Feature-based attention: it is all bottom-up priming

PubMed Central

Theeuwes, Jan

2013-01-01

Feature-based attention (FBA) enhances the representation of image characteristics throughout the visual field, a mechanism that is particularly useful when searching for a specific stimulus feature. Even though most theories of visual search implicitly or explicitly assume that FBA is under top-down control, we argue that the role of top-down processing in FBA may be limited. Our review of the literature indicates that all behavioural and neuro-imaging studies investigating FBA suffer from the shortcoming that they cannot rule out an effect of priming. The mere attending to a feature enhances the mandatory processing of that feature across the visual field, an effect that is likely to occur in an automatic, bottom-up way. Studies that have investigated the feasibility of FBA by means of cueing paradigms suggest that the role of top-down processing in FBA is limited (e.g. prepare for red). Instead, the actual processing of the stimulus is needed to cause the mandatory tuning of responses throughout the visual field. We conclude that it is likely that all FBA effects reported previously are the result of bottom-up priming. PMID:24018717

Construction and completion of flux balance models from pathway databases.

PubMed

Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

2012-02-01

Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.

Transport characteristics of three fluorescent conjugated bile acid analogs in isolated rat hepatocytes and couplets.

PubMed

Maglova, L M; Jackson, A M; Meng, X J; Carruth, M W; Schteingart, C D; Ton-Nu, H T; Hofmann, A F; Weinman, S A

1995-08-01

The transport properties of three different synthetically prepared fluorescent conjugated bile acid analogs (FBA), all with the fluorophore on the side chain, were determined using isolated rat hepatocytes and hepatocyte couplets. The compounds studied were cholylglycylamidofluorescein (CGamF), cholyl(N epsilon-nitrobenzoxadiazolyl [NBD])-lysine (C-NBD-L), and chenodeoxycholyl-(N epsilon-NBD)-lysine (CDC-NBD-L). When hepatocytes were incubated at 37 degrees C with 0.3 mumol/L of FBA and 0.15 mol/L of Na+, cell fluorescence increased linearly with time at a rate (U/min) of 7.8 +/- 0.5 for CGamF, 7.2 +/- 0.3 for C-NBD-L, and 13.7 +/- 1.0 for CDC-NBD-L (mean, +/- SE; n = 40 to 90). Uptake was concentration dependent for concentrations less than 20 mumol/L and was saturable. The Michaelis constant (Km) value (mumol/L) for CGamF was 10.8, for C-NBD-L was 3.8, and for CDC-NBD-L was 3.0. In the absence of Na+, the uptake rate was decreased by 50% for CGamF and by 38% for C-NBD-L; but uptake of CDC-NBD-L was unchanged and thus Na+ independent. Cellular uptake of all three derivatives was specific to hepatocytes and was absent in several nonhepatocyte cell lines. For CGamF and C-NBD-L, both Na(+)-dependent and Na(+)-independent uptake was inhibited by 200-fold excess concentrations of cholyltaurine, dehydrocholyltaurine, and cholate, but for CDC-NBD-L, these nonfluorescent bile acids did not inhibit initial uptake. The intracellular fluorescence of CGamF was strongly pH dependent at an excitation wavelength of 495 nm, but pH independent at 440 nm excitation. In contrast, intracellular fluorescence of C-NBD-L and CDC-NBD-L was pH independent. All three FBA were secreted into the canalicular space of approximately 50% to 60% of couplets. Cellular adenosine triphosphate (ATP) depletion with either CN- or atractyloside inhibited secretion of all three FBA. The multispecific organic anion transporter (MOAT) inhibitor, chlorodinitrobenzene, blocked secretion of fluorescent MOAT substrates at a concentration of 1 mumol/L. At this concentration it did not affect secretion of the three FBA. At higher concentrations, chlorodinitrobenzene partially inhibited the canalicular secretion of CGamF but not the other two FBA. In conclusion, all three FBA are secreted by canalicular membrane bile acid transporters, but the sinusoidal uptake characteristics of CGamF and C-NBD-L are more similar than those of CDC-NBD-L to the transport properties of cholyltaurine. Therefore, C-NBD-L appears to be the best of the three for studies of conjugated trihydroxy-bile acid transport in hepatocytes.

The Mechanism of Starch Over-Accumulation in Chlamydomonas reinhardtii High-Starch Mutants Identified by Comparative Transcriptome Analysis

PubMed Central

Koo, Kwang M.; Jung, Sera; Lee, Beom S.; Kim, Jin-Baek; Jo, Yeong D.; Choi, Hong-Il; Kang, Si-Yong; Chung, Gook-H.; Jeong, Won-Joong; Ahn, Joon-Woo

2017-01-01

The focus of this study was the mechanism of starch accumulation in Chlamydomonas reinhardtii high-starch mutants. Three C. reinhardtii mutants showing high-starch content were generated using gamma irradiation. When grown under nitrogen-deficient conditions, these mutants had more than twice as much starch than a wild-type control. The mechanism of starch over-accumulation in these mutants was studied with comparative transcriptome analysis. In all mutants, induction of phosphoglucomutase 1 (PGM1) expression was detected; PGM1 catalyzes the inter-conversion of glucose 1-phosphate and glucose 6-phosphate in both starch biosynthetic and glycolytic pathway. Interestingly, transcript levels of phosphoglucose isomerase 1 (PGI1), fructose 1,6-bisphosphate aldolase 1 and 2 (FBA1 and FBA2) were down-regulated in all mutants; PGI1, FBA1, and FBA2 act on downstream of glucose 6-phosphate conversion in glycolytic pathway. Therefore, down-regulations of PGI1, FBA1, and FBA2 may lead to accumulation of upstream metabolites, notably glucose 6-phosphate, resulting in induction of PGM1 expression through feed-forward regulation and that PGM1 overexpression caused starch over-accumulation in mutants. These results suggest that PGI1, FBA1, FBA2, and PGM1 correlate with each other in terms of coordinated transcriptional regulation and play central roles for starch over-accumulation in C. reinhardtii. PMID:28588557

Fructose-Bisphophate Aldolase Exhibits Functional Roles between Carbon Metabolism and the hrp System in Rice Pathogen Xanthomonas oryzae pv. oryzicola

PubMed Central

Li, Yu-rong; Cui, Yi-ping; Ji, Zhi-yuan; Cai, Lu-lu; Zou, Hua-song; Hutchins, William C.; Yang, Ching-hong; Chen, Gong-you

2012-01-01

Fructose-bisphophate aldolase (FbaB), is an enzyme in glycolysis and gluconeogenesis in living organisms. The mutagenesis in a unique fbaB gene of Xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak, led the pathogen not only unable to use pyruvate and malate for growth and delayed its growth when fructose was used as the sole carbon source, but also reduced extracellular polysaccharide (EPS) production and impaired bacterial virulence and growth in rice. Intriguingly, the fbaB promoter contains an imperfect PIP-box (plant-inducible promoter) (TTCGT-N9-TTCGT). The expression of fbaB was negatively regulated by a key hrp regulatory HrpG and HrpX cascade. Base substitution in the PIP-box altered the regulation of fbaB with the cascade. Furthermore, the expression of fbaB in X. oryzae pv. oryzicola RS105 strain was inducible in planta rather than in a nutrient-rich medium. Except other hrp-hrc-hpa genes, the expression of hrpG and hrpX was repressed and the transcripts of hrcC, hrpE and hpa3 were enhanced when fbaB was deleted. The mutation in hrcC, hrpE or hpa3 reduced the ability of the pathogen to acquire pyruvate and malate. In addition, bacterial virulence and growth in planta and EPS production in RΔfbaB mutant were completely restored to the wild-type level by the presence of fbaB in trans. This is the first report to demonstrate that carbohydrates, assimilated by X. oryzae pv. oryzicola, play critical roles in coordinating hrp gene expression through a yet unknown regulator. PMID:22384086

Identification and expression of fructose-1,6-bisphosphate aldolase genes and their relations to oil content in developing seeds of tea oil tree (Camellia oleifera).

PubMed

Zeng, Yanling; Tan, Xiaofeng; Zhang, Lin; Jiang, Nan; Cao, Heping

2014-01-01

Tea oil tree (Camellia oleifera, Co) provides a fine edible oil source in China. Tea oil from the seeds is very beneficial to human health. Fructose-1,6-bisphosphate aldolase (FBA) hydrolyzes fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, two critical metabolites for oil biosynthesis. The objectives of this study were to identify FBA genes and investigate the relationship between FBA gene expression and oil content in developing seeds of tea oil tree. In this paper, four developmentally up-regulated CoFBA genes were identified in Camellia oleifera seeds based on the transcriptome from two seed developmental stages corresponding to the initiation and peak stages of lipid biosynthesis. The expression of CoFBA genes, along with three key oil biosynthesis genes CoACP, CoFAD2 and CoSAD were analyzed in seeds from eight developmental stages by real-time quantitative PCR. The oil content and fatty acid composition were also analyzed. The results showed that CoFBA and CoSAD mRNA levels were well-correlated with oil content whereas CoFAD2 gene expression levels were correlated with fatty acid composition in Camellia seeds. We propose that CoFBA and CoSAD are two important factors for determining tea oil yield because CoFBA gene controls the flux of key intermediates for oil biosynthesis and CoSAD gene controls the synthesis of oleic acid, which accounts for 80% of fatty acids in tea oil. These findings suggest that tea oil yield could be improved by enhanced expression of CoFBA and CoSAD genes in transgenic plants.

Fructose-bisphosphate aldolase and enolase from Echinococcus granulosus: genes, expression patterns and protein interactions of two potential moonlighting proteins.

PubMed

Lorenzatto, Karina Rodrigues; Monteiro, Karina Mariante; Paredes, Rodolfo; Paludo, Gabriela Prado; da Fonsêca, Marbella Maria; Galanti, Norbel; Zaha, Arnaldo; Ferreira, Henrique Bunselmeyer

2012-09-10

Glycolytic enzymes, such as fructose-bisphosphate aldolase (FBA) and enolase, have been described as complex multifunctional proteins that may perform non-glycolytic moonlighting functions, but little is known about such functions, especially in parasites. We have carried out in silico genomic searches in order to identify FBA and enolase coding sequences in Echinococcus granulosus, the causative agent of cystic hydatid disease. Four FBA genes and 3 enolase genes were found, and their sequences and exon-intron structures were characterized and compared to those of their orthologs in Echinococcus multilocularis, the causative agent of alveolar hydatid disease. To gather evidence of possible non-glycolytic functions, the expression profile of FBA and enolase isoforms detected in the E. granulosus pathogenic larval form (hydatid cyst) (EgFBA1 and EgEno1) was assessed. Using specific antibodies, EgFBA1 and EgEno1 were detected in protoscolex and germinal layer cells, as expected, but they were also found in the hydatid fluid, which contains parasite's excretory-secretory (ES) products. Besides, both proteins were found in protoscolex tegument and in vitro ES products, further suggesting possible non-glycolytic functions in the host-parasite interface. EgFBA1 modeled 3D structure predicted a F-actin binding site, and the ability of EgFBA1 to bind actin was confirmed experimentally, which was taken as an additional evidence of FBA multifunctionality in E. granulosus. Overall, our results represent the first experimental evidences of alternative functions performed by glycolytic enzymes in E. granulosus and provide relevant information for the understanding of their roles in host-parasite interplay. Copyright © 2012 Elsevier B.V. All rights reserved.

Reflection and Transmission of Plane Electromagnetic Waves by a Geologic Layer.

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

Aldridge, David F.

Electric field and magnetic field reflection and transmission responses generated by a plane wave normally incident onto a finite - thickness geologic layer are mathematically derived and numerically evaluated. A thin layer with enhanced electric current conductivity and/or magnetic permeability is a reasonable geophysical representation of a hydraulic fracture inject ed with a high - contrast proppant pack. Both theory and numerics indicate that backward - and forward - scattered electromagnetic wavefields are potentially observable in a field experiment, despite the extreme thinness of a fracture compared to a typical low - frequency electromagnetic wavelength. The First Born Approximation (FBA)more » representation of layer scattering, significant for inversion studies, is shown to be accurate for a thin layer with mild medium parameter (i.e., conductivity, permeability, and per mittivity) contrasts with the surrounding homogeneous wholespace. However, FBA scattering theory breaks down for thick layers and strong parameter contrasts. ACKNOWLEDGEMENTS Sandia National Laboratories is a multi - mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE - AC04 - 94AL85000. This research is conducted under the auspices of CRADA (Cooperative Research and Development Agreement) SC11/01780.00 between Carbo Ceramics Inc. and Sandia National Laboratories. The author acknowledges former Carbo R&D Vic e - President Mr. Chad Cannan and former SNL Geophysics Department manage r Ms. Amy Halloran for their interest i n and support of this work. Technical discussions with Project Manager and Principal Investigator Dr. Chester J. Weiss of the SNL Geophysics Department greatly benefited this work. Dr. Lewis C. Bartel, formerly with S NL and presently a consultant to Carbo Ceramics, provided many useful and intuitive insights, and is acknowledged as the originator of the concept underpinning a recent patent grant (Aldridge and Bartel, 2016) involving electromagnetic wave scattering.« less

Streptococcus pneumoniae fructose-1,6-bisphosphate aldolase, a protein vaccine candidate, elicits Th1/Th2/Th17-type cytokine responses in mice.

PubMed

Elhaik Goldman, Shirin; Dotan, Shahar; Talias, Amir; Lilo, Amit; Azriel, Shalhevet; Malka, Itay; Portnoi, Maxim; Ohayon, Ariel; Kafka, Daniel; Ellis, Ronald; Elkabets, Moshe; Porgador, Angel; Levin, Ditza; Azhari, Rosa; Swiatlo, Edwin; Ling, Eduard; Feldman, Galia; Tal, Michael; Dagan, Ron; Mizrachi Nebenzahl, Yaffa

2016-04-01

Streptococcus pneumoniae (S. pneumoniae) is a major pathogen worldwide. The currently available polysaccharide-based vaccines significantly reduce morbidity and mortality. However, the inherent disadvantages of the currently available polysaccharide-based vaccines have motivated the search for other bacterial immunogens capable of eliciting a protective immune response against S. pneumoniae. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic enzyme, which was found to localize to the bacterial surface, where it functions as an adhesin. Previously, immunizing mice with recombinant FBA (rFBA) in the presence of alum elicited a protective immune response against a lethal challenge with S. pneumoniae. Thus, the aim of the present study was to determine the cytokine responses that are indicative of protective immunity following immunization with rFBA. The protective effects against pneumococcal challenge in mice immunized with rFBA with complete Freund's adjuvant (CFA) in the initial immunization and with incomplete Freund's adjuvant (IFA) in booster immunizations surpassed the protective effects observed following immunization with either rFBA + alum or pVACfba. CD4+ T-cells obtained from the rFBA/CFA/IFA/IFA-immunized mice co-cultured with rFBA-pulsed antigen-presenting cells (APCs), exhibited a significantly greater proliferative ability than CD4+ T-cells obtained from the adjuvant-immunized mice co-cultured with rFBA‑pulsed APCs. The levels of the Th1-type cytokines, interferon (IFN)-γ, interleukin (IL)-2, tumor necrosis factor (TNF)-α and IL-12, the Th2-type cytokines, IL-4, IL-5 and IL-10, and the Th17-type cytokine, IL-17A, significantly increased within 72 h of the initiation of co-culture with CD4+ T-cells obtained from the rFBA‑immunized mice, in comparison with the co-cultures with CD4+ T-cells obtained from the adjuvant-immunized mice. Immunizing mice with rFBA resulted in an IgG1/IgG2 ratio of 41, indicating a Th2 response with substantial Th1 involvement. In addition, rabbit and mouse anti-rFBA antisera significantly protected the mice against a lethal S. pneumoniae challenge in comparison with preimmune sera. Our results emphasize the mixed involvement of the Th1, Th2 and Th17 arms of the immune system in response to immunization with pneumococcal rFBA, a potential vaccine candidate.

Facile synthesis of magnetic Fe3O4@BiOI@AgI for water decontamination with visible light irradiation: Different mechanisms for different organic pollutants degradation and bacterial disinfection.

PubMed

Liang, Jialiang; Liu, Fuyang; Li, Mian; Liu, Wen; Tong, Meiping

2018-06-15

Magnetic Fe 3 O 4 @BiOI@AgI (FBA) spheres were synthesized through a multi-step process. The fabricated photocatalysts were characterized by different techniques. To testify the visible light driven photocatalytic activity of FBA, Rhodamine B and Bisphenol A were chosen as model common and emerging organic contaminants, respectively. While, gram-negative strain Escherichia coli was selected as model waterborne bacteria. The results showed that under visible light irradiation, FBA contained strong photocatalytic degradation capacity towards both RhB and BPA. Moreover, FBA was also found to exhibit excellent disinfection activity towards E. coli. The photocatalytic mechanisms for different pollutants by FBA were determined and found to vary for different pollutants. Specifically, scavenger experiments, degradation intermediates determination, as well as theoretical density functional theory (DFT) analysis showed that RhB and BPA were degraded via photosensitization (dominated by e - and ·O 2 - ) and direct photocatalytic oxidation (contributed by h + , e - and ·O 2 - ), respectively. Whereas, E. coli cells yet were found to be inactivated by the generation of e - and ·O 2 - rather than by the released Ag + . Since it contained superparamagnetic property, FBA could be easily separated from the reaction suspension after use. Due to the excellent photo stability, FBA exhibited strong photocatalytic activity in the fourth reused recycle. Therefore, FBA could serve as a promising alternative for water purification. Copyright © 2018 Elsevier Ltd. All rights reserved.

East Tennessee State University's "Make a Difference" Project: Using a Team-Based Consultative Model To Conduct Functional Behavioral Assessments.

ERIC Educational Resources Information Center

Vaughn, Kelley; Hales, Cindy; Bush, Marta; Fox, James

1998-01-01

Describes implementation of functional behavioral assessment (FBA) through collaboration between a university (East Tennessee State University) and the local school system. Discusses related issues such as factors in team training, team size, FBA adaptations, and replicability of the FBA team model. (Author/DB)

Fructose-1,6-bisphosphate aldolase (FBA)-a conserved glycolytic enzyme with virulence functions in bacteria: 'ill met by moonlight'.

PubMed

Shams, Fariza; Oldfield, Neil J; Wooldridge, Karl G; Turner, David P J

2014-12-01

Moonlighting proteins constitute an intriguing class of multifunctional proteins. Metabolic enzymes and chaperones, which are often highly conserved proteins in bacteria, archaea and eukaryotic organisms, are among the most commonly recognized examples of moonlighting proteins. Fructose-1,6-bisphosphate aldolase (FBA) is an enzyme involved in the Embden-Meyerhof-Parnas (EMP) glycolytic pathway and in gluconeogenesis. Increasingly, it is also recognized that FBA has additional functions beyond its housekeeping role in central metabolism. In the present review, we summarize the current knowledge of the moonlighting functions of FBA in bacteria.

Second generation engineering of transketolase for polar aromatic aldehyde substrates.

PubMed

Payongsri, Panwajee; Steadman, David; Hailes, Helen C; Dalby, Paul A

2015-04-01

Transketolase has significant industrial potential for the asymmetric synthesis of carboncarbon bonds with new chiral centres. Variants evolved on propanal were found previously with nascent activity on polar aromatic aldehydes 3-formylbenzoic acid (3-FBA), 4-formylbenzoic acid (4-FBA), and 3-hydroxybenzaldehyde (3-HBA), suggesting a potential novel route to analogues of chloramphenicol. Here we evolved improved transketolase activities towards aromatic aldehydes, by saturation mutagenesis of two active-site residues (R358 and S385), predicted to interact with the aromatic substituents. S385 variants selectively controlled the aromatic substrate preference, with up to 13-fold enhanced activities, and KM values comparable to those of natural substrates with wild-type transketolase. S385E even completely removed the substrate inhibition for 3-FBA, observed in all previous variants. The mechanisms of catalytic improvement were both mutation type and substrate dependent. S385E improved 3-FBA activity via kcat, but reduced 4-FBA activity via KM. Conversely, S385Y/T improved 3-FBA activity via KM and 4-FBA activity via kcat. This suggested that both substrate proximity and active-site orientation are very sensitive to mutation. Comparison of all variant activities on each substrate indicated different binding modes for the three aromatic substrates, supported by computational docking. This highlights a potential divergence in the evolution of different substrate specificities, with implications for enzyme engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2014-01-01

Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222

The involvement of wheat F-box protein gene TaFBA1 in the oxidative stress tolerance of plants.

PubMed

Zhou, Shu-Mei; Kong, Xiang-Zhu; Kang, Han-Han; Sun, Xiu-Dong; Wang, Wei

2015-01-01

As one of the largest gene families, F-box domain proteins have been found to play important roles in abiotic stress responses via the ubiquitin pathway. TaFBA1 encodes a homologous F-box protein contained in E3 ubiquitin ligases. In our previous study, we found that the overexpression of TaFBA1 enhanced drought tolerance in transgenic plants. To investigate the mechanisms involved, in this study, we investigated the tolerance of the transgenic plants to oxidative stress. Methyl viologen was used to induce oxidative stress conditions. Real-time PCR and western blot analysis revealed that TaFBA1 expression was up-regulated by oxidative stress treatments. Under oxidative stress conditions, the transgenic tobacco plants showed a higher germination rate, higher root length and less growth inhibition than wild type (WT). The enhanced oxidative stress tolerance of the transgenic plants was also indicated by lower reactive oxygen species (ROS) accumulation, malondialdehyde (MDA) content and cell membrane damage under oxidative stress compared with WT. Higher activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD), were observed in the transgenic plants than those in WT, which may be related to the upregulated expression of some antioxidant genes via the overexpression of TaFBA1. In others, some stress responsive elements were found in the promoter region of TaFBA1, and TaFBA1 was located in the nucleus, cytoplasm and plasma membrane. These results suggest that TaFBA1 plays an important role in the oxidative stress tolerance of plants. This is important for understanding the functions of F-box proteins in plants' tolerance to multiple stress conditions.

Fructose Degradation in the Haloarchaeon Haloferax volcanii Involves a Bacterial Type Phosphoenolpyruvate-Dependent Phosphotransferase System, Fructose-1-Phosphate Kinase, and Class II Fructose-1,6-Bisphosphate Aldolase

PubMed Central

Pickl, Andreas; Johnsen, Ulrike

2012-01-01

The halophilic archaeon Haloferax volcanii utilizes fructose as a sole carbon and energy source. Genes and enzymes involved in fructose uptake and degradation were identified by transcriptional analyses, deletion mutant experiments, and enzyme characterization. During growth on fructose, the gene cluster HVO_1495 to HVO_1499, encoding homologs of the five bacterial phosphotransferase system (PTS) components enzyme IIB (EIIB), enzyme I (EI), histidine protein (HPr), EIIA, and EIIC, was highly upregulated as a cotranscript. The in-frame deletion of HVO_1499, designated ptfC (ptf stands for phosphotransferase system for fructose) and encoding the putative fructose-specific membrane component EIIC, resulted in a loss of growth on fructose, which could be recovered by complementation in trans. Transcripts of HVO_1500 (pfkB) and HVO_1494 (fba), encoding putative fructose-1-phosphate kinase (1-PFK) and fructose-1,6-bisphosphate aldolase (FBA), respectively, as well as 1-PFK and FBA activities were specifically upregulated in fructose-grown cells. pfkB and fba knockout mutants did not grow on fructose, whereas growth on glucose was not inhibited, indicating the functional involvement of both enzymes in fructose catabolism. Recombinant 1-PFK and FBA obtained after homologous overexpression were characterized as having kinetic properties indicative of functional 1-PFK and a class II type FBA. From these data, we conclude that fructose uptake in H. volcanii involves a fructose-specific PTS generating fructose-1-phosphate, which is further converted via fructose-1,6-bisphosphate to triose phosphates by 1-PFK and FBA. This is the first report of the functional involvement of a bacterial-like PTS and of class II FBA in the sugar metabolism of archaea. PMID:22493022

The Involvement of Wheat F-Box Protein Gene TaFBA1 in the Oxidative Stress Tolerance of Plants

PubMed Central

Zhou, Shu-Mei; Kong, Xiang-Zhu; Kang, Han-Han; Sun, Xiu-Dong; Wang, Wei

2015-01-01

As one of the largest gene families, F-box domain proteins have been found to play important roles in abiotic stress responses via the ubiquitin pathway. TaFBA1 encodes a homologous F-box protein contained in E3 ubiquitin ligases. In our previous study, we found that the overexpression of TaFBA1 enhanced drought tolerance in transgenic plants. To investigate the mechanisms involved, in this study, we investigated the tolerance of the transgenic plants to oxidative stress. Methyl viologen was used to induce oxidative stress conditions. Real-time PCR and western blot analysis revealed that TaFBA1 expression was up-regulated by oxidative stress treatments. Under oxidative stress conditions, the transgenic tobacco plants showed a higher germination rate, higher root length and less growth inhibition than wild type (WT). The enhanced oxidative stress tolerance of the transgenic plants was also indicated by lower reactive oxygen species (ROS) accumulation, malondialdehyde (MDA) content and cell membrane damage under oxidative stress compared with WT. Higher activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD), were observed in the transgenic plants than those in WT, which may be related to the upregulated expression of some antioxidant genes via the overexpression of TaFBA1. In others, some stress responsive elements were found in the promoter region of TaFBA1, and TaFBA1 was located in the nucleus, cytoplasm and plasma membrane. These results suggest that TaFBA1 plays an important role in the oxidative stress tolerance of plants. This is important for understanding the functions of F-box proteins in plants’ tolerance to multiple stress conditions. PMID:25906259

Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase.

PubMed

Capodagli, Glenn C; Lee, Stephen A; Boehm, Kyle J; Brady, Kristin M; Pegan, Scott D

2014-12-09

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical data and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA's substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop's flexibility. Together the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.

Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans.

PubMed

Han, Xinya; Zhu, Xiuyun; Hong, Zongqin; Wei, Lin; Ren, Yanliang; Wan, Fen; Zhu, Shuaihua; Peng, Hao; Guo, Li; Rao, Li; Feng, Lingling; Wan, Jian

2017-06-26

Class II fructose-1,6-bisphosphate aldolases (FBA-II) are attractive new targets for the discovery of drugs to combat invasive fungal infection, because they are absent in animals and higher plants. Although several FBA-II inhibitors have been reported, none of these inhibitors exhibit antifungal effect so far. In this study, several novel inhibitors of FBA-II from C. albicans (Ca-FBA-II) with potent antifungal effects were rationally designed by jointly using a specific protocols of molecular docking-based virtual screening, accurate binding-conformation evaluation strategy, synthesis and enzymatic assays. The enzymatic assays reveal that the compounds 3c, 3e-g, 3j and 3k exhibit high inhibitory activity against Ca-FBA-II (IC 50 < 10 μM), and the most potential inhibitor is 3g, with IC 50 value of 2.7 μM. Importantly, the compounds 3f, 3g, and 3l possess not only high inhibitions against Ca-FBA-II, but also moderate antifungal activities against C. glabrata (MIC 80 = 4-64 μg/mL). The compounds 3g, 3l, and 3k in combination with fluconazole (8 μg/mL) displayed significantly synergistic antifungal activities (MIC 80 < 0.0625 μg/mL) against resistant Candida strains, which are resistant to azoles drugs. The probable binding modes between 3g and the active site of Ca-FBA-II have been proposed by using the DOX (docking, ONIOM, and XO) strategy. To our knowledge, no FBA-II inhibitors with antifungal activities against wild type and resistant strains from Candida were reported previously. The positive results suggest that the strategy adopted in this study are a promising method for the discovery of novel drugs against azole-resistant fungal pathogens in the future.

A Rational Design, Synthesis, Biological Evaluation and Structure--Activity Relationship Study of Novel Inhibitors against Cyanobacterial Fructose-1,6-bisphosphate Aldolase.

PubMed

Han, Xinya; Zhu, Xiuyun; Zhu, Shuaihua; Wei, Lin; Hong, Zongqin; Guo, Li; Chen, Haifeng; Chi, Bo; Liu, Yan; Feng, Lingling; Ren, Yanliang; Wan, Jian

2016-01-25

In the present study, a series of novel maleimide derivatives were rationally designed and optimized, and their inhibitory activities against cyanobacteria class-II fructose-1,6-bisphosphate aldolase (Cy-FBA-II) and Synechocystis sp. PCC 6803 were further evaluated. The experimental results showed that the introduction of a bigger group (Br, Cl, CH3, or C6H3-o-F) on the pyrrole-2',5'-dione ring resulted in a decrease in the Cy-FBA-II inhibitory activity of the hit compounds. Generally, most of the hit compounds with high Cy-FBA-II inhibitory activities could also exhibit high in vivo activities against Synechocystis sp. PCC 6803. Especially, compound 10 not only shows a high Cy-FBA-II activity (IC50 = 1.7 μM) but also has the highest in vivo activity against Synechocystis sp. PCC 6803 (EC50 = 0.6 ppm). Thus, compound 10 was selected as a representative molecule, and its probable interactions with the surrounding important residues in the active site of Cy-FBA-II were elucidated by the joint use of molecular docking, molecular dynamics simulations, ONIOM calculations, and enzymatic assays to provide new insight into the binding mode of the inhibitors and Cy-FBA-II. The positive results indicate that the design strategy used in the present study is very likely to be a promising way to find novel lead compounds with high inhibitory activities against Cy-FBA-II in the future. The enzymatic and algal inhibition assays suggest that Cy-FBA-II is very likely to be a promising target for the design, synthesis, and development of novel specific algicides to solve cyanobacterial harmful algal blooms.

A survey of functional behavior assessment methods used by behavior analysts in practice.

PubMed

Oliver, Anthony C; Pratt, Leigh A; Normand, Matthew P

2015-12-01

To gather information about the functional behavior assessment (FBA) methods behavior analysts use in practice, we sent a web-based survey to 12,431 behavior analysts certified by the Behavior Analyst Certification Board. Ultimately, 724 surveys were returned, with the results suggesting that most respondents regularly use FBA methods, especially descriptive assessments. Moreover, the data suggest that the majority of students are being formally taught about the various FBA methods and that educators are emphasizing the range of FBA methods in their teaching. However, less than half of the respondents reported using functional analyses in practice, although many considered descriptive assessments and functional analyses to be the most useful FBA methods. Most respondents reported using informant and descriptive assessments more frequently than functional analyses, and a majority of respondents indicated that they "never" or "almost never" used functional analyses to identify the function of behavior. © Society for the Experimental Analysis of Behavior.

Differential Development of Selectivity for Faces and Bodies in the Fusiform Gyrus

ERIC Educational Resources Information Center

Peelen, Marius V.; Glaser, Bronwyn; Vuilleumier, Patrik; Eliez, Stephan

2009-01-01

Viewing faces or bodies activates category-selective areas of visual cortex, including the fusiform face area (FFA), fusiform body area (FBA), and extrastriate body area (EBA). Here, using fMRI, we investigate the development of these areas, focusing on the right FFA and FBA. Despite the overlap of functionally defined FFA and FBA (54%-75%…

The role of the F-box gene TaFBA1 from wheat (Triticum aestivum L.) in drought tolerance.

PubMed

Zhou, Shumei; Sun, Xiudong; Yin, Suhong; Kong, Xiangzhu; Zhou, Shan; Xu, Ying; Luo, Yin; Wang, Wei

2014-11-01

Drought is one of the most important factors limiting plant growth and development. We identified a gene in wheat (Triticum aestivum L.) under drought stress named TaFBA1. TaFBA1 encodes a putative 325-amino-acid F-box protein with a conserved N-terminal F-box domain and a C-terminal AMN1 domain. Real-time RT-PCR analysis revealed that TaFBA1 transcript accumulation was upregulated by high-salinity, water stress, and abscisic acid (ABA) treatment. To evaluate the functions of TaFBA1 in the regulation of drought stress responses, we produced transgenic tobacco lines overexpressing TaFBA1. Under water stress conditions, the transgenic tobacco plants had a higher germination rate, higher relative water content, net photosynthesis rate (Pn), less chlorophyll loss, and less growth inhibition than WT. These results demonstrate the high tolerance of the transgenic plants to drought stress compared to the WT. The enhanced oxidative stress tolerance of these plants, which may be involved in their drought tolerance, was indicated by their lower levels of reactive oxygen species (ROS) accumulation, MDA content, and cell membrane damage under drought stress compared to WT. The antioxidant enzyme activities were higher in the transgenic plants than in WT, which may be related to the upregulated expression of some antioxidant genes via overexpression of TaFBA1. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Feature-based attention potentiates recovery of fine direction discrimination in cortically blind patients.

PubMed

Cavanaugh, Matthew R; Barbot, Antoine; Carrasco, Marisa; Huxlin, Krystel R

2017-12-10

Training chronic, cortically-blind (CB) patients on a coarse [left-right] direction discrimination and integration (CDDI) task recovers performance on this task at trained, blind field locations. However, fine direction difference (FDD) thresholds remain elevated at these locations, limiting the usefulness of recovered vision in daily life. Here, we asked if this FDD impairment can be overcome by training CB subjects with endogenous, feature-based attention (FBA) cues. Ten CB subjects were recruited and trained on CDDI and FDD with an FBA cue or FDD with a neutral cue. After completion of each training protocol, FDD thresholds were re-measured with both neutral and FBA cues at trained, blind-field locations and at corresponding, intact-field locations. In intact portions of the visual field, FDD thresholds were lower when tested with FBA than neutral cues. Training subjects in the blind field on the CDDI task improved FDD performance to the point that a threshold could be measured, but these locations remained impaired relative to the intact field. FDD training with neutral cues resulted in better blind field FDD thresholds than CDDI training, but thresholds remained impaired relative to intact field levels, regardless of testing cue condition. Importantly, training FDD in the blind field with FBA lowered FDD thresholds relative to CDDI training, and allowed the blind field to reach thresholds similar to the intact field, even when FBA trained subjects were tested with a neutral rather than FBA cue. Finally, FDD training appeared to also recover normal integration thresholds at trained, blind-field locations, providing an interesting double dissociation with respect to CDDI training. In summary, mechanisms governing FBA appear to function normally in both intact and impaired regions of the visual field following V1 damage. Our results mark the first time that FDD thresholds in CB fields have been seen to reach intact field levels of performance. Moreover, FBA can be leveraged during visual training to recover normal, fine direction discrimination and integration performance at trained, blind-field locations, potentiating visual recovery of more complex and precise aspects of motion perception in cortically-blinded fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of Paracoccidioides secreted proteins reveals fructose 1,6-bisphosphate aldolase as a plasminogen-binding protein.

PubMed

Chaves, Edilânia Gomes Araújo; Weber, Simone Schneider; Báo, Sonia Nair; Pereira, Luiz Augusto; Bailão, Alexandre Melo; Borges, Clayton Luiz; Soares, Célia Maria de Almeida

2015-02-27

Despite being important thermal dimorphic fungi causing Paracoccidioidomycosis, the pathogenic mechanisms that underlie the genus Paracoccidioides remain largely unknown. Microbial pathogens express molecules that can interact with human plasminogen, a protein from blood plasma, which presents fibrinolytic activity when activated into plasmin. Additionally, plasmin exhibits the ability of degrading extracellular matrix components, favoring the pathogen spread to deeper tissues. Previous work from our group demonstrated that Paracoccidioides presents enolase, as a protein able to bind and activate plasminogen, increasing the fibrinolytic activity of the pathogen, and the potential for adhesion and invasion of the fungus to host cells. By using proteomic analysis, we aimed to identify other proteins of Paracoccidioides with the ability of binding to plasminogen. In the present study, we employed proteomic analysis of the secretome, in order to identify plasminogen-binding proteins of Paracoccidioides, Pb01. Fifteen proteins were present in the fungal secretome, presenting the ability to bind to plasminogen. Those proteins are probable targets of the fungus interaction with the host; thus, they could contribute to the invasiveness of the fungus. For validation tests, we selected the protein fructose 1,6-bisphosphate aldolase (FBA), described in other pathogens as a plasminogen-binding protein. The protein FBA at the fungus surface and the recombinant FBA (rFBA) bound human plasminogen and promoted its conversion to plasmin, potentially increasing the fibrinolytic capacity of the fungus, as demonstrated in fibrin degradation assays. The addition of rFBA or anti-rFBA antibodies was capable of reducing the interaction between macrophages and Paracoccidioides, possibly by blocking the binding sites for FBA. These data reveal the possible participation of the FBA in the processes of cell adhesion and tissue invasion/dissemination of Paracoccidioides. These data indicate that Paracoccidioides is a pathogen that has several plasminogen-binding proteins that likely play important roles in pathogen-host interaction. In this context, FBA is a protein that might be involved somehow in the processes of invasion and spread of the fungus during infection.

Microscopic quantification of bacterial invasion by a novel antibody-independent staining method.

PubMed

Agerer, Franziska; Waeckerle, Stephanie; Hauck, Christof R

2004-10-01

Microscopic discrimination between extracellular and invasive, intracellular bacteria is a valuable technique in microbiology and immunology. We describe a novel fluorescence staining protocol, called FITC-biotin-avidin (FBA) staining, which allows the differentiation between extracellular and intracellular bacteria and is independent of specific antibodies directed against the microorganisms. FBA staining of eukaryotic cells infected with Gram-negative bacteria of the genus Neisseria or the Gram-positive pathogen Staphylococcus aureus are employed to validate the novel technique. The quantitative evaluation of intracellular pathogens by the FBA staining protocol yields identical results compared to parallel samples stained with conventional, antibody-dependent methods. FBA staining eliminates the need for cell permeabilization resulting in robust and rapid detection of invasive microbes. Taken together, FBA staining provides a reliable and convenient alternative for the differential detection of intracellular and extracellular bacteria and should be a valuable technical tool for the quantitative analysis of the invasive properties of pathogenic bacteria and other microorganisms.

Saccadic eye movements do not disrupt the deployment of feature-based attention.

PubMed

Kalogeropoulou, Zampeta; Rolfs, Martin

2017-07-01

The tight link of saccades to covert spatial attention has been firmly established, yet their relation to other forms of visual selection remains poorly understood. Here we studied the temporal dynamics of feature-based attention (FBA) during fixation and across saccades. Participants reported the orientation (on a continuous scale) of one of two sets of spatially interspersed Gabors (black or white). We tested performance at different intervals between the onset of a colored cue (black or white, indicating which stimulus was the most probable target; red: neutral condition) and the stimulus. FBA built up after cue onset: Benefits (errors for valid vs. neutral cues), costs (invalid vs. neutral), and the overall cueing effect (valid vs. invalid) increased with the cue-stimulus interval. Critically, we also tested visual performance at different intervals after a saccade, when FBA had been fully deployed before saccade initiation. Cueing effects were evident immediately after the saccade and were predicted most accurately and most precisely by fully deployed FBA, indicating that FBA was continuous throughout saccades. Finally, a decomposition of orientation reports into target reports and random guesses confirmed continuity of report precision and guess rates across the saccade. We discuss the role of FBA in perceptual continuity across saccades.

Software applications for flux balance analysis.

PubMed

Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

2014-01-01

Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers.

Incremental Contributions of FbaA and Other Impetigo-Associated Surface Proteins to Fitness and Virulence of a Classical Group A Streptococcal Skin Strain.

PubMed

Rouchon, Candace N; Ly, Anhphan T; Noto, John P; Luo, Feng; Lizano, Sergio; Bessen, Debra E

2017-11-01

Group A streptococci (GAS) are highly prevalent human pathogens whose primary ecological niche is the superficial epithelial layers of the throat and/or skin. Many GAS strains with a strong tendency to cause pharyngitis are distinct from strains that tend to cause impetigo; thus, genetic differences between them may confer host tissue-specific virulence. In this study, the FbaA surface protein gene was found to be present in most skin specialist strains but largely absent from a genetically related subset of pharyngitis isolates. In an Δ fbaA mutant constructed in the impetigo strain Alab49, loss of FbaA resulted in a slight but significant decrease in GAS fitness in a humanized mouse model of impetigo; the Δ fbaA mutant also exhibited decreased survival in whole human blood due to phagocytosis. In assays with highly sensitive outcome measures, Alab49ΔfbaA was compared to other isogenic mutants lacking virulence genes known to be disproportionately associated with classical skin strains. FbaA and PAM (i.e., the M53 protein) had additive effects in promoting GAS survival in whole blood. The pilus adhesin tip protein Cpa promoted Alab49 survival in whole blood and appears to fully account for the antiphagocytic effect attributable to pili. The finding that numerous skin strain-associated virulence factors make slight but significant contributions to virulence underscores the incremental contributions to fitness of individual surface protein genes and the multifactorial nature of GAS-host interactions. Copyright © 2017 American Society for Microbiology.

Structural and functional characterization of methicillin-resistant Staphylococcus aureus’s class IIb fructose 1,6-bisphosphate aldolase

DOE PAGES

Capodagli, Glenn C.; Lee, Stephen A.; Boehm, Kyle J.; ...

2014-11-12

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical datamore » and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop’s flexibility. Altogether the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.« less

Structural and functional characterization of methicillin-resistant Staphylococcus aureus’s class IIb fructose 1,6-bisphosphate aldolase

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

Capodagli, Glenn C.; Lee, Stephen A.; Boehm, Kyle J.

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical datamore » and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop’s flexibility. Altogether the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.« less

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

PubMed

Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2013-02-05

Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

SYMBMAT: Symbolic computation of quantum transition matrix elements

NASA Astrophysics Data System (ADS)

Ciappina, M. F.; Kirchner, T.

2012-08-01

We have developed a set of Mathematica notebooks to compute symbolically quantum transition matrices relevant for atomic ionization processes. The utilization of a symbolic language allows us to obtain analytical expressions for the transition matrix elements required in charged-particle and laser induced ionization of atoms. Additionally, by using a few simple commands, it is possible to export these symbolic expressions to standard programming languages, such as Fortran or C, for the subsequent computation of differential cross sections or other observables. One of the main drawbacks in the calculation of transition matrices is the tedious algebraic work required when initial states other than the simple hydrogenic 1s state need to be considered. Using these notebooks the work is dramatically reduced and it is possible to generate exact expressions for a large set of bound states. We present explicit examples of atomic collisions (in First Born Approximation and Distorted Wave Theory) and laser-matter interactions (within the Dipole and Strong Field Approximations and different gauges) using both hydrogenic wavefunctions and Slater-Type Orbitals with arbitrary nlm quantum numbers as initial states. Catalogue identifier: AEMI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 71 628 No. of bytes in distributed program, including test data, etc.: 444 195 Distribution format: tar.gz Programming language: Mathematica Computer: Single machines using Linux or Windows (with cores with any clock speed, cache memory and bits in a word) Operating system: Any OS that supports Mathematica. The notebooks have been tested under Windows and Linux and with versions 6.x, 7.x and 8.x Classification: 2.6 Nature of problem: The notebooks generate analytical expressions for quantum transition matrix elements required in diverse atomic processes: ionization by ion, electron, or photon impact and ionization within the framework of strong field physics. In charged-particle collisions approaches based on perturbation theory enjoy widespread utilization. Accordingly, we have chosen the First Born Approximation and Distorted Wave theories as examples. In light-matter interactions, the main ingredient for many types of calculations is the dipole transition matrix in its different formulations, i.e. length, velocity, and acceleration gauges. In all these cases the transitions of interest occur between a bound state and a continuum state which can be described in different ways. With the notebooks developed in the present work it is possible to calculate transition matrix elements analytically for any set of quantum numbers nlm of initial hydrogenic states or Slater-Type Orbitals and for plane waves or Coulomb waves as final continuum states. Solution method: The notebooks employ symbolic computation to generate analytical expressions for transition matrix elements used in both collision and light-matter interaction physics. fba_hyd.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in the First Born Approximation (FBA). The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a plane wave (PW) or a Coulomb wave (CW). distorted_hyd.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in Distorted Wave (DW) theories. The transitions considered are from a (distorted) bound hydrogenic state with arbitrary quantum numbers nlm to a distorted-wave continuum state. The computations are based on scalar and vectorial integrals (see the text for details). dipoleLength_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in length gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the Strong Field Approximation (SFA)) or a CW (the Coulomb-Volkov Approximation (CVA)). dipoleVelocity_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in velocity gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleAcceleration_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in acceleration gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA). For the case of the CVA we only include the transition from the 1s state to a continuum state represented by a CW. fba_STO.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in the FBA. The transitions considered are from a Slater-Type Orbital (STO) with arbitrary quantum numbers nlm to a continuum state represented by a PW or a CW. distorted_STO.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in DW theories. The transitions considered are from a (distorted) STO with arbitrary quantum numbers nlm to a distorted-wave continuum state. The computations are based on scalar and vectorial integrals (see the text for details). dipoleLength_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in length gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleVelocity_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in velocity gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleAcceleration_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in acceleration gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA). The symbolic expressions obtained within each notebook can be exported to standard programming languages such as Fortran or C using the Format.m package (see the text and Ref. Sofroniou (1993) [16] for details). Running time: Computational times vary according to the transition matrix selected and quantum numbers nlm of the initial state used. The typical running time is several minutes, but it will take longer for large values of nlm.

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

DOE PAGES

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe; ...

2017-04-07

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

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

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less

Fructose bisphosphate aldolase is involved in the control of RNA polymerase III-directed transcription.

PubMed

Cieśla, Małgorzata; Mierzejewska, Jolanta; Adamczyk, Małgorzata; Farrants, Ann-Kristin Östlund; Boguta, Magdalena

2014-06-01

Yeast Fba1 (fructose 1,6-bisphosphate aldolase) is a glycolytic enzyme essential for viability. The overproduction of Fba1 enables overcoming of a severe growth defect caused by a missense mutation rpc128-1007 in a gene encoding the C128 protein, the second largest subunit of the RNA polymerase III complex. The suppression of the growth phenotype by Fba1 is accompanied by enhanced de novo tRNA transcription in rpc128-1007 cells. We inactivated residues critical for the catalytic activity of Fba1. Overproduction of inactive aldolase still suppressed the rpc128-1007 phenotype, indicating that the function of this glycolytic enzyme in RNA polymerase III transcription is independent of its catalytic activity. Yeast Fba1 was determined to interact with the RNA polymerase III complex by coimmunoprecipitation. Additionally, a role of aldolase in control of tRNA transcription was confirmed by ChIP experiments. The results indicate a novel direct relationship between RNA polymerase III transcription and aldolase. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure-based prediction and identification of 4-epimerization activity of phosphate sugars in class II aldolases.

PubMed

Lee, Seon-Hwa; Hong, Seung-Hye; An, Jung-Ung; Kim, Kyoung-Rok; Kim, Dong-Eun; Kang, Lin-Woo; Oh, Deok-Kun

2017-05-16

Sugar 4-epimerization reactions are important for the production of rare sugars and their derivatives, which have various potential industrial applications. For example, the production of tagatose, a functional sweetener, from fructose by sugar 4-epimerization is currently constrained because a fructose 4-epimerase does not exist in nature. We found that class II D-fructose-1,6-bisphosphate aldolase (FbaA) catalyzed the 4-epimerization of D-fructose-6-phosphate (F6P) to D-tagatose-6-phosphate (T6P) based on the prediction via structural comparisons with epimerase and molecular docking and the identification of the condensed products of C3 sugars. In vivo, the 4-epimerization activity of FbaA is normally repressed. This can be explained by our results showing the catalytic efficiency of D-fructose-6-phosphate kinase for F6P phosphorylation was significantly higher than that of FbaA for F6P epimerization. Here, we identified the epimerization reactions and the responsible catalytic residues through observation of the reactions of FbaA and L-rhamnulose-1-phosphate aldolases (RhaD) variants with substituted catalytic residues using different substrates. Moreover, we obtained detailed potential epimerization reaction mechanism of FbaA and a general epimerization mechanism of the class II aldolases L-fuculose-1-phosphate aldolase, RhaD, and FbaA. Thus, class II aldolases can be used as 4-epimerases for the stereo-selective synthesis of valuable carbohydrates.

Capturing the essence of a metabolic network: a flux balance analysis approach.

PubMed

Murabito, Ettore; Simeonidis, Evangelos; Smallbone, Kieran; Swinton, Jonathan

2009-10-07

As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux balance analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented. Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here, we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of an FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole. Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined.

Fructose-bisphosphate aldolase and pyruvate kinase, two novel immunogens in Madurella mycetomatis.

PubMed

de Klerk, Nele; de Vogel, Corné; Fahal, Ahmed; van Belkum, Alex; van de Sande, Wendy W J

2012-02-01

Eumycetoma, a chronic granulomatous disease characterized by a subcutaneous mass, multiple sinuses and purulent discharge containing grains, remains difficult to diagnose and treat. Madurella mycetomatis is the most common causative agent of eumycetoma. Using a serum pool from patients with active mycetoma, we screened a M. mycetomatis-specific λgt11 cDNA library which was shown to contain 8% of cDNA inserts encoding proteins involved in glycolysis. Two of these enzymes, fructose-bisphosphate aldolase (FBA) and pyruvate kinase (PK), were produced in vitro and their antigenicity was studied with bead-based flow cytometry. It appeared that both FBA and PK IgG antibodies were present in eumycetoma patient sera. However, only FBA antibody levels were found to be significantly higher in eumycetoma patient sera when compared to healthy Sudanese controls. Furthermore, FBA and PK were also found to be expressed on the hyphae present in the mycetoma grain. In conclusion, this study presents two new antigenic proteins of M. mycetomatis next to the translationally controlled tumour protein (TCTP): the glycolytic enzymes FBA and PK. These antigens might be useful as vaccine-candidates in the prevention of mycetoma.

fMRI-adaptation studies of viewpoint tuning in the extrastriate and fusiform body areas.

PubMed

Taylor, John C; Wiggett, Alison J; Downing, Paul E

2010-03-01

People are easily able to perceive the human body across different viewpoints, but the neural mechanisms underpinning this ability are currently unclear. In three experiments, we used functional MRI (fMRI) adaptation to study the view-invariance of representations in two cortical regions that have previously been shown to be sensitive to visual depictions of the human body--the extrastriate and fusiform body areas (EBA and FBA). The BOLD response to sequentially presented pairs of bodies was treated as an index of view invariance. Specifically, we compared trials in which the bodies in each image held identical poses (seen from different views) to trials containing different poses. EBA and FBA adapted to identical views of the same pose, and both showed a progressive rebound from adaptation as a function of the angular difference between views, up to approximately 30 degrees. However, these adaptation effects were eliminated when the body stimuli were followed by a pattern mask. Delaying the mask onset increased the response (but not the adaptation effect) in EBA, leaving FBA unaffected. We interpret these masking effects as evidence that view-dependent fMRI adaptation is driven by later waves of neuronal responses in the regions of interest. Finally, in a whole brain analysis, we identified an anterior region of the left inferior temporal sulcus (l-aITS) that responded linearly to stimulus rotation, but showed no selectivity for bodies. Our results show that body-selective cortical areas exhibit a similar degree of view-invariance as other object selective areas--such as the lateral occipitotemporal area (LO) and posterior fusiform gyrus (pFs).

Microcompartmentation of cytosolic aldolase by interaction with the actin cytoskeleton in Arabidopsis.

PubMed

Garagounis, Constantine; Kostaki, Kalliopi-Ioanna; Hawkins, Tim J; Cummins, Ian; Fricker, Mark D; Hussey, Patrick J; Hetherington, Alistair M; Sweetlove, Lee J

2017-02-01

Evidence is accumulating for molecular microcompartments formed when proteins interact in localized domains with the cytoskeleton, organelle surfaces, and intracellular membranes. To understand the potential functional significance of protein microcompartmentation in plants, we studied the interaction of the glycolytic enzyme fructose bisphosphate aldolase with actin in Arabidopsis thaliana. Homology modelling of a major cytosolic isozyme of aldolase, FBA8, suggested that the tetrameric holoenzyme has two actin binding sites and could therefore act as an actin-bundling protein, as was reported for animal aldolases. This was confirmed by in vitro measurements of an increase in viscosity of F-actin polymerized in the presence of recombinant FBA8. Simultaneously, interaction with F-actin caused non-competitive inhibition of aldolase activity. We did not detect co-localization of an FBA8-RFP fusion protein, expressed in an fba8-knockout background, with the actin cytoskeleton using confocal laser-scanning microscopy. However, we did find evidence for a low level of interaction using FRET-FLIM analysis of FBA8-RFP co-expressed with the actin-binding protein GFP-Lifeact. Furthermore, knockout of FBA8 caused minor alterations of guard cell actin cytoskeleton morphology and resulted in a reduced rate of stomatal closure in response to decreased humidity. We conclude that cytosolic aldolase can be microcompartmented in vivo by interaction with the actin cytoskeleton and may subtly modulate guard cell behaviour as a result. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Structural Basis for Catalysis of a Tetrameric Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Ruskseree, Kamolchanok; Franzblau, Scott G.

2009-03-04

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), currently infects one-third of the world's population in its latent form. The emergence of multidrug-resistant and extensive drug-resistant strains has highlighted the need for new pharmacological targets within M. tuberculosis. The class IIa fructose 1,6-bisphosphate aldolase (FBA) enzyme from M. tuberculosis (MtFBA) has been proposed as one such target since it is upregulated in latent TB. Since the structure of MtFBA has not been determined and there is little information available on its reaction mechanism, we sought to determine the X-ray structure of MtFBA in complex with its substrates. By lowering themore » pH of the enzyme in the crystalline state, we were able to determine a series of high-resolution X-ray structures of MtFBA bound to dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, and fructose 1,6-bisphosphate at 1.5, 2.1, and 1.3 {angstrom}, respectively. Through these structures, it was discovered that MtFBA belongs to a novel tetrameric class of type IIa FBAs. The molecular details at the interface of the tetramer revealed important information for better predictability of the quaternary structures among the FBAs based on their primary sequences. These X-ray structures also provide interesting and new details on the reaction mechanism of class II FBAs. Substrates and products were observed in geometries poised for catalysis; in addition, unexpectedly, the hydroxyl-enolate intermediate of dihydroxyacetone phosphate was also captured and resolved structurally. These concise new details offer a better understanding of the reaction mechanisms for FBAs in general and provide a structural basis for inhibitor design efforts aimed at this class of enzymes.« less

Structural basis for catalysis of a tetrameric, class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Franzblau, Scott G.; Mesecar, Andrew D.

