postoperative RNFL better than the postoperative "reversed and smaller" cup-to-disc ratio. Cupping reversal in pediatric glaucoma may not predict improved ONH health and deserves further study. Copyright © 2014 Elsevier Inc. All rights reserved.

Does Informal Caregiving Lead to Parental Burnout? Comparing Parents Having (or Not) Children With Mental and Physical Issues.

PubMed

Gérain, Pierre; Zech, Emmanuelle

2018-01-01

Introduction: Parenting a child with special needs (CSN) may be an important challenge. Previous research has highlighted an increased risk of parental burnout among parents caring for their CSN. Yet, these studies only focused on children with specific issues and did not consider the wide variety of CSN. There is thus a need to take a more global approach to assessing the impact of caring for a CSN on parental burnout. In addition, the impact on parental burnout of personality and parenting (dis)agreement needs to be measured to have a better understanding of parent-caregivers' (PCgs) burnout. Method: An online survey was completed by a large sample of parents from which a subsample of PCgs was identified. Results: T -tests highlighted significantly more parental burnout among parents of CSN. However, further analyses showed that parents with only one child with one special need did not experience significantly more burnout than parents with typical children. The significant difference lay in the presence of comorbidity or the presence of multiple CSN in the family. Hierarchical regressions showed an important impact of Neuroticism for every burnout facet, along with co-parenting (dis)agreement. Subjective consequences of having to care for a CSN were also related to the burnout facets of both emotional exhaustion and emotional distancing. Discussion: The presence of comorbidity and of multiple CSN in the family were related to more PCg burnout, emphasizing the need to consider these situations in further research. The role of neuroticism in PCg burnout confirms previous research both in parental and professional contexts. Parenting (dis)agreement also highlights the importance of dyadic support among parents. Finally, the importance of subjective aspects suggests that parental perception of their situation remains a central element in understanding the consequences of caregiving.

TNF-alpha expression, evaluation of collagen, and TUNEL of Matricaria recutita L. extract and triamcinolone on oral ulcer in diabetic rats

PubMed Central

OLIVEIRA, Bruna Vasconcelos; BARROS SILVA, Paulo Goberlânio; NOJOSA, Jacqueline de Santiago; BRIZENO, Luiz André Cavalcante; FERREIRA, Jamile Magalhães; SOUSA, Fabrício Bitú; MOTA, Mário Rogério Lima; ALVES, Ana Paula Negreiros Nunes

2016-01-01

ABSTRACT Diabetes mellitus (DM) is a disease associated with delayed wound healing of oral ulcers by increased expression of proinflammatory cytokines and cellular apoptosis. Objective to evaluate the influence of Tumor Necrosis Factor alpha (TNF-α) and apoptosis in rats with DM treated with chamomile extract or triamcinolone. Material and Methods Wistar male rats (210.0±4.2 g) were divided into five groups: negative control group (NCG) without diabetes; positive control group (PCG) with DM (alloxan, 45 mg/kg); and groups treated with chamomile extract (normoglycemic= NCG group and diabetic= DCG group) and with triamcinolone (TG). Traumatic ulcers were performed on all animals that received topical triamcinolone, chamomile extract or saline 12/12 hours for ten days. Results On days five and ten the animals were euthanized and the ulcers were analyzed by light microscopy, TUNEL assay, and immunohistochemically (TNF-α). The NCG (p=0.0062), PCG (p=0.0285), NCG (p=0.0041), and DCG (p<0.0001) groups were completely healed on the 10th day, however, there was no healing on the TG (p=0.5127) group. The TNF-α expression showed a significant reduction from the 5th to the 10th day in NCG (p=0.0266) and DCG (p=0.0062). In connective tissue, the TUNEL assay showed a significant reduction in the number of positive cells in NCG (p=0.0273) and CNG (p=0.0469) and in the epithelium only in CDG (p=0.0320). Conclusions Chamomile extract can optimize the healing of traumatic oral ulcers in diabetic rats through the reduction of apoptosis in the epithelium and TNF-α expression. PMID:27383710

XIAP as a Molecular Target for Therapeutic Intervention in Prostate Cancer

DTIC Science & Technology

2007-10-01

receptor corepressor Clara Hwang Æ Veda N. Giri Æ John C. Wilkinson Æ Casey W. Wright Æ Amanda S. Wilkinson Æ Kathleen A. Cooney Æ Colin S. Duckett Received...including BRCA1, histone deacetylases (HDAC), and members of the polycomb group (PcG) of proteins. Clara Hwang and Veda N. Giri contributed equally to

(PCG) Protein Crystal Growth Canavalin Crystals grown on Earth and Space

NASA Technical Reports Server (NTRS)

1993-01-01

The major storage protein of leguminous plants and a major source of dietary protein for humans and domestic animals. It is studied in efforts to enhance nutritional value of proteins through protein engineerings. It is isolated from Jack Bean because of it's potential as a nutritional substance. Principal Investigator was Alexander McPherson.

Effect of the Creative Drama-Based Assertiveness Program on the Assertiveness Skill of Psychological Counsellor Candidates

ERIC Educational Resources Information Center

Gundogdu, Rezzan

2012-01-01

The purpose of this quasi-experimental research is to study the effects of the creative drama-based assertiveness program (CDBAP) on the assertiveness skill of Psychological Counselling and Guidance (PCG) department students. The opinions of experimental group students on the program were obtained through the CDBAP evaluation form. The sample of…

The Influence of Choice Theory Anger Management Program (CTAMP) on the Ability of Prospective Psychological Counselors for Anger Management

ERIC Educational Resources Information Center

Gündogdu, Rezzan

2018-01-01

This research is a quasi-experimental study with pretest-posttest-fallow up test and experiment-control group to investigate the influence of Choice Theory-based Anger Management Psychoeducation Program (CTAMP) on the ability of students of Department of Psychological Counseling and Guidance (PCG) for anger management. The Trait Anger-Anger Style…

Microgravity

NASA Image and Video Library

1989-02-03

(PCG) Protein Crystal Growth Human Serum Albumin. Contributes to many transport and regulatory processes and has multifunctional binding properties which range from various metals, to fatty acids, hormones, and a wide spectrum of therapeutic drugs. The most abundant protein of the circulatory system. It binds and transports an incredible variety of biological and pharmaceutical ligands throughout the blood stream. Principal Investigator on STS-26 was Larry DeLucas.

PCG, Pilot Kent Rominger transfers protein crystal vials to Sacco in Spacelab

NASA Image and Video Library

1995-11-05

STS073-351-009 (20 October - 5 November 1995) --- Astronaut Kent V. Rominger, STS-73 pilot, retrieves a protein sample on the middeck of the Earth-orbiting Space Shuttle Columbia. Rominger, along with four other NASA astronauts and two guest researchers, spent 16 full days in space in support of the United States Microgravity Laboratory (USML-2) mission.

Charting the Functional Relevance of Broca's Area for Visual Word Recognition and Picture Naming in Dutch Using fMRI-Guided TMS

ERIC Educational Resources Information Center

Wheat, Katherine L.; Cornelissen, Piers L.; Sack, Alexander T.; Schuhmann, Teresa; Goebel, Rainer; Blomert, Leo

2013-01-01

Magnetoencephalography (MEG) has shown pseudohomophone priming effects at Broca's area (specifically pars opercularis of left inferior frontal gyrus and precentral gyrus; LIFGpo/PCG) within [approximately]100 ms of viewing a word. This is consistent with Broca's area involvement in fast phonological access during visual word recognition. Here we…

Investigating the Attitude of PCG University Students towards Their Parents and towards Marriage

ERIC Educational Resources Information Center

Görkem, Anil; Bengisoy, Ayse

2018-01-01

The aim of this study is to investigate students in classes 1-2-3-4, studying Pyschological Guidance and Counselling (PGC) at a university in T.R.N.C. (Turkish Republic of Northern Cyprus) in their relationships with their parents and their attitudes towards marriage. The study includes 325 students and was conducted during the spring of…

Protein crystal growth results from shuttle flight 51-F

NASA Technical Reports Server (NTRS)

Bugg, C. E.

1985-01-01

The protein crystal growth (PCG) experiments run on 51-F were analyzed. It was found that: (1) sample stability is increased over that observed during the experiments on flight 51-D; (2) the dialysis experiments produced lysozyme crystals that were significantly larger than those obtained in our identical ground-based studies; (3) temperature fluctuations apparently caused problems during the crystallization experiments on 51-F; (4) it is indicated that teflon tape stabilizes droplets on the syringe tips; (5) samples survived during the reentry and landing in glass tips that were not stoppered with plungers; (6) from the ground-based studies, it was expected that equilibration should be complete within 2 to 4 days for all of these vapor-diffusion experiments, thus it appears that the vapor diffusion rates are somewhat slower under microgravity conditions; (7) drop tethering was highly successful, all four of the tethered drops were stable, even though they contained MPD solutions; (8) the PCG experiments on 51-F were done to assess the hardware and experimental procedures that are developed for future flights, when temperature control will be available. Lysozyme crystals obtained by microdialysis are considerably larger than those obtained on the ground, using the identical apparatus and procedures.

Increased Production of Food-Grade d-Tagatose from d-Galactose by Permeabilized and Immobilized Cells of Corynebacterium glutamicum, a GRAS Host, Expressing d-Galactose Isomerase from Geobacillus thermodenitrificans.

PubMed

Shin, Kyung-Chul; Sim, Dong-Hyun; Seo, Min-Ju; Oh, Deok-Kun

2016-11-02

The generally recognized as safe microorganism Corynebacterium glutamicum expressing Geobacillus thermodenitrificans d-galactose isomerase (d-GaI) was an efficient host for the production of d-tagatose, a functional sweetener. The d-tagatose production at 500 g/L d-galactose by the host was 1.4-fold higher than that by Escherichia coli expressing d-GaI. The d-tagatose-producing activity of permeabilized C. glutamicum (PCG) cells treated with 1% (w/v) Triton X-100 was 2.1-fold higher than that of untreated cells. Permeabilized and immobilized C. glutamicum (PICG) cells in 3% (w/v) alginate showed a 3.1-fold longer half-life at 50 °C and 3.1-fold higher total d-tagatose concentration in repeated batch reactions than PCG cells. PICG cells, which produced 165 g/L d-tagatose after 3 h, with a conversion of 55% (w/w) and a productivity of 55 g/L/h, showed significantly higher d-tagatose productivity than that reported for other cells. Thus, d-tagatose production by PICG cells may be an economical process to produce food-grade d-tagatose.

Cardiorespiratory system monitoring using a developed acoustic sensor.

PubMed

Abbasi-Kesbi, Reza; Valipour, Atefeh; Imani, Khadije

2018-02-01

This Letter proposes a wireless acoustic sensor for monitoring heartbeat and respiration rate based on phonocardiogram (PCG). The developed sensor comprises a processor, a transceiver which operates at industrial, scientific and medical band and the frequency of 2.54 GHz as well as two capacitor microphones which one for recording the heartbeat and another one for respiration rate. To evaluate the precision of the presented sensor in estimating heartbeat and respiration rate, the sensor is tested on the different volunteers and the obtained results are compared with a gold standard as a reference. The results reveal that root-mean-square error are determined <2.27 beats/min and 0.92 breaths/min for the heartbeat and respiration rate in turn. While the standard deviation of the error is obtained <1.26 and 0.63 for heartbeat and respiration rate, respectively. Also, the sensor estimate sounds of [Formula: see text] to [Formula: see text] obtained PCG signal with sensitivity and specificity 98.1% and 98.3% in turn that make 3% improvement than previous works. The results prove that the sensor can be appropriate candidate for recognising abnormal condition in the cardiorespiratory system.

Application of Russian Thermo-Electric Devices (TEDS) for the US Microgravity Program Protein Crystal Growth (PCG) Project

NASA Technical Reports Server (NTRS)

Aksamentov, Valery

1996-01-01

Changes in the former Soviet Union have opened the gate for the exchange of new technology. Interest in this work has been particularly related to Thermal Electric Cooling Devices (TED's) which have an application for the Thermal Enclosure System (TES) developed by NASA. Preliminary information received by NASA/MSFC indicates that Russian TED's have higher efficiency. Based on that assumption NASA/MSFC awarded a contract to the University of Alabama in Huntsville (UAH) in order to study the Russian TED's technology. In order to fulfill this a few steps should be made: (1) potential specifications and configurations should be defined for use of TED's in Protein Crystal Growing (PCG) thermal control hardware; and (2) work closely with the identified Russian source to define and identify potential Russian TED's to exceed the performance of available domestic TED's. Based on the data from Russia, it is possible to make plans for further steps such as buying and testing high performance TED's. To accomplish this goal two subcontracts have been released. One subcontract to Automated Sciences Group (ASG) located in Huntsville, AL and one to the International Center for Advanced Studies 'Cosmos' located in Moscow, Russia.

DMA Modulus as a Screening Parameter for Compatibility of Polymeric Containment Materials with Various Solutions for use in Space Shuttle Microgravity Protein Crystal Growth (PCG) Experiments

NASA Technical Reports Server (NTRS)

Wingard, Charles Doug; Munafo, Paul M. (Technical Monitor)

2002-01-01

Protein crystals are grown in microgravity experiments inside the Space Shuttle during orbit. Such crystals are basically grown in a five-component system containing a salt, buffer, polymer, organic and water. During these experiments, a number of different polymeric containment materials must be compatible with up to hundreds of different PCG solutions in various concentrations for durations up to 180 days. When such compatibility experiments are performed at NASA/MSFC (Marshall Space Flight Center) simultaneously on containment material samples immersed in various solutions in vials, the samples are rather small out of necessity. DMA4 modulus was often used as the primary screening parameter for such small samples as a pass/fail criterion for incompatibility issues. In particular, the TA Instruments DMA 2980 film tension clamp was used to test rubber O-rings as small in I.D. as 0.091 in. by cutting through the cross-section at one place, then clamping the stretched linear cord stock at each end. The film tension clamp was also used to successfully test short length samples of medical/surgical grade tubing with an O.D. of 0.125 in.

Aronia melanocarpa Treatment and Antioxidant Status in Selected Tissues in Wistar Rats

PubMed Central

Krośniak, Mirosław; Sanocka, Ilona; Bartoń, Henryk; Hebda, Tomasz; Francik, Sławomir

2014-01-01

Aronia juice is considered to be a source of compounds with high antioxidative potential. We conducted a study on the impact of compounds in the Aronia juice on oxidative stress in plasma and brain tissues. The influence of Aronia juice on oxidative stress parameters was tested with the use of a model with a high content of fructose and nonsaturated fats. Therefore, the activity of enzymatic (catalase, CAT, and paraoxonase, PON) and nonenzymatic (thiol groups, SH, and protein carbonyl groups, PCG) oxidative stress markers, which indicate changes in the carbohydrate and protein profiles, was marked in brain tissue homogenates. Adding Aronia caused statistically significant increase in the CAT activity in plasma in all tested diets, while the PON activity showed a statistically significant increase only in case of high fat diet. In animals fed with Aronia juice supplemented with carbohydrates or fat, statistically significant increase in the PON activity and the decrease in the CAT activity in brain tissue were observed. In case of the high fat diet, an increase in the number of SH groups and a decrease in the number of PCG groups in brain tissue were observed. PMID:25057488

Aronia melanocarpa treatment and antioxidant status in selected tissues in Wistar rats.

PubMed

Francik, Renata; Krośniak, Mirosław; Sanocka, Ilona; Bartoń, Henryk; Hebda, Tomasz; Francik, Sławomir

2014-01-01

Aronia juice is considered to be a source of compounds with high antioxidative potential. We conducted a study on the impact of compounds in the Aronia juice on oxidative stress in plasma and brain tissues. The influence of Aronia juice on oxidative stress parameters was tested with the use of a model with a high content of fructose and nonsaturated fats. Therefore, the activity of enzymatic (catalase, CAT, and paraoxonase, PON) and nonenzymatic (thiol groups, SH, and protein carbonyl groups, PCG) oxidative stress markers, which indicate changes in the carbohydrate and protein profiles, was marked in brain tissue homogenates. Adding Aronia caused statistically significant increase in the CAT activity in plasma in all tested diets, while the PON activity showed a statistically significant increase only in case of high fat diet. In animals fed with Aronia juice supplemented with carbohydrates or fat, statistically significant increase in the PON activity and the decrease in the CAT activity in brain tissue were observed. In case of the high fat diet, an increase in the number of SH groups and a decrease in the number of PCG groups in brain tissue were observed.

Determination of the Needs of University Students for Psychological Counseling and Guidance Services: The Case of Kocaeli University, Turkey

ERIC Educational Resources Information Center

Ulusoy, Yildiz Ö.; Varlikli, Gülsen; Dag, Funda; Sahranç, Ümit; Turan, Hakan

2014-01-01

The purpose of the study is to explain the needs of the students of Kocaeli University (KOU) for psychological counseling and guidance (PCG) services. KOU students constituted the population of the study and 6662 students chosen to represent minimum 10% of the total student number in all academic units from the same population constituted. A…

A post-Rosetta understanding of polarimetric observations of comets

NASA Astrophysics Data System (ADS)

Levasseur-Regourd, A. Chantal; Ciarletti, Valérie; Hadamcik, Edith; Lasue, Jérémie; Mannel, Thurid

2017-04-01

Numerous polarimetric observations of solar light scattered by dust in cometary comae have been obtained by various teams, providing phase angle and wavelength dependences for many comets and revealing different classes of comets [e.g., 1]. Besides, numerical and experimental simulations have suggested interpretations for such observations. The Rosetta long duration rendezvous with comet 67P/Churyumov-Gerasimenko (thereafter 67P/C-G) now allows us to compare our understanding of the polarimetric properties of cometary dust with the ground-truth provided by the Rosetta mission, at least for two typical results. First, some comets present a highly-polarized positive branch, the most conspicuous case being that of new comet C/1995 O1 Hale-Bopp [2], while other comets suffering a partial fragmentation or a total disruption, such as C/1995 S4 LINEAR [3], present a significant increase in polarization. We will discuss these observations in the context of evidence for changes between the porosity (and possibly the dust/ice ratio) of the subsurface and of the interior of 67P/C-G, a periodic Jupiter Family Comet, as derived from analyses [4] of the CONSERT bi-static radar measurements on board Rosetta and Philae. Secondly, numerical simulations of the phase and wavelength dependence of polarimetric observations of some comets (extensively observed on a wide range of wavelengths and phase angles) have suggested the presence of fractal, likely-porous aggregates and of compact particles within their comae [e.g., 5]. We will review such results in the context of evidence for porous and compact aggregates of submicron-sized grains in the inner coma of 67P/C-G [6], as given by 3D images (with a resolution down to tens of nanometers) of the MIDAS atomic force microscope on board Rosetta. References: [1] Kiselev et al., 2015, In Polarization of stars and planetary systems, CUP 379-404. [2] Levasseur-Regourd & Hadamcik, 2003, JQSRT 79-80, 903-910. [3] Hadamcik & Levasseur-Regourd, 2003, Icarus 166, 188-194. [4] Ciarletti et al., 2015, Astron. Astrophys. 583, A40. [5] Lasue et al., 2009, Icarus 199, 129-144. [6] Mannel et al., 2016, MNRAS 462, S 304-S311.

[Effects of granulocyte-macrophage colony stimulating factor on nuclear factor-KappaB activation in multiple organs of hemorrhage-induced acute lung injury in mice].

PubMed

Wang, Qian; Song, Yong; Shi, Yi

2007-05-01

To investigate the effects of nuclear factor-KappaB (NF-KappaB) activation in multiple organs of hemorrhage-induced acute lung injury (ALI) by the specific granulocyte-macrophage colony stimulating factor (GM-CSF)-neutralizing antibody (22E9) and dexamethasone (DEX) in mice. Twenty male C57BL/6 mice were used to reproduce a model of hemorrhagic shock by cardiac puncture. Before cardiac puncture, mice in different groups were transnasally administered with phosphate buffered solution (PBS, PCG group), PBS plus 1 microg 22E9 (HS1 group), PBS plus 10 microg 22E9 (HS10 group) and PBS plus 20 microg DEX (DEX group), respectively. In negative control group (NCG group) received cardiac puncture without shock followed by transnasal administration with PBS without shock. Lungs, hearts, livers and kidneys tissues of mice were harvested at 4 hours after hemorrhagic shock. The activities of NF-KappaB in different organs was determined by electrophoretic mobility shift assay (EMSA). The tumor necrosis factor-alpha (TNF-alpha) in lung and heart were determined by enzyme-linked immunosorbent assay (ELISA). 22E9 in both low or high doses could significantly inhibit NF-KappaB activities in lung, heart and liver, and elevated NF-KappaB activity in kidney compared with those of PCG group (all P<0.05). The effect of 22E9 was much better in HS1 group than in HS10 group (all P<0.05). DEX significantly strengthened NF-KappaB activity in kidney (P<0.05) and didn't significantly inhibit NF-KappaB activities in heart and liver compared with those of PCG group. 22E9 significantly inhibited TNF-alpha in lung and heart, while DEX significantly inhibited TNF-alpha in heart (all P<0.05). 22E9 can inhibit the NF-KappaB activation and inflammatory reaction in multiple organs after hemorrhage-induced ALI and reduce injury in multiple organs, while DEX has no significant effect.

Dai-Kou type conjugate gradient methods with a line search only using gradient.

PubMed

Huang, Yuanyuan; Liu, Changhe

2017-01-01

In this paper, the Dai-Kou type conjugate gradient methods are developed to solve the optimality condition of an unconstrained optimization, they only utilize gradient information and have broader application scope. Under suitable conditions, the developed methods are globally convergent. Numerical tests and comparisons with the PRP+ conjugate gradient method only using gradient show that the methods are efficient.

On the Convergence Analysis of the Optimized Gradient Method.

PubMed

Kim, Donghwan; Fessler, Jeffrey A

2017-01-01

This paper considers the problem of unconstrained minimization of smooth convex functions having Lipschitz continuous gradients with known Lipschitz constant. We recently proposed the optimized gradient method for this problem and showed that it has a worst-case convergence bound for the cost function decrease that is twice as small as that of Nesterov's fast gradient method, yet has a similarly efficient practical implementation. Drori showed recently that the optimized gradient method has optimal complexity for the cost function decrease over the general class of first-order methods. This optimality makes it important to study fully the convergence properties of the optimized gradient method. The previous worst-case convergence bound for the optimized gradient method was derived for only the last iterate of a secondary sequence. This paper provides an analytic convergence bound for the primary sequence generated by the optimized gradient method. We then discuss additional convergence properties of the optimized gradient method, including the interesting fact that the optimized gradient method has two types of worstcase functions: a piecewise affine-quadratic function and a quadratic function. These results help complete the theory of an optimal first-order method for smooth convex minimization.

On the Convergence Analysis of the Optimized Gradient Method

PubMed Central

Kim, Donghwan; Fessler, Jeffrey A.

2016-01-01

This paper considers the problem of unconstrained minimization of smooth convex functions having Lipschitz continuous gradients with known Lipschitz constant. We recently proposed the optimized gradient method for this problem and showed that it has a worst-case convergence bound for the cost function decrease that is twice as small as that of Nesterov’s fast gradient method, yet has a similarly efficient practical implementation. Drori showed recently that the optimized gradient method has optimal complexity for the cost function decrease over the general class of first-order methods. This optimality makes it important to study fully the convergence properties of the optimized gradient method. The previous worst-case convergence bound for the optimized gradient method was derived for only the last iterate of a secondary sequence. This paper provides an analytic convergence bound for the primary sequence generated by the optimized gradient method. We then discuss additional convergence properties of the optimized gradient method, including the interesting fact that the optimized gradient method has two types of worstcase functions: a piecewise affine-quadratic function and a quadratic function. These results help complete the theory of an optimal first-order method for smooth convex minimization. PMID:28461707

(PCG) Protein Crystal Growth Horse Serum Albumin

NASA Technical Reports Server (NTRS)

1995-01-01

Horse Serum Albumin crystals grown during the USML-1 (STS-50) mission's Protein Crystal Growth Glovebox Experiment. These crystals were grown using a vapor diffusion technique at 22 degrees C. The crystals were allowed to grow for nine days while in orbit. Crystals of 1.0 mm in length were produced. The most abundant blood serum protein, regulates blood pressure and transports ions, metabolites, and therapeutic drugs. Principal Investigator was Edward Meehan.

STS-67 Space Shuttle mission report

NASA Technical Reports Server (NTRS)

Fricke, Robert W., Jr.

1995-01-01

The STS-67 Space Shuttle Program Mission Report provides the results of the orbiter vehicle performance evaluation during this sixty-eighth flight of the Shuttle Program, the forty-third flight since the return to flight, and the eighth flight of the Orbiter vehicle Endeavour (OV-105). In addition, the report summarizes the payload activities and the performance of the External Tank (ET), Solid Rocket Booster (SRB), Reusable Solid Rocket Motor (RSRM), and the Space Shuttle Main Engines (SSME). The serial numbers of the other elements of the flight vehicle were ET-69 for the ET; 2012, 2033, and 2031 for SSME's 1, 2, and 3, respectively; and Bl-071 for the SRB's. The left-hand RSRM was designated 360W043A, and the right-hand RSRM was designated 360L043B. The primary objective of this flight was to successfully perform the operations of the ultraviolet astronomy (ASTRO-2) payload. Secondary objectives of this flight were to complete the operations of the Protein Crystal Growth - Thermal Enclosure System (PCG-TES), the Protein Crystal Growth - Single Locker Thermal Enclosure System (PCG-STES), the Commercial Materials Dispersion Apparatus ITA Experiments (CMIX), the Shuttle Amateur Radio Experiment-2 (SAREX-2), the Middeck Active Control Experiment (MACE), and two Get-Away Special (GAS) payloads.

Validation of the Choking Risk Assessment and Pneumonia Risk Assessment for adults with Intellectual and Developmental Disability (IDD).

PubMed

Sheppard, Justine Joan; Malandraki, Georgia A; Pifer, Paula; Cuff, Jill; Troche, Michelle; Hemsley, Bronwyn; Balandin, Susan; Mishra, Avinash; Hochman, Roberta

2017-10-01

Risk assessments are needed to identify adults with intellectual and developmental disability (IDD) at high risk of choking and pneumonia. To describe the development and validation of the Choking Risk Assessment (CRA) and the Pneumonia Risk Assessment (PRA) for adults with IDD. Test items were identified through literature review and focus groups. Five-year retrospective chart reviews identified a positive choking group (PCG), a negative choking group (NCG), a positive pneumonia group (PPG), and a negative pneumonia group (NPG). Participants were tested with the CRA and PRA by clinicians blind to these testing conditions. The CRA and PRA differentiated the PCG (n=93) from the NCG (n=526) and the PPG (n=63) from the NPG (n=209) with high specificity (0.91 and 0.92 respectively) and moderate to average sensitivity (0.53 and 0.62 respectively). Further analyses revealed associations between clinical diagnoses of dysphagia and choking (p=0.043), and pneumonia (p<0.001). The CRA and PRA are reliable, valid risk indicators for choking and pneumonia in adults with IDD. Precautions for mitigating choking and pneumonia risks can be applied selectively thus avoiding undue impacts on quality of life and unnecessary interventions for low risk individuals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level

PubMed Central

Liu, Jie; Bu, Cuiping; Wipfler, Benjamin; Liang, Aiping

2014-01-01

The present study compares the mitochondrial genomes of five species of the spittlebug tribe Callitettixini (Hemiptera: Cercopoidea: Cercopidae) from eastern Asia. All genomes of the five species sequenced are circular double-stranded DNA molecules and range from 15,222 to 15,637 bp in length. They contain 22 tRNA genes, 13 protein coding genes (PCGs) and 2 rRNA genes and share the putative ancestral gene arrangement of insects. The PCGs show an extreme bias of nucleotide and amino acid composition. Significant differences of the substitution rates among the different genes as well as the different codon position of each PCG are revealed by the comparative evolutionary analyses. The substitution speeds of the first and second codon position of different PCGs are negatively correlated with their GC content. Among the five species, the AT-rich region features great differences in length and pattern and generally shows a 2–5 times higher substitution rate than the fastest PCG in the mitochondrial genome, atp8. Despite the significant variability in length, short conservative segments were identified in the AT-rich region within Callitettixini, although absent from the other groups of the spittlebug superfamily Cercopoidea. PMID:25285442

Catastrophic disruptions as the origin of bilobate comets

NASA Astrophysics Data System (ADS)

Schwartz, Stephen R.; Michel, Patrick; Jutzi, Martin; Marchi, Simone; Zhang, Yun; Richardson, Derek C.

2018-05-01

Several comets observed at close range have bilobate shapes1, including comet 67P/Churyumov-Gerasimenko (67P/C-G), which was imaged by the European Space Agency's Rosetta mission2,3. Bilobate comets are thought to be primordial because they are rich in supervolatiles (for example, N2 and CO) and have a low bulk density, which implies that their formation requires a very low-speed accretion of two bodies. However, slow accretion does not only occur during the primordial phase of the Solar System; it can also occur at later epochs as part of the reaccumulation process resulting from the collisional disruption of a larger body4, so this cannot directly constrain the age of bilobate comets. Here, we show by numerical simulation that 67P/C-G and other elongated or bilobate comets can be formed in the wake of catastrophic collisional disruptions of larger bodies while maintaining their volatiles and low density throughout the process. Since this process can occur at any epoch of our Solar System's history, from early on through to the present day5, there is no need for these objects to be formed primordially. These findings indicate that observed prominent geological features, such as pits and stratified surface layers4,5, may not be primordial.

Protein crystal growth (5-IML-1)

NASA Technical Reports Server (NTRS)

Bugg, Charles E.

1992-01-01

Proteins (enzymes, hormones, immunoglobulins) account for 50 pct. or more of the dry weight of most living systems. A detailed understanding of the structural makeup of a protein is essential to any systematic research pertaining to it. Most macromolecules are extremely difficult to crystallize, and many otherwise exciting projects have terminated at the crystal growth stage. In principle, there are several aspects of microgravity that might be exploited to enhance protein crystal growth. The major factor is the elimination of density driven convective flow. Other factors that can be controlled in the absence of gravity is the sedimentation of growing crystals in a gravitational field, and the potential advantage of doing containerless crystal growth. As a result of these theories and facts, one can readily understand why the microgravity environment of an Earth orbiting vehicle seems to offer unique opportunities for the protein crystallographer. This perception has led to the establishment of the Protein Crystal Growth in a Microgravity Environment (PCG/ME) project. The results of experiments already performed during STS missions have in many cases resulted in large protein crystals which are structurally correct. Thus, the near term objective of the PCG/ME project is to continue to improve the techniques, procedures, and hardware systems used to grow protein crystals in Earth orbit.

Interpretation of the instantaneous frequency of phonocardiogram signals

NASA Astrophysics Data System (ADS)

Rey, Alexis B.

2005-06-01

Short-Time Fourier transforms, Wigner-Ville distribution, and Wavelet Transforms have been commonly used when dealing with non-stationary signals, and they have been known as time-frequency distributions. Also, it is commonly intended to investigate the behaviour of phonocardiogram signals as a means of prediction some oh the pathologies of the human hart. For this, this paper aims to analyze the relationship between the instantaneous frequency of a PCG signal and the so-mentioned time-frequency distributions; three algorithms using Matlab functions have been developed: the first one, the estimation of the IF using the normalized linear moment, the second one, the estimation of the IF using the periodic first moment, and the third one, the computing of the WVD. Meanwhile, the computing of the STFT spectrogram is carried out with a Matlab function. Several simulations of the spectrogram for a set of PCG signals and the estimation of the IF are shown, and its relationship is validated through correlation. Finally, the second algorithm is a better choice because the estimation is not biased, whereas the WVD is very computing-demanding and offers no benefit since the estimation of the IF by using this TFD has an equivalent result when using the derivative of the phase of the analytic signal, which is also less computing-demanding.

Does Informal Caregiving Lead to Parental Burnout? Comparing Parents Having (or Not) Children With Mental and Physical Issues

PubMed Central

Gérain, Pierre; Zech, Emmanuelle

2018-01-01

Introduction: Parenting a child with special needs (CSN) may be an important challenge. Previous research has highlighted an increased risk of parental burnout among parents caring for their CSN. Yet, these studies only focused on children with specific issues and did not consider the wide variety of CSN. There is thus a need to take a more global approach to assessing the impact of caring for a CSN on parental burnout. In addition, the impact on parental burnout of personality and parenting (dis)agreement needs to be measured to have a better understanding of parent-caregivers’ (PCgs) burnout. Method: An online survey was completed by a large sample of parents from which a subsample of PCgs was identified. Results: T-tests highlighted significantly more parental burnout among parents of CSN. However, further analyses showed that parents with only one child with one special need did not experience significantly more burnout than parents with typical children. The significant difference lay in the presence of comorbidity or the presence of multiple CSN in the family. Hierarchical regressions showed an important impact of Neuroticism for every burnout facet, along with co-parenting (dis)agreement. Subjective consequences of having to care for a CSN were also related to the burnout facets of both emotional exhaustion and emotional distancing. Discussion: The presence of comorbidity and of multiple CSN in the family were related to more PCg burnout, emphasizing the need to consider these situations in further research. The role of neuroticism in PCg burnout confirms previous research both in parental and professional contexts. Parenting (dis)agreement also highlights the importance of dyadic support among parents. Finally, the importance of subjective aspects suggests that parental perception of their situation remains a central element in understanding the consequences of caregiving. PMID:29928242

Large Airborne Full Tensor Gradient Data Inversion Based on a Non-Monotone Gradient Method

NASA Astrophysics Data System (ADS)

Sun, Yong; Meng, Zhaohai; Li, Fengting

2018-03-01

Following the development of gravity gradiometer instrument technology, the full tensor gravity (FTG) data can be acquired on airborne and marine platforms. Large-scale geophysical data can be obtained using these methods, making such data sets a number of the "big data" category. Therefore, a fast and effective inversion method is developed to solve the large-scale FTG data inversion problem. Many algorithms are available to accelerate the FTG data inversion, such as conjugate gradient method. However, the conventional conjugate gradient method takes a long time to complete data processing. Thus, a fast and effective iterative algorithm is necessary to improve the utilization of FTG data. Generally, inversion processing is formulated by incorporating regularizing constraints, followed by the introduction of a non-monotone gradient-descent method to accelerate the convergence rate of FTG data inversion. Compared with the conventional gradient method, the steepest descent gradient algorithm, and the conjugate gradient algorithm, there are clear advantages of the non-monotone iterative gradient-descent algorithm. Simulated and field FTG data were applied to show the application value of this new fast inversion method.

Multiscale Modeling of Hall Thrusters. Chapter 7: Plume Modeling

DTIC Science & Technology

2012-03-06

Quasineutral Potential Fix Finally, a ”quasi-neutral” switch has been implemented in the Draco Gauss - Seidel Solver. Implementation in the PCG solver is...unlimited. 4 (a) (b) Figure 7.2: Potential solution obtained for a single and multiple (16) zones Hence, part of the development effort went into...be seen from this plot, the two solutions are identical. The division of mesh into multiple zones had another benefit for parallel compu- tations

Microgravity

NASA Image and Video Library

2000-11-03

On the Space Shuttle Orbiter Atlantis' middeck, Astronaut Joseph R. Tarner, mission specialist, works at an area amidst several lockers which support the Protein Crystal Growth (PCG) experiment during the STS-66 mission. This particular section is called the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES). Together with the Vapor Diffusion Apparatus (VDA), housed in Single Locker Thermal Enclosure (SLTES), the COS/TES represents the continuing research into the structure of proteins and other macromolecules such as viruses.

A penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography.

PubMed

Shang, Shang; Bai, Jing; Song, Xiaolei; Wang, Hongkai; Lau, Jaclyn

2007-01-01

Conjugate gradient method is verified to be efficient for nonlinear optimization problems of large-dimension data. In this paper, a penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography (FMT) is presented. The algorithm combines the linear conjugate gradient method and the nonlinear conjugate gradient method together based on a restart strategy, in order to take advantage of the two kinds of conjugate gradient methods and compensate for the disadvantages. A quadratic penalty method is adopted to gain a nonnegative constraint and reduce the illposedness of the problem. Simulation studies show that the presented algorithm is accurate, stable, and fast. It has a better performance than the conventional conjugate gradient-based reconstruction algorithms. It offers an effective approach to reconstruct fluorochrome information for FMT.

Modified conjugate gradient method for diagonalizing large matrices.

PubMed

Jie, Quanlin; Liu, Dunhuan

2003-11-01

We present an iterative method to diagonalize large matrices. The basic idea is the same as the conjugate gradient (CG) method, i.e, minimizing the Rayleigh quotient via its gradient and avoiding reintroducing errors to the directions of previous gradients. Each iteration step is to find lowest eigenvector of the matrix in a subspace spanned by the current trial vector and the corresponding gradient of the Rayleigh quotient, as well as some previous trial vectors. The gradient, together with the previous trial vectors, play a similar role as the conjugate gradient of the original CG algorithm. Our numeric tests indicate that this method converges significantly faster than the original CG method. And the computational cost of one iteration step is about the same as the original CG method. It is suitable for first principle calculations.

Nucleus structure and dust morphology: Post-Rosetta understanding and implications

NASA Astrophysics Data System (ADS)

Levasseur-Regourd, A.; Bentley, Mark; Ciarletti, Valérie; Kofman, Woldek; Lasue, Jeremie; Mannel, Thurid; Herique, Alain

2017-10-01

The structure of cometary nuclei and the morphology of dust particles they eject have long been unknowns in cometary science. The combination of these two subjects, as revealed by the Rosetta mission at 67P/C-G, is currently providing an unprecedented insight about Solar System formation and early evolution.Rosetta has established that the bulk porosity of 67P/C-G nucleus is high, in the 70% to 85% range, both from the determination of its density and from permittivity measurements with CONSERT bistatic radar experiment [1-2]. CONSERT, through operations after Philae landing on 12-13 November 2014, has also allowed us to estimate that i) the porosity is likely to be higher inside the nucleus than on its subsurface, ii) a major component of the nucleus is refractory carbonaceous compounds, and iii) the small lobe is homogeneous at a scale of a few wavelengths (i.e., about 10 m), while heterogeneities in the 3-m range (similar to the rounded nodules noticed on walls of large pits) cannot be ruled out [2-4].Rosetta has also established, through its 26 months rendezvous with 67P/C-G, the aggregated structure of dust particles within a wide range of sizes in the inner cometary coma. The MIDAS atomic force microscope experiment has given us evidence (from 3D topographic images with nano- to micrometer resolution) for i) a hierarchical structure of aggregated dust particles, down to tens of nm-sized grains, ii) one extremely porous dust particle, with a fractal dimension of (1.7 ± 0.1) [5-6]. The accuracy of comparisons between cometary dust particles and interplanetary dust particles collected in the stratosphere (including CP-IDPs) could thus be improved.Such results should further refine the main processes (e.g., low velocity aggregation) that allowed the formation of comets in the early Solar System, and the implications of a possible late heavy bombardment on the interplanetary dust clouds and on telluric planets.References. 1. Pätzold et al. Nature 530 63 2016. 2. Kofman et al. Science 349 6247 2015. 3. Herique et al. MNRAS 462 S516 2016. 4. Ciarletti et al. A&A 583 A40 2015. 5. Bentley et al., Nature 537 73 2016. 6. Mannel et al., MNRAS 462 S304 2016.