2009-01-01

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), currently infects one third of the world’s population in its latent form. The emergence of multidrug resistant strains, MDR-TB and XDR-TB has highlighted the need for new pharmacological targets within M. tuberculosis. The Class IIa fructose 1,6-bisphosphate aldolase (FBA) enzyme from M. tuberculosis (MtFBA) has been proposed as one such target since its upregulated in latent TB. Since the structure of MtFBA had not been determined and since there was little information available on its reaction mechanism, we sought to determine the X-ray structure of MtFBA in complex with its substrates. By lowering the pH of the enzyme in the crystalline state, we were able to determine a series of high-resolution X-ray structures of MtFBA bound to dihydroxyacetonephosphate (DHAP), glyceraldehyde-3-phosphate (G3P), and fructose 1,6-bisphosphate (FBP) at 1.5 Å, 2.1 Å, and 1.3 Å respectively. Through these structures it was discovered that MtFBA belongs to a novel tetrameric class of the type IIa FBAs. The molecular details at the interface of the tetramer revealed important information for being able to better predict the quaternary structures among the FBAs based on their primary sequences. These X-ray structures also provide interesting and new details on the reaction mechanism of class II FBAs. Not only were the substrates and products observed in geometries poised for catalysis, but unexpectedly the hydroxyl enolate intermediate of DHAP was also captured and resolved structurally. These concise new details provide a better understanding of the reaction mechanisms for FBAs in general and provide a structural basis for inhibitor design efforts aimed at this class of enzymes. PMID:19167403

Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less

Glycolytic enzymes associated with the cell surface of Streptococcus pneumoniae are antigenic in humans and elicit protective immune responses in the mouse

PubMed Central

LING, E; FELDMAN, G; PORTNOI, M; DAGAN, R; OVERWEG, K; MULHOLLAND, F; CHALIFA-CASPI, V; WELLS, J; MIZRACHI-NEBENZAHL, Y

2004-01-01

Streptococcus pneumoniae is a leading cause of otitis media, sinusitis, pneumonia, bacteraemia and meningitis worldwide. The drawbacks associated with the limited number of various capsular polysaccharides that can be included in the polysaccharide-based vaccines focuses much attention on pneumococcal proteins as vaccine candidates. We extracted an enriched cell wall fraction from S. pneumoniae WU2. Approximately 150 soluble proteins could be identified by 2D gel electrophoresis. The proteins were screened by 2D-Western blotting using sera that were obtained longitudinally from children attending day-care centres at 18, 30 and 42 months of age and sera from healthy adult volunteers. The proteins were further identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Seventeen proteins were antigenic in children and adults, of which 13 showed an increasing antibody response with age in all eight children analysed. Two immunogenic proteins, fructose–bisphosphate aldolase (FBA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a control protein with known low immunogenicity, heat shock protein 70 (DnaK), were expressed in Escherichia coli, purified and used to immunize mice. Mouse antibodies elicited to the recombinant (r) FBA and rGAPDH were cross-reactive with several genetically unrelated strains of different serotypes and conferred protection to respiratory challenge with virulent pneumococci. In addition, the FBA used in this study (NP_345117) does not have a human ortholog and warrants further investigation as a candidate for a pneumococcal vaccine. In conclusion, the immunoproteomics based approach utilized in the present study appears to be a suitable tool for identification of novel S. pneumoniae vaccine candidates. PMID:15498039

Turbidimetric and photometric determination of total tannins in tea using a micro-flow-batch analyzer.

PubMed

Lima, Marcelo B; Andrade, Stéfani I E; Harding, David P; Pistonesi, Marcelo F; Band, Beatriz S F; Araújo, Mário C U

2012-01-15

Both turbidimetric and photometric determinations of total tannins in samples of green and black tea, using a micro-flow-batch analyzer (μFBA) were studied. The miniaturized system was formed using photocurable urethane-acrylate resin and ultraviolet lithography technique. The turbidimetric method was based on the precipitation reaction of Cu (II) with tannins in acetate medium at a pH of 4.5. The photometric method was based on the complexation reaction of tannins with ferrous tartrate. The turbidimetric μFBA was able to test 200 samples per hour. The photometric μFBA allowed 300 analyses per hour, generating 136μL of residue per analysis. The paired t test, at a 95% confidence level, showed no statistically significant differences between results obtained by both methods and the reference method. The urethane-acrylate μFBA maintained satisfactory physical and chemical properties, and represents an improvement over conventional flow-batch analyzer. Copyright © 2011 Elsevier B.V. All rights reserved.

Foreign body aspiration in children: A study of children who lived or died following aspiration.

PubMed

Mohammad, Maha; Saleem, Mohammad; Mahseeri, Mohamad; Alabdallat, Imad; Alomari, Ali; Za'atreh, Ala'; Qudaisat, Ibraheem; Shudifat, Abdulrahman; Nasri Alzoubi, Mohammad

2017-07-01

Foreign body aspiration (FBA) is a preventable cause of mortality and morbidity in children. We conducted a chart review of children who presented to a university hospital due to FBA in the period 1999-2014. Children were either managed with bronchoscopy for removal of the foreign body or died due to FBA. A total of 103 children were seen due to FBA including 27 deaths. The majority of children were boys and were less than 3 years old. Most aspirated foreign bodies were food-related, mainly peanuts. The majority of children presented with acute choking incidents, a smaller number presented with recurrent chest infections, and few children's choking incidents were unwitnessed. X-ray had a high rate of false negatives and bronchoscopy was the gold standard technique for assessment and management. Aspiration of foreign bodies is a preventable, life-threatening condition that calls for increased parent education and awareness. Copyright © 2017 Elsevier B.V. All rights reserved.

Neural correlates of human body perception.

PubMed

Aleong, Rosanne; Paus, Tomás

2010-03-01

The objective of this study was to investigate potential sex differences in the neural response to human bodies using fMRI carried out in healthy young adults. We presented human bodies in a block-design experiment to identify body-responsive regions of the brain, namely, extrastriate body area (EBA) and fusiform body area (FBA). In a separate event-related "adaptation" experiment, carried out in the same group of subjects, we presented sets of four human bodies of varying body size and shape. Varying levels of body morphing were introduced to assess the degree of morphing required for adaptation release. Analysis of BOLD signal in the block-design experiment revealed significant Sex x Hemisphere interactions in the EBA and the FBA responses to human bodies. Only women showed greater BOLD response to bodies in the right hemisphere compared with the left hemisphere for both EBA and FBA. The BOLD response in right EBA was higher in women compared with men. In the adaptation experiment, greater right versus left hemisphere response for EBA and FBA was also identified among women but not men. These findings are particularly novel in that they address potential sex differences in the lateralization of EBA and FBA responses to human body images. Although previous studies have found some degree of right hemisphere dominance in body perception, our results suggest that such a functional lateralization may differ between men and women.

Improving Preservice Teachers' Knowledge and Application of Functional Behavioral Assessments Using Multimedia

ERIC Educational Resources Information Center

Hirsch, Shanna Eisner; Kennedy, Michael J.; Haines, Shana J.; Thomas, Cathy Newman; Alves, Kat D.

2015-01-01

Functional behavioral assessment (FBA) is an empirically supported intervention associated with decreasing problem behavior and increasing appropriate behavior. To date, few studies have examined multimedia approaches to FBA training. This paper provides the outcomes of a randomized controlled trial across three university sites and evaluates…

A Survey of Functional Behavior Assessment Methods Used by Behavior Analysts in Practice

ERIC Educational Resources Information Center

Oliver, Anthony C.; Pratt, Leigh A.; Normand, Matthew P.

2015-01-01

To gather information about the functional behavior assessment (FBA) methods behavior analysts use in practice, we sent a web-based survey to 12,431 behavior analysts certified by the Behavior Analyst Certification Board. Ultimately, 724 surveys were returned, with the results suggesting that most respondents regularly use FBA methods, especially…

Functional Behavioral Assessment State Policies and Procedures. Quick Turn Around (QTA).

ERIC Educational Resources Information Center

National Association of State Directors of Special Education, Alexandria, VA.

This brief report provides an analysis of survey data collected from 45 states and territories about policies, procedures, and guidelines related to Functional Behavioral Assessment (FBA), plans to develop or revise policy in this area, and technical assistance needs related to FBA, especially for students who exhibit behavior that interferes with…

Examining the Efficacy of a Basic Functional Behavioral Assessment Training Package for School Personnel

ERIC Educational Resources Information Center

Loman, Sheldon L.; Horner, Robert H.

2014-01-01

This study evaluated the effects of manualized training in "Basic" functional behavioral assessment (FBA) for typical school professionals on the ability of these professionals to complete technically adequate FBAs. Twelve school professionals participated in four 1-hr training sessions using the Basic FBA training handbook. After…

Early Childhood Practitioner Involvement in Functional Behavioral Assessment and Function-Based Interventions: A Literature Review

ERIC Educational Resources Information Center

Wood, Brenna K.; Drogan, Robin R.; Janney, Donna M.

2014-01-01

Reviewers analyzed studies published from 1990 to 2012 to determine early childhood practitioner involvement in functional behavioral assessment (FBA) and function-based behavioral intervention plans (BIP) for children with challenging behavior, age 6 and younger. Coding of 30 studies included practitioner involvement in FBA and BIP processes,…

Improving Outcomes of Behavioral Intervention Plans

ERIC Educational Resources Information Center

Walker, Jennifer D.; Barry, Colleen

2017-01-01

According to federal mandates, if a student's behavior impedes their learning or the learning of others, the individualized education program team is required to address this with a functional behavioral assessment (FBA). The intent of the FBA is to determine the function, or reason, of the impeding behavior for the development of a behavioral…

FBA and BIP: Increasing the Behavior Adjustment of African American Boys in Schools

ERIC Educational Resources Information Center

Lo, Ya-yu; Cartledge, Gwendolyn

2006-01-01

Overrepresentation of African American boys in disciplinary and special education referrals has been a national concern. This study used functional behavioral assessments (FBAs) and behavioral intervention plans (BIPs) as a means to prevent disproportionality of African American boys. Based on FBA results, interventions were developed for four…

In vivo and in silico determination of essential genes of Campylobacter jejuni.

PubMed

Metris, Aline; Reuter, Mark; Gaskin, Duncan J H; Baranyi, Jozsef; van Vliet, Arnoud H M

2011-11-01

In the United Kingdom, the thermophilic Campylobacter species C. jejuni and C. coli are the most frequent causes of food-borne gastroenteritis in humans. While campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases Guillain-Barré syndrome. The rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predictions of metabolism and physiology of pathogenic micro-organisms. When combined, these datasets may allow for the identification of potential weaknesses that can be used for development of new antimicrobials to reduce or eliminate C. jejuni and C. coli from the food chain. A metabolic model of C. jejuni was constructed using the annotation of the NCTC 11168 genome sequence, a published model of the related bacterium Helicobacter pylori, and extensive literature mining. Using this model, we have used in silico Flux Balance Analysis (FBA) to determine key metabolic routes that are essential for generating energy and biomass, thus creating a list of genes potentially essential for growth under laboratory conditions. To complement this in silico approach, candidate essential genes have been determined using a whole genome transposon mutagenesis method. FBA and transposon mutagenesis (both this study and a published study) predict a similar number of essential genes (around 200). The analysis of the intersection between the three approaches highlights the shikimate pathway where genes are predicted to be essential by one or more method, and tend to be network hubs, based on a previously published Campylobacter protein-protein interaction network, and could therefore be targets for novel antimicrobial therapy. We have constructed the first curated metabolic model for the food-borne pathogen Campylobacter jejuni and have presented the resulting metabolic insights. We have shown that the combination of in silico and in vivo approaches could point to non-redundant, indispensable genes associated with the well characterised shikimate pathway, and also genes of unknown function specific to C. jejuni, which are all potential novel Campylobacter intervention targets.

Self-Adjuvanting Glycopeptide Conjugate Vaccine against Disseminated Candidiasis

PubMed Central

Xin, Hong; Cartmell, Jonathan; Bailey, Justin J.; Dziadek, Sebastian; Bundle, David R.; Cutler, Jim E.

2012-01-01

Our research on pathogenesis of disseminated candidiasis led to the discovery that antibodies specific for Candida albicans cell surface β-1, 2–mannotriose [β-(Man)3] protect mice. A 14 mer peptide Fba, which derived from the N-terminal portion of the C. albicans cytosolic/cell surface protein fructose-bisphosphate aldolase, was used as the glycan carrier and resulted in a novel synthetic glycopeptide vaccine β-(Man)3-Fba. By a dendritic cell-based immunization approach, this conjugate induced protective antibody responses against both the glycan and peptide parts of the vaccine. In this report, we modified the β-(Man)3-Fba conjugate by coupling it to tetanus toxoid (TT) in order to improve immunogenicity and allow for use of an adjuvant suitable for human use. By new immunization procedures entirely compatible with human use, the modified β-(Man)3-Fba-TT was administered either alone or as a mixture made with alum or monophosphoryl lipid A (MPL) adjuvants and given to mice by a subcutaneous (s.c.) route. Mice vaccinated with or, surprisingly, without adjuvant responded well by making robust antibody responses. The immunized groups showed a high degree of protection against a lethal challenge with C. albicans as evidenced by increased survival times and reduced kidney fungal burden as compared to control groups that received only adjuvant or DPBS buffer prior to challenge. To confirm that induced antibodies were protective, sera from mice immunized against the β-(Man)3-Fba-TT conjugate transferred protection against disseminated candidiasis to naïve mice, whereas C. albicans-absorbed immune sera did not. Similar antibody responses and protection induced by the β-(Man)3-Fba-TT vaccine was observed in inbred BALB/c and outbred Swiss Webster mice. We conclude that addition of TT to the glycopeptide conjugate results in a self-adjuvanting vaccine that promotes robust antibody responses without the need for additional adjuvant, which is novel and represents a major step forward in vaccine design against disseminated candidiasis. PMID:22563378

Using Multimodal Functional Behavioral Assessment to Inform Treatment Selection for Children with Either Emotional Disturbance or Social Maladjustment

ERIC Educational Resources Information Center

Miller, Jeffrey A.; Williams, Shelagh J.; McCoy, Erika L. B.

2004-01-01

Functional behavioral assessment (FBA) is an assessment procedure used to identify the reasons for children's misbehavior. In this article we provide an overview of one approach to FBA known as "multimodal functional behavioral assessment" (MFBA) that provides a comprehensive examination of the causes of children's disruptive behavior. The…

Professional Development and Learning by General Teachers Implementing Functional Behavioural Assessment in Thai Inclusive Classrooms

ERIC Educational Resources Information Center

Opartkiattikul, Watinee; Arthur-Kelly, Michael; Dempsey, Ian

2016-01-01

Functional Behavioural Assessment (FBA) is identified as a research-based approach used in many Western schools to support student behaviour. This study aimed to assist Thai classroom teachers by providing a professional development and learning programme in FBA to develop an effective and efficient process to address behaviour problems and allow…

Investigation on the Practice of the Functional Behavioral Assessment: Survey of Educators and Their Experiences in the Field

ERIC Educational Resources Information Center

Moreno, Gerardo; Wong-Lo, Mickie; Bullock, Lyndal M.

2017-01-01

The functional behavioral assessment (FBA) has been a hallmark practice amongst educators working with students demonstrating challenging behaviors. Although the process has been mandated in special education since the Individuals with Disabilities Education Act of 1997, the FBA varies in form and implementation across the United States of America…

From FBA to Implementation: A Look at What Is Actually Being Delivered

ERIC Educational Resources Information Center

Blood, Erika; Neel, Richard S.

2007-01-01

This study looks at the utilization of assessments on developing behavior intervention plans (BIPs) and their use in designing actual implementation for the children (elementary through high school) labeled EBD in a mid-sized district in eastern Washington. Files were reviewed to determine the types of assessments used, FBA components addressed,…

Special Considerations for Using Functional Behavior Assessment and Functionally-Indicated Interventions with Students in Alternative Educational Settings

ERIC Educational Resources Information Center

Ennis, Robin Parks; Jolivette, Kristine; Swoszowski, Nicole Cain

2017-01-01

Functional behavior assessment (FBA) is the process of collecting data to determine the function of an individual's behavior to develop a functionally-indicated behavioral intervention (BIP). Special adaptations may be needed to conduct FBA and implement BIPs in alternative educational settings. In this article, we highlight suggestions for…

FBAs and BIPs: Avoiding and Addressing Four Common Challenges Related to Fidelity

ERIC Educational Resources Information Center

Hirsch, Shanna E.; Bruhn, Allison L.; Lloyd, John Wills; Katsiyannis, Antonis

2017-01-01

There is substantial empirical evidence that the Functional Behavioral Assessment (FBA) process is an effective means to reduce student problem behavior and increase desirable behaviors (e.g., What Works Clearinghouse, 2016). The use of an FBA as the basis for a behavior intervention plan (BIP) has been a requirement for certain disciplinary…

Training School Personnel to Identify Interventions Based on Functional Behavioral Assessment

ERIC Educational Resources Information Center

Borgmeier, Chris; Loman, Sheldon L.; Hara, Motoaki; Rodriguez, Billie Jo

2015-01-01

Over 15 years after passage of legislation requiring the use of functional behavioral assessment (FBA) to inform the development of positive behavior support plans (BSPs) in special education, schools are still struggling to implement BSPs based on FBA and the function of behavior. A primary concern is that school teams regularly fail to use…

Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

PubMed Central

Rogers, Matthew B; Patron, Nicola J; Keeling, Patrick J

2007-01-01

Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA) are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes) of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group. PMID:17584924

Functional Behavior Assessment and Function-Based Intervention Planning: Considering the Simple Logic of the Process

ERIC Educational Resources Information Center

Scott, Terrance M.; Cooper, Justin T.

2017-01-01

While functional behavior assessment (FBA) has been a part of special education law and embedded in Individuals With Disabilities Education Act (IDEA) since 1997, a precise definition of what actions or processes constitute a legal FBA has never been adequately addressed in the law. This article provides an overview of the underlying logic of FBA…

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

PubMed

Chen, Xuewen; Alonso, Ana P; Allen, Doug K; Reed, Jennifer L; Shachar-Hill, Yair

2011-01-01

Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes. © 2010 Elsevier Inc. All rights reserved.

Vaccine and Monoclonal Antibody That Enhance Mouse Resistance to Candidiasis ▿

PubMed Central

Xin, Hong; Cutler, Jim E.

2011-01-01

Previously we showed that antibodies specific for the glycan β-1,2-mannotriose [β-(Man)3] on the cell surface of Candida albicans protect mice against disseminated candidiasis (H. Xin, S. Dziadek, D. R. Bundle, and J. E. Cutler, Proc. Natl. Acad. Sci. U. S. A. 105:13526–13531, 2008). Furthermore, six 14-mer peptides that are within the N-terminal portion of C. albicans wall proteins were conjugated to the glycan in an attempt to create immunogenic glycopeptide conjugates. By a dendritic cell (DC)-based immunization approach, all were immunogenic and three of the six conjugates induced a high degree of protection in mice. Interestingly, whereas all six peptides induced antibody responses when used alone to pulse DCs for subsequent immunizations, three peptides induced protection, and one in particular, peptide Fba (derived from fructose-bisphosphate aldolase), induced robust protective responses and is the focus of the current work. Fba peptide is not restricted by the major histocompatibility complex class II (MHC-II), as it induced anti-Fba antibodies in mice of different H-2 haplotypes and in rabbits. Furthermore, the peptide induced protection against disease caused by different C. albicans strains. Partial protection was achieved when alum was used in place of DCs for Fba immunizations. The passive transfer of immune sera from Fba-vaccinated mice, but not immune serum preabsorbed with fungal cells, conferred protection in naïve mice. This result, along with our finding that a monoclonal antibody specific for the peptide, E2-9 (IgM), protected mice against candidiasis, provide strong evidence that antibodies contribute to protection. Our work demonstrates the utility of cell wall peptides alone or as glycopeptides in vaccines designed for the induction of immunity against candidiasis and monoclonal antibodies as a rapid immunoprotective approach against the disease. PMID:21832099

Diagnostic value of immunoglobulin G antibodies against Candida enolase and fructose-bisphosphate aldolase for candidemia

PubMed Central

2013-01-01

Background The yeast Candida is one of the most frequent pathogens isolated from bloodstream infections and is associated with significant morbidity and mortality. Problems with clinical and microbiological diagnosis of invasive candidiasis (IC) have prompted the development of non-culture-based laboratory methods. Previous reports suggest that serological detection of antibodies might be useful for diagnosing systemic candidiasis. Methods Diagnosis of IC using antibodies against recombinant Candida albicans enolase (Eno) and fructose-bisphosphate aldolase (Fba1) was evaluated. Using recombinant Eno and Fba1 as coating antigens, enzyme-linked immunosorbent assays (ELISAs) were used to analyze sera from patients with candidemia (n = 101), Candida colonization (n = 50), bacteremia (n = 84), invasive aspergillosis (n = 40); and from healthy controls (n = 200). Results The results demonstrated that ELISA detection of anti-Eno and anti-Fba1 IgG distinguished IC from other pathogenic infections in patients and healthy individuals. The sensitivity, specificity, and positive and negative predictive values were 72.3%, 94.7%, 78.5% and 93% for anti-Eno, and 87.1%, 92.8%, 76.5% and 96.4% for anti-Fba1 antibodies, respectively. Combining these two tests improved sensitivity up to 90.1% and negative predictive value up to 97.1%, with specificity and positive predictive values of 90.6% and 72.2%. The tests were specific to the Candida genus and antibody titers were higher for candidemia patients than for controls. Positive antibody tests were obtained before blood culture results for 42.2% of patients for anti-Eno and 51.1% for anti-Fba1. Conclusion These data suggest that tests that detect IgG antibodies against Candida enolase and fructose-bisphosphate aldolase, especially when used in combination, could be a powerful tool for diagnosing IC. PMID:23725337

Diagnostic value of immunoglobulin G antibodies against Candida enolase and fructose-bisphosphate aldolase for candidemia.

PubMed

Li, Fang-Qiu; Ma, Chun-Fang; Shi, Li-Ning; Lu, Jing-Fen; Wang, Ying; Huang, Mei; Kong, Qian-Qian

2013-05-31

The yeast Candida is one of the most frequent pathogens isolated from bloodstream infections and is associated with significant morbidity and mortality. Problems with clinical and microbiological diagnosis of invasive candidiasis (IC) have prompted the development of non-culture-based laboratory methods. Previous reports suggest that serological detection of antibodies might be useful for diagnosing systemic candidiasis. Diagnosis of IC using antibodies against recombinant Candida albicans enolase (Eno) and fructose-bisphosphate aldolase (Fba1) was evaluated. Using recombinant Eno and Fba1 as coating antigens, enzyme-linked immunosorbent assays (ELISAs) were used to analyze sera from patients with candidemia (n = 101), Candida colonization (n = 50), bacteremia (n = 84), invasive aspergillosis (n = 40); and from healthy controls (n = 200). The results demonstrated that ELISA detection of anti-Eno and anti-Fba1 IgG distinguished IC from other pathogenic infections in patients and healthy individuals. The sensitivity, specificity, and positive and negative predictive values were 72.3%, 94.7%, 78.5% and 93% for anti-Eno, and 87.1%, 92.8%, 76.5% and 96.4% for anti-Fba1 antibodies, respectively. Combining these two tests improved sensitivity up to 90.1% and negative predictive value up to 97.1%, with specificity and positive predictive values of 90.6% and 72.2%. The tests were specific to the Candida genus and antibody titers were higher for candidemia patients than for controls. Positive antibody tests were obtained before blood culture results for 42.2% of patients for anti-Eno and 51.1% for anti-Fba1. These data suggest that tests that detect IgG antibodies against Candida enolase and fructose-bisphosphate aldolase, especially when used in combination, could be a powerful tool for diagnosing IC.

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

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

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE PAGES

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

2017-01-16

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

Tracheobronchial foreign body aspiration in children.

PubMed

Burton, E M; Brick, W G; Hall, J D; Riggs, W; Houston, C S

1996-02-01

In this retrospective study, we reviewed the demographic and radiographic findings of 155 children with bronchoscopy-proven tracheobronchial foreign body aspiration (FBA). Two thirds of the patients were male, and most were children between 1 and 2 years of age. An aspirated peanut accounted for one third of all cases. Foreign body location was distributed nearly evenly to the right and left primary bronchi; tracheal foreign body was noted in 16 patients. The most frequent symptoms of FBA were cough (85 patients) and wheezing (60 patients). Although most patients were seen within 1 day of aspiration, 30 patients had symptoms that lasted at least 1 week before diagnosis. The most common radiographic findings were unilateral or segmental hyperlucency (59) or atelectasis (38). The trachea was the site of the foreign body in one half of children with a normal chest radiograph and FBA.

Functional Behavioral Assessment-Based Interventions for Students with or at Risk for Emotional and/or Behavioral Disorders in School: A Hierarchical Linear Modeling Meta-Analysis

ERIC Educational Resources Information Center

Gage, Nicholas A.; Lewis, Timothy J.; Stichter, Janine P.

2012-01-01

Of the myriad practices currently utilized for students with disabilities, particularly students with or at risk for emotional and/or behavioral disorder (EBD), functional behavior assessment (FBA) is a practice with an emerging solid research base. However, the FBA research base relies on single-subject design (SSD) and synthesis has relied on…

Fructose-1,6-bisphosphate aldolase of Neisseria meningitidis binds human plasminogen via its C-terminal lysine residue.

PubMed

Shams, Fariza; Oldfield, Neil J; Lai, Si Kei; Tunio, Sarfraz A; Wooldridge, Karl G; Turner, David P J

2016-04-01

Neisseria meningitidis is a leading cause of fatal sepsis and meningitis worldwide. As for commensal species of human neisseriae, N. meningitidis inhabits the human nasopharynx and asymptomatic colonization is ubiquitous. Only rarely does the organism invade and survive in the bloodstream leading to disease. Moonlighting proteins perform two or more autonomous, often dissimilar, functions using a single polypeptide chain. They have been increasingly reported on the surface of both prokaryotic and eukaryotic organisms and shown to interact with a variety of host ligands. In some organisms moonlighting proteins perform virulence-related functions, and they may play a role in the pathogenesis of N. meningitidis. Fructose-1,6-bisphosphate aldolase (FBA) was previously shown to be surface-exposed in meningococci and involved in adhesion to host cells. In this study, FBA was shown to be present on the surface of both pathogenic and commensal neisseriae, and surface localization and anchoring was demonstrated to be independent of aldolase activity. Importantly, meningococcal FBA was found to bind to human glu-plasminogen in a dose-dependent manner. Site-directed mutagenesis demonstrated that the C-terminal lysine residue of FBA was required for this interaction, whereas subterminal lysine residues were not involved. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

DTIC Science & Technology

2014-11-14

problem. Modification of the PLOS ONE | www.plosone.org 1 November 2014 | Volume 9 | Issue 11 | e112524 Report Documentation Page Form ApprovedOMB No. 0704... Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 FBA algorithm to incorporate additional biological information from gene expression profiles is...We set the maximization of biomass production as the objective of FBA and implemented it in two different forms : without flux minimization (or

Born approximation in linear-time invariant system

NASA Astrophysics Data System (ADS)

Gumjudpai, Burin

2017-09-01

An alternative way of finding the LTI’s solution with the Born approximation, is investigated. We use Born approximation in the LTI and in the transformed LTI in form of Helmholtz equation. General solution are considered as infinite series or Feynman graph. Slow-roll approximation are explored. Transforming the LTI system into Helmholtz equation, approximated general solution can be found for any given forms of force with its initial value.

Interaction Between Spatial and Feature Attention in Posterior Parietal Cortex

PubMed Central

Ibos, Guilhem; Freedman, David J.

2016-01-01

Summary Lateral intraparietal (LIP) neurons encode a vast array of sensory and cognitive variables. Recently, we proposed that the flexibility of feature representations in LIP reflect the bottom-up integration of sensory signals, modulated by feature-based attention (FBA), from upstream feature-selective cortical neurons. Moreover, LIP activity is also strongly modulated by the position of space-based attention (SBA). However, the mechanisms by which SBA and FBA interact to facilitate the representation of task-relevant spatial and non-spatial features in LIP remain unclear. We recorded from LIP neurons during performance of a task which required monkeys to detect specific conjunctions of color, motion-direction, and stimulus position. Here we show that FBA and SBA potentiate each other’s effect in a manner consistent with attention gating the flow of visual information along the cortical visual pathway. Our results suggest that linear bottom-up integrative mechanisms allow LIP neurons to emphasize task-relevant spatial and non-spatial features. PMID:27499082

Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

PubMed

Henson, Michael A

2015-12-01

Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

Feature-based attentional weighting and spreading in visual working memory

PubMed Central

Niklaus, Marcel; Nobre, Anna C.; van Ede, Freek

2017-01-01

Attention can be directed at features and feature dimensions to facilitate perception. Here, we investigated whether feature-based-attention (FBA) can also dynamically weight feature-specific representations within multi-feature objects held in visual working memory (VWM). Across three experiments, participants retained coloured arrows in working memory and, during the delay, were cued to either the colour or the orientation dimension. We show that directing attention towards a feature dimension (1) improves the performance in the cued feature dimension at the expense of the uncued dimension, (2) is more efficient if directed to the same rather than to different dimensions for different objects, and (3) at least for colour, automatically spreads to the colour representation of non-attended objects in VWM. We conclude that FBA also continues to operate on VWM representations (with similar principles that govern FBA in the perceptual domain) and challenge the classical view that VWM representations are stored solely as integrated objects. PMID:28233830

Interaction between Spatial and Feature Attention in Posterior Parietal Cortex.

PubMed

Ibos, Guilhem; Freedman, David J

2016-08-17

Lateral intraparietal (LIP) neurons encode a vast array of sensory and cognitive variables. Recently, we proposed that the flexibility of feature representations in LIP reflect the bottom-up integration of sensory signals, modulated by feature-based attention (FBA), from upstream feature-selective cortical neurons. Moreover, LIP activity is also strongly modulated by the position of space-based attention (SBA). However, the mechanisms by which SBA and FBA interact to facilitate the representation of task-relevant spatial and non-spatial features in LIP remain unclear. We recorded from LIP neurons during performance of a task that required monkeys to detect specific conjunctions of color, motion direction, and stimulus position. Here we show that FBA and SBA potentiate each other's effect in a manner consistent with attention gating the flow of visual information along the cortical visual pathway. Our results suggest that linear bottom-up integrative mechanisms allow LIP neurons to emphasize task-relevant spatial and non-spatial features. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of optimality in natural and perturbed metabolic networks

PubMed Central

Segrè, Daniel; Vitkup, Dennis; Church, George M.

2002-01-01

An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that prokaryotes such as Escherichia coli have maximized their growth performance along evolution, flux balance analysis (FBA) predicts metabolic flux distributions at steady state by using linear programming. Corroborating earlier results, we show that recent intracellular flux data for wild-type E. coli JM101 display excellent agreement with FBA predictions. Although the assumption of optimality for a wild-type bacterium is justifiable, the same argument may not be valid for genetically engineered knockouts or other bacterial strains that were not exposed to long-term evolutionary pressure. We address this point by introducing the method of minimization of metabolic adjustment (MOMA), whereby we test the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type. MOMA employs quadratic programming to identify a point in flux space, which is closest to the wild-type point, compatibly with the gene deletion constraint. Comparing MOMA and FBA predictions to experimental flux data for E. coli pyruvate kinase mutant PB25, we find that MOMA displays a significantly higher correlation than FBA. Our method is further supported by experimental data for E. coli knockout growth rates. It can therefore be used for predicting the behavior of perturbed metabolic networks, whose growth performance is in general suboptimal. MOMA and its possible future extensions may be useful in understanding the evolutionary optimization of metabolism. PMID:12415116

Key glycolytic branch influences mesocarp oil content in oil palm.

PubMed

Ruzlan, Nurliyana; Low, Yoke Sum Jaime; Win, Wilonita; Azizah Musa, Noor; Ong, Ai-Ling; Chew, Fook-Tim; Appleton, David; Mohd Yusof, Hirzun; Kulaveerasingam, Harikrishna

2017-08-29

The fructose-1,6-bisphosphate aldolase catalyzed glycolysis branch that forms dihydroxyacetone phosphate and glyceraldehyde-3-phosphate was identified as a key driver of increased oil synthesis in oil palm and was validated in Saccharomyces cerevisiae. Reduction in triose phosphate isomerase (TPI) activity in a yeast knockdown mutant resulted in 19% increase in lipid content, while yeast strains overexpressing oil palm fructose-1,6-bisphosphate aldolase (EgFBA) and glycerol-3-phosphate dehydrogenase (EgG3PDH) showed increased lipid content by 16% and 21%, respectively. Genetic association analysis on oil palm SNPs of EgTPI SD_SNP_000035801 and EgGAPDH SD_SNP_000041011 showed that palms harboring homozygous GG in EgTPI and heterozygous AG in EgGAPDH exhibited higher mesocarp oil content based on dry weight. In addition, AG genotype of the SNP of EgG3PDH SD_SNP_000008411 was associated with higher mean mesocarp oil content, whereas GG genotype of the EgFBA SNP SD_SNP_000007765 was favourable. Additive effects were observed with a combination of favourable alleles in TPI and FBA in Nigerian x AVROS population (family F7) with highest allele frequency GG.GG being associated with a mean increase of 3.77% (p value = 2.3E -16 ) oil content over the Family 1. An analogous effect was observed in yeast, where overexpressed EgFBA in TPI - resulted in a 30% oil increment. These results provide insights into flux balances in glycolysis leading to higher yield in mesocarp oil-producing fruit.

Correction of the near threshold behavior of electron collisional excitation cross-sections in the plane-wave Born approximation

NASA Astrophysics Data System (ADS)

Kilcrease, D. P.; Brookes, S.

2013-12-01

The modeling of NLTE plasmas requires the solution of population rate equations to determine the populations of the various atomic levels relevant to a particular problem. The equations require many cross sections for excitation, de-excitation, ionization and recombination. A simple and computational fast way to calculate electron collisional excitation cross-sections for ions is by using the plane-wave Born approximation. This is essentially a high-energy approximation and the cross section suffers from the unphysical problem of going to zero near threshold. Various remedies for this problem have been employed with varying degrees of success. We present a correction procedure for the Born cross-sections that employs the Elwert-Sommerfeld factor to correct for the use of plane waves instead of Coulomb waves in an attempt to produce a cross-section similar to that from using the more time consuming Coulomb Born approximation. We compare this new approximation with other, often employed correction procedures. We also look at some further modifications to our Born Elwert procedure and its combination with Y.K. Kim's correction of the Coulomb Born approximation for singly charged ions that more accurately approximate convergent close coupling calculations.

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

PubMed Central

Hoppe, Andreas; Hoffmann, Sabrina; Holzhütter, Hermann-Georg

2007-01-01

Background In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions. Results To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of Escherichia coli (931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state. Conclusion Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered. PMID:17543097

Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms.

PubMed

Allen, Andrew E; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.

Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms

PubMed Central

Allen, Andrew E.; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G.; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively. PMID:21903677

A flow-batch analyzer with piston propulsion applied to automatic preparation of calibration solutions for Mn determination in mineral waters by ET AAS.

PubMed

Almeida, Luciano F; Vale, Maria G R; Dessuy, Morgana B; Silva, Márcia M; Lima, Renato S; Santos, Vagner B; Diniz, Paulo H D; Araújo, Mário C U

2007-10-31

The increasing development of miniaturized flow systems and the continuous monitoring of chemical processes require dramatically simplified and cheap flow schemes and instrumentation with large potential for miniaturization and consequent portability. For these purposes, the development of systems based on flow and batch technologies may be a good alternative. Flow-batch analyzers (FBA) have been successfully applied to implement analytical procedures, such as: titrations, sample pre-treatment, analyte addition and screening analysis. In spite of its favourable characteristics, the previously proposed FBA uses peristaltic pumps to propel the fluids and this kind of propulsion presents high cost and large dimension, making unfeasible its miniaturization and portability. To overcome these drawbacks, a low cost, robust, compact and non-propelled by peristaltic pump FBA is proposed. It makes use of a lab-made piston coupled to a mixing chamber and a step motor controlled by a microcomputer. The piston-propelled FBA (PFBA) was applied for automatic preparation of calibration solutions for manganese determination in mineral waters by electrothermal atomic-absorption spectrometry (ET AAS). Comparing the results obtained with two sets of calibration curves (five by manual and five by PFBA preparations), no significant statistical differences at a 95% confidence level were observed by applying the paired t-test. The standard deviation of manual and PFBA procedures were always smaller than 0.2 and 0.1mugL(-1), respectively. By using PFBA it was possible to prepare about 80 calibration solutions per hour.

Stress-Inducible Expression of an F-box Gene TaFBA1 from Wheat Enhanced the Drought Tolerance in Transgenic Tobacco Plants without Impacting Growth and Development.

PubMed

Kong, Xiangzhu; Zhou, Shumei; Yin, Suhong; Zhao, Zhongxian; Han, Yangyang; Wang, Wei

2016-01-01

E3 ligase plays an important role in the response to many environment stresses in plants. In our previous study, constitutive overexpression of an F-box protein gene TaFBA1 driven by 35S promoter improved the drought tolerance in transgenic tobacco plants, but the growth and development in transgenic plants was altered in normal conditions. In this study, we used stress-inducible promoter RD29A instead of 35S promoter, as a results, the stress-inducible transgenic tobacco plants exhibit a similar phenotype with wild type (WT) plants. However, the drought tolerance of the transgenic plants with stress-inducible expressed TaFBA1 was enhanced. The improved drought tolerance of transgenic plants was indicated by their higher seed germination rate and survival rate, greater biomass and photosynthesis than those of WT under water stress, which may be related to their greater water retention capability and osmotic adjustment. Moreover, the transgenic plants accumulated less reactive oxygen species, kept lower MDA content and membrane leakage under water stress, which may be related to their higher levels of antioxidant enzyme activity and upregulated gene expression of some antioxidant enzymes. These results suggest that stress induced expression of TaFBA1 confers drought tolerance via the improved water retention and antioxidative compete ability. Meanwhile, this stress-inducible expression strategy by RD29A promoter can minimize the unexpectable effects by 35S constitutive promoter on phenotypes of the transgenic plants.

Correction of the near threshold behavior of electron collisional excitation cross-sections in the plane-wave Born approximation

DOE PAGES

Kilcrease, D. P.; Brookes, S.

2013-08-19

The modeling of NLTE plasmas requires the solution of population rate equations to determine the populations of the various atomic levels relevant to a particular problem. The equations require many cross sections for excitation, de-excitation, ionization and recombination. Additionally, a simple and computational fast way to calculate electron collisional excitation cross-sections for ions is by using the plane-wave Born approximation. This is essentially a high-energy approximation and the cross section suffers from the unphysical problem of going to zero near threshold. Various remedies for this problem have been employed with varying degrees of success. We present a correction procedure formore » the Born cross-sections that employs the Elwert–Sommerfeld factor to correct for the use of plane waves instead of Coulomb waves in an attempt to produce a cross-section similar to that from using the more time consuming Coulomb Born approximation. We compare this new approximation with other, often employed correction procedures. Furthermore, we also look at some further modifications to our Born Elwert procedure and its combination with Y.K. Kim's correction of the Coulomb Born approximation for singly charged ions that more accurately approximate convergent close coupling calculations.« less

The national cost burden of bronchial foreign body aspiration in children.

PubMed

Kim, Irene A; Shapiro, Nina; Bhattacharyya, Neil

2015-05-01

Foreign body aspiration (FBA) continues to be a concerning pediatric problem, accounting for thousands of emergency room visits and more than 100 deaths each year in the United States. The costs incurred with hospitalizations and procedures following these events are the focus of this study. Retrospective review. The Nationwide Inpatient Sample from 2009 to 2011 was analyzed, and all cases with pediatric bronchial foreign body aspirations (International Classification of Diseases-9 codes: 934.0, 934.1, 934.8, and 934.9) were reviewed. Cases were analyzed to determine type of foreign body aspiration, procedural interventions performed, duration of inpatient stay, mortality rate, complications, and posthospitalization disposition. The median length of hospital stay and total costs associated with aspiration events were determined. An estimated 1,908 ± 273 pediatric bronchial FBA patients were admitted annually over the 3-year period (mean age, 3.6 ± 0.3 years; 61.3% ± 1.9% male). The ratio of foreign object aspiration to food aspiration was 5:3. Overall, 56%.0 ± 3.6% of the patients underwent a bronchoscopic procedure for foreign body removal; of those, 41.5% ± 2.5% had a foreign body removed at the time of the endoscopy. The hospital mortality rate associated with bronchial aspiration was 1.8% ± 0.4%; and 2.2% ± 0.5% of patients were diagnosed with anoxic brain injury. The median length of stay was 3 days (25th-75th interquartile range, 1-7 days).The median charges and actual costs per case were $20,820 ($10,800-$53,453) and $6,720 ($3,628-$16,723), respectively. The annual overall inpatient cost associated with pediatric bronchial foreign-body aspiration is approximately $12.8 million. Combined, the rate of death or anoxic brain injury associated with pediatric foreign body is approximately 4%. 2C. © 2014 The American Laryngological, Rhinological and Otological Society, Inc.

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

PubMed Central

2013-01-01

Background Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual simplifications for genome-scale dynamic analysis at steady states. Based on FBA, many current optimization methods for targeted bio-productions have been developed under the maximum cell growth assumption. The optimization problem to derive gene knockout strategies recently has been formulated as a bi-level programming problem in OptKnock for maximum targeted bio-productions with maximum growth rates. However, it has been shown that knockout mutants in fact reach the steady states with the minimization of metabolic adjustment (MOMA) from the corresponding wild-type strains instead of having maximal growth rates after genetic or metabolic intervention. In this work, we propose a new bi-level computational framework--MOMAKnock--which can derive robust knockout strategies under the MOMA flux distribution approximation. Methods In this new bi-level optimization framework, we aim to maximize the production of targeted chemicals by identifying candidate knockout genes or reactions under phenotypic constraints approximated by the MOMA assumption. Hence, the targeted chemical production is the primary objective of MOMAKnock while the MOMA assumption is formulated as the inner problem of constraining the knockout metabolic flux to be as close as possible to the steady-state phenotypes of wide-type strains. As this new inner problem becomes a quadratic programming problem, a novel adaptive piecewise linearization algorithm is developed in this paper to obtain the exact optimal solution to this new bi-level integer quadratic programming problem for MOMAKnock. Results Our new MOMAKnock model and the adaptive piecewise linearization solution algorithm are tested with a small E. coli core metabolic network and a large-scale iAF1260 E. coli metabolic network. The derived knockout strategies are compared with those from OptKnock. Our preliminary experimental results show that MOMAKnock can provide improved targeted productions with more robust knockout strategies. PMID:23368729

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints.

PubMed

Ren, Shaogang; Zeng, Bo; Qian, Xiaoning

2013-01-01

Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual simplifications for genome-scale dynamic analysis at steady states. Based on FBA, many current optimization methods for targeted bio-productions have been developed under the maximum cell growth assumption. The optimization problem to derive gene knockout strategies recently has been formulated as a bi-level programming problem in OptKnock for maximum targeted bio-productions with maximum growth rates. However, it has been shown that knockout mutants in fact reach the steady states with the minimization of metabolic adjustment (MOMA) from the corresponding wild-type strains instead of having maximal growth rates after genetic or metabolic intervention. In this work, we propose a new bi-level computational framework--MOMAKnock--which can derive robust knockout strategies under the MOMA flux distribution approximation. In this new bi-level optimization framework, we aim to maximize the production of targeted chemicals by identifying candidate knockout genes or reactions under phenotypic constraints approximated by the MOMA assumption. Hence, the targeted chemical production is the primary objective of MOMAKnock while the MOMA assumption is formulated as the inner problem of constraining the knockout metabolic flux to be as close as possible to the steady-state phenotypes of wide-type strains. As this new inner problem becomes a quadratic programming problem, a novel adaptive piecewise linearization algorithm is developed in this paper to obtain the exact optimal solution to this new bi-level integer quadratic programming problem for MOMAKnock. Our new MOMAKnock model and the adaptive piecewise linearization solution algorithm are tested with a small E. coli core metabolic network and a large-scale iAF1260 E. coli metabolic network. The derived knockout strategies are compared with those from OptKnock. Our preliminary experimental results show that MOMAKnock can provide improved targeted productions with more robust knockout strategies.

Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization.

PubMed

Sánchez, Benjamín J; Pérez-Correa, José R; Agosin, Eduardo

2014-09-01

Dynamic flux balance analysis (dFBA) has been widely employed in metabolic engineering to predict the effect of genetic modifications and environmental conditions in the cell׳s metabolism during dynamic cultures. However, the importance of the model parameters used in these methodologies has not been properly addressed. Here, we present a novel and simple procedure to identify dFBA parameters that are relevant for model calibration. The procedure uses metaheuristic optimization and pre/post-regression diagnostics, fixing iteratively the model parameters that do not have a significant role. We evaluated this protocol in a Saccharomyces cerevisiae dFBA framework calibrated for aerobic fed-batch and anaerobic batch cultivations. The model structures achieved have only significant, sensitive and uncorrelated parameters and are able to calibrate different experimental data. We show that consumption, suboptimal growth and production rates are more useful for calibrating dynamic S. cerevisiae metabolic models than Boolean gene expression rules, biomass requirements and ATP maintenance. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Coping with challenging behaviours of children with autism: effectiveness of brief training workshop for frontline staff in special education settings.

PubMed

Ling, C Y M; Mak, W W S

2012-03-01

The present study examined the effectiveness of three staff training elements: psychoeducation (PE) on autism, introduction of functional behavioural analysis (FBA) and emotional management (EM), on the reaction of challenging behaviours for frontline staff towards children with autism in Hong Kong special education settings. A sample of 311 frontline staff in educational settings was recruited to one of the three conditions: control, PE-FBA and PE-FBA-EM groups. A total of 175 participants completed all three sets of questionnaires during pre-training, immediate post-training and 1-month follow-up. Findings showed that the one-session staff training workshop increased staff knowledge of autism and perceived efficacy but decrease helping behavioural intention. In spite of the limited effectiveness of a one-session staff training workshop, continued staff training is still necessary for the improvement of service quality. Further exploration on how to change emotion response of staff is important. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

Impaired activity of adherens junctions contributes to endothelial dilator dysfunction in ageing rat arteries.

PubMed

Chang, Fumin; Flavahan, Sheila; Flavahan, Nicholas A

2017-08-01

Ageing-induced endothelial dysfunction contributes to organ dysfunction and progression of cardiovascular disease. VE-cadherin clustering at adherens junctions promotes protective endothelial functions, including endothelium-dependent dilatation. Ageing increased internalization and degradation of VE-cadherin, resulting in impaired activity of adherens junctions. Inhibition of VE-cadherin clustering at adherens junctions (function-blocking antibody; FBA) reduced endothelial dilatation in young arteries but did not affect the already impaired dilatation in old arteries. After junctional disruption with the FBA, dilatation was similar in young and old arteries. Src tyrosine kinase activity and tyrosine phosphorylation of VE-cadherin were increased in old arteries. Src inhibition increased VE-cadherin at adherens junctions and increased endothelial dilatation in old, but not young, arteries. Src inhibition did not increase dilatation in old arteries treated with the VE-cadherin FBA. Ageing impairs the activity of adherens junctions, which contributes to endothelial dilator dysfunction. Restoring the activity of adherens junctions could be of therapeutic benefit in vascular ageing. Endothelial dilator dysfunction contributes to pathological vascular ageing. Experiments assessed whether altered activity of endothelial adherens junctions (AJs) might contribute to this dysfunction. Aortas and tail arteries were isolated from young (3-4 months) and old (22-24 months) F344 rats. VE-cadherin immunofluorescent staining at endothelial AJs and AJ width were reduced in old compared to young arteries. A 140 kDa VE-cadherin species was present on the cell surface and in TTX-insoluble fractions, consistent with junctional localization. Levels of the 140 kDa VE-cadherin were decreased, whereas levels of a TTX-soluble 115 kDa VE-cadherin species were increased in old compared to young arteries. Acetylcholine caused endothelium-dependent dilatation that was decreased in old compared to young arteries. Disruption of VE-cadherin clustering at AJs (function-blocking antibody, FBA) inhibited dilatation to acetylcholine in young, but not old, arteries. After the FBA, there was no longer any difference in dilatation between old and young arteries. Src activity and tyrosine phosphorylation of VE-cadherin were increased in old compared to young arteries. In old arteries, Src inhibition (saracatinib) increased: (i) 140 kDa VE-cadherin in the TTX-insoluble fraction, (ii) VE-cadherin intensity at AJs, (iii) AJ width, and (iv) acetylcholine dilatation. In old arteries treated with the FBA, saracatinib no longer increased acetylcholine dilatation. Saracatinib did not affect dilatation in young arteries. Therefore, ageing impairs AJ activity, which appears to reflect Src-induced phosphorylation, internalization and degradation of VE-cadherin. Moreover, impaired AJ activity can account for the endothelial dilator dysfunction in old arteries. Restoring endothelial AJ activity may be a novel therapeutic approach to vascular ageing. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

Passive treatment of acid mine drainage using coal combustion by-products and spent mushroom substrate: Results of column study

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

Crisp, T.E.; Nairn, R.W.; Strevett, K.A.

1998-12-31

A column study was conducted to evaluate the feasibility of using of coal combustion by-products (CCB) as alkaline materials in a field scale downflow constructed wetlands for acid mine drainage treatment. Five columns (15.24 cm in diameter and 91.44 cm high) were constructed and filled with a combination of spent mushroom substrate (SMS) and one of three alkaline materials (limestone, hydrated fly ash, or fluidized bed ash). The five mixtures utilized were 10% fluidized bed ash/40% limestone (FBA/LS), 10% fluidized bed ash (FBA), 50% limestone (LS), 50% hydrated fly ash (HFA),m and 50% sieved (>1.5 cm) hydrated fly ash (S.more » HFA) with the remainder as SMS on a w/w basis. Column received synthetic acid mine drainage containing: 400 mg/L iron, 59 mg/L aluminum, 11 mg/L manganese, 50% mg/L magnesium, 40 mg/L calcium, and 1200 mg/L sulfate for 5 months. Anoxic conditions in the influent reservoirs were maintained by a positive nitrogen pressure head. Flow rates of 2.0 mL/minute to each column were maintained by a multichannel peristaltic pump. For all columns, effluent acidity concentrations were less than influent acidity concentration (877{sup {minus}}30, n = 75f). Mean effluent acidity concentrations were 241 mg/L (FBA/LS), 186 mg/L (FBA), 419 mg/L (LS), {minus}28.5 mg/L (HFA), and 351 mg/L (S. HFA), respectively. While all column produced measurable alkalinity, only the HFA column produced a net alkaline discharge. The results of these column studies are applicable to the design and sizing of innovative field scale systems using alkaline-rich CCB`s.« less

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

PubMed Central

2017-01-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository. PMID:28263984

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.

PubMed

Biggs, Matthew B; Papin, Jason A

2017-03-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository.

Rational synthetic combination genetic devices boosting high temperature ethanol fermentation.

PubMed

Sun, Huan; Jia, Haiyang; Li, Jun; Feng, Xudong; Liu, Yueqin; Zhou, Xiaohong; Li, Chun

2017-06-01

The growth and production of yeast in the industrial fermentation are seriously restrained by heat stress and exacerbated by heat induced oxidative stress. In this study, a novel synthetic biology approach was developed to globally boost the viability and production ability of S. cerevisiae at high temperature through rationally designing and combing heat shock protein (HSP) and superoxide dismutase (SOD) genetic devices to ultimately synergistically alleviate both heat stress and oxidative stress. HSP and SOD from extremophiles were constructed to be different genetic devices and they were preliminary screened by heat resistant experiments and anti-oxidative experiments, respectively. Then in order to customize and further improve thermotolerance of S. cerevisiae , the HSP genetic device and SOD genetic device were rationally combined. The results show the simply assemble of the same function genetic devices to solve heat stress or oxidative stress could not enhance the thermotolerance considerably. Only S. cerevisiae with the combination genetic device (FBA1p- sod-MB4 -FBA1p- shsp-HB8 ) solving both stress showed 250% better thermotolerance than the control and displayed further 55% enhanced cell density compared with the strains with single FBA1p- sod-MB4 or FBA1p- shsp-HB8 at 42 °C. Then the most excellent combination genetic device was introduced into lab S. cerevisiae and industrial S. cerevisiae for ethanol fermentation. The ethanol yields of the two strains were increased by 20.6% and 26.3% compared with the control under high temperature, respectively. These results indicate synergistically defensing both heat stress and oxidative stress is absolutely necessary to enhance the thermotolerance and production of S. cerevisiae .

Heisenberg-Langevin versus quantum master equation

NASA Astrophysics Data System (ADS)

Boyanovsky, Daniel; Jasnow, David

2017-12-01

The quantum master equation is an important tool in the study of quantum open systems. It is often derived under a set of approximations, chief among them the Born (factorization) and Markov (neglect of memory effects) approximations. In this article we study the paradigmatic model of quantum Brownian motion of a harmonic oscillator coupled to a bath of oscillators with a Drude-Ohmic spectral density. We obtain analytically the exact solution of the Heisenberg-Langevin equations, with which we study correlation functions in the asymptotic stationary state. We compare the exact correlation functions to those obtained in the asymptotic long time limit with the quantum master equation in the Born approximation with and without the Markov approximation. In the latter case we implement a systematic derivative expansion that yields the exact asymptotic limit under the factorization approximation only. We find discrepancies that could be significant when the bandwidth of the bath Λ is much larger than the typical scales of the system. We study the exact interaction energy as a proxy for the correlations missed by the Born approximation and find that its dependence on Λ is similar to the discrepancy between the exact solution and that of the quantum master equation in the Born approximation. We quantify the regime of validity of the quantum master equation in the Born approximation with or without the Markov approximation in terms of the system's relaxation rate γ , its unrenormalized natural frequency Ω and Λ : γ /Ω ≪1 and also γ Λ /Ω2≪1 . The reliability of the Born approximation is discussed within the context of recent experimental settings and more general environments.

On Born approximation in black hole scattering

NASA Astrophysics Data System (ADS)

Batic, D.; Kelkar, N. G.; Nowakowski, M.

2011-12-01

A massless field propagating on spherically symmetric black hole metrics such as the Schwarzschild, Reissner-Nordström and Reissner-Nordström-de Sitter backgrounds is considered. In particular, explicit formulae in terms of transcendental functions for the scattering of massless scalar particles off black holes are derived within a Born approximation. It is shown that the conditions on the existence of the Born integral forbid a straightforward extraction of the quasi normal modes using the Born approximation for the scattering amplitude. Such a method has been used in literature. We suggest a novel, well defined method, to extract the large imaginary part of quasinormal modes via the Coulomb-like phase shift. Furthermore, we compare the numerically evaluated exact scattering amplitude with the Born one to find that the approximation is not very useful for the scattering of massless scalar, electromagnetic as well as gravitational waves from black holes.

Bronchial Leech Infestation in a 15-Year-Old Female.

PubMed

Moslehi, Mohammad Ashkan; Imanieh, Mohammad Hadi; Adib, Ali

2016-01-01

Foreign body aspiration (FBA) is a common incidence in young children. Leeches are rarely reported as FBA at any age. This study describes a 15-year-old female who presented with hemoptysis, hematemesis, coughs, melena, and anemia seven months prior to admission. Chest X-ray showed a round hyperdensity in the right lower lobe. A chest computed tomography (CT) demonstrated an area of consolidation and surrounding ground glass opacities in the right lower lobe. Hematological investigations revealed anemia. Finally, bronchoscopy was performed and a 5 cm leech was found within the right B 7-8 bronchus and removed by forceps and a Dormia basket.

Bronchial Leech Infestation in a 15-Year-Old Female

PubMed Central

Moslehi, Mohammad Ashkan; Imanieh, Mohammad Hadi

2016-01-01

Foreign body aspiration (FBA) is a common incidence in young children. Leeches are rarely reported as FBA at any age. This study describes a 15-year-old female who presented with hemoptysis, hematemesis, coughs, melena, and anemia seven months prior to admission. Chest X-ray showed a round hyperdensity in the right lower lobe. A chest computed tomography (CT) demonstrated an area of consolidation and surrounding ground glass opacities in the right lower lobe. Hematological investigations revealed anemia. Finally, bronchoscopy was performed and a 5 cm leech was found within the right B7-8 bronchus and removed by forceps and a Dormia basket. PMID:27752380

Born approximation for scattering by evanescent waves: Comparison with exact scattering by an infinite fluid cylinder

NASA Astrophysics Data System (ADS)

Marston, Philip L.