Disruptive collisions as the origin of 67P/C-G and small bilobate comets

NASA Astrophysics Data System (ADS)

Michel, Patrick; Schwartz, Stephen R.; Jutzi, Martin; Marchi, Simone; Richardson, Derek C.; Zhang, Yun

2016-10-01

Images of comets sent by spacecraft have shown us that bilobate shapes seem to be common in the cometary population. This has been most recently evidenced by the images of comet 67P/C-G obtained by the ESA Rosetta mission, which show a low-density elongated body interpreted as a contact binary. The origin of such bilobate comets has been thought to be primordial because it requires the slow accretion of two bodies that become the two main components of the final object. However, slow accretion does not only occur during the primordial phase of the Solar System, but also later during the reaccumulation processes immediately following collisional disruptions of larger bodies. We perform numerical simulations of disruptions of large bodies. We demonstrate that during the ensuing gravitational phase, in which the generated fragments interact under their mutual gravity, aggregates with bi-lobed or elongated shapes formed form by reaccumulation at speeds that are at or below the range of those assumed in primordial accretion scenarios [1]. The same scenario has been demonstrated to occur in the asteroid belt to explain the origin of asteroid families [2] and has provided insight into the shapes of thus-far observed asteroids such as 25143 Itokawa [3]. Here we show that it is also a more general outcome that applies to disruption events in the outer Solar System. Moreover, we show that high temperature regions are very localized during the impact process, which solves the problem of the survival of organics and volatiles in the collisional process. The advantage of this scenario for the formation of small bilobate shapes, including 67P/C-G, is that it does not necessitate a primordial origin, as such disruptions can occur at later stages of the Solar System. This demonstrates how such comets can be relatively young, consistent with other studies that show that these shapes are unlikely to be formed early on and survive the entire history of the Solar System [4].[1] Schwartz, S.R. et al. 2016, in preparation; [2] Michel, P. et al. 2001, Science 294, 1696; [3] Michel, P., Richardson, D.C. 2013, A&A 554, L1; [4] Jutzi, M. et al. 2016 submitted to A&A.

Momentum-weighted conjugate gradient descent algorithm for gradient coil optimization.

PubMed

Lu, Hanbing; Jesmanowicz, Andrzej; Li, Shi-Jiang; Hyde, James S

2004-01-01

MRI gradient coil design is a type of nonlinear constrained optimization. A practical problem in transverse gradient coil design using the conjugate gradient descent (CGD) method is that wire elements move at different rates along orthogonal directions (r, phi, z), and tend to cross, breaking the constraints. A momentum-weighted conjugate gradient descent (MW-CGD) method is presented to overcome this problem. This method takes advantage of the efficiency of the CGD method combined with momentum weighting, which is also an intrinsic property of the Levenberg-Marquardt algorithm, to adjust step sizes along the three orthogonal directions. A water-cooled, 12.8 cm inner diameter, three axis torque-balanced gradient coil for rat imaging was developed based on this method, with an efficiency of 2.13, 2.08, and 4.12 mT.m(-1).A(-1) along X, Y, and Z, respectively. Experimental data demonstrate that this method can improve efficiency by 40% and field uniformity by 27%. This method has also been applied to the design of a gradient coil for the human brain, employing remote current return paths. The benefits of this design include improved gradient field uniformity and efficiency, with a shorter length than gradient coil designs using coaxial return paths. Copyright 2003 Wiley-Liss, Inc.

Prostate Cancer Aggressiveness Gene in Hereditary Prostate Cancer

DTIC Science & Technology

2007-03-01

with REA, and estrogen receptor corepressor. Breast Canc Res Treat., in press (2007). This grant provided research support for Dr Veda Giri while...an estrogen receptor corepressor Clara Hwang Æ Veda N. Giri Æ John C. Wilkinson Æ Casey W. Wright Æ Amanda S. Wilkinson Æ Kathleen A. Cooney Æ Colin S...histone deacetylases (HDAC), and members of the polycomb group (PcG) of proteins. Clara Hwang and Veda N. Giri contributed equally to this work. C

(PCG) Protein Crystal Growth HIV Reverse Transcriptase

NASA Technical Reports Server (NTRS)

1992-01-01

HIV Reverse Transcriptase crystals grown during the USML-1 (STS-50) mission using Commercial Refrigerator/Incubator Module (CR/IM) at 4 degrees C and the Vapor Diffusion Apparatus (VDA). Reverse transcriptase is an enzyme responsible for copying the nucleic acid genome of the AIDS virus from RNA to DNA. Studies indicated that the space-grown crystals were larger and better ordered (beyond 4 angstroms) than were comparable Earth-grown crystals. Principal Investigators were Charles Bugg and Larry DeLucas.

Cost and clinical consequence of antibiotic non-adherence in acute exacerbations of chronic bronchitis.

PubMed

Sorensen, S V; Baker, T; Fleurence, R; Dixon, J; Roberts, C; Haider, S; Hughes, D

2009-08-01

To quantify the impact of non-adherence on the clinical effectiveness of antibiotics for acute exacerbations of chronic bronchitis (AECB) and to estimate the economic consequences for Spain, Italy and the United States. Standard systematic reviewing procedures were followed to identify randomised controlled clinical trials of antibiotic treatment for acute respiratory tract infection for which adherence was reported. A decision-analytic model was then constructed to evaluate the impact of non-adherence to antibiotic treatment on clinical effectiveness and costs per AECB episode. The model compared the total treatment costs, cure rates and incremental costs per cure for a poor compliance group (PCG) against a good compliance group (GCG). Clinical and resource use estimates were from the published literature and physician surveys. Twenty-five articles met the criteria of the systematic review, although only one reported treatment success by adherence status. The relative risk of clinical effectiveness if non-adherent was 0.75 (95%CI 0.73-0.78). Based on this single study, the model predicted that 16-29% more patients would be cured in the GCG vs. the PCG, and payers would save up to euro122, euro179 and US$141 per AECB episode in Spain, Italy and the United States, respectively. Non-adherence to antibiotics for AECB may have an impact on clinical effectiveness, which is associated with increased costs.

The non-contact measure of the heart rate variability by laser Doppler vibrometry: comparison with electrocardiography

NASA Astrophysics Data System (ADS)

Cosoli, G.; Casacanditella, L.; Tomasini, E. P.; Scalise, L.

2016-06-01

The assessment of the heart rate variability (HRV) is of utmost importance, being one of the most promising markers of the activity of the autonomic nervous system and associated to cardiovascular mortality. Different signals can be used to perform HRV, primarily electrocardiography (ECG), photoplethysmography (PPG), phonocardiography (PCG) or vibrocardiography (VCG), since the fundamental aspect is the individuation of a periodic feature strictly correlated with cardiac activity (i.e. R-peak in ECG or the first sound in PCG). In this work, the authors demonstrate that the VCG performances in HRV analysis are sufficiently accurate if compared to the ones measured by ECG (i.e. standard methodology); moreover, the authors want to prove the feasibility of such measurement in correspondence of different measurement points (i.e. carotid artery—which is the typical VCG measurement point—and the radial artery on the wrist)1. Results show that VCG has a mean deviation of  <1 bpm with respect to ECG in heart rate (HR) measurement; carotid artery is the most accurate site for the assessment, but also the radial artery is a valid site, even if with a reduced SNR. With regards to HRV parameters, the mean percentage deviation is  <10% in correspondence of carotid artery, and  ≈16% for the radial artery. So, VCG allows for non-contact monitoring of the cardiac activity.

Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

PubMed Central

Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-01-01

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

Post-exercise cooling techniques in hot, humid conditions.

PubMed

Barwood, Martin James; Davey, Sarah; House, James R; Tipton, Michael J

2009-11-01

Major sporting events are often held in hot and humid environmental conditions. Cooling techniques have been used to reduce the risk of heat illness following exercise. This study compared the efficacy of five cooling techniques, hand immersion (HI), whole body fanning (WBF), an air cooled garment (ACG), a liquid cooled garment (LCG) and a phase change garment (PCG), against a natural cooling control condition (CON) over two periods between and following exercise bouts in 31 degrees C, 70%RH air. Nine males [age 22 (3) years; height 1.80 (0.04) m; mass 69.80 (7.10) kg] exercised on a treadmill at a maximal sustainable work intensity until rectal temperature (T (re)) reached 38.5 degrees C following which they underwent a resting recovery (0-15 min; COOL 1). They then recommenced exercise until T (re) again reached 38.5 degrees C and then undertook 30 min of cooling with (0-15 min; COOL 2A), and without face fanning (15-30 min; COOL 2B). Based on mean body temperature changes (COOL 1), WBF was most effective in extracting heat: CON 99 W; WBF: 235 W; PCG: 141 W; HI: 162 W; ACG: 101 W; LCG: 49 W) as a consequence of evaporating more sweat. Therefore, WBF represents a cheap and practical means of post-exercise cooling in hot, humid conditions in a sporting setting.

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

PubMed Central

Sasnauskas, Giedrius; Kauneckaitė, Kotryna; Siksnys, Virginijus

2018-01-01

Abstract Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5′-CATGCA-3′/5′-TGCATG-3′. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5′-TGCATG-3′ sequence. The VAL1-B3–DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences. PMID:29660015

Development, evaluation and application of a modified micrometeorological gradient method for long-term estimation of gaseous dry deposition over forest canopies.

EPA Science Inventory

Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air–surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen rati...

Fetal Heart Sounds Detection Using Wavelet Transform and Fractal Dimension

PubMed Central

Koutsiana, Elisavet; Hadjileontiadis, Leontios J.; Chouvarda, Ioanna; Khandoker, Ahsan H.

2017-01-01

Phonocardiography is a non-invasive technique for the detection of fetal heart sounds (fHSs). In this study, analysis of fetal phonocardiograph (fPCG) signals, in order to achieve fetal heartbeat segmentation, is proposed. The proposed approach (namely WT–FD) is a wavelet transform (WT)-based method that combines fractal dimension (FD) analysis in the WT domain for the extraction of fHSs from the underlying noise. Its adoption in this field stems from its successful use in the fields of lung and bowel sounds de-noising analysis. The efficiency of the WT–FD method in fHS extraction has been evaluated with 19 simulated fHS signals, created for the present study, with additive noise up to (3 dB), along with the simulated fPCGs database available at PhysioBank. Results have shown promising performance in the identification of the correct location and morphology of the fHSs, reaching an overall accuracy of 89% justifying the efficacy of the method. The WT–FD approach effectively extracts the fHS signals from the noisy background, paving the way for testing it in real fHSs and clearly contributing to better evaluation of the fetal heart functionality. PMID:28944222

Application of the conjugate-gradient method to ground-water models

USGS Publications Warehouse

Manteuffel, T.A.; Grove, D.B.; Konikow, Leonard F.

1984-01-01

The conjugate-gradient method can solve efficiently and accurately finite-difference approximations to the ground-water flow equation. An aquifer-simulation model using the conjugate-gradient method was applied to a problem of ground-water flow in an alluvial aquifer at the Rocky Mountain Arsenal, Denver, Colorado. For this application, the accuracy and efficiency of the conjugate-gradient method compared favorably with other available methods for steady-state flow. However, its efficiency relative to other available methods depends on the nature of the specific problem. The main advantage of the conjugate-gradient method is that it does not require the use of iteration parameters, thereby eliminating this partly subjective procedure. (USGS)

Comparison of genetic algorithms with conjugate gradient methods

NASA Technical Reports Server (NTRS)

Bosworth, J. L.; Foo, N. Y.; Zeigler, B. P.

1972-01-01

Genetic algorithms for mathematical function optimization are modeled on search strategies employed in natural adaptation. Comparisons of genetic algorithms with conjugate gradient methods, which were made on an IBM 1800 digital computer, show that genetic algorithms display superior performance over gradient methods for functions which are poorly behaved mathematically, for multimodal functions, and for functions obscured by additive random noise. Genetic methods offer performance comparable to gradient methods for many of the standard functions.

Astronauts Brent Jett and Koichi Wakata work with Protein Crystal Growth experiment

NASA Image and Video Library

1996-01-20

STS072-310-007 (11-20 Jan. 1996) --- Astronauts Brent W. Jett Jr. (left) and Koichi Wakata work with the Protein Crystal Growth (PCG) experiment at the Single Locker Thermal Enclosure System (STES) on the Space Shuttle Endeavour’s mid-deck. Jett, making his first flight in space, served as the crew’s pilot, while Wakata served as a mission specialist. Wakata, also a first time Shuttle crew member, represents Japan’s National Space Development Agency (NASDA).

The Role of microRNA miR-101 in Prostate Cancer Progression

DTIC Science & Technology

2012-09-01

genome -wide mapping of PcG binding in human fibroblasts, human ES cells, mouse ES cells, and Drosophila 37-41 . All of the studies demonstrated that...development. Mamm Genome 2002; 13(9): 493-503. 15. Simon J, Chiang A, Bender W, Shimell MJ, O’Connor M. Elements of the Drosophila bithorax complex... sequencing analysis of the miR-203 genomic region revealed cancer-specific DNA methylation in a region proximal to miR-203 in prostate cancer tissues

Crewmembers in the spacelab with Generic Bioprocessing Apparatus, Rack #10.

NASA Image and Video Library

1992-07-09

STS050-254-007 (25 June-9 July 1992) --- Lawrence J. DeLucas, payload specialist, handles a Protein Crystal Growth (PCG) sample at the multipurpose glovebox aboard the Earth-orbiting Space Shuttle Columbia. Astronaut Bonnie J. Dunbar, payload commander, communicates with ground controllers about the Solid Surface Combustion Experiment (SSCE), one of the United States Microgravity Laboratory 1’s (USML-1) three experiments on Rack 10. Five other crew members joined the pair for a record-setting 14-days of scientific data gathering.

The Maritime Environment, International Conference and Exhibition "Waste Water Treatment Technologies for Ships"

DTIC Science & Technology

1998-01-01

PEN 00 IJJ0 * PO PCg 0 M1 PM10 0M PON 0 PON *-4-) *% z * FIN* 0 -m PENA wo roe PORN OPW Ina 0 POO 0 Poo u U 0 ; 4-o sow 0P.4 P.4 OPM40 Poo Pssm-+NaPMO...than trying to guarantee, that even our children’s children can still enjoy beaches like this DEE -SYSE - MCL ’ESTPASSEGSA D-26120LZOEN I-RC ST eeon

Gradient optimization and nonlinear control

NASA Technical Reports Server (NTRS)

Hasdorff, L.

1976-01-01

The book represents an introduction to computation in control by an iterative, gradient, numerical method, where linearity is not assumed. The general language and approach used are those of elementary functional analysis. The particular gradient method that is emphasized and used is conjugate gradient descent, a well known method exhibiting quadratic convergence while requiring very little more computation than simple steepest descent. Constraints are not dealt with directly, but rather the approach is to introduce them as penalty terms in the criterion. General conjugate gradient descent methods are developed and applied to problems in control.

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.

A new smoothing modified three-term conjugate gradient method for [Formula: see text]-norm minimization problem.

PubMed

Du, Shouqiang; Chen, Miao

2018-01-01

We consider a kind of nonsmooth optimization problems with [Formula: see text]-norm minimization, which has many applications in compressed sensing, signal reconstruction, and the related engineering problems. Using smoothing approximate techniques, this kind of nonsmooth optimization problem can be transformed into a general unconstrained optimization problem, which can be solved by the proposed smoothing modified three-term conjugate gradient method. The smoothing modified three-term conjugate gradient method is based on Polak-Ribière-Polyak conjugate gradient method. For the Polak-Ribière-Polyak conjugate gradient method has good numerical properties, the proposed method possesses the sufficient descent property without any line searches, and it is also proved to be globally convergent. Finally, the numerical experiments show the efficiency of the proposed method.

Multiple polymer architectures of human Polyhomeotic homolog 3 (PHC3) SAM

PubMed Central

Nanyes, David R.; Junco, Sarah E.; Taylor, Alexander B.; Robinson, Angela K.; Patterson, Nicolle L.; Shivarajpur, Ambika; Halloran, Jonathan; Hale, Seth M.; Kaur, Yogeet; Hart, P. John; Kim, Chongwoo A.

2014-01-01

The self-association of sterile alpha motifs (SAMs) into a helical polymer architecture is a critical functional component of many different and diverse array of proteins. For the Drosophila Polycomb group (PcG) protein Polyhomeotic (Ph), its SAM polymerization serves as the structural foundation to cluster multiple PcG complexes, helping to maintain a silenced chromatin state. Ph SAM shares 64% sequence identity with its human ortholog, PHC3 SAM, and both SAMs polymerize. However, in the context of their larger protein regions, PHC3 SAM forms longer polymers compared to Ph SAM. Motivated to establish the precise structural basis for the differences, if any, between Ph and PHC3 SAM, we determined the crystal structure of the PHC3 SAM polymer. PHC3 SAM utilizes the same SAM-SAM interaction as the Ph SAM six-fold repeat polymer. Yet, PHC3 SAM polymerizes utilizing just five SAMs per turn of the helical polymer rather than the typical six per turn observed for all SAM polymers reported to date. Structural analysis suggested that malleability of the PHC3 SAM would allow formation of not just the five-fold repeat structure but possibly others. Indeed, a second PHC3 SAM polymer in a different crystal form forms a six-fold repeat polymer. These results suggest that the polymers formed by PHC3 SAM, and likely others, are quite dynamic. The functional consequence of the variable PHC3 SAM polymers may be to create different chromatin architectures. PMID:25044168

Regional amplitude of the low-frequency fluctuations at rest predicts word-reading skill.

PubMed

Xu, M; De Beuckelaer, A; Wang, X; Liu, L; Song, Y; Liu, J

2015-07-09

Individuals' reading skills are critical for their educational development, but variation in reading skills is known to be large. The present study used functional magnetic resonance imaging (fMRI) to examine the role of spontaneous brain activity at rest in individual differences in reading skills in a large sample of participants (N=263). Specifically, we correlated individuals' word-reading skill with their fractional amplitude of low-frequency fluctuation (fALFF) of the whole brain at rest and found that the fALFFs of both the bilateral precentral gyrus (PCG) and superior temporal plane (STP) were positively associated with reading skills. The fALFF-reading association observed in these two regions remained after controlling for general cognitive abilities and in-scanner head motion. A cross-validation confirmed that the individual differences in word-reading skills were reliably correlated with the fALFF values of the bilateral PCG and STP. A follow-up task-based fMRI experiment revealed that the reading-related regions overlapped with regions showing a higher response to sentences than to pseudo-sentences (strings of pseudo-words), suggesting the resting-state brain activity partly captures the characteristics of task-based brain activity. In short, our study provides one of the first pieces of evidence that links spontaneous brain activity to reading behavior and offers an easy-to-access neural marker for evaluating reading skill. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

TNF-alpha expression, evaluation of collagen, and TUNEL of Matricaria recutita L. extract and triamcinolone on oral ulcer in diabetic rats.

PubMed

Oliveira, Bruna Vasconcelos; Barros Silva, Paulo Goberlânio; Nojosa, Jacqueline de Santiago; Brizeno, Luiz André Cavalcante; Ferreira, Jamile Magalhães; Sousa, Fabrício Bitú; Mota, Mário Rogério Lima; Alves, Ana Paula Negreiros Nunes

2016-01-01

to evaluate the influence of Tumor Necrosis Factor alpha (TNF-α) and apoptosis in rats with DM treated with chamomile extract or triamcinolone. Wistar male rats (210.0±4.2 g) were divided into five groups: negative control group (NCG) without diabetes; positive control group (PCG) with DM (alloxan, 45 mg/kg); and groups treated with chamomile extract (normoglycemic= NCG group and diabetic= DCG group) and with triamcinolone (TG). Traumatic ulcers were performed on all animals that received topical triamcinolone, chamomile extract or saline 12/12 hours for ten days. On days five and ten the animals were euthanized and the ulcers were analyzed by light microscopy, TUNEL assay, and immunohistochemically (TNF-α). The NCG (p=0.0062), PCG (p=0.0285), NCG (p=0.0041), and DCG (p<0.0001) groups were completely healed on the 10th day, however, there was no healing on the TG (p=0.5127) group. The TNF-α expression showed a significant reduction from the 5th to the 10th day in NCG (p=0.0266) and DCG (p=0.0062). In connective tissue, the TUNEL assay showed a significant reduction in the number of positive cells in NCG (p=0.0273) and CNG (p=0.0469) and in the epithelium only in CDG (p=0.0320). Chamomile extract can optimize the healing of traumatic oral ulcers in diabetic rats through the reduction of apoptosis in the epithelium and TNF-α expression.

The histone demethylase Fbxl11/Kdm2a plays an essential role in embryonic development by repressing cell-cycle regulators.

PubMed

Kawakami, Eri; Tokunaga, Akinori; Ozawa, Manabu; Sakamoto, Reiko; Yoshida, Nobuaki

2015-02-01

Methylation and de-methylation of histone lysine residues play pivotal roles in mammalian early development; these modifications influence chromatin architecture and regulate gene transcription. Fbxl11 (F-box and leucine-rich repeat 11)/Kdm2a is a histone demethylase that selectively removes mono- and di-methylation from histone H3K36. Previously, two other histone H3K36 demethylases (Jmjd5 or Fbxl10) were analyzed based on the phenotypes of the corresponding knockout (KO) mice; the results of those studies implicated H3K36 demethylases in cell proliferation, apoptosis, and senescence (Fukuda et al., 2011; Ishimura et al., 2012). To elucidate the physiological role of Fbxl11, we generated and examined Fbxl11 KO mice. Fbxl11 was expressed throughout the body during embryogenesis, and the Fbxl11 KO mice exhibited embryonic lethality at E10.5-12.5, accompanied with severe growth defects leading to reduced body size. Furthermore, knockout of Fbxl11 decreased cell proliferation and increased apoptosis. The lack of Fbxl11 resulted in downregulation of the Polycomb group protein (PcG) Ezh2, PcG mediated H2A ubiquitination and upregulation of the cyclin-dependent kinase inhibitor p21Cip1. Taken together, our findings suggest that Fbxl11 plays an essential role in embryonic development and homeostasis by regulating cell proliferation and survival. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Evaluation of an alternate method for sampling benthic macroinvertebrates in low-gradient streams sampled as part of the National Rivers and Streams Assessment.

PubMed

Flotemersch, Joseph E; North, Sheila; Blocksom, Karen A

2014-02-01

Benthic macroinvertebrates are sampled in streams and rivers as one of the assessment elements of the US Environmental Protection Agency's National Rivers and Streams Assessment. In a 2006 report, the recommendation was made that different yet comparable methods be evaluated for different types of streams (e.g., low gradient vs. high gradient). Consequently, a research element was added to the 2008-2009 National Rivers and Streams Assessment to conduct a side-by-side comparison of the standard macroinvertebrate sampling method with an alternate method specifically designed for low-gradient wadeable streams and rivers that focused more on stream edge habitat. Samples were collected using each method at 525 sites in five of nine aggregate ecoregions located in the conterminous USA. Methods were compared using the benthic macroinvertebrate multimetric index developed for the 2006 Wadeable Streams Assessment. Statistical analysis did not reveal any trends that would suggest the overall assessment of low-gradient streams on a regional or national scale would change if the alternate method was used rather than the standard sampling method, regardless of the gradient cutoff used to define low-gradient streams. Based on these results, the National Rivers and Streams Survey should continue to use the standard field method for sampling all streams.

Gravity gradient preprocessing at the GOCE HPF

NASA Astrophysics Data System (ADS)

Bouman, J.; Rispens, S.; Gruber, T.; Schrama, E.; Visser, P.; Tscherning, C. C.; Veicherts, M.

2009-04-01

One of the products derived from the GOCE observations are the gravity gradients. These gravity gradients are provided in the Gradiometer Reference Frame (GRF) and are calibrated in-flight using satellite shaking and star sensor data. In order to use these gravity gradients for application in Earth sciences and gravity field analysis, additional pre-processing needs to be done, including corrections for temporal gravity field signals to isolate the static gravity field part, screening for outliers, calibration by comparison with existing external gravity field information and error assessment. The temporal gravity gradient corrections consist of tidal and non-tidal corrections. These are all generally below the gravity gradient error level, which is predicted to show a 1/f behaviour for low frequencies. In the outlier detection the 1/f error is compensated for by subtracting a local median from the data, while the data error is assessed using the median absolute deviation. The local median acts as a high-pass filter and it is robust as is the median absolute deviation. Three different methods have been implemented for the calibration of the gravity gradients. All three methods use a high-pass filter to compensate for the 1/f gravity gradient error. The baseline method uses state-of-the-art global gravity field models and the most accurate results are obtained if star sensor misalignments are estimated along with the calibration parameters. A second calibration method uses GOCE GPS data to estimate a low degree gravity field model as well as gravity gradient scale factors. Both methods allow to estimate gravity gradient scale factors down to the 10-3 level. The third calibration method uses high accurate terrestrial gravity data in selected regions to validate the gravity gradient scale factors, focussing on the measurement band. Gravity gradient scale factors may be estimated down to the 10-2 level with this method.

Preprocessing of gravity gradients at the GOCE high-level processing facility

NASA Astrophysics Data System (ADS)

Bouman, Johannes; Rispens, Sietse; Gruber, Thomas; Koop, Radboud; Schrama, Ernst; Visser, Pieter; Tscherning, Carl Christian; Veicherts, Martin

2009-07-01

One of the products derived from the gravity field and steady-state ocean circulation explorer (GOCE) observations are the gravity gradients. These gravity gradients are provided in the gradiometer reference frame (GRF) and are calibrated in-flight using satellite shaking and star sensor data. To use these gravity gradients for application in Earth scienes and gravity field analysis, additional preprocessing needs to be done, including corrections for temporal gravity field signals to isolate the static gravity field part, screening for outliers, calibration by comparison with existing external gravity field information and error assessment. The temporal gravity gradient corrections consist of tidal and nontidal corrections. These are all generally below the gravity gradient error level, which is predicted to show a 1/ f behaviour for low frequencies. In the outlier detection, the 1/ f error is compensated for by subtracting a local median from the data, while the data error is assessed using the median absolute deviation. The local median acts as a high-pass filter and it is robust as is the median absolute deviation. Three different methods have been implemented for the calibration of the gravity gradients. All three methods use a high-pass filter to compensate for the 1/ f gravity gradient error. The baseline method uses state-of-the-art global gravity field models and the most accurate results are obtained if star sensor misalignments are estimated along with the calibration parameters. A second calibration method uses GOCE GPS data to estimate a low-degree gravity field model as well as gravity gradient scale factors. Both methods allow to estimate gravity gradient scale factors down to the 10-3 level. The third calibration method uses high accurate terrestrial gravity data in selected regions to validate the gravity gradient scale factors, focussing on the measurement band. Gravity gradient scale factors may be estimated down to the 10-2 level with this method.

$L_{0}$ Gradient Projection.

PubMed

Ono, Shunsuke

2017-04-01

Minimizing L 0 gradient, the number of the non-zero gradients of an image, together with a quadratic data-fidelity to an input image has been recognized as a powerful edge-preserving filtering method. However, the L 0 gradient minimization has an inherent difficulty: a user-given parameter controlling the degree of flatness does not have a physical meaning since the parameter just balances the relative importance of the L 0 gradient term to the quadratic data-fidelity term. As a result, the setting of the parameter is a troublesome work in the L 0 gradient minimization. To circumvent the difficulty, we propose a new edge-preserving filtering method with a novel use of the L 0 gradient. Our method is formulated as the minimization of the quadratic data-fidelity subject to the hard constraint that the L 0 gradient is less than a user-given parameter α . This strategy is much more intuitive than the L 0 gradient minimization because the parameter α has a clear meaning: the L 0 gradient value of the output image itself, so that one can directly impose a desired degree of flatness by α . We also provide an efficient algorithm based on the so-called alternating direction method of multipliers for computing an approximate solution of the nonconvex problem, where we decompose it into two subproblems and derive closed-form solutions to them. The advantages of our method are demonstrated through extensive experiments.

Rapid analysis of charge variants of monoclonal antibodies using non-linear salt gradient in cation-exchange high performance liquid chromatography.

PubMed

Joshi, Varsha; Kumar, Vijesh; Rathore, Anurag S

2015-08-07

A method is proposed for rapid development of a short, analytical cation exchange high performance liquid chromatography method for analysis of charge heterogeneity in monoclonal antibody products. The parameters investigated and optimized include pH, shape of elution gradient and length of the column. It is found that the most important parameter for development of a shorter method is the choice of the shape of elution gradient. In this paper, we propose a step by step approach to develop a non-linear sigmoidal shape gradient for analysis of charge heterogeneity for two different monoclonal antibody products. The use of this gradient not only decreases the run time of the method to 4min against the conventional method that takes more than 40min but also the resolution is retained. Superiority of the phosphate gradient over sodium chloride gradient for elution of mAbs is also observed. The method has been successfully evaluated for specificity, sensitivity, linearity, limit of detection, and limit of quantification. Application of this method as a potential at-line process analytical technology tool has been suggested. Copyright © 2015 Elsevier B.V. All rights reserved.

Small angle neutron scattering study of the gemini nonionic surfactant in heavy water solutions

NASA Astrophysics Data System (ADS)

Rajewska, A.

2012-03-01

The nonionic gemini surfactant α α'-[2,4,7,9-tetramethyl-5-decyne-4,7diyl]bis[ω hydroxyl-polyoxyethylene] (S-10) was investigated in heavy water solutions only for concentrations: 2.3%, 2.5%,3%, 3.4%, 4% and 5% at temperature 25°C with small angle neutron scattering (SANS) method. All of surfactants solutions were prepared using D2O (99.9% deuterated, Prikladnaia Chimia, St. Petersburg, Russia) as a solvent. The nonionic gemini surfactant S-10 was obtained from Air Products & Chemicals, Inc., and used without further purification. All SANS measurements were performed on V-4 SANS spectrometer at BENSC, Berlin (Germany). Neutrons were used in wavelength range of 0.02 - 4 nm-1. For the measurements quartz cells of were used during experiment. Up to 14 such cells were placed in a holder. Results from experiment was calculated and evaluated with PCG 2.0 program from Graz University (Austria). In the investigated solutions two axis ellipsoidal micelles was observed.

The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications.

PubMed

Shen, Jinhui; Cong, Qian; Grishin, Nick V

2015-09-01

Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Generation Sequencing reads performed for whole-genome sequencing and report the complete mitogenome of Papilio (Pterourus) glaucus. The circular mitogenome is 15,306 bp in length and rich in A and T. It contains 13 protein-coding genes (PCGs), 22 transfer-RNA-coding genes (tRNA), and 2 ribosomal-RNA-coding genes (rRNA), with a gene order typical for mitogenomes of Lepidoptera. We performed phylogenetic analyses based on PCG and RNA-coding genes or protein sequences using Bayesian Inference and Maximum Likelihood methods. The phylogenetic trees consistently show that among species with available mitogenomes Papilio glaucus is the closest to Papilio (Agehana) maraho from Asia.

Gradients estimation from random points with volumetric tensor in turbulence

NASA Astrophysics Data System (ADS)

Watanabe, Tomoaki; Nagata, Koji

2017-12-01

We present an estimation method of fully-resolved/coarse-grained gradients from randomly distributed points in turbulence. The method is based on a linear approximation of spatial gradients expressed with the volumetric tensor, which is a 3 × 3 matrix determined by a geometric distribution of the points. The coarse grained gradient can be considered as a low pass filtered gradient, whose cutoff is estimated with the eigenvalues of the volumetric tensor. The present method, the volumetric tensor approximation, is tested for velocity and passive scalar gradients in incompressible planar jet and mixing layer. Comparison with a finite difference approximation on a Cartesian grid shows that the volumetric tensor approximation computes the coarse grained gradients fairly well at a moderate computational cost under various conditions of spatial distributions of points. We also show that imposing the solenoidal condition improves the accuracy of the present method for solenoidal vectors, such as a velocity vector in incompressible flows, especially when the number of the points is not large. The volumetric tensor approximation with 4 points poorly estimates the gradient because of anisotropic distribution of the points. Increasing the number of points from 4 significantly improves the accuracy. Although the coarse grained gradient changes with the cutoff length, the volumetric tensor approximation yields the coarse grained gradient whose magnitude is close to the one obtained by the finite difference. We also show that the velocity gradient estimated with the present method well captures the turbulence characteristics such as local flow topology, amplification of enstrophy and strain, and energy transfer across scales.

A new gradient shimming method based on undistorted field map of B0 inhomogeneity.

PubMed

Bao, Qingjia; Chen, Fang; Chen, Li; Song, Kan; Liu, Zao; Liu, Chaoyang

2016-04-01

Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method. Copyright © 2015 Elsevier Inc. All rights reserved.

Full magnetic gradient tensor from triaxial aeromagnetic gradient measurements: Calculation and application

NASA Astrophysics Data System (ADS)

Luo, Yao; Wu, Mei-Ping; Wang, Ping; Duan, Shu-Ling; Liu, Hao-Jun; Wang, Jin-Long; An, Zhan-Feng

2015-09-01

The full magnetic gradient tensor (MGT) refers to the spatial change rate of the three field components of the geomagnetic field vector along three mutually orthogonal axes. The tensor is of use to geological mapping, resources exploration, magnetic navigation, and others. However, it is very difficult to measure the full magnetic tensor gradient using existing engineering technology. We present a method to use triaxial aeromagnetic gradient measurements for deriving the full MGT. The method uses the triaxial gradient data and makes full use of the variation of the magnetic anomaly modulus in three dimensions to obtain a self-consistent magnetic tensor gradient. Numerical simulations show that the full MGT data obtained with the proposed method are of high precision and satisfy the requirements of data processing. We selected triaxial aeromagnetic gradient data from the Hebei Province for calculating the full MGT. Data processing shows that using triaxial tensor gradient data allows to take advantage of the spatial rate of change of the total field in three dimensions and suppresses part of the independent noise in the aeromagnetic gradient. The calculated tensor components have improved resolution, and the transformed full tensor gradient satisfies the requirement of geological mapping and interpretation.

Comparison between layers stacks of 67P/CG comet and spectrophotometric variability obtained from OSIRIS data

NASA Astrophysics Data System (ADS)

Ferrari, S.; Penasa, L.; La Forgia, F.; Massironi, M.; Naletto, G.; Lazzarin, M.; Fornasier, S.; Barucci, M. A.; Lucchetti, A.; Pajola, M.; Frattin, E.; Bertini, I.; Ferri, F.; Cremonese, G.

2017-09-01

The Rosetta/OSIRIS cameras unveiled the layered nature of comet 67P/Churyumov-Gerasimenko, suggesting that the comet bilobate shape results from the low-velocity merging of two independent onion-like objects. Several physiographical regions of the southern-hemisphere big lobe show stacks of layers forming high scarps, terraces and mesas. A spectrophotometric analysis of OSIRIS images based on multispectral data classifications was conducted in order to identify possible morphological, textural and/or compositional characters that allow to distinguish regional stacks of layers.

Astronaut Curtis Brown works with SAMS on Shuttle Atlantis middeck

NASA Image and Video Library

1994-11-14

STS066-14-021 (3-14 Nov 1994) --- On the Space Shuttle Atlantis' mid-deck, astronaut Curtis L. Brown, Jr., pilot, works with the Space Acceleration Measurement System (SAMS), which is making its eleventh Shuttle flight. This system supports the Protein Crystal Growth (PCG) experiments onboard by collecting and recording data characterizing the microgravity environment in the Shuttle mid-deck. Brown joined four other NASA astronauts and a European Space Agency (ESA) astronaut for 11-days aboard Atlantis in support of the Atmospheric Laboratory for Applications and Science (ATLAS-3) mission.

Magnetoelectrets prepared by using temperature gradient method

NASA Astrophysics Data System (ADS)

Ojha, Pragya; Qureshi, M. S.; Malik, M. M.

2015-05-01

A novel Temperature Gradient method for preparation of magnetoelectret is proposed. Non uniform magnetic field and temperature gradient are expected to be the main cause for the formation of magnetoelectrets (MEs). Being bad conductors of heat, during their formation, there is a possibility for the existence of a temperature gradient along the dielectric electrode interface. In this condition, the motion of, molecules and charge carriers are dependent on Temperature Gradient in a preferred direction. To increase this temperature gradient on both sides of the sample novel method for the preparation of MEs is developed for the first time. For this method the special sample holders are designed in our laboratory. MEs are prepared in such a way that one surface is cooled and the other is heated, during the process. With the help of XRD analysis using Type-E orientation pattern and surface charge studies on magnetoelectrets, the two main causes Non uniform magnetic field and temperature gradient for the formation of magnetoelectrets (MEs), are authenticated experimentally.

Radiofrequency pulse design using nonlinear gradient magnetic fields.

PubMed

Kopanoglu, Emre; Constable, R Todd

2015-09-01

An iterative k-space trajectory and radiofrequency (RF) pulse design method is proposed for excitation using nonlinear gradient magnetic fields. The spatial encoding functions (SEFs) generated by nonlinear gradient fields are linearly dependent in Cartesian coordinates. Left uncorrected, this may lead to flip angle variations in excitation profiles. In the proposed method, SEFs (k-space samples) are selected using a matching pursuit algorithm, and the RF pulse is designed using a conjugate gradient algorithm. Three variants of the proposed approach are given: the full algorithm, a computationally cheaper version, and a third version for designing spoke-based trajectories. The method is demonstrated for various target excitation profiles using simulations and phantom experiments. The method is compared with other iterative (matching pursuit and conjugate gradient) and noniterative (coordinate-transformation and Jacobian-based) pulse design methods as well as uniform density spiral and EPI trajectories. The results show that the proposed method can increase excitation fidelity. An iterative method for designing k-space trajectories and RF pulses using nonlinear gradient fields is proposed. The method can either be used for selecting the SEFs individually to guide trajectory design, or can be adapted to design and optimize specific trajectories of interest. © 2014 Wiley Periodicals, Inc.