2004-05-01

In some situations, evanescent waves can be an important component of the acoustic field within the sea bottom. For this reason (as well as to advance the understanding of scattering processes) it can be helpful to examine the modifications to scattering theory resulting from evanescence. Modifications to ray theory were examined in a prior approximation [P. L. Marston, J. Acoust. Soc. Am. 113, 2320 (2003)]. The new research concerns the modifications to the low-frequency Born approximation and confirmation by comparison with the exact two-dimensional scattering by a fluid cylinder. In the case of a circular cylinder having the same density as the surroundings but having a compressibility contrast with the surroundings, the Born approximation with a nonevanescent incident wave gives only monopole scattering. When the cylinder has a density contrast and the same compressibility as the surroundings the regular Born approximation gives only dipole scattering (with the dipole oriented along to the incident wavevector). In both cases when the Born approximation is modified to include the evanescence of the incident wave, an additional dipole scattering term is evident. In each case the new dipole is oriented along to the decay axis of the evanescent wave. [Research supported by ONR.

Photometric determination of phosphorus in mineralized biodiesel using a micro-flow-batch analyzer with solenoid micro-pumps.

PubMed

Lima, Marcelo B; Barreto, Inakã S; Andrade, Stéfani Iury E; Neta, Maria S S; Almeida, Luciano F; Araújo, Mário C U

2012-08-30

A method for the determination of phosphorus in mineralized biodiesel using a micro-flow-batch analyzer (μFBA) with solenoid micro-pumps was proposed. The samples were mineralized using an ashing procedure at 550 °C followed by dissolution of the residue. The determination of phosphorus was performed by employing the well-known molybdenum blue method. The measures of the absorbance were performed at 850 nm using an InfraRed LED integrated into the μFBA. Comparing with the reference method, no statistically significant differences were observed when applying the paired t-test at a 95% confidence level. Recovery study shows results between 97.9% and 105.8%. The proposed microsystem using solenoid micro-pumps presented satisfactory robustness and high sampling rate (190 h(-1)), with satisfactory reproducibility (relative standard deviation <4.5%, n=3), low reagents consumption (32 μL per analysis) and cost to build the device. Moreover, μFBA presents limit of detection (0.014 mg Kg(-1)), precision and accuracy compatible with the biodiesel regulations that establish a maximum concentration of 10 mg Kg(-1) (Brazil, USA, EU), suggesting that it is a good alternative for the determination of phosphorus in biodiesel. Copyright © 2012 Elsevier B.V. All rights reserved.

Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data.

PubMed

Kawasaki, Regiane; Baraúna, Rafael A; Silva, Artur; Carepo, Marta S P; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T J; Schneider, Maria P C

2016-01-01

Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.

Collisional excitation of the highly excited hydrogen atoms in the dipole form of the semiclassical impact parameter and Born approximations

NASA Technical Reports Server (NTRS)

Omidvar, K.

1971-01-01

Expressions for the excitation cross section of the highly excited states of the hydrogenlike atoms by fast charged particles have been derived in the dipole approximation of the semiclassical impact parameter and the Born approximations, making use of a formula for the asymptotic expansion of the oscillator strength of the hydrogenlike atoms given by Menzel. When only the leading term in the asymptotic expansion is retained, the expression for the cross section becomes identical to the expression obtained by the method of the classical collision and correspondence principle given by Percival and Richards. Comparisons are made between the Bethe coefficients obtained here and the Bethe coefficients of the Born approximation for transitions where the Born calculation is available. Satisfactory agreement is obtained only for n yields n + 1 transitions, with n the principal quantum number of the excited state.

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

Pin, F.G.

Sensor-based operation of autonomous robots in unstructured and/or outdoor environments has revealed to be an extremely challenging problem, mainly because of the difficulties encountered when attempting to represent the many uncertainties which are always present in the real world. These uncertainties are primarily due to sensor imprecisions and unpredictability of the environment, i.e., lack of full knowledge of the environment characteristics and dynamics. An approach. which we have named the {open_quotes}Fuzzy Behaviorist Approach{close_quotes} (FBA) is proposed in an attempt to remedy some of these difficulties. This approach is based on the representation of the system`s uncertainties using Fuzzy Set Theory-basedmore » approximations and on the representation of the reasoning and control schemes as sets of elemental behaviors. Using the FBA, a formalism for rule base development and an automated generator of fuzzy rules have been developed. This automated system can automatically construct the set of membership functions corresponding to fuzzy behaviors. Once these have been expressed in qualitative terms by the user. The system also checks for completeness of the rule base and for non-redundancy of the rules (which has traditionally been a major hurdle in rule base development). Two major conceptual features, the suppression and inhibition mechanisms which allow to express a dominance between behaviors are discussed in detail. Some experimental results obtained with the automated fuzzy, rule generator applied to the domain of sensor-based navigation in aprion unknown environments. using one of our autonomous test-bed robots as well as a real car in outdoor environments, are then reviewed and discussed to illustrate the feasibility of large-scale automatic fuzzy rule generation using the {open_quotes}Fuzzy Behaviorist{close_quotes} concepts.« less

Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

NASA Technical Reports Server (NTRS)

Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

2001-01-01

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

Stainless steel crown aspiration during sedation in pediatric dentistry.

PubMed

Adewumi, A; Kays, David W

2008-01-01

Foreign body aspiration (FBA) causes death in more than 300 children every year in the United States. Morbidity and mortality are increased in children due to narrow airways and immature protective mechanisms. Factors to consider in pediatric dentistry are: (1) the patient's age and behavior; (2) presence and extent of disability; (3) local anesthesia; (4) body positioning; and (5) loose teeth. FBA requires prompt recognition and early treatment to minimize potentially serious and sometimes fatal consequences. The purpose of this case report was to describe the aspiration of a stainless steel crown in a 5-year-old boy during conscious sedation. It also discusses how a prompt and accurate diagnosis, early referral, and immediate treatment helped prevent serious complications.

Topics in electron capture by fast ions

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

Hsin, S.H.

1987-01-01

The post-collision interaction (PCI) model was applied, together with the eikonal approximation, to study the (n = 2,3) capture cross sections in p + H(ls) collisions. The results indeed improve the previous eikonal calculations for l = 0 cases, and agree quite well with present experimental data. Calculations using the strong-potential Born (SPB) approximation, with the Sil and McGuire technique, for capture into the np, nd levels are also presented. While these cross sections are smaller than cross sections for capture into the ns levels at high velocities, nevertheless the Thomas peak is clearly evident in both the absolute valuemore » m = 2, absolute value m = 1 and m = 0 magnetic substates in p + H(ls) collisions. Also calculated were corrections to the SPB using the Distorted-Wave Born formalism of Taulbjerg and Briggs. In the sense of a plane-wave Born expansion, all terms of the third Born approximation and all single switching fourth Born terms are included, but a peaking approximation is needed to reduce the calculation to tractable form. Effects of the higher terms are most visible in the valley between the Thomas peak and the forward peak. The Thomas peak is visible in the correction term, even though it includes no second Born contributions.« less

An integrated model to simulate the scattering of ultrasounds by inclusions in steels.

PubMed

Darmon, Michel; Calmon, Pierre; Bèle, Bertrand

2004-04-01

We present a study performed to model and predict the ultrasonic response of alumina inclusions in steels. The Born and the extended quasistatic approximations have been applied and modified to improve their accuracy in the framework of this application. The modified Born approximation, called "doubly distorted wave (D(2)W) Born approximation" allowing to deal with various inclusion shapes, has been selected to be implemented in the CIVA software. The model reliability has been evaluated by comparison with Ying and Truell's exact analytical solution. In parallel, measurements have been carried out upon both natural and artificial alumina inclusions.

Validity of the Born approximation for beyond Gaussian weak lensing observables

DOE PAGES

Petri, Andrea; Haiman, Zoltan; May, Morgan

2017-06-06

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N-body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show thatmore » deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O(Φ 3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O(Φ 4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5σ. Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.« less

Validity of the Born approximation for beyond Gaussian weak lensing observables

NASA Astrophysics Data System (ADS)

Petri, Andrea; Haiman, Zoltán; May, Morgan

2017-06-01

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N -body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show that deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O (Φ3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O (Φ4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5 σ . Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.

Technique for evaluation of the strong potential Born approximation for electron capture

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

Sil, N.C.; McGuire, J.H.

1985-04-01

A technique is presented for evaluating differential cross sections in the strong potential Born (SPB) approximation. Our final expression is expressed as a finite sum of one-dimensional integrals, expressible as a finite sum of derivatives of hypergeometric functions.

Variationally consistent approximation scheme for charge transfer

NASA Technical Reports Server (NTRS)

Halpern, A. M.

1978-01-01

The author has developed a technique for testing various charge-transfer approximation schemes for consistency with the requirements of the Kohn variational principle for the amplitude to guarantee that the amplitude is correct to second order in the scattering wave functions. Applied to Born-type approximations for charge transfer it allows the selection of particular groups of first-, second-, and higher-Born-type terms that obey the consistency requirement, and hence yield more reliable approximation to the amplitude.

Natural products as sources of new fungicides (IV): Synthesis and biological evaluation of isobutyrophenone analogs as potential inhibitors of class-II fructose-1,6-bisphosphate aldolase.

PubMed

Li, Ding; Luong, Tuong Thi Mai; Dan, Wen-Jia; Ren, Yanliang; Nien, Hoang Xuan; Zhang, An-Ling; Gao, Jin-Ming

2018-01-15

Several recently identified antifungal compounds share the backbone structure of acetophenones. The aim of the present study was to develop new isobutyrophenone analogs as new antifungal agents. A series of new 2,4-dihydroxy-5-methyl isobutyrophenone derivatives were prepared and characterized by 1 H, 13 C NMR and MS spectroscopic data. These products were evaluated for in vitro antifungal activities against seven plant fungal pathogens by the mycelial growth inhibitory rate assay. Compounds 3, 4a, 5a, 5b, 5e, 5f and 5g showed a broad-spectrum high antifungal activity. On the other hand, for the first time, these compounds were also assayed as potential inhibitors against Class II fructose-1,6-bisphosphate aldolase (Fba) from the rice blast fungus, Magnaporthe grisea. Compounds 5e and 5g were found to exhibit the inhibition constants (Ki) for 15.12 and 14.27 μM, respectively, as the strongest competitive inhibitors against Fba activity. The possible binding-modes of compounds 5e and 5g were further analyzed by molecular docking algorithms. The results strongly suggested that compound 5g could be a promising lead for the discovery of new fungicides via targeting Class II Fba. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data

PubMed Central

Kawasaki, Regiane; Carepo, Marta S. P.; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T. J.; Schneider, Maria P. C.

2016-01-01

Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments. PMID:27595107

L-shell x-ray production cross sections of Ni, Cu, Ge, As, Rb, Sr, Y, Zr, and Pd by (0. 25--2. 5)-MeV protons

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

Duggan, J.L.; Kocur, P.M.; Price, J.L.

1985-10-01

L-shell x-ray production cross sections by /sub 1//sup 1/H/sup +/ ions are reported. The data are compared to the first Born approximation (plane-wave Born approximation for direct ionization and Oppenheimer-Brinkman-Kramers approximation for electron capture) and to the ECPSSR (energy-loss and Coulomb-deflection effects, perturbed stationary-state approximation with relativistic correction) theory. The energy of the protons ranged from 0.25 to 2.5 MeV in steps of 0.25 MeV. The targets used in these measurements were /sub 28/Ni, /sub 29/Cu, /sub 32/Ge, /sub 33/As, /sub 37/Rb, /sub 38/Sr, /sub 39/Y, /sub 40/Zr, and /sub 46/Pd. The first Born theory generally agrees with the datamore » found in the literature at high energies and overpredicts them below 1.5 MeV. The ECPSSR predictions are in better agreement with experimental cross sections. At 0.25 MeV our data, however, are underestimated by this theory and tend to agree with the first Born approximation.« less

Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

DTIC Science & Technology

2008-10-30

rigorous Poisson-based methods generally apply a Lee-Richards mo- lecular surface.9 This surface is considered the de facto description for continuum...definition and calculation of the Born radii. To evaluate the Born radii, two approximations are invoked. The first is the Coulomb field approximation (CFA...energy term, and depending on the particular GB formulation, higher-order non- Coulomb correction terms may be added to the Born radii to account for the

Potential-Energy Surfaces, the Born-Oppenheimer Approximations, and the Franck-Condon Principle: Back to the Roots.

PubMed

Mustroph, Heinz

2016-09-05

The concept of a potential-energy surface (PES) is central to our understanding of spectroscopy, photochemistry, and chemical kinetics. However, the terminology used in connection with the basic approximations is variously, and somewhat confusingly, represented with such phrases as "adiabatic", "Born-Oppenheimer", or "Born-Oppenheimer adiabatic" approximation. Concerning the closely relevant and important Franck-Condon principle (FCP), the IUPAC definition differentiates between a classical and quantum mechanical formulation. Consequently, in many publications we find terms such as "Franck-Condon (excited) state", or a vertical transition to the "Franck-Condon point" with the "Franck-Condon geometry" that relaxes to the excited-state equilibrium geometry. The Born-Oppenheimer approximation and the "classical" model of the Franck-Condon principle are typical examples of misused terms and lax interpretations of the original theories. In this essay, we revisit the original publications of pioneers of the PES concept and the FCP to help stimulate a lively discussion and clearer thinking around these important concepts. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of human activity and natural processes on groundwater arsenic in an urbanized area (South China) using multivariate statistical techniques.

PubMed

Huang, Guanxing; Chen, Zongyu; Liu, Fan; Sun, Jichao; Wang, Jincui

2014-11-01

Anthropogenic factors resulted from the urbanization may affect the groundwater As in urbanized areas. Groundwater samples from the Guangzhou city (South China) were collected for As and other parameter analysis, in order to assess the impact of urbanization and natural processes on As distribution in aquifers. Nearly 25.5 % of groundwater samples were above the WHO drinking water standard for As, and the As concentrations in the granular aquifer (GA) were generally far higher than that in the fractured bedrock aquifer (FBA). Samples were classified into four clusters by using hierarchical cluster analysis. Cluster 1 is mainly located in the FBA and controlled by natural processes. Anthropogenic pollution resulted from the urbanization is responsible for high As concentrations identified in cluster 2. Clusters 3 and 4 are mainly located in the GA and controlled by both natural processes and anthropogenic factors. Three main mechanisms control the source and mobilization of groundwater As in the study area. Firstly, the interaction of water and calcareous rocks appears to be responsible for As release in the FBA. Secondly, reduction of Fe/Mn oxyhydroxides and decomposition of organic matter are probably responsible for high As concentrations in the GA. Thirdly, during the process of urbanization, the infiltration of wastewater/leachate with a high As content is likely to be the main source for groundwater As, while NO3 (-) contamination diminishes groundwater As.

Microwave imaging by three-dimensional Born linearization of electromagnetic scattering

NASA Astrophysics Data System (ADS)

Caorsi, S.; Gragnani, G. L.; Pastorino, M.

1990-11-01

An approach to microwave imaging is proposed that uses a three-dimensional vectorial form of the Born approximation to linearize the equation of electromagnetic scattering. The inverse scattering problem is numerically solved for three-dimensional geometries by means of the moment method. A pseudoinversion algorithm is adopted to overcome ill conditioning. Results show that the method is well suited for qualitative imaging purposes, while its capability for exactly reconstructing the complex dielectric permittivity is affected by the limitations inherent in the Born approximation and in ill conditioning.

On the mathematical treatment of the Born-Oppenheimer approximation

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

Jecko, Thierry, E-mail: thierry.jecko@u-cergy.fr

2014-05-15

Motivated by the paper by Sutcliffe and Woolley [“On the quantum theory of molecules,” J. Chem. Phys. 137, 22A544 (2012)], we present the main ideas used by mathematicians to show the accuracy of the Born-Oppenheimer approximation for molecules. Based on mathematical works on this approximation for molecular bound states, in scattering theory, in resonance theory, and for short time evolution, we give an overview of some rigorous results obtained up to now. We also point out the main difficulties mathematicians are trying to overcome and speculate on further developments. The mathematical approach does not fit exactly to the common usemore » of the approximation in Physics and Chemistry. We criticize the latter and comment on the differences, contributing in this way to the discussion on the Born-Oppenheimer approximation initiated by Sutcliffe and Woolley. The paper neither contains mathematical statements nor proofs. Instead, we try to make accessible mathematically rigourous results on the subject to researchers in Quantum Chemistry or Physics.« less

Approximate solutions of acoustic 3D integral equation and their application to seismic modeling and full-waveform inversion

NASA Astrophysics Data System (ADS)

Malovichko, M.; Khokhlov, N.; Yavich, N.; Zhdanov, M.

2017-10-01

Over the recent decades, a number of fast approximate solutions of Lippmann-Schwinger equation, which are more accurate than classic Born and Rytov approximations, were proposed in the field of electromagnetic modeling. Those developments could be naturally extended to acoustic and elastic fields; however, until recently, they were almost unknown in seismology. This paper presents several solutions of this kind applied to acoustic modeling for both lossy and lossless media. We evaluated the numerical merits of those methods and provide an estimation of their numerical complexity. In our numerical realization we use the matrix-free implementation of the corresponding integral operator. We study the accuracy of those approximate solutions and demonstrate, that the quasi-analytical approximation is more accurate, than the Born approximation. Further, we apply the quasi-analytical approximation to the solution of the inverse problem. It is demonstrated that, this approach improves the estimation of the data gradient, comparing to the Born approximation. The developed inversion algorithm is based on the conjugate-gradient type optimization. Numerical model study demonstrates that the quasi-analytical solution significantly reduces computation time of the seismic full-waveform inversion. We also show how the quasi-analytical approximation can be extended to the case of elastic wavefield.

bb̅ud̅ four-quark systems in the Born-Oppenheimer approximation: prospects and challenges

NASA Astrophysics Data System (ADS)

Peters, Antje; Bicudo, Pedro; Wagner, Marc

2018-03-01

We summarize previous work on b̅b̅ud four-quark systems in the Born-Oppenheimer approximation and discuss first steps towards an extension to the theoretically more challenging bb̅ud̅ system. Strategies to identify a possibly existing bb̅ud̅ bound state are discussed and first numerical results are presented.

Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

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

R Daher; M Coincon; M Fonvielle

2011-12-31

We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very highmore » selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.« less

Pediatric airway foreign bodies.

PubMed

Fitzpatrick, P C; Guarisco, J L

1998-04-01

Foreign body aspiration (FBA) is a leading cause of accidental death in children less than one year old and is the cause of death in 7% of children less than four. Food items, especially peanuts, are the most common items aspirated in infants and toddlers, whereas older children are more likely to aspirate non-food items such as pen caps, pins, and paper clips. A high degree of suspicion is required to diagnose FBA. A history of a witnessed choking episode is most important in early diagnosis. An asymptomatic period is common after aspiration and contributes to a delay in diagnosis of greater than one week in 12% to 26% of patients. This delay in diagnosis causes increased morbidity from bronchial inflammation, obstruction, and pneumonia which is resistant to treatment. Prompt endoscopic removal of the foreign body with an open rigid bronchoscope under general anesthesia is the mainstay of therapy.

Fluxomics - connecting 'omics analysis and phenotypes.

PubMed

Winter, Gal; Krömer, Jens O

2013-07-01

In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies. © 2012 John Wiley & Sons Ltd and Society for Applied Microbiology.

MOST: a software environment for constraint-based metabolic modeling and strain design.

PubMed

Kelley, James J; Lane, Anatoliy; Li, Xiaowei; Mutthoju, Brahmaji; Maor, Shay; Egen, Dennis; Lun, Desmond S

2015-02-15

MOST (metabolic optimization and simulation tool) is a software package that implements GDBB (genetic design through branch and bound) in an intuitive user-friendly interface with excel-like editing functionality, as well as implementing FBA (flux balance analysis), and supporting systems biology markup language and comma-separated values files. GDBB is currently the fastest algorithm for finding gene knockouts predicted by FBA to increase production of desired products, but GDBB has only been available on a command line interface, which is difficult to use for those without programming knowledge, until the release of MOST. MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An individually tailored behavioral medicine treatment in physical therapy for tension-type headache - two experimental case studies.

PubMed

Söderlund, Anne; Lagerlöf, Helena

2016-01-01

The aim of this study was to describe and evaluate the effect of an individually tailored behavioral medicine treatment in physical therapy, based on a functional behavioral analysis (FBA), for tension-type headache (TTH). Two case studies with A1-A2-B-A3 design of two patients with TTH was conducted. Outcome variables were headache frequency, headache index (mean intensity), consumption of analgesics, self-efficacy in headache management (Headache Management Self-efficacy Scale [HMSE]), disability, and perceived loss of happiness for activities with family and friends. The results showed that headache frequency and headache index decreased for one of the patients. Self-efficacy in headache management increased markedly for both patients. A behavioral medicine treatment in physical therapy based on an FBA can be a way for physical therapists to handle patients with TTH. Future investigations should focus on large group studies with longer observation periods.

Effects of soya oligosaccharides and soya oligopeptides on lipid metabolism in hyperlipidaemic rats.

PubMed

Xie, Shali; Zhu, Jundong; Zhang, Yanqi; Shi, Kai; Shi, Yuangang; Ma, Xiao

2012-08-01

In the present study, we aimed to examine the effects of soya oligosaccharides (SOS) and soya oligopeptides (SOP) on blood lipid levels, release of vasoactive substances, antioxidant activity and faecal bile acid (FBA) excretion in rats fed a high-fat diet (HFD). Male Sprague-Dawley rats were evenly divided into five groups according to diets as follows: regular diet (control), HFD, HFD enriched with 2 % of SOS (SOS), HFD enriched with 3 % of SOP (SOP) and HFD enriched with 2 % SOS and 3 % SOP (SOSP). The results showed that SOS and SOP significantly reduced plasma total cholesterol, LDL-cholesterol and TAG, whereas HDL-cholesterol concentration was significantly increased. Furthermore, SOS and SOP reduced plasma apoB, apoE and the apoB:apoAI ratio, whereas apoAI was significantly increased. Moreover, SOS and SOP also reduced plasma thromboxane A₂ (TXA₂) and the TXA₂:prostacyclin (PGI₂) ratio, whereas plasma PGI₂ and nitric oxide were significantly increased. In addition, SOS and SOP significantly reduced serum and liver malondialdehyde concentrations and increased FBA excretion. However, we did not observe obvious influences of SOS and SOP on superoxide dismutase activities in the liver of HFD-fed rats. The combination of 2 % SOS and 3 % SOP showed a more marked effect than SOS or SOP alone in improving the lipid profile, release of vasoactive substances and increasing FBA excretion (P < 0.05). In summary, SOS and SOP might help prevent atherosclerosis through improving abnormal blood lipid levels, regulating vasoactive substances and protecting against oxidative stress.

Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.

PubMed

Samal, Areejit

2008-12-01

Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate. Almaas et al. have shown that the flux distribution follows a power law, and it is possible to associate with most metabolites two reactions which maximally produce and consume a given metabolite, respectively. This observation led to the concept of high-flux backbone (HFB) in metabolic networks. In previous work, the HFB has been computed using a particular optima obtained using FBA. In this paper, we investigate the conservation of HFB of a particular solution for a given medium across different alternate optima and near-optima in metabolic networks of E. coli and S. cerevisiae. Using flux variability analysis (FVA), we propose a method to determine reactions that are guaranteed to be in HFB regardless of alternate solutions. We find that the HFB of a particular optima is largely conserved across alternate optima in E. coli, while it is only moderately conserved in S. cerevisiae. However, the HFB of a particular near-optima shows a large variation across alternate near-optima in both organisms. We show that the conserved set of reactions in HFB across alternate near-optima has a large overlap with essential reactions and reactions which are both uniquely consuming (UC) and uniquely producing (UP). Our findings suggest that the structure of the metabolic network admits a high degree of redundancy and plasticity in near-optimal flow patterns enhancing system robustness for a given environmental condition.

Convergence of the strong-potential-Born approximation in Z/sub less-than//Z/sub greater-than/

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

McGuire, J.H.; Sil, N.C.

1986-01-01

Convergence of the strong-potential Born (SPB) approximation as a function of the charges of the projectile and target is studied numerically. Time-reversal invariance (or detailed balance) is satisfied at sufficiently high velocities even when the charges are asymmetric. This demonstarates that the SPB approximation converges to the correct result even when the charge of the ''weak'' potential, which is kept to first order, is larger than the charge of the ''strong'' potential, which is retained to all orders. Consequently, the SPB approximation is valid for systems of arbitrary charge symmetry (including symmetric systems) at sufficiently high velocities.

Microwave beam broadening due to turbulent plasma density fluctuations within the limit of the Born approximation and beyond

NASA Astrophysics Data System (ADS)

Köhn, A.; Guidi, L.; Holzhauer, E.; Maj, O.; Poli, E.; Snicker, A.; Weber, H.

2018-07-01

Plasma turbulence, and edge density fluctuations in particular, can under certain conditions broaden the cross-section of injected microwave beams significantly. This can be a severe problem for applications relying on well-localized deposition of the microwave power, like the control of MHD instabilities. Here we investigate this broadening mechanism as a function of fluctuation level, background density and propagation length in a fusion-relevant scenario using two numerical codes, the full-wave code IPF-FDMC and the novel wave kinetic equation solver WKBeam. The latter treats the effects of fluctuations using a statistical approach, based on an iterative solution of the scattering problem (Born approximation). The full-wave simulations are used to benchmark this approach. The Born approximation is shown to be valid over a large parameter range, including ITER-relevant scenarios.

A new probability distribution model of turbulent irradiance based on Born perturbation theory

NASA Astrophysics Data System (ADS)

Wang, Hongxing; Liu, Min; Hu, Hao; Wang, Qian; Liu, Xiguo

2010-10-01

The subject of the PDF (Probability Density Function) of the irradiance fluctuations in a turbulent atmosphere is still unsettled. Theory reliably describes the behavior in the weak turbulence regime, but theoretical description in the strong and whole turbulence regimes are still controversial. Based on Born perturbation theory, the physical manifestations and correlations of three typical PDF models (Rice-Nakagami, exponential-Bessel and negative-exponential distribution) were theoretically analyzed. It is shown that these models can be derived by separately making circular-Gaussian, strong-turbulence and strong-turbulence-circular-Gaussian approximations in Born perturbation theory, which denies the viewpoint that the Rice-Nakagami model is only applicable in the extremely weak turbulence regime and provides theoretical arguments for choosing rational models in practical applications. In addition, a common shortcoming of the three models is that they are all approximations. A new model, called the Maclaurin-spread distribution, is proposed without any approximation except for assuming the correlation coefficient to be zero. So, it is considered that the new model can exactly reflect the Born perturbation theory. Simulated results prove the accuracy of this new model.

A numerical analysis of the Born approximation for image formation modeling of differential interference contrast microscopy for human embryos

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Feigin, Micha; Greenspan, Hayit; Sochen, Nir

2008-03-01

The differential interference contrast (DIC) microscope is commonly used for the visualization of live biological specimens. It enables the view of the transparent specimens while preserving their viability, being a non-invasive modality. Fertility clinics often use the DIC microscope for evaluation of human embryos quality. Towards quantification and reconstruction of the visualized specimens, an image formation model for DIC imaging is sought and the interaction of light waves with biological matter is examined. In many image formation models the light-matter interaction is expressed via the first Born approximation. The validity region of this approximation is defined in a theoretical bound which limits its use to very small specimens with low dielectric contrast. In this work the Born approximation is investigated via the Helmholtz equation, which describes the interaction between the specimen and light. A solution on the lens field is derived using the Gaussian Legendre quadrature formulation. This numerical scheme is considered both accurate and efficient and has shortened significantly the computation time as compared to integration methods that required a great amount of sampling for satisfying the Whittaker - Shannon sampling theorem. By comparing the numerical results with the theoretical values it is shown that the theoretical bound is not directly relevant to microscopic imaging and is far too limiting. The numerical exhaustive experiments show that the Born approximation is inappropriate for modeling the visualization of thick human embryos.

/sub 1//sup 1/H/sup +/- and /sub 2//sup 4/He/sup +/-induced M-shell x-ray-production cross sections for selected elements in the rare-earth region

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

Mehta, R.; Duggan, J.L.; Price, J.L.

1983-12-01

The measurements of M-shell x-ray-production cross sections induced by /sub 1//sup 1/H/sup +/ and /sub 2//sup 4/He/sup +/ ions are compared to the first-Born-approximation and ECPSSR (energy loss, Coulomb-deflection effects; perturbed-stationary-state approximation, with relativistic corrections) theories. Most of the reported experimental data were measured in our laboratory and the other measurements were taken from the literature. The data from our laboratory were for incident H/sup +/ and He/sup +/ ions in the energy range from 0.25 to 2.5 MeV. The M-shell x-ray-production cross sections were measured for the following thin targets: /sub 59/Pr, /sub 60/Nd, /sub 63/Eu, /sub 64/Gd, /submore » 66/Dy, /sub 67/Ho, /sub 68/Er, /sub 70/Yb, and /sub 72/Hf. The data from the literature were for protons and He/sup +/ ions in the energy range from 30 keV to 40 MeV. These data were for the following elements: /sub 54/Xe, /sub 59/Pr, /sub 60/Nd, /sub 62/Sm, /sub 63/Eu, /sub 64/Gd, /sub 65/Tb, /sub 66/Dy, /sub 67/Ho, /sub 68/Er, /sub 70/Yb, /sub 72/Hf, /sub 73/Ta, /sub 74/W, /sub 78/Pt, /sub 79/Au, /sub 80/Hg, /sub 82/Pb, /sub 83/Bi, and /sub 92/U. The first-Born-approximation calculations of the ionization cross section were made using the plane-wave Born approximation for direct ionization and the Oppenheimer-Brinkman-Kramers approximation of Nikolaev for electron capture. The ECPSSR theory of Brandt and Lapicki (Phys. Rev. A 23, 1717 (1981)) goes beyond the first Born approximation and accounts for the energy loss, Coulomb deflection, and relativistic effects in the perturbed-stationary-state theory. The first Born approximation overpredicts all measurements. The ECPSSR theory predicts the M-shell production cross sections correctly for Z/sub 2/>70 and energies per ..mu..>0.25 MeV/..mu...« less

School-Aged Children Born Preterm: Review of Functioning across Multiple Domains and Guidelines for Assessment

ERIC Educational Resources Information Center

Dempsey, Allison G.; Keller-Margulis, Milena; Mire, Sarah; Abrahamson, Catherine; Dutt, Sonia; Llorens, Ashlie; Payan, Anita

2015-01-01

Children born preterm are at risk for developmental deficits across multiple functional domains. As the rate of survival for preterm infants increases due to medical advancements, a greater understanding is needed for how to meet the needs of this growing population in schools. Because approximately 50-70% of children born preterm require…

The Road to Prison is Paved with Bad Evaluations: The Case for Functional Behavioral Assessments and Behavior Intervention Plans.

PubMed

Poucher, Stephanie M

In 1997, Congress amended the Individuals with Disabilities Education Act ("IDEA") to include provisions meant to assist school districts in educating students with behavioral needs. These amendments required schools to use functional behavioral assessments ("FBA") and behavior intervention plans ("BIP") under certain circumstances. Congress did not, however, include a definition of or substantive requirements for either system of behavior management. As a result, although BIPs and FBAs are now federally mandated requirements, and it is clear that disregarding behavioral issues is a denial of a free appropriate public education ("FAPE"), the IDEA’s adjudicative standard, there is no clear consensus as to whether a student with behavioral needs must have an FBA or a BIP or what either must include. The IDEA’s lack of guidance has resulted in inconsistent and often contradictory court rulings, and the lack of specific definitions and procedures has allowed schools to develop purportedly legal but substantively deficient behavior evaluations and intervention plans for special needs students. Despite this confusion, some courts have properly looked to the administrative record for guidance on the substantive elements of FBAs and BIPs. Deference to hearing officers, along with other provisions within the IDEA, such as Child Find and inclusion obligations, may assist courts in determining whether a school’s failure to use an FBA and a BIP for a student with behavioral needs falls short of Board of Education v. Rowley’s requirements for FAPE. FBAs and BIPs aim to prevent and correct student misconduct before it escalates and results in drastic disciplinary action. Given the impact punitive school discipline policies have had on students with special needs, the added procedural safeguards these proactive behavior management schemes could provide are imperative to dismantling the school-to-prison pipeline.

Haptic perception and body representation in lateral and medial occipito-temporal cortices.

PubMed

Costantini, Marcello; Urgesi, Cosimo; Galati, Gaspare; Romani, Gian Luca; Aglioti, Salvatore M

2011-04-01

Although vision is the primary sensory modality that humans and other primates use to identify objects in the environment, we can recognize crucial object features (e.g., shape, size) using the somatic modality. Previous studies have shown that the occipito-temporal areas dedicated to the visual processing of object forms, faces and bodies also show category-selective responses when the preferred stimuli are haptically explored out of view. Visual processing of human bodies engages specific areas in lateral (extrastriate body area, EBA) and medial (fusiform body area, FBA) occipito-temporal cortex. This study aimed at exploring the relative involvement of EBA and FBA in the haptic exploration of body parts. During fMRI scanning, participants were asked to haptically explore either real-size fake body parts or objects. We found a selective activation of right and left EBA, but not of right FBA, while participants haptically explored body parts as compared to real objects. This suggests that EBA may integrate visual body representations with somatosensory information regarding body parts and form a multimodal representation of the body. Furthermore, both left and right EBA showed a comparable level of body selectivity during haptic perception and visual imagery. However, right but not left EBA was more activated during haptic exploration than visual imagery of body parts, ruling out that the response to haptic body exploration was entirely due to the use of visual imagery. Overall, the results point to the existence of different multimodal body representations in the occipito-temporal cortex which are activated during perception and imagery of human body parts. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.

PubMed

Cheung, C Y Maurice; Poolman, Mark G; Fell, David A; Ratcliffe, R George; Sweetlove, Lee J

2014-06-01

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C 3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO 2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis. © 2014 American Society of Plant Biologists. All Rights Reserved.

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves1[C][W][OPEN

PubMed Central

Cheung, C.Y. Maurice; Poolman, Mark G.; Fell, David. A.; Ratcliffe, R. George; Sweetlove, Lee J.

2014-01-01

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis. PMID:24596328

Tracheobronchial Foreign Bodies in Children: The Role of Emergency Rigid Bronchoscopy

PubMed Central

Baram, Aram; Sherzad, Hewa; Saeed, Sara; Kakamad, Fahmi H.; Hamawandi, Adnan M. H.

2017-01-01

Foreign body aspiration (FBA) is a common and lethal accident in the pediatric age group. It requires early recognition and treatment by rigid bronchoscopy to avoid fatal outcomes. Objective. The aim of this study was to study the pattern of FBA in the tracheobronchial tree as well as the success rate of rigid bronchoscopy in children admitted to a single center and to analyze the relationship of the type of foreign body (FB) with patients’ age, presentation, and complications. Methods. A retrospective cross-sectional study of FBA was conducted in children in the Sulaimani/Kurdistan region, Iraq, admitted to the emergency teaching hospital of the University of Sulaimani from January 2014 to March 2016. Result. Data of 83 patients between 6 months and 15 years old were studied. The most affected was the 1- to 5-year-old group. There was a slight female predominance (male to female ratio 0.93:1). The most common FB was sunflower seed (49.4%). History of choking was present in 92.8% of patients; 55.4% had normal air entry, and 37.3% had no added sound on chest auscultation. Normal chest X-ray (CXR) was found in 40% of patients. The most common site was the right bronchial tree (39.8%). Two patients needed mechanical ventilation; both of them died. There was a significant relationship between the type of FB (P = .013, .000, respectively). Conclusion. Medical history is the most important factor for reaching the diagnosis; bronchoscopy is mandatory if choking was witnessed, even if examination and CXR are normal. Organic material causes more local reaction than nonorganic material. PMID:29226187

The secreted fructose 1,6-bisphosphate aldolase as a broad spectrum vaccine candidate against pathogenic bacteria in aquaculture.

PubMed

Sun, Zhongyang; Shen, Binbing; Wu, Haizhen; Zhou, Xiangyu; Wang, Qiyao; Xiao, Jingfan; Zhang, Yuanxing

2015-10-01

The development of aquaculture has been hampered by different aquatic pathogens that can cause edwardsiellosis, vibriosis, or other diseases. Therefore, developing a broad spectrum vaccine against different fish diseases is necessary. In this study, fructose 1,6-bisphosphate aldolase (FBA), a conserved enzyme in the glycolytic pathway, was demonstrated to be located in the non-cytoplasmic components of five aquatic pathogenic bacteria and exhibited remarkable protection and cross-protection against these pathogens in turbot and zebrafish. Further analysis revealed that sera sampled from vaccinated turbot had a high level of specific antibody and bactericidal activity against these pathogens. Meanwhile, the increased expressions of immune response-related genes associated with antigen recognition and presentation indicated that the adaptive immune response was effectively aroused. Taken together, our results suggest that FBA can be utilized as a broad-spectrum vaccine against various pathogenic bacteria of aquaculture in the future. Copyright © 2015 Elsevier Ltd. All rights reserved.

An objective function exploiting suboptimal solutions in metabolic networks

PubMed Central

2013-01-01

Background Flux Balance Analysis is a theoretically elegant, computationally efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models exhibit persistent mathematical degeneracy that generally limits their predictive power. Results We propose a novel objective function for cellular metabolism that accounts for and exploits degeneracy in the metabolic network to improve flux predictions. In our model, regulation drives metabolism toward a region of flux space that allows nearly optimal growth. Metabolic mutants deviate minimally from this region, a function represented mathematically as a convex cone. Near-optimal flux configurations within this region are considered equally plausible and not subject to further optimizing regulation. Consistent with relaxed regulation near optimality, we find that the size of the near-optimal region predicts flux variability under experimental perturbation. Conclusion Accounting for suboptimal solutions can improve the predictive power of metabolic FBA models. Because fluctuations of enzyme and metabolite levels are inevitable, tolerance for suboptimality may support a functionally robust metabolic network. PMID:24088221

Constraint-based stoichiometric modelling from single organisms to microbial communities

PubMed Central

Olivier, Brett G.; Bruggeman, Frank J.; Teusink, Bas

2016-01-01

Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open. PMID:28334697

Removing lead in drinking water with activated carbon

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

Taylor, R.M.; Kuennen, R.W.

A point-of-use (POU) granular activated carbon (GAC) fixed bed adsorber (FBA) was evaluated for reduction of soluble and insoluble lead from drinking water. Some of the factors which affect lead removal by GAC were evaluated, such as carbon type, solution pH, and a limited amount of work on competitive interactions. The design criteria for lead reduction by a POU device are also addressed. Minicolumns were used to evaluate the capacity of carbon for lead under a variety of conditions. The importance of surface chemistry of the carbon and the relationship with the pH of the water for lead reduction wasmore » demonstrated. Results indicate that a properly designed POU-GAC-FBA can reduce lead in drinking water to below the EPA action level of 15 ppb while being tested under a variety of conditions as specified under the National Sanitation Foundation (NSF) International Standard 53 test protocol. 37 refs., 9 figs., 1 tab.« less

The metabolic enzyme fructose-1,6-bisphosphate aldolase acts as a transcriptional regulator in pathogenic Francisella.

PubMed

Ziveri, Jason; Tros, Fabiola; Guerrera, Ida Chiara; Chhuon, Cerina; Audry, Mathilde; Dupuis, Marion; Barel, Monique; Korniotis, Sarantis; Fillatreau, Simon; Gales, Lara; Cahoreau, Edern; Charbit, Alain

2017-10-11

The enzyme fructose-bisphosphate aldolase occupies a central position in glycolysis and gluconeogenesis pathways. Beyond its housekeeping role in metabolism, fructose-bisphosphate aldolase has been involved in additional functions and is considered as a potential target for drug development against pathogenic bacteria. Here, we address the role of fructose-bisphosphate aldolase in the bacterial pathogen Francisella novicida. We demonstrate that fructose-bisphosphate aldolase is important for bacterial multiplication in macrophages in the presence of gluconeogenic substrates. In addition, we unravel a direct role of this metabolic enzyme in transcription regulation of genes katG and rpoA, encoding catalase and an RNA polymerase subunit, respectively. We propose a model in which fructose-bisphosphate aldolase participates in the control of host redox homeostasis and the inflammatory immune response.The enzyme fructose-bisphosphate aldolase (FBA) plays central roles in glycolysis and gluconeogenesis. Here, Ziveri et al. show that FBA of the pathogen Francisella novicida acts, in addition, as a transcriptional regulator and is important for bacterial multiplication in macrophages.

CMB-lensing beyond the Born approximation

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

Marozzi, Giovanni; Fanizza, Giuseppe; Durrer, Ruth

2016-09-01

We investigate the weak lensing corrections to the cosmic microwave background temperature anisotropies considering effects beyond the Born approximation. To this aim, we use the small deflection angle approximation, to connect the lensed and unlensed power spectra, via expressions for the deflection angles up to third order in the gravitational potential. While the small deflection angle approximation has the drawback to be reliable only for multipoles ℓ ∼< 2500, it allows us to consistently take into account the non-Gaussian nature of cosmological perturbation theory beyond the linear level. The contribution to the lensed temperature power spectrum coming from the non-Gaussianmore » nature of the deflection angle at higher order is a new effect which has not been taken into account in the literature so far. It turns out to be the leading contribution among the post-Born lensing corrections. On the other hand, the effect is smaller than corrections coming from non-linearities in the matter power spectrum, and its imprint on CMB lensing is too small to be seen in present experiments.« less

Recovery of singularities from a backscattering Born approximation for a biharmonic operator in 3D

NASA Astrophysics Data System (ADS)

Tyni, Teemu

2018-04-01

We consider a backscattering Born approximation for a perturbed biharmonic operator in three space dimensions. Previous results on this approach for biharmonic operator use the fact that the coefficients are real-valued to obtain the reconstruction of singularities in the coefficients. In this text we drop the assumption about real-valued coefficients and also establish the recovery of singularities for complex coefficients. The proof uses mapping properties of the Radon transform.

Effects of Training in Functional Behavior Assessment

ERIC Educational Resources Information Center

Dukes, Charles; Rosenberg, Howard; Brady, Michael

2008-01-01

The purpose of this study was to investigate the effectiveness of training special education teachers in the process of functional behavioral assessment (FBA) and subsequent development of recommendations to promote behavior change. An original evaluation instrument was developed that included measures of special education teachers' knowledge of…

Individualized Positive Behavior Support in School Settings: A Meta-Analysis

ERIC Educational Resources Information Center

Goh, Ailsa E.; Bambara, Linda M.

2012-01-01

This meta-analysis examined school-based intervention research based on functional behavioral assessment (FBA) to determine the effectiveness of key individualized positive behavior support (IPBS) practices in school settings. In all, 83 studies representing 145 participants were included in the meta-analysis. Intervention, maintenance, and…

Semiclassical approximation of the Wheeler-DeWitt equation: arbitrary orders and the question of unitarity

NASA Astrophysics Data System (ADS)

Kiefer, Claus; Wichmann, David

2018-06-01

We extend the Born-Oppenheimer type of approximation scheme for the Wheeler-DeWitt equation of canonical quantum gravity to arbitrary orders in the inverse Planck mass squared. We discuss in detail the origin of unitarity violation in this scheme and show that unitarity can be restored by an appropriate modification which requires back reaction from matter onto the gravitational sector. In our analysis, we heavily rely on the gauge aspects of the standard Born-Oppenheimer scheme in molecular physics.

How will millennials impact freight flows in Texas? Final report.

DOT National Transportation Integrated Search

2017-01-01

Millennials (born between 1983 and 2000) represent approximately 25 percent of the population in the United States and already outnumber baby boomers (born between 1946 and 1964) in the current population (15,16,17). As young adults, millennials are ...

The Effects of Function-Based Self-Management Interventions on Student Behavior

ERIC Educational Resources Information Center

Hansen, Blake D.; Wills, Howard P.; Kamps, Debra M.; Greenwood, Charles R.

2014-01-01

Children with emotional and behavioral disorders (E/BD) struggle to achieve social and academic outcomes. Many studies have demonstrated self-management interventions to be effective at reducing problem behavior and increasing positive social and academic behaviors. Functional behavior assessment (FBA) information may be used in designing…

Acceptability of Functional Behavioral Assessment Procedures to Special Educators and School Psychologists

ERIC Educational Resources Information Center

O'Neill, Robert E.; Bundock, Kaitlin; Kladis, Kristin; Hawken, Leanne S.

2015-01-01

This survey study assessed the acceptability of a variety of functional behavioral assessment (FBA) procedures (i.e., functional assessment interviews, rating scales/questionnaires, systematic direct observations, functional analysis manipulations) to a national sample of 123 special educators and a state sample of 140 school psychologists.…

Recent Case Law Regarding Functional Behavioral Assessments: Implications for Practice

ERIC Educational Resources Information Center

Losinski, Mickey L.; Katsiyannis, Antonis; Ryan, Joseph B.

2014-01-01

While functional behavioral assessments (FBAs) are currently federally mandated requirements, public schools have not been provided clear federal guidance concerning what constitutes an acceptable FBA through Individuals With Disabilities Education Act or related regulations. The purpose of this article is to examine recent rulings regarding FBAs…

Functional Behavioral Assessment-Based Interventions. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2016

2016-01-01

This intervention report presents findings from a systematic review of "functional behavioral assessment-based interventions" conducted using the WWC Procedures and Standards Handbook, version 3.0, and the Children Identified With or At Risk for an Emotional Disturbance review protocol, version 3.0. Functional behavioral assessment (FBA)…

Promoting Self-Determination throughout the FBA/BIP Process

ERIC Educational Resources Information Center

Korinek, Lori

2015-01-01

Student behavior that interferes with teaching and learning remains a major concern for educators. In-school and postschool outcomes for students with challenging behaviors are among the poorest. Many of these students require a functional behavioral assessment and intervention plan to become more successful. Externally-driven behavior change…

Functional Behavioral Assessments and Intervention Plans in Early Intervention Settings.

ERIC Educational Resources Information Center

LaRocque, Michelle; Brown, Sharan E.; Johnson, Kurt L.

2001-01-01

This article advocates the use of functional behavioral assessments (FBAs) and behavior intervention plans (BIPs) in the development of Individualized Family Service Plans for children with or at risk of developing behavioral disorders. It describes the FBA and BIP processes and proposes a parent collaborative model for assessment and…

State Special Education Laws for Functional Behavioral Assessment and Behavior Intervention Plans

ERIC Educational Resources Information Center

Zirkel, Perry A.

2011-01-01

A comprehensive search identified 31 state statutes and regulations specific to functional behavioral assessments (FBA) and behavior intervention plans (BIP) in the special education context. A systematic tabulation of the state law provisions that exceed the rather narrow foundation requirements of the Individuals with Disabilities Education Act…

Factors in Teacher Adherence to Treatment.

ERIC Educational Resources Information Center

Gum, Louann

Treatment integrity, a measure of how accurately a treatment is carried out, is integral to the concept of effective behavioral analysis and intervention. This study sought to correlate teachers' perceptions of the functional behavior assessment and behavior intervention process (FBA/BIP) with their confidence that the process is an effective and…

Distorted-wave methods for electron capture in ion-atom collisions

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

Burgdoerfer, J.; Taulbjerg, K.

1986-05-01

Distorted-wave methods for electron capture are discussed with emphasis on the surface term in the T matrix and on the properties of the associated integral equations. The surface term is generally nonvanishing if the distorted waves are sufficiently accurate to include parts of the considered physical process. Two examples are considered in detail. If distorted waves of the strong-potential Born-approximation (SPB) type are employed the surface term supplies the first-Born-approximation part of the T matrix. The surface term is shown to vanish in the continuum-distorted-wave (CDW) method. The integral kernel is in either case free of the dangerous disconnected termsmore » discussed by Greider and Dodd but the CDW theory is peculiar in the sense that its first-order approximation (CDW1) excludes a specific on-shell portion of the double-scattering term that is closely connected with the classical Thomas process. The latter is described by the second-order term in the CDW series. The distorted-wave Born approximation with SPB waves is shown to be free of divergences. In the limit of asymmetric collisions the DWB suggests a modification of the SPB approximation to avoid the divergence problem recently identified by Dewangan and Eichler.« less

Many-body Green’s function theory for electron-phonon interactions: The Kadanoff-Baym approach to spectral properties of the Holstein dimer

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

Säkkinen, Niko; Peng, Yang; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin-Dahlem

2015-12-21

We present a Kadanoff-Baym formalism to study time-dependent phenomena for systems of interacting electrons and phonons in the framework of many-body perturbation theory. The formalism takes correctly into account effects of the initial preparation of an equilibrium state and allows for an explicit time-dependence of both the electronic and phononic degrees of freedom. The method is applied to investigate the charge neutral and non-neutral excitation spectra of a homogeneous, two-site, two-electron Holstein model. This is an extension of a previous study of the ground state properties in the Hartree (H), partially self-consistent Born (Gd) and fully self-consistent Born (GD) approximationsmore » published in Säkkinen et al. [J. Chem. Phys. 143, 234101 (2015)]. Here, the homogeneous ground state solution is shown to become unstable for a sufficiently strong interaction while a symmetry-broken ground state solution is shown to be stable in the Hartree approximation. Signatures of this instability are observed for the partially self-consistent Born approximation but are not found for the fully self-consistent Born approximation. By understanding the stability properties, we are able to study the linear response regime by calculating the density-density response function by time-propagation. This amounts to a solution of the Bethe-Salpeter equation with a sophisticated kernel. The results indicate that none of the approximations is able to describe the response function during or beyond the bipolaronic crossover for the parameters investigated. Overall, we provide an extensive discussion on when the approximations are valid and how they fail to describe the studied exact properties of the chosen model system.« less

Comment on “On the quantum theory of molecules” [J. Chem. Phys. 137, 22A544 (2012)

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

Sutcliffe, Brian T., E-mail: bsutclif@ulb.ac.be; Woolley, R. Guy

2014-01-21

In our previous paper [B. T. Sutcliffe and R. G. Woolley, J. Chem. Phys. 137, 22A544 (2012)] we argued that the Born-Oppenheimer approximation could not be based on an exact transformation of the molecular Schrödinger equation. In this Comment we suggest that the fundamental reason for the approximate nature of the Born-Oppenheimer model is the lack of a complete set of functions for the electronic space, and the need to describe the continuous spectrum using spectral projection.

Divergence of the total cross section for three body rearrangement collisions with coulomb interactions

NASA Technical Reports Server (NTRS)

Omidvar, K.

1972-01-01

Three charged particles 1, 2, 3 collide according to the reaction 1+(2+3) yields (1+3)+2, where (2+3) and (1+3) are hydrogenlike bound states. It is shown when (1+3) is in a highly excited state n, due to the repulsive potential, the cross section in the first Born approximation behaves as 1/n which makes the total cross section to diverge like ln n. The total cross sections in the higher orders of the Born approximation are similarly divergent logarithmically.

The Use of Structural Behavioral Assessment to Develop Interventions for Secondary Students Exhibiting Challenging Behaviors

ERIC Educational Resources Information Center

Losinski, Mickey; Maag, John W.; Katsiyannis, Antonis; Ryan, Joseph B.

2015-01-01

Structural behavioral assessment (SBA) involves a series of heuristic approaches similar to those used with functional behavioral assessment (FBA). It involves assessing contextual variables that precede the occurrence of a behavior. These variables have also been termed antecedents, setting events, or establishing operations. Once these variables…

Positive Behavior Support for a Child with Inattentive Behavior in a Japanese Regular Classroom

ERIC Educational Resources Information Center

Baba, Chiharu; Tanaka-Matsumi, Junko

2011-01-01

Nondisruptive problem behaviors exist to a large extent in group-oriented Japanese regular classrooms. However, many children remain untreated. We implemented an antecedent-based functional behavioral assessment (FBA) and developed a behavioral support program for a first-grade boy who exhibited inattentive behavior in a Japanese regular…

Questions about Behavioral Function (QABF): Adaptation and Validation of the Spanish Version

ERIC Educational Resources Information Center

Simo-Pinatella, David; Alomar-Kurz, Elisabeth; Font-Roura, Josep; Gine, Climent; Matson, Johnny L.; Cifre, Ignacio

2013-01-01

People with intellectual disabilities (ID) often engage in problem behaviors, such as verbal or physical aggression, property destruction, or self-injury. These behaviors become a challenge for the families and for professionals. Functional behavioral assessment (FBA) is a method used to identify variables that influence or maintain challenging…

Multidimensional Functional Behaviour Assessment within a Problem Analysis Framework.

ERIC Educational Resources Information Center

Ryba, Ken; Annan, Jean

This paper presents a new approach to contextualized problem analysis developed for use with multimodal Functional Behaviour Assessment (FBA) at Massey University in Auckland, New Zealand. The aim of problem analysis is to simplify complex problems that are difficult to understand. It accomplishes this by providing a high order framework that can…

Transitioning Non-Traditional Students to an Undergraduate Business Program

ERIC Educational Resources Information Center

Bailey, April E.; Marsh, Michael T.

2010-01-01

This paper reports experiences of non-traditional students in a specially designed section of seminar course which was primarily designed for first-year traditional business students. The College of Business's BSN101, Foundations of Business Administration (FBA), is designed to serves as a course to assist the students with transitioning into the…

Implementing and Evaluating Effective Professional Development in Functional Behavioral Assessment in Rural Schools.

ERIC Educational Resources Information Center

Mitchem, Katherine; Richards, Ann; Wells, Deborah

The use of positive behavior supports (PBS) based on functional behavioral assessment (FBA) has produced dramatic improvements in problem behaviors of challenging students. This approach is a long-term strategy to reduce inappropriate behavior, teach more appropriate behavior, and provide contextual supports necessary for successful outcomes. Yet…

An Evidence-Driven, Solution-Focused Approach to Functional Behavior Assessment Report Writing

ERIC Educational Resources Information Center

Farmer, Ryan L.; Floyd, Randy G.

2016-01-01

School-based practitioners are to implement and report functional behavior assessments (FBAs) that are consistent with both the research literature and the law, both federal and state. However, the literature regarding how best to document the FBA process is underdeveloped. A review of applied behavior analytic and school psychology literature as…

Facilitating Effective Team-Based Functional Behavioral Assessments in Typical School Settings

ERIC Educational Resources Information Center

Park, Kristy Lee

2007-01-01

School systems face the challenge of effectively and efficiently addressing the disciplinary needs of their students and providing a safe environment conducive to learning. The 1997 and 2004 reauthorization of the Individuals With Disabilities Education Act (IDEA) mandates the use of functional behavioral assessment (FBA) for students who, because…

An Evaluation of the Relative Effectiveness of Function-Based Consequent and Antecedent Interventions in a Preschool Setting

ERIC Educational Resources Information Center

von Schulz, Jonna H.; Dufrene, Brad A.; LaBrot, Zachary C.; Tingstrom, Daniel H.; Olmi, D. Joe; Radley, Keith; Mitchell, Rachel; Maldonado, Aimee

2018-01-01

Although there is substantial functional behavioral assessment (FBA) literature suggesting that function-based interventions are effective for improving problem behavior, only a limited number of studies have examined the effectiveness of function-based antecedent versus consequent interventions. Additionally, although there has been a recent…

Respiratory-aspirated 35-mm hairpin successfully retrieved with a Teflon® snare system under fluoroscopic guidance via a split endotracheal tube: a useful technique in cases of failed extraction by bronchoscopy and avoiding the need for a thoracotomy.

PubMed

Gill, S S; Pease, R A; Ashwin, C J; Gill, S S; Tait, N P

2012-09-01

Respiratory foreign body aspiration (FBA) is a common global health problem requiring prompt recognition and early treatment to prevent potentially fatal complications. The majority of FBAs are due to organic objects and treatment is usually via either endoscopic or surgical extraction. FBA of a straight hairpin has been described as a unique entity in the literature, occurring most commonly in females, particularly during adolescence. In the process of inserting hairpins, the pins will typically be between the teeth with the head tilted backwards, while tying their hair with both hands. This position increases the risk of aspiration, particularly if there is any sudden coughing or laughing. To our knowledge, this is the first case report of a 35-mm straight metallic hairpin foreign body that has been successfully retrieved by a radiological snare system under fluoroscopic guidance. This was achieved with the use of a split endotracheal tube, and therefore avoided the need for a thoracotomy in an adolescent female patient.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

PubMed

Toya, Yoshihiro; Shimizu, Hiroshi

2013-11-01

Rational engineering of metabolism is important for bio-production using microorganisms. Metabolic design based on in silico simulations and experimental validation of the metabolic state in the engineered strain helps in accomplishing systematic metabolic engineering. Flux balance analysis (FBA) is a method for the prediction of metabolic phenotype, and many applications have been developed using FBA to design metabolic networks. Elementary mode analysis (EMA) and ensemble modeling techniques are also useful tools for in silico strain design. The metabolome and flux distribution of the metabolic pathways enable us to evaluate the metabolic state and provide useful clues to improve target productivity. Here, we reviewed several computational applications for metabolic engineering by using genome-scale metabolic models of microorganisms. We also discussed the recent progress made in the field of metabolomics and (13)C-metabolic flux analysis techniques, and reviewed these applications pertaining to bio-production development. Because these in silico or experimental approaches have their respective advantages and disadvantages, the combined usage of these methods is complementary and effective for metabolic engineering. Copyright © 2013 Elsevier Inc. All rights reserved.

Systematic development and optimization of chemically defined medium supporting high cell density growth of Bacillus coagulans.

PubMed

Chen, Yu; Dong, Fengqing; Wang, Yonghong

2016-09-01

With determined components and experimental reducibility, the chemically defined medium (CDM) and the minimal chemically defined medium (MCDM) are used in many metabolism and regulation studies. This research aimed to develop the chemically defined medium supporting high cell density growth of Bacillus coagulans, which is a promising producer of lactic acid and other bio-chemicals. In this study, a systematic methodology combining the experimental technique with flux balance analysis (FBA) was proposed to design and simplify a CDM. The single omission technique and single addition technique were employed to determine the essential and stimulatory compounds, before the optimization of their concentrations by the statistical method. In addition, to improve the growth rationally, in silico omission and addition were performed by FBA based on the construction of a medium-size metabolic model of B. coagulans 36D1. Thus, CDMs were developed to obtain considerable biomass production of at least five B. coagulans strains, in which two model strains B. coagulans 36D1 and ATCC 7050 were involved.

Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies.

PubMed

Banerjee, Chiranjib; Singh, Puneet Kumar; Shukla, Pratyoosh

2016-03-01

Exploring the efficiency of algae to produce remarkable products can be directly benefitted by studying its mechanism at systems level. Recent advents in biotechnology like flux balance analysis (FBA), genomics and in silico proteomics minimize the wet lab exertion. It is understood that FBA predicts the metabolic products, metabolic pathways and alternative pathway to maximize the desired product, and these are key components for microalgae bio-engineering. This review encompasses recent transgenesis techniques and metabolic engineering strategies applied to different microalgae for improving different traits. Further it also throws light on RNAi and riboswitch engineering based methods which may be advantageous for high throughput microalgal research. A valid and optimally designed microalga can be developed where every engineering strategies meet each other successfully and will definitely fulfill the market needs. It is also to be noted that Omics (viz. genetic and metabolic manipulation with bioinformatics) should be integrated to develop a strain which could prove to be a futuristic solution for sustainable development for energy. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using foreground/background analysis to determine leaf and canopy chemistry

NASA Technical Reports Server (NTRS)

Pinzon, J. E.; Ustin, S. L.; Hart, Q. J.; Jacquemoud, S.; Smith, M. O.

1995-01-01

Spectral Mixture Analysis (SMA) has become a well established procedure for analyzing imaging spectrometry data, however, the technique is relatively insensitive to minor sources of spectral variation (e.g., discriminating stressed from unstressed vegetation and variations in canopy chemistry). Other statistical approaches have been tried e.g., stepwise multiple linear regression analysis to predict canopy chemistry. Grossman et al. reported that SMLR is sensitive to measurement error and that the prediction of minor chemical components are not independent of patterns observed in more dominant spectral components like water. Further, they observed that the relationships were strongly dependent on the mode of expressing reflectance (R, -log R) and whether chemistry was expressed on a weight (g/g) or are basis (g/sq m). Thus, alternative multivariate techniques need to be examined. Smith et al. reported a revised SMA that they termed Foreground/Background Analysis (FBA) that permits directing the analysis along any axis of variance by identifying vectors through the n-dimensional spectral volume orthonormal to each other. Here, we report an application of the FBA technique for the detection of canopy chemistry using a modified form of the analysis.

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

PubMed Central

Orman, Mehmet A.; Berthiaume, Francois; Androulakis, Ioannis P.; Ierapetritou, Marianthi G.

2013-01-01

Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted. PMID:22196224

Vehicle tracking using fuzzy-based vehicle detection window with adaptive parameters

NASA Astrophysics Data System (ADS)

Chitsobhuk, Orachat; Kasemsiri, Watjanapong; Glomglome, Sorayut; Lapamonpinyo, Pipatphon

2018-04-01

In this paper, fuzzy-based vehicle tracking system is proposed. The proposed system consists of two main processes: vehicle detection and vehicle tracking. In the first process, the Gradient-based Adaptive Threshold Estimation (GATE) algorithm is adopted to provide the suitable threshold value for the sobel edge detection. The estimated threshold can be adapted to the changes of diverse illumination conditions throughout the day. This leads to greater vehicle detection performance compared to a fixed user's defined threshold. In the second process, this paper proposes the novel vehicle tracking algorithms namely Fuzzy-based Vehicle Analysis (FBA) in order to reduce the false estimation of the vehicle tracking caused by uneven edges of the large vehicles and vehicle changing lanes. The proposed FBA algorithm employs the average edge density and the Horizontal Moving Edge Detection (HMED) algorithm to alleviate those problems by adopting fuzzy rule-based algorithms to rectify the vehicle tracking. The experimental results demonstrate that the proposed system provides the high accuracy of vehicle detection about 98.22%. In addition, it also offers the low false detection rates about 3.92%.

Born Hartree Bethe approximation in the theory of inelastic electron molecule scattering

NASA Astrophysics Data System (ADS)

Kretinin, I. Yu; Krisilov, A. V.; Zon, B. A.

2008-11-01

We propose a new approximation in the theory of inelastic electron atom and electron molecule scattering. Taking into account the completeness property of atomic and molecular wavefunctions, considered in the Hartree approximation, and using Bethe's parametrization for electronic excitations during inelastic collisions via the mean excitation energy, we show that the calculation of the inelastic total integral cross-sections (TICS), in the framework of the first Born approximation, involves only the ground-state wavefunction. The final analytical formula obtained for the TICS, i.e. for the sum of elastic and inelastic ones, contains no adjusting parameters. Calculated TICS for electron scattering by light atoms and molecules (He, Ne, and H2) are in good agreement within the experimental data; results show asymptotic coincidence for heavier ones (Ar, Kr, Xe and N2).

A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast

PubMed Central

Cankorur-Cetinkaya, Ayca; Dereli, Elif; Eraslan, Serpil; Karabekmez, Erkan; Dikicioglu, Duygu; Kirdar, Betul

2012-01-01

Background Understanding the dynamic mechanism behind the transcriptional organization of genes in response to varying environmental conditions requires time-dependent data. The dynamic transcriptional response obtained by real-time RT-qPCR experiments could only be correctly interpreted if suitable reference genes are used in the analysis. The lack of available studies on the identification of candidate reference genes in dynamic gene expression studies necessitates the identification and the verification of a suitable gene set for the analysis of transient gene expression response. Principal Findings In this study, a candidate reference gene set for RT-qPCR analysis of dynamic transcriptional changes in Saccharomyces cerevisiae was determined using 31 different publicly available time series transcriptome datasets. Ten of the twelve candidates (TPI1, FBA1, CCW12, CDC19, ADH1, PGK1, GCN4, PDC1, RPS26A and ARF1) we identified were not previously reported as potential reference genes. Our method also identified the commonly used reference genes ACT1 and TDH3. The most stable reference genes from this pool were determined as TPI1, FBA1, CDC19 and ACT1 in response to a perturbation in the amount of available glucose and as FBA1, TDH3, CCW12 and ACT1 in response to a perturbation in the amount of available ammonium. The use of these newly proposed gene sets outperformed the use of common reference genes in the determination of dynamic transcriptional response of the target genes, HAP4 and MEP2, in response to relaxation from glucose and ammonium limitations, respectively. Conclusions A candidate reference gene set to be used in dynamic real-time RT-qPCR expression profiling in yeast was proposed for the first time in the present study. Suitable pools of stable reference genes to be used under different experimental conditions could be selected from this candidate set in order to successfully determine the expression profiles for the genes of interest. PMID:22675547

Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools

PubMed Central

Reznik, Ed; Mehta, Pankaj; Segrè, Daniel

2013-01-01

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price) cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady state constraints carries biologically significant information on the processes that control intracellular metabolites in the cell. PMID:24009492

My Body Looks Like That Girl’s: Body Mass Index Modulates Brain Activity during Body Image Self-Reflection among Young Women

PubMed Central

Wen, Xin; She, Ying; Vinke, Petra Corianne; Chen, Hong

2016-01-01

Body image distress or body dissatisfaction is one of the most common consequences of obesity and overweight. We investigated the neural bases of body image processing in overweight and average weight young women to understand whether brain regions that were previously found to be involved in processing self-reflective, perspective and affective components of body image would show different activation between two groups. Thirteen overweight (O-W group, age = 20.31±1.70 years) and thirteen average weight (A-W group, age = 20.15±1.62 years) young women underwent functional magnetic resonance imaging while performing a body image self-reflection task. Among both groups, whole-brain analysis revealed activations of a brain network related to perceptive and affective components of body image processing. ROI analysis showed a main effect of group in ACC as well as a group by condition interaction within bilateral EBA, bilateral FBA, right IPL, bilateral DLPFC, left amygdala and left MPFC. For the A-W group, simple effect analysis revealed stronger activations in Thin-Control compared to Fat-Control condition within regions related to perceptive (including bilateral EBA, bilateral FBA, right IPL) and affective components of body image processing (including bilateral DLPFC, left amygdala), as well as self-reference (left MPFC). The O-W group only showed stronger activations in Fat-Control than in Thin-Control condition within regions related to the perceptive component of body image processing (including left EBA and left FBA). Path analysis showed that in the Fat-Thin contrast, body dissatisfaction completely mediated the group difference in brain response in left amygdala across the whole sample. Our data are the first to demonstrate differences in brain response to body pictures between average weight and overweight young females involved in a body image self-reflection task. These results provide insights for understanding the vulnerability to body image distress among overweight or obese young females. PMID:27764116

Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures-Systems biology-based interpretation using genome-scale metabolic flux balance model and multivariate data analysis.

PubMed

Reimonn, Thomas M; Park, Seo-Young; Agarabi, Cyrus D; Brorson, Kurt A; Yoon, Seongkyu

2016-09-01

Genome-scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745-753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome-scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163-1173, 2016. © 2016 American Institute of Chemical Engineers.

My Body Looks Like That Girl's: Body Mass Index Modulates Brain Activity during Body Image Self-Reflection among Young Women.

PubMed

Gao, Xiao; Deng, Xiao; Wen, Xin; She, Ying; Vinke, Petra Corianne; Chen, Hong

2016-01-01

Body image distress or body dissatisfaction is one of the most common consequences of obesity and overweight. We investigated the neural bases of body image processing in overweight and average weight young women to understand whether brain regions that were previously found to be involved in processing self-reflective, perspective and affective components of body image would show different activation between two groups. Thirteen overweight (O-W group, age = 20.31±1.70 years) and thirteen average weight (A-W group, age = 20.15±1.62 years) young women underwent functional magnetic resonance imaging while performing a body image self-reflection task. Among both groups, whole-brain analysis revealed activations of a brain network related to perceptive and affective components of body image processing. ROI analysis showed a main effect of group in ACC as well as a group by condition interaction within bilateral EBA, bilateral FBA, right IPL, bilateral DLPFC, left amygdala and left MPFC. For the A-W group, simple effect analysis revealed stronger activations in Thin-Control compared to Fat-Control condition within regions related to perceptive (including bilateral EBA, bilateral FBA, right IPL) and affective components of body image processing (including bilateral DLPFC, left amygdala), as well as self-reference (left MPFC). The O-W group only showed stronger activations in Fat-Control than in Thin-Control condition within regions related to the perceptive component of body image processing (including left EBA and left FBA). Path analysis showed that in the Fat-Thin contrast, body dissatisfaction completely mediated the group difference in brain response in left amygdala across the whole sample. Our data are the first to demonstrate differences in brain response to body pictures between average weight and overweight young females involved in a body image self-reflection task. These results provide insights for understanding the vulnerability to body image distress among overweight or obese young females.

Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling.

PubMed

Chaudhary, Neha; Tøndel, Kristin; Bhatnagar, Rakesh; dos Santos, Vítor A P Martins; Puchałka, Jacek

2016-03-01

Genome-Scale Metabolic Reconstructions (GSMRs), along with optimization-based methods, predominantly Flux Balance Analysis (FBA) and its derivatives, are widely applied for assessing and predicting the behavior of metabolic networks upon perturbation, thereby enabling identification of potential novel drug targets and biotechnologically relevant pathways. The abundance of alternate flux profiles has led to the evolution of methods to explore the complete solution space aiming to increase the accuracy of predictions. Herein we present a novel, generic algorithm to characterize the entire flux space of GSMR upon application of FBA, leading to the optimal value of the objective (the optimal flux space). Our method employs Modified Latin-Hypercube Sampling (LHS) to effectively border the optimal space, followed by Principal Component Analysis (PCA) to identify and explain the major sources of variability within it. The approach was validated with the elementary mode analysis of a smaller network of Saccharomyces cerevisiae and applied to the GSMR of Pseudomonas aeruginosa PAO1 (iMO1086). It is shown to surpass the commonly used Monte Carlo Sampling (MCS) in providing a more uniform coverage for a much larger network in less number of samples. Results show that although many fluxes are identified as variable upon fixing the objective value, majority of the variability can be reduced to several main patterns arising from a few alternative pathways. In iMO1086, initial variability of 211 reactions could almost entirely be explained by 7 alternative pathway groups. These findings imply that the possibilities to reroute greater portions of flux may be limited within metabolic networks of bacteria. Furthermore, the optimal flux space is subject to change with environmental conditions. Our method may be a useful device to validate the predictions made by FBA-based tools, by describing the optimal flux space associated with these predictions, thus to improve them.

Functional Behavioral Assessment for a Boy with Duchenne Muscular Dystrophy and Problem Behavior: A Case Study from Greece

ERIC Educational Resources Information Center

Theodoridou, Zoe; Koutsoklenis, Athanasios

2013-01-01

This article focuses on the application of functional behavioral assessment (FBA) to design a positive behavior intervention (PBI) for a boy with Duchenne muscular dystrophy (DMD) who encounters serious difficulties at the mainstream school because of behavioral problems and physical limitations. After the definition of problem behavior and its…

Coping with Challenging Behaviours of Children with Autism: Effectiveness of Brief Training Workshop for Frontline Staff in Special Education Settings

ERIC Educational Resources Information Center

Ling, C. Y. M.; Mak, W. W. S.

2012-01-01

Background: The present study examined the effectiveness of three staff training elements: psychoeducation (PE) on autism, introduction of functional behavioural analysis (FBA) and emotional management (EM), on the reaction of challenging behaviours for frontline staff towards children with autism in Hong Kong special education settings. Methods:…

A Comparison of Functional Behavioral Assessment and Functional Analysis Methodology among Students with Mild Disabilities

ERIC Educational Resources Information Center

Lewis, Timothy J.; Mitchell, Barbara S.; Harvey, Kristin; Green, Ambra; McKenzie, Jennifer

2015-01-01

Functional behavioral assessment (FBA) and functional analyses (FA) are grounded in the applied behavior analysis principle that posits problem behavior is functionally related to the environment in which it occurs and is maintained by either providing access to reinforcing outcomes or allowing the individual to avoid or escape that which they…

The Role of the Replacement Behavior in Function-Based Intervention

ERIC Educational Resources Information Center

Reeves, Linda M.; Ferro, Jolenea B.; Umbreit, John; Liaupsin, Carl J.

2017-01-01

Three students with autism spectrum disorder (ASD) who displayed off-task behavior participated in a two-phase study. In Phase 1, a functional behavioral assessment (FBA) was conducted for each student. In addition, an assessment of each student's ability to perform the replacement behavior identified that none of the participants was able to do…

Exploring the Link among Behavior Intervention Plans, Treatment Integrity, and Student Outcomes under Natural Educational Conditions

ERIC Educational Resources Information Center

Cook, Clayton R.; Mayer, G. Roy; Wright, Diana Browning; Kraemer, Bonnie; Wallace, Michele D.; Dart, Evan; Collins, Tai; Restori, Alberto

2012-01-01

Several researchers have argued that the functional behavior assessment (FBA) and behavior intervention plan (BIP) mandates in the Individuals With Disabilities Education Act of 2004 have gone beyond the current research base. For instance, although BIPs have been shown to improve student outcomes when implemented with strict control and oversight…

When to Use Functional Behavioral Assessment? Best Practice vs. Legal Guidance

ERIC Educational Resources Information Center

von Ravensberg, Heidi; Blakely, Allison

2014-01-01

When to conduct a functional behavioral assessment (FBA) is a question answered by both best practice and the law. The special education field continues to improve the effectiveness and efficiency of the functional behavioral assessment, an evidence-based technology that is the basis of a behavior intervention plan (BIP) and a cornerstone of the…

Teacher Involvement in the Development of Function-Based Behaviour Intervention Plans for Students with Challenging Behaviour

ERIC Educational Resources Information Center

O'Neill, Sue; Stephenson, Jennifer

2009-01-01

This article examines literature published since 1997 on functional behaviour assessment (FBA) and behaviour intervention plans (BIPs), involving school-based personnel, for children identified as having or being at risk of emotional/behavioural disorder (E/BD) in school settings. Of interest was the level of involvement of school-based personnel…

The Use of a Functional Behavioral Assessment-Based Self Management Intervention for Students with Emotional/Behavioral Disorders

ERIC Educational Resources Information Center

Rasheed, Saleem A.; Fore, Cecil, III; Jones, Arthur; Smith, Latisha

2012-01-01

The research literature on the use of Functional Behavioral Assessments (FBA) to develop Behavior Intervention Plans (BIP) for students with emotional/behavioral disorders, who present problem classroom behaviors for use in the schools, is well documented. There are school-wide, district-wide, and state-wide plans that are currently being…

Are We on the Right Course? Lessons Learned about Current FBA/BIP Practices in Schools

ERIC Educational Resources Information Center

Van Acker, Richard; Boreson, Lynn; Gable, Robert A.; Potterton, Thomas

2005-01-01

Schools across the nation have been charged with the task of conducting functional behavioral assessments (FBAs) to aid in the development of behavior intervention plans (BIPs) to address the challenging behavior of students with special education needs. In response, schools have initiated efforts to provide the various members of their student…

Determination of the charge of relativistic heavy nuclei from emulsion tracks

NASA Technical Reports Server (NTRS)

Morgan, S. H., Jr.; Eby, P. B.

1971-01-01

The number of delta rays with energies between 50 and 150 keV that are produced by heavy nuclei in emulsions is calculated. The Z(2) dependence predicted by the first Born approximation is corrected by a direct calculation of the Mott exact phase-shift scattering cross section. Comparisons are made with corrections predicted by the second Born approximation. When the phase-shift results are applied to the problem of charge identification, corrections of up to 4 units of charge for 1.457-GeV/nucleon nuclei with charge Z = 75 are found.

Measurements of the scattering of sound by a line vortex

NASA Technical Reports Server (NTRS)

Horne, W. C.

1983-01-01

This paper presents measurements of the phase and magnitude of the scattered field arising from the incidence of a monochromatic plane sound field as a steady vortex. The amplitude of the scattered field was found to vary linearly with the vortex strength, and with the incident wave amplitude and frequency as predicted by solutions based on the Born approximation. The scattered field was observed to be nonsingular in the incidence direction, and this was similar to predictions by the Parabolic Equation Method (PEM) rather than the Born approximation, which predicts singular behavior in the incidence direction.

Initial results from the Caltech/DSRI balloon-borne isotope experiment

NASA Technical Reports Server (NTRS)

Schindler, S. M.; Buffington, A.; Christian, E. C.; Grove, J. E.; Lau, K. H.; Stone, E. C.; Rasmussen, I. L.; Laursen, S.

1985-01-01

The Caltech/DSRI balloon-borne High Energy Isotope Spectrometer Telescope (HEIST) was flown successfully from Palestine, Texas on 14 May 1984. The experiment was designed to measure cosmic ray isotopic abundances from neon through iron, with incident particle energies from approximately 1.5 to 2.2 GeV/nucleon, depending on the element. During approximately 38 hours at float altitude, 10 to the 5th events were recorded with Z or = 6 and incident energies 1.5 GeV/nucleon. We present results from the ongoing data analysis associated with both the pre-flight Bevalac calibration and the flight data.

Coherent states, quantum gravity, and the Born-Oppenheimer approximation. I. General considerations

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

Stottmeister, Alexander, E-mail: alexander.stottmeister@gravity.fau.de; Thiemann, Thomas, E-mail: thomas.thiemann@gravity.fau.de

2016-06-15

This article, as the first of three, aims at establishing the (time-dependent) Born-Oppenheimer approximation, in the sense of space adiabatic perturbation theory, for quantum systems constructed by techniques of the loop quantum gravity framework, especially the canonical formulation of the latter. The analysis presented here fits into a rather general framework and offers a solution to the problem of applying the usual Born-Oppenheimer ansatz for molecular (or structurally analogous) systems to more general quantum systems (e.g., spin-orbit models) by means of space adiabatic perturbation theory. The proposed solution is applied to a simple, finite dimensional model of interacting spin systems,more » which serves as a non-trivial, minimal model of the aforesaid problem. Furthermore, it is explained how the content of this article and its companion affect the possible extraction of quantum field theory on curved spacetime from loop quantum gravity (including matter fields).« less

Generalized Born Models of Macromolecular Solvation Effects

NASA Astrophysics Data System (ADS)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Comparing University Academic Performances of HSC Students at the Three Art-Based Faculties

ERIC Educational Resources Information Center

Ismail, Noor Azina; Othman, Azmah

2006-01-01

University Malaya enrolls students from all states in Malaysia as well as a small number of students from overseas. The objective of this paper is to investigate the effect of past performance on students at three faculties, namely, Faculty of Economics and Administration(FEA), Faculty of Business and Accounting(FBA) and Faculty of Arts and Social…

Identification and expression of fructose-1,6-bisphosphate aldolase genes and their relations to oil content in developing seeds of tea oil tree (Camellia oleifera)

USDA-ARS?s Scientific Manuscript database

Tea oil tree (Camellia oleifera, Co) provides a fine edible oil source in China. Tea oil from the seeds is very beneficial to human health. Fructose-1,6-bisphosphate aldolase (FBA) hydrolyzes fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, two critical metab...

Addressing Challenging Behaviours in the General Education Setting: Conducting a Teacher-Based Functional Behavioural Assessment (FBA)

ERIC Educational Resources Information Center

Moreno, Gerardo

2011-01-01

When a student demonstrates a challenging or problematic behaviour in the classroom, the climate and the instructional experience can change dramatically for both the students and the classroom teacher. Before resorting to sanctions and punitive consequences, there is a series of steps a classroom teacher can conduct to reduce and replace the…

Functional Behavioral Assessment and Students at Risk for or with Emotional Disabilities: Current Issues and Considerations

ERIC Educational Resources Information Center

Gable, Robert A.; Park, Kristy Lee; Scott, Terrance M.

2014-01-01

The use of functional behavioral assessment (FBA) is an effective tool to address a wide range of severe behavior problems of students at risk for or with emotional disabilities (ED). However, the transformation of a procedure proven effective under highly-controlled clinical conditions to a practical and effective strategy for use in applied…

You Can Help Every Provider Have a Better Understanding of Functional Behavior Assessment! A Review of the Website: Basic FBA to BSP

ERIC Educational Resources Information Center

Shultz, Gwendolyn Joy; Havens, Nathan; Gurney, Beth Newberry; Burt, Jon

2017-01-01

Managing problematic classroom behavior is a challenge for many teachers, regardless of population. The website, www.basicfba.com, designed by researchers at Portland State University, offers teachers and practitioners a wealth of materials to assist them in conducting and maintaining a functional behavior assessment and behavior support plan.…

The Shock and Vibration Digest. Volume 16, Number 5

DTIC Science & Technology

1984-05-01

Lu, Y.P. and Everstine, G.C., "More on Finite Element Modelling of Damped Composite 45. Narayanan, S., Verma, J.P., and Mallik , A.K., Systems," J...78-78-FBA, p 461 (1978). 46. Narayanan, S. and Mallik , A.K., "Free Vibrations of Thin Walled Open Section Beams with Con- 34. Lunden, R., "Damping of

Implementation of a Single Comprehensive Function-Based Intervention across Multiple Classrooms for a High School Student

ERIC Educational Resources Information Center

Whitford, Denise K.; Liaupsin, Carl J.; Umbreit, John; Ferro, Jolenea B.

2013-01-01

A comprehensive function-based intervention was developed to address the chronic, high levels of off-task behavior by a 15-year-old ninth grade Caucasian male with learning disabilities and ADHD. A descriptive FBA identified that the student's off-task behavior was reinforced by peer attention and task avoidance. Intervention involved the…

Commentary on Zirkel: Judicial Rulings Specific to FBAs or BIPs under the IDEA and Corollary State Laws--An Update

ERIC Educational Resources Information Center

Horner, Robert H.; Yell, Mitchell L.

2017-01-01

The authors discuss the journal article by Perry Zirkel on legal action in regard to functional behavioral assessment (FBA) and behavior intervention plans (BIPs). They contend that the Zirkel article opens larger questions that will be central to ongoing discussions at the national, state, district, school, and family levels. Such issues include…

A Comparison of Functional Behavior Assessment Methodologies with Young Children: Descriptive Methods and Functional Analysis

ERIC Educational Resources Information Center

Alter, Peter J.; Conroy, Maureen A.; Mancil, G. Rich; Haydon, Todd

2008-01-01

The use of functional behavior assessment (FBA) to guide the development of behavior intervention plans continues to increase since they were first mandated in IDEA (Individuals with Disabilities Education Act Amendments of 1997, 20 U.S.C. Section 1400 et seq, 1997). A variety of indirect and direct instruments have been developed to facilitate…

An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies.

PubMed

Toro, León; Pinilla, Laura; Avignone-Rossa, Claudio; Ríos-Estepa, Rigoberto

2018-05-01

In this work, we expanded and updated a genome-scale metabolic model of Streptomyces clavuligerus. The model includes 1021 genes and 1494 biochemical reactions; genome-reaction information was curated and new features related to clavam metabolism and to the biomass synthesis equation were incorporated. The model was validated using experimental data from the literature and simulations were performed to predict cellular growth and clavulanic acid biosynthesis. Flux balance analysis (FBA) showed that limiting concentrations of phosphate and an excess of ammonia accumulation are unfavorable for growth and clavulanic acid biosynthesis. The evaluation of different objective functions for FBA showed that maximization of ATP yields the best predictions for cellular behavior in continuous cultures, while the maximization of growth rate provides better predictions for batch cultures. Through gene essentiality analysis, 130 essential genes were found using a limited in silico media, while 100 essential genes were identified in amino acid-supplemented media. Finally, a strain design was carried out to identify candidate genes to be overexpressed or knocked out so as to maximize antibiotic biosynthesis. Interestingly, potential metabolic engineering targets, identified in this study, have not been tested experimentally.

Fast flux module detection using matroid theory.

PubMed

Reimers, Arne C; Bruggeman, Frank J; Olivier, Brett G; Stougie, Leen

2015-05-01

Flux balance analysis (FBA) is one of the most often applied methods on genome-scale metabolic networks. Although FBA uniquely determines the optimal yield, the pathway that achieves this is usually not unique. The analysis of the optimal-yield flux space has been an open challenge. Flux variability analysis is only capturing some properties of the flux space, while elementary mode analysis is intractable due to the enormous number of elementary modes. However, it has been found by Kelk et al. (2012) that the space of optimal-yield fluxes decomposes into flux modules. These decompositions allow a much easier but still comprehensive analysis of the optimal-yield flux space. Using the mathematical definition of module introduced by Müller and Bockmayr (2013b), we discovered useful connections to matroid theory, through which efficient algorithms enable us to compute the decomposition into modules in a few seconds for genome-scale networks. Using that every module can be represented by one reaction that represents its function, in this article, we also present a method that uses this decomposition to visualize the interplay of modules. We expect the new method to replace flux variability analysis in the pipelines for metabolic networks.

Expressive Language in Preschoolers Born Preterm: Results of Language Sample Analysis and Standardized Assessment

ERIC Educational Resources Information Center

Imgrund, Caitlin

2017-01-01

Children born preterm constitute one of the largest populations of children at risk for the development of language impairments. A little over one in ten pregnancies result in a preterm birth and approximately 25% of these children go on to experience subsequent difficulties with language (CDC, 2015; Foster-Cohen, Friesen, Champion, &…

Immunological control of ticks and tick-borne diseases that impact cattle health and production in Mexico

USDA-ARS?s Scientific Manuscript database

The cattle industry is one of the most important agroeconomic activities in Mexico. The national herd is estimated to include approximately 33.5 million head of cattle. Ticks and tick-borne diseases are principal factors with a negative impact on cattle health and production in Mexico. The most econ...

Communication: On the calculation of time-dependent electron flux within the Born-Oppenheimer approximation: A flux-flux reflection principle

NASA Astrophysics Data System (ADS)

Albert, Julian; Hader, Kilian; Engel, Volker

2017-12-01

It is commonly assumed that the time-dependent electron flux calculated within the Born-Oppenheimer (BO) approximation vanishes. This is not necessarily true if the flux is directly determined from the continuity equation obeyed by the electron density. This finding is illustrated for a one-dimensional model of coupled electronic-nuclear dynamics. There, the BO flux is in perfect agreement with the one calculated from a solution of the time-dependent Schrödinger equation for the coupled motion. A reflection principle is derived where the nuclear BO flux is mapped onto the electronic flux.

First-principles calculations reveal controlling principles for carrier mobilities in semiconductors

DOE PAGES

Wu, Yu -Ning; Zhang, Xiaoguang; Pantelides, Sokrates T.; ...

2016-10-11

It has long been believed that carrier mobilities in semiconductors can be calculated by Fermi s golden rule (Born approximation). Phenomenological models for scattering amplitudes are typically used for engineering- level device modeling. Here we introduce a parameter-free, first-principles approach based on complex- wavevector energy bands that does not invoke the Born approximation. We show that phonon-limited mobility is controlled by low-resistivity percolation paths and that in ionized-impurity scattering one must account for the effect of the screening charge, which cancels most of the Coulomb tail.Finally, calculated electron mobilities in silicon are in agreement with experimental data.

Comparing the role of the height of men and women in the marriage market.

PubMed

Yamamura, Eiji; Tsutsui, Yoshiro

2017-08-01

This paper explores how the role of men and women's height in the marriage market has changed across generations. Using individual-level data from Japan, we compared the effect of height on marriages between men and women, and investigated how the effect of height on marriage has changed across generations. Our key findings are: (1) for men born before 1965, a 1% increase in height led to an approximately 0.56% increase in the probability of being married. Conversely, for women born before 1965, a 1% increase in height led to an approximately 0.56% decrease in the probability of being married. (2) For men born in or after 1965, a 1% increase in height led to an approximately 1.05% (0.18%) increase (decrease) in the probability of being married (divorced). However, the height effect was not present for women. Japan experienced astounding economic development after World War II, which resulted in changes in its economic and social structure. These changes may have also altered the role of height for Japanese men and women in the marriage market. Copyright © 2017 Elsevier B.V. All rights reserved.

Many-body Green’s function theory for electron-phonon interactions: Ground state properties of the Holstein dimer

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

Säkkinen, Niko; Leeuwen, Robert van; Peng, Yang

2015-12-21

We study ground-state properties of a two-site, two-electron Holstein model describing two molecules coupled indirectly via electron-phonon interaction by using both exact diagonalization and self-consistent diagrammatic many-body perturbation theory. The Hartree and self-consistent Born approximations used in the present work are studied at different levels of self-consistency. The governing equations are shown to exhibit multiple solutions when the electron-phonon interaction is sufficiently strong, whereas at smaller interactions, only a single solution is found. The additional solutions at larger electron-phonon couplings correspond to symmetry-broken states with inhomogeneous electron densities. A comparison to exact results indicates that this symmetry breaking is stronglymore » correlated with the formation of a bipolaron state in which the two electrons prefer to reside on the same molecule. The results further show that the Hartree and partially self-consistent Born solutions obtained by enforcing symmetry do not compare well with exact energetics, while the fully self-consistent Born approximation improves the qualitative and quantitative agreement with exact results in the same symmetric case. This together with a presented natural occupation number analysis supports the conclusion that the fully self-consistent approximation describes partially the bipolaron crossover. These results contribute to better understanding how these approximations cope with the strong localizing effect of the electron-phonon interaction.« less

Scattering and absorption of massless scalar waves by Born-Infeld black holes

NASA Astrophysics Data System (ADS)

Sanchez, Pablo Alejandro; Bretón, Nora; Bergliaffa, Santiago Esteban Perez

2018-06-01

We present the results of a study of the scattering of massless planar scalar waves by a Born-Infeld black hole. The scattering and absorption cross sections are calculated using partial-wave methods. The numerical results are checked by reproducing those of the Reissner-Nordstrom black hole, and also using several approximations, with which our results are in very good agreement. The dependence of these phenomena on the effective potential, the charge of the black hole, and the value of the Born-Infeld parameter is discussed.

Migration timing and parenting practices: Contributions to social development in preschoolers with foreign-born and native-born mothers

PubMed Central

Glick, Jennifer E.; Hanish, Laura D.; Yabiku, Scott T.; Bradley, Robert H.

2012-01-01

Little is known about how key aspects of parental migration or child-rearing history affect social development across children from immigrant families. Relying on data on approximately 6,400 children from the Early Childhood Longitudinal Study – Birth Cohort, analyses assessed the role of mothers’ age at migration on children’s social development in the United States (sociability and problem behaviors). Consistent with models of divergent adaptation and assimilation, the relationship between age at arrival and children’s social development is not linear. Parenting practices, observed when children were approximately 24 months of age, partially mediated the relation between mothers’ age at arrival and children’s social development reported at approximate age 48 months, particularly in the case of mothers who arrived as adults. PMID:22966921

Second-order Born calculation of coplanar symmetric (e, 2e) process on Mg

NASA Astrophysics Data System (ADS)

Zhang, Yong-Zhi; Wang, Yang; Zhou, Ya-Jun

2014-06-01

The second-order distorted wave Born approximation (DWBA) method is employed to investigate the triple differential cross sections (TDCS) of coplanar doubly symmetric (e, 2e) collisions for magnesium at excess energies of 6 eV-20 eV. Comparing with the standard first-order DWBA calculations, the inclusion of the second-order Born term in the scattering amplitude improves the degree of agreement with experiments, especially for backward scattering region of TDCS. This indicates that the present second-order Born term is capable to give a reasonable correction to DWBA model in studying coplanar symmetric (e, 2e) problems of two-valence-electron target in low energy range.

Migration Timing and Parenting Practices: Contributions to Social Development in Preschoolers with Foreign-Born and Native-Born Mothers

ERIC Educational Resources Information Center

Glick, Jennifer E.; Hanish, Laura D.; Yabiku, Scott T.; Bradley, Robert H.

2012-01-01

Little is known about how key aspects of parental migration or childrearing history affect social development across children from immigrant families. Relying on data on approximately 6,400 children from the Early Childhood Longitudinal Study-Birth Cohort, analyses assessed the role of mother's age at migration on children's social development in…

CMB weak-lensing beyond the Born approximation: a numerical approach

NASA Astrophysics Data System (ADS)

Fabbian, Giulio; Calabrese, Matteo; Carbone, Carmelita

2018-02-01

We perform a complete study of the gravitational lensing effect beyond the Born approximation on the Cosmic Microwave Background (CMB) anisotropies using a multiple-lens raytracing technique through cosmological N-body simulations of the DEMNUni suite. The impact of second-order effects accounting for the non-linear evolution of large-scale structures is evaluated propagating for the first time the full CMB lensing jacobian together with the light rays trajectories. We carefully investigate the robustness of our approach against several numerical effects in the raytracing procedure and in the N-body simulation itself, and find no evidence of large contaminations. We discuss the impact of beyond-Born corrections on lensed CMB observables, and compare our results with recent analytical predictions that appeared in the literature, finding a good agreement, and extend these results to smaller angular scales. We measure the gravitationally-induced CMB polarization rotation that appears in the geodesic equation at second order, and compare this result with the latest analytical predictions. We then present the detection prospect of beyond-Born effects with the future CMB-S4 experiment. We show that corrections to the temperature power spectrum can be measured only if a good control of the extragalactic foregrounds is achieved. Conversely, the beyond-Born corrections on E and B-modes power spectra will be much more difficult to detect.

The Use of Functional Behavioural Assessment for Students with Challenging Behaviours: Current Patterns and Experience of Australian Practitioners.

ERIC Educational Resources Information Center

O'Neill, Sue; Stephenson, Jennifer

2010-01-01

With the growing adoption of the Positive Behaviour Support (PBS) system state-wide in New South Wales, Australia, it was of interest to determine the readiness of behaviour specialists to conduct Functional Behaviour Assessments (FBA) as part of the third tier of School-wide PBS provision. This article presents the findings from a survey…

Molecular and biochemical characterizations of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis.

PubMed

Li, Shan; Bian, Meng; Wang, Xiaoyun; Chen, Xueqing; Xie, Zhizhi; Sun, Hengchang; Jia, Feifei; Liang, Pei; Zhou, Chenhui; He, Lei; Mao, Qiang; Huang, Bo; Liang, Chi; Wu, Zhongdao; Li, Xuerong; Xu, Jin; Huang, Yan; Yu, Xinbing

2014-01-01

Fructose-1,6-bisphosphate aldolase (FbA) is a ubiquitous enzyme in glycolysis. In the present study, we screened out three distinct genes encoding FbA isozymes (CsFbAs, CsFbA-1/2/3) from Clonorchis sinensis (C. sinensis) and characterized their sequences and structures profiles as well as biochemical properties. The amino acid sequences of CsFbAs shared homology with those of Class I FbAs from other species. The putative quaternary structures revealed that CsFbA-2 and CsFbA-3 were tetramers, while CsFbA-1 was dimer. Recombinant CsFbA-2 and CsFbA-3 (rCsFbA-2/3) were confirmed to be Class I FbAs for their stable enzymatic activities in the presence of EDTA or metal ions. However, recombinant CsFbA-1 (rCsFbA-1) did not show the catalytic activity, which might be due to the inappropriate fold and interaction between its subunits. Both rCsFbA-2 and rCsFbA-3 showed similar enzymatic properties such as optimal temperatures and broad pH ranges that similar to human FbA isozymes. They showed relatively higher affinities for fructose-1,6-bisphosphate (FBP) than fructose-1-phosphate (F-1-P). Their kcat ratios of FBP to F-1-P were in accordance with those of human FbA-A or C. In addition, CsFbAs were differentially transcribed in the developmental stages of C. sinensis, suggesting their essential roles throughout the life stages. Extensive distribution of CsFbAs in adult worms indicated that ubiquitous activities of CsFbAs took place in these organs. Collectively, these results suggested that long-term parasitic environment might adapt these isozymes similar to host FbAs for metabolic requirement. Our study will provide new insight into CsFbAs in the glycometabolism of C. sinensis and relationship between the host and the parasite. Copyright © 2014 Elsevier B.V. All rights reserved.

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.

PubMed

Boyle, Nanette R; Morgan, John A

2009-01-07

Photosynthetic organisms convert atmospheric carbon dioxide into numerous metabolites along the pathways to make new biomass. Aquatic photosynthetic organisms, which fix almost half of global inorganic carbon, have great potential: as a carbon dioxide fixation method, for the economical production of chemicals, or as a source for lipids and starch which can then be converted to biofuels. To harness this potential through metabolic engineering and to maximize production, a more thorough understanding of photosynthetic metabolism must first be achieved. A model algal species, C. reinhardtii, was chosen and the metabolic network reconstructed. Intracellular fluxes were then calculated using flux balance analysis (FBA). The metabolic network of primary metabolism for a green alga, C. reinhardtii, was reconstructed using genomic and biochemical information. The reconstructed network accounts for the intracellular localization of enzymes to three compartments and includes 484 metabolic reactions and 458 intracellular metabolites. Based on BLAST searches, one newly annotated enzyme (fructose-1,6-bisphosphatase) was added to the Chlamydomonas reinhardtii database. FBA was used to predict metabolic fluxes under three growth conditions, autotrophic, heterotrophic and mixotrophic growth. Biomass yields ranged from 28.9 g per mole C for autotrophic growth to 15 g per mole C for heterotrophic growth. The flux balance analysis model of central and intermediary metabolism in C. reinhardtii is the first such model for algae and the first model to include three metabolically active compartments. In addition to providing estimates of intracellular fluxes, metabolic reconstruction and modelling efforts also provide a comprehensive method for annotation of genome databases. As a result of our reconstruction, one new enzyme was annotated in the database and several others were found to be missing; implying new pathways or non-conserved enzymes. The use of FBA to estimate intracellular fluxes also provides flux values that can be used as a starting point for rational engineering of C. reinhardtii. From these initial estimates, it is clear that aerobic heterotrophic growth on acetate has a low yield on carbon, while mixotrophically and autotrophically grown cells are significantly more carbon efficient.

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

PubMed

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion.

PubMed

Albert, Julian; Falge, Mirjam; Gomez, Sandra; Sola, Ignacio R; Hildenbrand, Heiko; Engel, Volker

2015-07-28

We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.

Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion

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

Albert, Julian; Falge, Mirjam; Hildenbrand, Heiko

2015-07-28

We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.

Spatial Risk Assessments Based on Vector-Borne Disease Epidemiologic Data: Importance of Scale for West Nile Virus Disease in Colorado

PubMed Central

Winters, Anna M.; Eisen, Rebecca J.; Delorey, Mark J.; Fischer, Marc; Nasci, Roger S.; Zielinski-Gutierrez, Emily; Moore, Chester G.; Pape, W. John; Eisen, Lars

2010-01-01

We used epidemiologic data for human West Nile virus (WNV) disease in Colorado from 2003 and 2007 to determine 1) the degree to which estimates of vector-borne disease occurrence is influenced by spatial scale of data aggregation (county versus census tract), and 2) the extent of concordance between spatial risk patterns based on case counts versus incidence. Statistical analyses showed that county, compared with census tract, accounted for approximately 50% of the overall variance in WNV disease incidence, and approximately 33% for the subset of cases classified as West Nile neuroinvasive disease. These findings indicate that sub-county scale presentation provides valuable risk information for stakeholders. There was high concordance between spatial patterns of WNV disease incidence and case counts for census tract (83%) but not for county (50%) or zip code (31%). We discuss how these findings impact on practices to develop spatial epidemiologic data for vector-borne diseases and present data to stakeholders. PMID:20439980

Three-dimensional inversion of multisource array electromagnetic data

NASA Astrophysics Data System (ADS)

Tartaras, Efthimios

Three-dimensional (3-D) inversion is increasingly important for the correct interpretation of geophysical data sets in complex environments. To this effect, several approximate solutions have been developed that allow the construction of relatively fast inversion schemes. One such method that is fast and provides satisfactory accuracy is the quasi-linear (QL) approximation. It has, however, the drawback that it is source-dependent and, therefore, impractical in situations where multiple transmitters in different positions are employed. I have, therefore, developed a localized form of the QL approximation that is source-independent. This so-called localized quasi-linear (LQL) approximation can have a scalar, a diagonal, or a full tensor form. Numerical examples of its comparison with the full integral equation solution, the Born approximation, and the original QL approximation are given. The objective behind developing this approximation is to use it in a fast 3-D inversion scheme appropriate for multisource array data such as those collected in airborne surveys, cross-well logging, and other similar geophysical applications. I have developed such an inversion scheme using the scalar and diagonal LQL approximation. It reduces the original nonlinear inverse electromagnetic (EM) problem to three linear inverse problems. The first of these problems is solved using a weighted regularized linear conjugate gradient method, whereas the last two are solved in the least squares sense. The algorithm I developed provides the option of obtaining either smooth or focused inversion images. I have applied the 3-D LQL inversion to synthetic 3-D EM data that simulate a helicopter-borne survey over different earth models. The results demonstrate the stability and efficiency of the method and show that the LQL approximation can be a practical solution to the problem of 3-D inversion of multisource array frequency-domain EM data. I have also applied the method to helicopter-borne EM data collected by INCO Exploration over the Voisey's Bay area in Labrador, Canada. The results of the 3-D inversion successfully delineate the shallow massive sulfides and show that the method can produce reasonable results even in areas of complex geology and large resistivity contrasts.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

PubMed

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

Non-linear 3-D Born shear waveform tomography in Southeast Asia

NASA Astrophysics Data System (ADS)

Panning, Mark P.; Cao, Aimin; Kim, Ahyi; Romanowicz, Barbara A.

2012-07-01

Southeast (SE) Asia is a tectonically complex region surrounded by many active source regions, thus an ideal test bed for developments in seismic tomography. Much recent development in tomography has been based on 3-D sensitivity kernels based on the first-order Born approximation, but there are potential problems with this approach when applied to waveform data. In this study, we develop a radially anisotropic model of SE Asia using long-period multimode waveforms. We use a theoretical 'cascade' approach, starting with a large-scale Eurasian model developed using 2-D Non-linear Asymptotic Coupling Theory (NACT) sensitivity kernels, and then using a modified Born approximation (nBorn), shown to be more accurate at modelling waveforms, to invert a subset of the data for structure in a subregion (longitude 75°-150° and latitude 0°-45°). In this subregion, the model is parametrized at a spherical spline level 6 (˜200 km). The data set is also inverted using NACT and purely linear 3-D Born kernels. All three final models fit the data well, with just under 80 per cent variance reduction as calculated using the corresponding theory, but the nBorn model shows more detailed structure than the NACT model throughout and has much better resolution at depths greater than 250 km. Based on variance analysis, the purely linear Born kernels do not provide as good a fit to the data due to deviations from linearity for the waveform data set used in this modelling. The nBorn isotropic model shows a stronger fast velocity anomaly beneath the Tibetan Plateau in the depth range of 150-250 km, which disappears at greater depth, consistent with other studies. It also indicates moderate thinning of the high-velocity plate in the middle of Tibet, consistent with a model where Tibet is underplated by Indian lithosphere from the south and Eurasian lithosphere from the north, in contrast to a model with continuous underplating by Indian lithosphere across the entire plateau. The nBorn anisotropic model detects negative ξ anomalies suggestive of vertical deformation associated with subducted slabs and convergent zones at the Himalayan front and Tien Shan at depths near 150 km.

A Stochastic Tick-Borne Disease Model: Exploring the Probability of Pathogen Persistence.

PubMed

Maliyoni, Milliward; Chirove, Faraimunashe; Gaff, Holly D; Govinder, Keshlan S

2017-09-01

We formulate and analyse a stochastic epidemic model for the transmission dynamics of a tick-borne disease in a single population using a continuous-time Markov chain approach. The stochastic model is based on an existing deterministic metapopulation tick-borne disease model. We compare the disease dynamics of the deterministic and stochastic models in order to determine the effect of randomness in tick-borne disease dynamics. The probability of disease extinction and that of a major outbreak are computed and approximated using the multitype Galton-Watson branching process and numerical simulations, respectively. Analytical and numerical results show some significant differences in model predictions between the stochastic and deterministic models. In particular, we find that a disease outbreak is more likely if the disease is introduced by infected deer as opposed to infected ticks. These insights demonstrate the importance of host movement in the expansion of tick-borne diseases into new geographic areas.

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

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

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

DOE PAGES

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...

2015-04-21

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Human body perception and higher-level person perception are dissociated in early development.

PubMed

Slaughter, Virginia

2011-01-01

Abstract Developmental data support the proposal that human body perceptual processing is distinct from other aspects of person perception. Infants are sensitive to human bodily motion and attribute goals to human arm movements before they demonstrate recognition of human body structure. The developmental data suggest the possibility of bidirectional linkages between EBA- and FBA-mediated representations and these higher-level elements of person perception.

Acquisition: Direct Care Medical Services Contracts

DTIC Science & Technology

2004-06-24

System FAR Federal Acquisition Regulation FBA Franchise Business Activity FICA Federal Insurance Contributions Act FISC Fleet Industrial Supply Center...regarding the use of Franchise Business Activity contracts to forward fund appropriations from one fiscal year for work performed in the next fiscal year...2002 to 63 in FY 2003. 3 As discussed in Inspector General of the Department of Defense Report No. D-2003-113, “ Franchise Business Activity Contracts

Dynamic leaching behavior of geogenic As in soils after cement-based stabilization/solidification.

PubMed

Li, Jiang-Shan; Wang, Lei; Tsang, Daniel C W; Beiyuan, Jingzi; Poon, Chi Sun

2017-12-01

Cement-based stabilization/solidification (S/S) is a practical treatment approach for hazardous waste with anthropogenic As sources; however, its applicability for geogenic As-containing soil and the long-term leaching potential remain uncertain. In this study, semi-dynamic leaching test was performed to investigate the influence of S/S binders (cement blended with fuel ash (FA), furnace bottom ash (FBA), or ground granulated blast furnace slag (GGBS)) on the long-term leaching characteristics of geogenic As. The results showed that mineral admixtures with higher Ca content and pozzolanic activity were more effective in reducing the leached As concentrations. Thus, cement blended with FBA was inferior to other binders in suppressing the As leaching, while 20% replacement of ordinary Portland cement by GGBS was considered most feasible for the S/S treatment of As-containing soils. The leachability of geogenic As was suppressed by the encapsulation effect of solidified matrix and interlocking network of hydration products that were supported by scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) results. The long-term leaching of geogenic As from the monolithic samples was diffusion-controlled. Increasing the Ca content in the samples led to a decrease in diffusion coefficient and an increase in feasibility for "controlled utilization" of the S/S-treated soils.

A triple-bridged azido-Cu(II) chain compound fine-tuned by mixed carboxylate/ethanol linkers displays slow-relaxation and ferromagnetic order: synthesis, crystal structure, magnetic properties and DFT calculations.

PubMed

Liu, Xiangyu; Chen, Sanping; Grancha, Thais; Pardo, Emilio; Ke, Hongshan; Yin, Bing; Wei, Qing; Xie, Gang; Gao, Shengli

2014-11-07

A new azido-Cu(II) compound, [Cu(4-fba)(N3)(C2H5OH)] (4-fba = 4-fluorobenzoic acid) (1), has been synthesized and characterized. The X-ray crystal structure analysis demonstrates that only one crystallographically independent Cu(II) ion in the asymmetric unit of 1 exhibits a stretched octahedral geometry in which two azido N atoms and two carboxylic O atoms locate in the equatorial square, while two ethanol O atoms occupy the apical positions, forming a 1D Cu(II) chain with an alternating triple-bridge of EO-azido, syn,syn-carboxylate, and μ2-ethanol. The title compound consists of ferromagnetically interacting ferromagnetic chains, which exhibit ferromagnetic order (T(c) = 7.0 K). The strong ferromagnetic coupling between adjacent Cu(II) ions within each chain is due to the countercomplementarity of the super-exchange pathways, whereas the ferromagnetic interchain interactions--responsible for the long-range magnetic ordering--are most likely due to the presence of coordinated ethanol molecules establishing hydrogen bonds with neighboring chains. DFT calculations have been performed on compound 1 to offer a qualitative theoretical explanation of the magnetic behavior.

Steady-state visually evoked potential correlates of human body perception.

PubMed

Giabbiconi, Claire-Marie; Jurilj, Verena; Gruber, Thomas; Vocks, Silja

2016-11-01

In cognitive neuroscience, interest in the neuronal basis underlying the processing of human bodies is steadily increasing. Based on functional magnetic resonance imaging studies, it is assumed that the processing of pictures of human bodies is anchored in a network of specialized brain areas comprising the extrastriate and the fusiform body area (EBA, FBA). An alternative to examine the dynamics within these networks is electroencephalography, more specifically so-called steady-state visually evoked potentials (SSVEPs). In SSVEP tasks, a visual stimulus is presented repetitively at a predefined flickering rate and typically elicits a continuous oscillatory brain response at this frequency. This brain response is characterized by an excellent signal-to-noise ratio-a major advantage for source reconstructions. The main goal of present study was to demonstrate the feasibility of this method to study human body perception. To that end, we presented pictures of bodies and contrasted the resulting SSVEPs to two control conditions, i.e., non-objects and pictures of everyday objects (chairs). We found specific SSVEPs amplitude differences between bodies and both control conditions. Source reconstructions localized the SSVEP generators to a network of temporal, occipital and parietal areas. Interestingly, only body perception resulted in activity differences in middle temporal and lateral occipitotemporal areas, most likely reflecting the EBA/FBA.

Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.

Metabolism and evolution: A comparative study of reconstructed genome-level metabolic networks

NASA Astrophysics Data System (ADS)

Almaas, Eivind

2008-03-01

The availability of high-quality annotations of sequenced genomes has made it possible to generate organism-specific comprehensive maps of cellular metabolism. Currently, more than twenty such metabolic reconstructions are publicly available, with the majority focused on bacteria. A typical metabolic reconstruction for a bacterium results in a complex network containing hundreds of metabolites (nodes) and reactions (links), while some even contain more than a thousand. The constrain-based optimization approach of flux-balance analysis (FBA) is used to investigate the functional characteristics of such large-scale metabolic networks, making it possible to estimate an organism's growth behavior in a wide variety of nutrient environments, as well as its robustness to gene loss. We have recently completed the genome-level metabolic reconstruction of Yersinia pseudotuberculosis, as well as the three Yersinia pestis biovars Antiqua, Mediaevalis, and Orientalis. While Y. pseudotuberculosis typically only causes fever and abdominal pain that can mimic appendicitis, the evolutionary closely related Y. pestis strains are the aetiological agents of the bubonic plague. In this presentation, I will discuss our results and conclusions from a comparative study on the evolution of metabolic function in the four Yersiniae networks using FBA and related techniques, and I will give particular focus to the interplay between metabolic network topology and evolutionary flexibility.