Determination of boundaries between ranges of high and low gradient of beam profile.

PubMed

Wendykier, Jacek; Bieniasiewicz, Marcin; Grządziel, Aleksandra; Jedynak, Tadeusz; Kośniewski, Wiktor; Reudelsdorf, Marta; Wendykier, Piotr

2016-01-01

This work addresses the problem of treatment planning system commissioning by introducing a new method of determination of boundaries between high and low gradient in beam profile. The commissioning of a treatment planning system is a very important task in the radiation therapy. One of the main goals of this task is to compare two field profiles: measured and calculated. Applying points of 80% and 120% of nominal field size can lead to the incorrect determination of boundaries, especially for small field sizes. The method that is based on the beam profile gradient allows for proper assignment of boundaries between high and low gradient regions even for small fields. TRS 430 recommendations for commissioning were used. The described method allows a separation between high and low gradient, because it directly uses the value of the gradient of a profile. For small fields, the boundaries determined by the new method allow a commissioning of a treatment planning system according to the TRS 430, while the point of 80% of nominal field size is already in the high gradient region. The method of determining the boundaries by using the beam profile gradient can be extremely helpful during the commissioning of the treatment planning system for Intensity Modulated Radiation Therapy or for other techniques which require very small field sizes.

Pure phase encode magnetic field gradient monitor.

PubMed

Han, Hui; MacGregor, Rodney P; Balcom, Bruce J

2009-12-01

Numerous methods have been developed to measure MRI gradient waveforms and k-space trajectories. The most promising new strategy appears to be magnetic field monitoring with RF microprobes. Multiple RF microprobes may record the magnetic field evolution associated with a wide variety of imaging pulse sequences. The method involves exciting one or more test samples and measuring the time evolution of magnetization through the FIDs. Two critical problems remain. The gradient waveform duration is limited by the sample T(2)*, while the k-space maxima are limited by gradient dephasing. The method presented is based on pure phase encode FIDs and solves the above two problems in addition to permitting high strength gradient measurement. A small doped water phantom (1-3 mm droplet, T(1), T(2), T(2)* < 100 micros) within a microprobe is excited by a series of closely spaced broadband RF pulses each followed by FID single point acquisition. Two trial gradient waveforms have been chosen to illustrate the technique, neither of which could be measured by the conventional RF microprobe measurement. The first is an extended duration gradient waveform while the other illustrates the new method's ability to measure gradient waveforms with large net area and/or high amplitude. The new method is a point monitor with simple implementation and low cost hardware requirements.

The Acoustical Properties of the Polyurethane Concrete Made of Oyster Shell Waste Comparing Other Concretes as Architectural Design Components

NASA Astrophysics Data System (ADS)

Setyowati, Erni; Hardiman, Gagoek; Purwanto

2018-02-01

This research aims to determine the acoustical properties of concrete material made of polyurethane and oyster shell waste as both fine aggregate and coarse aggregate comparing to other concrete mortar. Architecture needs aesthetics materials, so the innovation in architectural material should be driven through the efforts of research on materials for building designs. The DOE methods was used by mixing cement, oyster shell, sands, and polyurethane by composition of 160 ml:40 ml:100 ml: 120 ml respectively. Refer to the results of previous research, then cement consumption is reduced up to 20% to keep the concept of green material. This study compared three different compositions of mortars, namely portland cement concrete with gravel (PCG), polyurethane concrete of oyster shell (PCO) and concrete with plastics aggregate (PCP). The methods of acoustical tests were conducted refer to the ASTM E413-04 standard. The research results showed that polyurethane concrete with oyster shell waste aggregate has absorption coefficient 0.52 and STL 63 dB and has a more beautiful appearance when it was pressed into moulding. It can be concluded that polyurethane concrete with oyster shell aggregate (PCO) is well implemented in architectural acoustics-components.

Non-Gradient Blue Native Polyacrylamide Gel Electrophoresis.

PubMed

Luo, Xiaoting; Wu, Jinzi; Jin, Zhen; Yan, Liang-Jun

2017-02-02

Gradient blue native polyacrylamide gel electrophoresis (BN-PAGE) is a well established and widely used technique for activity analysis of high-molecular-weight proteins, protein complexes, and protein-protein interactions. Since its inception in the early 1990s, a variety of minor modifications have been made to this gradient gel analytical method. Here we provide a major modification of the method, which we call non-gradient BN-PAGE. The procedure, similar to that of non-gradient SDS-PAGE, is simple because there is no expensive gradient maker involved. The non-gradient BN-PAGE protocols presented herein provide guidelines on the analysis of mitochondrial protein complexes, in particular, dihydrolipoamide dehydrogenase (DLDH) and those in the electron transport chain. Protocols for the analysis of blood esterases or mitochondrial esterases are also presented. The non-gradient BN-PAGE method may be tailored for analysis of specific proteins according to their molecular weight regardless of whether the target proteins are hydrophobic or hydrophilic. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

A critical analysis of some popular methods for the discretisation of the gradient operator in finite volume methods

NASA Astrophysics Data System (ADS)

Syrakos, Alexandros; Varchanis, Stylianos; Dimakopoulos, Yannis; Goulas, Apostolos; Tsamopoulos, John

2017-12-01

Finite volume methods (FVMs) constitute a popular class of methods for the numerical simulation of fluid flows. Among the various components of these methods, the discretisation of the gradient operator has received less attention despite its fundamental importance with regards to the accuracy of the FVM. The most popular gradient schemes are the divergence theorem (DT) (or Green-Gauss) scheme and the least-squares (LS) scheme. Both are widely believed to be second-order accurate, but the present study shows that in fact the common variant of the DT gradient is second-order accurate only on structured meshes whereas it is zeroth-order accurate on general unstructured meshes, and the LS gradient is second-order and first-order accurate, respectively. This is explained through a theoretical analysis and is confirmed by numerical tests. The schemes are then used within a FVM to solve a simple diffusion equation on unstructured grids generated by several methods; the results reveal that the zeroth-order accuracy of the DT gradient is inherited by the FVM as a whole, and the discretisation error does not decrease with grid refinement. On the other hand, use of the LS gradient leads to second-order accurate results, as does the use of alternative, consistent, DT gradient schemes, including a new iterative scheme that makes the common DT gradient consistent at almost no extra cost. The numerical tests are performed using both an in-house code and the popular public domain partial differential equation solver OpenFOAM.

A modified micrometeorological gradient method for estimating O3 dry depositions over a forest canopy

NASA Astrophysics Data System (ADS)

Wu, Z. Y.; Zhang, L.; Wang, X. M.; Munger, J. W.

2015-07-01

Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air-surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake in the top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts, during 1993-2000. All three gradient methods (AGM, MBR, and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR, and MGM method being 2.28, 1.45, and 1.18 times that of the EC, respectively. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach to monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.

A different approach to estimate nonlinear regression model using numerical methods

NASA Astrophysics Data System (ADS)

Mahaboob, B.; Venkateswarlu, B.; Mokeshrayalu, G.; Balasiddamuni, P.

2017-11-01

This research paper concerns with the computational methods namely the Gauss-Newton method, Gradient algorithm methods (Newton-Raphson method, Steepest Descent or Steepest Ascent algorithm method, the Method of Scoring, the Method of Quadratic Hill-Climbing) based on numerical analysis to estimate parameters of nonlinear regression model in a very different way. Principles of matrix calculus have been used to discuss the Gradient-Algorithm methods. Yonathan Bard [1] discussed a comparison of gradient methods for the solution of nonlinear parameter estimation problems. However this article discusses an analytical approach to the gradient algorithm methods in a different way. This paper describes a new iterative technique namely Gauss-Newton method which differs from the iterative technique proposed by Gorden K. Smyth [2]. Hans Georg Bock et.al [10] proposed numerical methods for parameter estimation in DAE’s (Differential algebraic equation). Isabel Reis Dos Santos et al [11], Introduced weighted least squares procedure for estimating the unknown parameters of a nonlinear regression metamodel. For large-scale non smooth convex minimization the Hager and Zhang (HZ) conjugate gradient Method and the modified HZ (MHZ) method were presented by Gonglin Yuan et al [12].

The q-G method : A q-version of the Steepest Descent method for global optimization.

PubMed

Soterroni, Aline C; Galski, Roberto L; Scarabello, Marluce C; Ramos, Fernando M

2015-01-01

In this work, the q-Gradient (q-G) method, a q-version of the Steepest Descent method, is presented. The main idea behind the q-G method is the use of the negative of the q-gradient vector of the objective function as the search direction. The q-gradient vector, or simply the q-gradient, is a generalization of the classical gradient vector based on the concept of Jackson's derivative from the q-calculus. Its use provides the algorithm an effective mechanism for escaping from local minima. The q-G method reduces to the Steepest Descent method when the parameter q tends to 1. The algorithm has three free parameters and it is implemented so that the search process gradually shifts from global exploration in the beginning to local exploitation in the end. We evaluated the q-G method on 34 test functions, and compared its performance with 34 optimization algorithms, including derivative-free algorithms and the Steepest Descent method. Our results show that the q-G method is competitive and has a great potential for solving multimodal optimization problems.

Linear solvation energy relationships in normal phase chromatography based on gradient separations.

PubMed

Wu, Di; Lucy, Charles A

2017-09-22

Coupling the modified Soczewiñski model and one gradient run, a gradient method was developed to build a linear solvation energy relationship (LSER) for normal phase chromatography. The gradient method was tested on dinitroanilinopropyl (DNAP) and silica columns with hexane/dichloromethane (DCM) mobile phases. LSER models built based on the gradient separation agree with those derived from a series of isocratic separations. Both models have similar LSER coefficients and comparable goodness of fit, but the LSER model based on gradient separation required fewer trial and error experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

RF Pulse Design using Nonlinear Gradient Magnetic Fields

PubMed Central

Kopanoglu, Emre; Constable, R. Todd

2014-01-01

Purpose An iterative k-space trajectory and radio-frequency (RF) pulse design method is proposed for Excitation using Nonlinear Gradient Magnetic fields (ENiGMa). Theory and Methods The spatial encoding functions (SEFs) generated by nonlinear gradient fields (NLGFs) are linearly dependent in Cartesian-coordinates. Left uncorrected, this may lead to flip-angle variations in excitation profiles. In the proposed method, SEFs (k-space samples) are selected using a Matching-Pursuit algorithm, and the RF pulse is designed using a Conjugate-Gradient algorithm. Three variants of the proposed approach are given: the full-algorithm, a computationally-cheaper version, and a third version for designing spoke-based trajectories. The method is demonstrated for various target excitation profiles using simulations and phantom experiments. Results The method is compared to other iterative (Matching-Pursuit and Conjugate Gradient) and non-iterative (coordinate-transformation and Jacobian-based) pulse design methods as well as uniform density spiral and EPI trajectories. The results show that the proposed method can increase excitation fidelity significantly. Conclusion An iterative method for designing k-space trajectories and RF pulses using nonlinear gradient fields is proposed. The method can either be used for selecting the SEFs individually to guide trajectory design, or can be adapted to design and optimize specific trajectories of interest. PMID:25203286

A weighted variational gradient-based fusion method for high-fidelity thin cloud removal of Landsat images

NASA Astrophysics Data System (ADS)

Huang, Wei; Chen, Xiu; Wang, Yueyun

2018-03-01

Landsat data are widely used in various earth observations, but the clouds interfere with the applications of the images. This paper proposes a weighted variational gradient-based fusion method (WVGBF) for high-fidelity thin cloud removal of Landsat images, which is an improvement of the variational gradient-based fusion (VGBF) method. The VGBF method integrates the gradient information from the reference band into visible bands of cloudy image to enable spatial details and remove thin clouds. The VGBF method utilizes the same gradient constraints to the entire image, which causes the color distortion in cloudless areas. In our method, a weight coefficient is introduced into the gradient approximation term to ensure the fidelity of image. The distribution of weight coefficient is related to the cloud thickness map. The map is built on Independence Component Analysis (ICA) by using multi-temporal Landsat images. Quantitatively, we use R value to evaluate the fidelity in the cloudless regions and metric Q to evaluate the clarity in the cloud areas. The experimental results indicate that the proposed method has the better ability to remove thin cloud and achieve high fidelity.

Neural mechanisms of voluntary and involuntary recall: a PET study.

PubMed

Hall, Nicoline Marie; Gjedde, Albert; Kupers, Ron

2008-01-25

Neuropsychological and neuroimaging studies on episodic memory retrieval have primarily focused on volitional memory tasks. However, some conscious memories arise involuntarily, i.e. without a strategic retrieval attempt, yet little is known about the neural network underlying involuntary episodic memory. The aim of this study was to determine whether voluntary and involuntary recall are mediated by separate cortical networks. We used positron emission tomography (PET) to measure changes in regional cerebral blood flow (rCBF) in 12 healthy subjects during voluntary and involuntary cued recall of pictures and a control condition with no episodic memory requirements. Involuntary recall was elicited by using an incidental memory task. Compared to the control condition, voluntary and involuntary recall were both associated with significant regional cerebral blood flow (rCBF) increases in posterior cingulate gyrus (PCG; BA 23), left precuneus (BA 7), and right parahippocampal gyrus (BA 35/36). In addition, rCBF in right dorsolateral prefrontal cortex (PFC; BA 8/9) and left precuneus (BA 7) was significantly larger during voluntary compared to involuntary recall, while rCBF was enhanced in left dorsolateral PFC (BA 9) during involuntary recall. The findings corroborate an association of the right PFC with a strategic component of episodic memory retrieval. Moreover, they show for the first time that it is possible to activate the medial temporal lobe, the PCG, and the precuneus, regions normally associated with retrieval success, without this strategic element. The relatively higher activity in precuneus during voluntary compared to involuntary recall suggests that activity in this region co-varies not only with retrieval success but also with retrieval intentionality.

Hydrodeoxygenation of prairie cordgrass bio-oil over Ni based activated carbon synergistic catalysts combined with different metals.

PubMed

Cheng, Shouyun; Wei, Lin; Zhao, Xianhui; Kadis, Ethan; Cao, Yuhe; Julson, James; Gu, Zhengrong

2016-06-25

Bio-oil can be upgraded through hydrodeoxygenation (HDO). Low-cost and effective catalysts are crucial for the HDO process. In this study, four inexpensive combinations of Ni based activated carbon synergistic catalysts including Ni/AC, Ni-Fe/AC, Ni-Mo/AC and Ni-Cu/AC were evaluated for HDO of prairie cordgrass (PCG) bio-oil. The tests were carried out in the autoclave under mild operating conditions with 500psig of H2 pressure and 350°C temperature. The catalysts were characterized by X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) and transmission electron microscope (TEM). The results show that all synergistic catalysts had significant improvements on the physicochemical properties (water content, pH, oxygen content, higher heating value and chemical compositions) of the upgraded PCG bio-oil. The higher heating value of the upgraded bio-oil (ranging from 29.65MJ/kg to 31.61MJ/kg) improved significantly in comparison with the raw bio-oil (11.33MJ/kg), while the oxygen content reduced to only 21.70-25.88% from 68.81% of the raw bio-oil. Compared to raw bio-oil (8.78% hydrocarbons and no alkyl-phenols), the Ni/AC catalysts produced the highest content of gasoline range hydrocarbons (C6-C12) at 32.63% in the upgraded bio-oil, while Ni-Mo/AC generated the upgraded bio-oil with the highest content of gasoline blending alkyl-phenols at 38.41%. Copyright © 2016 Elsevier B.V. All rights reserved.

Gray matter volume correlates of global positive alcohol expectancy in non-dependent adult drinkers

PubMed Central

Ide, Jaime S.; Zhang, Sheng; Hu, Sien; Matuskey, David; Bednarski, Sarah R.; Erdman, Emily; Farr, Olivia M.; Li, Chiang-shan R.

2013-01-01

Alcohol use and misuse is known to involve structural brain changes. Numerous imaging studies have examined changes in gray matter (GM) volumes in dependent drinkers, but there is little information on whether non-dependent drinking is associated with structural changes and whether these changes are related to psychological factors – such as alcohol expectancy – that influence drinking behavior. We used voxel based morphometry (VBM) to examine whether the global positive scale of alcohol expectancy, as measured by the Alcohol Expectancy Questionnaire AEQ-3, is associated with specific structural markers and whether such markers are associated with drinking behavior in 113 adult non-dependent drinkers (66 women). Alcohol expectancy is positively correlated with GM volume of left precentrral gyrus (PCG) in men and women combined and bilateral superior frontal gyri (SFG) in women, and negatively correlated with GM volume of the right ventral putamen in men. Furthermore, mediation analyses showed that the GM volume of PCG mediate the correlation of alcohol expectancy and the average number of drinks consumed per occasion and monthly total number of drinks in the past year. When recent drinking was directly accounted for in multiple regressions, GM volume of bilateral dorsolateral prefrontal cortices (DLPFC) correlated positively with alcohol expectancy in the combined sample. To our knowledge, these results are the first to identify the structural brain correlates of alcohol expectancy and its mediation of drinking behaviors. These findings suggest that more studies are needed to investigate increased GM volume in the frontal cortices as a neural correlate of alcohol expectancy. PMID:23461484

Laboratory study of methyl isocyanate ices under astrophysical conditions

NASA Astrophysics Data System (ADS)

Maté, B.; Molpeceres, G.; Timón, V.; Tanarro, I.; Escribano, R.; Guillemin, J. C.; Cernicharo, J.; Herrero, V. J.

2017-10-01

Methyl isocyanate has been recently detected in comet 67P/Churyumov-Gerasimenko (67P/CG) and in the interstellar medium. New physicochemical studies on this species are now necessary as tools for subsequent studies in astrophysics. In this work, infrared spectra of solid CH3NCO have been obtained at temperatures of relevance for astronomical environments. The spectra are dominated by a strong, characteristic multiplet feature at 2350-2250 cm-1, which can be attributed to the asymmetric stretching of the NCO group. A phase transition from amorphous to crystalline methyl isocyanate is observed at ˜90 K. The band strengths for the absorptions of CH3NCO in ice at 20 K have been measured. Deuterated methyl isocyanate is used to help with the spectral assignment. No X-ray structure has been reported for crystalline CH3NCO. Here we advance a tentative theoretical structure, based on density functional theory (DFT) calculations, derived taking the crystal of isocyanic acid as a starting point. A harmonic theoretical spectrum is then calculated for the proposed structure and compared with the experimental data. A mixed ice of H2O and CH3NCO was formed by simultaneous deposition of water and methyl isocyanate at 20 K. The absence of new spectral features indicates that methyl isocyanate and water do not react appreciably at 20 K, but form a stable mixture. The high CH3NCO/H2O ratio reported for comet 67P/CG, and the characteristic structure of the 2350-2250 cm-1 band, makes it a very good candidate for future astronomical searches.

The shared neural basis of music and language.

PubMed

Yu, Mengxia; Xu, Miao; Li, Xueting; Chen, Zhencai; Song, Yiying; Liu, Jia

2017-08-15

Human musical ability is proposed to play a key phylogenetical role in the evolution of language, and the similarity of hierarchical structure in music and language has led to considerable speculation about their shared mechanisms. While behavioral and electrophysioglocial studies have revealed associations between music and linguistic abilities, results from functional magnetic resonance imaging (fMRI) studies on their relations are contradictory, possibly because these studies usually treat music or language as single entities without breaking down to their components. Here, we examined the relations between different components of music (i.e., melodic and rhythmic analysis) and language (i.e., semantic and phonological processing) using both behavioral tests and resting-state fMRI. Behaviorally, we found that individuals with music training experiences were better at semantic processing, but not at phonological processing, than those without training. Further correlation analyses showed that semantic processing of language was related to melodic, but not rhythmic, analysis of music. Neurally, we found that performances in both semantic processing and melodic analysis were correlated with spontaneous brain activities in the bilateral precentral gyrus (PCG) and superior temporal plane at the regional level, and with the resting-state functional connectivity of the left PCG with the left supramarginal gyrus and left superior temporal gyrus at the network level. Together, our study revealed the shared spontaneous neural basis of music and language based on the behavioral link between melodic analysis and semantic processing, which possibly relied on a common mechanism of automatic auditory-motor integration. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

INCURVATA2 Encodes the Catalytic Subunit of DNA Polymerase α and Interacts with Genes Involved in Chromatin-Mediated Cellular Memory in Arabidopsis thaliana

PubMed Central

Barrero, José María; González-Bayón, Rebeca; del Pozo, Juan Carlos; Ponce, María Rosa; Micol, José Luis

2007-01-01

Cell type–specific gene expression patterns are maintained by the stable inheritance of transcriptional states through mitosis, requiring the action of multiprotein complexes that remodel chromatin structure. Genetic and molecular interactions between chromatin remodeling factors and components of the DNA replication machinery have been identified in Schizosaccharomyces pombe, indicating that some epigenetic marks are replicated simultaneously to DNA with the participation of the DNA replication complexes. This model of epigenetic inheritance might be extended to the plant kingdom, as we report here with the positional cloning and characterization of INCURVATA2 (ICU2), which encodes the putative catalytic subunit of the DNA polymerase α of Arabidopsis thaliana. The strong icu2-2 and icu2-3 insertional alleles caused fully penetrant zygotic lethality when homozygous and incompletely penetrant gametophytic lethality, probably because of loss of DNA polymerase activity. The weak icu2-1 allele carried a point mutation and caused early flowering, leaf incurvature, and homeotic transformations of sepals into carpels and of petals into stamens. Further genetic analyses indicated that ICU2 interacts with TERMINAL FLOWER2, the ortholog of HETEROCHROMATIN PROTEIN1 of animals and yeasts, and with the Polycomb group (PcG) gene CURLY LEAF. Another PcG gene, EMBRYONIC FLOWER2, was found to be epistatic to ICU2. Quantitative RT-PCR analyses indicated that a number of regulatory genes were derepressed in the icu2-1 mutant, including genes associated with flowering time, floral meristem, and floral organ identity. PMID:17873092

Heart Rate assessment by means of a novel approach applied to signals of different nature

NASA Astrophysics Data System (ADS)

Cosoli, G.; Casacanditella, L.; Tomasini, EP; Scalise, L.

2017-01-01

Electrocardiographic (ECG) signal presents many clinically relevant features (e.g. QT-interval, that is the duration of the ventricular depolarization). A novel processing technique has been demonstrated to be capable to measure some important characteristics according to the morphology of the waveform. Basing on that, the aim of this work is to propose an improved algorithm and to prove its efficacy in the assessment of the subject’s Heart Rate (HR) in comparison to standard algorithms (i.e. Pan & Tompkins). Results obtained in experimentally collected ECG signals for the identification of the main feature (R-peak) are comparable to those obtained with the traditional approach (sensitivity of 99.55% and 99.95%, respectively). Moreover, the use of this algorithm has been broaden to signals coming from different biomedical sensors (based on optical, acoustical and mechanical principles), all related to blood flow, for the computation of HR. In particular, it has been employed to PCG (Phonocardiography), PPG (Photoplethysmography) and VCG (Vibrocardiography), where standard algorithms could not be widely applied. HR results from a measurement campaign on 8 healthy subjects have shown, with respect to ECG, deviations (calculated as 2σ) of ±3.3 bpm, ±2.3 bpm and ±1.5 bpm for PCG, PPG and VCG, respectively. In conclusion, it is possible to state that the adopted algorithm is able to measure HR accurately from different biosignals. Future work will involve the extraction of additional morphological features in order to characterise the waveforms more deeply and to better describe the subject’s health status.

A new method of determining moisture gradient in wood

Treesearch

Zhiyong Cai

2008-01-01

Moisture gradient in wood and wood composites is one of most important factors that affects both physical stability and mechanical performance. This paper describes a method for measuring moisture gradient in lumber and engineering wood composites as it varies across material thickness. This innovative method employs a collimated radiation beam (x rays or [gamma] rays...

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.

A three-term conjugate gradient method under the strong-Wolfe line search

NASA Astrophysics Data System (ADS)

Khadijah, Wan; Rivaie, Mohd; Mamat, Mustafa

2017-08-01

Recently, numerous studies have been concerned in conjugate gradient methods for solving large-scale unconstrained optimization method. In this paper, a three-term conjugate gradient method is proposed for unconstrained optimization which always satisfies sufficient descent direction and namely as Three-Term Rivaie-Mustafa-Ismail-Leong (TTRMIL). Under standard conditions, TTRMIL method is proved to be globally convergent under strong-Wolfe line search. Finally, numerical results are provided for the purpose of comparison.

The equivalent magnetizing method applied to the design of gradient coils for MRI.

PubMed

Lopez, Hector Sanchez; Liu, Feng; Crozier, Stuart

2008-01-01

This paper presents a new method for the design of gradient coils for Magnetic Resonance Imaging systems. The method is based on the equivalence between a magnetized volume surrounded by a conducting surface and its equivalent representation in surface current/charge density. We demonstrate that the curl of the vertical magnetization induces a surface current density whose stream line defines the coil current pattern. This method can be applied for coils wounds on arbitrary surface shapes. A single layer unshielded transverse gradient coil is designed and compared, with the designs obtained using two conventional methods. Through the presented example we demonstrate that the generated unconventional current patterns obtained using the magnetizing current method produces a superior gradient coil performance than coils designed by applying conventional methods.

Approximate error conjugation gradient minimization methods

DOEpatents

Kallman, Jeffrey S

2013-05-21

In one embodiment, a method includes selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, calculating an approximate error using the subset of rays, and calculating a minimum in a conjugate gradient direction based on the approximate error. In another embodiment, a system includes a processor for executing logic, logic for selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, logic for calculating an approximate error using the subset of rays, and logic for calculating a minimum in a conjugate gradient direction based on the approximate error. In other embodiments, computer program products, methods, and systems are described capable of using approximate error in constrained conjugate gradient minimization problems.

Biomaterials with persistent growth factor gradients in vivo accelerate vascularized tissue formation.

PubMed

Akar, Banu; Jiang, Bin; Somo, Sami I; Appel, Alyssa A; Larson, Jeffery C; Tichauer, Kenneth M; Brey, Eric M

2015-12-01

Gradients of soluble factors play an important role in many biological processes, including blood vessel assembly. Gradients can be studied in detail in vitro, but methods that enable the study of spatially distributed soluble factors and multi-cellular processes in vivo are limited. Here, we report on a method for the generation of persistent in vivo gradients of growth factors in a three-dimensional (3D) biomaterial system. Fibrin loaded porous poly (ethylene glycol) (PEG) scaffolds were generated using a particulate leaching method. Platelet derived growth factor BB (PDGF-BB) was encapsulated into poly (lactic-co-glycolic acid) (PLGA) microspheres which were placed distal to the tissue-material interface. PLGA provides sustained release of PDGF-BB and its diffusion through the porous structure results in gradient formation. Gradients within the scaffold were confirmed in vivo using near-infrared fluorescence imaging and gradients were present for more than 3 weeks. The diffusion of PDGF-BB was modeled and verified with in vivo imaging findings. The depth of tissue invasion and density of blood vessels formed in response to the biomaterial increased with magnitude of the gradient. This biomaterial system allows for generation of sustained growth factor gradients for the study of tissue response to gradients in vivo. Published by Elsevier Ltd.

Determination of wall shear stress from mean velocity and Reynolds shear stress profiles

NASA Astrophysics Data System (ADS)

Volino, Ralph J.; Schultz, Michael P.

2018-03-01

An analytical method is presented for determining the Reynolds shear stress profile in steady, two-dimensional wall-bounded flows using the mean streamwise velocity. The method is then utilized with experimental data to determine the local wall shear stress. The procedure is applicable to flows on smooth and rough surfaces with arbitrary pressure gradients. It is based on the streamwise component of the boundary layer momentum equation, which is transformed into inner coordinates. The method requires velocity profiles from at least two streamwise locations, but the formulation of the momentum equation reduces the dependence on streamwise gradients. The method is verified through application to laminar flow solutions and turbulent DNS results from both zero and nonzero pressure gradient boundary layers. With strong favorable pressure gradients, the method is shown to be accurate for finding the wall shear stress in cases where the Clauser fit technique loses accuracy. The method is then applied to experimental data from the literature from zero pressure gradient studies on smooth and rough walls, and favorable and adverse pressure gradient cases on smooth walls. Data from very near the wall are not required for determination of the wall shear stress. Wall friction velocities obtained using the present method agree with those determined in the original studies, typically to within 2%.

The discrete adjoint method for parameter identification in multibody system dynamics.

PubMed

Lauß, Thomas; Oberpeilsteiner, Stefan; Steiner, Wolfgang; Nachbagauer, Karin

2018-01-01

The adjoint method is an elegant approach for the computation of the gradient of a cost function to identify a set of parameters. An additional set of differential equations has to be solved to compute the adjoint variables, which are further used for the gradient computation. However, the accuracy of the numerical solution of the adjoint differential equation has a great impact on the gradient. Hence, an alternative approach is the discrete adjoint method , where the adjoint differential equations are replaced by algebraic equations. Therefore, a finite difference scheme is constructed for the adjoint system directly from the numerical time integration method. The method provides the exact gradient of the discretized cost function subjected to the discretized equations of motion.

Brain vascular image enhancement based on gradient adjust with split Bregman

NASA Astrophysics Data System (ADS)

Liang, Xiao; Dong, Di; Hui, Hui; Zhang, Liwen; Fang, Mengjie; Tian, Jie

2016-04-01

Light Sheet Microscopy is a high-resolution fluorescence microscopic technique which enables to observe the mouse brain vascular network clearly with immunostaining. However, micro-vessels are stained with few fluorescence antibodies and their signals are much weaker than large vessels, which make micro-vessels unclear in LSM images. In this work, we developed a vascular image enhancement method to enhance micro-vessel details which should be useful for vessel statistics analysis. Since gradient describes the edge information of the vessel, the main idea of our method is to increase the gradient values of the enhanced image to improve the micro-vessels contrast. Our method contained two steps: 1) calculate the gradient image of LSM image, and then amplify high gradient values of the original image to enhance the vessel edge and suppress low gradient values to remove noises. Then we formulated a new L1-norm regularization optimization problem to find an image with the expected gradient while keeping the main structure information of the original image. 2) The split Bregman iteration method was used to deal with the L1-norm regularization problem and generate the final enhanced image. The main advantage of the split Bregman method is that it has both fast convergence and low memory cost. In order to verify the effectiveness of our method, we applied our method to a series of mouse brain vascular images acquired from a commercial LSM system in our lab. The experimental results showed that our method could greatly enhance micro-vessel edges which were unclear in the original images.

Technical Note: Interleaved Bipolar Acquisition and Low-rank Reconstruction for Water-Fat Separation in MRI.

PubMed

Cho, JaeJin; Park, HyunWook

2018-05-17

To acquire interleaved bipolar data and reconstruct the full data using low-rank property for water fat separation. Bipolar acquisition suffers from issues related to gradient switching, the opposite gradient polarities, and other system imperfections, which prevent accurate water-fat separation. In this study, an interleaved bipolar acquisition scheme and a low-rank reconstruction method were proposed to reduce issues from the bipolar gradients while achieving a short imaging time. The proposed interleaved bipolar acquisition scheme collects echo-time signals from both gradient polarities; however, the sequence increases the imaging time. To reduce the imaging time, the signals were subsampled at every dimension of k-space. The low-rank property of the bipolar acquisition was defined and exploited to estimate the full data from the acquired subsampled data. To eliminate the bipolar issues, in the proposed method, the water-fat separation was performed separately for each gradient polarity, and the results for the positive and negative gradient polarities were combined after the water-fat separation. A phantom study and in-vivo experiments were conducted on a 3T Siemens Verio system. The results for the proposed method were compared with the results of the fully sampled interleaved bipolar acquisition and Soliman's method, which was the previous water-fat separation approach for reducing the issues of bipolar gradients and accelerating the interleaved bipolar acquisition. The proposed method provided accurate water and fat images without the issues of bipolar gradients and demonstrated a better performance compared with the results of the previous methods. The water-fat separation using the bipolar acquisition has several benefits including a short echo-spacing time. However, it suffers from bipolar-gradient issues such as strong gradient switching, system imperfection, and eddy current effects. This study demonstrated that accurate water-fat separated images can be obtained using the proposed interleaved bipolar acquisition and low-rank reconstruction by using the benefits of the bipolar acquisition while reducing the bipolar-gradient issues with a short imaging time. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A support vector machine-based method to identify mild cognitive impairment with multi-level characteristics of magnetic resonance imaging.

PubMed

Long, Zhuqing; Jing, Bin; Yan, Huagang; Dong, Jianxin; Liu, Han; Mo, Xiao; Han, Ying; Li, Haiyun

2016-09-07

Mild cognitive impairment (MCI) represents a transitional state between normal aging and Alzheimer's disease (AD). Non-invasive diagnostic methods are desirable to identify MCI for early therapeutic interventions. In this study, we proposed a support vector machine (SVM)-based method to discriminate between MCI patients and normal controls (NCs) using multi-level characteristics of magnetic resonance imaging (MRI). This method adopted a radial basis function (RBF) as the kernel function, and a grid search method to optimize the two parameters of SVM. The calculated characteristics, i.e., the Hurst exponent (HE), amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo) and gray matter density (GMD), were adopted as the classification features. A leave-one-out cross-validation (LOOCV) was used to evaluate the classification performance of the method. Applying the proposed method to the experimental data from 29 MCI patients and 33 healthy subjects, we achieved a classification accuracy of up to 96.77%, with a sensitivity of 93.10% and a specificity of 100%, and the area under the curve (AUC) yielded up to 0.97. Furthermore, the most discriminative features for classification were found to predominantly involve default-mode regions, such as hippocampus (HIP), parahippocampal gyrus (PHG), posterior cingulate gyrus (PCG) and middle frontal gyrus (MFG), and subcortical regions such as lentiform nucleus (LN) and amygdala (AMYG). Therefore, our method is promising in distinguishing MCI patients from NCs and may be useful for the diagnosis of MCI. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

A feasible DY conjugate gradient method for linear equality constraints

NASA Astrophysics Data System (ADS)

LI, Can

2017-09-01

In this paper, we propose a feasible conjugate gradient method for solving linear equality constrained optimization problem. The method is an extension of the Dai-Yuan conjugate gradient method proposed by Dai and Yuan to linear equality constrained optimization problem. It can be applied to solve large linear equality constrained problem due to lower storage requirement. An attractive property of the method is that the generated direction is always feasible and descent direction. Under mild conditions, the global convergence of the proposed method with exact line search is established. Numerical experiments are also given which show the efficiency of the method.

Quantification of susceptibility change at high-concentrated SPIO-labeled target by characteristic phase gradient recognition.

PubMed

Zhu, Haitao; Nie, Binbin; Liu, Hua; Guo, Hua; Demachi, Kazuyuki; Sekino, Masaki; Shan, Baoci

2016-05-01

Phase map cross-correlation detection and quantification may produce highlighted signal at superparamagnetic iron oxide nanoparticles, and distinguish them from other hypointensities. The method may quantify susceptibility change by performing least squares analysis between a theoretically generated magnetic field template and an experimentally scanned phase image. Because characteristic phase recognition requires the removal of phase wrap and phase background, additional steps of phase unwrapping and filtering may increase the chance of computing error and enlarge the inconsistence among algorithms. To solve problem, phase gradient cross-correlation and quantification method is developed by recognizing characteristic phase gradient pattern instead of phase image because phase gradient operation inherently includes unwrapping and filtering functions. However, few studies have mentioned the detectable limit of currently used phase gradient calculation algorithms. The limit may lead to an underestimation of large magnetic susceptibility change caused by high-concentrated iron accumulation. In this study, mathematical derivation points out the value of maximum detectable phase gradient calculated by differential chain algorithm in both spatial and Fourier domain. To break through the limit, a modified quantification method is proposed by using unwrapped forward differentiation for phase gradient generation. The method enlarges the detectable range of phase gradient measurement and avoids the underestimation of magnetic susceptibility. Simulation and phantom experiments were used to quantitatively compare different methods. In vivo application performs MRI scanning on nude mice implanted by iron-labeled human cancer cells. Results validate the limit of detectable phase gradient and the consequent susceptibility underestimation. Results also demonstrate the advantage of unwrapped forward differentiation compared with differential chain algorithms for susceptibility quantification at high-concentrated iron accumulation. Copyright © 2015 Elsevier Inc. All rights reserved.

Constraints on the subsurface structure and density of the nucleus of Comet 67P/Churyumov-Gerasimenko from Arecibo radar observations

NASA Astrophysics Data System (ADS)

Kamoun, P.; Lamy, P. L.; Toth, I.; Herique, A.

2014-08-01

Context. Little is known about the internal structure of cometary nuclei. In addition to understanding their accretion in the early solar nebula and their subsequent evolution in the solar system, we find this question to be of acute and timely interest in the case of 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) due to be visited by the Rosetta spacecraft in the second half of 2014. In particular, the successful landing of the Philae surface module depends critically upon the bulk density of the nucleus and the structure of its surface layer. Aims: In addition to fostering our general knowledge of these properties, it is important to exploit all possible information to assist in preparing the delivery of Philae. Methods: We performed an in-depth analysis of the observations done with the radar system of the Arecibo Observatory in November 1982 when comet 67P/C-G had a close encounter with Earth at a geocentric distance of 0.4AU taking our present knowledge of the properties of its nucleus (size, rotational state) into account. Results: In the absence of a detectable radar echo, we determined a maximum radar cross section of 0.7 km2, leading to a maximum radar albedo of 0.05. This low albedo probably results from a combination of a low radar reflectivity material and a lightly packed upper layer of the nucleus with substantial roughness (rms slope of ≈55°), consistent with its low thermal inertia. Based on radar observations of other cometary nuclei and asteroids, it is unlikely that the albedo can be lower than 0.04 so that we were able to constrain the dielectric permittivity of the subsurface layer to a narrow range of 1.9 to 2.1. Laboratory measurements and our modeling of mixtures of ice and dust have led to a porosity in the range of approximately 55 to 65% and a density in the range of ≈600 to ≈1000 kg m-3 for the top ≈2.5 m layer of the nucleus. This would be the bulk density range for a homogeneous nucleus and would place the success of the landing at risk, but an inhomogeneous nucleus with an overall density below this range remains a possibility.

Iterative and multigrid methods in the finite element solution of incompressible and turbulent fluid flow

NASA Astrophysics Data System (ADS)

Lavery, N.; Taylor, C.

1999-07-01

Multigrid and iterative methods are used to reduce the solution time of the matrix equations which arise from the finite element (FE) discretisation of the time-independent equations of motion of the incompressible fluid in turbulent motion. Incompressible flow is solved by using the method of reduce interpolation for the pressure to satisfy the Brezzi-Babuska condition. The k-l model is used to complete the turbulence closure problem. The non-symmetric iterative matrix methods examined are the methods of least squares conjugate gradient (LSCG), biconjugate gradient (BCG), conjugate gradient squared (CGS), and the biconjugate gradient squared stabilised (BCGSTAB). The multigrid algorithm applied is based on the FAS algorithm of Brandt, and uses two and three levels of grids with a V-cycling schedule. These methods are all compared to the non-symmetric frontal solver. Copyright

A comparison of two closely-related approaches to aerodynamic design optimization

NASA Technical Reports Server (NTRS)

Shubin, G. R.; Frank, P. D.

1991-01-01

Two related methods for aerodynamic design optimization are compared. The methods, called the implicit gradient approach and the variational (or optimal control) approach, both attempt to obtain gradients necessary for numerical optimization at a cost significantly less than that of the usual black-box approach that employs finite difference gradients. While the two methods are seemingly quite different, they are shown to differ (essentially) in that the order of discretizing the continuous problem, and of applying calculus, is interchanged. Under certain circumstances, the two methods turn out to be identical. We explore the relationship between these methods by applying them to a model problem for duct flow that has many features in common with transonic flow over an airfoil. We find that the gradients computed by the variational method can sometimes be sufficiently inaccurate to cause the optimization to fail.

Joint design of large-tip-angle parallel RF pulses and blipped gradient trajectories.

PubMed

Cao, Zhipeng; Donahue, Manus J; Ma, Jun; Grissom, William A

2016-03-01

To design multichannel large-tip-angle kT-points and spokes radiofrequency (RF) pulses and gradient waveforms for transmit field inhomogeneity compensation in high field magnetic resonance imaging. An algorithm to design RF subpulse weights and gradient blip areas is proposed to minimize a magnitude least-squares cost function that measures the difference between realized and desired state parameters in the spin domain, and penalizes integrated RF power. The minimization problem is solved iteratively with interleaved target phase updates, RF subpulse weights updates using the conjugate gradient method with optimal control-based derivatives, and gradient blip area updates using the conjugate gradient method. Two-channel parallel transmit simulations and experiments were conducted in phantoms and human subjects at 7 T to demonstrate the method and compare it to small-tip-angle-designed pulses and circularly polarized excitations. The proposed algorithm designed more homogeneous and accurate 180° inversion and refocusing pulses than other methods. It also designed large-tip-angle pulses on multiple frequency bands with independent and joint phase relaxation. Pulses designed by the method improved specificity and contrast-to-noise ratio in a finger-tapping spin echo blood oxygen level dependent functional magnetic resonance imaging study, compared with circularly polarized mode refocusing. A joint RF and gradient waveform design algorithm was proposed and validated to improve large-tip-angle inversion and refocusing at ultrahigh field. © 2015 Wiley Periodicals, Inc.

A wet/wet differential pressure sensor for measuring vertical hydraulic gradient.

PubMed

Fritz, Brad G; Mackley, Rob D

2010-01-01

Vertical hydraulic gradient is commonly measured in rivers, lakes, and streams for studies of groundwater-surface water interaction. While a number of methods with subtle differences have been applied, these methods can generally be separated into two categories; measuring surface water elevation and pressure in the subsurface separately or making direct measurements of the head difference with a manometer. Making separate head measurements allows for the use of electronic pressure sensors, providing large datasets that are particularly useful when the vertical hydraulic gradient fluctuates over time. On the other hand, using a manometer-based method provides an easier and more rapid measurement with a simpler computation to calculate the vertical hydraulic gradient. In this study, we evaluated a wet/wet differential pressure sensor for use in measuring vertical hydraulic gradient. This approach combines the advantage of high-temporal frequency measurements obtained with instrumented piezometers with the simplicity and reduced potential for human-induced error obtained with a manometer board method. Our results showed that the wet/wet differential pressure sensor provided results comparable to more traditional methods, making it an acceptable method for future use.

New head gradient coil design and construction techniques

PubMed Central

Handler, William B; Harris, Chad T; Scholl, Timothy J; Parker, Dennis L; Goodrich, K Craig; Dalrymple, Brian; Van Sass, Frank; Chronik, Blaine A

2013-01-01

Purpose To design and build a head insert gradient coil to use in conjunction with body gradients for superior imaging. Materials and Methods The use of the Boundary Element Method to solve for a gradient coil wire pattern on an arbitrary surface has allowed us to incorporate engineering changes into the electromagnetic design of a gradient coil directly. Improved wire pattern design has been combined with robust manufacturing techniques and novel cooling methods. Results The finished coil had an efficiency of 0.15 mT/m/A in all three axes and allowed the imaging region to extend across the entire head and upper part of the neck. Conclusion The ability to adapt your electromagnetic design to necessary changes from an engineering perspective leads to superior coil performance. PMID:24123485

A modified form of conjugate gradient method for unconstrained optimization problems

NASA Astrophysics Data System (ADS)

Ghani, Nur Hamizah Abdul; Rivaie, Mohd.; Mamat, Mustafa

2016-06-01

Conjugate gradient (CG) methods have been recognized as an interesting technique to solve optimization problems, due to the numerical efficiency, simplicity and low memory requirements. In this paper, we propose a new CG method based on the study of Rivaie et al. [7] (Comparative study of conjugate gradient coefficient for unconstrained Optimization, Aus. J. Bas. Appl. Sci. 5(2011) 947-951). Then, we show that our method satisfies sufficient descent condition and converges globally with exact line search. Numerical results show that our proposed method is efficient for given standard test problems, compare to other existing CG methods.

Coupling temporal and spatial gradient information in high-density unstructured Lagrangian measurements

NASA Astrophysics Data System (ADS)

Wong, Jaime G.; Rosi, Giuseppe A.; Rouhi, Amirreza; Rival, David E.

2017-10-01

Particle tracking velocimetry (PTV) produces high-quality temporal information that is often neglected when computing spatial gradients. A method is presented here to utilize this temporal information in order to improve the estimation of spatial gradients for spatially unstructured Lagrangian data sets. Starting with an initial guess, this method penalizes any gradient estimate where the substantial derivative of vorticity along a pathline is not equal to the local vortex stretching/tilting. Furthermore, given an initial guess, this method can proceed on an individual pathline without any further reference to neighbouring pathlines. The equivalence of the substantial derivative and vortex stretching/tilting is based on the vorticity transport equation, where viscous diffusion is neglected. By minimizing the residual of the vorticity-transport equation, the proposed method is first tested to reduce error and noise on a synthetic Taylor-Green vortex field dissipating in time. Furthermore, when the proposed method is applied to high-density experimental data collected with `Shake-the-Box' PTV, noise within the spatial gradients is significantly reduced. In the particular test case investigated here of an accelerating circular plate captured during a single run, the method acts to delineate the shear layer and vortex core, as well as resolve the Kelvin-Helmholtz instabilities, which were previously unidentifiable without the use of ensemble averaging. The proposed method shows promise for improving PTV measurements that require robust spatial gradients while retaining the unstructured Lagrangian perspective.

Longitudinal gradient coil optimization in the presence of transient eddy currents.

PubMed

Trakic, A; Liu, F; Lopez, H Sanchez; Wang, H; Crozier, S

2007-06-01

The switching of magnetic field gradient coils in magnetic resonance imaging (MRI) inevitably induces transient eddy currents in conducting system components, such as the cryostat vessel. These secondary currents degrade the spatial and temporal performance of the gradient coils, and compensation methods are commonly employed to correct for these distortions. This theoretical study shows that by incorporating the eddy currents into the coil optimization process, it is possible to modify a gradient coil design so that the fields created by the coil and the eddy currents combine together to generate a spatially homogeneous gradient that follows the input pulse. Shielded and unshielded longitudinal gradient coils are used to exemplify this novel approach. To assist in the evaluation of transient eddy currents induced within a realistic cryostat vessel, a low-frequency finite-difference time-domain (FDTD) method using the total-field scattered-field (TFSF) scheme was performed. The simulations demonstrate the effectiveness of the proposed method for optimizing longitudinal gradient fields while taking into account the spatial and temporal behavior of the eddy currents.

Systematic generation of buffer systems for pH gradient ion exchange chromatography and their application.

PubMed

Kröner, Frieder; Hubbuch, Jürgen

2013-04-12

pH gradient protein separations are widely used techniques in the field of protein analytics, of which isoelectric focusing is the most well known application. The chromatographic variant, based on the formation of pH gradients in ion exchange columns is only rarely applied due to the difficulties to form controllable, linear pH gradients over a broad pH range. This work describes a method for the systematic generation of buffer compositions with linear titration curves, resulting in well controllable pH gradients. To generate buffer compositions with linear titration curves an in silico method was successfully developed. With this tool, buffer compositions for pH gradient ion exchange chromatography with pH ranges spanning up to 7.5 pH units were established and successfully validated. Subsequently, the buffer systems were used to characterize the elution behavior of 22 different model proteins in cation and anion exchange pH gradient chromatography. The results of both chromatographic modes as well as isoelectric focusing were compared to describe differences in between the methods. Copyright © 2013 Elsevier B.V. All rights reserved.

Calibration of a rotating accelerometer gravity gradiometer using centrifugal gradients

NASA Astrophysics Data System (ADS)

Yu, Mingbiao; Cai, Tijing

2018-05-01

The purpose of this study is to calibrate scale factors and equivalent zero biases of a rotating accelerometer gravity gradiometer (RAGG). We calibrate scale factors by determining the relationship between the centrifugal gradient excitation and RAGG response. Compared with calibration by changing the gravitational gradient excitation, this method does not need test masses and is easier to implement. The equivalent zero biases are superpositions of self-gradients and the intrinsic zero biases of the RAGG. A self-gradient is the gravitational gradient produced by surrounding masses, and it correlates well with the RAGG attitude angle. We propose a self-gradient model that includes self-gradients and the intrinsic zero biases of the RAGG. The self-gradient model is a function of the RAGG attitude, and it includes parameters related to surrounding masses. The calibration of equivalent zero biases determines the parameters of the self-gradient model. We provide detailed procedures and mathematical formulations for calibrating scale factors and parameters in the self-gradient model. A RAGG physical simulation system substitutes for the actual RAGG in the calibration and validation experiments. Four point masses simulate four types of surrounding masses producing self-gradients. Validation experiments show that the self-gradients predicted by the self-gradient model are consistent with those from the outputs of the RAGG physical simulation system, suggesting that the presented calibration method is valid.

Cognitive Behaviour therapy for Older Adults with Insomnia and Depression: A Randomized Controlled Trial in Community Mental Health Services.

PubMed

Sadler, Paul; McLaren, Suzanne; Klein, Britt; Harvey, Jack; Jenkins, Megan

2018-05-24

To investigate whether cognitive behaviour therapy was effective for older adults with comorbid insomnia and depression in a community mental health setting, and explore whether an advanced form of cognitive behaviour therapy for insomnia produced better outcomes compared to a standard form of cognitive behaviour therapy for insomnia. An 8 week randomized controlled clinical trial was conducted within community mental health services, Victoria, Australia. Seventy-two older adults (56% female, M age 75 years ± 7) with diagnosed comorbid insomnia and depression participated. Three conditions were tested using a group therapy format: cognitive behaviour therapy for insomnia (CBT-I, standard), cognitive behaviour therapy for insomnia plus positive mood strategies (CBT-I+, advanced), psychoeducation control group (PCG, control). The primary outcomes were insomnia severity (Insomnia Severity Index) and depression severity (Geriatric Depression Scale). Primary and secondary measures were collected at pre (week 0), post (week 8), and follow-up (week 20). CBT-I and CBT-I+ both generated significantly greater reductions in insomnia and depression severity compared to PCG from pre to post (p < .001), which were maintained at follow-up. Although the differences between outcomes of the two treatment conditions were not statistically significant, the study was not sufficiently powered to detect either superiority of one treatment or equivalence of the two treatment conditions. CBT-I and CBT-I+ were both effective at reducing insomnia and depression severity for older adults. Mental health services that deliver treatment for comorbid insomnia with cognitive behaviour therapy may improve recovery outcomes for older adults with depression. Australian and New Zealand Clinical Trials Registry (ANZCTR) URL: https://www.anzctr.org.au Trial ID: ACTRN12615000067572 Date Registered: 12th December 2014.

Function of YY1 in Long-Distance DNA Interactions

PubMed Central

Atchison, Michael L.

2014-01-01

During B cell development, long-distance DNA interactions are needed for V(D)J somatic rearrangement of the immunoglobulin (Ig) loci to produce functional Ig genes, and for class switch recombination (CSR) needed for antibody maturation. The tissue-specificity and developmental timing of these mechanisms is a subject of active investigation. A small number of factors are implicated in controlling Ig locus long-distance interactions including Pax5, Yin Yang 1 (YY1), EZH2, IKAROS, CTCF, cohesin, and condensin proteins. Here we will focus on the role of YY1 in controlling these mechanisms. YY1 is a multifunctional transcription factor involved in transcriptional activation and repression, X chromosome inactivation, Polycomb Group (PcG) protein DNA recruitment, and recruitment of proteins required for epigenetic modifications (acetylation, deacetylation, methylation, ubiquitination, sumoylation, etc.). YY1 conditional knock-out indicated that YY1 is required for B cell development, at least in part, by controlling long-distance DNA interactions at the immunoglobulin heavy chain and Igκ loci. Our recent data show that YY1 is also required for CSR. The mechanisms implicated in YY1 control of long-distance DNA interactions include controlling non-coding antisense RNA transcripts, recruitment of PcG proteins to DNA, and interaction with complexes involved in long-distance DNA interactions including the cohesin and condensin complexes. Though common rearrangement mechanisms operate at all Ig loci, their distinct temporal activation along with the ubiquitous nature of YY1 poses challenges for determining the specific mechanisms of YY1 function in these processes, and their regulation at the tissue-specific and B cell stage-specific level. The large numbers of post-translational modifications that control YY1 functions are possible candidates for regulation. PMID:24575094

Effect of β-hydroxy-β-methylbutyrate in masticatory muscles of rats

PubMed Central

Daré, Leticia R; Dias, Daniel V; Rosa Junior, Geraldo M; Bueno, Cleuber R S; Buchaim, Rogerio L; Rodrigues, Antonio de C; Andreo, Jesus C

2015-01-01

The aim of this research was to examine the influence of β-hydroxy-β-methylbutyrate (HMB) on changes in the profile of muscle fibers, whether these alterations were similar between the elevator and depressor muscles of the jaw, and whether the effects would be similar in male and female animals. Fifty-eight rats aged 60 days (29 animals of each gender) were divided into four groups: the initial control group (ICG) was sacrificed at the beginning of the experiment; the placebo control group (PCG) received saline and was fed ad libitum; the experimental group (EG) received 0.3 g kg−1 of HMB daily for 4 weeks by gavage as well as the same amount of food consumed by the PCG in the previous day; and the experimental ad libitum group (EAG) received the same dose of the supplement along with food ad libitum. Samples included the digastric and masseter muscles for the histoenzymological analysis. Data were subjected to statistical analysis with a significance level of P < 0.05. Use of HMB caused a decrease in the percentage of fast twitch glycolytic (FG) fibers and an increase in fast twitch oxidative glycolytic (FOG) fibers in males in both experimental groups (EG and EAG). However, it produced no increase in the muscle fiber area, in either gender, in the masseter muscle. In the digastric muscle, the HMB did not change the frequency or the area of any muscle fiber types in either gender. Our data suggest that the use of HMB caused small changes in the enzymological profile of fibers of the mastication muscles; the changes were different in the elevator and depressor muscles of the jaw and the results were different depending on gender. PMID:25400135

Altered effective connectivity anchored in the posterior cingulate cortex and the medial prefrontal cortex in cognitively intact elderly APOE ε4 carriers: a preliminary study.

PubMed

Luo, Xiao; Li, Kaicheng; Jia, Y L; Zeng, Qingze; Jiaerken, Yeerfan; Qiu, Tiantian; Huang, Peiyu; Xu, Xiaojun; Shen, Zhujing; Guan, Xiaojun; Zhou, Jiong; Wang, Chao; Xu, J J; Zhang, Minming

2018-03-17

The APOE ε4 allele is associated with impaired intrinsic functional connectivity in neural networks, especially in the default mode network (DMN). However, effective connectivity (EC) reflects the direct causal effects of one brain region to another, which has rarely been investigated. Recently, Granger causality analysis (GCA) proved suitable for the study of directionality in neuronal interactions. Using GCA, we examined the differences in the EC between the anterior medial prefrontal cortex/posterior cingulate cortex (aMPFC/PCC) and the whole brain in 17 ε4 carrying and 32 non-carrying cognitively intact elderly individuals. Furthermore, correlation analyses were performed between the abnormal EC and cognition/neuropathological indices. Compared with the non-carriers, the results showed that the ε4 carriers exhibited decreased EC from the PCC to the whole brain in the middle temporal gyrus (MTG), the anterior cingulate cortex (ACC), and the precuneus (PCu). Meanwhile, the ε4 carriers demonstrated increased EC from the whole brain to the aMPFC in the inferior parietal lobe (IPL) and the postcentral gyrus (PCG). The correlation analyses suggested that the EC from the IPL/PCG to the aMPFC was related to episodic memory in non-carriers, while the decreased EC from the PCC to the ACC was associated with increased levels of t-tau in the ε4 carriers. In ε4 carriers, a negative influence can be traced from the PCC to both the anterior and posterior DMN subsystems; meanwhile, the anterior DMN subsystem receives compensatory effects from the parietal cortex. Early increases in AD-related pathologies in the PCC may act as first factors during this pathological process.

Effects of rearrangement and allelic exclusion of JJAZ1/SUZ12 on cell proliferation and survival

PubMed Central

Li, Hui; Ma, XianYong; Wang, Jinglan; Koontz, Jason; Nucci, Marisa; Sklar, Jeffrey

2007-01-01

Polycomb group genes (PcGs) have been implicated in cancer based on altered levels of expression observed in certain tumors and the behavior of cultured cells containing inserted PcG transgenes. Endometrial stromal tumors provide evidence for a direct causal relationship because they contain several chromosomal translocations and resultant gene fusions involving PcGs, the most common of which joins portions of theJAZF1 gene to the PcGJJAZ1/SUZ12. We show here that both benign and malignant forms of this tumor have theJAZF1–JJAZ1 fusion but only the malignant form also exhibits exclusion of the unrearrangedJJAZ1 allele. To evaluate the effects of both theJJAZ1/SUZ12 fusion and allelic exclusion on functions related to cell growth, we studied HEK293 cells that were modified with respect toJJAZ1 expression. We found that theJAZF1–JJAZ1 fusion restored levels of the polycomb protein EZH2 and histone 3 lysine 27 trimethylation, which were reduced by knockdown of endogenous JJAZ1. At the same time, the presence ofJAZF1–JJAZ1 markedly inhibited apoptosis and induced above normal proliferation rates, although the latter effect occurred only when normalJJAZ1 was suppressed. Our findings suggest a genetic pathway for progression of a benign precursor to a sarcoma involving increased cell survival associated with acquisition of a PcG rearrangement, followed by accelerated cellular proliferation upon allelic exclusion of the unrearranged copy of that gene. Furthermore, these results indicate the likely functional importance of allelic exclusion of genes disrupted by chromosomal translocations, as seen in a variety of other cancers. PMID:18077430

Efficacy of photobiomodulation therapy on masseter thickness and oral health-related quality of life in children with spastic cerebral palsy.

PubMed

Santos, Maria Teresa Botti Rodrigues; Nascimento, Karla Santos; Carazzato, Simone; Barros, Alina Oliveira; Mendes, Fausto Medeiros; Diniz, Michele Baffi

2017-08-01

The study aimed to evaluate the efficacy of photobiomodulation therapy (PBMT) on bilateral masseter muscle thickness and amplitude of mouth opening in children with spastic cerebral palsy (CP), and the impact on their oral health-related quality of life (OHRQOL). Three groups were included: experimental CP group (EG: n = 26 with oral complaints), positive control CP group (PCG: n = 26 without complaints), and negative control group (NCG: n = 26 without CP). In the EG, the masseter muscles on both sides were irradiated with an infrared low-level Ga-Al-As laser (λ = 808 ± 3 nm, 120 mW) using a 3 J/cm 2 energy dose per site, with a 20 s exposure time per site (spot area: 4 mm 2 ; irradiance: 3 W/cm 2 ; energy delivery per point: 2.4 J) six times over six consecutive weeks. Masseter thickness, assessed through ultrasonography, and the amplitude of mouth opening were measured in the EG before and after six applications of PBMT and once in the PCG and NCG. The Parental-Caregiver Perception Questionnaire (P-CPQ) was used to evaluate OHRQOL. ANOVA, chi-square, t tests, and multilevel linear regression were used for statistical analysis. In the EG, the study results revealed average increments of 0.77 (0.08) millimeter in masseter thickness (P < 0.05) and 7.39 (0.58) millimeter for mouth opening (P < 0.05) and reduction in all P-CPQ domains (P < 0.001), except for social well-being. The six applications of PBMT increased masseter thickness and mouth opening amplitude and reduced the impact of spastic CP on OHRQOL.

Association between depression in carers and malnutrition in children aged 6 months to 5 years.

PubMed

Motlhatlhedi, Keneilwe; Setlhare, Vincent; Ganiyu, Adewale; Firth, Jacqueline

2017-01-30

 Childhood malnutrition is an important risk factor for child mortality and underlies close to 50% of child deaths worldwide. Previous studies have found an association between maternal depression and child malnutrition, but it is not known whether this association exists in Botswana. In addition, previous studies excluded non-maternal primary caregivers (PCGs). It is unclear whether the association between primary caregiver depression and child malnutrition remains when non-maternal PCGs are included. The aim of this study was to determine if there is an association between PCG depression and malnutrition in children aged between 6 months and 5 years in Mahalapye, Botswana. The study was conducted in the child welfare clinics of Xhosa and Airstrip clinics, two primary health care facilities in Mahalapye, Botswana. This was a case control study. Cases were malnourished children aged between 6 months and 5 years, and controls were non-malnourished children matched for age and gender. The outcome of interest was depression in the PCGs of the cases and controls, which was assessed using the Patient Health Questionnaire 9 (PHQ 9), a depression screening tool. From a sample of 171 children, 84 of whom were malnourished, we found that the malnourished children were significantly more likely to have depressed PCGs (odds ratio = 4.33; 95% CI: 1.89, 9.89) than non-malnourished children in the 6-month to 5-year age group; the PCGs of malnourished children also had lower educational status. This study found a significant association between PCG depression and child malnutrition.

Continuous recovery of valine in a model mixture of amino acids and salt from Corynebacterium bacteria fermentation using a simulated moving bed chromatography.

PubMed

Park, Chanhun; Nam, Hee-Geun; Jo, Se-Hee; Wang, Nien-Hwa Linda; Mun, Sungyong

2016-02-26

The economical efficiency of valine production in related industries is largely affected by the performance of a valine separation process, in which valine is to be separated from leucine, alanine, and ammonium sulfate. Such separation is currently handled by a batch-mode hybrid process based on ion-exchange and crystallization schemes. To make a substantial improvement in the economical efficiency of an industrial valine production, such a batch-mode process based on two different separation schemes needs to be converted into a continuous-mode separation process based on a single separation scheme. To address this issue, a simulated moving bed (SMB) technology was applied in this study to the development of a continuous-mode valine-separation chromatographic process with uniformity in adsorbent and liquid phases. It was first found that a Chromalite-PCG600C resin could be eligible for the adsorbent of such process, particularly in an industrial scale. The intrinsic parameters of each component on the Chromalite-PCG600C adsorbent were determined and then utilized in selecting a proper set of configurations for SMB units, columns, and ports, under which the SMB operating parameters were optimized with a genetic algorithm. Finally, the optimized SMB based on the selected configurations was tested experimentally, which confirmed its effectiveness in continuous separation of valine from leucine, alanine, ammonium sulfate with high purity, high yield, high throughput, and high valine product concentration. It is thus expected that the developed SMB process in this study will be able to serve as one of the trustworthy ways of improving the economical efficiency of an industrial valine production process. Copyright © 2016 Elsevier B.V. All rights reserved.

SSX and the synovial-sarcoma-specific chimaeric protein SYT-SSX co-localize with the human Polycomb group complex.

PubMed

Soulez, M; Saurin, A J; Freemont, P S; Knight, J C

1999-04-29

Chromosome translocation t(X;18)(p11.2;q11.2) is unique to synovial sarcomas and results in an 'in frame' fusion of the SYT gene with the SSX1 or closely-related SSX2 gene. Wild-type SYT and SSX proteins, and the SYT-SSX chimaeric proteins, can modulate transcription in gene reporter assays. To help elucidate the role of these proteins in cell function and neoplasia we have performed immunolabelling experiments to determine their subcellular localization in three cell types. Transient expression of epitope-tagged proteins produced distinctive nuclear staining patterns. The punctate staining of SYT and SYT-SSX proteins showed some similarities. We immunolabelled a series of endogenous nuclear antigens and excluded the SYT and SYT-SSX focal staining from association with these domains (e.g. sites of active transcription, snRNPs). In further experiments we immunolabelled the Polycomb group (PcG) proteins RING1 or BMI-1 and showed that SSX and SYT-SSX proteins, but not SYT, co-localized with these markers. Consistent with this we show that SSX and SYT-SSX associate with chromatin, and also associate with condensed chromatin at metaphase. Noteably, SSX produced a dense signal over the surface of metaphase chromosomes whereas SYT-SSX produced discrete focal staining. Our data indicate that SSX and SYT-SSX proteins are recruited to nuclear domains occupied by PcG complexes, and this provides us with a new insight into the possible function of wild-type SSX and the mechanism by which the aberrant SYT-SSX protein might disrupt fundamental mechanisms controlling cell division and cell fate.

Monetary Reward and Punishment to Response Inhibition Modulate Activation and Synchronization Within the Inhibitory Brain Network.

PubMed

Chikara, Rupesh K; Chang, Erik C; Lu, Yi-Chen; Lin, Dar-Shong; Lin, Chin-Teng; Ko, Li-Wei

2018-01-01

A reward or punishment can modulate motivation and emotions, which in turn affect cognitive processing. The present simultaneous functional magnetic resonance imaging-electroencephalography study examines neural mechanisms of response inhibition under the influence of a monetary reward or punishment by implementing a modified stop-signal task in a virtual battlefield scenario. The participants were instructed to play as snipers who open fire at a terrorist target but withhold shooting in the presence of a hostage. The participants performed the task under three different feedback conditions in counterbalanced order: a reward condition where each successfully withheld response added a bonus (i.e., positive feedback) to the startup credit, a punishment condition where each failure in stopping deduced a penalty (i.e., negative feedback), and a no-feedback condition where response outcome had no consequences and served as a control setting. Behaviorally both reward and punishment conditions led to significantly down-regulated inhibitory function in terms of the critical stop-signal delay. As for the neuroimaging results, increased activities were found for the no-feedback condition in regions previously reported to be associated with response inhibition, including the right inferior frontal gyrus and the pre-supplementary motor area. Moreover, higher activation of the lingual gyrus, posterior cingulate gyrus (PCG) and inferior parietal lobule were found in the reward condition, while stronger activation of the precuneus gyrus was found in the punishment condition. The positive feedback was also associated with stronger changes of delta, theta, and alpha synchronization in the PCG than were the negative or no-feedback conditions. These findings depicted the intertwining relationship between response inhibition and motivation networks.

Methods for Fabricating Gradient Alloy Articles with Multi-Functional Properties

NASA Technical Reports Server (NTRS)

Hofmann, Douglas C. (Inventor); Suh, Eric J. (Inventor); Borgonia, John Paul C. (Inventor); Dillon, Robert P. (Inventor); Mulder, Jerry L. (Inventor); Gardner, Paul B. (Inventor)

2015-01-01

Systems and methods for fabricating multi-functional articles comprised of additively formed gradient materials are provided. The fabrication of multi-functional articles using the additive deposition of gradient alloys represents a paradigm shift from the traditional way that metal alloys and metal/metal alloy parts are fabricated. Since a gradient alloy that transitions from one metal to a different metal cannot be fabricated through any conventional metallurgy techniques, the technique presents many applications. Moreover, the embodiments described identify a broad range of properties and applications.

An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels.

PubMed

Gonçalves, A M; Nehme, N S; Morel, C M

1990-01-01

A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980)]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels are applied to gradient gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

Limited-memory trust-region methods for sparse relaxation

NASA Astrophysics Data System (ADS)

Adhikari, Lasith; DeGuchy, Omar; Erway, Jennifer B.; Lockhart, Shelby; Marcia, Roummel F.

2017-08-01

In this paper, we solve the l2-l1 sparse recovery problem by transforming the objective function of this problem into an unconstrained differentiable function and applying a limited-memory trust-region method. Unlike gradient projection-type methods, which uses only the current gradient, our approach uses gradients from previous iterations to obtain a more accurate Hessian approximation. Numerical experiments show that our proposed approach eliminates spurious solutions more effectively while improving computational time.

Biodegradable Polymers Induce CD54 on THP-1 Cells in Skin Sensitization Test.

PubMed

Jung, Yeon Suk; Kato, Reiko; Tsuchiya, Toshie

2011-01-01

Currently, nonanimal methods of skin sensitization testing for various chemicals, biodegradable polymers, and biomaterials are being developed in the hope of eliminating the use of animals. The human cell line activation test (h-CLAT) is a skin sensitization assessment that mimics the functions of dendritic cells (DCs). DCs are specialized antigen-presenting cells, and they interact with T cells and B cells to initiate immune responses. Phenotypic changes in DCs, such as the production of CD86 and CD54 and internalization of MHC class II molecules, have become focal points of the skin sensitization test. In this study, we used h-CLAT to assess the effects of biodegradable polymers. The results showed that several biodegradable polymers increased the expression of CD54, and the relative skin sensitizing abilities of biodegradable polymers were PLLG (75 : 25) < PLLC (40 : 60) < PLGA (50 : 50) < PCG (50 : 50). These results may contribute to the creation of new guidelines for the use of biodegradable polymers in scaffolds or allergenic hazards.

Evaluation of multiple tracer methods to estimate low groundwater flow velocities.

PubMed

Reimus, Paul W; Arnold, Bill W

2017-04-01

Four different tracer methods were used to estimate groundwater flow velocity at a multiple-well site in the saturated alluvium south of Yucca Mountain, Nevada: (1) two single-well tracer tests with different rest or "shut-in" periods, (2) a cross-hole tracer test with an extended flow interruption, (3) a comparison of two tracer decay curves in an injection borehole with and without pumping of a downgradient well, and (4) a natural-gradient tracer test. Such tracer methods are potentially very useful for estimating groundwater velocities when hydraulic gradients are flat (and hence uncertain) and also when water level and hydraulic conductivity data are sparse, both of which were the case at this test location. The purpose of the study was to evaluate the first three methods for their ability to provide reasonable estimates of relatively low groundwater flow velocities in such low-hydraulic-gradient environments. The natural-gradient method is generally considered to be the most robust and direct method, so it was used to provide a "ground truth" velocity estimate. However, this method usually requires several wells, so it is often not practical in systems with large depths to groundwater and correspondingly high well installation costs. The fact that a successful natural gradient test was conducted at the test location offered a unique opportunity to compare the flow velocity estimates obtained by the more easily deployed and lower risk methods with the ground-truth natural-gradient method. The groundwater flow velocity estimates from the four methods agreed very well with each other, suggesting that the first three methods all provided reasonably good estimates of groundwater flow velocity at the site. The advantages and disadvantages of the different methods, as well as some of the uncertainties associated with them are discussed. Published by Elsevier B.V.

What is the best way to contour lung tumors on PET scans? Multiobserver validation of a gradient-based method using a NSCLC digital PET phantom.

PubMed

Werner-Wasik, Maria; Nelson, Arden D; Choi, Walter; Arai, Yoshio; Faulhaber, Peter F; Kang, Patrick; Almeida, Fabio D; Xiao, Ying; Ohri, Nitin; Brockway, Kristin D; Piper, Jonathan W; Nelson, Aaron S

2012-03-01

To evaluate the accuracy and consistency of a gradient-based positron emission tomography (PET) segmentation method, GRADIENT, compared with manual (MANUAL) and constant threshold (THRESHOLD) methods. Contouring accuracy was evaluated with sphere phantoms and clinically realistic Monte Carlo PET phantoms of the thorax. The sphere phantoms were 10-37 mm in diameter and were acquired at five institutions emulating clinical conditions. One institution also acquired a sphere phantom with multiple source-to-background ratios of 2:1, 5:1, 10:1, 20:1, and 70:1. One observer segmented (contoured) each sphere with GRADIENT and THRESHOLD from 25% to 50% at 5% increments. Subsequently, seven physicians segmented 31 lesions (7-264 mL) from 25 digital thorax phantoms using GRADIENT, THRESHOLD, and MANUAL. For spheres <20 mm in diameter, GRADIENT was the most accurate with a mean absolute % error in diameter of 8.15% (10.2% SD) compared with 49.2% (51.1% SD) for 45% THRESHOLD (p < 0.005). For larger spheres, the methods were statistically equivalent. For varying source-to-background ratios, GRADIENT was the most accurate for spheres >20 mm (p < 0.065) and <20 mm (p < 0.015). For digital thorax phantoms, GRADIENT was the most accurate (p < 0.01), with a mean absolute % error in volume of 10.99% (11.9% SD), followed by 25% THRESHOLD at 17.5% (29.4% SD), and MANUAL at 19.5% (17.2% SD). GRADIENT had the least systematic bias, with a mean % error in volume of -0.05% (16.2% SD) compared with 25% THRESHOLD at -2.1% (34.2% SD) and MANUAL at -16.3% (20.2% SD; p value <0.01). Interobserver variability was reduced using GRADIENT compared with both 25% THRESHOLD and MANUAL (p value <0.01, Levene's test). GRADIENT was the most accurate and consistent technique for target volume contouring. GRADIENT was also the most robust for varying imaging conditions. GRADIENT has the potential to play an important role for tumor delineation in radiation therapy planning and response assessment. Copyright © 2012. Published by Elsevier Inc.

BLIPPED (BLIpped Pure Phase EncoDing) high resolution MRI with low amplitude gradients

NASA Astrophysics Data System (ADS)

Xiao, Dan; Balcom, Bruce J.

2017-12-01

MRI image resolution is proportional to the maximum k-space value, i.e. the temporal integral of the magnetic field gradient. High resolution imaging usually requires high gradient amplitudes and/or long spatial encoding times. Special gradient hardware is often required for high amplitudes and fast switching. We propose a high resolution imaging sequence that employs low amplitude gradients. This method was inspired by the previously proposed PEPI (π Echo Planar Imaging) sequence, which replaced EPI gradient reversals with multiple RF refocusing pulses. It has been shown that when the refocusing RF pulse is of high quality, i.e. sufficiently close to 180°, the magnetization phase introduced by the spatial encoding magnetic field gradient can be preserved and transferred to the following echo signal without phase rewinding. This phase encoding scheme requires blipped gradients that are identical for each echo, with low and constant amplitude, providing opportunities for high resolution imaging. We now extend the sequence to 3D pure phase encoding with low amplitude gradients. The method is compared with the Hybrid-SESPI (Spin Echo Single Point Imaging) technique to demonstrate the advantages in terms of low gradient duty cycle, compensation of concomitant magnetic field effects and minimal echo spacing, which lead to superior image quality and high resolution. The 3D imaging method was then applied with a parallel plate resonator RF probe, achieving a nominal spatial resolution of 17 μm in one dimension in the 3D image, requiring a maximum gradient amplitude of only 5.8 Gauss/cm.

An historical survey of computational methods in optimal control.

NASA Technical Reports Server (NTRS)

Polak, E.

1973-01-01

Review of some of the salient theoretical developments in the specific area of optimal control algorithms. The first algorithms for optimal control were aimed at unconstrained problems and were derived by using first- and second-variation methods of the calculus of variations. These methods have subsequently been recognized as gradient, Newton-Raphson, or Gauss-Newton methods in function space. A much more recent addition to the arsenal of unconstrained optimal control algorithms are several variations of conjugate-gradient methods. At first, constrained optimal control problems could only be solved by exterior penalty function methods. Later algorithms specifically designed for constrained problems have appeared. Among these are methods for solving the unconstrained linear quadratic regulator problem, as well as certain constrained minimum-time and minimum-energy problems. Differential-dynamic programming was developed from dynamic programming considerations. The conditional-gradient method, the gradient-projection method, and a couple of feasible directions methods were obtained as extensions or adaptations of related algorithms for finite-dimensional problems. Finally, the so-called epsilon-methods combine the Ritz method with penalty function techniques.

Performance comparison of a new hybrid conjugate gradient method under exact and inexact line searches

NASA Astrophysics Data System (ADS)

Ghani, N. H. A.; Mohamed, N. S.; Zull, N.; Shoid, S.; Rivaie, M.; Mamat, M.

2017-09-01

Conjugate gradient (CG) method is one of iterative techniques prominently used in solving unconstrained optimization problems due to its simplicity, low memory storage, and good convergence analysis. This paper presents a new hybrid conjugate gradient method, named NRM1 method. The method is analyzed under the exact and inexact line searches in given conditions. Theoretically, proofs show that the NRM1 method satisfies the sufficient descent condition with both line searches. The computational result indicates that NRM1 method is capable in solving the standard unconstrained optimization problems used. On the other hand, the NRM1 method performs better under inexact line search compared with exact line search.

Gradient Pre-Emphasis to Counteract First-Order Concomitant Fields on Asymmetric MRI Gradient Systems

PubMed Central

Tao, Shengzhen; Weavers, Paul T.; Trzasko, Joshua D.; Shu, Yunhong; Huston, John; Lee, Seung-Kyun; Frigo, Louis M.; Bernstein, Matt A.