Dynamic flux balancing elucidates NAD(P)H production as limiting response to furfural inhibition in Saccharomyces cerevisiae.

PubMed

Pornkamol, Unrean; Franzen, Carl J

2015-08-01

Achieving efficient and economical lignocellulose-based bioprocess requires a robust organism tolerant to furfural, a major inhibitory compound present in lignocellulosic hydrolysate. The aim of this study was to develop a model that could generate quantitative descriptions of cell metabolism for elucidating the cell's adaptive response to furfural. Such a modelling tool could provide strategies for the design of more robust cells. A dynamic flux balance (dFBA) model of Saccharomyces cerevisiae was created by coupling a kinetic fermentation model with a previously published genome-scale stoichiometric model. The dFBA model was used for studying intracellular and extracellular flux responses to furfural perturbations under steady state and dynamic conditions. The predicted effects of furfural on dynamic flux profiles agreed well with previously published experimental results. The model showed that the yeast cell adjusts its metabolism in response to furfural challenge by increasing fluxes through the pentose phosphate pathway, TCA cycle, and proline and serine biosynthesis in order to meet the high demand of NAD(P)H cofactors. The model described here can be used to aid in systematic optimization of the yeast, as well as of the fermentation process, for efficient lignocellulosic ethanol production. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach.

PubMed

Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

2015-10-28

The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data.

Phenomenological Study of Interaction between Solar Acoustic Waves and Sunspots from Measured Scattered Wavefunctions

NASA Astrophysics Data System (ADS)

Yang, Ming-Hsu; Chou, Dean-Yi; Zhao, Hui; Liang, Zhi-Chao

2012-08-01

The solar acoustic waves around a sunspot are modified because of the interaction with the sunspot. The interaction can be viewed as that the sunspot, excited by the incident wave, generates the scattered wave, and the scattered wave is added to the incident wave to form the total wave around the sunspot. We define an interaction parameter, which could be complex, describing the interaction between the acoustic waves and the sunspot. The scattered wavefunction on the surface can be expressed as a two-dimensional integral of the product of the Green's function, the wavefunction, and the two-dimensional interaction parameter over the sunspot area for the Born approximation of different orders. We assume a simple model for the two-dimensional interaction parameter distribution: its absolute value is axisymmetric with a Gaussian distribution and its phase is a constant. The measured scattered wavefunctions of various modes for NOAAs 11084 and 11092 are fitted to the theoretical scattered wavefunctions to determine the three model parameters, magnitude, Gaussian radius, and phase, for the Born approximation of different orders. The three model parameters converge to some values at high-order Born approximations. The result of the first-order Born approximation is significantly different from the convergent value in some cases. The rate of convergence depends on the sunspot size and wavelength. It converges more rapidly for the smaller sunspot and longer wavelength. The magnitude increases with mode frequency and degree for each radial order. The Gaussian radius is insensitive to frequency and degree. The spatial range of the interaction parameter is greater than that of the continuum intensity deficit, but smaller than that of the acoustic power deficit of the sunspot. The phase versus phase speed falls into a small range. This suggests that the phase could be a function phase speed. NOAAs 11084 and 11092 have a similar magnitude and phase, although the ratio of their sizes is 0.75.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

PubMed Central

2012-01-01

Background The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context. Results We have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. In particular the ouput of the program entails, depending on user's requirement: 1) the generalized Born radius of each atom; 2) the electrostatic solvation free energy; 3) the electrostatic forces on each atom (currently in a dvelopmental stage); 4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18; 5) the pKa of all ionizable groups; 6) the electrostatic potential at the surface of the molecule; 7) the electrostatic potential in a volume surrounding the molecule; Conclusions Although at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material. PMID:22536964

Interpretation of ES, CS, and IOS approximations within a translational--internal coupling scheme. IV. ES and IOS molecule--molecule cross sections

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

Snider, R.F.; Parvatiyar, M.G.

1981-05-15

Properties of energy sudden and infinite order sudden translational--internal reduced S matrices are given for general molecule--molecule collisions. Formal similarities with the distorted wave Born approximation are discussed. Structural simplifications of energy dependent and kinetic cross sections associated with making the ES approximation are described. Conceptual difficulties associated with applying the ES and IOS approximations to kinetic processes dominated by energetically inelastic collisions are pointed out.

Birth Order and Injury-Related Infant Mortality in the U.S.

PubMed

Ahrens, Katherine A; Rossen, Lauren M; Thoma, Marie E; Warner, Margaret; Simon, Alan E

2017-10-01

The purpose of this study was to evaluate the risk of death during the first year of life due to injury, such as unintentional injury and homicide, by birth order in the U.S. Using national birth cohort-linked birth-infant death data (births, 2000-2010; deaths, 2000-2011), risks of infant mortality due to injury in second-, third-, fourth-, and fifth or later-born singleton infants were compared with first-born singleton infants. Risk ratios were estimated using log-binomial models adjusted for maternal age, marital status, race/ethnicity, and education. The statistical analyses were conducted in 2016. Approximately 40%, 32%, 16%, 7%, and 4% of singleton live births were first, second, third, fourth, and fifth or later born, respectively. From 2000 to 2011, a total of 15,866 infants died as a result of injury (approximately 1,442 deaths per year). Compared with first-born infants (2.9 deaths per 10,000 live births), second or later-born infants were at increased risk of infant mortality due to injury (second, 3.6 deaths; third, 4.2 deaths; fourth, 4.8 deaths; fifth or later, 6.4 deaths). The corresponding adjusted risk ratios were as follows: second, 1.84 (95% CI=1.76, 1.91); third, 2.42 (95% CI=2.30, 2.54); fourth, 2.96 (95% CI=2.77, 3.16); and fifth or later, 4.26 (95% CI=3.96, 4.57). Singleton infants born second or later were at increased risk of mortality due to injury during their first year of life in the U.S. This study's findings highlight the importance of investigating underlying mechanisms behind this increased risk. Published by Elsevier Inc.

Strong-potential Born calculations for electron capture

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

McGuire, J.H.; Sil, N.C.

1983-12-01

A closed-form expression for 1s-1s electron capture has been developed in the strong-potential Born (SPB) approximation. Terms of the order (Z/sub p//v)/sup 2/ are ignored in our expression, where Z/sub p/ is the charge of the projectile and v is the collision velocity. Our errors of order (Z/sub p//v)/sup 2/ are within the accuracy of the SPB approximation itself, which is valid to first order in the projectile-electron interaction V/sub p/ (and all orders in the stronger target potential V/sub T/). Calculations using our expression are in better agreement with experimental observations of the shape of the Thomas peak thanmore » are other calculations.« less

Electromagnetic backscattering from a random distribution of lossy dielectric scatterers

NASA Technical Reports Server (NTRS)

Lang, R. H.

1980-01-01

Electromagnetic backscattering from a sparse distribution of discrete lossy dielectric scatterers occupying a region 5 was studied. The scatterers are assumed to have random position and orientation. Scattered fields are calculated by first finding the mean field and then by using it to define an equivalent medium within the volume 5. The scatterers are then viewed as being embedded in the equivalent medium; the distorted Born approximation is then used to find the scattered fields. This technique represents an improvement over the standard Born approximation since it takes into account the attenuation of the incident and scattered waves in the equivalent medium. The method is used to model a leaf canopy when the leaves are modeled by lossy dielectric discs.

Time-dependent calculations of transfer ionization by fast proton-helium collision in one-dimensional kinematics

NASA Astrophysics Data System (ADS)

Serov, Vladislav V.; Kheifets, A. S.

2014-12-01

We analyze a transfer ionization (TI) reaction in the fast proton-helium collision H++He →H0+He2 ++ e- by solving a time-dependent Schrödinger equation (TDSE) under the classical projectile motion approximation in one-dimensional kinematics. In addition, we construct various time-independent analogs of our model using lowest-order perturbation theory in the form of the Born series. By comparing various aspects of the TDSE and the Born series calculations, we conclude that the recent discrepancies of experimental and theoretical data may be attributed to deficiency of the Born models used by other authors. We demonstrate that the correct Born series for TI should include the momentum-space overlap between the double-ionization amplitude and the wave function of the transferred electron.

BORN CROSS SECTIONS FOR INELASTIC SCATTERING OF ELECTRONS BY HYDROGEN ATOMS. III. 5s, 5p, 5d, 5f, 5g STATES

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

Milford, S.N.; Morrissey, J.J.; Scanlon, J.H.

1960-12-01

Born total cross sections were computed for the strong optically allowed transitions from n = 5 to n' = 6, at incident energies between 0.2 and 1361 ev. Thirty energy values were considered for the 5s to 6p and 5g to 6h cases, and nine for the other transitions. The cross sections obtained were larger than those of comparable transitions for lower n. The Bethe (dipole) approximation was also used, and was found to give good agreement with the Born results down to relatively low energies ( approx equal 3 ev). (auth)

Developing Positive Behavioral Support for Students with Challenging Behaviors. From the Third CCBD Mini-Library Series, What Works for Children and Youth with E/BD: Linking Yesterday and Today with Tomorrow.

ERIC Educational Resources Information Center

Sugai, George, Ed.; Lewis, Timothy J., Ed.

This monograph is a guide to positive behavioral intervention and support (PBIS) and functional behavioral assessment (FBA) in the special education of students with behavior disorders as emphasized in the 1997 amendments to the Individuals with Disabilities Act (IDEA 97). An introduction explains that positive behavioral support represents the…

Testability Design Rating System: Testability Handbook. Volume 1

DTIC Science & Technology

1992-02-01

4-10 4.7.5 Summary of False BIT Alarms (FBA) ............................. 4-10 4.7.6 Smart BIT Technique...Circuit Board PGA Pin Grid Array PLA Programmable Logic Array PLD Programmable Logic Device PN Pseudo-Random Number PREDICT Probabilistic Estimation of...11 4.7.6 Smart BIT ( reference: RADC-TR-85-198). " Smart " BIT is a term given to BIT circuitry in a system LRU which includes dedicated processor/memory

Categorical discrimination of human body parts by magnetoencephalography

PubMed Central

Nakamura, Misaki; Yanagisawa, Takufumi; Okamura, Yumiko; Fukuma, Ryohei; Hirata, Masayuki; Araki, Toshihiko; Kamitani, Yukiyasu; Yorifuji, Shiro

2015-01-01

Humans recognize body parts in categories. Previous studies have shown that responses in the fusiform body area (FBA) and extrastriate body area (EBA) are evoked by the perception of the human body, when presented either as whole or as isolated parts. These responses occur approximately 190 ms after body images are visualized. The extent to which body-sensitive responses show specificity for different body part categories remains to be largely clarified. We used a decoding method to quantify neural responses associated with the perception of different categories of body parts. Nine subjects underwent measurements of their brain activities by magnetoencephalography (MEG) while viewing 14 images of feet, hands, mouths, and objects. We decoded categories of the presented images from the MEG signals using a support vector machine (SVM) and calculated their accuracy by 10-fold cross-validation. For each subject, a response that appeared to be a body-sensitive response was observed and the MEG signals corresponding to the three types of body categories were classified based on the signals in the occipitotemporal cortex. The accuracy in decoding body-part categories (with a peak at approximately 48%) was above chance (33.3%) and significantly higher than that for random categories. According to the time course and location, the responses are suggested to be body-sensitive and to include information regarding the body-part category. Finally, this non-invasive method can decode category information of a visual object with high temporal and spatial resolution and this result may have a significant impact in the field of brain–machine interface research. PMID:26582986

Categorical discrimination of human body parts by magnetoencephalography.

PubMed

Nakamura, Misaki; Yanagisawa, Takufumi; Okamura, Yumiko; Fukuma, Ryohei; Hirata, Masayuki; Araki, Toshihiko; Kamitani, Yukiyasu; Yorifuji, Shiro

2015-01-01

Humans recognize body parts in categories. Previous studies have shown that responses in the fusiform body area (FBA) and extrastriate body area (EBA) are evoked by the perception of the human body, when presented either as whole or as isolated parts. These responses occur approximately 190 ms after body images are visualized. The extent to which body-sensitive responses show specificity for different body part categories remains to be largely clarified. We used a decoding method to quantify neural responses associated with the perception of different categories of body parts. Nine subjects underwent measurements of their brain activities by magnetoencephalography (MEG) while viewing 14 images of feet, hands, mouths, and objects. We decoded categories of the presented images from the MEG signals using a support vector machine (SVM) and calculated their accuracy by 10-fold cross-validation. For each subject, a response that appeared to be a body-sensitive response was observed and the MEG signals corresponding to the three types of body categories were classified based on the signals in the occipitotemporal cortex. The accuracy in decoding body-part categories (with a peak at approximately 48%) was above chance (33.3%) and significantly higher than that for random categories. According to the time course and location, the responses are suggested to be body-sensitive and to include information regarding the body-part category. Finally, this non-invasive method can decode category information of a visual object with high temporal and spatial resolution and this result may have a significant impact in the field of brain-machine interface research.

Three-dimensional imaging of buried objects in very lossy earth by inversion of VETEM data

USGS Publications Warehouse

Cui, T.J.; Aydiner, A.A.; Chew, W.C.; Wright, D.L.; Smith, D.V.

2003-01-01

The very early time electromagnetic system (VETEM) is an efficient tool for the detection of buried objects in very lossy earth, which allows a deeper penetration depth compared to the ground-penetrating radar. In this paper, the inversion of VETEM data is investigated using three-dimensional (3-D) inverse scattering techniques, where multiple frequencies are applied in the frequency range from 0-5 MHz. For small and moderately sized problems, the Born approximation and/or the Born iterative method have been used with the aid of the singular value decomposition and/or the conjugate gradient method in solving the linearized integral equations. For large-scale problems, a localized 3-D inversion method based on the Born approximation has been proposed for the inversion of VETEM data over a large measurement domain. Ways to process and to calibrate the experimental VETEM data are discussed to capture the real physics of buried objects. Reconstruction examples using synthesized VETEM data and real-world VETEM data are given to test the validity and efficiency of the proposed approach.

Towards a complete North American Anabaptist Genealogy II: analysis of inbreeding.

PubMed

Agarwala, R; Schäffer, A A; Tomlin, J F

2001-08-01

We describe a large genealogy data base, which can be searched by computer, of 295,095 Amish and Mennonite individuals. The data base was constructed by merging our existing Anabaptist Genealogy Database 2.0 containing approximately 85,000 individuals with a genealogy file containing approximately 242,000 individuals, kindly provided by Mr. James Hostetler. The merging process corrected thousands of inconsistencies and eliminated hundreds of duplicate individuals. Geneticists have long been interested in Anabaptist populations because they are closed and have detailed written genealogies. The creation of an enlarged and unified data base affords the opportunity to examine inbreeding trends and correlates in these populations. We show the following results. The frequency of consanguineous marriages shows steady increase over time and reached approximately 85% for individuals born in 1940-1959. Among consanguineous marriages, the median kinship coefficient stayed stable in the 19th century, but rose from 0.0115 to 0.0151 in the 20th century. There are statistically significant associations (p < 0.0001) between inbreeding and family size and interbirth intervals in the 20th century. There is an association (p < 0.0005) between inbreeding and early death for individuals born in 1920-1959. However, this association reverses dramatically (p < 0.0005 in the opposite direction) for individuals born in 1960-1979. We tested for an association between inbreeding and being the mother of twins, but found none.

Effects of a finite aperture on the Inverse Born Approximation

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

Kogan, V.G.; Rose, J.H.

1983-01-01

One of the most important effects of complex part geometry is that the available entrance and exit angles for ultrasound are limited. We will present a study of the Inverse Born approximation in which we have data for incident (and exit) directions confined to a conical aperture. Modeling the direct problem by the Born Approximation, we obtained analytical results for (1) a weak spherical inclusion, and (2) a penny shaped crack (modeled by an oblate spheroid). General results are: (a) the value of the characteristic function ..gamma.. is constant in the interior of the flaw, but reduced in value; (b)more » the discontinuity at the boundary of the flaw occurs over the lighted portion of the flaw; (c) this discontinuity is contrasted by a region where ..gamma.. is negative; and (d) new non-physical discontinuities and non-analyticities appear in the reconstructed characteristic function. These general features also appear in numerical calculations which use as input strong scattering data from a spherical void and a flat penny shaped crack in Titanium. The numerical results can be straightforwardly interpreted in terms of the analytical calculation mentioned above, indicating that they will be useful in the study of realistic flaws. We conclude by discussing the stabilization of the aperture limited inversion problem and the removal of non-physical features in the reconstruction.« less

Does really Born Oppenheimer approximation break down in charge transfer processes? An exactly solvable model

NASA Astrophysics Data System (ADS)

Kuznetsov, Alexander M.; Medvedev, Igor G.

2006-05-01

Effects of deviation from the Born-Oppenheimer approximation (BOA) on the non-adiabatic transition probability for the transfer of a quantum particle in condensed media are studied within an exactly solvable model. The particle and the medium are modeled by a set of harmonic oscillators. The dynamic interaction of the particle with a single local mode is treated explicitly without the use of BOA. Two particular situations (symmetric and non-symmetric systems) are considered. It is shown that the difference between the exact solution and the true BOA is negligibly small at realistic parameters of the model. However, the exact results differ considerably from those of the crude Condon approximation (CCA) which is usually considered in the literature as a reference point for BOA (Marcus-Hush-Dogonadze formula). It is shown that the exact rate constant can be smaller (symmetric system) or larger (non-symmetric one) than that obtained in CCA. The non-Condon effects are also studied.

Cross sections and rate coefficients for inner-shell excitation of Li-like ions with 6 < Z < 42

NASA Astrophysics Data System (ADS)

Safronova, U. I.; Safronova, M. S.; Kato, T.

1996-07-01

Excitation cross sections and rate coefficients by electron impact were calculated for the 1s22s-1s2s2p, 1s22s-1s2s2 and 1s22s-1s2p2 transitions of the Li-like ions (C IV, N V, O VI, Ne VIII, Mg X, Al XI, Si XII, S XIV, Ar XVI, Ca XVIII, Ti XX, Fe XXIV, Ni XXVI, Zn XXVIII, Ge XXX, Se XXXII, Kr XXXIV and Mo XXXX) in the Coulomb-Born approximation with exchange including relativistic effects and configuration interaction. Level energies, mixing coefficients and transition wavelengths and probabilities were also computed. Calculations performed by the 1/Z perturbation theory and Coulomb-Born approximation are compared with the R-matrix method and the distorted-wave approximation were Z is the nuclear charge. Formulae obtained for the angular factors of n-electron atomic system allow one to generalize this method to an arbitrary system of highly charged ions.

Corrections to the one-photon approximation in the 0+-->2+ transition of 12C

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

Paul Gueye; Madeleine Bernheim; J. F. Danel

2001-04-18

Contribution of higher order effects to the one-photon exchange approximation were studied in the first excited state of 12C by comparing inclusive inelastic scattering cross sections of electrons and positrons obtained at the Saclay Linear Accelerator. The data were compared to a distorted wave Born approximation (DWBA)calculation. The results indicate an effect less than 2% within 2sigma, compatible with what was observed in recent elastic scattering measurements.

The graviton luminosity of the sun and other stars

NASA Technical Reports Server (NTRS)

Gould, R. J.

1985-01-01

Graviton production in electron-electron (e-e) and electron-ion (e-z) scattering is evaluated in the Born approximation. The calculation is compared with that for photon production, that is, Coulomb quadrupole bremsstrahlung, and a number of results are taken over from that problem. Application is made to the sun, and it is found that for the solar plasma the main contribution to the graviton luminosity comes from the central core at r/R approximately 0.1. The total luminosity (Lg) in gravitons is about 7.9 x 10 to the 14th ergs/s, close to an earlier estimate by Weinberg (1965, 1972); about 33 percent of the total results from e-e collisions with the rest from e-z collisions (mainly e-p and e-alpha). Approximate corrections to Born formulas are evaluated, and this Lg includes the associated (approximately + or - 10 percent, respectively) modification. The quantum-mechanical aspects of the solar Lg problem are discussed, and it is shown why a previous classical calculation overestimated Lg by about an order of magnitude. Production of gravitons in binary collisions in other types of stars is discussed briefly. It is found that Lg varies very little along the main sequence. White dwarfs have a typical graviton luminosity LWD approximately 10 to the 19th ergs/s, while neutron stars have LNS approximately 10 to the 25th ergs/s; these estimates are very rough.

Postural Complexity Differs Between Infant Born Full Term and Preterm During the Development of Early Behaviors

PubMed Central

Dusing, Stacey C; Izzo, Theresa A.; Thacker, Leroy R.; Galloway, James C

2014-01-01

Background and Aims Postural control differs between infants born preterm and full term at 1–3 weeks of age. It is unclear if differences persist or alter the development of early behaviors. The aim of this longitudinal study was to compare changes in postural control variability during development of head control and reaching in infants born preterm and full term. Methods Eighteen infants born preterm (mean gestational age 28.3±3.1 weeks) were included in this study and compared to existing data from 22 infants born full term. Postural variability was assessed longitudinally using root mean squared displacement and approximate entropy of the center of pressure displacement from birth to 6 months as measures of the magnitude of the variability and complexity of postural control. Behavioral coding was used to quantify development of head control and reaching. Results Group differences were identified in postural complexity during the development of head control and reaching. Infants born preterm used more repetitive and less adaptive postural control strategies than infants born full term. Both groups changed their postural complexity utilized during the development of head control and reaching. Discussion Early postural complexity was decreased in infants born preterm, compared to infants born full term. Commonly used clinical assessments did not identify these early differences in postural control. Altered postural control in infants born preterm influenced ongoing skill development in the first six months of life. PMID:24485170

Genetic Characterization of the Tick-Borne Orbiviruses

PubMed Central

Belaganahalli, Manjunatha N.; Maan, Sushila; Maan, Narender S.; Brownlie, Joe; Tesh, Robert; Attoui, Houssam; Mertens, Peter P. C.

2015-01-01

The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in ‘conserved’ Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a ~1 kb smaller genome. PMID:25928203

Genetic characterization of the tick-borne orbiviruses.

PubMed

Belaganahalli, Manjunatha N; Maan, Sushila; Maan, Narender S; Brownlie, Joe; Tesh, Robert; Attoui, Houssam; Mertens, Peter P C

2015-04-28

The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in 'conserved' Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a ~1 kb smaller genome.

Elastic scattering of spin-polarized electrons and positrons from 23Na nuclei

NASA Astrophysics Data System (ADS)

Jakubassa-Amundsen, D. H.

2018-07-01

Differential cross sections and polarization correlations for the scattering of relativistic spin-polarized leptons from unpolarized ground-state sodium nuclei are calculated within the distorted-wave Born approximation (DWBA). Various nuclear ground-state charge distributions are probed. Besides potential scattering, also electric C2 and magnetic M1 and M3 transitions are taken into account. It is shown that even for a light nucleus such as 23Na there are considerable electron-positron differences at high collision energies and large scattering angles. In particular, the symmetry of the Sherman function with respect to a global sign change, as predicted by the second-order Born approximation when replacing electrons by positrons, is broken whenever the diffraction structures come into play beyond 100 MeV.

Born-Oppenheimer approximation for a singular system

NASA Astrophysics Data System (ADS)

Akbas, Haci; Turgut, O. Teoman

2018-01-01

We discuss a simple singular system in one dimension, two heavy particles interacting with a light particle via an attractive contact interaction and not interacting among themselves. It is natural to apply the Born-Oppenheimer approximation to this problem. We present a detailed discussion of this approach; the advantage of this simple model is that one can estimate the error terms self-consistently. Moreover, a Fock space approach to this problem is presented where an expansion can be proposed to get higher order corrections. A slight modification of the same problem in which the light particle is relativistic is discussed in a later section by neglecting pair creation processes. Here, the second quantized description is more challenging, but with some care, one can recover the first order expression exactly.

Coupled-Sturmian and perturbative treatments of electron transfer and ionization in high-energy p-He+ collisions

NASA Astrophysics Data System (ADS)

Winter, Thomas G.; Alston, Steven G.

1992-02-01

Cross sections have been determined for electron transfer and ionization in collisions between protons and He+ ions at proton energies from several hundred kilo-electron-volts to 2 MeV. A coupled-Sturmian approach is taken, extending the work of Winter [Phys. Rev. A 35, 3799 (1987)] and Stodden et al. [Phys. Rev. A 41, 1281 (1990)] to high energies where perturbative approaches are expected to be valid. An explicit connection is made with the first-order Born approximation for ionization and the impulse version of the distorted, strong-potential Born approximation for electron transfer. The capture cross section is shown to be affected by the presence of target basis functions of positive energy near v2/2, corresponding to the Thomas mechanism.

Calculation of the total electron excitation cross section in the Born approximation using Slater wave functions for the Li (2s yields 2p), Li (2s yields 3p), Na (3s yields 4p), Mg (3p yields 4s), Ca (4s yields 4p) and K (4s yields 4p) excitations. M.S. Thesis

NASA Technical Reports Server (NTRS)

Simsic, P. L.

1974-01-01

Excitation of neutral atoms by inelastic scattering of incident electrons in gaseous nebulae were investigated using Slater Wave functions to describe the initial and final states of the atom. Total cross sections using the Born Approximation are calculated for: Li(2s yields 2p), Na(3s yields 4p), k(4s yields 4p). The intensity of emitted radiation from gaseous nebulae is also calculated, and Maxwell distribution is employed to average the kinetic energy of electrons.

West nile virus and equine encephalitis viruses: new perspectives.

PubMed

Long, Maureen T

2014-12-01

Mosquito-borne diseases affect horses worldwide. Mosquito-borne diseases generally cause encephalomyelitis in the horse and can be difficult to diagnose antemortem. In addition to general disease, and diagnostic and treatment aspects, this review article summarizes the latest information on these diseases, covering approximately the past 5 years, with a focus on new equine disease encroachments, diagnostic and vaccination aspects, and possible therapeutics on the horizon. Copyright © 2014 Elsevier Inc. All rights reserved.

Active Immunizations with Peptide-DC Vaccines and Passive Transfer with Antibodies Protect Neutropenic Mice against Disseminated Candidiasis

PubMed Central

Xin, Hong

2015-01-01

We previously report that peptide-pulsed dendritic cell (DC) vaccination, which targeting two peptides (Fba and Met6) expressed on the cell surface of Candida albicans, can induce high degree of protection against disseminated candidiasis in immunocompetent mice. Passive transfer of immune sera from the peptide immunized mice or peptide-related monoclonal antibodies demonstrated that protection was medicated by peptide-specific antibodies. In this study the efficacy of active and passive immunization against disseminated candidiasis was tested in mice with cyclophosphamide-induced neutropenia. Peptide-DC vaccines were given to mice prior to induction of neutropenia. We show active immunization with either Fba or Met6 peptide-DC vaccine significantly improved the survival and reduced the fungal burden of disseminated candidiasis in those immunocompromised mice. Importantly, we show that administration of two protective monoclonal antibodies also protect neutropenic mice against the disease, implying possibility of developing a successful passive immunotherapy strategy to treat the disease and protect against disseminated candidiasis. The results of this study are crucial as they address the fundamental questions as to whether the synthetic peptide vaccine induced immunity protects the host during a neutropenic episode. We anticipate that this peptide-vaccine study will serve as the foundation of future investigations into new peptide vaccines comprised of cell surface peptides from other medically important Candida species, as well as other fungi. PMID:26620842

A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef.

PubMed

Kamies, Rizqah; Farrant, Jill M; Tadele, Zerihun; Cannarozzi, Gina; Rafudeen, Mohammed Suhail

2017-11-15

The orphan crop, Eragrostis tef , was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.

A micro-flow-batch analyzer with solenoid micro-pumps for the photometric determination of iodate in table salt.

PubMed

Lima, Marcelo B; Barreto, Inakã S; Andrade, Stéfani Iury E; Almeida, Luciano F; Araújo, Mário C U

2012-10-15

In this study, a micro-flow-batch analyzer (μFBA) with solenoid micro-pumps for the photometric determination of iodate in table salt is described. The method is based on the reaction of iodate with iodide to form molecular iodine followed by the reaction with N,N-diethyl-p-phenylenediamine (DPD). The analytical signal was measured at 520 nm using a green LED integrated into the μFBA built in the urethane-acrylate resin. The analytical curve for iodate was linear in the range of 0.01-10.0 mg L(-1) with a correlation coefficient of 0.997. The limit of detection and relative standard deviation were estimated at 0.004 mg L(-1) and<1.5% (n=3), respectively. The accuracy was assessed through recovery test (97.6-103.5%) and independent analysis by a conventional titrimetric method. Comparing this technique with the conventional method, no statistically significant differences were observed when applying the paired t-test at a 95% confidence level. The proposed microsystem using solenoid micro-pumps presented satisfactory robustness and high sampling rate (170 h(-1)), with a low reagents consumption and a low cost to build the device. The proposed microsystem is a new alternative for automatic determination of iodate in table salt, comparing satisfactory to the recently flow system. Copyright © 2012 Elsevier B.V. All rights reserved.

Second Order Born Effects in the Perpendicular Plane Ionization of Xe (5p) Atoms

NASA Astrophysics Data System (ADS)

Purohit, G.; Singh, Prithvi; Patidar, Vinod

We report triple differential cross section (TDCS) results for the perpendicular plane ionization of xenon atoms at incident electron energies 5, 10, 20, 30, and 40 eV above ionization potential. The TDCS calculation have been preformed within the modified distorted wave Born approximation formalism including the second order Born (SBA) amplitude. We compare the (e, 2e) TDCS result of our calculation with the very recent measurements of Nixon and Murray [Phys. Rev. A 85, 022716 (2012)] and relativistic DWBA-G results of Illarionov and Stauffer [J. Phys. B: At. Mol. Opt. Phys. 45, 225202 (2012)] and discuss the process contributing to structure seen in the differential cross section.

Few-particle quantum dynamics-comparing nonequilibrium Green functions with the generalized Kadanoff-Baym ansatz to density operator theory

NASA Astrophysics Data System (ADS)

Hermanns, S.; Balzer, K.; Bonitz, M.

2013-03-01

The nonequilibrium description of quantum systems requires, for more than two or three particles, the use of a reduced description to be numerically tractable. Two possible approaches are based on either reduced density matrices or nonequilibrium Green functions (NEGF). Both concepts are formulated in terms of hierarchies of coupled equations—the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy for the reduced density operators and the Martin-Schwinger-hierarchy (MS) for the Green functions, respectively. In both cases, similar approximations are introduced to decouple the hierarchy, yet still many questions regarding the correspondence of both approaches remain open. Here we analyze this correspondence by studying the generalized Kadanoff-Baym ansatz (GKBA) that reduces the NEGF to a single-time theory. Starting from the BBGKY-hierarchy we present the approximations that are necessary to recover the GKBA result both, with Hartree-Fock propagators (HF-GKBA) and propagators in second Born approximation. To test the quality of the HF-GKBA, we study the dynamics of a 4-electron Hubbard nanocluster starting from a strong nonequilibrium initial state and compare to exact results and the Wang-Cassing approximation to the BBGKY hierarchy presented recently by Akbari et al. [1].

Ab initio design of laser pulses to control molecular motion

NASA Astrophysics Data System (ADS)

Balint-Kurti, Gabriel; Ren, Qinghua; Manby, Frederick; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel; Zou, Shiyang; Singh, Harjinder

2007-03-01

Our recent attempts to design laser pulses entirely theoretically, in a quantitative and accurate manner, so as to fully understand the underlying mechanisms active in the control process will be outlined. We have developed a new Born-Oppenheimer like separation called the electric-nuclear Born-Oppenheimer (ENBO) approximation. In this approximation variations of both the nuclear geometry and of the external electric field are assumed to be slow compared with the speed at which the electronic degrees of freedom respond to these changes. This assumption permits the generation of a potential energy surface that depends not only on the relative geometry of the nuclei, but also on the electric field strength and on the orientation of the molecule with respect to the electric field. The range of validity of the ENBO approximation is discussed. Optimal control theory is used along with the ENBO approximation to design laser pulses for exciting vibrational and rotational motion in H2 and CO molecules. Progress on other applications, including controlling photodissociation processes, isotope separation, stabilization of molecular Bose-Einstein condensates as well as applications to biological molecules also be presented. *Support acknowledged from EPSRC.

The effect of bi-terminal PEGylation of an integrin  α vβ 6-targeted 18F peptide on pharmacokinetics and tumor uptake

DOE PAGES

Hausner, Sven H.; Bauer, Nadine; Hu, Lina Y.; ...

2015-03-26

Radiotracers based on the peptide A20FMDV2 selectively target the cell surface receptor integrin α vβ 6. This integrin has been identified as a prognostic indicator correlating with the severity of disease for several challenging malignancies. In previous studies of A20FMDV2 peptides labeled with 4- 18F-fluorobenzoic acid ( 18F-FBA), we have shown that the introduction of poly(ethylene glycol) (PEG) improves pharmacokinetics, including increased uptake in α vβ 6-expressing tumors. The present study evaluated the effect of site-specific C-terminal or dual (N- and C-terminal) PEGylation, yielding 18F-FBA-A20FMDV2-PEG 28 (4) and 18F-FBA-PEG 28-A20FMDV2-PEG 28 (5), on α vβ 6-targeted tumor uptake and pharmacokinetics.more » The results are compared with 18F-FBA–labeled A20FMDV2 radiotracers (1–3) bearing either no PEG or different PEG units at the N terminus. The radiotracers were prepared and radiolabeled on solid phase. Using 3 cell lines, DX3puroβ6 (α vβ 6+), DX3puro (α vβ 6–), and BxPC-3 (α vβ 6+), we evaluated the radiotracers in vitro (serum stability; cell binding and internalization) and in vivo in mouse models bearing paired DX3puroβ6–DX3puro and, for 5, BxPC-3 xenografts. Here, the size and location of the PEG units significantly affected α vβ 6 targeting and pharmacokinetics. Although the C-terminally PEGylated 4 showed some improvements over the un-PEGylated 18F-FBA-A20FMDV2 (1), it was the bi-terminally PEGylated 5 that displayed the more favorable combination of high α vβ 6 affinity, selectivity, and pharmacokinetic profile. In vitro, 5 bound to α vβ 6-expressing DX3puroβ6 and BxPC-3 cells with 60.5% ± 3.3% and 48.8% ± 8.3%, respectively, with a significant fraction of internalization (37.2% ± 4.0% and 37.6% ± 4.1% of total radioactivity, respectively). By comparison, in the DX3puro control 5 showed only 3.0% ± 0.5% binding and 0.9% ± 0.2% internalization. In vivo, 5 maintained high, α vβ 6-directed binding in the paired DX3puroβ6–DX3puro model (1 h: DX3puroβ6, 2.3 ± 0.2 percentage injected dose per gram [%ID/g]; DX3puroβ6/DX3puro ratio, 6.5:1; 4 h: 10.7:1). In the pancreatic BxPC-3 model, uptake was 4.7 ± 0.9 %ID/g (1 h) despite small tumor sizes (20–80 mg). In conclusion, the bi-PEGylated radiotracer 5 showed a greatly improved pharmacokinetic profile, beyond what was predicted from individual N- or C-terminal PEGylation. It appears that the 2 PEG units acted synergistically to result in an improved metabolic profile including high α vβ 6+ tumor uptake and retention.« less

The effect of bi-terminal PEGylation of an integrin  α vβ 6-targeted 18F peptide on pharmacokinetics and tumor uptake

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

Hausner, Sven H.; Bauer, Nadine; Hu, Lina Y.

Radiotracers based on the peptide A20FMDV2 selectively target the cell surface receptor integrin α vβ 6. This integrin has been identified as a prognostic indicator correlating with the severity of disease for several challenging malignancies. In previous studies of A20FMDV2 peptides labeled with 4- 18F-fluorobenzoic acid ( 18F-FBA), we have shown that the introduction of poly(ethylene glycol) (PEG) improves pharmacokinetics, including increased uptake in α vβ 6-expressing tumors. The present study evaluated the effect of site-specific C-terminal or dual (N- and C-terminal) PEGylation, yielding 18F-FBA-A20FMDV2-PEG 28 (4) and 18F-FBA-PEG 28-A20FMDV2-PEG 28 (5), on α vβ 6-targeted tumor uptake and pharmacokinetics.more » The results are compared with 18F-FBA–labeled A20FMDV2 radiotracers (1–3) bearing either no PEG or different PEG units at the N terminus. The radiotracers were prepared and radiolabeled on solid phase. Using 3 cell lines, DX3puroβ6 (α vβ 6+), DX3puro (α vβ 6–), and BxPC-3 (α vβ 6+), we evaluated the radiotracers in vitro (serum stability; cell binding and internalization) and in vivo in mouse models bearing paired DX3puroβ6–DX3puro and, for 5, BxPC-3 xenografts. Here, the size and location of the PEG units significantly affected α vβ 6 targeting and pharmacokinetics. Although the C-terminally PEGylated 4 showed some improvements over the un-PEGylated 18F-FBA-A20FMDV2 (1), it was the bi-terminally PEGylated 5 that displayed the more favorable combination of high α vβ 6 affinity, selectivity, and pharmacokinetic profile. In vitro, 5 bound to α vβ 6-expressing DX3puroβ6 and BxPC-3 cells with 60.5% ± 3.3% and 48.8% ± 8.3%, respectively, with a significant fraction of internalization (37.2% ± 4.0% and 37.6% ± 4.1% of total radioactivity, respectively). By comparison, in the DX3puro control 5 showed only 3.0% ± 0.5% binding and 0.9% ± 0.2% internalization. In vivo, 5 maintained high, α vβ 6-directed binding in the paired DX3puroβ6–DX3puro model (1 h: DX3puroβ6, 2.3 ± 0.2 percentage injected dose per gram [%ID/g]; DX3puroβ6/DX3puro ratio, 6.5:1; 4 h: 10.7:1). In the pancreatic BxPC-3 model, uptake was 4.7 ± 0.9 %ID/g (1 h) despite small tumor sizes (20–80 mg). In conclusion, the bi-PEGylated radiotracer 5 showed a greatly improved pharmacokinetic profile, beyond what was predicted from individual N- or C-terminal PEGylation. It appears that the 2 PEG units acted synergistically to result in an improved metabolic profile including high α vβ 6+ tumor uptake and retention.« less

Eastern Equine Encephalitis

MedlinePlus

... EEE is one of the most severe mosquito-transmitted diseases in the United States with approximately 33% mortality ... Emerging and Zoonotic Infectious Diseases (NCEZID) Division of Vector-Borne Diseases (DVBD) Email Recommend Tweet YouTube Instagram Listen Watch ...

Electron impact excitation of H2 - Rydberg band systems and the benchmark dissociative cross section for H Lyman-alpha

NASA Technical Reports Server (NTRS)

Shemansky, D. E.; Hall, D. T.; Ajello, J. M.

1985-01-01

The cross sections sigma R 1 (2p) for excitation of H Ly-alpha emission produced by electron impact on H2 is reexamined. A more accurate estimate for sigma R 1 (2p) is obtained based on Born approximation estimates of the H2 Rydberg system cross sections using measured relative excitation functions. The obtained value is (8.18 + or -1.2) x 10 to the -18th sq cm at 100 eV, a factor of 0.69 below the value universally applied to cross section measurements over the past decade. Cross sections for the H2 Rydberg systems fixed in magnitude by the Born approximation have also been obtained using experimentally determined excitation functions. Accurate analytic expressions for these cross sections allow the direct calculation of rate coefficients.

Quantitative assessment of submicron scale anisotropy in tissue multifractality by scattering Mueller matrix in the framework of Born approximation

NASA Astrophysics Data System (ADS)

Das, Nandan Kumar; Dey, Rajib; Chakraborty, Semanti; Panigrahi, Prasanta K.; Meglinski, Igor; Ghosh, Nirmalya

2018-04-01

A number of tissue-like disordered media exhibit local anisotropy of scattering in the scaling behavior. Scaling behavior contains wealth of fractal or multifractal properties. We demonstrate that the spatial dielectric fluctuations in a sample of biological tissue exhibit multifractal anisotropy. Multifractal anisotropy encoded in the wavelength variation of the light scattering Mueller matrix and manifesting as an intriguing spectral diattenuation effect. We developed an inverse method for the quantitative assessment of the multifractal anisotropy. The method is based on the processing of relevant Mueller matrix elements in Fourier domain by using Born approximation, followed by the multifractal analysis. The approach promises for probing subtle micro-structural changes in biological tissues associated with the cancer and precancer, as well as for non-destructive characterization of a wide range of scattering materials.

Single electron impact ionization of the methane molecule

NASA Astrophysics Data System (ADS)

Bouamoud, Mammar; Sahlaoui, Mohammed; Benmansour, Nour El Houda; Atomic and Molecular Collisions Team

2014-10-01

Triply differential cross sections (TDCS) results of electron-impact ionization of the inner 2a1 molecular orbital of CH4 are presented in the framework of the Second Born Approximation and compared with the experimental data performed in coplanar asymmetric geometry. The cross sections are averaged on the random orientations of the molecular target for accurate comparison with experiments and are compared also with the theoretical calculations of the Three Coulomb wave (3CW) model. Our results are in good agreement with experiments and 3CW results in the binary peak. In contrast the Second Born Approximation yields a significant higher values compared to the 3CW results for the recoil peak and seems to describe suitably the recoil region where higher order effects can occur with the participation of the recoiling ion in the collision process.

Precise calculations in simulations of the interaction of low energy neutrons with nano-dispersed media

NASA Astrophysics Data System (ADS)

Artem'ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.

2016-01-01

We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2-5 nm and for neutron energies 3 × 10-7-10-3 eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.

Immigration, race/ethnicity, and social and economic factors as predictors of breastfeeding initiation.

PubMed

Celi, Ann C; Rich-Edwards, Janet W; Richardson, Marcie K; Kleinman, Ken P; Gillman, Matthew W

2005-03-01

To determine the impact of immigration status as well as race/ethnicity and social and economic factors on breastfeeding initiation. Cohort. Multisite group practice in eastern Massachusetts. One thousand eight hundred twenty-nine pregnant women prospectively followed up in Project Viva. Whether the participant breastfed her infant. The overall breastfeeding initiation rate was 83%. In multivariate models that included race/ethnicity and social, economic, and demographic factors, foreign-born women were more likely to initiate breastfeeding than US-born women (odds ratio [OR], 3.2 [95% confidence interval (CI), 2.0-5.2]). In models stratified by both race/ethnicity and immigration status, and further adjusted for whether the mother herself was breastfed as an infant and the mother's parents' immigration status, US-born and foreign-born black and Hispanic women initiated breastfeeding at rates at least as high as US-born white women (US-born black vs US-born white women, OR, 1.2 [95% CI, 0.8-1.9], US-born Hispanic vs US-born white women, OR, 1.1 [95% CI, 0.6-1.9], foreign-born black vs US-born white women, OR, 2.6 [95% CI, 1.1-6.0], and foreign-born Hispanic vs US-born white women, OR, 1.8 [95% CI, 0.7-4.8]). Calculations of predicted prevalences showed that, for example, the 2.6-fold increase in odds for the foreign-born black vs US-born white women translated to an increase in probability of approximately 1.4. Higher maternal education and household income also predicted higher initiation rates. Immigration status was strongly associated with increased breastfeeding initiation in this cohort, implying that cultural factors are important in the decision to breastfeed. Immigrants of all races/ethnicities initiated breastfeeding more often than their US-born counterparts. In addition, US-born minority groups initiated breastfeeding at rates at least as high as their white counterparts, likely due in part to high levels of education and income as well as to access to a medical care system that explicitly supports breastfeeding.

Fast inverse scattering solutions using the distorted Born iterative method and the multilevel fast multipole algorithm

PubMed Central

Hesford, Andrew J.; Chew, Weng C.

2010-01-01

The distorted Born iterative method (DBIM) computes iterative solutions to nonlinear inverse scattering problems through successive linear approximations. By decomposing the scattered field into a superposition of scattering by an inhomogeneous background and by a material perturbation, large or high-contrast variations in medium properties can be imaged through iterations that are each subject to the distorted Born approximation. However, the need to repeatedly compute forward solutions still imposes a very heavy computational burden. To ameliorate this problem, the multilevel fast multipole algorithm (MLFMA) has been applied as a forward solver within the DBIM. The MLFMA computes forward solutions in linear time for volumetric scatterers. The typically regular distribution and shape of scattering elements in the inverse scattering problem allow the method to take advantage of data redundancy and reduce the computational demands of the normally expensive MLFMA setup. Additional benefits are gained by employing Kaczmarz-like iterations, where partial measurements are used to accelerate convergence. Numerical results demonstrate both the efficiency of the forward solver and the successful application of the inverse method to imaging problems with dimensions in the neighborhood of ten wavelengths. PMID:20707438

A differential equation for the Generalized Born radii.

PubMed

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

2013-06-28

The Generalized Born (GB) model offers a convenient way of representing electrostatics in complex macromolecules like proteins or nucleic acids. The computation of atomic GB radii is currently performed by different non-local approaches involving volume or surface integrals. Here we obtain a non-linear second-order partial differential equation for the Generalized Born radius, which may be solved using local iterative algorithms. The equation is derived under the assumption that the usual GB approximation to the reaction field obeys Laplace's equation. The equation admits as particular solutions the correct GB radii for the sphere and the plane. The tests performed on a set of 55 different proteins show an overall agreement with other reference GB models and "perfect" Poisson-Boltzmann based values.

Simulating the spread of malaria using a generic transmission model for mosquito-borne infectious diseases

NASA Astrophysics Data System (ADS)

Kon, Cynthia Mui Lian; Labadin, Jane

2016-06-01

Malaria is a critical infection caused by parasites which are spread to humans through mosquito bites. Approximately half of the world's population is in peril of getting infected by malaria. Mosquito-borne diseases have a standard behavior where they are transmitted in the same manner, only through vector mosquito. Taking this into account, a generic spatial-temporal model for transmission of multiple mosquito-borne diseases had been formulated. Our interest is to reproduce the actual cases of different mosquito-borne diseases using the generic model and then predict future cases so as to improve control and target measures competently. In this paper, we utilize notified weekly malaria cases in four districts in Sarawak, Malaysia, namely Kapit, Song, Belaga and Marudi. The actual cases for 36 weeks, which is from week 39 in 2012 to week 22 in 2013, are compared with simulations of the generic spatial-temporal transmission mosquito-borne diseases model. We observe that the simulation results display corresponding result to the actual malaria cases in the four districts.

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

120 DEG C Cure, Durable, Corrosion Protection Powder Coatings for Temperature Sensitive Substrates

DTIC Science & Technology

2005-01-28

Extrudate was passed through water-cooled pinch-rolls and collected onto a stainless steel belt; from exit of the extruder, approximately 60 sec... stainless steel belt; from exit of the extruder, approximately 60 sec. was required to reach ambient temperature. Production scale processing at...inherently free from volatile organic compounds, chromates, and hazardous air pollutants. Relative to the incumbent solvent-borne urethane paint

Prevalence of small for gestational age (SGA) and short stature in children born SGA who qualify for growth hormone treatment at 3 years of age: Population-based study.

PubMed

Fujita, Kaori; Nagasaka, Miwako; Iwatani, Sota; Koda, Tsubasa; Kurokawa, Daisuke; Yamana, Keiji; Nishida, Kosuke; Taniguchi-Ikeda, Mariko; Uchino, Eiko; Shirai, Chika; Iijima, Kazumoto; Morioka, Ichiro

2016-05-01

To treat children born small for gestational age (SGA) with severe short stature, treatment with growth hormone (GH) has been approved in the USA, Europe, and Japan, but no population-based studies have reported their prevalence. The aims of this study were to investigate the prevalence of SGA and short stature in children born SGA who qualify for GH treatment at 3 years of age in a Japanese population. A population-based study was conducted in Kobe, Japan with 27 228 infants who were born between 2006 and 2008 and followed until 3 years of age. Prevalence of birthweight (BW) or birth length (BL) ≤ -2.0 standard deviation scores (SDS) for gestational age (GA; definition of SGA) was calculated. Short children born SGA who qualify for GH treatment at 3 years of age were estimated using the following criteria: BW and BL below the 10th percentile for GA, BW or BL ≤ -2.0 SDS for GA, and 2.5 SDS below the mean height for age. The prevalence of SGA was 3.5%. The estimated prevalence of short stature in children born SGA who met the criteria for GH treatment was 0.06%. The prevalence in infants born <34 weeks (0.39%) was significantly higher than that in infants born 34-41 weeks GA (0.05%, P = 0.02). The prevalence of SGA and short stature in children born SGA who qualify for GH treatment is approximately 1 of 30 infants and 1 of 1800 children, respectively. The risk is increased when children are born <34 weeks GA. © 2015 Japan Pediatric Society.

Active immunizations with peptide-DC vaccines and passive transfer with antibodies protect neutropenic mice against disseminated candidiasis.

PubMed

Xin, Hong

2016-01-04

We previously report that peptide-pulsed dendritic cell (DC) vaccination, which targeting two peptides (Fba and Met6) expressed on the cell surface of Candida albicans, can induce high degree of protection against disseminated candidiasis in immunocompetent mice. Passive transfer of immune sera from the peptide immunized mice or peptide-related monoclonal antibodies demonstrated that protection was medicated by peptide-specific antibodies. In this study the efficacy of active and passive immunization against disseminated candidiasis was tested in mice with cyclophosphamide-induced neutropenia. Peptide-DC vaccines were given to mice prior to induction of neutropenia. We show active immunization with either Fba or Met6 peptide-DC vaccine significantly improved the survival and reduced the fungal burden of disseminated candidiasis in those immunocompromised mice. Importantly, we show that administration of two protective monoclonal antibodies also protect neutropenic mice against the disease, implying possibility of developing a successful passive immunotherapy strategy to treat the disease and protect against disseminated candidiasis. The results of this study are crucial as they address the fundamental questions as to whether the synthetic peptide vaccine induced immunity protects the host during a neutropenic episode. We anticipate that this peptide-vaccine study will serve as the foundation of future investigations into new peptide vaccines comprised of cell surface peptides from other medically important Candida species, as well as other fungi. Copyright © 2015 Elsevier Ltd. All rights reserved.

Human attention filters for single colors.

PubMed

Sun, Peng; Chubb, Charles; Wright, Charles E; Sperling, George

2016-10-25

The visual images in the eyes contain much more information than the brain can process. An important selection mechanism is feature-based attention (FBA). FBA is best described by attention filters that specify precisely the extent to which items containing attended features are selectively processed and the extent to which items that do not contain the attended features are attenuated. The centroid-judgment paradigm enables quick, precise measurements of such human perceptual attention filters, analogous to transmission measurements of photographic color filters. Subjects use a mouse to locate the centroid-the center of gravity-of a briefly displayed cloud of dots and receive precise feedback. A subset of dots is distinguished by some characteristic, such as a different color, and subjects judge the centroid of only the distinguished subset (e.g., dots of a particular color). The analysis efficiently determines the precise weight in the judged centroid of dots of every color in the display (i.e., the attention filter for the particular attended color in that context). We report 32 attention filters for single colors. Attention filters that discriminate one saturated hue from among seven other equiluminant distractor hues are extraordinarily selective, achieving attended/unattended weight ratios >20:1. Attention filters for selecting a color that differs in saturation or lightness from distractors are much less selective than attention filters for hue (given equal discriminability of the colors), and their filter selectivities are proportional to the discriminability distance of neighboring colors, whereas in the same range hue attention-filter selectivity is virtually independent of discriminabilty.

Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm.

PubMed

Xie, Zhengwei; Zhang, Tianyu; Ouyang, Qi

2018-02-01

One of the long-expected goals of genome-scale metabolic modelling is to evaluate the influence of the perturbed enzymes on flux distribution. Both ordinary differential equation (ODE) models and constraint-based models, like Flux balance analysis (FBA), lack the capacity to perform metabolic control analysis (MCA) for large-scale networks. In this study, we developed a hyper-cube shrink algorithm (HCSA) to incorporate the enzymatic properties into the FBA model by introducing a pseudo reaction V constrained by enzymatic parameters. Our algorithm uses the enzymatic information quantitatively rather than qualitatively. We first demonstrate the concept by applying HCSA to a simple three-node network, whereby we obtained a good correlation between flux and enzyme abundance. We then validate its prediction by comparison with ODE and with a synthetic network producing voilacein and analogues in Saccharomyces cerevisiae. We show that HCSA can mimic the state-state results of ODE. Finally, we show its capability of predicting the flux distribution in genome-scale networks by applying it to sporulation in yeast. We show the ability of HCSA to operate without biomass flux and perform MCA to determine rate-limiting reactions. Algorithm was implemented by Matlab and C ++. The code is available at https://github.com/kekegg/HCSA. xiezhengwei@hsc.pku.edu.cn or qi@pku.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Is chloroplastic class IIA aldolase a marine enzyme?

PubMed

Miyasaka, Hitoshi; Ogata, Takeru; Tanaka, Satoshi; Ohama, Takeshi; Kano, Sanae; Kazuhiro, Fujiwara; Hayashi, Shuhei; Yamamoto, Shinjiro; Takahashi, Hiro; Matsuura, Hideyuki; Hirata, Kazumasa

2016-11-01

Expressed sequence tag analyses revealed that two marine Chlorophyceae green algae, Chlamydomonas sp. W80 and Chlamydomonas sp. HS5, contain genes coding for chloroplastic class IIA aldolase (fructose-1, 6-bisphosphate aldolase: FBA). These genes show robust monophyly with those of the marine Prasinophyceae algae genera Micromonas, Ostreococcus and Bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior to the divergence of the core chlorophytes (Chlorophyceae and Trebouxiophyceae) and the prasinophytes. The absence of this gene in some freshwater chlorophytes, such as Chlamydomonas reinhardtii, Volvox carteri, Chlorella vulgaris, Chlorella variabilis and Coccomyxa subellipsoidea, can therefore be explained by the loss of this gene somewhere in the evolutionary process. Our survey on the distribution of this gene in genomic and transcriptome databases suggests that this gene occurs almost exclusively in marine algae, with a few exceptions, and as such, we propose that chloroplastic class IIA FBA is a marine environment-adapted enzyme. This hypothesis was also experimentally tested using Chlamydomonas W80, for which we found that the transcript levels of this gene to be significantly lower under low-salt (that is, simulated terrestrial) conditions. Expression analyses of transcriptome data for two algae, Prymnesium parvum and Emiliania huxleyi, taken from the Sequence Read Archive database also indicated that the expression of this gene under terrestrial conditions (low NaCl and low sulfate) is significantly downregulated. Thus, these experimental and transcriptome data provide support for our hypothesis.

A Method to Constrain Genome-Scale Models with 13C Labeling Data

PubMed Central

García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel; Ghosh, Amit; Chubukov, Victor; Mukhopadhyay, Aindrila; Arkin, Adam; Keasling, Jay D.

2015-01-01

Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems. PMID:26379153

Structural Control of Metabolic Flux

PubMed Central

Sajitz-Hermstein, Max; Nikoloski, Zoran

2013-01-01

Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions. PMID:24367246

Fluxes through plant metabolic networks: measurements, predictions, insights and challenges.