2016-01-01

PURPOSE To develop a gradient pre-emphasis scheme that prospectively counteracts the effects of the first-order concomitant fields for any arbitrary gradient waveform played on asymmetric gradient systems, and to demonstrate the effectiveness of this approach using a real-time implementation on a compact gradient system. METHODS After reviewing the first-order concomitant fields that are present on asymmetric gradients, a generalized gradient pre-emphasis model assuming arbitrary gradient waveforms is developed to counteract their effects. A numerically straightforward, simple to implement approximate solution to this pre-emphasis problem is derived, which is compatible with the current hardware infrastructure used on conventional MRI scanners for eddy current compensation. The proposed method was implemented on the gradient driver sub-system, and its real-time use was tested using a series of phantom and in vivo data acquired from 2D Cartesian phase-difference, echo-planar imaging (EPI) and spiral acquisitions. RESULTS The phantom and in vivo results demonstrate that unless accounted for, first-order concomitant fields introduce considerable phase estimation error into the measured data and result in images exhibiting spatially dependent blurring/distortion. The resulting artifacts are effectively prevented using the proposed gradient pre-emphasis. CONCLUSION An efficient and effective gradient pre-emphasis framework is developed to counteract the effects of first-order concomitant fields of asymmetric gradient systems. PMID:27373901

Testing thermal gradient driving force for grain boundary migration using molecular dynamics simulations

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

Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

2015-02-01

Strong thermal gradients in low-thermal-conductivity ceramics may drive extended defects, such as grain boundaries and voids, to migrate in preferential directions. In this work, molecular dynamics simulations are conducted to study thermal gradient driven grain boundary migration and to verify a previously proposed thermal gradient driving force equation, using uranium dioxide as a model system. It is found that a thermal gradient drives grain boundaries to migrate up the gradient and the migration velocity increases under a constant gradient owing to the increase in mobility with temperature. Different grain boundaries migrate at very different rates due to their different intrinsicmore » mobilities. The extracted mobilities from the thermal gradient driven simulations are compared with those calculated from two other well-established methods and good agreement between the three different methods is found, demonstrating that the theoretical equation of the thermal gradient driving force is valid, although a correction of one input parameter should be made. The discrepancy in the grain boundary mobilities between modeling and experiments is also discussed.« less

Directional phytoscreening: contaminant gradients in trees for plume delineation.

PubMed

Limmer, Matt A; Shetty, Mikhil K; Markus, Samantha; Kroeker, Ryan; Parker, Beth L; Martinez, Camilo; Burken, Joel G

2013-08-20

Tree sampling methods have been used in phytoscreening applications to delineate contaminated soil and groundwater, augmenting traditional investigative methods that are time-consuming, resource-intensive, invasive, and costly. In the past decade, contaminant concentrations in tree tissues have been shown to reflect the extent and intensity of subsurface contamination. This paper investigates a new phytoscreening tool: directional tree coring, a concept originating from field data that indicated azimuthal concentrations in tree trunks reflected the concentration gradients in the groundwater around the tree. To experimentally test this hypothesis, large diameter trees were subjected to subsurface contaminant concentration gradients in a greenhouse study. These trees were then analyzed for azimuthal concentration gradients in aboveground tree tissues, revealing contaminant centroids located on the side of the tree nearest the most contaminated groundwater. Tree coring at three field sites revealed sufficiently steep contaminant gradients in trees reflected nearby groundwater contaminant gradients. In practice, trees possessing steep contaminant gradients are indicators of steep subsurface contaminant gradients, providing compass-like information about the contaminant gradient, pointing investigators toward higher concentration regions of the plume.

Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

NASA Technical Reports Server (NTRS)

Navon, I. M.

1984-01-01

A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

Boundedness and convergence of online gradient method with penalty for feedforward neural networks.

PubMed

Zhang, Huisheng; Wu, Wei; Liu, Fei; Yao, Mingchen

2009-06-01

In this brief, we consider an online gradient method with penalty for training feedforward neural networks. Specifically, the penalty is a term proportional to the norm of the weights. Its roles in the method are to control the magnitude of the weights and to improve the generalization performance of the network. By proving that the weights are automatically bounded in the network training with penalty, we simplify the conditions that are required for convergence of online gradient method in literature. A numerical example is given to support the theoretical analysis.

Computational methods for aerodynamic design using numerical optimization

NASA Technical Reports Server (NTRS)

Peeters, M. F.

1983-01-01

Five methods to increase the computational efficiency of aerodynamic design using numerical optimization, by reducing the computer time required to perform gradient calculations, are examined. The most promising method consists of drastically reducing the size of the computational domain on which aerodynamic calculations are made during gradient calculations. Since a gradient calculation requires the solution of the flow about an airfoil whose geometry was slightly perturbed from a base airfoil, the flow about the base airfoil is used to determine boundary conditions on the reduced computational domain. This method worked well in subcritical flow.

Iterative methods for elliptic finite element equations on general meshes

NASA Technical Reports Server (NTRS)

Nicolaides, R. A.; Choudhury, Shenaz

1986-01-01

Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

Tailoring magnetic field gradient design to magnet cryostat geometry.

PubMed

Trakic, A; Liu, F; Lopez, H S; Wang, H; Crozier, S

2006-01-01

Eddy currents induced within a magnetic resonance imaging (MRI) cryostat bore during pulsing of gradient coils can be applied constructively together with the gradient currents that generate them, to obtain good quality gradient uniformities within a specified imaging volume over time. This can be achieved by simultaneously optimizing the spatial distribution and temporal pre-emphasis of the gradient coil current, to account for the spatial and temporal variation of the secondary magnetic fields due to the induced eddy currents. This method allows the tailored design of gradient coil/magnet configurations and consequent engineering trade-offs. To compute the transient eddy currents within a realistic cryostat vessel, a low-frequency finite-difference time-domain (FDTD) method using total-field scattered-field (TFSF) scheme has been performed and validated.

Structural optimization with approximate sensitivities

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Hopkins, D. A.; Coroneos, R.

1994-01-01

Computational efficiency in structural optimization can be enhanced if the intensive computations associated with the calculation of the sensitivities, that is, gradients of the behavior constraints, are reduced. Approximation to gradients of the behavior constraints that can be generated with small amount of numerical calculations is proposed. Structural optimization with these approximate sensitivities produced correct optimum solution. Approximate gradients performed well for different nonlinear programming methods, such as the sequence of unconstrained minimization technique, method of feasible directions, sequence of quadratic programming, and sequence of linear programming. Structural optimization with approximate gradients can reduce by one third the CPU time that would otherwise be required to solve the problem with explicit closed-form gradients. The proposed gradient approximation shows potential to reduce intensive computation that has been associated with traditional structural optimization.

Simultaneous auto-calibration and gradient delays estimation (SAGE) in non-Cartesian parallel MRI using low-rank constraints.

PubMed

Jiang, Wenwen; Larson, Peder E Z; Lustig, Michael

2018-03-09

To correct gradient timing delays in non-Cartesian MRI while simultaneously recovering corruption-free auto-calibration data for parallel imaging, without additional calibration scans. The calibration matrix constructed from multi-channel k-space data should be inherently low-rank. This property is used to construct reconstruction kernels or sensitivity maps. Delays between the gradient hardware across different axes and RF receive chain, which are relatively benign in Cartesian MRI (excluding EPI), lead to trajectory deviations and hence data inconsistencies for non-Cartesian trajectories. These in turn lead to higher rank and corrupted calibration information which hampers the reconstruction. Here, a method named Simultaneous Auto-calibration and Gradient delays Estimation (SAGE) is proposed that estimates the actual k-space trajectory while simultaneously recovering the uncorrupted auto-calibration data. This is done by estimating the gradient delays that result in the lowest rank of the calibration matrix. The Gauss-Newton method is used to solve the non-linear problem. The method is validated in simulations using center-out radial, projection reconstruction and spiral trajectories. Feasibility is demonstrated on phantom and in vivo scans with center-out radial and projection reconstruction trajectories. SAGE is able to estimate gradient timing delays with high accuracy at a signal to noise ratio level as low as 5. The method is able to effectively remove artifacts resulting from gradient timing delays and restore image quality in center-out radial, projection reconstruction, and spiral trajectories. The low-rank based method introduced simultaneously estimates gradient timing delays and provides accurate auto-calibration data for improved image quality, without any additional calibration scans. © 2018 International Society for Magnetic Resonance in Medicine.

Single fiber lignin distributions based on the density gradient column method

Treesearch

Brian Boyer; Alan W. Rudie

2007-01-01

The density gradient column method was used to determine the effects of uniform and non-uniform pulping processes on variation in individual fiber lignin concentrations of the resulting pulps. A density gradient column uses solvents of different densities and a mixing process to produce a column of liquid with a smooth transition from higher density at the bottom to...

Optimization with artificial neural network systems - A mapping principle and a comparison to gradient based methods

NASA Technical Reports Server (NTRS)

Leong, Harrison Monfook

1988-01-01

General formulae for mapping optimization problems into systems of ordinary differential equations associated with artificial neural networks are presented. A comparison is made to optimization using gradient-search methods. The performance measure is the settling time from an initial state to a target state. A simple analytical example illustrates a situation where dynamical systems representing artificial neural network methods would settle faster than those representing gradient-search. Settling time was investigated for a more complicated optimization problem using computer simulations. The problem was a simplified version of a problem in medical imaging: determining loci of cerebral activity from electromagnetic measurements at the scalp. The simulations showed that gradient based systems typically settled 50 to 100 times faster than systems based on current neural network optimization methods.

Determining the mean hydraulic gradient of ground water affected by tidal fluctuations

USGS Publications Warehouse

Serfes, Michael E.

1991-01-01

Tidal fluctuations in surface-water bodies produce progressive pressure waves in adjacent aquifers. As these pressure waves propagate inland, ground-water levels and hydraulic gradients continuously fluctuate, creating a situation where a single set of water-level measurements cannot be used to accurately characterize ground-water flow. For example, a time series of water levels measured in a confined aquifer in Atlantic City, New Jersey, showed that the hydraulic gradient ranged from .01 to .001 with a 22-degree change in direction during a tidal day of approximately 25 hours. At any point where ground water tidally fluctuates, the magnitude and direction of the hydraulic gradient fluctuates about the mean or regional hydraulic gradient. The net effect of these fluctuations on ground-water flow can be determined using the mean hydraulic gradient, which can be calculated by comparing mean ground- and surface-water elevations. Filtering methods traditionally used to determine daily mean sea level can be similarly applied to ground water to determine mean levels. Method (1) uses 71 consecutive hourly water-level observations to accurately determine the mean level. Method (2) approximates the mean level using only 25 consecutive hourly observations; however, there is a small error associated with this method.

Analysis and calculation by integral methods of laminar compressible boundary-layer with heat transfer and with and without pressure gradient

NASA Technical Reports Server (NTRS)

Morduchow, Morris

1955-01-01

A survey of integral methods in laminar-boundary-layer analysis is first given. A simple and sufficiently accurate method for practical purposes of calculating the properties (including stability) of the laminar compressible boundary layer in an axial pressure gradient with heat transfer at the wall is presented. For flow over a flat plate, the method is applicable for an arbitrarily prescribed distribution of temperature along the surface and for any given constant Prandtl number close to unity. For flow in a pressure gradient, the method is based on a Prandtl number of unity and a uniform wall temperature. A simple and accurate method of determining the separation point in a compressible flow with an adverse pressure gradient over a surface at a given uniform wall temperature is developed. The analysis is based on an extension of the Karman-Pohlhausen method to the momentum and the thermal energy equations in conjunction with fourth- and especially higher degree velocity and stagnation-enthalpy profiles.

The formation of stable pH gradients with weak monovalent buffers for isoelectric focusing in free solution

NASA Technical Reports Server (NTRS)

Mosher, Richard A.; Thormann, Wolfgang; Graham, Aly; Bier, Milan

1985-01-01

Two methods which utilize simple buffers for the generation of stable pH gradients (useful for preparative isoelectric focusing) are compared and contrasted. The first employs preformed gradients comprised of two simple buffers in density-stabilized free solution. The second method utilizes neutral membranes to isolate electrolyte reservoirs of constant composition from the separation column. It is shown by computer simulation that steady-state gradients can be formed at any pH range with any number of components in such a system.

Design and Performance of Property Gradient Ternary Nitride Coating Based on Process Control.

PubMed

Yan, Pei; Chen, Kaijie; Wang, Yubin; Zhou, Han; Peng, Zeyu; Jiao, Li; Wang, Xibin

2018-05-09

Surface coating is an effective approach to improve cutting tool performance, and multiple or gradient coating structures have become a common development strategy. However, composition mutations at the interfaces decrease the performance of multi-layered coatings. The key mitigation technique has been to reduce the interface effect at the boundaries. This study proposes a structure design method for property-component gradient coatings based on process control. The method produces coatings with high internal cohesion and high external hardness, which could reduce the composition and performance mutations at the interface. A ZrTiN property gradient ternary nitride coating was deposited on cemented carbide by multi-arc ion plating with separated Ti and Zr targets. The mechanical properties, friction behaviors, and cutting performances were systematically investigated, compared with a single-layer coating. The results indicated that the gradient coating had better friction and wear performance with lower wear rate and higher resistance to peeling off during sliding friction. The gradient coating had better wear and damage resistance in cutting processes, with lower machined surface roughness Ra. Gradient-structured coatings could effectively inhibit micro crack initiation and growth under alternating force and temperature load. This method could be extended to similar ternary nitride coatings.

Evolution of Cometary Activity at 67P/Churyumov-Gerasimenko as seen by ROSINA/Rosetta

NASA Astrophysics Data System (ADS)

Jäckel, A.; Altwegg, K.; Balsiger, H.; Calmonte, U.; Gasc, S.; Le Roy, L.; Rubin, M.; Tzou, C. Y.; Wurz, P.; Bieler, A.; Berthelier, J.-J.; Fiethe, B.; Hässig, M.; deKeyser, J.; Mall, U.; Rème, H.

2015-10-01

Since nine months the European Space Agency's spacecraft Rosetta, with the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) onboard, is in the comet escort phase. ROSINA is a suite of three instruments, consisting of the COmetary Pressure Sensor (COPS), the Double Focusing Mass Spectrometer (DFMS), and the Reflectron-type Time-Of-Flight (RTOF) mass spectrometer [1]. The two mass spectrometers measure in situ the neutral and ionized volatile material in the coma of comet 67P/Churyumov- Gerasimenko (67P/C-G). With COPS we are able to derive the total gas density, bulk velocities and temperatures of the coma.

Crystal growth and annealing method and apparatus

DOEpatents

Gianoulakis, Steven E.; Sparrow, Robert

2001-01-01

A method and apparatus for producing crystals that minimizes birefringence even at large crystal sizes, and is suitable for production of CaF.sub.2 crystals. The method of the present invention comprises annealing a crystal by maintaining a minimal temperature gradient in the crystal while slowly reducing the bulk temperature of the crystal. An apparatus according to the present invention includes a thermal control system added to a crystal growth and annealing apparatus, wherein the thermal control system allows a temperature gradient during crystal growth but minimizes the temperature gradient during crystal annealing. An embodiment of the present invention comprises a secondary heater incorporated into a conventional crystal growth and annealing apparatus. The secondary heater supplies heat to minimize the temperature gradients in the crystal during the annealing process. The secondary heater can mount near the bottom of the crucible to effectively maintain appropriate temperature gradients.

Computational study of the effect of gradient magnetic field in navigation of spherical particles

NASA Astrophysics Data System (ADS)

Karvelas, E. G.; Lampropoulos, N. K.; Papadimitriou, D. I.; Karakasidis, T. E.; Sarris, I. E.

2017-11-01

The use of spherical magnetic nanoparticles that are coated with drugs and can be navigated in arteries to attack tumors is proposed as an alternative to chemotherapy. Navigation of particles is due to magnetic field gradients that may be produced in an MRI device. In the present work, a computational study for the evaluation of the magnitude of the gradient magnetic field for particles navigation in Y bifurcations is presented. For this purpose, the presented method solves for the fluid flow and includes all the important forces that act on the particles in their discrete motion. The method is based on an iteration algorithm that adjusts the gradient magnetic field to minimize the particles’ deviation from a desired trajectory. Using the above mentioned method, the appropriate range of the gradient magnetic field for optimum navigation of nanoparticles’s aggregation is found.

Canceling the Gravity Gradient Phase Shift in Atom Interferometry.

PubMed

D'Amico, G; Rosi, G; Zhan, S; Cacciapuoti, L; Fattori, M; Tino, G M

2017-12-22

Gravity gradients represent a major obstacle in high-precision measurements by atom interferometry. Controlling their effects to the required stability and accuracy imposes very stringent requirements on the relative positioning of freely falling atomic clouds, as in the case of precise tests of Einstein's equivalence principle. We demonstrate a new method to exactly compensate the effects introduced by gravity gradients in a Raman-pulse atom interferometer. By shifting the frequency of the Raman lasers during the central π pulse, it is possible to cancel the initial position- and velocity-dependent phase shift produced by gravity gradients. We apply this technique to simultaneous interferometers positioned along the vertical direction and demonstrate a new method for measuring local gravity gradients that does not require precise knowledge of the relative position between the atomic clouds. Based on this method, we also propose an improved scheme to determine the Newtonian gravitational constant G towards the 10 ppm relative uncertainty.

Canceling the Gravity Gradient Phase Shift in Atom Interferometry

NASA Astrophysics Data System (ADS)

D'Amico, G.; Rosi, G.; Zhan, S.; Cacciapuoti, L.; Fattori, M.; Tino, G. M.

2017-12-01

Gravity gradients represent a major obstacle in high-precision measurements by atom interferometry. Controlling their effects to the required stability and accuracy imposes very stringent requirements on the relative positioning of freely falling atomic clouds, as in the case of precise tests of Einstein's equivalence principle. We demonstrate a new method to exactly compensate the effects introduced by gravity gradients in a Raman-pulse atom interferometer. By shifting the frequency of the Raman lasers during the central π pulse, it is possible to cancel the initial position- and velocity-dependent phase shift produced by gravity gradients. We apply this technique to simultaneous interferometers positioned along the vertical direction and demonstrate a new method for measuring local gravity gradients that does not require precise knowledge of the relative position between the atomic clouds. Based on this method, we also propose an improved scheme to determine the Newtonian gravitational constant G towards the 10 ppm relative uncertainty.

Patterns of macromycete community assemblage along an elevation gradient: options for fungal gradient and metacommunity analyse

Treesearch

Marko Gómez-Hernández; Guadalupe Williams-Linera; Roger Guevara; D. Jean Lodge

2012-01-01

Gradient analysis is rarely used in studies of fungal communities. Data on macromycetes from eight sites along an elevation gradient in central Veracruz, Mexico, were used to demonstrate methods for gradient analysis that can be applied to studies of communities of fungi. Selected sites from 100 to 3,500 m altitude represent tropical dry forest, tropical montane cloud...

Mathematical modeling of sample stacking methods in microfluidic systems

NASA Astrophysics Data System (ADS)

Horek, Jon

Gradient focusing methods are a general class of experimental techniques used to simultaneously separate and increase the cross-sectionally averaged concentration of charged particle mixtures. In comparison, Field Amplified Sample Stacking (FASS) techniques first concentrate the collection of molecules before separating them. Together, we denote gradient focusing and FASS methods "sample stacking" and study the dynamics of a specific method, Temperature Gradient Focusing (TGF), in which an axial temperature gradient is applied along a channel filled with weak buffer. Gradients in electroosmotic fluid flow and electrophoretic species velocity create the simultaneous separating and concentrating mechanism mentioned above. In this thesis, we begin with the observation that very little has been done to model the dynamics of gradient focusing, and proceed to solve the fundamental equations of fluid mechanics and scalar transport, assuming the existence of slow axial variations and the Taylor-Aris dispersion coefficient. In doing so, asymptotic methods reduce the equations from 3D to 1D, and we arrive at a simple 1D model which can be used to predict the transient evolution of the cross-sectionally averaged analyte concentration. In the second half of this thesis, we run several numerical focusing experiments with a 3D finite volume code. Comparison of the 1D theory and 3D simulations illustrates not only that the asymptotic theory converges as a certain parameter tends to zero, but also that fairly large axial slip velocity gradients lead to quite small errors in predicted steady variance. Additionally, we observe that the axial asymmetry of the electrophoretic velocity model leads to asymmetric peak shapes, a violation of the symmetric Gaussians predicted by the 1D theory. We conclude with some observations on the effect of Peclet number and gradient strength on the performance of focusing experiments, and describe a method for experimental optimization. Such knowledge is useful for design of lab-on-a-chip devices.

Testing the limits of gradient sensing

PubMed Central

Lakhani, Vinal

2017-01-01

The ability to detect a chemical gradient is fundamental to many cellular processes. In multicellular organisms gradient sensing plays an important role in many physiological processes such as wound healing and development. Unicellular organisms use gradient sensing to move (chemotaxis) or grow (chemotropism) towards a favorable environment. Some cells are capable of detecting extremely shallow gradients, even in the presence of significant molecular-level noise. For example, yeast have been reported to detect pheromone gradients as shallow as 0.1 nM/μm. Noise reduction mechanisms, such as time-averaging and the internalization of pheromone molecules, have been proposed to explain how yeast cells filter fluctuations and detect shallow gradients. Here, we use a Particle-Based Reaction-Diffusion model of ligand-receptor dynamics to test the effectiveness of these mechanisms and to determine the limits of gradient sensing. In particular, we develop novel simulation methods for establishing chemical gradients that not only allow us to study gradient sensing under steady-state conditions, but also take into account transient effects as the gradient forms. Based on reported measurements of reaction rates, our results indicate neither time-averaging nor receptor endocytosis significantly improves the cell’s accuracy in detecting gradients over time scales associated with the initiation of polarized growth. Additionally, our results demonstrate the physical barrier of the cell membrane sharpens chemical gradients across the cell. While our studies are motivated by the mating response of yeast, we believe our results and simulation methods will find applications in many different contexts. PMID:28207738

Efficient method to design RF pulses for parallel excitation MRI using gridding and conjugate gradient

PubMed Central

Feng, Shuo

2014-01-01

Parallel excitation (pTx) techniques with multiple transmit channels have been widely used in high field MRI imaging to shorten the RF pulse duration and/or reduce the specific absorption rate (SAR). However, the efficiency of pulse design still needs substantial improvement for practical real-time applications. In this paper, we present a detailed description of a fast pulse design method with Fourier domain gridding and a conjugate gradient method. Simulation results of the proposed method show that the proposed method can design pTx pulses at an efficiency 10 times higher than that of the conventional conjugate-gradient based method, without reducing the accuracy of the desirable excitation patterns. PMID:24834420

Efficient method to design RF pulses for parallel excitation MRI using gridding and conjugate gradient.

PubMed

Feng, Shuo; Ji, Jim

2014-04-01

Parallel excitation (pTx) techniques with multiple transmit channels have been widely used in high field MRI imaging to shorten the RF pulse duration and/or reduce the specific absorption rate (SAR). However, the efficiency of pulse design still needs substantial improvement for practical real-time applications. In this paper, we present a detailed description of a fast pulse design method with Fourier domain gridding and a conjugate gradient method. Simulation results of the proposed method show that the proposed method can design pTx pulses at an efficiency 10 times higher than that of the conventional conjugate-gradient based method, without reducing the accuracy of the desirable excitation patterns.

Iterative solution of the inverse Cauchy problem for an elliptic equation by the conjugate gradient method

NASA Astrophysics Data System (ADS)

Vasil'ev, V. I.; Kardashevsky, A. M.; Popov, V. V.; Prokopev, G. A.

2017-10-01

This article presents results of computational experiment carried out using a finite-difference method for solving the inverse Cauchy problem for a two-dimensional elliptic equation. The computational algorithm involves an iterative determination of the missing boundary condition from the override condition using the conjugate gradient method. The results of calculations are carried out on the examples with exact solutions as well as at specifying an additional condition with random errors are presented. Results showed a high efficiency of the iterative method of conjugate gradients for numerical solution

In situ synthesis of bilayered gradient poly(vinyl alcohol)/hydroxyapatite composite hydrogel by directional freezing-thawing and electrophoresis method.

PubMed

Su, Cui; Su, Yunlan; Li, Zhiyong; Haq, Muhammad Abdul; Zhou, Yong; Wang, Dujin

2017-08-01

Bilayered poly(vinyl alcohol) (PVA)/hydroxyapatite (HA) composite hydrogels with anisotropic and gradient mechanical properties were prepared by the combination of directional freezing-thawing (DFT) and electrophoresis method. Firstly, PVA hydrogels with aligned channel structure were prepared by the DFT method. Then, HA nanoparticles were in situ synthesized within the PVA hydrogels via electrophoresis. By controlling the time of the electrophoresis process, a bilayered gradient hydrogel containing HA particles in only half of the gel region was obtained. The PVA/HA composite hydrogel exhibited gradient mechanical strength depending on the distance to the cathode. The gradient initial tensile modulus ranging from 0.18MPa to 0.27MPa and the gradient initial compressive modulus from 0.33MPa to 0.51MPa were achieved. The binding strength of the two regions was relatively high and no apparent internal stress or defect was observed at the boundary. The two regions of the bilayered hydrogel also showed different osteoblast cell adhesion properties. Copyright © 2017 Elsevier B.V. All rights reserved.

The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient

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

Bykov, Dmytro; Kristensen, Kasper; Kjærgaard, Thomas

We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems. A test set of supramolecular complexes containing up to 158 atoms and 1960 contracted basis functions has been employed to demonstrate the general applicability of the DEC-RI-MP2 methodmore » and to analyze the errors of the DEC approximation. Moreover, the test set contains molecules of complicated electronic structures and is thus deliberately chosen to stress test the DEC-RI-MP2 gradient implementation. Additionally, as a showcase example the full molecular gradient for insulin (787 atoms and 7604 contracted basis functions) has been evaluated.« less

Quantification and Compensation of Eddy-Current-Induced Magnetic Field Gradients

PubMed Central

Spees, William M.; Buhl, Niels; Sun, Peng; Ackerman, Joseph J.H.; Neil, Jeffrey J.; Garbow, Joel R.

2011-01-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or 6-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom’s free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner’s gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. PMID:21764614

Quantification and compensation of eddy-current-induced magnetic-field gradients.

PubMed

Spees, William M; Buhl, Niels; Sun, Peng; Ackerman, Joseph J H; Neil, Jeffrey J; Garbow, Joel R

2011-09-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or six-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom's free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner's gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. Copyright © 2011 Elsevier Inc. All rights reserved.

Improving the accuracy of the gradient method for determining soil carbon dioxide efflux

USDA-ARS?s Scientific Manuscript database

Continuous soil CO2 efflux (Fsoil) estimates can be obtained by the gradient method (GM), but the utility of the method is hindered by uncertainties in the application of published models for the diffusion coefficient (Ds). We compared two in-situ methods for determining Ds, one based calibrating th...

A projection gradient method for computing ground state of spin-2 Bose–Einstein condensates

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

Wang, Hanquan, E-mail: hanquan.wang@gmail.com; Yunnan Tongchang Scientific Computing and Data Mining Research Center, Kunming, Yunnan Province, 650221

In this paper, a projection gradient method is presented for computing ground state of spin-2 Bose–Einstein condensates (BEC). We first propose the general projection gradient method for solving energy functional minimization problem under multiple constraints, in which the energy functional takes real functions as independent variables. We next extend the method to solve a similar problem, where the energy functional now takes complex functions as independent variables. We finally employ the method into finding the ground state of spin-2 BEC. The key of our method is: by constructing continuous gradient flows (CGFs), the ground state of spin-2 BEC can bemore » computed as the steady state solution of such CGFs. We discretized the CGFs by a conservative finite difference method along with a proper way to deal with the nonlinear terms. We show that the numerical discretization is normalization and magnetization conservative and energy diminishing. Numerical results of the ground state and their energy of spin-2 BEC are reported to demonstrate the effectiveness of the numerical method.« less

Functional linear models to test for differences in prairie wetland hydraulic gradients

USGS Publications Warehouse

Greenwood, Mark C.; Sojda, Richard S.; Preston, Todd M.; Swayne, David A.; Yang, Wanhong; Voinov, A.A.; Rizzoli, A.; Filatova, T.

2010-01-01

Functional data analysis provides a framework for analyzing multiple time series measured frequently in time, treating each series as a continuous function of time. Functional linear models are used to test for effects on hydraulic gradient functional responses collected from three types of land use in Northeastern Montana at fourteen locations. Penalized regression-splines are used to estimate the underlying continuous functions based on the discretely recorded (over time) gradient measurements. Permutation methods are used to assess the statistical significance of effects. A method for accommodating missing observations in each time series is described. Hydraulic gradients may be an initial and fundamental ecosystem process that responds to climate change. We suggest other potential uses of these methods for detecting evidence of climate change.

Phase gradient algorithm based on co-axis two-step phase-shifting interferometry and its application

NASA Astrophysics Data System (ADS)

Wang, Yawei; Zhu, Qiong; Xu, Yuanyuan; Xin, Zhiduo; Liu, Jingye

2017-12-01

A phase gradient method based on co-axis two-step phase-shifting interferometry, is used to reveal the detailed information of a specimen. In this method, the phase gradient distribution can only be obtained by calculating both the first-order derivative and the radial Hilbert transformation of the intensity difference between two phase-shifted interferograms. The feasibility and accuracy of this method were fully verified by the simulation results for a polystyrene sphere and a red blood cell. The empirical results demonstrated that phase gradient is sensitive to changes in the refractive index and morphology. Because phase retrieval and tedious phase unwrapping are not required, the calculation speed is faster. In addition, co-axis interferometry has high spatial resolution.

Study of translational dynamics in molten polymer by variation of gradient pulse-width of PGSE.

PubMed

Stepišnik, Janez; Lahajnar, Gojmir; Zupančič, Ivan; Mohorič, Aleš

2013-11-01

Pulsed gradient spin echo is a method of measuring molecular translation. Changing Δ makes it sensitive to diffusion spectrum. Spin translation effects the buildup of phase structure during the application of gradient pulses as well. The time scale of the self-diffusion measurement shortens if this is taken into account. The method of diffusion spectrometry with variable δ is also less sensitive to artifacts caused by spin relaxation and internal gradient fields. Here the method is demonstrated in the case of diffusion spectrometry of molten polyethylene. The results confirm a model of constraint release in a system of entangled polymer chains as a sort of tube Rouse motion. Copyright © 2013 Elsevier Inc. All rights reserved.

Numerical methods for the design of gradient-index optical coatings.

PubMed

Anzengruber, Stephan W; Klann, Esther; Ramlau, Ronny; Tonova, Diana

2012-12-01

We formulate the problem of designing gradient-index optical coatings as the task of solving a system of operator equations. We use iterative numerical procedures known from the theory of inverse problems to solve it with respect to the coating refractive index profile and thickness. The mathematical derivations necessary for the application of the procedures are presented, and different numerical methods (Landweber, Newton, and Gauss-Newton methods, Tikhonov minimization with surrogate functionals) are implemented. Procedures for the transformation of the gradient coating designs into quasi-gradient ones (i.e., multilayer stacks of homogeneous layers with different refractive indices) are also developed. The design algorithms work with physically available coating materials that could be produced with the modern coating technologies.

Contour Detection and Completion for Inpainting and Segmentation Based on Topological Gradient and Fast Marching Algorithms

PubMed Central

Auroux, Didier; Cohen, Laurent D.; Masmoudi, Mohamed

2011-01-01

We combine in this paper the topological gradient, which is a powerful method for edge detection in image processing, and a variant of the minimal path method in order to find connected contours. The topological gradient provides a more global analysis of the image than the standard gradient and identifies the main edges of an image. Several image processing problems (e.g., inpainting and segmentation) require continuous contours. For this purpose, we consider the fast marching algorithm in order to find minimal paths in the topological gradient image. This coupled algorithm quickly provides accurate and connected contours. We present then two numerical applications, to image inpainting and segmentation, of this hybrid algorithm. PMID:22194734

New head gradient coil design and construction techniques.

PubMed

Handler, William B; Harris, Chad T; Scholl, Timothy J; Parker, Dennis L; Goodrich, K Craig; Dalrymple, Brian; Van Sass, Frank; Chronik, Blaine A

2014-05-01

To design and build a head insert gradient coil to use in conjunction with body gradients for superior imaging. The use of the boundary element method to solve for a gradient coil wire pattern on an arbitrary surface allowed us to incorporate engineering changes into the electromagnetic design of a gradient coil directly. Improved wire pattern design was combined with robust manufacturing techniques and novel cooling methods. The finished coil had an efficiency of 0.15 mT/m/A in all three axes and allowed the imaging region to extend across the entire head and upper part of the neck. The ability to adapt an electromagnetic design to necessary changes from an engineering perspective leads to superior coil performance. Copyright © 2013 Wiley Periodicals, Inc.

Evaluation of multiple tracer methods to estimate low groundwater flow velocities

DOE PAGES

Reimus, Paul W.; Arnold, Bill W.

2017-02-20

Here, four different tracer methods were used to estimate groundwater flow velocity at a multiple-well site in the saturated alluvium south of Yucca Mountain, Nevada: (1) two single-well tracer tests with different rest or “shut-in” periods, (2) a cross-hole tracer test with an extended flow interruption, (3) a comparison of two tracer decay curves in an injection borehole with and without pumping of a downgradient well, and (4) a natural-gradient tracer test. Such tracer methods are potentially very useful for estimating groundwater velocities when hydraulic gradients are flat (and hence uncertain) and also when water level and hydraulic conductivity datamore » are sparse, both of which were the case at this test location. The purpose of the study was to evaluate the first three methods for their ability to provide reasonable estimates of relatively low groundwater flow velocities in such low-hydraulic-gradient environments. The natural-gradient method is generally considered to be the most robust and direct method, so it was used to provide a “ground truth” velocity estimate. However, this method usually requires several wells, so it is often not practical in systems with large depths to groundwater and correspondingly high well installation costs. The fact that a successful natural gradient test was conducted at the test location offered a unique opportunity to compare the flow velocity estimates obtained by the more easily deployed and lower risk methods with the ground-truth natural-gradient method. The groundwater flow velocity estimates from the four methods agreed very well with each other, suggesting that the first three methods all provided reasonably good estimates of groundwater flow velocity at the site. We discuss the advantages and disadvantages of the different methods, as well as some of the uncertainties associated with them.« less

Evaluation of multiple tracer methods to estimate low groundwater flow velocities

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

Reimus, Paul W.; Arnold, Bill W.

Here, four different tracer methods were used to estimate groundwater flow velocity at a multiple-well site in the saturated alluvium south of Yucca Mountain, Nevada: (1) two single-well tracer tests with different rest or “shut-in” periods, (2) a cross-hole tracer test with an extended flow interruption, (3) a comparison of two tracer decay curves in an injection borehole with and without pumping of a downgradient well, and (4) a natural-gradient tracer test. Such tracer methods are potentially very useful for estimating groundwater velocities when hydraulic gradients are flat (and hence uncertain) and also when water level and hydraulic conductivity datamore » are sparse, both of which were the case at this test location. The purpose of the study was to evaluate the first three methods for their ability to provide reasonable estimates of relatively low groundwater flow velocities in such low-hydraulic-gradient environments. The natural-gradient method is generally considered to be the most robust and direct method, so it was used to provide a “ground truth” velocity estimate. However, this method usually requires several wells, so it is often not practical in systems with large depths to groundwater and correspondingly high well installation costs. The fact that a successful natural gradient test was conducted at the test location offered a unique opportunity to compare the flow velocity estimates obtained by the more easily deployed and lower risk methods with the ground-truth natural-gradient method. The groundwater flow velocity estimates from the four methods agreed very well with each other, suggesting that the first three methods all provided reasonably good estimates of groundwater flow velocity at the site. We discuss the advantages and disadvantages of the different methods, as well as some of the uncertainties associated with them.« less

Defect Detection of Steel Surfaces with Global Adaptive Percentile Thresholding of Gradient Image

NASA Astrophysics Data System (ADS)

Neogi, Nirbhar; Mohanta, Dusmanta K.; Dutta, Pranab K.

2017-12-01

Steel strips are used extensively for white goods, auto bodies and other purposes where surface defects are not acceptable. On-line surface inspection systems can effectively detect and classify defects and help in taking corrective actions. For detection of defects use of gradients is very popular in highlighting and subsequently segmenting areas of interest in a surface inspection system. Most of the time, segmentation by a fixed value threshold leads to unsatisfactory results. As defects can be both very small and large in size, segmentation of a gradient image based on percentile thresholding can lead to inadequate or excessive segmentation of defective regions. A global adaptive percentile thresholding of gradient image has been formulated for blister defect and water-deposit (a pseudo defect) in steel strips. The developed method adaptively changes the percentile value used for thresholding depending on the number of pixels above some specific values of gray level of the gradient image. The method is able to segment defective regions selectively preserving the characteristics of defects irrespective of the size of the defects. The developed method performs better than Otsu method of thresholding and an adaptive thresholding method based on local properties.

A fast random walk algorithm for computing the pulsed-gradient spin-echo signal in multiscale porous media.

PubMed

Grebenkov, Denis S

2011-02-01

A new method for computing the signal attenuation due to restricted diffusion in a linear magnetic field gradient is proposed. A fast random walk (FRW) algorithm for simulating random trajectories of diffusing spin-bearing particles is combined with gradient encoding. As random moves of a FRW are continuously adapted to local geometrical length scales, the method is efficient for simulating pulsed-gradient spin-echo experiments in hierarchical or multiscale porous media such as concrete, sandstones, sedimentary rocks and, potentially, brain or lungs. Copyright © 2010 Elsevier Inc. All rights reserved.

Three-dimensional Gravity Inversion with a New Gradient Scheme on Unstructured Grids

NASA Astrophysics Data System (ADS)

Sun, S.; Yin, C.; Gao, X.; Liu, Y.; Zhang, B.

2017-12-01

Stabilized gradient-based methods have been proved to be efficient for inverse problems. Based on these methods, setting gradient close to zero can effectively minimize the objective function. Thus the gradient of objective function determines the inversion results. By analyzing the cause of poor resolution on depth in gradient-based gravity inversion methods, we find that imposing depth weighting functional in conventional gradient can improve the depth resolution to some extent. However, the improvement is affected by the regularization parameter and the effect of the regularization term becomes smaller with increasing depth (shown as Figure 1 (a)). In this paper, we propose a new gradient scheme for gravity inversion by introducing a weighted model vector. The new gradient can improve the depth resolution more efficiently, which is independent of the regularization parameter, and the effect of regularization term will not be weakened when depth increases. Besides, fuzzy c-means clustering method and smooth operator are both used as regularization terms to yield an internal consecutive inverse model with sharp boundaries (Sun and Li, 2015). We have tested our new gradient scheme with unstructured grids on synthetic data to illustrate the effectiveness of the algorithm. Gravity forward modeling with unstructured grids is based on the algorithm proposed by Okbe (1979). We use a linear conjugate gradient inversion scheme to solve the inversion problem. The numerical experiments show a great improvement in depth resolution compared with regular gradient scheme, and the inverse model is compact at all depths (shown as Figure 1 (b)). AcknowledgeThis research is supported by Key Program of National Natural Science Foundation of China (41530320), China Natural Science Foundation for Young Scientists (41404093), and Key National Research Project of China (2016YFC0303100, 2017YFC0601900). ReferencesSun J, Li Y. 2015. Multidomain petrophysically constrained inversion and geology differentiation using guided fuzzy c-means clustering. Geophysics, 80(4): ID1-ID18. Okabe M. 1979. Analytical expressions for gravity anomalies due to homogeneous polyhedral bodies and translations into magnetic anomalies. Geophysics, 44(4), 730-741.

Single image super-resolution using self-optimizing mask via fractional-order gradient interpolation and reconstruction.

PubMed

Yang, Qi; Zhang, Yanzhu; Zhao, Tiebiao; Chen, YangQuan

2017-04-04

Image super-resolution using self-optimizing mask via fractional-order gradient interpolation and reconstruction aims to recover detailed information from low-resolution images and reconstruct them into high-resolution images. Due to the limited amount of data and information retrieved from low-resolution images, it is difficult to restore clear, artifact-free images, while still preserving enough structure of the image such as the texture. This paper presents a new single image super-resolution method which is based on adaptive fractional-order gradient interpolation and reconstruction. The interpolated image gradient via optimal fractional-order gradient is first constructed according to the image similarity and afterwards the minimum energy function is employed to reconstruct the final high-resolution image. Fractional-order gradient based interpolation methods provide an additional degree of freedom which helps optimize the implementation quality due to the fact that an extra free parameter α-order is being used. The proposed method is able to produce a rich texture detail while still being able to maintain structural similarity even under large zoom conditions. Experimental results show that the proposed method performs better than current single image super-resolution techniques. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Uncertainty based pressure reconstruction from velocity measurement with generalized least squares

NASA Astrophysics Data System (ADS)

Zhang, Jiacheng; Scalo, Carlo; Vlachos, Pavlos

2017-11-01

A method using generalized least squares reconstruction of instantaneous pressure field from velocity measurement and velocity uncertainty is introduced and applied to both planar and volumetric flow data. Pressure gradients are computed on a staggered grid from flow acceleration. The variance-covariance matrix of the pressure gradients is evaluated from the velocity uncertainty by approximating the pressure gradient error to a linear combination of velocity errors. An overdetermined system of linear equations which relates the pressure and the computed pressure gradients is formulated and then solved using generalized least squares with the variance-covariance matrix of the pressure gradients. By comparing the reconstructed pressure field against other methods such as solving the pressure Poisson equation, the omni-directional integration, and the ordinary least squares reconstruction, generalized least squares method is found to be more robust to the noise in velocity measurement. The improvement on pressure result becomes more remarkable when the velocity measurement becomes less accurate and more heteroscedastic. The uncertainty of the reconstructed pressure field is also quantified and compared across the different methods.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

A simple method for MR elastography: a gradient-echo type multi-echo sequence.

PubMed

Numano, Tomokazu; Mizuhara, Kazuyuki; Hata, Junichi; Washio, Toshikatsu; Homma, Kazuhiro

2015-01-01

To demonstrate the feasibility of a novel MR elastography (MRE) technique based on a conventional gradient-echo type multi-echo MR sequence which does not need additional bipolar magnetic field gradients (motion encoding gradient: MEG), yet is sensitive to vibration. In a gradient-echo type multi-echo MR sequence, several images are produced from each echo of the train with different echo times (TEs). If these echoes are synchronized with the vibration, each readout's gradient lobes achieve a MEG-like effect, and the later generated echo causes a greater MEG-like effect. The sequence was tested for the tissue-mimicking agarose gel phantoms and the psoas major muscles of healthy volunteers. It was confirmed that the readout gradient lobes caused an MEG-like effect and the later TE images had higher sensitivity to vibrations. The magnitude image of later generated echo suffered the T2 decay and the susceptibility artifacts, but the wave image and elastogram of later generated echo were unaffected by these effects. In in vivo experiments, this method was able to measure the mean shear modulus of the psoas major muscle. From the results of phantom experiments and volunteer studies, it was shown that this method has clinical application potential. Copyright © 2014 Elsevier Inc. All rights reserved.

A note on the effective evaluation height for flux-gradient relationships and its application to herbicide fluxes

USDA-ARS?s Scientific Manuscript database

Volatilization represents a significant loss pathway for many pesticides, herbicides and other agrochemicals. One common method for measuring the volatilization of agrochemicals is the flux-gradient method. Using this method, the chemical flux is estimated as the product of the vertical concentratio...

Interfacial free energy and stiffness of aluminum during rapid solidification

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

Brown, Nicholas T.; Martinez, Enrique; Qu, Jianmin

Using molecular dynamics simulations and the capillary fluctuation method, we have calculated the anisotropic crystal-melt interfacial free energy and stiffness of aluminum in a rapid solidification system where a temperature gradient is applied to enforce thermal non-equilibrium. To calculate these material properties, the standard capillary fluctuation method typically used for systems in equilibrium has been modified to incorporate a second-order Taylor expansion of the interfacial free energy term. The result is a robust method for calculating interfacial energy, stiffness and anisotropy as a function of temperature gradient using the fluctuations in the defined interface height. This work includes the calculationmore » of interface characteristics for temperature gradients ranging from 11 to 34 K/nm. The captured results are compared to a thermal equilibrium case using the same model and simulation technique with a zero gradient definition. We define the temperature gradient as the change in temperature over height perpendicular to the crystal-melt interface. The gradients are applied in MD simulations using defined thermostat regions on a stable solid-liquid interface initially in thermal equilibrium. The results of this work show that the interfacial stiffness and free energy for aluminum are dependent on the magnitude of the temperature gradient, however the anisotropic parameters remain independent of the non-equilibrium conditions applied in this analysis. As a result, the relationships of the interfacial free energy/stiffness are determined to be linearly related to the thermal gradient, and can be interpolated to find material characteristics at additional temperature gradients.« less

Interfacial free energy and stiffness of aluminum during rapid solidification

DOE PAGES

Brown, Nicholas T.; Martinez, Enrique; Qu, Jianmin

2017-05-01

Using molecular dynamics simulations and the capillary fluctuation method, we have calculated the anisotropic crystal-melt interfacial free energy and stiffness of aluminum in a rapid solidification system where a temperature gradient is applied to enforce thermal non-equilibrium. To calculate these material properties, the standard capillary fluctuation method typically used for systems in equilibrium has been modified to incorporate a second-order Taylor expansion of the interfacial free energy term. The result is a robust method for calculating interfacial energy, stiffness and anisotropy as a function of temperature gradient using the fluctuations in the defined interface height. This work includes the calculationmore » of interface characteristics for temperature gradients ranging from 11 to 34 K/nm. The captured results are compared to a thermal equilibrium case using the same model and simulation technique with a zero gradient definition. We define the temperature gradient as the change in temperature over height perpendicular to the crystal-melt interface. The gradients are applied in MD simulations using defined thermostat regions on a stable solid-liquid interface initially in thermal equilibrium. The results of this work show that the interfacial stiffness and free energy for aluminum are dependent on the magnitude of the temperature gradient, however the anisotropic parameters remain independent of the non-equilibrium conditions applied in this analysis. As a result, the relationships of the interfacial free energy/stiffness are determined to be linearly related to the thermal gradient, and can be interpolated to find material characteristics at additional temperature gradients.« less

Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI.

PubMed

Jeurissen, Ben; Leemans, Alexander; Sijbers, Jan

2014-10-01

Ensuring one is using the correct gradient orientations in a diffusion MRI study can be a challenging task. As different scanners, file formats and processing tools use different coordinate frame conventions, in practice, users can end up with improperly oriented gradient orientations. Using such wrongly oriented gradient orientations for subsequent diffusion parameter estimation will invalidate all rotationally variant parameters and fiber tractography results. While large misalignments can be detected by visual inspection, small rotations of the gradient table (e.g. due to angulation of the acquisition plane), are much more difficult to detect. In this work, we propose an automated method to align the coordinate frame of the gradient orientations with that of the corresponding diffusion weighted images, using a metric based on whole brain fiber tractography. By transforming the gradient table and measuring the average fiber trajectory length, we search for the transformation that results in the best global 'connectivity'. To ensure a fast calculation of the metric we included a range of algorithmic optimizations in our tractography routine. To make the optimization routine robust to spurious local maxima, we use a stochastic optimization routine that selects a random set of seed points on each evaluation. Using simulations, we show that our method can recover the correct gradient orientations with high accuracy and precision. In addition, we demonstrate that our technique can successfully recover rotated gradient tables on a wide range of clinically realistic data sets. As such, our method provides a practical and robust solution to an often overlooked pitfall in the processing of diffusion MRI. Copyright © 2014 Elsevier B.V. All rights reserved.

Positive Contrast Visualization of Nitinol Devices using Susceptibility Gradient Mapping

PubMed Central

Vonken, Evert-jan P.A.; Schär, Michael; Stuber, Matthias

2008-01-01

MRI visualization of devices is traditionally based on the signal loss due to T2* effects originating from the local susceptibility differences. To visualize nitinol devices with positive contrast a recently introduced post processing method is adapted to map the induced susceptibility gradients. This method operates on regular gradient echo MR images and maps the shift in k-space in a (small) neighborhood of every voxel by Fourier analysis followed by a center of mass calculation. The quantitative map of the local shifts generates the positive contrast image of the devices, while areas without susceptibility gradients render a background with noise only. The positive signal response of this method depends only on the choice of the voxel neighborhood size. The properties of the method are explained and the visualization of a nitinol wire and two stents are shown for illustration. PMID:18727096

Refractive index gradient measurement across the thickness of a dielectric film by the prism coupling method

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

Sokolov, Viktor I; Panchenko, Vladislav Ya; Seminogov, V N

2012-08-31

A method is proposed for measuring the refractive index gradient n(z) in nonuniformly thick dielectric films. The method is based on the excitation of waveguide modes in a film using the prism coupling technique and on the calculation of n(z) and film thickness H{sub f} with the help of the angular positions of the TE or TM modes. The method can be used for an arbitrary shape of the index modulation over the film thickness in the limit of a small gradient [{Delta} n(z)/n(z) || 1]. (laser applications and other topics in quantum electronics)

Contrast Gradient-Based Blood Velocimetry With Computed Tomography: Theory, Simulations, and Proof of Principle in a Dynamic Flow Phantom.

PubMed

Korporaal, Johannes G; Benz, Matthias R; Schindera, Sebastian T; Flohr, Thomas G; Schmidt, Bernhard

2016-01-01

The aim of this study was to introduce a new theoretical framework describing the relationship between the blood velocity, computed tomography (CT) acquisition velocity, and iodine contrast enhancement in CT images, and give a proof of principle of contrast gradient-based blood velocimetry with CT. The time-averaged blood velocity (v(blood)) inside an artery along the axis of rotation (z axis) is described as the mathematical division of a temporal (Hounsfield unit/second) and spatial (Hounsfield unit/centimeter) iodine contrast gradient. From this new theoretical framework, multiple strategies for calculating the time-averaged blood velocity from existing clinical CT scan protocols are derived, and contrast gradient-based blood velocimetry was introduced as a new method that can calculate v(blood) directly from contrast agent gradients and the changes therein. Exemplarily, the behavior of this new method was simulated for image acquisition with an adaptive 4-dimensional spiral mode consisting of repeated spiral acquisitions with alternating scan direction. In a dynamic flow phantom with flow velocities between 5.1 and 21.2 cm/s, the same acquisition mode was used to validate the simulations and give a proof of principle of contrast gradient-based blood velocimetry in a straight cylinder of 2.5 cm diameter, representing the aorta. In general, scanning with the direction of blood flow results in decreased and scanning against the flow in increased temporal contrast agent gradients. Velocity quantification becomes better for low blood and high acquisition speeds because the deviation of the measured contrast agent gradient from the temporal gradient will increase. In the dynamic flow phantom, a modulation of the enhancement curve, and thus alternation of the contrast agent gradients, can be observed for the adaptive 4-dimensional spiral mode and is in agreement with the simulations. The measured flow velocities in the downslopes of the enhancement curves were in good agreement with the expected values, although the accuracy and precision worsened with increasing flow velocities. The new theoretical framework increases the understanding of the relationship between the blood velocity, CT acquisition velocity, and iodine contrast enhancement in CT images, and it interconnects existing blood velocimetry methods with research on transluminary attenuation gradients. With these new insights, novel strategies for CT blood velocimetry, such as the contrast gradient-based method presented in this article, may be developed.

High-Resolution Autoradiography

DTIC Science & Technology

1955-01-01

alloy the tungsten concontrationl of it 1-mnicron culbe is: (8,9 gmI) (8.88 mcg m1-2nl/micron gradient will probably not be so sharp am fit( gradients ...phases of Ilite work: (a) Applicattion and( develop- lie( iiirkeh used. ment (If the( wet-process autorodiographic method will (b)i Trwo methods exist...34 concentration gradients are sufficiently large, the same solution since the range of beta particles in water Wet-process autoradiography as developed for

Analytical energy gradient based on spin-free infinite-order Douglas-Kroll-Hess method with local unitary transformation

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

Nakajima, Yuya; Seino, Junji; Nakai, Hiromi, E-mail: nakai@waseda.jp

In this study, the analytical energy gradient for the spin-free infinite-order Douglas-Kroll-Hess (IODKH) method at the levels of the Hartree-Fock (HF), density functional theory (DFT), and second-order Møller-Plesset perturbation theory (MP2) is developed. Furthermore, adopting the local unitary transformation (LUT) scheme for the IODKH method improves the efficiency in computation of the analytical energy gradient. Numerical assessments of the present gradient method are performed at the HF, DFT, and MP2 levels for the IODKH with and without the LUT scheme. The accuracies are examined for diatomic molecules such as hydrogen halides, halogen dimers, coinage metal (Cu, Ag, and Au) halides,more » and coinage metal dimers, and 20 metal complexes, including the fourth–sixth row transition metals. In addition, the efficiencies are investigated for one-, two-, and three-dimensional silver clusters. The numerical results confirm the accuracy and efficiency of the present method.« less

A general strategy for performing temperature-programming in high performance liquid chromatography--further improvements in the accuracy of retention time predictions of segmented temperature gradients.

PubMed

Wiese, Steffen; Teutenberg, Thorsten; Schmidt, Torsten C

2012-01-27

In the present work it is shown that the linear elution strength (LES) model which was adapted from temperature-programming gas chromatography (GC) can also be employed for systematic method development in high-temperature liquid chromatography (HT-HPLC). The ability to predict isothermal retention times based on temperature-gradient as well as isothermal input data was investigated. For a small temperature interval of ΔT=40°C, both approaches result in very similar predictions. Average relative errors of predicted retention times of 2.7% and 1.9% were observed for simulations based on isothermal and temperature-gradient measurements, respectively. Concurrently, it was investigated whether the accuracy of retention time predictions of segmented temperature gradients can be further improved by temperature dependent calculation of the parameter S(T) of the LES relationship. It was found that the accuracy of retention time predictions of multi-step temperature gradients can be improved to around 1.5%, if S(T) was also calculated temperature dependent. The adjusted experimental design making use of four temperature-gradient measurements was applied for systematic method development of selected food additives by high-temperature liquid chromatography. Method development was performed within a temperature interval from 40°C to 180°C using water as mobile phase. Two separation methods were established where selected food additives were baseline separated. In addition, a good agreement between simulation and experiment was observed, because an average relative error of predicted retention times of complex segmented temperature gradients less than 5% was observed. Finally, a schedule of recommendations to assist the practitioner during systematic method development in high-temperature liquid chromatography was established. Copyright © 2011 Elsevier B.V. All rights reserved.

Areal-averaged trace gas emission rates from long-range open-path measurements in stable boundary layer conditions

NASA Astrophysics Data System (ADS)

Schäfer, K.; Grant, R. H.; Emeis, S.; Raabe, A.; von der Heide, C.; Schmid, H. P.

2012-07-01

Measurements of land-surface emission rates of greenhouse and other gases at large spatial scales (10 000 m2) are needed to assess the spatial distribution of emissions. This can be readily done using spatial-integrating micro-meteorological methods like flux-gradient methods which were evaluated for determining land-surface emission rates of trace gases under stable boundary layers. Non-intrusive path-integrating measurements are utilized. Successful application of a flux-gradient method requires confidence in the gradients of trace gas concentration and wind, and in the applicability of boundary-layer turbulence theory; consequently the procedures to qualify measurements that can be used to determine the flux is critical. While there is relatively high confidence in flux measurements made under unstable atmospheres with mean winds greater than 1 m s-1, there is greater uncertainty in flux measurements made under free convective or stable conditions. The study of N2O emissions of flat grassland and NH3 emissions from a cattle lagoon involves quality-assured determinations of fluxes under low wind, stable or night-time atmospheric conditions when the continuous "steady-state" turbulence of the surface boundary layer breaks down and the layer has intermittent turbulence. Results indicate that following the Monin-Obukhov similarity theory (MOST) flux-gradient methods that assume a log-linear profile of the wind speed and concentration gradient incorrectly determine vertical profiles and thus flux in the stable boundary layer. An alternative approach is considered on the basis of turbulent diffusivity, i.e. the measured friction velocity as well as height gradients of horizontal wind speeds and concentrations without MOST correction for stability. It is shown that this is the most accurate of the flux-gradient methods under stable conditions.

A gradient system solution to Potts mean field equations and its electronic implementation.

PubMed

Urahama, K; Ueno, S

1993-03-01

A gradient system solution method is presented for solving Potts mean field equations for combinatorial optimization problems subject to winner-take-all constraints. In the proposed solution method the optimum solution is searched by using gradient descent differential equations whose trajectory is confined within the feasible solution space of optimization problems. This gradient system is proven theoretically to always produce a legal local optimum solution of combinatorial optimization problems. An elementary analog electronic circuit implementing the presented method is designed on the basis of current-mode subthreshold MOS technologies. The core constituent of the circuit is the winner-take-all circuit developed by Lazzaro et al. Correct functioning of the presented circuit is exemplified with simulations of the circuits implementing the scheme for solving the shortest path problems.

Local CC2 response method based on the Laplace transform: analytic energy gradients for ground and excited states.

PubMed

Ledermüller, Katrin; Schütz, Martin

2014-04-28

A multistate local CC2 response method for the calculation of analytic energy gradients with respect to nuclear displacements is presented for ground and electronically excited states. The gradient enables the search for equilibrium geometries of extended molecular systems. Laplace transform is used to partition the eigenvalue problem in order to obtain an effective singles eigenvalue problem and adaptive, state-specific local approximations. This leads to an approximation in the energy Lagrangian, which however is shown (by comparison with the corresponding gradient method without Laplace transform) to be of no concern for geometry optimizations. The accuracy of the local approximation is tested and the efficiency of the new code is demonstrated by application calculations devoted to a photocatalytic decarboxylation process of present interest.

On the constrained minimization of smooth Kurdyka—Łojasiewicz functions with the scaled gradient projection method

NASA Astrophysics Data System (ADS)

Prato, Marco; Bonettini, Silvia; Loris, Ignace; Porta, Federica; Rebegoldi, Simone

2016-10-01

The scaled gradient projection (SGP) method is a first-order optimization method applicable to the constrained minimization of smooth functions and exploiting a scaling matrix multiplying the gradient and a variable steplength parameter to improve the convergence of the scheme. For a general nonconvex function, the limit points of the sequence generated by SGP have been proved to be stationary, while in the convex case and with some restrictions on the choice of the scaling matrix the sequence itself converges to a constrained minimum point. In this paper we extend these convergence results by showing that the SGP sequence converges to a limit point provided that the objective function satisfies the Kurdyka-Łojasiewicz property at each point of its domain and its gradient is Lipschitz continuous.

Minimum maximum temperature gradient coil design.

PubMed

While, Peter T; Poole, Michael S; Forbes, Larry K; Crozier, Stuart

2013-08-01

Ohmic heating is a serious problem in gradient coil operation. A method is presented for redesigning cylindrical gradient coils to operate at minimum peak temperature, while maintaining field homogeneity and coil performance. To generate these minimaxT coil windings, an existing analytic method for simulating the spatial temperature distribution of single layer gradient coils is combined with a minimax optimization routine based on sequential quadratic programming. Simulations are provided for symmetric and asymmetric gradient coils that show considerable improvements in reducing maximum temperature over existing methods. The winding patterns of the minimaxT coils were found to be heavily dependent on the assumed thermal material properties and generally display an interesting "fish-eye" spreading of windings in the dense regions of the coil. Small prototype coils were constructed and tested for experimental validation and these demonstrate that with a reasonable estimate of material properties, thermal performance can be improved considerably with negligible change to the field error or standard figures of merit. © 2012 Wiley Periodicals, Inc.

Stochastic Spectral Descent for Discrete Graphical Models

DOE PAGES

Carlson, David; Hsieh, Ya-Ping; Collins, Edo; ...

2015-12-14

Interest in deep probabilistic graphical models has in-creased in recent years, due to their state-of-the-art performance on many machine learning applications. Such models are typically trained with the stochastic gradient method, which can take a significant number of iterations to converge. Since the computational cost of gradient estimation is prohibitive even for modestly sized models, training becomes slow and practically usable models are kept small. In this paper we propose a new, largely tuning-free algorithm to address this problem. Our approach derives novel majorization bounds based on the Schatten- norm. Intriguingly, the minimizers of these bounds can be interpreted asmore » gradient methods in a non-Euclidean space. We thus propose using a stochastic gradient method in non-Euclidean space. We both provide simple conditions under which our algorithm is guaranteed to converge, and demonstrate empirically that our algorithm leads to dramatically faster training and improved predictive ability compared to stochastic gradient descent for both directed and undirected graphical models.« less

Determination of reversed-phase high performance liquid chromatography based octanol-water partition coefficients for neutral and ionizable compounds: Methodology evaluation.

PubMed

Liang, Chao; Qiao, Jun-Qin; Lian, Hong-Zhen

2017-12-15

Reversed-phase liquid chromatography (RPLC) based octanol-water partition coefficient (logP) or distribution coefficient (logD) determination methods were revisited and assessed comprehensively. Classic isocratic and some gradient RPLC methods were conducted and evaluated for neutral, weak acid and basic compounds. Different lipophilicity indexes in logP or logD determination were discussed in detail, including the retention factor logk w corresponding to neat water as mobile phase extrapolated via linear solvent strength (LSS) model from isocratic runs and calculated with software from gradient runs, the chromatographic hydrophobicity index (CHI), apparent gradient capacity factor (k g ') and gradient retention time (t g ). Among the lipophilicity indexes discussed, logk w from whether isocratic or gradient elution methods best correlated with logP or logD. Therefore logk w is recommended as the preferred lipophilicity index for logP or logD determination. logk w easily calculated from methanol gradient runs might be the main candidate to replace logk w calculated from classic isocratic run as the ideal lipophilicity index. These revisited RPLC methods were not applicable for strongly ionized compounds that are hardly ion-suppressed. A previously reported imperfect ion-pair RPLC method was attempted and further explored for studying distribution coefficients (logD) of sulfonic acids that totally ionized in the mobile phase. Notably, experimental logD values of sulfonic acids were given for the first time. The IP-RPLC method provided a distinct way to explore logD values of ionized compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

Spiral Gradient Coil Design for Use in Cylindrical MRI Systems.

PubMed

Wang, Yaohui; Xin, Xuegang; Liu, Feng; Crozier, Stuart

2018-04-01

In magnetic resonance imaging, the stream function based method is commonly used in the design of gradient coils. However, this method can be prone to errors associated with the discretization of continuous current density and wire connections. In this paper, we propose a novel gradient coil design scheme that works directly in the wire space, avoiding the system errors that may appear in the stream function approaches. Specifically, the gradient coil pattern is described with dedicated spiral functions adjusted to allow the coil to produce the required field gradients in the imaging area, minimal stray field, and other engineering terms. The performance of a designed spiral gradient coil was compared with its stream-function counterpart. The numerical evaluation shows that when compared with the conventional solution, the inductance and resistance was reduced by 20.9 and 10.5%, respectively. The overall coil performance (evaluated by the figure of merit (FoM)) was improved up to 26.5% for the x -gradient coil design; for the z-gradient coil design, the inductance and resistance were reduced by 15.1 and 6.7% respectively, and the FoM was increased by 17.7%. In addition, by directly controlling the wire distributions, the spiral gradient coil design was much sparser than conventional coils.

Designing gradient coils with reduced hot spot temperatures.

PubMed

While, Peter T; Forbes, Larry K; Crozier, Stuart

2010-03-01

Gradient coil temperature is an important concern in the design and construction of MRI scanners. Closely spaced gradient coil windings cause temperature hot spots within the system as a result of Ohmic heating associated with large current being driven through resistive material, and can strongly affect the performance of the coils. In this paper, a model is presented for predicting the spatial temperature distribution of a gradient coil, including the location and extent of temperature hot spots. Subsequently, a method is described for designing gradient coils with improved temperature distributions and reduced hot spot temperatures. Maximum temperature represents a non-linear constraint and a relaxed fixed point iteration routine is proposed to adjust coil windings iteratively to minimise this coil feature. Several examples are considered that assume different thermal material properties and cooling mechanisms for the gradient system. Coil winding solutions are obtained for all cases considered that display a considerable drop in hot spot temperature (>20%) when compared to standard minimum power gradient coils with equivalent gradient homogeneity, efficiency and inductance. The method is semi-analytical in nature and can be adapted easily to consider other non-linear constraints in the design of gradient coils or similar systems. Crown Copyright (c) 2009. Published by Elsevier Inc. All rights reserved.

On the electromagnetic scattering from infinite rectangular grids with finite conductivity

NASA Technical Reports Server (NTRS)

Christodoulou, C. G.; Kauffman, J. F.

1986-01-01

A variety of methods can be used in constructing solutions to the problem of mesh scattering. However, each of these methods has certain drawbacks. The present paper is concerned with a new technique which is valid for all spacings. The new method involved, called the fast Fourier transform-conjugate gradient method (FFT-CGM), represents an iterative technique which employs the conjugate gradient method to improve upon each iterate, utilizing the fast Fourier transform. The FFT-CGM method provides a new accurate model which can be extended and applied to the more difficult problems of woven mesh surfaces. The formulation of the FFT-conjugate gradient method for aperture fields and current densities for a planar periodic structure is considered along with singular operators, the formulation of the FFT-CG method for thin wires with finite conductivity, and reflection coefficients.

Controlled droplet transport to target on a high adhesion surface with multi-gradients

PubMed Central

Deng, Siyan; Shang, Weifeng; Feng, Shile; Zhu, Shiping; Xing, Yan; Li, Dan; Hou, Yongping; Zheng, Yongmei

2017-01-01

We introduce multi-gradients including Laplace pressure gradient, wettable gradient and wettable different gradient on a high adhesion surface via special wedge-pattern and improved anodic oxidation method. As a result of the cooperative effect mentioned above, controlled directional motion of a droplet on a high adhesion surface is realized, even when the surface is turned upside down. The droplet motion can be predicted and the movement distances can be controlled by simply adjusting the wedge angle and droplet volume. More interestingly, when Laplace pressure gradient is introduced on a V-shaped wettable gradient surface, two droplets can move toward one another as designed. PMID:28368020

Fast conjugate phase image reconstruction based on a Chebyshev approximation to correct for B0 field inhomogeneity and concomitant gradients.

PubMed

Chen, Weitian; Sica, Christopher T; Meyer, Craig H

2008-11-01

Off-resonance effects can cause image blurring in spiral scanning and various forms of image degradation in other MRI methods. Off-resonance effects can be caused by both B0 inhomogeneity and concomitant gradient fields. Previously developed off-resonance correction methods focus on the correction of a single source of off-resonance. This work introduces a computationally efficient method of correcting for B0 inhomogeneity and concomitant gradients simultaneously. The method is a fast alternative to conjugate phase reconstruction, with the off-resonance phase term approximated by Chebyshev polynomials. The proposed algorithm is well suited for semiautomatic off-resonance correction, which works well even with an inaccurate or low-resolution field map. The proposed algorithm is demonstrated using phantom and in vivo data sets acquired by spiral scanning. Semiautomatic off-resonance correction alone is shown to provide a moderate amount of correction for concomitant gradient field effects, in addition to B0 imhomogeneity effects. However, better correction is provided by the proposed combined method. The best results were produced using the semiautomatic version of the proposed combined method.

RES: Regularized Stochastic BFGS Algorithm

NASA Astrophysics Data System (ADS)

Mokhtari, Aryan; Ribeiro, Alejandro

2014-12-01

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

Automatic extraction of planetary image features

NASA Technical Reports Server (NTRS)

LeMoigne-Stewart, Jacqueline J. (Inventor); Troglio, Giulia (Inventor); Benediktsson, Jon A. (Inventor); Serpico, Sebastiano B. (Inventor); Moser, Gabriele (Inventor)

2013-01-01

A method for the extraction of Lunar data and/or planetary features is provided. The feature extraction method can include one or more image processing techniques, including, but not limited to, a watershed segmentation and/or the generalized Hough Transform. According to some embodiments, the feature extraction method can include extracting features, such as, small rocks. According to some embodiments, small rocks can be extracted by applying a watershed segmentation algorithm to the Canny gradient. According to some embodiments, applying a watershed segmentation algorithm to the Canny gradient can allow regions that appear as close contours in the gradient to be segmented.

DISENTANGLING AGN AND STAR FORMATION ACTIVITY AT HIGH REDSHIFT USING HUBBLE SPACE TELESCOPE GRISM SPECTROSCOPY

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

Bridge, Joanna S.; Zeimann, Gregory R.; Trump, Jonathan R.

2016-08-01

Differentiating between active galactic nucleus (AGN) activity and star formation in z ∼ 2 galaxies is difficult because traditional methods, such as line-ratio diagnostics, change with redshift, while multi-wavelength methods (X-ray, radio, IR) are sensitive to only the brightest AGNs. We have developed a new method for spatially resolving emission lines using the Hubble Space Telescope /Wide Field Camera 3 G141 grism spectra and quantifying AGN activity through the spatial gradient of the [O iii]/H β line ratio. Through detailed simulations, we show that our novel line-ratio gradient approach identifies ∼40% more low-mass and obscured AGNs than obtained by classicalmore » methods. Based on our simulations, we developed a relationship that maps the stellar mass, star formation rate, and measured [O iii]/H β gradient to the AGN Eddington ratio. We apply our technique to previously studied stacked samples of galaxies at z ∼ 2 and find that our results are consistent with these studies. This gradient method will also be able to inform other areas of galaxy evolution science, such as inside-out quenching and metallicity gradients, and will be widely applicable to future spatially resolved James Webb Space Telescope data.« less

Retention prediction and separation optimization under multilinear gradient elution in liquid chromatography with Microsoft Excel macros.

PubMed

Fasoula, S; Zisi, Ch; Gika, H; Pappa-Louisi, A; Nikitas, P

2015-05-22

A package of Excel VBA macros have been developed for modeling multilinear gradient retention data obtained in single or double gradient elution mode by changing organic modifier(s) content and/or eluent pH. For this purpose, ten chromatographic models were used and four methods were adopted for their application. The methods were based on (a) the analytical expression of the retention time, provided that this expression is available, (b) the retention times estimated using the Nikitas-Pappa approach, (c) the stepwise approximation, and (d) a simple numerical approximation involving the trapezoid rule for integration of the fundamental equation for gradient elution. For all these methods, Excel VBA macros have been written and implemented using two different platforms; the fitting and the optimization platform. The fitting platform calculates not only the adjustable parameters of the chromatographic models, but also the significance of these parameters and furthermore predicts the analyte elution times. The optimization platform determines the gradient conditions that lead to the optimum separation of a mixture of analytes by using the Solver evolutionary mode, provided that proper constraints are set in order to obtain the optimum gradient profile in the minimum gradient time. The performance of the two platforms was tested using experimental and artificial data. It was found that using the proposed spreadsheets, fitting, prediction, and optimization can be performed easily and effectively under all conditions. Overall, the best performance is exhibited by the analytical and Nikitas-Pappa's methods, although the former cannot be used under all circumstances. Copyright © 2015 Elsevier B.V. All rights reserved.

3D Printed Programmable Release Capsules.

PubMed

Gupta, Maneesh K; Meng, Fanben; Johnson, Blake N; Kong, Yong Lin; Tian, Limei; Yeh, Yao-Wen; Masters, Nina; Singamaneni, Srikanth; McAlpine, Michael C

2015-08-12

The development of methods for achieving precise spatiotemporal control over chemical and biomolecular gradients could enable significant advances in areas such as synthetic tissue engineering, biotic-abiotic interfaces, and bionanotechnology. Living organisms guide tissue development through highly orchestrated gradients of biomolecules that direct cell growth, migration, and differentiation. While numerous methods have been developed to manipulate and implement biomolecular gradients, integrating gradients into multiplexed, three-dimensional (3D) matrices remains a critical challenge. Here we present a method to 3D print stimuli-responsive core/shell capsules for programmable release of multiplexed gradients within hydrogel matrices. These capsules are composed of an aqueous core, which can be formulated to maintain the activity of payload biomolecules, and a poly(lactic-co-glycolic) acid (PLGA, an FDA approved polymer) shell. Importantly, the shell can be loaded with plasmonic gold nanorods (AuNRs), which permits selective rupturing of the capsule when irradiated with a laser wavelength specifically determined by the lengths of the nanorods. This precise control over space, time, and selectivity allows for the ability to pattern 2D and 3D multiplexed arrays of enzyme-loaded capsules along with tunable laser-triggered rupture and release of active enzymes into a hydrogel ambient. The advantages of this 3D printing-based method include (1) highly monodisperse capsules, (2) efficient encapsulation of biomolecular payloads, (3) precise spatial patterning of capsule arrays, (4) "on the fly" programmable reconfiguration of gradients, and (5) versatility for incorporation in hierarchical architectures. Indeed, 3D printing of programmable release capsules may represent a powerful new tool to enable spatiotemporal control over biomolecular gradients.

A hybrid neural learning algorithm using evolutionary learning and derivative free local search method.

PubMed

Ghosh, Ranadhir; Yearwood, John; Ghosh, Moumita; Bagirov, Adil

2006-06-01

In this paper we investigate a hybrid model based on the Discrete Gradient method and an evolutionary strategy for determining the weights in a feed forward artificial neural network. Also we discuss different variants for hybrid models using the Discrete Gradient method and an evolutionary strategy for determining the weights in a feed forward artificial neural network. The Discrete Gradient method has the advantage of being able to jump over many local minima and find very deep local minima. However, earlier research has shown that a good starting point for the discrete gradient method can improve the quality of the solution point. Evolutionary algorithms are best suited for global optimisation problems. Nevertheless they are cursed with longer training times and often unsuitable for real world application. For optimisation problems such as weight optimisation for ANNs in real world applications the dimensions are large and time complexity is critical. Hence the idea of a hybrid model can be a suitable option. In this paper we propose different fusion strategies for hybrid models combining the evolutionary strategy with the discrete gradient method to obtain an optimal solution much quicker. Three different fusion strategies are discussed: a linear hybrid model, an iterative hybrid model and a restricted local search hybrid model. Comparative results on a range of standard datasets are provided for different fusion hybrid models.

Exploring versioned distributed arrays for resilience in scientific applications: Global view resilience

DOE PAGES

Chien, Andrew A.; Balaji, Pavan; Dun, Nan; ...

2016-09-08

Exascale studies project reliability challenges for future HPC systems. We present the Global View Resilience (GVR) system, a library for portable resilience. GVR begins with a subset of the Global Arrays interface, and adds new capabilities to create versions, name versions, and compute on version data. Applications can focus versioning where and when it is most productive, and customize for each application structure independently. This control is portable, and its embedding in application source makes it natural to express and easy to maintain. The ability to name multiple versions and “partially materialize” them efficiently makes ambitious forward-recovery based on “datamore » slices” across versions or data structures both easy to express and efficient. Using several large applications (OpenMC, preconditioned conjugate gradient (PCG) solver, ddcMD, and Chombo), we evaluate the programming effort to add resilience. The required changes are small (< 2% lines of code (LOC)), localized and machine-independent, and perhaps most important, require no software architecture changes. We also measure the overhead of adding GVR versioning and show that overheads < 2% are generally achieved. This overhead suggests that GVR can be implemented in large-scale codes and support portable error recovery with modest investment and runtime impact. Our results are drawn from both IBM BG/Q and Cray XC30 experiments, demonstrating portability. We also present two case studies of flexible error recovery, illustrating how GVR can be used for multi-version rollback recovery, and several different forward-recovery schemes. GVR’s multi-version enables applications to survive latent errors (silent data corruption) with significant detection latency, and forward recovery can make that recovery extremely efficient. Lastly, our results suggest that GVR is scalable, portable, and efficient. GVR interfaces are flexible, supporting a variety of recovery schemes, and altogether GVR embodies a gentle-slope path to tolerate growing error rates in future extreme-scale systems.« less

Exploring versioned distributed arrays for resilience in scientific applications: Global view resilience

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

Chien, Andrew A.; Balaji, Pavan; Dun, Nan

Exascale studies project reliability challenges for future HPC systems. We present the Global View Resilience (GVR) system, a library for portable resilience. GVR begins with a subset of the Global Arrays interface, and adds new capabilities to create versions, name versions, and compute on version data. Applications can focus versioning where and when it is most productive, and customize for each application structure independently. This control is portable, and its embedding in application source makes it natural to express and easy to maintain. The ability to name multiple versions and “partially materialize” them efficiently makes ambitious forward-recovery based on “datamore » slices” across versions or data structures both easy to express and efficient. Using several large applications (OpenMC, preconditioned conjugate gradient (PCG) solver, ddcMD, and Chombo), we evaluate the programming effort to add resilience. The required changes are small (< 2% lines of code (LOC)), localized and machine-independent, and perhaps most important, require no software architecture changes. We also measure the overhead of adding GVR versioning and show that overheads < 2% are generally achieved. This overhead suggests that GVR can be implemented in large-scale codes and support portable error recovery with modest investment and runtime impact. Our results are drawn from both IBM BG/Q and Cray XC30 experiments, demonstrating portability. We also present two case studies of flexible error recovery, illustrating how GVR can be used for multi-version rollback recovery, and several different forward-recovery schemes. GVR’s multi-version enables applications to survive latent errors (silent data corruption) with significant detection latency, and forward recovery can make that recovery extremely efficient. Lastly, our results suggest that GVR is scalable, portable, and efficient. GVR interfaces are flexible, supporting a variety of recovery schemes, and altogether GVR embodies a gentle-slope path to tolerate growing error rates in future extreme-scale systems.« less

A marker-based watershed method for X-ray image segmentation.