PubMed

Kruger, Nicholas J; Ratcliffe, R George

2015-01-01

Although the flows of material through metabolic networks are central to cell function, they are not easy to measure other than at the level of inputs and outputs. This is particularly true in plant cells, where the network spans multiple subcellular compartments and where the network may function either heterotrophically or photoautotrophically. For many years, kinetic modelling of pathways provided the only method for describing the operation of fragments of the network. However, more recently, it has become possible to map the fluxes in central carbon metabolism using the stable isotope labelling techniques of metabolic flux analysis (MFA), and to predict intracellular fluxes using constraints-based modelling procedures such as flux balance analysis (FBA). These approaches were originally developed for the analysis of microbial metabolism, but over the last decade, they have been adapted for the more demanding analysis of plant metabolic networks. Here, the principal features of MFA and FBA as applied to plants are outlined, followed by a discussion of the insights that have been gained into plant metabolic networks through the application of these time-consuming and non-trivial methods. The discussion focuses on how a system-wide view of plant metabolism has increased our understanding of network structure, metabolic perturbations and the provision of reducing power and energy for cell function. Current methodological challenges that limit the scope of plant MFA are discussed and particular emphasis is placed on the importance of developing methods for cell-specific MFA.

Is chloroplastic class IIA aldolase a marine enzyme?

PubMed Central

Miyasaka, Hitoshi; Ogata, Takeru; Tanaka, Satoshi; Ohama, Takeshi; Kano, Sanae; Kazuhiro, Fujiwara; Hayashi, Shuhei; Yamamoto, Shinjiro; Takahashi, Hiro; Matsuura, Hideyuki; Hirata, Kazumasa

2016-01-01

Expressed sequence tag analyses revealed that two marine Chlorophyceae green algae, Chlamydomonas sp. W80 and Chlamydomonas sp. HS5, contain genes coding for chloroplastic class IIA aldolase (fructose-1, 6-bisphosphate aldolase: FBA). These genes show robust monophyly with those of the marine Prasinophyceae algae genera Micromonas, Ostreococcus and Bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior to the divergence of the core chlorophytes (Chlorophyceae and Trebouxiophyceae) and the prasinophytes. The absence of this gene in some freshwater chlorophytes, such as Chlamydomonas reinhardtii, Volvox carteri, Chlorella vulgaris, Chlorella variabilis and Coccomyxa subellipsoidea, can therefore be explained by the loss of this gene somewhere in the evolutionary process. Our survey on the distribution of this gene in genomic and transcriptome databases suggests that this gene occurs almost exclusively in marine algae, with a few exceptions, and as such, we propose that chloroplastic class IIA FBA is a marine environment-adapted enzyme. This hypothesis was also experimentally tested using Chlamydomonas W80, for which we found that the transcript levels of this gene to be significantly lower under low-salt (that is, simulated terrestrial) conditions. Expression analyses of transcriptome data for two algae, Prymnesium parvum and Emiliania huxleyi, taken from the Sequence Read Archive database also indicated that the expression of this gene under terrestrial conditions (low NaCl and low sulfate) is significantly downregulated. Thus, these experimental and transcriptome data provide support for our hypothesis. PMID:27058504

How large are nonadiabatic effects in atomic and diatomic systems?

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

Yang, Yubo, E-mail: yyang173@illinois.edu, E-mail: normantubman2015@u.northwestern.edu; Tubman, Norm M., E-mail: yyang173@illinois.edu, E-mail: normantubman2015@u.northwestern.edu; Ceperley, David M.

2015-09-28

With recent developments in simulating nonadiabatic systems to high accuracy, it has become possible to determine how much energy is attributed to nuclear quantum effects beyond zero-point energy. In this work, we calculate the non-relativistic ground-state energies of atomic and molecular systems without the Born-Oppenheimer approximation. For this purpose, we utilize the fixed-node diffusion Monte Carlo method, in which the nodes depend on both the electronic and ionic positions. We report ground-state energies for all systems studied, ionization energies for the first-row atoms and atomization energies for the first-row hydrides. We find the ionization energies of the atoms to bemore » nearly independent of the Born-Oppenheimer approximation, within the accuracy of our results. The atomization energies of molecular systems, however, show small effects of the nonadiabatic coupling between electrons and nuclei.« less

Elastic and inelastic scattering of /sup 58/Ni+/sup 208/Pb at bombarding energies from 598 to 1011 MeV

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

Beckerman, M.; Auble, R.L.; Bertrand, F.E.

1987-08-01

High-resolution measurements have been made of elastic and inelastic scattering of /sup 58/Ni+ /sup 208/Pb at four bombarding energies from 10.3 to 17.4 MeV/nucleon. The considerable inelastic strength observed for excitation energies up to at least 7 MeV is dominated by Coulomb-driven quadrupole transitions. Analyses were done using both the distorted-wave Born approximation and coupled-channels models. At the highest bombarding energies the data can be described equally well by distorted-wave Born approximations and coupled channels analyses. We find that B(E2) = 0.062 e/sup 2/b/sup 2/ for the 1.454 MeV 2/sup +/ state in /sup 58/Ni and B(E2) = 0.34 e/supmore » 2/b/sup 2/ for the 4.09 MeV 2/sup +/ state in /sup 208/Pb.« less

u d b \\xAF b \\xAF tetraquark resonances with lattice QCD potentials and the Born-Oppenheimer approximation

NASA Astrophysics Data System (ADS)

Bicudo, Pedro; Cardoso, Marco; Peters, Antje; Pflaumer, Martin; Wagner, Marc

2017-09-01

We study tetraquark resonances with lattice QCD potentials computed for a static b ¯b ¯ pair in the presence of two lighter quarks u d , the Born-Oppenheimer approximation and the emergent wave method. As a proof of concept we focus on the system with isospin I =0 , but consider different relative angular momenta l of the heavy quarks b ¯b ¯. For l =0 a bound state has already been predicted with quantum numbers I (JP)=0 (1+). Exploring various angular momenta we now compute the phase shifts and search for S and T matrix poles in the second Riemann sheet. We predict a tetraquark resonance for l =1 , decaying into two B mesons, with quantum numbers I (JP)=0 (1-) , mass m =10 57 6-4+4 MeV and decay width Γ =11 2-103+90 MeV .

How large are nonadiabatic effects in atomic and diatomic systems?

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

Yang, Yubo; Kylänpää, Ilkka; Tubman, Norm M.

2015-09-29

With recent developments in simulating nonadiabatic systems to high accuracy, it has become possible to determine how much energy is attributed to nuclear quantum effects beyond zero-point energy. Here, we calculate the non-relativistic ground-state energies of atomic and molecular systems without the Born-Oppenheimer approximation. For this purpose, we utilize the fixed-node diffusion Monte Carlo method, in which the nodes depend on both the electronic and ionic positions. Our report shows the ground-state energies for all systems studied, ionization energies for the first-row atoms and atomization energies for the first-row hydrides. We find the ionization energies of the atoms to bemore » nearly independent of the Born-Oppenheimer approximation, within the accuracy of our results. The atomization energies of molecular systems, however, show small effects of the nonadiabatic coupling between electrons and nuclei.« less

On proton excitation of forbidden lines in positive ions

NASA Astrophysics Data System (ADS)

Burgess, Alan; Tully, John A.

2005-08-01

The semi-classical impact parameter approximations used by Bahcall and Wolf and by Bely and Faucher, for proton excitation of electric quadrupole transitions in positive ions, both fail at high energies, giving cross sections which do not fall off correctly as constant/E. This is in contrast with the pioneering example of Seaton for Fe+13 and of Reid and Schwarz for S+3, both of whom achieve the correct functional form, but do not ensure the correct constant of proportionality. By combining the Born and semi-classical approximations one can obtain cross sections which have the full correct behaviour as E → ∞, and hence, rate coefficients which have the correct high temperature behaviour (~C/T1/2 with the correct value of C). We provide a computer program for calculating these. An error in Faucher's derivation of the Born formula is also discussed.

Born distorted-wave approximation applied to the H+ + He collisions at intermediate and high energies

NASA Astrophysics Data System (ADS)

Rahmanian, M.; Fathi, R.; Shojaei, F.

2017-11-01

The single-charge transfer process in collision of protons with helium atoms in their ground states is investigated. The model utilizes the second-order three-body Born distorted-wave approximation (BDW-3B) with correct Coulomb boundary conditions to calculate the differential and total cross sections at intermediate and high energies. The role of the passive electrons and electron-electron correlations are studied by comparing our results and the BDW-4B calculations with the complete perturbation potential. The present results are also compared with other theories, and the Thomas scattering mechanism is investigated. The obtained results are also compared with the recent experimental measurements. For the prior differential cross sections, the comparisons show better agreement with the experiments at smaller scattering angles. The agreement between the total cross sections and the BDW-4B results as well as the experimental data is good at higher impact energies.

The He+H¯→He p¯+e+ rearrangement

NASA Astrophysics Data System (ADS)

Todd, Allan C.; Armour, Edward A. G.

2006-06-01

In this paper, we present a summary of our work in progress on calculating cross sections for the He+H¯→He p¯+e+ rearrangement process in He H¯ scattering. This has involved a study of the system He p¯ within the Born-Oppenheimer (BO) approximation using the Rayleigh-Ritz variational method. This work has been reported in [A.C. Todd, E.A.G. Armour, J. Phys. B 38 (2005) 3367] and is summarised here. Similar calculations are in progress for the He+H¯ entrance channel. We intend to use the entrance channel and rearrangement channel wave functions to obtain the cross sections for the rearrangement using the distorted wave Born approximation T-matrix method described elsewhere in these proceedings [E.A.G. Armour, S. Jonsell, Y. Liu, A.C. Todd, these Proceedings, doi:10.1016/j.nimb.2006.01.049].

High-frequency Born synthetic seismograms based on coupled normal modes

USGS Publications Warehouse

Pollitz, Fred F.

2011-01-01

High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ∼4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD).

Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

PubMed

Albaugh, Alex; Head-Gordon, Teresa; Niklasson, Anders M N

2018-02-13

Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

Direct pair production in heavy-ion--atom collisions

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

Anholt, R.; Jakubassa-Amundsen, D.H.; Amundsen, P.A.

1983-02-01

Direct pair production in approx.5-MeV/amu heavy-ion--atom collisions with uranium target atoms is calculated with the plane-wave Born approximation and the semiclassical approximation. Briggs's approximation is used to obtain the electron and positron wave functions. Since pair production involves high momentum transfer q from the moving projectile to the vacuum, use is made of a high-q approximation to greatly simplify the numerical computations. Coulomb deflection of the projectile, the effect of finite nuclear size on the elec- tronic wave functions, and the energy loss by the projectile exciting the pair are all taken into account in these calculations.

Current and Future Repellent Technologies: The Potential of Spatial Repellents and Their Place in Mosquito-Borne Disease Control.

PubMed

Norris, Edmund J; Coats, Joel R

2017-01-29

Every year, approximately 700,000 people die from complications associated with etiologic disease agents transmitted by mosquitoes. While insecticide-based vector control strategies are important for the management of mosquito-borne diseases, insecticide-resistance and other logistical hurdles may lower the efficacy of this approach, especially in developing countries. Repellent technologies represent another fundamental aspect of preventing mosquito-borne disease transmission. Among these technologies, spatial repellents are promising alternatives to the currently utilized contact repellents and may significantly aid in the prevention of mosquito-borne disease if properly incorporated into integrated pest management approaches. As their deployment would not rely on prohibitively expensive or impractical novel accessory technologies and resources, they have potential utility in developing countries where the burden of mosquito-borne disease is most prevalent. This review aims to describe the history of various repellent technologies, highlight the potential of repellent technologies in preventing the spread of mosquito-borne disease, and discuss currently known mechanisms that confer resistance to current contact and spatial repellents, which may lead to the failures of these repellents. In the subsequent section, current and future research projects aimed at exploring long-lasting non-pyrethroid spatial repellent molecules along with new paradigms and rationale for their development will be discussed.

Current and Future Repellent Technologies: The Potential of Spatial Repellents and Their Place in Mosquito-Borne Disease Control

PubMed Central

Norris, Edmund J.; Coats, Joel R.

2017-01-01

Every year, approximately 700,000 people die from complications associated with etiologic disease agents transmitted by mosquitoes. While insecticide-based vector control strategies are important for the management of mosquito-borne diseases, insecticide-resistance and other logistical hurdles may lower the efficacy of this approach, especially in developing countries. Repellent technologies represent another fundamental aspect of preventing mosquito-borne disease transmission. Among these technologies, spatial repellents are promising alternatives to the currently utilized contact repellents and may significantly aid in the prevention of mosquito-borne disease if properly incorporated into integrated pest management approaches. As their deployment would not rely on prohibitively expensive or impractical novel accessory technologies and resources, they have potential utility in developing countries where the burden of mosquito-borne disease is most prevalent. This review aims to describe the history of various repellent technologies, highlight the potential of repellent technologies in preventing the spread of mosquito-borne disease, and discuss currently known mechanisms that confer resistance to current contact and spatial repellents, which may lead to the failures of these repellents. In the subsequent section, current and future research projects aimed at exploring long-lasting non-pyrethroid spatial repellent molecules along with new paradigms and rationale for their development will be discussed. PMID:28146066

Quantifying Fusion Born Ion Populations in Magnetically Confined Plasmas using Ion Cyclotron Emission

DOE PAGES

Carbajal, L.; Warwick Univ., Coventry; Dendy, R. O.; ...

2017-03-07

Ion cyclotron emission (ICE) offers unique promise as a diagnostic of the fusion born alpha-particle population in magnetically confined plasmas. Pioneering observations from JET and TFTR found that ICE intensity P ICE scales approximately linearly with the measured neutron flux from fusion reactions, and with the inferred concentration, n /n i , of fusion-born alpha-particles confined within the plasma. We present fully nonlinear self-consistent kinetic simulations that reproduce this scaling for the first time. This resolves a longstanding question in the physics of fusion alpha particle confinement and stability in MCF plasmas. It confirms the MCI as the likely emissionmore » mechanism and greatly strengthens the basis for diagnostic exploitation of ICE in future burning plasmas.« less

Quantifying Fusion Born Ion Populations in Magnetically Confined Plasmas using Ion Cyclotron Emission

NASA Astrophysics Data System (ADS)

Carbajal, L.; Dendy, R. O.; Chapman, S. C.; Cook, J. W. S.

2017-03-01

Ion cyclotron emission (ICE) offers a unique promise as a diagnostic of the fusion born alpha-particle population in magnetically confined plasmas. Pioneering observations from JET and TFTR found that ICE intensity PICE scales approximately linearly with the measured neutron flux from fusion reactions, and with the inferred concentration, nα/ni, of fusion born alpha particles confined within the plasma. We present fully nonlinear self-consistent kinetic simulations that reproduce this scaling for the first time. This resolves a long-standing question in the physics of fusion alpha-particle confinement and stability in magnetic confinement fusion plasmas. It confirms the magnetoacoustic cyclotron instability as the likely emission mechanism and greatly strengthens the basis for diagnostic exploitation of ICE in future burning plasmas.

Quantifying Fusion Born Ion Populations in Magnetically Confined Plasmas using Ion Cyclotron Emission.

PubMed

Carbajal, L; Dendy, R O; Chapman, S C; Cook, J W S

2017-03-10

Ion cyclotron emission (ICE) offers a unique promise as a diagnostic of the fusion born alpha-particle population in magnetically confined plasmas. Pioneering observations from JET and TFTR found that ICE intensity P_{ICE} scales approximately linearly with the measured neutron flux from fusion reactions, and with the inferred concentration, n_{α}/n_{i}, of fusion born alpha particles confined within the plasma. We present fully nonlinear self-consistent kinetic simulations that reproduce this scaling for the first time. This resolves a long-standing question in the physics of fusion alpha-particle confinement and stability in magnetic confinement fusion plasmas. It confirms the magnetoacoustic cyclotron instability as the likely emission mechanism and greatly strengthens the basis for diagnostic exploitation of ICE in future burning plasmas.

VLF Trimpi modelling on the path NWC-Dunedin using both finite element and 3D Born modelling

NASA Astrophysics Data System (ADS)

Nunn, D.; Hayakawa, K. B. M.

1998-10-01

This paper investigates the numerical modelling of VLF Trimpis, produced by a D region inhomogeneity on the great circle path. Two different codes are used to model Trimpis on the path NWC-Dunedin. The first is a 2D Finite Element Method Code (FEM), whose solutions are rigorous and valid in the strong scattering or non-Born limit. The second code is a 3D model that invokes the Born approximation. The predicted Trimpis from these codes compare very closely, thus confirming the validity of both models. The modal scattering matrices for both codes are analysed in some detail and are found to have a comparable structure. They indicate strong scattering between the dominant TM modes. Analysis of the scattering matrix from the FEM code shows that departure from linear Born behaviour occurs when the inhomogeneity has a horizontal scale size of about 100 km and a maximum electron density enhancement at 75 km altitude of about 6 electrons.

Asymptotic form for the cross section for the Coulomb interacting rearrangement collisions

NASA Technical Reports Server (NTRS)

Omidvar, K.

1973-01-01

It is shown that in a rearrangement collision leading to the formation of the highly excited hydrogenlike states the cross section in all orders of the Born approximation behaves as 1/n sq, with n the principal quantum number, thus invalidating the Brinkman-Kramers approximation for large n. Similarly, in high energy inelastic electron-hydrogenlike atom collisions the exchange cross section for sufficiently large n dominates the direct excitation cross section.

Functional neural bases of numerosity judgments in healthy adults born preterm.

PubMed

Clark, Caron A C; Liu, Yating; Wright, Nicolas Lee Abbot; Bedrick, Alan; Edgin, Jamie O

2017-11-01

High rates of mathematics learning disabilities among individuals born preterm (<37weeksGA) have spurred calls for a greater understanding of the nature of these weaknesses and their neural underpinnings. Groups of healthy, high functioning young adults born preterm and full term (n=20) completed a symbolic and non-symbolic magnitude comparison task while undergoing functional MRI scanning. Collectively, participants showed activation in superior and inferior frontal and parietal regions previously linked to numeric processing when comparing non-symbolic magnitude arrays separated by small numeric distances. Simultaneous deactivation of the default mode network also was evident during these trials. Individuals born preterm showed increased signal change relative to their full term peers in right inferior frontal and parietal regions when comparing the non-symbolic magnitude arrays. Elevated signal change during non-symbolic task blocks was associated with poorer performance on a calculation task administered outside of the scanner. These findings indicate that healthy, high-functioning adults born preterm may recruit fronto-parietal networks more extensively when processing non-symbolic magnitudes, suggesting that approximate number system training may be an inroad for early intervention to prevent mathematics difficulties in this population. Copyright © 2017 Elsevier Inc. All rights reserved.

Race differences in infant mortality from endogenous causes: a population-based study in North Carolina.

PubMed

Michielutte, R; Moore, M L; Meis, P J; Ernest, J M; Wells, H B

1994-02-01

This study examines the associations between race, birth weight, and mortality from endogenous causes for all singleton births born in 1984-1987 in a 20-county region of North Carolina. A more detailed analysis of preterm low birth weight infants examines these associations according to the proximate medical causes (medical etiology) of the preterm birth. Overall, black infants were found to have approximately twice the mortality risk of white infants. Most of the excess black mortality risk is explained by the larger proportion of black infants born at lower birth weights. The pattern of race differences in infant mortality by birth weight generally replicates the results of earlier studies, but the relative risk ratios within specific birth weight categories are smaller than previously reported. Among preterm low birth weight infants, the association between race and endogenous mortality differs within categories of medical etiology. The mortality risk is the same for black and white infants born preterm due to premature rupture of the membranes (PROM), lower for black infants born preterm due to medical problems, and higher for black infants born preterm due to idiopathic premature labor (IPL).

Variation in Differential and Total Cross Sections Due to Different Radial Wave Functions

ERIC Educational Resources Information Center

Williamson, W., Jr.; Greene, T.

1976-01-01

Three sets of analytical wave functions are used to calculate the Na (3s---3p) transition differential and total electron excitation cross sections by Born approximations. Results show expected large variations in values. (Author/CP)

An approximate inverse scattering technique for reconstructing blockage profiles in water pipelines using acoustic transients.

PubMed

Jing, Liwen; Li, Zhao; Wang, Wenjie; Dubey, Amartansh; Lee, Pedro; Meniconi, Silvia; Brunone, Bruno; Murch, Ross D

2018-05-01

An approximate inverse scattering technique is proposed for reconstructing cross-sectional area variation along water pipelines to deduce the size and position of blockages. The technique allows the reconstructed blockage profile to be written explicitly in terms of the measured acoustic reflectivity. It is based upon the Born approximation and provides good accuracy, low computational complexity, and insight into the reconstruction process. Numerical simulations and experimental results are provided for long pipelines with mild and severe blockages of different lengths. Good agreement is found between the inverse result and the actual pipe condition for mild blockages.

Ionization potential depression and optical spectra in a Debye plasma model

NASA Astrophysics Data System (ADS)

Lin, Chengliang; Röpke, Gerd; Reinholz, Heidi; Kraeft, Wolf-Dietrich

2017-11-01

We show how optical spectra in dense plasmas are determined by the shift of energy levels as well as the broadening owing to collisions with the plasma particles. In lowest approximation, the interaction with the plasma particles is described by the RPA dielectric function, leading to the Debye shift of the continuum edge. The bound states remain nearly un-shifted, their broadening is calculated in Born approximation. The role of ionization potential depression as well as the Inglis-Teller effect are shown. The model calculations have to be improved going beyond the lowest (RPA) approximation when applying to WDM spectra.

Accounting for Location Error in Kalman Filters: Integrating Animal Borne Sensor Data into Assimilation Schemes

PubMed Central

Sengupta, Aritra; Foster, Scott D.; Patterson, Toby A.; Bravington, Mark

2012-01-01

Data assimilation is a crucial aspect of modern oceanography. It allows the future forecasting and backward smoothing of ocean state from the noisy observations. Statistical methods are employed to perform these tasks and are often based on or related to the Kalman filter. Typically Kalman filters assumes that the locations associated with observations are known with certainty. This is reasonable for typical oceanographic measurement methods. Recently, however an alternative and abundant source of data comes from the deployment of ocean sensors on marine animals. This source of data has some attractive properties: unlike traditional oceanographic collection platforms, it is relatively cheap to collect, plentiful, has multiple scientific uses and users, and samples areas of the ocean that are often difficult of costly to sample. However, inherent uncertainty in the location of the observations is a barrier to full utilisation of animal-borne sensor data in data-assimilation schemes. In this article we examine this issue and suggest a simple approximation to explicitly incorporate the location uncertainty, while staying in the scope of Kalman-filter-like methods. The approximation stems from a Taylor-series approximation to elements of the updating equation. PMID:22900005

On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

NASA Astrophysics Data System (ADS)

Scherrer, Arne; Agostini, Federica; Sebastiani, Daniel; Gross, E. K. U.; Vuilleumier, Rodolphe

2017-07-01

Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the computation of high-precision molecular spectra.

Few-body quark dynamics for doubly heavy baryons and tetraquarks

NASA Astrophysics Data System (ADS)

Richard, Jean-Marc; Valcarce, Alfredo; Vijande, Javier

2018-03-01

We discuss the adequate treatment of the three- and four-body dynamics for the quark model picture of double-charm baryons and tetraquarks. We stress that the variational and Born-Oppenheimer approximations give energies very close to the exact ones, while the diquark approximation might be somewhat misleading. The Hall-Post inequalities also provide very useful lower bounds that exclude the possibility of stable tetraquarks for some mass ratios and some color wave functions.

Density functional theory of electron transfer beyond the Born-Oppenheimer approximation: Case study of LiF.

PubMed

Li, Chen; Requist, Ryan; Gross, E K U

2018-02-28

We perform model calculations for a stretched LiF molecule, demonstrating that nonadiabatic charge transfer effects can be accurately and seamlessly described within a density functional framework. In alkali halides like LiF, there is an abrupt change in the ground state electronic distribution due to an electron transfer at a critical bond length R = R c , where an avoided crossing of the lowest adiabatic potential energy surfaces calls the validity of the Born-Oppenheimer approximation into doubt. Modeling the R-dependent electronic structure of LiF within a two-site Hubbard model, we find that nonadiabatic electron-nuclear coupling produces a sizable elongation of the critical R c by 0.5 bohr. This effect is very accurately captured by a simple and rigorously derived correction, with an M -1 prefactor, to the exchange-correlation potential in density functional theory, M = reduced nuclear mass. Since this nonadiabatic term depends on gradients of the nuclear wave function and conditional electronic density, ∇ R χ(R) and ∇ R n(r, R), it couples the Kohn-Sham equations at neighboring R points. Motivated by an observed localization of nonadiabatic effects in nuclear configuration space, we propose a local conditional density approximation-an approximation that reduces the search for nonadiabatic density functionals to the search for a single function y(n).

Environmental effects on long term behavior of composite laminates

NASA Astrophysics Data System (ADS)

Singhal, S. N.; Chamis, C. C.

Model equations are presented for approximate methods simulating the long-term behavior of composite materials and structures in hot/humid service environments. These equations allow laminate property upgradings with time, and can account for the effects of service environments on creep response. These methodologies are illustrated for various individual and coupled temperature/moisture, longitudinal/transverse, and composite material type cases. Creep deformation is noted to rise dramatically for cases of matrix-borne, but not of fiber-borne, loading in hot, humid environments; the coupled influence of temperature and moisture is greater than a mere combination of their individual influences.

Environmental effects on long term behavior of composite laminates

NASA Technical Reports Server (NTRS)

Singhal, S. N.; Chamis, C. C.

1992-01-01

Model equations are presented for approximate methods simulating the long-term behavior of composite materials and structures in hot/humid service environments. These equations allow laminate property upgradings with time, and can account for the effects of service environments on creep response. These methodologies are illustrated for various individual and coupled temperature/moisture, longitudinal/transverse, and composite material type cases. Creep deformation is noted to rise dramatically for cases of matrix-borne, but not of fiber-borne, loading in hot, humid environments; the coupled influence of temperature and moisture is greater than a mere combination of their individual influences.

Balloon borne Antarctic frost point measurements and their impact on polar stratospheric cloud theories

NASA Technical Reports Server (NTRS)

Rosen, James M.; Hofmann, D. J.; Carpenter, J. R.; Harder, J. W.; Oltsmans, S. J.

1988-01-01

Balloon-borne frost point measurements were performed over Antarctica during September-October 1987 as part of the NOZE II effort at McMurdo. The results show water mixing ratios on the order of 2 ppmv in the 20 km region, suggesting that models of the springtime Antarctic stratosphere should be based on approximately 2 ppmv water vapor. Evidence indicating that some PSCs form at temperatures higher than the frost point in the 15 to 20 km region is discussed. This supports the binary HNO3-H2O theory of PSC composition.

Born-Oppenheimer approximation in an effective field theory language

NASA Astrophysics Data System (ADS)

Brambilla, Nora; Krein, Gastão; Tarrús Castellà, Jaume; Vairo, Antonio

2018-01-01

The Born-Oppenheimer approximation is the standard tool for the study of molecular systems. It is founded on the observation that the energy scale of the electron dynamics in a molecule is larger than that of the nuclei. A very similar physical picture can be used to describe QCD states containing heavy quarks as well as light-quarks or gluonic excitations. In this work, we derive the Born-Oppenheimer approximation for QED molecular systems in an effective field theory framework by sequentially integrating out degrees of freedom living at energies above the typical energy scale where the dynamics of the heavy degrees of freedom occurs. In particular, we compute the matching coefficients of the effective field theory for the case of the H2+ diatomic molecule that are relevant to compute its spectrum up to O (m α5). Ultrasoft photon loops contribute at this order, being ultimately responsible for the molecular Lamb shift. In the effective field theory the scaling of all the operators is homogeneous, which facilitates the determination of all the relevant contributions, an observation that may become useful for high-precision calculations. Using the above case as a guidance, we construct under some conditions an effective field theory for QCD states formed by a color-octet heavy quark-antiquark pair bound with a color-octet light-quark pair or excited gluonic state, highlighting the similarities and differences between the QED and QCD systems. Assuming that the multipole expansion is applicable, we construct the heavy-quark potential up to next-to-leading order in the multipole expansion in terms of nonperturbative matching coefficients to be obtained from lattice QCD.

Disparities in vaccinations and cancer screening among U.S.- and foreign-born Arab and European American non-Hispanic White women.

PubMed

Dallo, Florence J; Kindratt, Tiffany B

2015-01-01

Disparities in vaccinations and cancer screening exist when comparing foreign-born and U.S.-born women collectively and disaggregated by race and ethnicity. The purpose of this study was to estimate and compare the age-adjusted prevalence of not receiving a flu or pneumonia vaccine, clinical breast examination, mammogram or Pap smear among U.S.- and foreign-born White women by region of birth and examine associations while controlling for potential confounders. We pooled 12 years of National Health Interview Survey data (n = 117,893). To approximate an "Arab-American" ethnicity, we identified 15 "Arab" countries from the Middle East region that comprise the Arab Nations. Data was requested from the National Center for Health Statistics Research Data Center. We used the χ(2) statistic to compare descriptive statistics and odds ratios (ORs) with 95% CIs were used for inferential statistics. Compared to U.S.-born, foreign-born Whites from the Arab Nations had higher estimates of not receiving recommended vaccinations and cancer screenings. In crude and adjusted analyses, foreign-born Arab-American women were less likely to report receiving a flu vaccine (OR, 0.34; 95% CI, 0.21-0.58), pneumonia vaccine (OR, 0.14; 95% CI, 0.06-0.32), Pap smear (OR, 0.13; 95% CI, 0.05-0.31), or clinical breast examination (OR, 0.16; 95% CI, 0.07-0.37) compared with U.S.-born White women. There were no differences for mammography. This national study examining uptake of flu and pneumonia vaccines and preventive cancer screenings suggests that estimates are lower for foreign-born Arab-American women compared with U.S.-born White women. Future studies should collect qualitative data that assess the cultural context surrounding prevention and screening behaviors among Arab-American women. Copyright © 2015 Jacobs Institute of Women's Health. Published by Elsevier Inc. All rights reserved.

Numerical simulation of the generation of reactive oxygen and nitrogen species (RONS) in water by atmospheric-pressure plasmas and their effects on Escherichia coli (E. coli)

NASA Astrophysics Data System (ADS)

Ikuse, Kazumasa; Hamaguchi, Satoshi

2016-09-01

We have used two types of numerical simulations to examine biological effects of reactive oxygen and nitrogen species (RONS) generated in water by an atmospheric-pressure plasma (APP) that irradiates the water surface. One is numerical simulation for the generation and transport of RONS in water based on the reaction-diffusion-advection equations coupled with Poisson equation. The rate constants, mobilities, and diffusion coefficients used in the equations are obtained from the literature. The gaseous species are given as boundary conditions and time evolution of the concentrations of chemical species in pure water is solved numerically as functions of the depth in one dimension. Although it is not clear how living organisms respond to such exogenous RONS, we also use numerical simulation for metabolic reactions of Escherichia coli (E. coli) and examine possible effects of such RONS on an in-silico model organism. The computation model is based on the flux balance analysis (FBA), where the fluxes of the metabolites in a biological system are evaluated in steady state, i.e., under the assumption that the fluxes do not change in time. The fluxes are determined with liner programming to maximize the growth rate of the bacteria under the given conditions. Although FBA cannot be directly applied to dynamical responses of metabolic reactions, the simulation still gives insight into the biological reactions to exogenous chemical species generated by an APP. Partially supported by JSPS Grants-in-Aid for Scientific Research.

Neural adaptation to thin and fat bodies in the fusiform body area and middle occipital gyrus: an fMRI adaptation study.

PubMed

Hummel, Dennis; Rudolf, Anne K; Brandi, Marie-Luise; Untch, Karl-Heinz; Grabhorn, Ralph; Hampel, Harald; Mohr, Harald M

2013-12-01

Visual perception can be strongly biased due to exposure to specific stimuli in the environment, often causing neural adaptation and visual aftereffects. In this study, we investigated whether adaptation to certain body shapes biases the perception of the own body shape. Furthermore, we aimed to evoke neural adaptation to certain body shapes. Participants completed a behavioral experiment (n = 14) to rate manipulated pictures of their own bodies after adaptation to demonstratively thin or fat pictures of their own bodies. The same stimuli were used in a second experiment (n = 16) using functional magnetic resonance imaging (fMRI) adaptation. In the behavioral experiment, after adapting to a thin picture of the own body participants also judged a thinner than actual body picture to be the most realistic and vice versa, resembling a typical aftereffect. The fusiform body area (FBA) and the right middle occipital gyrus (rMOG) show neural adaptation to specific body shapes while the extrastriate body area (EBA) bilaterally does not. The rMOG cluster is highly selective for bodies and perhaps body parts. The findings of the behavioral experiment support the existence of a perceptual body shape aftereffect, resulting from a specific adaptation to thin and fat pictures of one's own body. The fMRI results imply that body shape adaptation occurs in the FBA and the rMOG. The role of the EBA in body shape processing remains unclear. The results are also discussed in the light of clinical body image disturbances. Copyright © 2012 Wiley Periodicals, Inc.

Human attention filters for single colors

PubMed Central

Sun, Peng; Chubb, Charles; Wright, Charles E.; Sperling, George

2016-01-01

The visual images in the eyes contain much more information than the brain can process. An important selection mechanism is feature-based attention (FBA). FBA is best described by attention filters that specify precisely the extent to which items containing attended features are selectively processed and the extent to which items that do not contain the attended features are attenuated. The centroid-judgment paradigm enables quick, precise measurements of such human perceptual attention filters, analogous to transmission measurements of photographic color filters. Subjects use a mouse to locate the centroid—the center of gravity—of a briefly displayed cloud of dots and receive precise feedback. A subset of dots is distinguished by some characteristic, such as a different color, and subjects judge the centroid of only the distinguished subset (e.g., dots of a particular color). The analysis efficiently determines the precise weight in the judged centroid of dots of every color in the display (i.e., the attention filter for the particular attended color in that context). We report 32 attention filters for single colors. Attention filters that discriminate one saturated hue from among seven other equiluminant distractor hues are extraordinarily selective, achieving attended/unattended weight ratios >20:1. Attention filters for selecting a color that differs in saturation or lightness from distractors are much less selective than attention filters for hue (given equal discriminability of the colors), and their filter selectivities are proportional to the discriminability distance of neighboring colors, whereas in the same range hue attention-filter selectivity is virtually independent of discriminabilty. PMID:27791040

Human functional magnetic resonance imaging reveals separation and integration of shape and motion cues in biological motion processing.

PubMed

Jastorff, Jan; Orban, Guy A

2009-06-03

In a series of human functional magnetic resonance imaging experiments, we systematically manipulated point-light stimuli to identify the contributions of the various areas implicated in biological motion processing (for review, see Giese and Poggio, 2003). The first experiment consisted of a 2 x 2 factorial design with global shape and kinematics as factors. In two additional experiments, we investigated the contributions of local opponent motion, the complexity of the portrayed movement and a one-back task to the activation pattern. Experiment 1 revealed a clear separation between shape and motion processing, resulting in two branches of activation. A ventral region, extending from the lateral occipital sulcus to the posterior inferior temporal gyrus, showed a main effect of shape and its extension into the fusiform gyrus also an interaction. The dorsal region, including the posterior inferior temporal sulcus and the posterior superior temporal sulcus (pSTS), showed a main effect of kinematics together with an interaction. Region of interest analysis identified these interaction sites as the extrastriate and fusiform body areas (EBA and FBA). The local opponent motion cue yielded only little activation, limited to the ventral region (experiment 3). Our results suggest that the EBA and the FBA correspond to the initial stages in visual action analysis, in which the performed action is linked to the body of the actor. Moreover, experiment 2 indicates that the body areas are activated automatically even in the absence of a task, whereas other cortical areas like pSTS or frontal regions depend on the complexity of movements or task instructions for their activation.

Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory.

PubMed

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-05-15

Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA).

Testicular cancer risk and maternal parity: a population-based cohort study.

PubMed

Westergaard, T; Andersen, P K; Pedersen, J B; Frisch, M; Olsen, J H; Melbye, M

1998-04-01

The aim was to study, in a population-based cohort design, whether first-born sons run a higher risk of testicular cancer than later born sons; to investigate whether this difference in risk was affected by birth cohort, age of the son, maternal age, interval to previous delivery and other reproductive factors; and, finally, to evaluate to what extent changes in women's parity over time might explain the increasing incidence of testicular cancer. By using data from the Civil Registration System, a database was established of all women born in Denmark since 1935 and all their children alive in 1968 or born later. Sons with testicular cancer were identified in the Danish Cancer Registry. Among 1015994 sons followed for 15981 967 person-years, 626 developed testicular cancer (443 non-seminomas, 183 seminomas). Later born sons had a decreased risk of testicular cancer (RR = 0.80, 95% CI = 0.67-0.95) compared with first-born sons. The RR was 0.79 (95% CI = 0.64-0.98) for non-seminomas and 0.81 (95% CI = 0.58-1.13) for seminomas. There was no association between testicular cancer risk and overall parity of the mother, maternal or paternal age at the birth of the son, or maternal age at first birth. The decreased risk of testicular cancer among later born sons was not modified by age, birth cohort, interval to the previous birth, sex of the first-born child, or maternal age at birth of the son or at first birth. The increased proportion of first-borns from birth cohort 1946 to birth cohort 1969 only explained around 3% of an approximated two-fold increase in incidence between the cohorts. Our data document a distinctly higher risk of testicular cancer in first-born compared with later born sons and suggest that the most likely explanation should be sought among exposures in utero. The increase in the proportion of first-borns in the population has only contributed marginally to the increase in testicular cancer incidence.

Suburban migration and the birth outcome of Chicago-born white and African-American women: the merit of the healthy migrant theory?

PubMed

Collins, James W; Rankin, Kristin M; Janowiak, Christine M

2013-11-01

The healthy migrant theory posits that women who migrate before pregnancy are intrinsically healthier and therefore have better birth outcomes than those who don't move. Objective. To determine whether migration to the suburbs is associated with lower rates of preterm (<37 weeks) birth among Chicago-born White and African-American mothers. We performed stratified and multilevel logistic regression analyses on an Illinois transgenerational dataset of non-Latino White and African-American infants (1989-1991) and their mothers (1956-1976) with appended US census income information. Forty percent of Chicago-born White mothers (N = 45,135) migrated to Suburban Cook County and 30 % migrated to the more geographically distant collar counties. In contrast, 10 % of Chicago-born African-American mothers (N = 41,221) migrated to Suburban Cook and only two percent migrated to the collar counties. Chicago-born White and African-American migrant mothers to Suburban Cook County had lower preterm birth rates than their non-migrant counterparts; RR = 0.8 (0.8-0.9) and 0.8 (0.7-0.8), respectively. When neighborhood income was singularly taken into account, the protective association of suburban migration and preterm birth disappeared among Chicago-born Whites. In race-specific multilevel multivariate regression models which included neighborhood income, the adjusted odds ratio of preterm birth, low birth weight, and small for gestational-age for Chicago-born White and African-American migrant (compared to non-migrant) mothers approximated unity. Neighborhood income underlies the protective association of suburban migration and birth outcome among Chicago-born White and African-American mothers. These findings do not support the healthy migrant hypothesis of reproductive outcome.

Students' Moral Reasoning as Related to Cultural Background and Educational Experience.

ERIC Educational Resources Information Center

Bar-Yam, Miriam; And Others

The relationship between moral development and cultural and educational background is examined. Approximately 120 Israeli youth representing different social classes, sex, religious affiliation, and educational experience were interviewed. The youth interviewed included urban middle and lower class students, Kibbutz-born, Youth Aliyah…

Research notes : pavement markings using waterborne paint and Visibeads in Region 2.

DOT National Transportation Integrated Search

1995-01-01

In order to address the problems associated with solvent-borne patins, ODOT Region 2 staff bought sufficient waterborne paint to place approximately 760 linear miles of stripes. This enabled the Region staff to evaluate state-of-the-art materials and...

Aharonov-Casher effect and quantum transport in graphene based nano rings: A self-consistent Born approximation

NASA Astrophysics Data System (ADS)

Ghaderzadeh, A.; Rahbari, S. H. Ebrahimnazhad; Phirouznia, A.

2018-03-01

In this study, Rashba coupling induced Aharonov-Casher effect in a graphene based nano ring is investigated theoretically. The graphene based nano ring is considered as a central device connected to semi-infinite graphene nano ribbons. In the presence of the Rashba spin-orbit interaction, two armchair shaped edge nano ribbons are considered as semi-infinite leads. The non-equilibrium Green's function approach is utilized to obtain the quantum transport characteristics of the system. The relaxation and dephasing mechanisms within the self-consistent Born approximation is scrutinized. The Lopez-Sancho method is also applied to obtain the self-energy of the leads. We unveil that the non-equilibrium current of the system possesses measurable Aharonov-Casher oscillations with respect to the Rashba coupling strength. In addition, we have observed the same oscillations in dilute impurity regimes in which amplitude of the oscillations is shown to be suppressed as a result of the relaxations.

High-frequency Born synthetic seismograms based on coupled normal modes

USGS Publications Warehouse

Pollitz, F.

2011-01-01

High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ~4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD). ?? The Author Geophysical Journal International ?? 2011 RAS.

Electron-impact ionization of Ne (2 p ) and Ar (3 p ) at intermediate energies: Role of the postcollision interaction

NASA Astrophysics Data System (ADS)

Hu, Xiaoqing; Gao, Cong-Zhang; Chen, Zhanbin; Wang, Jianguo; Wu, Yong; Wang, Yang

2017-11-01

We present the absolute triple differential cross section (TDCS) for single ionization of Ne (2 p ) at an impact energy of 599.6 eV and Ar (3 p ) at 195 eV. The role of the postcollision interaction (PCI) is studied using a high-order distorted-wave Born approximation model with a continuum distorted-waves expansion. Both the second- and third-order effects are considered in the present calculations, and the third-order distorted wave Born approximation model is reported in the (e ,2 e ) reaction. The calculated results show satisfactory agreement with experimental data. The magnitude of the absolute TDCS is enhanced by a factor 2-3 when the strength factor γ of the PCI amplitude is summarized just from 0 to 2. This proves that the PCI plays an important role in the absolute TDCS of the (e ,2 e ) reaction in the intermediate-energy region.

General relativistic corrections to the weak lensing convergence power spectrum

NASA Astrophysics Data System (ADS)

Giblin, John T.; Mertens, James B.; Starkman, Glenn D.; Zentner, Andrew R.

2017-11-01

We compute the weak lensing convergence power spectrum, Cℓκκ, in a dust-filled universe using fully nonlinear general relativistic simulations. The spectrum is then compared to more standard, approximate calculations by computing the Bardeen (Newtonian) potentials in linearized gravity and partially utilizing the Born approximation. We find corrections to the angular power spectrum amplitude of order ten percent at very large angular scales, ℓ˜2 - 3 , and percent-level corrections at intermediate angular scales of ℓ˜20 - 30 .

Positronium formation in e+ plus H- collisions

NASA Technical Reports Server (NTRS)

Straton, Jack C.; Drachman, Richard J.

1990-01-01

Cross sections for positronium formation by capture from the negative hydrogen ion are given. Orthogonalization corrections to the Coulomb (First) Born Approximation (CBA) differential and total cross sections are calculated using approximate H- wave functions of both Lowdin and Chandrasekhar. Various methods of orthogonalizing the unbound projectile to the possible bound states are considered. It is found that treating the atomic nuclei as if they were isotopic spin projections of a single type of nucleon gives cross sections that are an improvement over the CBA.

The fading American dream: Trends in absolute income mobility since 1940.

PubMed

Chetty, Raj; Grusky, David; Hell, Maximilian; Hendren, Nathaniel; Manduca, Robert; Narang, Jimmy

2017-04-28

We estimated rates of "absolute income mobility"-the fraction of children who earn more than their parents-by combining data from U.S. Census and Current Population Survey cross sections with panel data from de-identified tax records. We found that rates of absolute mobility have fallen from approximately 90% for children born in 1940 to 50% for children born in the 1980s. Increasing Gross Domestic Product (GDP) growth rates alone cannot restore absolute mobility to the rates experienced by children born in the 1940s. However, distributing current GDP growth more equally across income groups as in the 1940 birth cohort would reverse more than 70% of the decline in mobility. These results imply that reviving the "American dream" of high rates of absolute mobility would require economic growth that is shared more broadly across the income distribution. Copyright © 2017, American Association for the Advancement of Science.

Diagonal Born-Oppenheimer correction for coupled-cluster wave-functions

NASA Astrophysics Data System (ADS)

Shamasundar, K. R.

2018-06-01

We examine how geometry-dependent normalisation freedom of electronic wave-functions affects extraction of a meaningful diagonal Born-Oppenheimer correction (DBOC) to the ground-state Born-Oppenheimer potential energy surface (PES). By viewing this freedom as a kind of gauge-freedom, it is shown that DBOC and the resulting associated mass-dependent adiabatic PES are gauge-invariant quantities. A sum-over-states (SOS) formula for DBOC which explicitly exhibits this invariance is derived. A biorthogonal formulation suitable for DBOC computations using standard unnormalised coupled-cluster (CC) wave-functions is presented. This is shown to lead to a biorthogonal version of SOS formula with similar properties. On this basis, different computational schemes for evaluating DBOC using approximate CC wave-functions are derived. One of this agrees with the formula used in the current literature. The connection to adiabatic-to-diabatic transformations in non-adiabatic dynamics is explored and complications arising from biorthogonal nature of CC theory are identified.

A multiplex serologic platform for diagnosis of tick-borne diseases.

PubMed

Tokarz, Rafal; Mishra, Nischay; Tagliafierro, Teresa; Sameroff, Stephen; Caciula, Adrian; Chauhan, Lokendrasingh; Patel, Jigar; Sullivan, Eric; Gucwa, Azad; Fallon, Brian; Golightly, Marc; Molins, Claudia; Schriefer, Martin; Marques, Adriana; Briese, Thomas; Lipkin, W Ian

2018-02-16

Tick-borne diseases are the most common vector-borne diseases in the United States, with serology being the primary method of diagnosis. We developed the first multiplex, array-based assay for serodiagnosis of tick-borne diseases called the TBD-Serochip. The TBD-Serochip was designed to discriminate antibody responses to 8 major tick-borne pathogens present in the United States, including Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Borrelia miyamotoi, Ehrlichia chaffeensis, Rickettsia rickettsii, Heartland virus and Powassan virus. Each assay contains approximately 170,000 12-mer linear peptides that tile along the protein sequence of the major antigens from each agent with 11 amino acid overlap. This permits accurate identification of a wide range of specific immunodominant IgG and IgM epitopes that can then be used to enhance diagnostic accuracy and integrate differential diagnosis into a single assay. To test the performance of the TBD-Serochip, we examined sera from patients with confirmed Lyme disease, babesiosis, anaplasmosis, and Powassan virus disease. We identified a wide range of specific discriminatory epitopes that facilitated accurate diagnosis of each disease. We also identified previously undiagnosed infections. Our results indicate that the TBD-Serochip is a promising tool for a differential diagnosis not available with currently employed serologic assays for TBDs.

Electrical excitability: a spectrum of properties in the progeny of a single embryonic neuroblast.

PubMed Central

Goodman, C S; Pearson, K G; Spitzer, N C

1980-01-01

We have examined the range of some properties of the progeny of a single embryonic precursor cell in the grasshopper. The approximately 100 progeny of this single neuroblast share certain features such as their transmitter and some aspects of their morphology; at the same time, however, they demonstrate a broad spectrum of electrical properties, from spiking to non-spiking neurons. The first-born progeny are spiking neurons with peripheral axons. Many of the progeny, including all of the last-born, do not generate action potentials. The nonspiking progeny are local intraganglionic neurons and appear to compose a major proportion of the progeny of this neuroblast. All of the nonspiking neurons have calcium inward current channels and can make action potentials when outward current channels are blocked. We propose a model for grasshopper neurogenesis based on cell lineage such that (i) certain features (e.g., transmitter) are shared by the progeny of all cell divisions from a single neuroblast, and (ii) other features (e.g., electrical properties) are shared by the progeny of a given birth position (e.g., first versus last born) from all of the neuroblasts. According to this model, the first-born progeny from all neuroblasts are spiking neurons, whereas the last-born are nonspiking. Images PMID:6246499

Design of an 8-40 GHz Antenna for the Wideband Instrument for Snow Measurements (WISM)

NASA Technical Reports Server (NTRS)

Durham, Timothy E.; Vanhille, Kenneth J.; Trent, Christopher R.; Lambert, Kevin M.; Miranda, Felix A.

2015-01-01

This poster describes the implementation of a 6x6 element, dual linear polarized array with beamformer that operates from about 8-40 GHz. It is implemented using a relatively new multi-layer microfabrication process. The beamformer includes baluns that feed dual-polarized differential antenna elements and reactive splitters that cover the full frequency range of operation. This fixed beam array (FBA) serves as the feed for a multi-band instrument designed to measure snow water equivalent (SWE) from an airborne platform known as the Wideband Instrument for Snow Measurements (WISM).

A randomised, double-blind, placebo-controlled phase 1 study of the safety, tolerability and pharmacodynamics of volixibat in overweight and obese but otherwise healthy adults: implications for treatment of non-alcoholic steatohepatitis.

PubMed

Palmer, Melissa; Jennings, Lee; Silberg, Debra G; Bliss, Caleb; Martin, Patrick

2018-03-16

Accumulation of toxic free cholesterol in hepatocytes may cause hepatic inflammation and fibrosis. Volixibat inhibits bile acid reuptake via the apical sodium bile acid transporter located on the luminal surface of the ileum. The resulting increase in bile acid synthesis from cholesterol could be beneficial in patients with non-alcoholic steatohepatitis. This adaptive dose-finding study investigated the safety, tolerability, pharmacodynamics, and pharmacokinetics of volixibat. Overweight and obese adults were randomised 3:1 to double-blind volixibat or placebo, respectively, for 12 days. Volixibat was initiated at a once-daily dose of 20 mg, 40 mg or 80 mg. Based on the assessment of predefined safety events, volixibat dosing was either escalated or reduced. Other dose regimens (titrations and twice-daily dosing) were also evaluated. Assessments included safety, tolerability, stool hardness, faecal bile acid (FBA) excretion, and serum levels of 7α-hydroxy-4-cholesten-3-one (C4) and lipids. All 84 randomised participants (volixibat, 63; placebo, 21) completed the study, with no serious adverse events at doses of up to 80 mg per day (maximum assessed dose). The median number of daily bowel evacuations increased from 1 (range 0-4) to 2 (0-8) during volixibat treatment, and stool was looser with volixibat than placebo. Volixibat was minimally absorbed; serum levels were rarely quantifiable at any dose or sampling time point, thereby precluding pharmacokinetic analyses. Mean daily FBA excretion was 930.61 μmol (standard deviation [SD] 468.965) with volixibat and 224.75 μmol (195.403) with placebo; effects were maximal at volixibat doses ≥20 mg/day. Mean serum C4 concentrations at day 12 were 98.767 ng/mL (standard deviation, 61.5841) with volixibat and 16.497 ng/mL (12.9150) with placebo. Total and low-density lipoprotein cholesterol levels decreased in the volixibat group, with median changes of - 0.70 mmol/L (range - 2.8 to 0.4) and - 0.6990 mmol/L (- 3.341 to 0.570), respectively. This study indicates that maximal inhibition of bile acid reabsorption, as assessed by FBA excretion, occurs at volixibat doses of ≥20 mg/day in obese and overweight adults, without appreciable change in gastrointestinal tolerability. These findings guided dose selection for an ongoing phase 2 study in patients with non-alcoholic steatohepatitis. ClinicalTrials.gov identifier: NCT02287779 (registration first received 6 November 2014).

Predictability of tick-borne encephalitis fluctuations.

PubMed

Zeman, P

2017-10-01

Tick-borne encephalitis is a serious arboviral infection with unstable dynamics and profound inter-annual fluctuations in case numbers. A dependable predictive model has been sought since the discovery of the disease. The present study demonstrates that four superimposed cycles, approximately 2·4, 3, 5·4, and 10·4 years long, can account for three-fifths of the variation in the disease fluctuations over central Europe. Using harmonic regression, these cycles can be projected into the future, yielding forecasts of sufficient accuracy for up to 4 years ahead. For the years 2016-2018, this model predicts elevated incidence levels in most parts of the region.

The extreme ultraviolet spectrograph: A radial groove grating, sounding rocket-borne, astronomical instrument

NASA Technical Reports Server (NTRS)

Wilkinson, Erik; Green, James C.; Cash, Webster

1993-01-01

The design, calibration, and sounding rocket flight performance of a novel spectrograph suitable for moderate-resolution EUV spectroscopy are presented. The sounding rocket-borne instrument uses a radial groove grating to maintain a high system efficiency while controlling the aberrations induced when doing spectroscopy in a converging beam. The instrument has a resolution of approximately 2 A across the 200-330 A bandpass with an average effective area of 2 sq cm. The instrument, called the Extreme Ultraviolet Spectrograph, acquired the first EUV spectra in this wavelength region of the hot white dwarf G191-B2B and the late-type star Capella.

Full-Genome Characterisation of Orungo, Lebombo and Changuinola Viruses Provides Evidence for Co-Evolution of Orbiviruses with Their Arthropod Vectors

PubMed Central

Mohd Jaafar, Fauziah; Belhouchet, Mourad; Belaganahalli, Manjunatha; Tesh, Robert B.; Mertens, Peter P. C.; Attoui, Houssam

2014-01-01

The complete genomes of Orungo virus (ORUV), Lebombo virus (LEBV) and Changuinola virus (CGLV) were sequenced, confirming that they each encode 11 distinct proteins (VP1-VP7 and NS1-NS4). Phylogenetic analyses of cell-attachment protein ‘outer-capsid protein 1′ (OC1), show that orbiviruses fall into three large groups, identified as: VP2(OC1), in which OC1 is the 2nd largest protein, including the Culicoides transmitted orbiviruses; VP3(OC1), which includes the mosquito transmitted orbiviruses; and VP4(OC1) which includes the tick transmitted viruses. Differences in the size of OC1 between these groups, places the T2 ‘subcore-shell protein’ as the third largest protein ‘VP3(T2)’ in the first of these groups, but the second largest protein ‘VP3(T2)’ in the other two groups. ORUV, LEBV and CGLV all group with the Culicoides-borne VP2(OC1)/VP3(T2) viruses. The G+C content of the ORUV, LEBV and CGLV genomes is also similar to that of the Culicoides-borne, rather than the mosquito-borne, or tick borne orbiviruses. These data suggest that ORUV and LEBV are Culicoides- rather than mosquito-borne. Multiple isolations of CGLV from sand flies suggest that they are its primary vector. OC1 of the insect-borne orbiviruses is approximately twice the size of the equivalent protein of the tick borne viruses. Together with internal sequence similarities, this suggests its origin by duplication (concatermerisation) of a smaller OC1 from an ancestral tick-borne orbivirus. Phylogenetic comparisons showing linear relationships between the dates of evolutionary-separation of their vector species, and genetic-distances between tick-, mosquito- or Culicoides-borne virus-groups, provide evidence for co-evolution of the orbiviruses with their arthropod vectors. PMID:24475112

Density functional theory of electron transfer beyond the Born-Oppenheimer approximation: Case study of LiF

NASA Astrophysics Data System (ADS)

Li, Chen; Requist, Ryan; Gross, E. K. U.

2018-02-01

We perform model calculations for a stretched LiF molecule, demonstrating that nonadiabatic charge transfer effects can be accurately and seamlessly described within a density functional framework. In alkali halides like LiF, there is an abrupt change in the ground state electronic distribution due to an electron transfer at a critical bond length R = Rc, where an avoided crossing of the lowest adiabatic potential energy surfaces calls the validity of the Born-Oppenheimer approximation into doubt. Modeling the R-dependent electronic structure of LiF within a two-site Hubbard model, we find that nonadiabatic electron-nuclear coupling produces a sizable elongation of the critical Rc by 0.5 bohr. This effect is very accurately captured by a simple and rigorously derived correction, with an M-1 prefactor, to the exchange-correlation potential in density functional theory, M = reduced nuclear mass. Since this nonadiabatic term depends on gradients of the nuclear wave function and conditional electronic density, ∇Rχ(R) and ∇Rn(r, R), it couples the Kohn-Sham equations at neighboring R points. Motivated by an observed localization of nonadiabatic effects in nuclear configuration space, we propose a local conditional density approximation—an approximation that reduces the search for nonadiabatic density functionals to the search for a single function y(n).

Infant born preterm have delayed development of adaptive postural control in the first 5 months of life.

PubMed

Dusing, Stacey C; Thacker, Leroy R; Galloway, James C

2016-08-01

Infants born preterm are at increased risk of developmental disabilities, that may be attributed to their early experiences and ability to learn. The purpose of this paper was to evaluate the ability of infants born preterm to adapt their postural control to changing task demands. This study included 18 infants born at 32 weeks of gestation or less whose posture was compared in supine under 2 conditions, with and without a visual stimulus presented. The postural variability, measured with root mean squared displacement of the center of pressure, and postural complexity, measured with the approximate entropy of the center of pressure displacement were measured longitudinally from 2.5 to 5 months of age. The infants looked at the toys in midline for several months prior to adapting their postural variability in a manner similar to full term infants. Only after postural variability was reduced in both the caudal cephalic and medial lateral direction in the toy condition did the infants learn to reach for the toy. Postural complexity did not vary between conditions. These findings suggest that infants used a variety of strategies to control their posture. In contrast to research with infants born full term, the infants born preterm in this study did not identify the successful strategy of reducing movement of the center of pressure until months after showing interest in the toy. This delayed adaptation may impact the infants ability to learn over time. Copyright © 2016 Elsevier Inc. All rights reserved.

THE NATIONAL CHILDREN'S STUDY: BEGINNING THE IMPLEMENTATION OF A NATIONAL-PROBABILITY SAMPLE

EPA Science Inventory

Introduction: The National Children's Study (NCS) is a longitudinal cohort study that will follow a sample of approximately 100,000 children born in the United States from before birth until 21 years of age. The NCS will investigate the separate and combined effects of environmen...

Helping Young Hispanic Learners

ERIC Educational Resources Information Center

Garcia, Eugene E.; Jensen, Bryant

2007-01-01

Hispanics are the largest and youngest ethnic group in the United States. Moreover, young Hispanic children make up approximately 80 percent of the U.S. English language learner population. They are a heterogeneous group, born both inside and outside the United States and having origins in Mexico, Cuba, Central America, South America, and the…

Johanna and Tommy: Two Preschoolers in Sweden with Brittle Bones.

ERIC Educational Resources Information Center

Millde, Kristina; Brodin, Jane

Information is presented for caregivers of Swedish children with osteogenesis imperfecta (brittle bones) and their families. Approximately five children with brittle bones are born in Sweden annually. Two main types of brittle bone disease have been identified: congenita and tarda. Typical symptoms include numerous and unexpected fractures, bluish…

Earth Observation

NASA Image and Video Library

2014-05-31

ISS040-E-006165 (31 May 2014 ) --- One of the Expedition 40 crew members aboard the International Space Station photographed this nadir image of the volcanic-born Banks Peninsula, on the east coast of the South Island of New Zealand on May 31, 2014. Banks Peninsula covers an area of approximately 1,150 square kilometers.

Combined active and passive microwave remote sensing of vegetated surfaces at l-band

USDA-ARS?s Scientific Manuscript database

In previous work the distorted Born approximation (DBA) of volume scattering was combined with the numerical solutions of Maxwell equations (NMM3D) for a rough surface to calculate the radar backscattering coefficient for the Soil Moisture Active Passive (SMAP) mission. The model results were valida...

Leucine is a major regulator of muscle protein synthesis in neonates

USDA-ARS?s Scientific Manuscript database

Approximately 10 % of infants born in the United States are of low birth weight. Growth failure during the neonatal period is a common occurrence in low birth weight infants due to their inability to tolerate full feeds, concerns about advancing protein supply, and high nutrient requirements for gro...

Inelastic cross sections for low-energy electrons in liquid water: exchange and correlation effects.

PubMed

Emfietzoglou, Dimitris; Kyriakou, Ioanna; Garcia-Molina, Rafael; Abril, Isabel; Nikjoo, Hooshang

2013-11-01

Low-energy electrons play a prominent role in radiation therapy and biology as they are the largest contributor to the absorbed dose. However, no tractable theory exists to describe the interaction of low-energy electrons with condensed media. This article presents a new approach to include exchange and correlation (XC) effects in inelastic electron scattering at low energies (below ∼10 keV) in the context of the dielectric theory. Specifically, an optical-data model of the dielectric response function of liquid water is developed that goes beyond the random phase approximation (RPA) by accounting for XC effects using the concept of the many-body local-field correction (LFC). It is shown that the experimental energy-loss-function of liquid water can be reproduced by including into the RPA dispersion relations XC effects (up to second order) calculated in the time-dependent local-density approximation with the addition of phonon-induced broadening in N. D. Mermin's relaxation-time approximation. Additional XC effects related to the incident and/or struck electrons are included by means of the vertex correction calculated by a modified Hubbard formula for the exchange-only LFC. Within the first Born approximation, the present XC corrections cause a significantly larger reduction (∼10-50%) to the inelastic cross section compared to the commonly used Mott and Ochkur approximations, while also yielding much better agreement with the recent experimental data for amorphous ice. The current work offers a manageable, yet rigorous, approach for including non-Born effects in the calculation of inelastic cross sections for low-energy electrons in liquid water, which due to its generality, can be easily extended to other condensed media.

Digestive Symptoms in Healthy People and Subjects With Irritable Bowel Syndrome

PubMed Central

Guyonnet, Denis; Donazzolo, Yves; Gendre, David; Tanguy, Jérôme; Guarner, Francisco

2015-01-01

Goals: The aim of this study was to validate the ability of symptom frequency questionnaire to differentiate between irritable bowel syndrome (IBS) patients and healthy subjects. Background: A digestive symptom frequency questionnaire (DSFQ) was previously used in a food efficacy trial in a non-IBS population with mild gastrointestinal symptoms. Study: We compared 2 well-defined populations: 100 IBS patients fulfilling Rome III criteria (mean age 32 y; range, 18 to 59 y), and 100 sex-matched and age-matched healthy subjects. Frequency of individual digestive symptoms (abdominal pain/discomfort, bloating, flatulence, borborygmi) was assessed using a 5-point Likert scale (from none to everyday of the week) and the IBS severity with the IBS-SSS questionnaire. Health-Related Quality of life (HRQoL) was assessed with the Food and Benefits Assessment (FBA) and Functional Digestive Disorders Quality of Life (FDDQL) questionnaires. The digestive (dis)comfort dimension of these questionnaires was considered as the main dimension for HRQoL. Results: The DSFQ discriminated IBS from healthy subjects with a significant difference (P<0.001) between groups (estimated mean difference=5.58; 95% CI, 4.91-6.28). On the basis of the ROC curve (AUC=0.9479), a cutoff value of 5 gives a sensitivity of 92% and a specificity of 84%, with a positive likelihood ratio of 5.75. Composite score of symptoms correlated strongly (P<0.0001) with digestive discomfort measured by FDDQL (−0.816), digestive comfort measured by FBA (−0.789), and the IBS-SSS score (0.762). Conclusions: Measurement of digestive symptom frequency by means of the DSFQ can differentiate IBS from healthy subjects, and shows a good correlation with other validated questionnaires (clinical trial #NCT01457378). PMID:25014236

Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production.

PubMed

Mao, Longfei; Verwoerd, Wynand S

2013-01-01

Saccharomyces cerevisiae possesses numerous advantageous biological features, such as being robust, easily handled, mostly non-pathogenic and having high catabolic rates, etc., which can be considered as merits for being used as a promising biocatalyst in microbial fuel cells (MFCs) for electricity generation. Previous studies have developed efficient MFC configurations to convert metabolic electron shuttles, such as cytoplasmic NADH, into usable electric current. However, no studies have elucidated the maximum potential of S. cerevisiae for current output and the underlying metabolic pathways, resulting from the interaction of thousands of reactions inside the cell during MFC operation. To address these two key issues, this study used in silico metabolic engineering techniques, flux balance analysis (FBA), and flux variability analysis with target flux minimization (FATMIN), to model the metabolic perturbation of S. cerevisiae under the MFC-energy extraction. The FBA results showed that, in the cytoplasmic NADH-dependent mediated electron transfer (MET) mode, S. cerevisiae had a potential to produce currents at up to 5.781 A/gDW for the anaerobic and 6.193 A/gDW for the aerobic environments. The FATMIN results showed that the aerobic and anaerobic metabolisms are resilient, relying on six and five contributing reactions respectively for high current production. Two reactions, catalyzed by glutamate dehydrogenase (NAD) (EC 1.4.1.3) and methylene tetrahydrofolate dehydrogenase (NAD) (EC 1.5.1.5), were shared in both current-production modes and contributed to over 80% of the identified maximum current outputs. It is also shown that the NADH regeneration was much less energy costly than biomass production rate. Taken together, our finding suggests that S. cerevisiae should receive more research effort for MFC electricity production.

Simultaneous Analyses and Applications of Multiple Fluorobenzoate and Halide Tracers in Hydrologic Studies

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

Hu, Q; Moran, J E

2004-01-22

An analytical method that employs ion chromatography has been developed to more fully exploit the use of fluorobenzoic acids (FBAs) and halides as hydrologic tracers. In a single run, this reliable, sensitive, and robust method can simultaneously separate and quantify halides (fluoride, chloride, bromide, and iodide) and up to seven FBAs from other common groundwater constituents (e.g., nitrate and sulfate). The usefulness of this ion chromatographic (IC) analytical method is demonstrated in both field and laboratory tracer experiments. Field experiments in unsaturated tuff featuring fractures or a fault show that this efficient and cost-effective method helps achieve the objectives ofmore » tracer studies that use multiple FBAs and/or diffusivity tracers (simultaneous use of one or more FBA and halide). The field study examines the hydrologic response of fractures and the matrix to different flow rates and the contribution of matrix diffusion in chemical transport. Laboratory tracer experiments with eight geologic media from across the United States--mostly from Department of Energy facilities where groundwater contamination is prevalent and where subsurface characterization employing tracers has been ongoing or is in need--reveal several insights about tracer transport behavior: (1) Bromide and FBAs are not always transported conservatively. (2) The delayed transport of these anionic tracers is likely related to geologic media characteristics, such as organic matter, pH, iron oxide content, and clay mineralogy. (3) Any use of iodine as a hydrologic tracer should take into account the different sorption behaviors of iodide and iodate and the possible conversion of iodine's initial chemical form. (4) The transport behavior of potential FBA and halide tracers under relevant geochemical conditions should be evaluated before beginning ambitious, large-scale field tracer experiments.« less

Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production

PubMed Central

Mao, Longfei; Verwoerd, Wynand S

2013-01-01

Saccharomyces cerevisiae possesses numerous advantageous biological features, such as being robust, easily handled, mostly non-pathogenic and having high catabolic rates, etc., which can be considered as merits for being used as a promising biocatalyst in microbial fuel cells (MFCs) for electricity generation. Previous studies have developed efficient MFC configurations to convert metabolic electron shuttles, such as cytoplasmic NADH, into usable electric current. However, no studies have elucidated the maximum potential of S. cerevisiae for current output and the underlying metabolic pathways, resulting from the interaction of thousands of reactions inside the cell during MFC operation. To address these two key issues, this study used in silico metabolic engineering techniques, flux balance analysis (FBA), and flux variability analysis with target flux minimization (FATMIN), to model the metabolic perturbation of S. cerevisiae under the MFC-energy extraction. The FBA results showed that, in the cytoplasmic NADH-dependent mediated electron transfer (MET) mode, S. cerevisiae had a potential to produce currents at up to 5.781 A/gDW for the anaerobic and 6.193 A/gDW for the aerobic environments. The FATMIN results showed that the aerobic and anaerobic metabolisms are resilient, relying on six and five contributing reactions respectively for high current production. Two reactions, catalyzed by glutamate dehydrogenase (NAD) (EC 1.4.1.3) and methylene tetrahydrofolate dehydrogenase (NAD) (EC 1.5.1.5), were shared in both current-production modes and contributed to over 80% of the identified maximum current outputs. It is also shown that the NADH regeneration was much less energy costly than biomass production rate. Taken together, our finding suggests that S. cerevisiae should receive more research effort for MFC electricity production. PMID:23969939

Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory

PubMed Central

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-01-01

Background Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA). PMID:18482450

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

PubMed

Klamt, Steffen; Regensburger, Georg; Gerstl, Matthias P; Jungreuthmayer, Christian; Schuster, Stefan; Mahadevan, Radhakrishnan; Zanghellini, Jürgen; Müller, Stefan

2017-04-01

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks.

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

PubMed Central

Klamt, Steffen; Gerstl, Matthias P.; Jungreuthmayer, Christian; Mahadevan, Radhakrishnan; Müller, Stefan

2017-01-01

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks. PMID:28406903

Status of serum-calcium and -albumin measurement in Argentina assessed in 300 representative laboratories with 20 fresh frozen single donation sera.

PubMed

Stepman, Hedwig C M; Stöckl, Dietmar; Acheme, Rosana; Sesini, Sandra; Mazziotta, Daniel; Thienpont, Linda M

2011-11-01

The Fundación Bioquímica Argentina (FBA) performs external quality assessment (EQA) of >3200 laboratories. However, FBA realizes that sample non-commutability and predominant use of heterogeneous systems may bias the estimated performance and standardization status. To eliminate these confounding factors, a study using frozen single donation sera was undertaken with the focus on serum-calcium and -albumin measurement. Target values were established from the results produced with homogeneous systems. In groups of n=7, system effects were investigated. Laboratory performance was evaluated from the correlation coefficient r between the measurement results for all sera and the target values. This allowed ranking of the laboratories and judgment of the deviation for individual samples (total error) against a 10% limit. The total error specification was a deviation for ≥ 5 samples exceeding 10% and/or causing a result outside the laboratory's reference interval. For calcium (n=303) (range: 2.06-2.42 mmol/L), 81 laboratories had an r-value <0.6, 43 even <0.4; the total error was relevant for 97 (10% limit) and 111 (reference interval) laboratories. For albumin (n=311) (range: 34.7-45.7 g/L) r was <0.7 (<0.4) in 44 (16) laboratories; 83 and 36 laboratories exceeded the total error criteria. Laboratories using homogeneous systems were generally ranked higher by correlation. System effects were moderate for calcium, but significant for albumin. The study demonstrated the need to improve the quality and harmonization of calcium and albumin testing in the investigated laboratories. To achieve this objective, we promote co-operation between laboratories, EQA provider and manufacturers.

Immunological control of ticks and tick-borne diseases that impact cattle health and production.

PubMed

Almazan, Consuelo; Tipacamu, Gabriela Aguilar; Rodriguez, Sergio; Mosqueda, Juan; Perez de Leon, Adalberto

2018-03-01

The cattle industry is one of the most important agroeconomic activities in Mexico. The national herd is estimated to include approximately 33.5. million head of cattle. Ticks and tick-borne diseases are principal factors with a negative impact on cattle health and production. The most economically important tick species parasitizing cattle in Mexico are Rhipicephalus microplus , R. annulatus , and Amblyomma mixtum . Parasitism by ticks affects cattle health and production directly. Morbidity and mortality caused by tick-borne diseases augment the detrimental effect of tick infestation in cattle. Bovine babesiosis and anaplasmosis are the most important tick-borne diseases of cattle, which are caused by infectious agents transmitted by R. microplus and R. annulatus . However, there are no prophylactic therapies to control bovine babesiosis and anaplasmosis. Chemical control is the most common way to treat animals against ticks, and the use of acaricides can also help manage tick-borne diseases. However, the evolution of resistance to acaricides among cattle tick populations renders chemical control ineffective; which represents a challenge for sustainable ticks and tick-borne diseases control. The only anti-tick vaccine commercially available globally is based on the recombinant antigen Bm86. Because of its mode of immunity against R. microplus and R. annulatus , the Bm86-based vaccine also decreases the exposition of bovines to babesiosis and anaplasmosis. Research with Bm86-based vaccines documented high efficacy against R. annulatus , the efficacy levels against R. microplus varies according to the geographic origin of tick populations, and there is not effect against other ticks species such as Amblyomma spp. The impact of ticks and tick-borne diseases, the problem of chemical control due to acaricide resistance, and progress with anti-tick vaccine research efforts in Mexico are reviewed herein.

Rotational-vibrational coupling in the theory of electron-molecule scattering

NASA Technical Reports Server (NTRS)

Temkin, A.; Sullivan, E. C.

1974-01-01

The adiabatic-nuclei approximation of vibrational-rotational excitation of homonuclear diatomic molecules can be simply augmented to describe the vibrational-rotational coupling by including the dependence of the vibrational wave function on j. Appropriate formulas are given, and the theory, is applied to e-H2 excitation, whereby it is shown that deviations from the simple Born-Oppenheimer approximation measured by Wong and Schultz can be explained. More important, it can be seen that the inclusion of the j-dependent centrifugal term is essential for transitions involving high-rotational quantum numbers.

Onsets of hierarchy truncation and self–consistent Born approximation with quantum mechanics prescriptions invariance

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

Zhang, Hou-Dao; Yan, YiJing, E-mail: yyan@ust.hk; iChEM and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026

2015-12-07

The issue of efficient hierarchy truncation is related to many approximate theories. In this paper, we revisit this issue from both the numerical efficiency and quantum mechanics prescription invariance aspects. The latter requires that the truncation approximation made in Schrödinger picture, such as the quantum master equations and their self–consistent–Born–approximation improvements, should be transferable to their Heisenberg–picture correspondences, without further approximations. We address this issue with the dissipaton equation of motion (DEOM), which is a unique theory for the dynamics of not only reduced systems but also hybrid bath environments. We also highlight the DEOM theory is not only aboutmore » how its dynamical variables evolve in time, but also the underlying dissipaton algebra. We demonstrate this unique feature of DEOM with model systems and report some intriguing nonlinear Fano interferences characteristics that are experimentally measurable.« less

Mosquito-borne viruses circulating in Kinshasa, Democratic Republic of the Congo.

PubMed

Mbanzulu, Kennedy Makola; Wumba, Roger; Mukendi, Jean-Pierre Kambala; Zanga, Josué Kikana; Shija, Fortunate; Bobanga, Thierry Lengu; Aloni, Michel Ntetani; Misinzo, Gerald

2017-04-01

Diseases caused by mosquito-borne viruses are among the most important emerging diseases that threaten human and animal health, particularly in Africa. However, little attention has been paid to these diseases in the Democratic Republic of the Congo (DRC). The present cross-sectional study was undertaken between March and May 2014 to investigate the presence of mosquito-borne viruses in mosquitoes collected from five municipalities of Kinshasa, DRC. Mosquitoes were collected using BG-Sentinel traps and battery-powered aspirators. Female mosquitoes were pooled according to their genera and sampling locations, preserved in RNAlater, and later screened for viruses using reverse transcription PCR (RT-PCR) assays. A total of 2922 mosquitoes were collected and 29 pools of female mosquitoes, containing approximately 30 mosquitoes each, were tested. Twelve of the 29 (41.4%) mosquito pools were found to be infected with at least one arbovirus, with eight (27.5%) pools positive for Alphavirus, nine (31%) for Flavivirus, and five (17.2%) for Bunyaviridae. Chikungunya, o'nyong'nyong, and Rift valley fever viruses were detected. The present study shows that mosquitoes in Kinshasa carry mosquito-borne viruses that may have serious public health implications. Further investigations on the presence of mosquito-borne viruses in the human and livestock populations of Kinshasa and DRC are recommended. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

The influence of cross-order terms in interface mobilities for structure-borne sound source characterization

NASA Astrophysics Data System (ADS)

Bonhoff, H. A.; Petersson, B. A. T.

2010-08-01

For the characterization of structure-borne sound sources with multi-point or continuous interfaces, substantial simplifications and physical insight can be obtained by incorporating the concept of interface mobilities. The applicability of interface mobilities, however, relies upon the admissibility of neglecting the so-called cross-order terms. Hence, the objective of the present paper is to clarify the importance and significance of cross-order terms for the characterization of vibrational sources. From previous studies, four conditions have been identified for which the cross-order terms can become more influential. Such are non-circular interface geometries, structures with distinctively differing transfer paths as well as a suppression of the zero-order motion and cases where the contact forces are either in phase or out of phase. In a theoretical study, the former four conditions are investigated regarding the frequency range and magnitude of a possible strengthening of the cross-order terms. For an experimental analysis, two source-receiver installations are selected, suitably designed to obtain strong cross-order terms. The transmitted power and the source descriptors are predicted by the approximations of the interface mobility approach and compared with the complete calculations. Neglecting the cross-order terms can result in large misinterpretations at certain frequencies. On average, however, the cross-order terms are found to be insignificant and can be neglected with good approximation. The general applicability of interface mobilities for structure-borne sound source characterization and the description of the transmission process thereby is confirmed.

Pleural mesothelioma and lung cancer risks in relation to occupational history and asbestos lung burden

PubMed Central

Gilham, Clare; Rake, Christine; Burdett, Garry; Nicholson, Andrew G; Davison, Leslie; Franchini, Angelo; Carpenter, James; Hodgson, John; Darnton, Andrew; Peto, Julian

2016-01-01

Background We have conducted a population-based study of pleural mesothelioma patients with occupational histories and measured asbestos lung burdens in occupationally exposed workers and in the general population. The relationship between lung burden and risk, particularly at environmental exposure levels, will enable future mesothelioma rates in people born after 1965 who never installed asbestos to be predicted from their asbestos lung burdens. Methods Following personal interview asbestos fibres longer than 5 µm were counted by transmission electron microscopy in lung samples obtained from 133 patients with mesothelioma and 262 patients with lung cancer. ORs for mesothelioma were converted to lifetime risks. Results Lifetime mesothelioma risk is approximately 0.02% per 1000 amphibole fibres per gram of dry lung tissue over a more than 100-fold range, from 1 to 4 in the most heavily exposed building workers to less than 1 in 500 in most of the population. The asbestos fibres counted were amosite (75%), crocidolite (18%), other amphiboles (5%) and chrysotile (2%). Conclusions The approximate linearity of the dose–response together with lung burden measurements in younger people will provide reasonably reliable predictions of future mesothelioma rates in those born since 1965 whose risks cannot yet be seen in national rates. Burdens in those born more recently will indicate the continuing occupational and environmental hazards under current asbestos control regulations. Our results confirm the major contribution of amosite to UK mesothelioma incidence and the substantial contribution of non-occupational exposure, particularly in women. PMID:26715106

The F-box family genes as key elements in response to salt, heavy mental, and drought stresses in Medicago truncatula.

PubMed

Song, Jian Bo; Wang, Yan Xiang; Li, Hai Bo; Li, Bo Wen; Zhou, Zhao Sheng; Gao, Shuai; Yang, Zhi Min

2015-07-01

F-box protein is a subunit of Skp1-Rbx1-Cul1-F-box protein (SCF) complex with typically conserved F-box motifs of approximately 40 amino acids and is one of the largest protein families in eukaryotes. F-box proteins play critical roles in selective and specific protein degradation through the 26S proteasome. In this study, we bioinformatically identified 972 putative F-box proteins from Medicago truncatula genome. Our analysis showed that in addition to the conserved motif, the F-box proteins have several other functional domains in their C-terminal regions (e.g., LRRs, Kelch, FBA, and PP2), some of which were found to be M. truncatula species-specific. By phylogenetic analysis of the F-box motifs, these proteins can be classified into three major families, and each family can be further grouped into more subgroups. Analysis of the genomic distribution of F-box genes on M. truncatula chromosomes revealed that the evolutional expansion of F-box genes in M. truncatula was probably due to localized gene duplications. To investigate the possible response of the F-box genes to abiotic stresses, both publicly available and customer-prepared microarrays were analyzed. Most of the F-box protein genes can be responding to salt and heavy metal stresses. Real-time PCR analysis confirmed that some of the F-box protein genes containing heat, drought, salicylic acid, and abscisic acid responsive cis-elements were able to respond to the abiotic stresses.

Emissivity of half-space random media. [in passive remote sensing

NASA Technical Reports Server (NTRS)

Tsang, L.; Kong, J. A.

1976-01-01

Scattering of electromagnetic waves by a half-space random medium with three-dimensional correlation functions is studied with the Born approximation. The emissivity is calculated from a simple integral and is illustrated for various cases. The results are valid over a wavelength range smaller or larger than the correlation lengths.

Handle with Care

ERIC Educational Resources Information Center

Merrill, Margaret C.

2006-01-01

The Centers for Disease Control estimates that every year 76 million Americans get some kind of food poisoning, more than 300,000 are hospitalized, and approximately 5,000 people die. A 2004 analysis by the Center for Science in the Public Interest indicates that contaminated produce is responsible for the greatest number of food-borne illnesses.…

Transitioning Young Adults with Autism: Hopes & Challenges for Parents

ERIC Educational Resources Information Center

Mookerjee, Veera

2012-01-01

Data generated by the Center for Disease Control (CDC) from the 2010 census indicates that out of four million children born in the United States "approximately 36,500 children will eventually be diagnosed with an [Autism Spectrum Disorder] ASD" ("http://www.cdc.gov/ncbddd/autism/data.html"). The process of caring for an…

A Cartoon in One Dimension of the Hydrogen Molecular Ion

ERIC Educational Resources Information Center

Dutta, Sourav; Ganguly, Shreemoyee; Dutta-Roy, Binayak

2008-01-01

To illustrate the basic methodology involved in the quantum mechanics of molecules, a one-dimensional caricature of the hydrogen molecular ion (H[superscript +][subscript 2]) is presented, which is exactly solvable, in the Born-Oppenheimer approximation, in terms of elementary functions. The purpose of the exercise is to elucidate in a simple…

Dietary Patterns and Intelligence in Early and Middle Childhood

ERIC Educational Resources Information Center

Theodore, Reremoana F.; Thompson, John M. D.; Waldie, Karen E.; Wall, Clare; Becroft, David M. O.; Robinson, Elizabeth; Wild, Chris J.; Clark, Philippa M.; Mitchell, Ed A.

2009-01-01

The association between intelligence and diet at 3.5 and 7 years was examined in 591 children of European descent. Approximately half of the children were born small-for-gestational age (birth weight @?10th percentile). The relationship between IQ and diet (measured by food frequency) was investigated using multiple regression analyses. Eating…

Magnetic Resonance Imaging--Insights into Brain Injury and Outcomes in Premature Infants

ERIC Educational Resources Information Center

Mathur, Amit; Inder, Terrie

2009-01-01

Preterm birth is a major public-health issue because of its increasing incidence combined with the frequent occurrence of subsequent behavioral, neurological, and psychiatric challenges faced by surviving infants. Approximately 10-15% of very preterm children (born less than 30 weeks gestational age) develop cerebral palsy, and 30-60% of them…

Lessons in Learning: More Education, Less Employment--Immigrants and the Labour Market

ERIC Educational Resources Information Center

Canadian Council on Learning, 2008

2008-01-01

Nearly one out of five Canadian residents was born outside of Canada and approximately two-thirds of Canada's population growth results from net international migration. Only Australia, where immigrants represent 24% of the population, has a greater percentage of immigrants than Canada (18%). Immigration is a major factor in Canada's economic…

Microbial profiling, neural network and semantic web: an integrated information system for human pathogen risk management, prevention and surveillance in food safety

USDA-ARS?s Scientific Manuscript database

It is estimated that food-borne pathogens cause approximately 76 million cases of gastrointestinal illnesses, 325,000 hospitalizations, and 5,000 deaths in the United States annually. Genomic, proteomic, and metabolomic studies, particularly, genome sequencing projects are providing valuable inform...

New approach to description of (d,xn) spectra at energies below 50 MeV in Monte Carlo simulation by intra-nuclear cascade code with Distorted Wave Born Approximation

NASA Astrophysics Data System (ADS)

Hashimoto, S.; Iwamoto, Y.; Sato, T.; Niita, K.; Boudard, A.; Cugnon, J.; David, J.-C.; Leray, S.; Mancusi, D.

2014-08-01

A new approach to describing neutron spectra of deuteron-induced reactions in the Monte Carlo simulation for particle transport has been developed by combining the Intra-Nuclear Cascade of Liège (INCL) and the Distorted Wave Born Approximation (DWBA) calculation. We incorporated this combined method into the Particle and Heavy Ion Transport code System (PHITS) and applied it to estimate (d,xn) spectra on natLi, 9Be, and natC targets at incident energies ranging from 10 to 40 MeV. Double differential cross sections obtained by INCL and DWBA successfully reproduced broad peaks and discrete peaks, respectively, at the same energies as those observed in experimental data. Furthermore, an excellent agreement was observed between experimental data and PHITS-derived results using the combined method in thick target neutron yields over a wide range of neutron emission angles in the reactions. We also applied the new method to estimate (d,xp) spectra in the reactions, and discussed the validity for the proton emission spectra.

Calculation of the age of the first infection for skin sores and scabies in five remote communities in northern Australia.

PubMed

Lydeamore, M J; Campbell, P T; Cuningham, W; Andrews, R M; Kearns, T; Clucas, D; Gundjirryirr Dhurrkay, R; Carapetis, J; Tong, S Y C; McCaw, J M; McVernon, J

2018-05-08

Prevalence of skin sores and scabies in remote Australian Aboriginal communities remains unacceptably high, with Group A Streptococcus (GAS) the dominant pathogen. We aim to better understand the drivers of GAS transmission using mathematical models. To estimate the force of infection, we quantified the age of first skin sores and scabies infection by pooling historical data from three studies conducted across five remote Aboriginal communities for children born between 2001 and 2005. We estimated the age of the first infection using the Kaplan-Meier estimator; parametric exponential mixture model; and Cox proportional hazards. For skin sores, the mean age of the first infection was approximately 10 months and the median was 7 months, with some heterogeneity in median observed by the community. For scabies, the mean age of the first infection was approximately 9 months and the median was 8 months, with significant heterogeneity by the community and an enhanced risk for children born between October and December. The young age of the first infection with skin sores and scabies reflects the high disease burden in these communities.

Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions

PubMed Central

Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán

2013-01-01

Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory. PMID:24790954

Relativistic corrections to the ground state of H2 calculated without using the Born-Oppenheimer approximation

NASA Astrophysics Data System (ADS)

Wang, L. M.; Yan, Z.-C.

2018-06-01

The Schrödinger equation for the ground state of the hydrogen molecule H2 is solved by applying the Rayleigh-Ritz variational method in Hylleraas coordinates without using the Born-Oppenheimer approximation. The nonrelativistic energy eigenvalue is converged to -1.164 025 030 880 (7 ) atomic units. The leading-order relativistic corrections, including the mass-velocity, Darwin, orbit-orbit, spin-spin, and relativistic recoil terms, are evaluated perturbatively. Together with the higher-order relativistic and quantum electrodynamic corrections obtained by Puchalski et al. [Phys. Rev. Lett. 117, 263002 (2016), 10.1103/PhysRevLett.117.263002], we determine the dissociation energy of the hydrogen molecule, D0=36 118.069 71 (33 ) cm-1 , which agrees with the two recent experimental results of Liu et al. [J. Chem. Phys. 130, 174306 (2009), 10.1063/1.3120443], 36 118.069 62 (37 ) cm-1 , and Altmann et al. [Phys. Rev. Lett. 120, 043204 (2018), 10.1103/PhysRevLett.120.043204], 36 118.069 45 (31 ) cm-1 .

Nonequilibrium Green's functions and atom-surface dynamics: Simple views from a simple model system

NASA Astrophysics Data System (ADS)

Boström, E.; Hopjan, M.; Kartsev, A.; Verdozzi, C.; Almbladh, C.-O.

2016-03-01

We employ Non-equilibrium Green's functions (NEGF) to describe the real-time dynamics of an adsorbate-surface model system exposed to ultrafast laser pulses. For a finite number of electronic orbitals, the system is solved exactly and within different levels of approximation. Specifically i) the full exact quantum mechanical solution for electron and nuclear degrees of freedom is used to benchmark ii) the Ehrenfest approximation (EA) for the nuclei, with the electron dynamics still treated exactly. Then, using the EA, electronic correlations are treated with NEGF within iii) 2nd Born and with iv) a recently introduced hybrid scheme, which mixes 2nd Born self-energies with non-perturbative, local exchange- correlation potentials of Density Functional Theory (DFT). Finally, the effect of a semi-infinite substrate is considered: we observe that a macroscopic number of de-excitation channels can hinder desorption. While very preliminary in character and based on a simple and rather specific model system, our results clearly illustrate the large potential of NEGF to investigate atomic desorption, and more generally, the non equilibrium dynamics of material surfaces subject to ultrafast laser fields.

Multiple outer-shell ionization effect in inner-shell x-ray production by light ions

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

Lapicki, G.; Mehta, R.; Duggan, J.L.

1986-11-01

L-shell x-ray production cross sections by 0.25--2.5-MeV /sub 2//sup 4/He/sup +/ ions in /sub 28/Ni, /sub 29/Cu, /sub 32/Ge, /sub 33/As, /sub 37/Rb, /sub 38/Sr, /sub 39/Y, /sub 40/Zr, and /sub 46/Pd are reported. The data are compared to the first Born approximation and the ECPSSR theory that accounts for the projectile energy loss (E) and Coulomb deflection (C) as well as the perturbed-stationary-state (PSS) and relativistic (R) effects in the treatment of the target L-shell electron. Surprisingly, the first Born approximation appears to converge to the data while the ECPSSR predictions underestimate them in the low-velocity limit. This ismore » explained as the result of improper use of single-hole fluorescence yields. A heuristic formula is proposed to account for multiple ionizations in terms of a classical probability for these phenomena and, after it is applied, the ECPSSR theory of L-shell ionization is found to be in good agreement with the data.« less

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

Carbajal, L.; Warwick Univ., Coventry; Dendy, R. O.

Ion cyclotron emission (ICE) offers unique promise as a diagnostic of the fusion born alpha-particle population in magnetically confined plasmas. Pioneering observations from JET and TFTR found that ICE intensity P ICE scales approximately linearly with the measured neutron flux from fusion reactions, and with the inferred concentration, n /n i , of fusion-born alpha-particles confined within the plasma. We present fully nonlinear self-consistent kinetic simulations that reproduce this scaling for the first time. This resolves a longstanding question in the physics of fusion alpha particle confinement and stability in MCF plasmas. It confirms the MCI as the likely emissionmore » mechanism and greatly strengthens the basis for diagnostic exploitation of ICE in future burning plasmas.« less

Calculation of total electron excitation cross-sections and partial electron ionization cross-sections for the elements. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Green, T. J.

1973-01-01

Computer programs were used to calculate the total electron excitation cross-section for atoms and the partial ionization cross-section. The approximations to the scattering amplitude used are as follows: (1) Born, Bethe, and Modified Bethe for non-exchange excitation; (2) Ochkur for exchange excitation; and (3) Coulomb-Born of non-exchange ionization. The amplitudes are related to the differential cross-sections which are integrated to give the total excitation (or partial ionization) cross-section for the collision. The atomic wave functions used are Hartree-Fock-Slater functions for bound states and the coulomb wave function for the continuum. The programs are presented and the results are examined.

The PoGO+ Ballon-Borne Hard X-ray Polarimetry Mission

NASA Astrophysics Data System (ADS)

Friis, Mette; Kiss, Mózsi; Mikhalev, Victor; Pearce, Mark; Takahashi, Hiromitsu

2018-03-01

The PoGO mission, including the PoGOLite Pathfinder and PoGO+, aims to provide polarimetric measurements of the Crab system and Cygnus X-1 in the hard X-ray band. Measurements are conducted from a stabilized balloon-borne platform, launched on a 1 million cubic meter balloon from the Esrange Space Center in Sweden to an altitude of approximately 40 km. Several flights have been conducted, resulting in two independent measurements of the Crab polarization and one of Cygnus X-1. Here, a review of the PoGO mission is presented, including a description of the payload and the flight campaigns, and a discussion of some of the scientific results obtained to date.

2-D Fused Image Reconstruction approach for Microwave Tomography: a theoretical assessment using FDTD Model.

PubMed

Bindu, G; Semenov, S

2013-01-01

This paper describes an efficient two-dimensional fused image reconstruction approach for Microwave Tomography (MWT). Finite Difference Time Domain (FDTD) models were created for a viable MWT experimental system having the transceivers modelled using thin wire approximation with resistive voltage sources. Born Iterative and Distorted Born Iterative methods have been employed for image reconstruction with the extremity imaging being done using a differential imaging technique. The forward solver in the imaging algorithm employs the FDTD method of solving the time domain Maxwell's equations with the regularisation parameter computed using a stochastic approach. The algorithm is tested with 10% noise inclusion and successful image reconstruction has been shown implying its robustness.

Are Canadian-born Major League Baseball players more likely to bat left-handed? A partial test of the hockey-influence on batting hypothesis.

PubMed

Cairney, John; Chirico, Daniele; Li, Yao-Chuen; Bremer, Emily; Graham, Jeffrey D

2018-01-01

It has been suggested that Canadian-born Major League Baseball (MLB) players are more likely to bat left-handed, possibly owing to the fact that they learn to play ice hockey before baseball, and that there is no clear hand-preference when shooting with a hockey stick; approximately half of all ice hockey players shoot left. We constructed a database on active (i.e., October, 2016) MLB players from four countries/regions based on place of birth (Canada, United States of America [USA], Dominican Republic and South Asia [i.e., Japan, Taiwan and South Korea]), including information on which hand they use to bat and throw. We also extracted information on all Canadian-born MLB players, dating back to 1917. Our results confirm that the proportion of left-handed batters born in Canada is higher when compared to the other countries selected; also, since 1917, the proportion of Canadian MLB players who bat left has been consistently higher than the league average. We also compared the proportion of left-handed batters in Canada with players born in states in the USA grouped into high, average and low based on hockey participation. The proportion of MLB players born in states with a high level of hockey participation were more likely to bat left, although the differences were significant at trend level only (p < .10). Lastly, we found that while Canadians were more likely to bat left-handed, this did not correspond with a greater left-hand dominance, as determined by throwing hand. In conclusion, the present study confirms that Canadian-born MLB players are more likely to bat left-handed when compared to American, Dominican Republic and South Asian-born MLB players, providing partial support for the hockey influence on batting hypothesis.

Women in Free Clinics: An Assessment of Health-Related Quality of Life for Prevention and Health Education.

PubMed

Kamimura, Akiko; Myers, Kyl; Ashby, Jeanie; Trinh, Ha Ngoc; Nourian, Maziar M; Reel, Justine J

2015-08-01

Understanding gender influences on health-related quality of life (HRQoL) is important to improve women's health when considering diseases that afflict women specifically. The target population of this study was uninsured female free clinic patients who are low socio-economic status and lack access to healthcare resources. Free clinics provide free or reduced fee healthcare to individuals who lack access to primary care and are socio-economically disadvantaged. While approximately half of free clinic patients are women, there is a paucity of comprehensive health-related data for female free clinic patients. US born English, non-US born English, and Spanish speaking female free clinic patients completed a self-administered survey using a standardized women's HRQoL measure in Fall 2014 (N = 389). Female free clinic patients reported lower HRQoL on all aspects of women's health compared to the US baseline scores, and were less likely to utilize preventive care including: mammograms, Pap smear, and HPV vaccination compared to the US general population. Spanish speakers reported a higher percentage of having had mammography and Pap smear, and heard about HPV compared to the other two groups. US born English speakers reported lower levels of HRQoL in vasomotor symptoms and sleep symptoms, and the lowest percentage of breast health and Pap smear screenings compared to non-US born English and Spanish speakers. Non-US born English speakers reported higher preference for female physician compared to US born English speakers and Spanish speakers. Free clinic female patients need preventative interventions and educational opportunities to improve their overall HRQoL.

Mapping the landscape of metabolic goals of a cell

DOE PAGES

Zhao, Qi; Stettner, Arion I.; Reznik, Ed; ...

2016-05-23

Here, genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptationmore » trajectories.« less

Metabolic network modeling with model organisms.

PubMed

Yilmaz, L Safak; Walhout, Albertha Jm

2017-02-01

Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions. Published by Elsevier Ltd.

Metabolic network modeling with model organisms

PubMed Central

Yilmaz, L. Safak; Walhout, Albertha J.M.

2017-01-01

Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions. PMID:28088694

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

PubMed

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

Electron-Phonon and Electron-Electron Interactions in Individual Suspended Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Cronin, Stephen

2010-03-01

The fabrication of pristine, nearly defect-free, suspended carbon nanotubes (CNTs) enables the observation of several phenomena not seen before in carbon nanotubes, including breakdown of the Born-Oppenheimer approximation^1, mode selective electron-phonon coupling^2, and a Mott insulator transition^3. Raman spectroscopy of these nanotubes under applied gate and bias potentials reveals exceptionally strong electron-phonon coupling, arising from Kohn anomalies, which result in mode selective electron-phonon coupling, negative differential conductance (NDC), and non-equilibrium phonon populations^2,4. Due to the extremely long electron lifetimes, we observe a breakdown of the Born-Oppenheimer approximation, as deduced from the gate voltage-induced changes in the vibrational energies of suspended carbon nanotubes^1. We also report strikingly large variations in the Raman intensity of pristine metallic CNTs in response to gate voltages, which are attributed to a Mott insulating state of the strongly correlated electrons^3. As will be shown, preparing clean, defect-free devices is an essential prerequisite for studying the rich low-dimensional physics of CNTs. (1.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Direct Observation of Born-Oppenheimer Approximation Breakdown in Carbon Nanotubes.'' Nano Letters, 9, 607 (2009). (2.) Bushmaker, A.W., Deshpande, V.V., Bockrath, M.W., and Cronin, S.B., ``Direct Observation of Mode Selective Electron-Phonon Coupling in Suspended Carbon Nanotubes.'' Nano Letters, 7, 3618 (2007) (3.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Large Modulations in the Intensity of Raman-Scattered Light from Pristine Carbon Nanotubes.'' Physical Review Letters, 103, 067401 (2009). (4.) Bushmaker, A.W., Deshpande, V.V., Hsieh, S., Bockrath, M.W., and Cronin, S.B., ``Gate Voltage Controlled Non-Equilibrium and Non-Ohmic Behavior in Suspended Carbon Nanotubes.'' Nano Letters, 9, 2862 (2009)

Hypertrophic pyloric stenosis in infants following pertussis prophylaxis with erythromycin--Knoxville, Tennessee, 1999.

PubMed

1999-12-17

In February 1999, pertussis was diagnosed in six neonates born at hospital A in Knoxville, Tennessee. Because a health-care worker at hospital A was most likely the source of exposure, the local health department recommended on February 25, 1999, that erythromycin be prescribed as postexposure prophylaxis for the approximately 200 infants born at hospital A during February 1-24, 1999. In March 1999, local pediatric surgeons noticed an increased number of cases of infantile hypertrophic pyloric stenosis (IHPS) in the area, with seven cases occurring during a 2-week period. All seven IHPS cases were in infants born in hospital A during February who were given erythromycin orally for prophylaxis following possible exposure to pertussis, although none had pertussis diagnosed. The Tennessee Department of Health and CDC investigated the cluster of IHPS cases and its possible association with use of erythromycin. This report summarizes the results of the investigation, which suggest a causal role of erythromycin in this cluster of IHPS cases.

Neonatal infrared axillary thermometry.

PubMed

Seguin, J; Terry, K

1999-01-01

The authors compared axillary skin temperatures (AT) measured with an infrared (IR) thermometer (Lightouch Neonate, Exergen Corp) with rectal temperatures (RT) in 16 newly born term infants under radiant warmers (RW) and in cribs. Twelve stable, growing premature infants in incubators were also studied. This new device may be useful because of safety and rapid results (1 second), but clinical accuracy is unknown. For term infants, mean (SD) RT-AT difference was 0.1 (0.48) degree C under RW and 0.25 (0.17) degree C 2 hours later in cribs. For premature infants in incubators the mean RT-AT difference was 0.09 (0.16) degree C. Axillary temperatures measured by IR thermometer approximate RT for newly born term infants in cribs and stable premature infants in incubators. For newly born term infants under RW, RT-AT differences vary more widely, limiting clinical usefulness in this setting. The device, the unique age of this population, and the RW environment may play a role.

Average-atom treatment of relaxation time in x-ray Thomson scattering from warm dense matter.

PubMed

Johnson, W R; Nilsen, J

2016-03-01

The influence of finite relaxation times on Thomson scattering from warm dense plasmas is examined within the framework of the average-atom approximation. Presently most calculations use the collision-free Lindhard dielectric function to evaluate the free-electron contribution to the Thomson cross section. In this work, we use the Mermin dielectric function, which includes relaxation time explicitly. The relaxation time is evaluated by treating the average atom as an impurity in a uniform electron gas and depends critically on the transport cross section. The calculated relaxation rates agree well with values inferred from the Ziman formula for the static conductivity and also with rates inferred from a fit to the frequency-dependent conductivity. Transport cross sections determined by the phase-shift analysis in the average-atom potential are compared with those evaluated in the commonly used Born approximation. The Born approximation converges to the exact cross sections at high energies; however, differences that occur at low energies lead to corresponding differences in relaxation rates. The relative importance of including relaxation time when modeling x-ray Thomson scattering spectra is examined by comparing calculations of the free-electron dynamic structure function for Thomson scattering using Lindhard and Mermin dielectric functions. Applications are given to warm dense Be plasmas, with temperatures ranging from 2 to 32 eV and densities ranging from 2 to 64 g/cc.

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

Johnson, W. R.; Nilsen, J.

Here, the influence of finite relaxation times on Thomson scattering from warm dense plasmas is examined within the framework of the average-atom approximation. Presently most calculations use the collision-free Lindhard dielectric function to evaluate the free-electron contribution to the Thomson cross section. In this work, we use the Mermin dielectric function, which includes relaxation time explicitly. The relaxation time is evaluated by treating the average atom as an impurity in a uniform electron gas and depends critically on the transport cross section. The calculated relaxation rates agree well with values inferred from the Ziman formula for the static conductivity andmore » also with rates inferred from a fit to the frequency-dependent conductivity. Transport cross sections determined by the phase-shift analysis in the average-atom potential are compared with those evaluated in the commonly used Born approximation. The Born approximation converges to the exact cross sections at high energies; however, differences that occur at low energies lead to corresponding differences in relaxation rates. The relative importance of including relaxation time when modeling x-ray Thomson scattering spectra is examined by comparing calculations of the free-electron dynamic structure function for Thomson scattering using Lindhard and Mermin dielectric functions. Applications are given to warm dense Be plasmas, with temperatures ranging from 2 to 32 eV and densities ranging from 2 to 64 g/cc.« less

Average-atom treatment of relaxation time in x-ray Thomson scattering from warm dense matter

DOE PAGES

Johnson, W. R.; Nilsen, J.

2016-03-14

Here, the influence of finite relaxation times on Thomson scattering from warm dense plasmas is examined within the framework of the average-atom approximation. Presently most calculations use the collision-free Lindhard dielectric function to evaluate the free-electron contribution to the Thomson cross section. In this work, we use the Mermin dielectric function, which includes relaxation time explicitly. The relaxation time is evaluated by treating the average atom as an impurity in a uniform electron gas and depends critically on the transport cross section. The calculated relaxation rates agree well with values inferred from the Ziman formula for the static conductivity andmore » also with rates inferred from a fit to the frequency-dependent conductivity. Transport cross sections determined by the phase-shift analysis in the average-atom potential are compared with those evaluated in the commonly used Born approximation. The Born approximation converges to the exact cross sections at high energies; however, differences that occur at low energies lead to corresponding differences in relaxation rates. The relative importance of including relaxation time when modeling x-ray Thomson scattering spectra is examined by comparing calculations of the free-electron dynamic structure function for Thomson scattering using Lindhard and Mermin dielectric functions. Applications are given to warm dense Be plasmas, with temperatures ranging from 2 to 32 eV and densities ranging from 2 to 64 g/cc.« less

Strong-potential Born calculations for 1s-1s electron capture from atoms by protons

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

McGuire, J.H.; Kletke, R.E.; Sil, N.C.

1985-08-01

The strong-potential Born (SPB) approximation is examined by comparing various SPB calculations of high-velocity 1s-1s electron capture cross sections with one another and with experimental data. Above about 1 MeV, calculations using the SPB method of McGuire and Sil (SPMS) (Phys. Rev. A 28, 3679 (1983)) are in good agreement with total-cross-section observations for protons on H, He, C, Ne, and Ar as expected. For p+H and p+He, the SPB full-peaking (SPB-FP) approximation of Macek and Alston (Phys. Rev. A 26, 250 (1982)) and the SPB transverse-peaking (SPB-TP) approximation of Alston (Phys. Rev. A 27, 2342 (1982)) differ from ourmore » SPMS total cross sections by typically a factor of 2, as expected from general validity criteria. However, the differential cross sections at very forward angles (well within the Thomas angle) are the same in SPMS, SPB-FP, and SPB-TP methods in all cases. Below 1 MeV, cross sections obtained with use of various SPB methods differ considerably from one another, placing a limit of validity for these SPB calculations. We also suggest that in the gap between those energies where continuum intermediate states simply dominate, and above those energies where bound intermediate states simply dominate, detailed conceptual understanding of electron capture is incomplete.« less

Interpretation of ES, CS, and IOS approximations within a translational-internal coupling scheme. II. Application to atom--diatom kinetic cross sections

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

Coombe, D.A.; Snider, R.F.

1980-02-15

ES, CS, and IOS approximations to atom--diatom kinetic cross sections are derived. In doing so, reduced S-matrices in a translational-internal coupling scheme are stressed. This entails the insertion of recently obtained approximate reduced S-matrices in the translational-internal coupling scheme into previously derived general expressions for the kinetic cross sections. Of special interest is the structure (rotational j quantum number dependence) of the kinetic cross sections associated with the Senftleben Beenakker effects and of pure internal state relaxation phenomena. The viscomagnetic effect is used as an illustrative example. It is found in particular that there is a great similarity of structuremore » between the energy sudden (and IOS) approximation and the previously derived distorted wave Born results.« less

Strong potential wave functions with elastic channel distortion

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

Macek, J.; Taulbjerg, K.

1989-06-01

The strong-potential Born approximation is analyzed in a channel-distorted-wave approach. Channel-distorted SPB wave functions are reduced to a conventional form in which the standard off-energy-shell factor /ital g/ has been replaced by a modified factor ..gamma.., which represents a suitable average of /ital g/ over the momentum distribution of the distorted-channel function. The modified factor is evaluated in a physically realistic model for the distortion potential, and it is found that ..gamma.. is well represented by a slowly varying phase factor. The channel-distorted SPB approximation is accordingly identical to the impulse approximation if the phase variation of ..gamma.. can bemore » ignored. This is generally the case in applications to radiative electron capture and to a good approximation for ordinary capture at not too small velocities.« less

Evaluation of the Impact of Mandating Health Care Providers to Offer Hepatitis C Virus Screening to All Persons Born During 1945-1965 - New York, 2014.

PubMed

Flanigan, Colleen A; Leung, Shu-Yin J; Rowe, Kirsten A; Levey, Wendy K; King, Andrea; Sommer, Jamie N; Morne, Johanne E; Zucker, Howard A

2017-09-29

Approximately 75% of all hepatitis C virus (HCV) infections in the United States and 73% of HCV-associated mortality occur in persons born during 1945-1965, placing this birth cohort at increased risk for liver cancer and other HCV-related liver disease (1). In the United States, an estimated 2.7 million persons are living with HCV infection, and it is estimated that up to 75% of these persons do not know their status. Since 2012, CDC has recommended that persons born during 1945-1965 receive one-time HCV testing. To increase the number of persons tested for HCV and to ensure timely diagnosis and linkage to care, in 2014, New York enacted a hepatitis C testing law that requires health care providers to offer HCV antibody screening to all persons born during 1945-1965 who are receiving services in primary care settings or as hospital inpatients, and to refer persons with positive HCV antibody tests for follow-up health care, including an HCV diagnostic test (i.e., HCV RNA).* The New York State Department of Health (NYSDOH) used survey data from clinical laboratories and Medicaid claims and encounter data, and state and New York City (NYC) HCV surveillance data to assess the number of persons tested for HCV and number of persons with newly diagnosed HCV infections who were linked to care. During the first year of the HCV law implementation, there was a 51% increase in specimens submitted for HCV testing to surveyed clinical laboratories; testing rates among active Medicaid clients increased 52%, and linkage to care among persons with newly diagnosed HCV infection increased approximately 40% in New York and 11% in NYC. These findings highlight the potential for state laws to promote HCV testing and the utility of HCV surveillance and Medicaid claims data to monitor the quality of HCV testing and linkage to care for HCV-infected persons.

Functional Brain Organization for Number Processing in Pre-Verbal Infants

ERIC Educational Resources Information Center

Edwards, Laura A.; Wagner, Jennifer B.; Simon, Charline E.; Hyde, Daniel C.

2016-01-01

Humans are born with the ability to mentally represent the approximate numerosity of a set of objects, but little is known about the brain systems that sub-serve this ability early in life and their relation to the brain systems underlying symbolic number and mathematics later in development. Here we investigate processing of numerical magnitudes…

Genetic evaluation of the probability of lambing in yearling Targhee ewes

USDA-ARS?s Scientific Manuscript database

The objective of this study was to determine the additive genetic control of lambing percentage in yearling Targhee ewes. The records of 3,103 ewe lambs born from 1989 to 2011 and mated at approximately 7.5 mo of age were analyzed. Records included sire, dam, weaning weight, breeding pen, age of dam...

New Utrecht High School Project IMPACT. O.E.E. Evaluation Report, 1982-1983.

ERIC Educational Resources Information Center

Bulkin, Elly; Sica, Michael

Project IMPACT, a magnet program in its third and final year of funding, provided instruction in ESL and Italian language skills, as well as bilingual instruction in mathematics, social studies and typing to approximately 200 students of limited English proficiency in a Brooklyn, New York, high school. Nearly all program students were born in…

Project KANPE, 1982-1983. O.E.E. Evaluation Report.

ERIC Educational Resources Information Center

Clesca, Monique; And Others

This report describes Project KANPE, a multi-site program. In its final year of a three-year funding cycle, the project served approximately 275 Haitian students of limited English proficiency in grades nine through twelve at three New York City high schools. Ninety-six percent of the target population were born in Haiti and all spoke either…

Do Twins Have Lower Cognitive Ability than Singletons?