PubMed

Zhang, Xiaodong; Jia, Fucang; Luo, Suhuai; Liu, Guiying; Hu, Qingmao

2014-03-01

Digital X-ray images are the most frequent modality for both screening and diagnosis in hospitals. To facilitate subsequent analysis such as quantification and computer aided diagnosis (CAD), it is desirable to exclude image background. A marker-based watershed segmentation method was proposed to segment background of X-ray images. The method consisted of six modules: image preprocessing, gradient computation, marker extraction, watershed segmentation from markers, region merging and background extraction. One hundred clinical direct radiograph X-ray images were used to validate the method. Manual thresholding and multiscale gradient based watershed method were implemented for comparison. The proposed method yielded a dice coefficient of 0.964±0.069, which was better than that of the manual thresholding (0.937±0.119) and that of multiscale gradient based watershed method (0.942±0.098). Special means were adopted to decrease the computational cost, including getting rid of few pixels with highest grayscale via percentile, calculation of gradient magnitude through simple operations, decreasing the number of markers by appropriate thresholding, and merging regions based on simple grayscale statistics. As a result, the processing time was at most 6s even for a 3072×3072 image on a Pentium 4 PC with 2.4GHz CPU (4 cores) and 2G RAM, which was more than one time faster than that of the multiscale gradient based watershed method. The proposed method could be a potential tool for diagnosis and quantification of X-ray images. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Detection of thermal gradients through fiber-optic Chirped Fiber Bragg Grating (CFBG): Medical thermal ablation scenario

NASA Astrophysics Data System (ADS)

Korganbayev, Sanzhar; Orazayev, Yerzhan; Sovetov, Sultan; Bazyl, Ali; Schena, Emiliano; Massaroni, Carlo; Gassino, Riccardo; Vallan, Alberto; Perrone, Guido; Saccomandi, Paola; Arturo Caponero, Michele; Palumbo, Giovanna; Campopiano, Stefania; Iadicicco, Agostino; Tosi, Daniele

2018-03-01

In this paper, we describe a novel method for spatially distributed temperature measurement with Chirped Fiber Bragg Grating (CFBG) fiber-optic sensors. The proposed method determines the thermal profile in the CFBG region from demodulation of the CFBG optical spectrum. The method is based on an iterative optimization that aims at minimizing the mismatch between the measured CFBG spectrum and a CFBG model based on coupled-mode theory (CMT), perturbed by a temperature gradient. In the demodulation part, we simulate different temperature distribution patterns with Monte-Carlo approach on simulated CFBG spectra. Afterwards, we obtain cost function that minimizes difference between measured and simulated spectra, and results in final temperature profile. Experiments and simulations have been carried out first with a linear gradient, demonstrating a correct operation (error 2.9 °C); then, a setup has been arranged to measure the temperature pattern on a 5-cm long section exposed to medical laser thermal ablation. Overall, the proposed method can operate as a real-time detection technique for thermal gradients over 1.5-5 cm regions, and turns as a key asset for the estimation of thermal gradients at the micro-scale in biomedical applications.

Accuracy of Gradient Reconstruction on Grids with High Aspect Ratio

NASA Technical Reports Server (NTRS)

Thomas, James

2008-01-01

Gradient approximation methods commonly used in unstructured-grid finite-volume schemes intended for solutions of high Reynolds number flow equations are studied comprehensively. The accuracy of gradients within cells and within faces is evaluated systematically for both node-centered and cell-centered formulations. Computational and analytical evaluations are made on a series of high-aspect-ratio grids with different primal elements, including quadrilateral, triangular, and mixed element grids, with and without random perturbations to the mesh. Both rectangular and cylindrical geometries are considered; the latter serves to study the effects of geometric curvature. The study shows that the accuracy of gradient reconstruction on high-aspect-ratio grids is determined by a combination of the grid and the solution. The contributors to the error are identified and approaches to reduce errors are given, including the addition of higher-order terms in the direction of larger mesh spacing. A parameter GAMMA characterizing accuracy on curved high-aspect-ratio grids is discussed and an approximate-mapped-least-square method using a commonly-available distance function is presented; the method provides accurate gradient reconstruction on general grids. The study is intended to be a reference guide accompanying the construction of accurate and efficient methods for high Reynolds number applications

Biocompatible patterning of proteins on wettability gradient surface by thermo-transfer printing.

PubMed

Kim, Sungho; Ryu, Yong-Sang; Suh, Jeng-Hun; Keum, Chang-Min; Sohn, Youngjoo; Lee, Sin-Doo

2014-08-01

We develop a simple and biocompatible method of patterning proteins on a wettability gradient surface by thermo-transfer printing. The wettability gradient is produced on a poly(dimethylsiloxane) (PDMS)-modified glass substrate through the temperature gradient during thermo-transfer printing. The water contact angle on the PDMS-modified surface is found to gradually increase along the direction of the temperature gradient from a low to a high temperature region. Based on the wettability gradient, the gradual change in the adsorption and immobilization of proteins (cholera toxin B subunit) is achieved in a microfluidic cell with the PDMS-modified surface.

Generalization of the van der Pauw Method: Analyzing Longitudinal Magnetoresistance Asymmetry to Quantify Doping Gradients

NASA Astrophysics Data System (ADS)

Grayson, M.; Zhou, Wang; Yoo, Heun-Mo; Prabhu-Gaunkar, S.; Tiemann, L.; Reichl, C.; Wegscheider, W.

A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients. Results will be shown of various semoconductor systems where this method is applied, from bulk doped semiconductors, to exfoliated 2D materials. McCormick Catalyst Award from Northwestern University, EECS Bridge Funding, and AFOSR FA9550-15-1-0247.

Gradient Calculation Methods on Arbitrary Polyhedral Unstructured Meshes for Cell-Centered CFD Solvers

NASA Technical Reports Server (NTRS)

Sozer, Emre; Brehm, Christoph; Kiris, Cetin C.

2014-01-01

A survey of gradient reconstruction methods for cell-centered data on unstructured meshes is conducted within the scope of accuracy assessment. Formal order of accuracy, as well as error magnitudes for each of the studied methods, are evaluated on a complex mesh of various cell types through consecutive local scaling of an analytical test function. The tests highlighted several gradient operator choices that can consistently achieve 1st order accuracy regardless of cell type and shape. The tests further offered error comparisons for given cell types, leading to the observation that the "ideal" gradient operator choice is not universal. Practical implications of the results are explored via CFD solutions of a 2D inviscid standing vortex, portraying the discretization error properties. A relatively naive, yet largely unexplored, approach of local curvilinear stencil transformation exhibited surprisingly favorable properties

On the relation between phase-field crack approximation and gradient damage modelling

NASA Astrophysics Data System (ADS)

Steinke, Christian; Zreid, Imadeddin; Kaliske, Michael

2017-05-01

The finite element implementation of a gradient enhanced microplane damage model is compared to a phase-field model for brittle fracture. Phase-field models and implicit gradient damage models share many similarities despite being conceived from very different standpoints. In both approaches, an additional differential equation and a length scale are introduced. However, while the phase-field method is formulated starting from the description of a crack in fracture mechanics, the gradient method starts from a continuum mechanics point of view. At first, the scope of application for both models is discussed to point out intersections. Then, the analysis of the employed mathematical methods and their rigorous comparison are presented. Finally, numerical examples are introduced to illustrate the findings of the comparison which are summarized in a conclusion at the end of the paper.

Performance analysis of structured gradient algorithm. [for adaptive beamforming linear arrays

NASA Technical Reports Server (NTRS)

Godara, Lal C.

1990-01-01

The structured gradient algorithm uses a structured estimate of the array correlation matrix (ACM) to estimate the gradient required for the constrained least-mean-square (LMS) algorithm. This structure reflects the structure of the exact array correlation matrix for an equispaced linear array and is obtained by spatial averaging of the elements of the noisy correlation matrix. In its standard form the LMS algorithm does not exploit the structure of the array correlation matrix. The gradient is estimated by multiplying the array output with the receiver outputs. An analysis of the two algorithms is presented to show that the covariance of the gradient estimated by the structured method is less sensitive to the look direction signal than that estimated by the standard method. The effect of the number of elements on the signal sensitivity of the two algorithms is studied.

Use of shift gradient in the second dimension to improve the separation space in comprehensive two-dimensional liquid chromatography.

PubMed

Li, Duxin; Schmitz, Oliver J

2013-08-01

Comprehensive two-dimensional liquid chromatography (LC × LC) has received much attention because it offers much higher peak capacities than separation in a single dimension. The advantageous peak capacity makes it attractive for the separation of complex samples. Various gradient methods have been used in LC × LC systems. The use of continuous shift gradient is advantageous because it combines the peak compression effect of full gradient mode and the tailed gradient program in parallel gradient mode. Here, a comparison of LC × LC analysis of Chinese herbal medicine with full gradient mode and shift gradient mode in the second dimension was performed. A correlation between the first and second dimensions was found in full gradient mode, and this was significantly reduced with shift gradient mode. The orthogonality increased by 43.7%. The effective peak distribution area increased significantly, which produced better separation.

Mini-batch optimized full waveform inversion with geological constrained gradient filtering

NASA Astrophysics Data System (ADS)

Yang, Hui; Jia, Junxiong; Wu, Bangyu; Gao, Jinghuai

2018-05-01

High computation cost and generating solutions without geological sense have hindered the wide application of Full Waveform Inversion (FWI). Source encoding technique is a way to dramatically reduce the cost of FWI but subject to fix-spread acquisition setup requirement and slow convergence for the suppression of cross-talk. Traditionally, gradient regularization or preconditioning is applied to mitigate the ill-posedness. An isotropic smoothing filter applied on gradients generally gives non-geological inversion results, and could also introduce artifacts. In this work, we propose to address both the efficiency and ill-posedness of FWI by a geological constrained mini-batch gradient optimization method. The mini-batch gradient descent optimization is adopted to reduce the computation time by choosing a subset of entire shots for each iteration. By jointly applying the structure-oriented smoothing to the mini-batch gradient, the inversion converges faster and gives results with more geological meaning. Stylized Marmousi model is used to show the performance of the proposed method on realistic synthetic model.

Formulation and Evaluation of Guggul Lipid Nanovesicles for Transdermal Delivery of Aceclofenac

PubMed Central

Gaur, Praveen Kumar; Mishra, Shikha; Aeri, Vidhu

2014-01-01

Context. Most new drugs have low water solubility and liposome is an important formulation to administer such drugs; however, it is quite unstable and has negligible systemic absorption. Objective. Aceclofenac nanovesicles were made using guggul lipid for formulating stable transdermal formulation. Materials and Methods. Guggul lipid was formulated into vesicles along with cholesterol and dicetyl phosphate using film hydration method. The formulations were analyzed for physicochemical properties and stability. Then its skin permeation and anti-inflammatory activity were determined. Results. Both categories of vesicles (PC and GL) showed optimum physicochemical properties; however, accelerated stability study showed considerable differences. GL-1 was appreciably stable for over 6 months at 4°C. Corresponding gels (PCG-1 and GLG-1) showed C max values at 4.98 and 7.32 μg/mL along with the T max values at 4 and 8 hours, respectively. GLG-1 inhibited edema production by 90.81% in 6 hours. Discussion. PC liposomes are unstable at higher temperature and upon longer storage. The formulation with higher lipid content (GL-1) showed good drug retention after 24 hours and appreciable stability both at higher temperature and for longer duration. Guggul lipid being a planar molecule might be stacked in vesicle wall with cholesterol. Conclusion. The composition of the nanovesicle played an important role in stability and drug permeation. Guggul lipid is suitable for producing stable vesicles. PMID:24672328

Aeromagnetic gradient compensation method for helicopter based on ɛ-support vector regression algorithm

NASA Astrophysics Data System (ADS)

Wu, Peilin; Zhang, Qunying; Fei, Chunjiao; Fang, Guangyou

2017-04-01

Aeromagnetic gradients are typically measured by optically pumped magnetometers mounted on an aircraft. Any aircraft, particularly helicopters, produces significant levels of magnetic interference. Therefore, aeromagnetic compensation is essential, and least square (LS) is the conventional method used for reducing interference levels. However, the LSs approach to solving the aeromagnetic interference model has a few difficulties, one of which is in handling multicollinearity. Therefore, we propose an aeromagnetic gradient compensation method, specifically targeted for helicopter use but applicable on any airborne platform, which is based on the ɛ-support vector regression algorithm. The structural risk minimization criterion intrinsic to the method avoids multicollinearity altogether. Local aeromagnetic anomalies can be retained, and platform-generated fields are suppressed simultaneously by constructing an appropriate loss function and kernel function. The method was tested using an unmanned helicopter and obtained improvement ratios of 12.7 and 3.5 in the vertical and horizontal gradient data, respectively. Both of these values are probably better than those that would have been obtained from the conventional method applied to the same data, had it been possible to do so in a suitable comparative context. The validity of the proposed method is demonstrated by the experimental result.

Application of modified Rosenbrock's method for optimization of nutrient media used in microorganism culturing.

PubMed

Votruba, J; Pilát, P; Prokop, A

1975-12-01

The Rosenbrock's procedure has been modified for optimization of nutrient medium composition and has been found to be less tedious than the Box-Wilson method, especially for larger numbers of optimized parameters. Its merits are particularly obvious with multiparameter optimization where the gradient method, so far the only one employed in microbiology from a variety of optimization methods (e.g., refs, 9 and 10), becomes impractical because of the excessive number of experiments required. The method suggested is also more stable during optimization than the gradient methods which are very sensitive to the selection of steps in the direction of the gradient and may thus easily shoot out of the optimized region. It is also anticipated that other direct search methods, particularly simplex design, may be easily adapted for optimization of medium composition. It is obvious that direct search methods may find an application in process improvement in antibiotic and related industries.

An M-step preconditioned conjugate gradient method for parallel computation

NASA Technical Reports Server (NTRS)

Adams, L.

1983-01-01

This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.

The effect of density gradients on hydrometers

NASA Astrophysics Data System (ADS)

Heinonen, Martti; Sillanpää, Sampo

2003-05-01

Hydrometers are simple but effective instruments for measuring the density of liquids. In this work, we studied the effect of non-uniform density of liquid on a hydrometer reading. The effect induced by vertical temperature gradients was investigated theoretically and experimentally. A method for compensating for the effect mathematically was developed and tested with experimental data obtained with the MIKES hydrometer calibration system. In the tests, the method was found reliable. However, the reliability depends on the available information on the hydrometer dimensions and density gradients.

Peak-Seeking Control Using Gradient and Hessian Estimates

NASA Technical Reports Server (NTRS)

Ryan, John J.; Speyer, Jason L.

2010-01-01

A peak-seeking control method is presented which utilizes a linear time-varying Kalman filter. Performance function coordinate and magnitude measurements are used by the Kalman filter to estimate the gradient and Hessian of the performance function. The gradient and Hessian are used to command the system toward a local extremum. The method is naturally applied to multiple-input multiple-output systems. Applications of this technique to a single-input single-output example and a two-input one-output example are presented.

Method of Lines Transpose an Implicit Vlasov Maxwell Solver for Plasmas

DTIC Science & Technology

2015-04-17

boundary crossings should be rare. Numerical results for the Bennett pinch are given in Figure 9. In order to resolve large gradients near the center of the...contributing to the large error at the center of the beam due to large gradients there) and with the finite beam cut-off radius and the outflow boundary...usable time step size can be limited by the numerical accuracy of the method when there are large gradients (high-frequency content) in the solution. We

Method and means for a spatial and temporal probe for laser-generated plumes based on density gradients

DOEpatents

Yeung, Edward S.; Chen, Guoying

1990-05-01

A method and means for a spatial and temporal probe for laser generated plumes based on density gradients includes generation of a plume of vaporized material from a surface by an energy source. The probe laser beam is positioned so that the plume passes through the probe laser beam. Movement of the probe laser beam caused by refraction from the density gradient of the plume is monitored. Spatial and temporal information, correlated to one another, is then derived.

A new family of Polak-Ribiere-Polyak conjugate gradient method with the strong-Wolfe line search

NASA Astrophysics Data System (ADS)

Ghani, Nur Hamizah Abdul; Mamat, Mustafa; Rivaie, Mohd

2017-08-01

Conjugate gradient (CG) method is an important technique in unconstrained optimization, due to its effectiveness and low memory requirements. The focus of this paper is to introduce a new CG method for solving large scale unconstrained optimization. Theoretical proofs show that the new method fulfills sufficient descent condition if strong Wolfe-Powell inexact line search is used. Besides, computational results show that our proposed method outperforms to other existing CG methods.

3D printing for the design and fabrication of polymer-based gradient scaffolds.

PubMed

Bracaglia, Laura G; Smith, Brandon T; Watson, Emma; Arumugasaamy, Navein; Mikos, Antonios G; Fisher, John P

2017-07-01

To accurately mimic the native tissue environment, tissue engineered scaffolds often need to have a highly controlled and varied display of three-dimensional (3D) architecture and geometrical cues. Additive manufacturing in tissue engineering has made possible the development of complex scaffolds that mimic the native tissue architectures. As such, architectural details that were previously unattainable or irreproducible can now be incorporated in an ordered and organized approach, further advancing the structural and chemical cues delivered to cells interacting with the scaffold. This control over the environment has given engineers the ability to unlock cellular machinery that is highly dependent upon the intricate heterogeneous environment of native tissue. Recent research into the incorporation of physical and chemical gradients within scaffolds indicates that integrating these features improves the function of a tissue engineered construct. This review covers recent advances on techniques to incorporate gradients into polymer scaffolds through additive manufacturing and evaluate the success of these techniques. As covered here, to best replicate different tissue types, one must be cognizant of the vastly different types of manufacturing techniques available to create these gradient scaffolds. We review the various types of additive manufacturing techniques that can be leveraged to fabricate scaffolds with heterogeneous properties and discuss methods to successfully characterize them. Additive manufacturing techniques have given tissue engineers the ability to precisely recapitulate the native architecture present within tissue. In addition, these techniques can be leveraged to create scaffolds with both physical and chemical gradients. This work offers insight into several techniques that can be used to generate graded scaffolds, depending on the desired gradient. Furthermore, it outlines methods to determine if the designed gradient was achieved. This review will help to condense the abundance of information that has been published on the creation and characterization of gradient scaffolds and to provide a single review discussing both methods for manufacturing gradient scaffolds and evaluating the establishment of a gradient. Copyright © 2017. Published by Elsevier Ltd.

Development of a Novel, Bicombinatorial Approach to Alloy Development, and Application to Rapid Screening of Creep Resistant Titanium Alloys

NASA Astrophysics Data System (ADS)

Martin, Brian

Combinatorial approaches have proven useful for rapid alloy fabrication and optimization. A new method of producing controlled isothermal gradients using the Gleeble Thermomechanical simulator has been developed, and demonstrated on the metastable beta-Ti alloy beta-21S, achieving a thermal gradient of 525-700 °C. This thermal gradient method has subsequently been coupled with existing combinatorial methods of producing composition gradients using the LENS(TM) additive manufacturing system, through the use of elemental blended powders. This has been demonstrated with a binary Ti-(0-15) wt% Cr build, which has subsequently been characterized with optical and electron microscopy, with special attention to the precipitate of TiCr2 Laves phases. The TiCr2 phase has been explored for its high temperature mechanical properties in a new oxidation resistant beta-Ti alloy, which serves as a demonstration of the new bicombinatorial methods developed as applied to a multicomponent alloy system.

Development, validation, and comparison of ICA-based gradient artifact reduction algorithms for simultaneous EEG-spiral in/out and echo-planar fMRI recordings

PubMed Central

Ryali, S; Glover, GH; Chang, C; Menon, V

2009-01-01

EEG data acquired in an MRI scanner are heavily contaminated by gradient artifacts that can significantly compromise signal quality. We developed two new methods based on Independent Component Analysis (ICA) for reducing gradient artifacts from spiral in-out and echo-planar pulse sequences at 3T, and compared our algorithms with four other commonly used methods: average artifact subtraction (Allen et al. 2000), principal component analysis (Niazy et al. 2005), Taylor series (Wan et al. 2006) and a conventional temporal ICA algorithm. Models of gradient artifacts were derived from simulations as well as a water phantom and performance of each method was evaluated on datasets constructed using visual event-related potentials (ERPs) as well as resting EEG. Our new methods recovered ERPs and resting EEG below the beta band (< 12.5 Hz) with high signal-to-noise ratio (SNR > 4). Our algorithms outperformed all of these methods on resting EEG in the theta- and alpha-bands (SNR > 4); however, for all methods, signal recovery was modest (SNR ~ 1) in the beta-band and poor (SNR < 0.3) in the gamma-band and above. We found that the conventional ICA algorithm performed poorly with uniformly low SNR (< 0.1). Taken together, our new ICA-based methods offer a more robust technique for gradient artifact reduction when scanning at 3T using spiral in-out and echo-planar pulse sequences. We provide new insights into the strengths and weaknesses of each method using a unified subspace framework. PMID:19580873

Hybrid DFP-CG method for solving unconstrained optimization problems

NASA Astrophysics Data System (ADS)

Osman, Wan Farah Hanan Wan; Asrul Hery Ibrahim, Mohd; Mamat, Mustafa

2017-09-01

The conjugate gradient (CG) method and quasi-Newton method are both well known method for solving unconstrained optimization method. In this paper, we proposed a new method by combining the search direction between conjugate gradient method and quasi-Newton method based on BFGS-CG method developed by Ibrahim et al. The Davidon-Fletcher-Powell (DFP) update formula is used as an approximation of Hessian for this new hybrid algorithm. Numerical result showed that the new algorithm perform well than the ordinary DFP method and proven to posses both sufficient descent and global convergence properties.

Shielded resistive electromagnets of arbitrary surface geometry using the boundary element method and a minimum energy constraint.

PubMed

Harris, Chad T; Haw, Dustin W; Handler, William B; Chronik, Blaine A

2013-09-01

Eddy currents are generated in MR by the use of rapidly switched electromagnets, resulting in time varying and spatially varying magnetic fields that must be either minimized or corrected. This problem is further complicated when non-cylindrical insert magnets are used for specialized applications. Interruption of the coupling between an insert coil and the MR system is typically accomplished using active magnetic shielding. A new method of actively shielding insert gradient and shim coils of any surface geometry by use of the boundary element method for coil design with a minimum energy constraint is presented. This method was applied to shield x- and z-gradient coils for two separate cases: a traditional cylindrical primary gradient with cylindrical shield and, to demonstrate its versatility in surface geometry, the same cylindrical primary gradients with a rectangular box-shaped shield. For the cylindrical case this method produced shields that agreed with analytic solutions. For the second case, the rectangular box-shaped shields demonstrated very good shielding characteristics despite having a different geometry than the primary coils. Copyright © 2013 Elsevier Inc. All rights reserved.

Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: An efficient implementation for the density-fitted second-order Møller–Plesset perturbation theory

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

Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr

General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller–Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele,more » Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.« less

Subpixel displacement measurement method based on the combination of particle swarm optimization and gradient algorithm

NASA Astrophysics Data System (ADS)

Guang, Chen; Qibo, Feng; Keqin, Ding; Zhan, Gao

2017-10-01

A subpixel displacement measurement method based on the combination of particle swarm optimization (PSO) and gradient algorithm (GA) was proposed for accuracy and speed optimization in GA, which is a subpixel displacement measurement method better applied in engineering practice. An initial integer-pixel value was obtained according to the global searching ability of PSO, and then gradient operators were adopted for a subpixel displacement search. A comparison was made between this method and GA by simulated speckle images and rigid-body displacement in metal specimens. The results showed that the computational accuracy of the combination of PSO and GA method reached 0.1 pixel in the simulated speckle images, or even 0.01 pixels in the metal specimen. Also, computational efficiency and the antinoise performance of the improved method were markedly enhanced.

A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization

PubMed Central

Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

2015-01-01

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence—with at most a linear convergence rate—because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method. PMID:26381742

A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization.

PubMed

Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

2015-01-01

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence--with at most a linear convergence rate--because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method.

A z-gradient array for simultaneous multi-slice excitation with a single-band RF pulse.

PubMed

Ertan, Koray; Taraghinia, Soheil; Sadeghi, Alireza; Atalar, Ergin

2018-07-01

Multi-slice radiofrequency (RF) pulses have higher specific absorption rates, more peak RF power, and longer pulse durations than single-slice RF pulses. Gradient field design techniques using a z-gradient array are investigated for exciting multiple slices with a single-band RF pulse. Two different field design methods are formulated to solve for the required current values of the gradient array elements for the given slice locations. The method requirements are specified, optimization problems are formulated for the minimum current norm and an analytical solution is provided. A 9-channel z-gradient coil array driven by independent, custom-designed gradient amplifiers is used to validate the theory. Performance measures such as normalized slice thickness error, gradient strength per unit norm current, power dissipation, and maximum amplitude of the magnetic field are provided for various slice locations and numbers of slices. Two and 3 slices are excited by a single-band RF pulse in simulations and phantom experiments. The possibility of multi-slice excitation with a single-band RF pulse using a z-gradient array is validated in simulations and phantom experiments. Magn Reson Med 80:400-412, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Simulated Design Strategies for SPECT Collimators to Reduce the Eddy Currents Induced by MRI Gradient Fields

NASA Astrophysics Data System (ADS)

Samoudi, Amine M.; Van Audenhaege, Karen; Vermeeren, Günter; Verhoyen, Gregory; Martens, Luc; Van Holen, Roel; Joseph, Wout

2015-10-01

Combining single photon emission computed tomography (SPECT) with magnetic resonance imaging (MRI) requires the insertion of highly conductive SPECT collimators inside the MRI scanner, resulting in an induced eddy current disturbing the combined system. We reduced the eddy currents due to the insert of a novel tungsten collimator inside transverse and longitudinal gradient coils. The collimator was produced with metal additive manufacturing, that is part of a microSPECT insert for a preclinical SPECT/MRI scanner. We characterized the induced magnetic field due to the gradient field and adapted the collimators to reduce the induced eddy currents. We modeled the x-, y-, and z-gradient coil and the different collimator designs and simulated them with FEKO, a three-dimensional method of moments / finite element methods (MoM/FEM) full-wave simulation tool. We used a time analysis approach to generate the pulsed magnetic field gradient. Simulation results show that the maximum induced field can be reduced by 50.82% in the final design bringing the maximum induced magnetic field to less than 2% of the applied gradient for all the gradient coils. The numerical model was validated with measurements and was proposed as a tool for studying the effect of a SPECT collimator within the MRI gradient coils.

Lateral Temperature-Gradient Method for High-Throughput Characterization of Material Processing by Millisecond Laser Annealing.

PubMed

Bell, Robert T; Jacobs, Alan G; Sorg, Victoria C; Jung, Byungki; Hill, Megan O; Treml, Benjamin E; Thompson, Michael O

2016-09-12

A high-throughput method for characterizing the temperature dependence of material properties following microsecond to millisecond thermal annealing, exploiting the temperature gradients created by a lateral gradient laser spike anneal (lgLSA), is presented. Laser scans generate spatial thermal gradients of up to 5 °C/μm with peak temperatures ranging from ambient to in excess of 1400 °C, limited only by laser power and materials thermal limits. Discrete spatial property measurements across the temperature gradient are then equivalent to independent measurements after varying temperature anneals. Accurate temperature calibrations, essential to quantitative analysis, are critical and methods for both peak temperature and spatial/temporal temperature profile characterization are presented. These include absolute temperature calibrations based on melting and thermal decomposition, and time-resolved profiles measured using platinum thermistors. A variety of spatially resolved measurement probes, ranging from point-like continuous profiling to large area sampling, are discussed. Examples from annealing of III-V semiconductors, CdSe quantum dots, low-κ dielectrics, and block copolymers are included to demonstrate the flexibility, high throughput, and precision of this technique.

Bistatic Radar Observations of 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Andert, T.; Remus, S.; Simpson, R. A.; Paetzold, M.; Häusler, B.; Tellmann, S.; González Peytavi, G.; Bird, M. K.

2017-12-01

Objectives of the Rosetta Radio Science investigations included determining the dielectric properties, small-scale roughness, and rotational state of the nucleus of comet 67P/Churyumov-Gerasimenko (67P/C-G) from bistatic radar (BSR) measurements. The radio transmitter and high gain antenna (HGA) on the spacecraft beamed right circularly polarized (RCP) radio signals at two wavelengths - 3.6 cm (X-Band) and 13 cm (S-Band) - toward the nucleus surface. Part of the impinging radiation was then scattered toward a 70-m ground station of the NASA Deep Space Network (DSN) on Earth where it was received and recorded coherently in both RCP and left circular polarization (LCP). Between late September and mid-December 2014 six BSR experiments at 67P/C-G were successfully conducted. Such measurements had never before been attempted at such a small body in interplanetary space. The distances between the spacecraft and the comet varied from 10 km (September) to 30 km (December) and the incident angles ranged from 42° to 56°. In five experiments the HGA footprint was close to the equator; on 29 November the footprint was close to the rotation axis. Both RCP and LCP echoes were detected at X-band during the experiments; the echoes on 29 November were strongest. Rosetta's ultra-stable oscillator provided a very stable frequency reference for transmission; such stability was required because the direct and reflected signals were separated during the experiments by only a fraction of 1 Hz. For a known incidence angle and measured RCP/LCP power ratio, the surface dielectric constant may be obtained by applying Fresnel theory if the surface is sufficiently smooth. In the Rosetta case the resulting power ratios on 29 November yielded non-physical dielectric constants, possibly because of the irregularly shaped surface. The paper will investigate the possibility that a cloud of discrete scatters might be responsible for the observed RCP/LCP ratios.

Inventory of Volatiles in the Coma of Comet 67P/Churyumov-Gerasimenko from Rosetta ROSINA - An Overview of First Results

NASA Astrophysics Data System (ADS)

Altwegg, K.; Rubin, M.; Balsiger, H. R.; Jäckel, A.; Le Roy, L.; Wurz, P.; Gasc, S.; Calmonte, U.; Tzou, C. Y.; Mall, U. A.; Fiethe, B.; De Keyser, J. M.; Berthelier, J. J.; Reme, H.; Gombosi, T. I.; Fuselier, S.

2014-12-01

The European Space Agency's Rosetta spacecraft is now close in a bound orbit around comet 67P/Churyumov-Gerasimenko (67P/C-G). On board is the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) instrument suite. ROSINA consists of two mass spectrometers, the Double Focusing Mass Spectrometer (DFMS) and the Reflectron-type Time-Of-Flight (RTOF), as well as the COmet Pressure Sensor (COPS). ROSINA is designed to detect and monitor the neutral gas and thermal plasma environment in the comet's coma by in situ investigation. The two mass spectrometers have high dynamic ranges and complement each other with high mass resolution (DFMS) and high time resolution and large mass range (RTOF). Especially the unprecedented sensitivity and mass resolution of DFMS together with the large mass range of RTOF will allow determining precisely light species (e.g. isotopologues) as well as detecting heavy organics. The pressure sensor COPS is capable to derive total gas densities, velocities, and temperatures. To date only limited data for the composition of cometary comae at heliocentric distances of more than 2.5 AU are available. The set is dominated by CO and daughter species of water from bright comets originating in the Oort cloud. While some molecules can be detected from far by remote sensing (e.g. CO) other molecules are much more difficult to observe from ground (e.g. CO2). The Rosetta mission presents a unique opportunity to directly probe the parent species in the thin cometary atmosphere of a Kuiper-belt object at more than 2.5 AU from the Sun and relate it to ground-based observations. Distances that far from the Sun are of particular interest as the comet's activity transitions from being super volatiles dominated to being water dominated. We will report on the first measurements of the volatile inventory obtained from ROSINA observations as Rosetta is following comet 67P/C-G in close vicinity.

The first mitochondrial genome for the butterfly family Riodinidae (Abisara fylloides) and its systematic implications.

PubMed

Zhao, Fang; Huang, Dun-Yuan; Sun, Xiao-Yan; Shi, Qing-Hui; Hao, Jia-Sheng; Zhang, Lan-Lan; Yang, Qun

2013-10-01

The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene (PCG) sequences of 19 available butterfly species covering all the five butterfly families (Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae, which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon. The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides , the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene (PCG) sequences of 19 available butterfly species covering all the five butterfly families (Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae, which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.

Rosetta/VIRTIS-M spectral data: Comet 67P/CG compared to other primitive small bodies.

NASA Astrophysics Data System (ADS)

De Sanctis, M. C.; Capaccioni, F.; Filacchione, G.; Erard, S.; Tosi, F.; Ciarniello, M.; Raponi, A.; Piccioni, G.; Leyrat, C.; Bockelée-Morvan, D.; Drossart, P.; Fornasier, S.

2014-12-01

VIRTIS-M, the Visible InfraRed Thermal Imaging Spectrometer, onboard the Rosetta Mission orbiter (Coradini et al., 2007) acquired data of the comet 67P/Churyumov-Gerasimenko in the 0.25-5.1 µm spectral range. The initial data, obtained during the first mission phases to the comet, allow us to derive albedo and global spectral properties of the comet nucleus as well as spectra of different areas on the nucleus. The characterization of cometary nuclei surfaces and their comparison with those of related populations such as extinct comet candidates, Centaurs, near-Earth asteroids (NEAs), trans-Neptunian objects (TNOs), and primitive asteroids is critical to understanding the origin and evolution of small solar system bodies. The acquired VIRTIS data are used to compare the global spectral properties of comet 67P/CG to published spectra of other cometary nuclei observed from ground or visited by space mission. Moreover, the spectra of 67P/Churyumov-Gerasimenko are also compared to those of primitive asteroids and centaurs. The comparison can give us clues on the possible common formation and evolutionary environment for primitive asteroids, centaurs and Jupiter-family comets. Authors acknowledge the funding from Italian and French Space Agencies. References: Coradini, A., Capaccioni, F., Drossart, P., Arnold, G., Ammannito, E., Angrilli, F., Barucci, A., Bellucci, G., Benkhoff, J., Bianchini, G., Bibring, J. P., Blecka, M., Bockelee-Morvan, D., Capria, M. T., Carlson, R., Carsenty, U., Cerroni, P., Colangeli, L., Combes, M., Combi, M., Crovisier, J., De Sanctis, M. C., Encrenaz, E. T., Erard, S., Federico, C., Filacchione, G., Fink, U., Fonti, S., Formisano, V., Ip, W. H., Jaumann, R., Kuehrt, E., Langevin, Y., Magni, G., McCord, T., Mennella, V., Mottola, S., Neukum, G., Palumbo, P., Piccioni, G., Rauer, H., Saggin, B., Schmitt, B., Tiphene, D., Tozzi, G., Space Science Reviews, Volume 128, Issue 1-4, 529-559, 2007.

The ALMA-PILS survey: the sulphur connection between protostars and comets: IRAS 16293-2422 B and 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Drozdovskaya, Maria N.; van Dishoeck, Ewine F.; Jørgensen, Jes K.; Calmonte, Ursina; van der Wiel, Matthijs H. D.; Coutens, Audrey; Calcutt, Hannah; Müller, Holger S. P.; Bjerkeli, Per; Persson, Magnus V.; Wampfler, Susanne F.; Altwegg, Kathrin

2018-06-01

The evolutionary past of our Solar system can be pieced together by comparing analogous low-mass protostars with remnants of our Protosolar Nebula - comets. Sulphur-bearing molecules may be unique tracers of the joint evolution of the volatile and refractory components. ALMA Band 7 data from the large unbiased Protostellar Interferometric Line Survey are used to search for S-bearing molecules in the outer disc-like structure, ˜60 au from IRAS 16293-2422 B, and are compared with data on 67P/Churyumov-Gerasimenko (67P/C-G) stemming from the ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) instrument aboard Rosetta. Species such as SO2, SO, OCS, CS, H2CS, H2S, and CH3SH are detected via at least one of their isotopologues towards IRAS 16293-2422 B. The search reveals a first-time detection of OC33S towards this source and a tentative first-time detection of C36S towards a low-mass protostar. The data show that IRAS 16293-2422 B contains much more OCS than H2S in comparison to 67P/C-G; meanwhile, the SO/SO2 ratio is in close agreement between the two targets. IRAS 16293-2422 B has a CH3SH/H2CS ratio in range of that of our Solar system (differences by a factor of 0.7-5.3). It is suggested that the levels of UV radiation during the initial collapse of the systems may have varied and have potentially been higher for IRAS 16293-2422 B due to its binary nature; thereby, converting more H2S into OCS. It remains to be conclusively tested if this also promotes the formation of S-bearing complex organics. Elevated UV levels of IRAS 16293-2422 B and a warmer birth cloud of our Solar system may jointly explain the variations between the two low-mass systems.

Enhancer of zeste acts as a major developmental regulator of Ciona intestinalis embryogenesis

PubMed Central

Le Goff, Emilie; Martinand-Mari, Camille; Martin, Marianne; Feuillard, Jérôme; Boublik, Yvan; Godefroy, Nelly; Mangeat, Paul; Baghdiguian, Stephen; Cavalli, Giacomo

2015-01-01

ABSTRACT The paradigm of developmental regulation by Polycomb group (PcG) proteins posits that they maintain silencing outside the spatial expression domains of their target genes, particularly of Hox genes, starting from mid embryogenesis. The Enhancer of zeste [E(z)] PcG protein is the catalytic subunit of the PRC2 complex, which silences its targets via deposition of the H3K27me3 mark. Here, we studied the ascidian Ciona intestinalis counterpart of E(z). Ci-E(z) is detected by immunohistochemistry as soon as the 2- and 4-cell stages as a cytoplasmic form and becomes exclusively nuclear thereafter, whereas the H3K27me3 mark is detected starting from the gastrula stage and later. Morpholino invalidation of Ci-E(z) leads to the total disappearance of both Ci-E(z) protein and its H3K27me3 mark. Ci-E(z) morphants display a severe phenotype. Strikingly, the earliest defects occur at the 4-cell stage with the dysregulation of cell positioning and mitotic impairment. At later stages, Ci-E(z)-deficient embryos are affected by terminal differentiation defects of neural, epidermal and muscle tissues, by the failure to form a notochord and by the absence of caudal nerve. These major phenotypic defects are specifically rescued by injection of a morpholino-resistant Ci-E(z) mRNA, which restores expression of Ci-E(z) protein and re-deposition of the H3K27me3 mark. As observed by qPCR analyses, Ci-E(z) invalidation leads to the early derepression of tissue-specific developmental genes, whereas late-acting developmental genes are generally down-regulated. Altogether, our results suggest that Ci-E(z) plays a major role during embryonic development in Ciona intestinalis by silencing early-acting developmental genes in a Hox-independent manner. PMID:26276097

Gradient-based interpolation method for division-of-focal-plane polarimeters.

PubMed

Gao, Shengkui; Gruev, Viktor

2013-01-14

Recent advancements in nanotechnology and nanofabrication have allowed for the emergence of the division-of-focal-plane (DoFP) polarization imaging sensors. These sensors capture polarization properties of the optical field at every imaging frame. However, the DoFP polarization imaging sensors suffer from large registration error as well as reduced spatial-resolution output. These drawbacks can be improved by applying proper image interpolation methods for the reconstruction of the polarization results. In this paper, we present a new gradient-based interpolation method for DoFP polarimeters. The performance of the proposed interpolation method is evaluated against several previously published interpolation methods by using visual examples and root mean square error (RMSE) comparison. We found that the proposed gradient-based interpolation method can achieve better visual results while maintaining a lower RMSE than other interpolation methods under various dynamic ranges of a scene ranging from dim to bright conditions.

Energy minimization in medical image analysis: Methodologies and applications.

PubMed

Zhao, Feng; Xie, Xianghua

2016-02-01

Energy minimization is of particular interest in medical image analysis. In the past two decades, a variety of optimization schemes have been developed. In this paper, we present a comprehensive survey of the state-of-the-art optimization approaches. These algorithms are mainly classified into two categories: continuous method and discrete method. The former includes Newton-Raphson method, gradient descent method, conjugate gradient method, proximal gradient method, coordinate descent method, and genetic algorithm-based method, while the latter covers graph cuts method, belief propagation method, tree-reweighted message passing method, linear programming method, maximum margin learning method, simulated annealing method, and iterated conditional modes method. We also discuss the minimal surface method, primal-dual method, and the multi-objective optimization method. In addition, we review several comparative studies that evaluate the performance of different minimization techniques in terms of accuracy, efficiency, or complexity. These optimization techniques are widely used in many medical applications, for example, image segmentation, registration, reconstruction, motion tracking, and compressed sensing. We thus give an overview on those applications as well. Copyright © 2015 John Wiley & Sons, Ltd.

The Modified HZ Conjugate Gradient Algorithm for Large-Scale Nonsmooth Optimization.

PubMed

Yuan, Gonglin; Sheng, Zhou; Liu, Wenjie

2016-01-01

In this paper, the Hager and Zhang (HZ) conjugate gradient (CG) method and the modified HZ (MHZ) CG method are presented for large-scale nonsmooth convex minimization. Under some mild conditions, convergent results of the proposed methods are established. Numerical results show that the presented methods can be better efficiency for large-scale nonsmooth problems, and several problems are tested (with the maximum dimensions to 100,000 variables).

Magnetic method for stimulating transport in fluids

DOEpatents

Martin, James E.; Solis, Kyle J.

2016-10-18

A method for producing mass and heat transport in fluids, wherein the method does not rely on conventional convection, that is, it does not require gravity, a thermal gradient, or a magnetic field gradient. This method gives rise to a unique class of vigorous, field-controllable flow patterns termed advection lattices. The advection lattices can be used to transport heat and/or mass in any desired direction using only magnetic fields.

Finite difference time domain (FDTD) method for modeling the effect of switched gradients on the human body in MRI.

PubMed

Zhao, Huawei; Crozier, Stuart; Liu, Feng

2002-12-01

Numerical modeling of the eddy currents induced in the human body by the pulsed field gradients in MRI presents a difficult computational problem. It requires an efficient and accurate computational method for high spatial resolution analyses with a relatively low input frequency. In this article, a new technique is described which allows the finite difference time domain (FDTD) method to be efficiently applied over a very large frequency range, including low frequencies. This is not the case in conventional FDTD-based methods. A method of implementing streamline gradients in FDTD is presented, as well as comparative analyses which show that the correct source injection in the FDTD simulation plays a crucial rule in obtaining accurate solutions. In particular, making use of the derivative of the input source waveform is shown to provide distinct benefits in accuracy over direct source injection. In the method, no alterations to the properties of either the source or the transmission media are required. The method is essentially frequency independent and the source injection method has been verified against examples with analytical solutions. Results are presented showing the spatial distribution of gradient-induced electric fields and eddy currents in a complete body model. Copyright 2002 Wiley-Liss, Inc.

A progressive gradient moment nulling design technique.

PubMed

Pipe, J G; Chenevert, T L

1991-05-01

A method is presented for designing motion-compensated gradients in a progressive manner. The method is easily applicable to many types of waveforms, and can compensate for any order of motion. It can be implemented graphically or numerically. Underlying theory and examples of its application are provided.

Bidirectional composition on lie groups for gradient-based image alignment.

PubMed

Mégret, Rémi; Authesserre, Jean-Baptiste; Berthoumieu, Yannick

2010-09-01

In this paper, a new formulation based on bidirectional composition on Lie groups (BCL) for parametric gradient-based image alignment is presented. Contrary to the conventional approaches, the BCL method takes advantage of the gradients of both template and current image without combining them a priori. Based on this bidirectional formulation, two methods are proposed and their relationship with state-of-the-art gradient based approaches is fully discussed. The first one, i.e., the BCL method, relies on the compositional framework to provide the minimization of the compensated error with respect to an augmented parameter vector. The second one, the projected BCL (PBCL), corresponds to a close approximation of the BCL approach. A comparative study is carried out dealing with computational complexity, convergence rate and frequence of convergence. Numerical experiments using a conventional benchmark show the performance improvement especially for asymmetric levels of noise, which is also discussed from a theoretical point of view.

Isolation of purified oocyst walls and sporocysts from Toxoplasma gondii.

PubMed

Everson, William V; Ware, Michael W; Dubey, J P; Lindquist, H D Alan

2002-01-01

Toxoplasma gondii oocysts are environmentally resistant and can infect virtually all warm-blooded hosts, including humans and livestock. Little is known about the biochemical basis for this resistance of oocysts, and mechanism for excystation of T. gondii sporozoites. The objective of the present study was to evaluate different methods (mechanical fragmentation, gradients, flow cytometry) to separate and purify T. gondii oocyst walls and sporocysts. Oocyst walls were successfully separated and purified using iodixanol gradients. Sporocysts were successfully separated and purified using iodixanol and Percoll gradients. Purification was also achieved by flow cytometry. Flow cytometry with fluorescence-activated cell sorting (FACS) yielded analytical quantities of oocyst walls and intact sporocysts. Flow cytometry with FACS also proved useful for quantitation of purity obtained following iodixanol gradient fractionation. Methods reported in this paper will be useful for analytical purposes, such as proteomic analysis of components unique to this life cycle stage, development of detection methods, or excystation studies.

Conjugate gradient type methods for linear systems with complex symmetric coefficient matrices

NASA Technical Reports Server (NTRS)

Freund, Roland

1989-01-01

We consider conjugate gradient type methods for the solution of large sparse linear system Ax equals b with complex symmetric coefficient matrices A equals A(T). Such linear systems arise in important applications, such as the numerical solution of the complex Helmholtz equation. Furthermore, most complex non-Hermitian linear systems which occur in practice are actually complex symmetric. We investigate conjugate gradient type iterations which are based on a variant of the nonsymmetric Lanczos algorithm for complex symmetric matrices. We propose a new approach with iterates defined by a quasi-minimal residual property. The resulting algorithm presents several advantages over the standard biconjugate gradient method. We also include some remarks on the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

Surface Profile and Stress Field Evaluation using Digital Gradient Sensing Method

DOE PAGES

Miao, C.; Sundaram, B. M.; Huang, L.; ...

2016-08-09

Shape and surface topography evaluation from measured orthogonal slope/gradient data is of considerable engineering significance since many full-field optical sensors and interferometers readily output accurate data of that kind. This has applications ranging from metrology of optical and electronic elements (lenses, silicon wafers, thin film coatings), surface profile estimation, wave front and shape reconstruction, to name a few. In this context, a new methodology for surface profile and stress field determination based on a recently introduced non-contact, full-field optical method called digital gradient sensing (DGS) capable of measuring small angular deflections of light rays coupled with a robust finite-difference-based least-squaresmore » integration (HFLI) scheme in the Southwell configuration is advanced here. The method is demonstrated by evaluating (a) surface profiles of mechanically warped silicon wafers and (b) stress gradients near growing cracks in planar phase objects.« less

Aircraft symmetric flight optimization. [gradient techniques for supersonic aircraft control

NASA Technical Reports Server (NTRS)

Falco, M.; Kelley, H. J.

1973-01-01

Review of the development of gradient techniques and their application to aircraft optimal performance computations in the vertical plane of flight. Results obtained using the method of gradients are presented for attitude- and throttle-control programs which extremize the fuel, range, and time performance indices subject to various trajectory and control constraints, including boundedness of engine throttle control. A penalty function treatment of state inequality constraints which generally appear in aircraft performance problems is outlined. Numerical results for maximum-range, minimum-fuel, and minimum-time climb paths for a hypothetical supersonic turbojet interceptor are presented and discussed. In addition, minimum-fuel climb paths subject to various levels of ground overpressure intensity constraint are indicated for a representative supersonic transport. A variant of the Gel'fand-Tsetlin 'method of ravines' is reviewed, and two possibilities for further development of continuous gradient processes are cited - namely, a projection version of conjugate gradients and a curvilinear search.

Gradient-based Electrical Properties Tomography (gEPT): a Robust Method for Mapping Electrical Properties of Biological Tissues In Vivo Using Magnetic Resonance Imaging

PubMed Central

Liu, Jiaen; Zhang, Xiaotong; Schmitter, Sebastian; Van de Moortele, Pierre-Francois; He, Bin

2014-01-01

Purpose To develop high-resolution electrical properties tomography (EPT) methods and investigate a gradient-based EPT (gEPT) approach which aims to reconstruct the electrical properties (EP), including conductivity and permittivity, of an imaged sample from experimentally measured B1 maps with improved boundary reconstruction and robustness against measurement noise. Theory and Methods Using a multi-channel transmit/receive stripline head coil, with acquired B1 maps for each coil element, by assuming negligible Bz component compared to transverse B1 components, a theory describing the relationship between B1 field, EP value and their spatial gradient has been proposed. The final EP images were obtained through spatial integration over the reconstructed EP gradient. Numerical simulation, physical phantom and in vivo human experiments at 7 T have been conducted to evaluate the performance of the proposed methods. Results Reconstruction results were compared with target EP values in both simulations and phantom experiments. Human experimental results were compared with EP values in literature. Satisfactory agreement was observed with improved boundary reconstruction. Importantly, the proposed gEPT method proved to be more robust against noise when compared to previously described non-gradient-based EPT approaches. Conclusion The proposed gEPT approach holds promises to improve EP mapping quality by recovering the boundary information and enhancing robustness against noise. PMID:25213371

Fast conjugate phase image reconstruction based on a Chebyshev approximation to correct for B0 field inhomogeneity and concomitant gradients

PubMed Central

Chen, Weitian; Sica, Christopher T.; Meyer, Craig H.

2008-01-01

Off-resonance effects can cause image blurring in spiral scanning and various forms of image degradation in other MRI methods. Off-resonance effects can be caused by both B0 inhomogeneity and concomitant gradient fields. Previously developed off-resonance correction methods focus on the correction of a single source of off-resonance. This work introduces a computationally efficient method of correcting for B0 inhomogeneity and concomitant gradients simultaneously. The method is a fast alternative to conjugate phase reconstruction, with the off-resonance phase term approximated by Chebyshev polynomials. The proposed algorithm is well suited for semiautomatic off-resonance correction, which works well even with an inaccurate or low-resolution field map. The proposed algorithm is demonstrated using phantom and in vivo data sets acquired by spiral scanning. Semiautomatic off-resonance correction alone is shown to provide a moderate amount of correction for concomitant gradient field effects, in addition to B0 imhomogeneity effects. However, better correction is provided by the proposed combined method. The best results were produced using the semiautomatic version of the proposed combined method. PMID:18956462

Monitoring gradient profile on-line in micro- and nano-high performance liquid chromatography using conductivity detection.

PubMed

Zhang, Min; Chen, Apeng; Lu, Joann J; Cao, Chengxi; Liu, Shaorong

2016-08-19

In micro- or nano-flow high performance liquid chromatography (HPLC), flow-splitters and gradient elutions are commonly used for reverse phase HPLC separations. When a flow splitter was used at a high split-ratio (e.g., 1000:1 or higher), the actual gradient may deviate away from the programmed gradient. Sometimes, mobile phase concentrations can deviate by as much as 5%. In this work, we noticed that the conductivity (σ) of a gradient decreased with the increasing organic-solvent fraction (φ). Based on the relationship between σ and φ, a method was developed for monitoring gradient profile on-line to record any deviations in these HPLC systems. The conductivity could be measured by a traditional conductivity detector or a capacitively coupled contactless conductivity detector (C(4)D). The method was applied for assessing the performance of an electroosmotic pump (EOP) based nano-HPLC. We also observed that σ value of the gradient changed with system pressure; a=0.0175ΔP (R(2)=0.964), where a is the percentage of the conductivity increase and ΔP is the system pressure in bar. This effect was also investigated. Copyright © 2016. Published by Elsevier B.V.

Magnetic Resonance Imaging of Solids Using Oscillating Field Gradients

NASA Astrophysics Data System (ADS)

Daud, Yaacob Mat

1992-01-01

Available from UMI in association with The British Library. A fully automatic solid state NMR imaging spectrometer is described. Use has been made of oscillating field gradients to frequency and phase encode the spatial localisation of the nuclear spins. The RF pulse is applied during the zero crossing of the field gradient, so only low RF power is needed to cover the narrow spectral width of the spins. The oscillating field gradient coils were operated on resonance hence large gradient strength could be applied (up to 200G/cm). Two image reconstruction methods were used, filtered back-projection and two dimensional Fourier transformation. The use of phase encoding, both with oscillating and with pulsed field gradients, enabled us to acquire the data when the gradients were off, and this method proved to be insensitive to eddy currents. It also allowed the use of narrow bandwidth receiver thus improving the signal to noise ratio. The maximum entropy method was used in an effort to remove data truncation effects, although the results were not too convincing. The application of these new imaging schemes, was tested by mapping the T_1 and T_2 of polymers. The calculated relaxation maps produced precise spatial information about T_1 and T_2 which is not possible to achieve by conventional relaxation weight mapping. In a second application, the diffusion of water vapour into dried zeolite powder was studied. We found that the diffusion process is not Fickian.

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation.

PubMed

Xu, Jinshi; Chen, Yu; Zhang, Lixia; Chai, Yongfu; Wang, Mao; Guo, Yaoxin; Li, Ting; Yue, Ming

2017-07-01

Community assembly processes is the primary focus of community ecology. Using phylogenetic-based and functional trait-based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits' variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis . Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle- and low-altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large-scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.

Maximum Power Point Tracking with Dichotomy and Gradient Method for Automobile Exhaust Thermoelectric Generators

NASA Astrophysics Data System (ADS)

Fang, W.; Quan, S. H.; Xie, C. J.; Tang, X. F.; Wang, L. L.; Huang, L.

2016-03-01

In this study, a direct-current/direct-current (DC/DC) converter with maximum power point tracking (MPPT) is developed to down-convert the high voltage DC output from a thermoelectric generator to the lower voltage required to charge batteries. To improve the tracking accuracy and speed of the converter, a novel MPPT control scheme characterized by an aggregated dichotomy and gradient (ADG) method is proposed. In the first stage, the dichotomy algorithm is used as a fast search method to find the approximate region of the maximum power point. The gradient method is then applied for rapid and accurate tracking of the maximum power point. To validate the proposed MPPT method, a test bench composed of an automobile exhaust thermoelectric generator was constructed for harvesting the automotive exhaust heat energy. Steady-state and transient tracking experiments under five different load conditions were carried out using a DC/DC converter with the proposed ADG and with three traditional methods. The experimental results show that the ADG method can track the maximum power within 140 ms with a 1.1% error rate when the engine operates at 3300 rpm@71 NM, which is superior to the performance of the single dichotomy method, the single gradient method and the perturbation and observation method from the viewpoint of improved tracking accuracy and speed.

Nonnegative least-squares image deblurring: improved gradient projection approaches

NASA Astrophysics Data System (ADS)

Benvenuto, F.; Zanella, R.; Zanni, L.; Bertero, M.

2010-02-01

The least-squares approach to image deblurring leads to an ill-posed problem. The addition of the nonnegativity constraint, when appropriate, does not provide regularization, even if, as far as we know, a thorough investigation of the ill-posedness of the resulting constrained least-squares problem has still to be done. Iterative methods, converging to nonnegative least-squares solutions, have been proposed. Some of them have the 'semi-convergence' property, i.e. early stopping of the iteration provides 'regularized' solutions. In this paper we consider two of these methods: the projected Landweber (PL) method and the iterative image space reconstruction algorithm (ISRA). Even if they work well in many instances, they are not frequently used in practice because, in general, they require a large number of iterations before providing a sensible solution. Therefore, the main purpose of this paper is to refresh these methods by increasing their efficiency. Starting from the remark that PL and ISRA require only the computation of the gradient of the functional, we propose the application to these algorithms of special acceleration techniques that have been recently developed in the area of the gradient methods. In particular, we propose the application of efficient step-length selection rules and line-search strategies. Moreover, remarking that ISRA is a scaled gradient algorithm, we evaluate its behaviour in comparison with a recent scaled gradient projection (SGP) method for image deblurring. Numerical experiments demonstrate that the accelerated methods still exhibit the semi-convergence property, with a considerable gain both in the number of iterations and in the computational time; in particular, SGP appears definitely the most efficient one.

Algorithms for accelerated convergence of adaptive PCA.

PubMed

Chatterjee, C; Kang, Z; Roychowdhury, V P

2000-01-01

We derive and discuss new adaptive algorithms for principal component analysis (PCA) that are shown to converge faster than the traditional PCA algorithms due to Oja, Sanger, and Xu. It is well known that traditional PCA algorithms that are derived by using gradient descent on an objective function are slow to converge. Furthermore, the convergence of these algorithms depends on appropriate choices of the gain sequences. Since online applications demand faster convergence and an automatic selection of gains, we present new adaptive algorithms to solve these problems. We first present an unconstrained objective function, which can be minimized to obtain the principal components. We derive adaptive algorithms from this objective function by using: 1) gradient descent; 2) steepest descent; 3) conjugate direction; and 4) Newton-Raphson methods. Although gradient descent produces Xu's LMSER algorithm, the steepest descent, conjugate direction, and Newton-Raphson methods produce new adaptive algorithms for PCA. We also provide a discussion on the landscape of the objective function, and present a global convergence proof of the adaptive gradient descent PCA algorithm using stochastic approximation theory. Extensive experiments with stationary and nonstationary multidimensional Gaussian sequences show faster convergence of the new algorithms over the traditional gradient descent methods.We also compare the steepest descent adaptive algorithm with state-of-the-art methods on stationary and nonstationary sequences.

Edge gradients evaluation for 2D hybrid finite volume method model

USDA-ARS?s Scientific Manuscript database

In this study, a two-dimensional depth-integrated hydrodynamic model was developed using FVM on a hybrid unstructured collocated mesh system. To alleviate the negative effects of mesh irregularity and non-uniformity, a conservative evaluation method for edge gradients based on the second-order Tayl...

Enrichment of Undifferentiated Type A Spermatogonia from Goat Testis Using Discontinuous Percoll Density Gradient and Differential Plating

PubMed Central

Heidari, Banafsheh; Gifani, Minoo; Shirazi, Abolfazl; Zarnani, Amir-Hassan; Baradaran, Behzad; Naderi, Mohammad Mehdi; Behzadi, Bahareh; Borjian-Boroujeni, Sara; Sarvari, Ali; Lakpour, Niknam; Akhondi, Mohammad Mehdi

2014-01-01

Background The well documented source for adult multipotent stem cells is Spermatogonial Stem Cells (SSCs). They are the foundation of spermatogenesis in the testis throughout adult life by balancing self-renewal and differentiation. The aim of this study was to assess the effect of percoll density gradient and differential plating on enrichment of undifferentiated type A spermatogonia in dissociated cellular suspension of goat testes. Additionally, we evaluated the separated fractions of the gradients in percoll and samples in differential plating at different times for cell number, viability and purification rate of goat SSCs in culture. Methods Testicular cells were successfully isolated from one month old goat testis using two-step enzymatic digestion and followed by two purification protocols, differential plating with different times of culture (3, 4, 5, and 6 hr) and discontinuous percoll density with different gradients (20, 28, 30, and 32%). The difference of percentage of undifferentiated SSCs (PGP9.5 positive) in each method was compared using ANOVA and comparison between the highest percentage of corresponding value between two methods was carried out by t-test using Sigma Stat (ver. 3.5). Results The highest PGP9.5 (94.6±0.4) and the lowest c-Kit positive (25.1±0.7) in Percoll method was significantly (p ≤ 0.001) achieved in 32% percoll gradient. While the corresponding rates in differential plating method for the highest PGP9.5 positive cells (81.3±1.1) and lowest c-Kit (17.1±1.4) was achieved after 5 hr culturing (p < 0.001). The enrichment of undifferentiated type A spermatogonia using Percoll was more efficient than differential plating method (p < 0.001). Conclusion Percoll density gradient and differential plating were efficient and fast methods for enrichment of type A spermatogonial stem cells from goat testes. PMID:24834311

Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

DOE PAGES

Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

2015-08-06

This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performingmore » microcanonical excited state molecular dynamics with p-nitroaniline.« less

A family of conjugate gradient methods for large-scale nonlinear equations.

PubMed

Feng, Dexiang; Sun, Min; Wang, Xueyong

2017-01-01

In this paper, we present a family of conjugate gradient projection methods for solving large-scale nonlinear equations. At each iteration, it needs low storage and the subproblem can be easily solved. Compared with the existing solution methods for solving the problem, its global convergence is established without the restriction of the Lipschitz continuity on the underlying mapping. Preliminary numerical results are reported to show the efficiency of the proposed method.

Crystal growth and annealing for minimized residual stress

DOEpatents

Gianoulakis, Steven E.

2002-01-01

A method and apparatus for producing crystals that minimizes birefringence even at large crystal sizes, and is suitable for production of CaF.sub.2 crystals. The method of the present invention comprises annealing a crystal by maintaining a minimal temperature gradient in the crystal while slowly reducing the bulk temperature of the crystal. An apparatus according to the present invention includes a thermal control system added to a crystal growth and annealing apparatus, wherein the thermal control system allows a temperature gradient during crystal growth but minimizes the temperature gradient during crystal annealing.

Method for single crystal growth of photovoltaic perovskite material and devices

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

Huang, Jinsong; Dong, Qingfeng

Systems and methods for perovskite single crystal growth include using a low temperature solution process that employs a temperature gradient in a perovskite solution in a container, also including at least one small perovskite single crystal, and a substrate in the solution upon which substrate a perovskite crystal nucleates and grows, in part due to the temperature gradient in the solution and in part due to a temperature gradient in the substrate. For example, a top portion of the substrate external to the solution may be cooled.

Method and means for a spatial and temporal probe for laser-generated plumes based on density gradients

DOEpatents

Yeung, E.S.; Chen, G.

1990-05-01

A method and means are disclosed for a spatial and temporal probe for laser generated plumes based on density gradients includes generation of a plume of vaporized material from a surface by an energy source. The probe laser beam is positioned so that the plume passes through the probe laser beam. Movement of the probe laser beam caused by refraction from the density gradient of the plume is monitored. Spatial and temporal information, correlated to one another, is then derived. 15 figs.

Four-body trajectory optimization

NASA Technical Reports Server (NTRS)

Pu, C. L.; Edelbaum, T. N.

1974-01-01

A comprehensive optimization program has been developed for computing fuel-optimal trajectories between the earth and a point in the sun-earth-moon system. It presents methods for generating fuel optimal two-impulse trajectories which may originate at the earth or a point in space and fuel optimal three-impulse trajectories between two points in space. The extrapolation of the state vector and the computation of the state transition matrix are accomplished by the Stumpff-Weiss method. The cost and constraint gradients are computed analytically in terms of the terminal state and the state transition matrix. The 4-body Lambert problem is solved by using the Newton-Raphson method. An accelerated gradient projection method is used to optimize a 2-impulse trajectory with terminal constraint. The Davidon's Variance Method is used both in the accelerated gradient projection method and the outer loop of a 3-impulse trajectory optimization problem.

On the accurate analysis of vibroacoustics in head insert gradient coils.

PubMed

Winkler, Simone A; Alejski, Andrew; Wade, Trevor; McKenzie, Charles A; Rutt, Brian K

2017-10-01

To accurately analyze vibroacoustics in MR head gradient coils. A detailed theoretical model for gradient coil vibroacoustics, including the first description and modeling of Lorentz damping, is introduced and implemented in a multiphysics software package. Numerical finite-element method simulations were used to establish a highly accurate vibroacoustic model in head gradient coils in detail, including the newly introduced Lorentz damping effect. Vibroacoustic coupling was examined through an additional modal analysis. Thorough experimental studies were used to validate simulations. Average experimental sound pressure levels (SPLs) and accelerations over the 0-3000 Hz frequency range were 97.6 dB, 98.7 dB, and 95.4 dB, as well as 20.6 g, 8.7 g, and 15.6 g for the X-, Y-, and Z-gradients, respectively. A reasonable agreement between simulations and measurements was achieved. Vibroacoustic coupling showed a coupled resonance at 2300 Hz for the Z-gradient that is responsible for a sharp peak and the highest SPL value in the acoustic spectrum. We have developed and used more realistic multiphysics simulation methods to gain novel insights into the underlying concepts for vibroacoustics in head gradient coils, which will permit improved analyses of existing gradient coils and novel SPL reduction strategies for future gradient coil designs. Magn Reson Med 78:1635-1645, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Projection methods for line radiative transfer in spherical media.

NASA Astrophysics Data System (ADS)

Anusha, L. S.; Nagendra, K. N.

An efficient numerical method called the Preconditioned Bi-Conjugate Gradient (Pre-BiCG) method is presented for the solution of radiative transfer equation in spherical geometry. A variant of this method called Stabilized Preconditioned Bi-Conjugate Gradient (Pre-BiCG-STAB) is also presented. These methods are based on projections on the subspaces of the n dimensional Euclidean space mathbb {R}n called Krylov subspaces. The methods are shown to be faster in terms of convergence rate compared to the contemporary iterative methods such as Jacobi, Gauss-Seidel and Successive Over Relaxation (SOR).

SAGRAD: A Program for Neural Network Training with Simulated Annealing and the Conjugate Gradient Method.

PubMed

Bernal, Javier; Torres-Jimenez, Jose

2015-01-01

SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks for classification using batch learning, is discussed. Neural network training in SAGRAD is based on a combination of simulated annealing and Møller's scaled conjugate gradient algorithm, the latter a variation of the traditional conjugate gradient method, better suited for the nonquadratic nature of neural networks. Different aspects of the implementation of the training process in SAGRAD are discussed, such as the efficient computation of gradients and multiplication of vectors by Hessian matrices that are required by Møller's algorithm; the (re)initialization of weights with simulated annealing required to (re)start Møller's algorithm the first time and each time thereafter that it shows insufficient progress in reaching a possibly local minimum; and the use of simulated annealing when Møller's algorithm, after possibly making considerable progress, becomes stuck at a local minimum or flat area of weight space. Outlines of the scaled conjugate gradient algorithm, the simulated annealing procedure and the training process used in SAGRAD are presented together with results from running SAGRAD on two examples of training data.

Stem cell migration and mechanotransduction on linear stiffness gradient hydrogels

PubMed Central

Hadden, William J.; Young, Jennifer L.; Holle, Andrew W.; McFetridge, Meg L.; Kim, Du Yong; Wijesinghe, Philip; Taylor-Weiner, Hermes; Wen, Jessica H.; Lee, Andrew R.; Bieback, Karen; Vo, Ba-Ngu; Sampson, David D.; Kennedy, Brendan F.; Spatz, Joachim P.; Choi, Yu Suk

2017-01-01

The spatial presentation of mechanical information is a key parameter for cell behavior. We have developed a method of polymerization control in which the differential diffusion distance of unreacted cross-linker and monomer into a prepolymerized hydrogel sink results in a tunable stiffness gradient at the cell–matrix interface. This simple, low-cost, robust method was used to produce polyacrylamide hydrogels with stiffness gradients of 0.5, 1.7, 2.9, 4.5, 6.8, and 8.2 kPa/mm, spanning the in vivo physiological and pathological mechanical landscape. Importantly, three of these gradients were found to be nondurotactic for human adipose-derived stem cells (hASCs), allowing the presentation of a continuous range of stiffnesses in a single well without the confounding effect of differential cell migration. Using these nondurotactic gradient gels, stiffness-dependent hASC morphology, migration, and differentiation were studied. Finally, the mechanosensitive proteins YAP, Lamin A/C, Lamin B, MRTF-A, and MRTF-B were analyzed on these gradients, providing higher-resolution data on stiffness-dependent expression and localization. PMID:28507138

Thermal Management Techniques for Oil-Free Turbomachinery Systems

NASA Technical Reports Server (NTRS)

Radil, Kevin; DellaCorte, Chris; Zeszotek, Michelle

2006-01-01

Tests were performed to evaluate three different methods of utilizing air to provide thermal management control for compliant journal foil air bearings. The effectiveness of the methods was based on bearing bulk temperature and axial thermal gradient reductions during air delivery. The first method utilized direct impingement of air on the inner surface of a hollow test journal during operation. The second, less indirect method achieved heat removal by blowing air inside the test journal to simulate air flowing axially through a hollow, rotating shaft. The third method emulated the most common approach to removing heat by forcing air axially through the bearing s support structure. Internal bearing temperatures were measured with three, type K thermocouples embedded in the bearing that measured general internal temperatures and axial thermal gradients. Testing was performed in a 1 atm, 260 C ambient environment with the bearing operating at 60 krpm and supporting a load of 222 N. Air volumetric flows of 0.06, 0.11, and 0.17 cubic meters per minute at approximately 150 to 200 C were used. The tests indicate that all three methods provide thermal management but at different levels of effectiveness. Axial cooling of the bearing support structure had a greater effect on bulk temperature for each air flow and demonstrated that the thermal gradients could be influenced by the directionality of the air flow. Direct air impingement on the journal's inside surface provided uniform reductions in both bulk temperature and thermal gradients. Similar to the direct method, indirect journal cooling had a uniform cooling effect on both bulk temperatures and thermal gradients but was the least effective of the three methods.

Test of Shi et al. Method to Infer the Magnetic Reconnection Geometry from Spacecraft Data: MHD Simulation with Guide Field and Antiparallel Kinetic Simulation

NASA Technical Reports Server (NTRS)

Denton, R.; Sonnerup, B. U. O.; Swisdak, M.; Birn, J.; Drake, J. F.; Heese, M.

2012-01-01

When analyzing data from an array of spacecraft (such as Cluster or MMS) crossing a site of magnetic reconnection, it is desirable to be able to accurately determine the orientation of the reconnection site. If the reconnection is quasi-two dimensional, there are three key directions, the direction of maximum inhomogeneity (the direction across the reconnection site), the direction of the reconnecting component of the magnetic field, and the direction of rough invariance (the "out of plane" direction). Using simulated spacecraft observations of magnetic reconnection in the geomagnetic tail, we extend our previous tests of the direction-finding method developed by Shi et al. (2005) and the method to determine the structure velocity relative to the spacecraft Vstr. These methods require data from four proximate spacecraft. We add artificial noise and calibration errors to the simulation fields, and then use the perturbed gradient of the magnetic field B and perturbed time derivative dB/dt, as described by Denton et al. (2010). Three new simulations are examined: a weakly three-dimensional, i.e., quasi-two-dimensional, MHD simulation without a guide field, a quasi-two-dimensional MHD simulation with a guide field, and a two-dimensional full dynamics kinetic simulation with inherent noise so that the apparent minimum gradient was not exactly zero, even without added artificial errors. We also examined variations of the spacecraft trajectory for the kinetic simulation. The accuracy of the directions found varied depending on the simulation and spacecraft trajectory, but all the directions could be found within about 10 for all cases. Various aspects of the method were examined, including how to choose averaging intervals and the best intervals for determining the directions and velocity. For the kinetic simulation, we also investigated in detail how the errors in the inferred gradient directions from the unmodified Shi et al. method (using the unperturbed gradient) depended on the amplitude of the calibration errors. For an accuracy of 3 for the maximum gradient direction, the calibration errors could be as large as 3% of reconnection magnetic field, while for the same accuracy for the minimum gradient direction, the calibration errors could only be as large as 0.03% of the reconnection magnetic field. These results suggest that the maximum gradient direction can normally be determined by the unmodified Shi et al. method, while the modified method or some other method must be used to accurately determine the minimum gradient direction. The structure velocity was found with magnitude accurate to 2% and direction accurate to within 5%.

M-step preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

Adams, L.

1983-01-01

Preconditioned conjugate gradient methods for solving sparse symmetric and positive finite systems of linear equations are described. Necessary and sufficient conditions are given for when these preconditioners can be used and an analysis of their effectiveness is given. Efficient computer implementations of these methods are discussed and results on the CYBER 203 and the Finite Element Machine under construction at NASA Langley Research Center are included.

Validation of continuous-wave Doppler echocardiographic measurements of mitral and tricuspid prosthetic valve gradients: a simultaneous Doppler-catheter study.

PubMed

Wilkins, G T; Gillam, L D; Kritzer, G L; Levine, R A; Palacios, I F; Weyman, A E

1986-10-01

For patients with stenotic native valves, the modified Bernoulli equation (delta P = 4V2) may be applied to Doppler-measured transvalvular velocities to yield an accurate estimate of transvalvular gradients. Although it would be useful if the same approach could be used for those with stenotic prosthetic valves, no previous study has validated the Doppler technique in this setting. We therefore recorded simultaneous continuous-wave Doppler flow profiles and transvalvular manometric gradients in 12 catheterized patients in whom all atrial and ventricular pressures were directly measured (transseptal left atrial catheterization and transthoracic ventricular puncture were performed where necessary). A total of 13 prostheses were studied: 11 mitral (seven porcine, three Starr-Edwards, and one Björk-Shiley) and two tricuspid (one porcine and one Björk-Shiley). The Doppler-determined mean gradient was calculated as the mean of the instantaneous gradients (delta P = 4V2) at 10 msec intervals throughout diastole. The correlation of simultaneous Doppler (DMG) and manometric mean gradients (MG) for the whole group (n = 13) demonstrated a highly significant relationship (MG = 1.07 DMG + 0.28; r = .96, p = .0001). The correlation was equally good for porcine valves alone (n = 8) (MG = 1.06 DMG + 0.55; r = .96, p = .001) and for mechanical valves alone (n = 5) (MG = 1.06 DMG - 0.04; r = .93, p = .02). In a subset of patients without regurgitation (n = 8), prosthetic valve areas were estimated by two Doppler methods originally described by Holen and Hatle, as well as by the invasive Gorlin method. As expected from theoretical considerations, a close correlation was not demonstrated between results of the Gorlin method and those of either Hatle's Doppler method (r = .65, fp = NS) or Holen's method (r = .14, p = NS). Comparison of the results of the two Doppler methods yielded a somewhat closer correlation (r = .73, p less than or equal to .05). These results suggest that in patients with disk-occluder, ball-occluder, and porcine prosthetic valves, Doppler estimates of transvalvular gradients are virtually identical to those obtained invasively.

Steepest descent with momentum for quadratic functions is a version of the conjugate gradient method.

PubMed

Bhaya, Amit; Kaszkurewicz, Eugenius

2004-01-01

It is pointed out that the so called momentum method, much used in the neural network literature as an acceleration of the backpropagation method, is a stationary version of the conjugate gradient method. Connections with the continuous optimization method known as heavy ball with friction are also made. In both cases, adaptive (dynamic) choices of the so called learning rate and momentum parameters are obtained using a control Liapunov function analysis of the system.

Optimization Based Efficiencies in First Order Reliability Analysis

NASA Technical Reports Server (NTRS)

Peck, Jeffrey A.; Mahadevan, Sankaran

2003-01-01

This paper develops a method for updating the gradient vector of the limit state function in reliability analysis using Broyden's rank one updating technique. In problems that use commercial code as a black box, the gradient calculations are usually done using a finite difference approach, which becomes very expensive for large system models. The proposed method replaces the finite difference gradient calculations in a standard first order reliability method (FORM) with Broyden's Quasi-Newton technique. The resulting algorithm of Broyden updates within a FORM framework (BFORM) is used to run several example problems, and the results compared to standard FORM results. It is found that BFORM typically requires fewer functional evaluations that FORM to converge to the same answer.

Exploration Opportunity Search of Near-earth Objects Based on Analytical Gradients

NASA Astrophysics Data System (ADS)

Ren, Yuan; Cui, Ping-Yuan; Luan, En-Jie

2008-07-01

The problem of search of opportunity for the exploration of near-earth minor objects is investigated. For rendezvous missions, the analytical gradients of the performance index with respect to the free parameters are derived using the variational calculus and the theory of state-transition matrix. After generating randomly some initial guesses in the search space, the performance index is optimized, guided by the analytical gradients, leading to the local minimum points representing the potential launch opportunities. This method not only keeps the global-search property of the traditional method, but also avoids the blindness in the latter, thereby increasing greatly the computing speed. Furthermore, with this method, the searching precision could be controlled effectively.

Search of exploration opportunity for near earth objects based on analytical gradients

NASA Astrophysics Data System (ADS)

Ren, Y.; Cui, P. Y.; Luan, E. J.

2008-01-01

The problem of searching for exploration opportunity of near Earth objects is investigated. For rendezvous missions, the analytical gradients of performance index with respect to free parameters are derived by combining the calculus of variation with the theory of state-transition matrix. Then, some initial guesses are generated random in the search space, and the performance index is optimized with the guidance of analytical gradients from these initial guesses. This method not only keeps the property of global search in traditional method, but also avoids the blindness in the traditional exploration opportunity search; hence, the computing speed could be increased greatly. Furthermore, by using this method, the search precision could be controlled effectively.