ERIC Educational Resources Information Center

Webbink, Dinand; Posthuma, Danielle; Boomsma, Dorret I.; de Geus, Eco J. C.; Visscher, Peter M.

2008-01-01

Previous studies based on population cohorts born at least 35 years ago, have reported appreciable childhood cognitive deficits for twins. We compared longitudinal IQ scores from approximately 188,000 singletons and some 6000 twins who went to primary school in the Netherlands from 1994 to 2003. In addition, we used a family-based design in which…

Combined active and passive microwave remote sensing of soil moisture for vegetated surfaces at L-band

USDA-ARS?s Scientific Manuscript database

The distorted Born approximation (DBA) combined with the numerical solutions of Maxwell equations (NMM3D) has been used for the radar backscattering model for the SMAP mission. The models for vegetated surfaces such as wheat, grass, soybean and corn have been validated with the Soil Moisture Active ...

Numicon, Numeracy and a Special Need

ERIC Educational Resources Information Center

Horner, Vikki

2002-01-01

Charlotte, the author's 11-year-old daughter, was born with Down syndrome, and is currently attending the local middle school. In terms of her disability Charlotte is developing very well and has a reading age of 9+, however her maths skills age is approximately 4 years. It is not necessarily the case that if a child has good language and literacy…

Semiclassical Origin of Superdeformed Shell Structure in the Spheroidal Cavity Model

NASA Astrophysics Data System (ADS)

Arita, K.; Sugita, A.; Matsuyanagi, K.

1998-12-01

Classical periodic orbits responsible for emergence of the superdeformed shell structures of single-particle motion in spheroidal cavities are identified and their relative contributions to the shell structures are evaluated. Both prolate and oblate superdeformations (axis ratio approximately 2:1) as well as prolate hyperdeformation (axis ratio approximately 3:1) are investigated. Fourier transforms of quantum spectra clearly show that three-dimensional periodic orbits born out of bifurcations of planar orbits in the equatorial plane become predominant at large prolate deformations, while butterfly-shaped planar orbits bifurcated from linear orbits along the minor axis are important at large oblate deformations.

Born iterative reconstruction using perturbed-phase field estimates.

PubMed

Astheimer, Jeffrey P; Waag, Robert C

2008-10-01

A method of image reconstruction from scattering measurements for use in ultrasonic imaging is presented. The method employs distorted-wave Born iteration but does not require using a forward-problem solver or solving large systems of equations. These calculations are avoided by limiting intermediate estimates of medium variations to smooth functions in which the propagated fields can be approximated by phase perturbations derived from variations in a geometric path along rays. The reconstruction itself is formed by a modification of the filtered-backpropagation formula that includes correction terms to account for propagation through an estimated background. Numerical studies that validate the method for parameter ranges of interest in medical applications are presented. The efficiency of this method offers the possibility of real-time imaging from scattering measurements.

Systems and methods for locating and imaging proppant in an induced fracture

DOEpatents

Aldridge, David F.; Bartel, Lewis C.

2016-02-02

Born Scattering Inversion (BSI) systems and methods are disclosed. A BSI system may be incorporated in a well system for accessing natural gas, oil and geothermal reserves in a geologic formation beneath the surface of the Earth. The BSI system may be used to generate a three-dimensional image of a proppant-filled hydraulically-induced fracture in the geologic formation. The BSI system may include computing equipment and sensors for measuring electromagnetic fields in the vicinity of the fracture before and after the fracture is generated, adjusting the parameters of a first Born approximation model of a scattered component of the surface electromagnetic fields using the measured electromagnetic fields, and generating the image of the proppant-filled fracture using the adjusted parameters.

2-D Fused Image Reconstruction approach for Microwave Tomography: a theoretical assessment using FDTD Model

PubMed Central

Bindu, G.; Semenov, S.

2013-01-01

This paper describes an efficient two-dimensional fused image reconstruction approach for Microwave Tomography (MWT). Finite Difference Time Domain (FDTD) models were created for a viable MWT experimental system having the transceivers modelled using thin wire approximation with resistive voltage sources. Born Iterative and Distorted Born Iterative methods have been employed for image reconstruction with the extremity imaging being done using a differential imaging technique. The forward solver in the imaging algorithm employs the FDTD method of solving the time domain Maxwell’s equations with the regularisation parameter computed using a stochastic approach. The algorithm is tested with 10% noise inclusion and successful image reconstruction has been shown implying its robustness. PMID:24058889

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

Implicit solvation models provide, for many applications, an effective way of describing the electrostatic effects of aqueous solvation. Here we outline the main approximations behind the popular Generalized Born solvation model. We show how its accuracy, relative to the Poisson-Boltzmann treatment, can be significantly improved in a computationally inexpensive manner to make the model useful in the studies of large-scale conformational transitions at the atomic level. The improved model is tested in a molecular dynamics simulation of folding of a 46-residue (three helix bundle) protein. Starting from an extended structure at 450K, the protein folds to the lowest energy conformation within 6 ns of simulation time, and the predicted structure differs from the native one by 2.4 A (backbone RMSD).

[Occupational exposure to blood in multiple trauma care].

PubMed

Wicker, S; Wutzler, S; Schachtrupp, A; Zacharowski, K; Scheller, B

2015-01-01

Trauma care personnel are at risk of occupational exposure to blood-borne pathogens. Little is known regarding compliance with standard precautions or occupational exposure to blood and body fluids among multiple trauma care personnel in Germany. Compliance rates of multiple trauma care personnel in applying standard precautions, knowledge about transmission risks of blood-borne pathogens, perceived risks of acquiring hepatitis B, hepatitis C and human immunodeficiency virus (HIV) and the personal attitude towards testing of the index patient for blood-borne pathogens after a needlestick injury were evaluated. In the context of an advanced multiple trauma training an anonymous questionnaire was administered to the participants. Almost half of the interviewees had sustained a needlestick injury within the last 12 months. Approximately three quarters of the participants were concerned about the risk of HIV and hepatitis. Trauma care personnel had insufficient knowledge of the risk of blood-borne pathogens, overestimated the risk of hepatitis C infection and underused standard precautionary measures. Although there was excellent compliance for using gloves, there was poor compliance in using double gloves (26.4 %), eye protectors (19.7 %) and face masks (15.8 %). The overwhelming majority of multiple trauma care personnel believed it is appropriate to test an index patient for blood-borne pathogens following a needlestick injury. The process of treatment in prehospital settings is less predictable than in other settings in which invasive procedures are performed. Periodic training and awareness programs for trauma care personnel are required to increase the knowledge of occupational infections and the compliance with standard precautions. The legal and ethical aspects of testing an index patient for blood-borne pathogens after a needlestick injury of a healthcare worker have to be clarified in Germany.

Health Disparities and Delayed Health care among Older Adults in California: A Perspective from Race, Ethnicity, and Immigration.

PubMed

Du, Yan; Xu, Qingwen

2016-09-01

To examine racial/ethnic/immigration disparities in health and to investigate the relationships among race/ethnic/immigration status, delayed health care, and health of the elderly. Responses from 13,508 people aged 65 and above were analyzed based on the California Health Interview Survey (CHIS) 2011-2012. Key variables include race/ethnicity/immigration status, health outcome, and delayed health care. Age, gender, education, work status, and annual family income are used as covariates. The findings indicate that Whites (regardless of country of birth) and U.S.-born Asians enjoy better health than Latinos, African-Americans, and Foreign-born Asians. Foreign-born Asians and foreign-born Latinos have the poorest self-reported health and mental health, respectively. Delayed use of health care is negatively associated with both self-reported health and mental health status. Health disparities exist among older adult populations; the combined effects of minority and immigrant status can be approximated from the results in this study. Health care accessibility and the quality of care should be promoted in minority/immigrant populations. Public health nurses have a strong potential to aide in reducing health disparities among an aging American population that continues to exhibit increasing racial/ethnic diversity. © 2016 Wiley Periodicals, Inc.

Aging in Australia: country of birth and language preferences of residents in aged care facilities.

PubMed

Petrov, Ljubica; Joyce, Catherine; Gucciardo-Masci, Tonina

2017-09-05

Objective There is a need to better understand the use of aged care services by people from culturally and linguistically diverse backgrounds. The aim of the present study was to describe the prevalence of people living in residential aged care facilities (RACFs) who were born in non-English-speaking countries and/or have a preferred language other than English and to describe service utilisation rates. Methods The present study consisted of a secondary analysis of data from the Australian Institute of Health and Welfare National Aged Care Data Clearinghouse. Data were analysed by country of birth, preferred language, state or territory and Aged Care Planning Regions within Victoria. Results Nationally, over 30000 (18.3%) RACF residents were born in a non-English-speaking country. In Victoria, almost one in four RACF residents (23.9%) was born in a non-English-speaking country, and approximately one in eight (13.1%) has a preferred language other than English. Most Victorian RACFs (72.4%) have at least one resident with a preferred language other than English. Approximately one in four residents (26.1%) with a preferred language other than English are the sole speaker of the language in their facility. Conclusion All RACFs need to effectively address the needs and preferences of their residents, including those who were born in a non-English-speaking country or prefer to speak a language other than English. What is known about the topic? The number of older people from a non-English-speaking background continues to increase, but little is known about the prevalence of this cohort living in RACFs and how aged care providers are responding to their needs and preferences. What does this paper add? The present study provides detailed, service- and policy-relevant information, demonstrating a substantial degree of diversity among people living in RACFs, with wide distribution across facilities and regions. The findings confirm the need for a systematic, sector-wide approach to addressing linguistic diversity and developing inclusive practices. What are the implications for practitioners? All RACFs are required to develop policies and procedures in order to cater to the needs and preferences of residents who were born in non-English-speaking countries and/or who prefer to speak a language other than English.

Excitation of levels in Li6 by inelastic electron scattering

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

Bernheim, M.; Bishop, G. R.

1963-07-01

Inelastic scattering of electrons from metallic targets of Li 6 was studied as part of a program to establish the validity of the Born approximation calculation of the cross section. This calculation predicts the separation of the inelastic form factor into two contributions corresponding to the absorption of longitudinal and transverse virtual photons by the bombarded system. (R.E.U.)

Parametrization of electron impact ionization cross sections for CO, CO2, NH3 and SO2

NASA Technical Reports Server (NTRS)

Srivastava, Santosh K.; Nguyen, Hung P.

1987-01-01

The electron impact ionization and dissociative ionization cross section data of CO, CO2, CH4, NH3, and SO2, measured in the laboratory, were parameterized utilizing an empirical formula based on the Born approximation. For this purpose an chi squared minimization technique was employed which provided an excellent fit to the experimental data.

Theoretical and experimental quantification of doubly and singly differential cross sections for electron-induced ionization of isolated tetrahydrofuran molecules

DOE PAGES

Champion, Christophe; Quinto, Michele A.; Bug, Marion U.; ...

2014-07-29

Electron-induced ionization of the commonly used surrogate of the DNA sugar-phosphate backbone, namely, the tetrahydrofuran molecule, is here theoretically described within the 1 st Born approximation by means of quantum-mechanical approach. Comparisons between theory and recent experiments are reported in terms of doubly and singly differential cross sections.

Reprint of: Ionization probabilities of Ne, Ar, Kr, and Xe by proton impact for different initial states and impact energies

NASA Astrophysics Data System (ADS)

Montanari, C. C.; Miraglia, J. E.

2018-01-01

In this contribution we present ab initio results for ionization total cross sections, probabilities at zero impact parameter, and impact parameter moments of order +1 and -1 of Ne, Ar, Kr, and Xe by proton impact in an extended energy range from 100 keV up to 10 MeV. The calculations were performed by using the continuum distorted wave eikonal initial state approximation (CDW-EIS) for energies up to 1 MeV, and using the first Born approximation for larger energies. The convergence of the CDW-EIS to the first Born above 1 MeV is clear in the present results. Our inner-shell ionization cross sections are compared with the available experimental data and with the ECPSSR results. We also include in this contribution the values of the ionization probabilities at the origin, and the impact parameter dependence. These values have been employed in multiple ionization calculations showing very good description of the experimental data. Tables of the ionization probabilities are presented, disaggregated for the different initial bound states, considering all the shells for Ne and Ar, the M-N shells of Kr and the N-O shells of Xe.

Perturbations of the seismic reflectivity of a fluid-saturated depth-dependent poroelastic medium.

PubMed

de Barros, Louis; Dietrich, Michel

2008-03-01

Analytical formulas are derived to compute the first-order effects produced by plane inhomogeneities on the point source seismic response of a fluid-filled stratified porous medium. The derivation is achieved by a perturbation analysis of the poroelastic wave equations in the plane-wave domain using the Born approximation. This approach yields the Frechet derivatives of the P-SV- and SH-wave responses in terms of the Green's functions of the unperturbed medium. The accuracy and stability of the derived operators are checked by comparing, in the time-distance domain, differential seismograms computed from these analytical expressions with complete solutions obtained by introducing discrete perturbations into the model properties. For vertical and horizontal point forces, it is found that the Frechet derivative approach is remarkably accurate for small and localized perturbations of the medium properties which are consistent with the Born approximation requirements. Furthermore, the first-order formulation appears to be stable at all source-receiver offsets. The porosity, consolidation parameter, solid density, and mineral shear modulus emerge as the most sensitive parameters in forward and inverse modeling problems. Finally, the amplitude-versus-angle response of a thin layer shows strong coupling effects between several model parameters.

Role of the 3He optical model potential ambiguity in the distorted-wave Born approximation description of the 58Ni(3He, d)59Cu reaction at 130 MeV incident energy

NASA Astrophysics Data System (ADS)

Djaloeis, A.; Alderliesten, C.; Bojowald, J.; Mayer-Böricke, C.; Oelert, W.; Turek, P.

1983-04-01

Angular distributions of 58Ni(3He, d)59Cu transitions leading to the (0.0 MeV, 32-), (0.91 MeV, 52-), and (3.04 MeV, 92+) states in 59Cu have been measured at an incident energy of 130 MeV. The experimental data have been used to study mainly the role of the 3He optical model potential ambiguity in the distorted-wave Born approximation description of the reaction. Satisfactory fits to the data are obtained using a deep helion potential in standard local zero-range calculations. For a shallow 3He potential a comparable description can be achieved if the depth of the real part of the deuteron optical potential is reduced considerably, and nonlocality as well as finite-range corrections are taken into account. Under these conditions, the use of a 3He potential constructed according to the Johnson-Soper prescription yields similar results. NUCLEAR REACTIONS 58Ni (3He, d)59Cu, E=130 MeV; measured dσ(θ)dΩ. Enriched target; DWBA analysis; discussed reaction mechanism.

Cavity Born-Oppenheimer Approximation for Correlated Electron-Nuclear-Photon Systems.

PubMed

Flick, Johannes; Appel, Heiko; Ruggenthaler, Michael; Rubio, Angel

2017-04-11

In this work, we illustrate the recently introduced concept of the cavity Born-Oppenheimer approximation [ Flick et al. PNAS 2017 , 10.1073/pnas.1615509114 ] for correlated electron-nuclear-photon problems in detail. We demonstrate how an expansion in terms of conditional electronic and photon-nuclear wave functions accurately describes eigenstates of strongly correlated light-matter systems. For a GaAs quantum ring model in resonance with a photon mode we highlight how the ground-state electronic potential-energy surface changes the usual harmonic potential of the free photon mode to a dressed mode with a double-well structure. This change is accompanied by a splitting of the electronic ground-state density. For a model where the photon mode is in resonance with a vibrational transition, we observe in the excited-state electronic potential-energy surface a splitting from a single minimum to a double minimum. Furthermore, for a time-dependent setup, we show how the dynamics in correlated light-matter systems can be understood in terms of population transfer between potential energy surfaces. This work at the interface of quantum chemistry and quantum optics paves the way for the full ab initio description of matter-photon systems.

Scaling Cross Sections for Ion-atom Impact Ionization

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

Igor D. Kaganovich; Edward Startsev; Ronald C. Davidson

2003-06-06

The values of ion-atom ionization cross sections are frequently needed for many applications that utilize the propagation of fast ions through matter. When experimental data and theoretical calculations are not available, approximate formulas are frequently used. This paper briefly summarizes the most important theoretical results and approaches to cross section calculations in order to place the discussion in historical perspective and offer a concise introduction to the topic. Based on experimental data and theoretical predictions, a new fit for ionization cross sections is proposed. The range of validity and accuracy of several frequently used approximations (classical trajectory, the Born approximation,more » and so forth) are discussed using, as examples, the ionization cross sections of hydrogen and helium atoms by various fully stripped ions.« less

Scattering of electromagnetic waves from a half-space of randomly distributed discrete scatterers and polarized backscattering ratio law

NASA Technical Reports Server (NTRS)

Zhu, P. Y.

1991-01-01

The effective-medium approximation is applied to investigate scattering from a half-space of randomly and densely distributed discrete scatterers. Starting from vector wave equations, an approximation, called effective-medium Born approximation, a particular way, treating Green's functions, and special coordinates, of which the origin is set at the field point, are used to calculate the bistatic- and back-scatterings. An analytic solution of backscattering with closed form is obtained and it shows a depolarization effect. The theoretical results are in good agreement with the experimental measurements in the cases of snow, multi- and first-year sea-ice. The root product ratio of polarization to depolarization in backscattering is equal to 8; this result constitutes a law about polarized scattering phenomena in the nature.

Estimating the impact of newly arrived foreign-born persons on tuberculosis in the United States.

PubMed

Liu, Yecai; Painter, John A; Posey, Drew L; Cain, Kevin P; Weinberg, Michelle S; Maloney, Susan A; Ortega, Luis S; Cetron, Martin S

2012-01-01

Among approximately 163.5 million foreign-born persons admitted to the United States annually, only 500,000 immigrants and refugees are required to undergo overseas tuberculosis (TB) screening. It is unclear what extent of the unscreened nonimmigrant visitors contributes to the burden of foreign-born TB in the United States. We defined foreign-born persons within 1 year after arrival in the United States as "newly arrived", and utilized data from U.S. Department of Homeland Security, U.S. Centers for Disease Control and Prevention, and World Health Organization to estimate the incidence of TB among newly arrived foreign-born persons in the United States. During 2001 through 2008, 11,500 TB incident cases, including 291 multidrug-resistant TB incident cases, were estimated to occur among 20,989,738 person-years for the 1,479,542,654 newly arrived foreign-born persons in the United States. Of the 11,500 estimated TB incident cases, 41.6% (4,783) occurred among immigrants and refugees, 36.6% (4,211) among students/exchange visitors and temporary workers, 13.8% (1,589) among tourists and business travelers, and 7.3% (834) among Canadian and Mexican nonimmigrant visitors without an I-94 form (e.g., arrival-departure record). The top 3 newly arrived foreign-born populations with the largest estimated TB incident cases per 100,000 admissions were immigrants and refugees from high-incidence countries (e.g., 2008 WHO-estimated TB incidence rate of ≥100 cases/100,000 population/year; 235.8 cases/100,000 admissions, 95% confidence interval [CI], 228.3 to 243.3), students/exchange visitors and temporary workers from high-incidence countries (60.9 cases/100,000 admissions, 95% CI, 58.5 to 63.3), and immigrants and refugees from medium-incidence countries (e.g., 2008 WHO-estimated TB incidence rate of 15-99 cases/100,000 population/year; 55.2 cases/100,000 admissions, 95% CI, 51.6 to 58.8). Newly arrived nonimmigrant visitors contribute substantially to the burden of foreign-born TB in the United States. To achieve the goals of TB elimination, direct investment in global TB control and strategies to target nonimmigrant visitors should be considered.

Cardiovascular Disease Risk Factor Profiles of 263,356 Older Australians According to Region of Birth and Acculturation, with a Focus on Migrants Born in Asia

PubMed Central

Guo, Shuyu; Lucas, Robyn M.; Joshy, Grace; Banks, Emily

2015-01-01

Risk factors for cardiovascular disease (CVD), such as obesity, diabetes, hypertension and physical inactivity, are common in Australia, but the prevalence varies according to cultural background. We examined the relationship between region of birth, measures of acculturation, and CVD risk profiles in immigrant, compared to Australian-born, older Australians. Cross-sectional data from 263,356 participants aged 45 and over joining the population-based 45 and Up Study cohort from 2006–2008 were used. Prevalence ratios for CVD risk factors in Australian- versus overseas-born participants were calculated using modified Poisson regression, adjusting for age, sex and socioeconomic factors and focusing on Asian migrants. The association between time resident in Australia and age at migration and CVD risk factors in Asian migrants was also examined. Migrants from Northeast (n = 3,213) and Southeast Asia (n = 3,942) had lower levels of overweight/obesity, physical activity and female smoking than Australian-born participants (n = 199,356), although differences in prevalence of overweight/obesity were sensitive to body-mass-index cut-offs used. Compared to Australian-born participants, migrants from Northeast Asia were 20–30% less likely, and from Southeast Asia 10–20% more likely, to report being treated for hypertension and/or hypercholesterolaemia; Southeast Asian migrants were 40–60% more likely to report diabetes. Northeast Asian-born individuals were less likely than Australian-born to have 3 or more CVD risk factors. Diabetes, treated hypertension and hypercholesterolaemia occurred at relatively low average body-mass-index in Southeast Asian migrants. The CVD risk factor profiles of migrants tended to approximate those of Australian-born with increasing acculturation, in both favourable (e.g., increased physical activity) and unfavourable directions (e.g., increased female smoking). Minimizing CVD risk in migrant populations may be achieved through efforts to retain the healthy facets of the traditional lifestyle, such as a normal body mass index and low prevalence of smoking in women, in addition to adopting healthy aspects of the host country lifestyle, such as increased physical activity. PMID:25695771

Gravitational corrections to light propagation in a perturbed FLRW universe and corresponding weak-lensing spectra

NASA Astrophysics Data System (ADS)

Cuesta-Lazaro, Carolina; Quera-Bofarull, Arnau; Reischke, Robert; Schäfer, Björn Malte

2018-06-01

When the gravitational lensing of the large-scale structure is calculated from a cosmological model a few assumptions enter: (i) one assumes that the photons follow unperturbed background geodesics, which is usually referred to as the Born approximation, (ii) the lenses move slowly, (iii) the source-redshift distribution is evaluated relative to the background quantities, and (iv) the lensing effect is linear in the gravitational potential. Even though these approximations are small individually they could sum up, especially since they include local effects such as the Sachs-Wolfe and peculiar motion, but also non-local ones like the Born approximation and the integrated Sachs-Wolfe effect. In this work, we will address all points mentioned and perturbatively calculate the effect on a tomographic cosmic shear power spectrum of each effect individually as well as all cross-correlations. Our findings show that each effect is at least 4-5 orders of magnitude below the leading order lensing signal. Finally, we sum up all effects to estimate the overall impact on parameter estimation by a future cosmological weak-lensing survey such as Euclid in a wcold dark matter cosmology with parametrization Ωm, σ8, ns, h, w0, and wa, using five tomographic bins. We consistently find a parameter bias of 10-5, which is therefore completely negligible for all practical purposes, confirming that other effects such as intrinsic alignments, magnification bias and uncertainties in the redshift distribution will be the dominant systematic source in future surveys.

[Study on national active monitoring for food borne pathogens and antimicrobial resistance in China 2001].

PubMed

Wang, Maoqi; Ran, Lu; Wang, Zhutian; Li, Zhigang

2004-01-01

To survey food borne pathogens and antimicrobial resistance in China. A total of 4034 samples of foods (raw meats, raw milk, cooked meats, ice cream, yoghurt, aquatic product and vegetable) were examined for the presence of Escherichia coli O157:H7 Salmonella spp and Listeria monocytogens by national active foodborne pathogens surveillance system. The samples were obtained from 11 provinces in 2001. Approximate 5.50% of the all samples yielded 3 pathogenes, whereas Escherichia coli O157:H7 (0.82%), Salmonella servoars (3.32%) and Listeria monocytogens (1.29%). The most heavy contamination by three food borne pathogens are in raw meat (12.96%). Top seven serotype of the 137 Salmonella isolates are S. derby, S. agona, S. enteritidis, S. reading, S. anatum. S. muenster, S. typhimurium. Serotypes and antibiotic resistance patterns of Salmonella isolates are different in 11 provinces. E. coli O157:H7 strains that are isolated from raw meat and cooked meat have VT2, eae, Hly genes. Salmonella and E. coli strains of multidrug resistance were isolated and identified.

Electric transition dipole moment in pre-Born-Oppenheimer molecular structure theory.

PubMed

Simmen, Benjamin; Mátyus, Edit; Reiher, Markus

2014-10-21

This paper presents the calculation of the electric transition dipole moment in a pre-Born-Oppenheimer framework. Electrons and nuclei are treated equally in terms of the parametrization of the non-relativistic total wave function, which is written as a linear combination of basis functions constructed from explicitly correlated Gaussian functions and the global vector representation. The integrals of the electric transition dipole moment are derived corresponding to these basis functions in both the length and the velocity representation. The calculations are performed in laboratory-fixed Cartesian coordinates without relying on coordinates which separate the center of mass from the translationally invariant degrees of freedom. The effect of the overall motion is eliminated through translationally invariant integral expressions. The electric transition dipole moment is calculated between two rovibronic levels of the H2 molecule assignable to the lowest rovibrational states of the X (1)Σ(g)(+) and B (1)Σ(u)(+) electronic states in the clamped-nuclei framework. This is the first evaluation of this quantity in a full quantum mechanical treatment without relying on the Born-Oppenheimer approximation.

Persistent and progressive long-term lung disease in survivors of preterm birth.

PubMed

Urs, Rhea; Kotecha, Sailesh; Hall, Graham L; Simpson, Shannon J

2018-04-13

Preterm birth accounts for approximately 11% of births globally, with rates increasing across many countries. Concurrent advances in neonatal care have led to increased survival of infants of lower gestational age (GA). However, infants born <32 weeks of GA experience adverse respiratory outcomes, manifesting with increased respiratory symptoms, hospitalisation and health care utilisation into early childhood. The development of bronchopulmonary dysplasia (BPD) - the chronic lung disease of prematurity - further increases the risk of poor respiratory outcomes throughout childhood, into adolescence and adulthood. Indeed, survivors of preterm birth have shown increased respiratory symptoms, altered lung structure, persistent and even declining lung function throughout childhood. The mechanisms behind this persistent and sometimes progressive lung disease are unclear, and the implications place those born preterm at increased risk of respiratory morbidity into adulthood. This review aims to summarise what is known about the long-term pulmonary outcomes of contemporary preterm birth, examine the possible mechanisms of long-term respiratory morbidity in those born preterm and discuss addressing the unknowns and potentials for targeted treatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mental Health of Aging Immigrants and Native-Born Men Across 11 European Countries

PubMed Central

2013-01-01

Objectives. Though working-age immigrants exhibit lower mortality compared with those domestic-born immigrants, consequences of immigration for mental health remain unclear. We examine whether older immigrants exhibit a mental advantage and whether factors believed to underlie immigrant vulnerability explain disparities. Method. The sample includes 12,247 noninstitutionalized men more than 50 years in 11 European countries. Multivariate logistic regression models estimated the impact of physical health, health behaviors, availability of social support, social participation, citizenship, time since immigration, socioeconomic status (SES), and employment on the mental health of immigrants. Results. Immigrants face 1.60 increased odds of depression despite a physical health advantage, evidenced by 0.74 lower odds of chronic illness. SES and availability of social support were predictive, though acculturation measures were not. Decomposition analysis revealed that only approximately 20% of the variation in depression rates between immigrants and native-born peers were explained by commonly cited risk factors. Conclusions. Despite physical health advantages, older immigrants suffer substantially higher depression rates. Time since immigration does not appear to mitigate depressive symptoms. PMID:23325505

Treecode-based generalized Born method

NASA Astrophysics Data System (ADS)

Xu, Zhenli; Cheng, Xiaolin; Yang, Haizhao

2011-02-01

We have developed a treecode-based O(Nlog N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

Molecular Detection of Tick-Borne Pathogens in Humans with Tick Bites and Erythema Migrans, in the Netherlands

PubMed Central

Jahfari, Setareh; Hofhuis, Agnetha; Fonville, Manoj; van der Giessen, Joke; van Pelt, Wilfrid; Sprong, Hein

2016-01-01

Background Tick-borne diseases are the most prevalent vector-borne diseases in Europe. Knowledge on the incidence and clinical presentation of other tick-borne diseases than Lyme borreliosis and tick-borne encephalitis is minimal, despite the high human exposure to these pathogens through tick bites. Using molecular detection techniques, the frequency of tick-borne infections after exposure through tick bites was estimated. Methods Ticks, blood samples and questionnaires on health status were collected from patients that visited their general practitioner with a tick bite or erythema migrans in 2007 and 2008. The presence of several tick-borne pathogens in 314 ticks and 626 blood samples of this cohort were analyzed using PCR-based methods. Using multivariate logistic regression, associations were explored between pathogens detected in blood and self-reported symptoms at enrolment and during a three-month follow-up period. Results Half of the ticks removed from humans tested positive for Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Candidatus Neoehrlichia mikurensis, Rickettsia helvetica, Rickettsia monacensis, Borrelia miyamotoi and several Babesia species. Among 92 Borrelia burgdorferi s. l. positive ticks, 33% carried another pathogen from a different genus. In blood of sixteen out of 626 persons with tick bites or erythema migrans, DNA was detected from Candidatus Neoehrlichia mikurensis (n = 7), Anaplasma phagocytophilum (n = 5), Babesia divergens (n = 3), Borrelia miyamotoi (n = 1) and Borrelia burgdorferi s. l. (n = 1). None of these sixteen individuals reported any overt symptoms that would indicate a corresponding illness during the three-month follow-up period. No associations were found between the presence of pathogen DNA in blood and; self-reported symptoms, with pathogen DNA in the corresponding ticks (n = 8), reported tick attachment duration, tick engorgement, or antibiotic treatment at enrolment. Conclusions Based on molecular detection techniques, the probability of infection with a tick-borne pathogen other than Lyme spirochetes after a tick bite is roughly 2.4%, in the Netherlands. Similarly, among patients with erythema migrans, the probability of a co-infection with another tick-borne pathogen is approximately 2.7%. How often these infections cause disease symptoms or to what extend co-infections affect the course of Lyme borreliosis needs further investigations. PMID:27706159

Nuclear Fusion Rate Study of a Muonic Molecule via Nuclear Threshold Resonances

NASA Astrophysics Data System (ADS)

Faghihi, F.; Eskandari, M. R.

This work follows our previous calculations of the ground state binding energy, size, and the effective nuclear charge of the muonic T3 molecule, using the Born-Oppenheimer adiabatic approximation. In our past articles, we showed that the system possesses two minimum positions, the first one at the muonic distance and the second at the atomic distance. Also, the symmetric planner vibrational model assumed between the two minima and the approximated potential were calculated. Following from the previous studies, we now calculate the fusion rate of the T3 muonic molecule according to the overlap integral of the resonance nuclear compound nucleus and the molecular wave functions.

ANALYSIS OF DEUTERON STRIPPING EXPERIMENTS

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

Amado, R.D.

1959-05-01

Deuteron stripping experiments analyzed according to the theory of Butter are a nearly unique source of information on the orbital angular momentum and single-particle widths of nuclear bound states. A number of problems in the Butter theory remain. Chew and Low show that in reactions in which there is a contribution from thc exchange of a single particles there can appear isolated poles in the normalized Born approximation to the cross section and that the residue at these poles can be related to quantities of physical interest. Stripping is such a reactions and the Butter theory is the renormalized Bornmore » approximation. (A.C.)« less

Quantum gravitational contributions to the cosmic microwave background anisotropy spectrum.

PubMed

Kiefer, Claus; Krämer, Manuel

2012-01-13

We derive the primordial power spectrum of density fluctuations in the framework of quantum cosmology. For this purpose we perform a Born-Oppenheimer approximation to the Wheeler-DeWitt equation for an inflationary universe with a scalar field. In this way, we first recover the scale-invariant power spectrum that is found as an approximation in the simplest inflationary models. We then obtain quantum gravitational corrections to this spectrum and discuss whether they lead to measurable signatures in the cosmic microwave background anisotropy spectrum. The nonobservation so far of such corrections translates into an upper bound on the energy scale of inflation.

Improved distorted wave theory with the localized virial conditions

NASA Astrophysics Data System (ADS)

Hahn, Y. K.; Zerrad, E.

2009-12-01

The distorted wave theory is operationally improved to treat the full collision amplitude, such that the corrections to the distorted wave Born amplitude can be systematically calculated. The localized virial conditions provide the tools necessary to test the quality of successive approximations at each stage and to optimize the solution. The details of the theoretical procedure are explained in concrete terms using a collisional ionization model and variational trial functions. For the first time, adjustable parameters associated with an approximate scattering solution can be fully determined by the theory. A small number of linear parameters are introduced to examine the convergence property and the effectiveness of the new approach.

Born Oppenheimer potential energy for interaction of antihydrogen with molecular hydrogen

NASA Astrophysics Data System (ADS)

Strasburger, Krzysztof

2005-09-01

Inelastic collisions with hydrogen molecules are claimed to be an important channel of antihydrogen (\\overlineH) losses (Armour and Zeman 1999 Int. J. Quantum Chem. 74 645). In the present work, interaction energies for the H_{2}\\--\\overlineH system in the ground state have been calculated within the Born-Oppenheimer approximation. The leptonic problem was solved variationally with the basis of explicitly correlated Gaussian functions. The geometry of H2 was fixed at equilibrium geometry and the \\overlineH atom approached the molecule from two directions—along or perpendicularly to the bond axis. Purely attractive potential energy curve has been obtained for the first nuclear configuration, while a local maximum (lower than the energy at infinite separation) has been found for the second one.

Non-Born-Oppenheimer calculations of the pure vibrational spectrum of HeH+.

PubMed

Pavanello, Michele; Bubin, Sergiy; Molski, Marcin; Adamowicz, Ludwik

2005-09-08

Very accurate calculations of the pure vibrational spectrum of the HeH(+) ion are reported. The method used does not assume the Born-Oppenheimer approximation, and the motion of both the electrons and the nuclei are treated on equal footing. In such an approach the vibrational motion cannot be decoupled from the motion of electrons, and thus the pure vibrational states are calculated as the states of the system with zero total angular momentum. The wave functions of the states are expanded in terms of explicitly correlated Gaussian basis functions multipled by even powers of the internuclear distance. The calculations yielded twelve bound states and corresponding eleven transition energies. Those are compared with the pure vibrational transition energies extracted from the experimental rovibrational spectrum.

Born iterative reconstruction using perturbed-phase field estimates

PubMed Central

Astheimer, Jeffrey P.; Waag, Robert C.

2008-01-01

A method of image reconstruction from scattering measurements for use in ultrasonic imaging is presented. The method employs distorted-wave Born iteration but does not require using a forward-problem solver or solving large systems of equations. These calculations are avoided by limiting intermediate estimates of medium variations to smooth functions in which the propagated fields can be approximated by phase perturbations derived from variations in a geometric path along rays. The reconstruction itself is formed by a modification of the filtered-backpropagation formula that includes correction terms to account for propagation through an estimated background. Numerical studies that validate the method for parameter ranges of interest in medical applications are presented. The efficiency of this method offers the possibility of real-time imaging from scattering measurements. PMID:19062873

A study of the geographic coverage properties of a satellite borne Doppler lidar wind velocity measuring system

NASA Technical Reports Server (NTRS)

Pate, T. H.

1982-01-01

Geographic coverage frequency and geographic shot density for a satellite borne Doppler lidar wind velocity measuring system are measured. The equations of motion of the light path on the ground were derived and a computer program devised to compute shot density and coverage frequency by latitude-longitude sections. The equations for the coverage boundaries were derived and a computer program developed to plot these boundaries, thus making it possible, after an application of a map coloring algorithm, to actually see the areas of multiple coverage. A theoretical cross-swath shot density function that gives close approximations in certain cases was also derived. This information should aid in the design of an efficient data-processing system for the Doppler lidar.

The impact and implications of undocumented immigration on individual and collective health in the United States.

PubMed

Hilfinger Messias, DeAnne K; McEwen, Marylyn Morris; Clark, Lauren

2015-01-01

A nation of immigrants, the United States currently has more foreign-born residents than any other country; approximately 28% of these foreign-born residents are undocumented immigrants--individuals who either entered or are currently residing in the country without valid immigration or residency documents. The complex and constantly changing social, political, and economic context of undocumented migration has profound effects on individuals, families, and communities. The lack of demographic and epidemiologic data on undocumented immigrants is a major public health challenge. In this article, we identify multiple dimensions of vulnerability among undocumented persons; examine how undocumentedness impacts health and health care access and utilization; and consider the professional, practice, and policy issues and implications for nurses. Copyright © 2015 Elsevier Inc. All rights reserved.

The growth of railway ground vibration problems - A review.

PubMed

Connolly, David P; Marecki, Grzegorz P; Kouroussis, Georges; Thalassinakis, Ioannis; Woodward, Peter K

2016-10-15

Ground-borne noise and vibration from railway lines can cause human distress/annoyance, and also negatively affect real estate property values. Therefore this paper analyses a collection of technical ground-borne noise and vibration reports, detailing commercial vibration assessments undertaken at 1604 railway track sections, in 9 countries across the world. A wide range of rail projects are considered including light rail, tram lines, underground/tunnelled lines, freight, conventional rail and high speed rail. It documents the rise in ground-borne vibration problems and trends in the prediction industry, with the aim of informing the current research area. Firstly, the reports are analysed chronologically and it is found that railway vibration is a growing global concern, and as such, assessments have become more prevalent. International assessment metrics are benchmarked and it is found that velocity decibels (VdB), vibration dose value (VDV) and peak particle velocity (PPV) are the most commonly used methods of assessment. Furthermore, to predict vibration levels, the physical measurement of frequency transfer functions is preferential to numerical modelling. Results from the reports show that ground vibration limits are exceeded in 44% of assessments, and that ground-borne noise limits are exceeded in 31%. Moreover, mitigation measures were required on approximately 50% of projects, revealing that ground-borne noise and vibration is a widespread railroad engineering challenge. To solve these problems, the most commonly used abatement strategy is a modification of the railtrack structure (active mitigation), rather than the implementation of a more passive solution in the far-field. Copyright © 2015 Elsevier B.V. All rights reserved.

Selection, Language Heritage, and the Earnings Trajectories of Black Immigrants in the United States

PubMed Central

Hamilton, Tod G.

2014-01-01

Research suggests that immigrants from the English-speaking Caribbean surpass the earnings of U.S.-born blacks approximately one decade after arriving in the United States. Using data from the 1980–2000 U.S. censuses and the 2005–2007 American Community Surveys on U.S.-born black and non-Hispanic white men as well as black immigrant men from all the major sending regions of the world, I evaluate whether selective migration and language heritage of immigrants’ birth countries account for the documented earnings crossover. I validate the earnings pattern of black immigrants documented in previous studies, but I also find that the earnings of most arrival cohorts of immigrants from the English-speaking Caribbean, after residing in the United States for more than 20 years, are projected to converge with or slightly overtake those of U.S.-born black internal migrants. The findings also show three arrival cohorts of black immigrants from English-speaking African countries are projected to surpass the earnings of U.S.-born black internal migrants. No arrival cohort of black immigrants is projected to surpass the earnings of U.S.-born non-Hispanic whites. Birth-region analysis shows that black immigrants from English-speaking countries experience more rapid earnings growth than immigrants from non-English-speaking countries. The arrival-cohort and birth-region variation in earnings documented in this study suggest that selective migration and language heritage of black immigrants’ birth countries are important determinants of their initial earnings and earnings trajectories in the United States. PMID:24854004

Increasing lung cancer death rates among young women in southern and midwestern States.

PubMed

Jemal, Ahmedin; Ma, Jiemin; Rosenberg, Philip S; Siegel, Rebecca; Anderson, William F

2012-08-01

Previous studies reported that declines in age-specific lung cancer death rates among women in the United States abruptly slowed in women younger than age 50 years (ie, women born after the 1950s). However, in view of substantial geographic differences in antitobacco measures and sociodemographic factors that affect smoking prevalence, it is unknown whether this change in the trend was similar across all states. We examined female age-specific lung cancer death rates (1973 through 2007) by year of death and birth in each state by using age-period-cohort models. Cohort relative risks adjusted for age and period effects were used to compare the lung cancer death rate for a given birth cohort to a referent birth cohort (ie, the 1933 cohort herein). Age-specific lung cancer death rates declined continuously in white women in California, but the rates declined less quickly or even increased in the remaining states among women younger than age 50 years and women born after the 1950s, especially in several southern and midwestern states. For example, in some southern states (eg, Alabama), lung cancer death rates among women born in the 1960s were approximately double those of women born in the 1930s. The unfavorable lung cancer trend in white women born after circa 1950 in southern and midwestern states underscores the need for additional interventions to promote smoking cessation in these high-risk populations, which could lead to more favorable future mortality trends for lung cancer and other smoking-related diseases.

Increasing Lung Cancer Death Rates Among Young Women in Southern and Midwestern States

PubMed Central

Jemal, Ahmedin; Ma, Jiemin; Rosenberg, Philip S.; Siegel, Rebecca; Anderson, William F.

2012-01-01

Purpose Previous studies reported that declines in age-specific lung cancer death rates among women in the United States abruptly slowed in women younger than age 50 years (ie, women born after the 1950s). However, in view of substantial geographic differences in antitobacco measures and sociodemographic factors that affect smoking prevalence, it is unknown whether this change in the trend was similar across all states. Methods We examined female age-specific lung cancer death rates (1973 through 2007) by year of death and birth in each state by using age-period-cohort models. Cohort relative risks adjusted for age and period effects were used to compare the lung cancer death rate for a given birth cohort to a referent birth cohort (ie, the 1933 cohort herein). Results Age-specific lung cancer death rates declined continuously in white women in California, but the rates declined less quickly or even increased in the remaining states among women younger than age 50 years and women born after the 1950s, especially in several southern and midwestern states. For example, in some southern states (eg, Alabama), lung cancer death rates among women born in the 1960s were approximately double those of women born in the 1930s. Conclusion The unfavorable lung cancer trend in white women born after circa 1950 in southern and midwestern states underscores the need for additional interventions to promote smoking cessation in these high-risk populations, which could lead to more favorable future mortality trends for lung cancer and other smoking-related diseases. PMID:22734032

Food choking hazards in children.

PubMed

Sidell, Douglas R; Kim, Irene A; Coker, Tumaini R; Moreno, Candice; Shapiro, Nina L

2013-12-01

To review the literature on pediatric food choking risks, with the long-term goal of supporting legislation regulating the production, labeling, and distribution of high-risk foods. A PubMed search (Keywords: choking, obstruction, asphyxiation, foreign body, food) was conducted in July-September 2010 with publication dates ranging from 1966 to 2010. Articles related to pediatric foreign body aspiration (FBA) were selected by three independent reviewers. 1145 articles were initially identified. Abstracts were then screened utilizing a tool designed to isolate relevant pediatric choking events; this tool helped to only select abstracts which presented data on patients younger than 18 years of age who had choked on food items. Through this, a total of 72 pertinent articles were isolated (55 observational studies, 17 case reports/series). For each study, patient age, sex, foreign body location, presenting signs and symptoms, utility of radiographic studies, and type of foreign body detected in the majority of study participants were determined. A "majority" of patients for each study was predetermined arbitrarily to be 2/3 of the studied population. The majority of patients in each observational study was determined to be: male (87% of all studies) and age <5 years (95% of all studies). Aspirated foreign bodies were mostly detected in the right main bronchus foreign body (72% of all studies), and there were abnormal radiographic signs (81% of all studies) at the time of evaluation. Food-object foreign bodies were the most frequent factors associated with choking (94% of all studies). Childhood aspiration of food-objects is a significant public health issue. Although there is substantial legislation regulating non-food items that pose a choking hazard, equivalent guidelines do not exist for high-risk foods. Our study identifies and confirms several risk factors for pediatric FBA events. In doing so, it echoes the concerns and suggestions of various groups in supporting the development of legislation which may reduce the incidence of food-object aspiration. Copyright © 2013. Published by Elsevier Ireland Ltd.

An integrated pathway system modeling of Saccharomyces cerevisiae HOG pathway: a Petri net based approach.

PubMed

Tomar, Namrata; Choudhury, Olivia; Chakrabarty, Ankush; De, Rajat K

2013-02-01

Biochemical networks comprise many diverse components and interactions between them. It has intracellular signaling, metabolic and gene regulatory pathways which are highly integrated and whose responses are elicited by extracellular actions. Previous modeling techniques mostly consider each pathway independently without focusing on the interrelation of these which actually functions as a single system. In this paper, we propose an approach of modeling an integrated pathway using an event-driven modeling tool, i.e., Petri nets (PNs). PNs have the ability to simulate the dynamics of the system with high levels of accuracy. The integrated set of signaling, regulatory and metabolic reactions involved in Saccharomyces cerevisiae's HOG pathway has been collected from the literature. The kinetic parameter values have been used for transition firings. The dynamics of the system has been simulated and the concentrations of major biological species over time have been observed. The phenotypic characteristics of the integrated system have been investigated under two conditions, viz., under the absence and presence of osmotic pressure. The results have been validated favorably with the existing experimental results. We have also compared our study with the study of idFBA (Lee et al., PLoS Comput Biol 4:e1000-e1086, 2008) and pointed out the differences between both studies. We have simulated and monitored concentrations of multiple biological entities over time and also incorporated feedback inhibition by Ptp2 which has not been included in the idFBA study. We have concluded that our study is the first to the best of our knowledge to model signaling, metabolic and regulatory events in an integrated form through PN model framework. This study is useful in computational simulation of system dynamics for integrated pathways as there are growing evidences that the malfunctioning of the interplay among these pathways is associated with disease.

Age of Onset of Blindness and the Development of the Semantics of Color Names.

ERIC Educational Resources Information Center

Marmor, Gloria Strauss

The relationship between age of onset of blindness and development of knowledge of color relations was examined with 16 college students who had been born totally blind, 16 who had been blinded totally at approximately 15 years of age, and 16 who had normal vision. Ss were asked to judge the similarities between color names, and judgments were…

Born in Hope and Controversy: The Challenges of Infusing Sustainability in the Campus Operations and Curriculum at Florida Gulf Coast University

ERIC Educational Resources Information Center

Wohlpart, A. James; Shepard, Joseph; Corcoran, Peter Blaze

2009-01-01

Florida Gulf Coast University, located in southwest Florida in the United States, opened its doors in 1997 with approximately 1,500 students as the tenth institution in the State University System. The site of the campus was a topic of disagreement between proponents of economic growth and development and proponents of sustainability and…

SAR Imaging through the Earth’s Ionosphere

DTIC Science & Technology

2013-11-06

or, otherwise, if polarimetry puts too high of a demand on storage, downlink capacity, etc.), then the approach based on the Faraday rotation is not...reflected fields for both are the same in the first Born approximation. Modern practical applications of radar polarimetry employ different empirical and...Fruneau, and J.-P. Rudant. Classification of tropical vegetation using multifrequency partial SAR polarimetry . IEEE Geoscience and Remote Sensing Letters

Encouraging the next generation into land-based industries.

PubMed

Rowarth, Js

2008-12-01

Members of the Y-Generation (born between approximately 1978 and 1994) have expectations of careers, rewards and 'work-life balance' that are very different from those of previous generations. This paper discusses these differences, how the land-based industries can position in order to offer 'the career path of choice', and how doing so will be of benefit not only to employers but also to New Zealand.

Generational Differences in Knowledge Markets

DTIC Science & Technology

2010-03-01

and Generation X generations. Following Generation X, Generation Y , or the Millennial Generation, includes those born between 1979 and 1994. The...positions but their numbers are small—approximately half the Baby Boomer population—and they’ll be leading Generation Y which is three times their size...boom” resulted in the 98.8 million-strong Generation Y (Sincavage, 2004). The resulting unevenness of the population distribution by age in the

Genetic evaluation of weaning weight and probability of lambing at 1 year of age in Targhee lambs

USDA-ARS?s Scientific Manuscript database

The objective of this study was to investigate genetic control of 120-day weaning weight and the probability of lambing at 1 year of age in Targhee ewe lambs. Records of 5,967 ewe lambs born from 1989 to 2012 and first exposed to rams for breeding at approximately 7 months of age were analyzed. Reco...

Racial Gaps in Early Childhood: Socio-Emotional Health, Developmental, and Educational Outcomes among African-American Boys. Report

ERIC Educational Resources Information Center

Aratani, Yumiko; Wight, Vanessa R.; Cooper, Janice L.

2011-01-01

This study uses the Early Childhood Longitudinal Study-Birth Cohort (child-B) data, collected by the National Center for Education Statistics in the U.S. Department of Education. The EC LS-B is a nationally representative longitudinal study of approximately 11,000 children who were born in 2001. The children in the EC LS-B have been followed…

Pleural mesothelioma and lung cancer risks in relation to occupational history and asbestos lung burden.

PubMed

Gilham, Clare; Rake, Christine; Burdett, Garry; Nicholson, Andrew G; Davison, Leslie; Franchini, Angelo; Carpenter, James; Hodgson, John; Darnton, Andrew; Peto, Julian

2016-05-01

We have conducted a population-based study of pleural mesothelioma patients with occupational histories and measured asbestos lung burdens in occupationally exposed workers and in the general population. The relationship between lung burden and risk, particularly at environmental exposure levels, will enable future mesothelioma rates in people born after 1965 who never installed asbestos to be predicted from their asbestos lung burdens. Following personal interview asbestos fibres longer than 5 µm were counted by transmission electron microscopy in lung samples obtained from 133 patients with mesothelioma and 262 patients with lung cancer. ORs for mesothelioma were converted to lifetime risks. Lifetime mesothelioma risk is approximately 0.02% per 1000 amphibole fibres per gram of dry lung tissue over a more than 100-fold range, from 1 to 4 in the most heavily exposed building workers to less than 1 in 500 in most of the population. The asbestos fibres counted were amosite (75%), crocidolite (18%), other amphiboles (5%) and chrysotile (2%). The approximate linearity of the dose-response together with lung burden measurements in younger people will provide reasonably reliable predictions of future mesothelioma rates in those born since 1965 whose risks cannot yet be seen in national rates. Burdens in those born more recently will indicate the continuing occupational and environmental hazards under current asbestos control regulations. Our results confirm the major contribution of amosite to UK mesothelioma incidence and the substantial contribution of non-occupational exposure, particularly in women. 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/

Born scattering of long-period body waves

NASA Astrophysics Data System (ADS)

Dalkolmo, Jörg; Friederich, Wolfgang

2000-09-01

The Born approximation is applied to the modelling of the propagation of deeply turning long-period body waves through heterogeneities in the lowermost mantle. We use an exact Green's function for a spherically symmetric earth model that also satisfies the appropriate boundary conditions at internal boundaries and the surface of the earth. The scattered displacement field is obtained by a numerical quadrature of the product of the Green's function, the exciting wavefield and structural perturbations. We study three examples: scattering of long-period P waves from a plume rising from the core-mantle boundary (CMB), generation of long-period precursors to PKIKP by strong, localized scatterers at the CMB, and propagation of core-diffracted P waves through large-scale heterogeneities in D''. The main results are as follows: (1) the signals scattered from a realistic plume are small with relative amplitudes of less than 2 per cent at a period of 20s, rendering plume detection a fairly difficult task; (2) strong heterogeneities at the CMB of appropriate size may produce observable long-period precursors to PKIKP in spite of the presence of a diffraction from the PKP-B caustic; (3) core-diffracted P waves (Pdiff) are sensitive to structure in D'' far off the geometrical ray path and also far beyond the entry and exit points of the ray into and out of D'' sensitivity kernels exhibit ring-shaped patterns of alternating sign reminiscent of Fresnel zones; (4) Pdiff also shows a non-negligible sensitivity to shear wave velocity in D'' (5) down to periods of 40s, the Born approximation is sufficiently accurate to allow waveform modelling of Pdiff through large-scale heterogeneities in D'' of up to 5 per cent.

Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy.

PubMed

McKemmish, Laura K; McKenzie, Ross H; Hush, Noel S; Reimers, Jeffrey R

2015-10-14

Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion, qualitatively differently behavior is found compared to traditional properties of the density matrix and hence entanglement provides new information about system properties. For chemical reactions, this type of entanglement simply builds up as the transition-state region is crossed. It is robust to small changes in parameter values and is therefore more attractive for making quantum qubits than is the related fragile ground-state entanglement, provided that coherent motion at the transition state can be sustained.

Direct Measurement of Wave Kernels in Time-Distance Helioseismology

NASA Technical Reports Server (NTRS)

Duvall, T. L., Jr.

2006-01-01

Solar f-mode waves are surface-gravity waves which propagate horizontally in a thin layer near the photosphere with a dispersion relation approximately that of deep water waves. At the power maximum near 3 mHz, the wavelength of 5 Mm is large enough for various wave scattering properties to be observable. Gizon and Birch (2002,ApJ,571,966)h ave calculated kernels, in the Born approximation, for the sensitivity of wave travel times to local changes in damping rate and source strength. In this work, using isolated small magnetic features as approximate point-sourc'e scatterers, such a kernel has been measured. The observed kernel contains similar features to a theoretical damping kernel but not for a source kernel. A full understanding of the effect of small magnetic features on the waves will require more detailed modeling.

Genetic correlations between body weight change and reproduction traits in Merino ewes depend on age.

PubMed

Rose, G; Mulder, H A; van der Werf, J H J; Thompson, A N; van Arendonk, J A M

2014-08-01

Merino sheep in Australia experience periods of variable feed supply. Merino sheep can be bred to be more resilient to this variation by losing less BW when grazing poor quality pasture and gaining more BW when grazing good quality pasture. Therefore, selection on BW change might be economically attractive but correlations with other traits in the breeding objective need to be known. The genetic correlations (rg) between BW, BW change, and reproduction were estimated using records from approximately 7,350 fully pedigreed Merino ewes managed at Katanning in Western Australia. Number of lambs and total weight of lambs born and weaned were measured on approximately 5,300 2-yr-old ewes, approximately 4,900 3-yr-old ewes, and approximately 3,600 4-yr-old ewes. On a proportion of these ewes BW change was measured: approximately 1,950 2-yr-old ewes, approximately 1,500 3-yr-old ewes, and approximately 1,100 4-yr-old ewes. The BW measurements were for 3 periods. The first period was during mating period over 42 d on poor pasture. The second period was during pregnancy over 90 d for ewes that got pregnant on poor and medium quality pasture. The third period was during lactation over 130 d for ewes that weaned a lamb on good quality pasture. Genetic correlations between weight change and reproduction were estimated within age classes. Genetic correlations were tested to be significantly greater magnitude than 0 using likelihood ratio tests. Nearly all BW had significant positive genetic correlations with all reproduction traits. In 2-yr-old ewes, BW change during the mating period had a positive genetic correlation with number of lambs weaned (rg = 0.58); BW change during pregnancy had a positive genetic correlation with total weight of lambs born (rg = 0.33) and a negative genetic correlation with number of lambs weaned (rg = -0.49). All other genetic correlations were not significantly greater magnitude than 0 but estimates of genetic correlations for 3-yr-old ewes were generally consistent with these findings. The direction of the genetic correlations mostly coincided with the energy requirements of the ewes and the stage of maturity of the ewes. In conclusion, optimized selection strategies on BW changes to increase resilience will depend on the genetic correlations with reproduction and are dependent on age.

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.