Multifunctional curing agents and their use in improving strength of composites containing carbon fibers embedded in a polymeric matrix

DOEpatents

Vautard, Frederic; Ozcan, Soydan

2017-04-11

A functionalized carbon fiber having covalently bound on its surface a sizing agent containing epoxy groups, at least some of which are engaged in covalent bonds with crosslinking molecules, wherein each of said crosslinking molecules possesses at least two epoxy-reactive groups and at least one free functional group reactive with functional groups of a polymer matrix in which the carbon fiber is to be incorporated, wherein at least a portion of said crosslinking molecules are engaged, via at least two of their epoxy-reactive groups, in crosslinking bonds between at least two epoxy groups of the sizing agent. Composites comprised of these functionalized carbon fibers embedded in a polymeric matrix are also described. Methods for producing the functionalized carbon fibers and composites thereof are also described.

Site-Specific Attachment of gold Nanoparticles to DNA Templates

DTIC Science & Technology

2001-01-01

1 -ethyl- 3 -( 3 - dimethylaminopropyl ) carbodiimide hydrochloride (Pierce) and -2.0rmg N...functionalized gold nanoparticles. The gold particles were covalently bound to the amino groups on the DNA using standard 1 -ethyl- 3 - ( 3 - dimethylaminopropyl ...nm). The reaction between the amino group on the DNA and the carboxyl group on the gold particle was facilitated by 1 -ethyl- 3 -( 3 - dimethylaminopropyl

Integration of two RAB5 groups during endosomal transport in plants

PubMed Central

Ebine, Kazuo; Choi, Seung-won; Ichinose, Sakura; Uemura, Tomohiro; Nakano, Akihiko

2018-01-01

RAB5 is a key regulator of endosomal functions in eukaryotic cells. Plants possess two different RAB5 groups, canonical and plant-unique types, which act via unknown counteracting mechanisms. Here, we identified an effector molecule of the plant-unique RAB5 in Arabidopsis thaliana, ARA6, which we designated PLANT-UNIQUE RAB5 EFFECTOR 2 (PUF2). Preferential colocalization with canonical RAB5 on endosomes and genetic interaction analysis indicated that PUF2 coordinates vacuolar transport with canonical RAB5, although PUF2 was identified as an effector of ARA6. Competitive binding of PUF2 with GTP-bound ARA6 and GDP-bound canonical RAB5, together interacting with the shared activating factor VPS9a, showed that ARA6 negatively regulates canonical RAB5-mediated vacuolar transport by titrating PUF2 and VPS9a. These results suggest a unique and unprecedented function for a RAB effector involving the integration of two RAB groups to orchestrate endosomal trafficking in plant cells. PMID:29749929

Synthesis and Applications of (ONO Pincer)Ruthenium‐Complex‐Bound Norvalines

PubMed Central

Yokoi, Tomoya; Yoshida, Ryota; Ogata, Kazuki; Hashizume, Daisuke; Yasuda, Nobuhiro; Sadakane, Koichiro

2016-01-01

Abstract Two (ONO pincer)ruthenium‐complex‐bound norvalines, Boc−[Ru(pydc)(terpy)]Nva−OMe (1; Boc=tert‐butyloxycarbonyl, terpy=terpyridyl, Nva=norvaline) and Boc−[Ru(pydc)(tBu‐terpy)]Nva−OMe (5), were successfully synthesized and their molecular structures and absolute configurations were unequivocally determined by single‐crystal X‐ray diffraction. The robustness of the pincer Ru complexes and norvaline scaffolds against acidic/basic, oxidizing, and high‐temperature conditions enabled us to perform selective transformations of the N‐Boc and C−OMe termini into various functional groups, such as alkyl amide, alkyl urea, and polyether groups, without the loss of the Ru center or enantiomeric purity. The resulting dialkylated Ru‐bound norvaline, n‐C11H23CO−l‐[Ru(pydc)(terpy)]Nva−NH‐n‐C11H23 (l‐4) was found to have excellent self‐assembly properties in organic solvents, thereby affording the corresponding supramolecular gels. Ru‐bound norvaline l‐1 exhibited a higher catalytic activity for the oxidation of alcohols by H2O2 than parent complex [Ru(pydc)(terpy)] (11 a). PMID:26879368

Explicit construction of quadratic Lyapunov functions for the small gain, positivity, circle, and Popov theorems and their application to robust stability

NASA Technical Reports Server (NTRS)

Haddad, Wassim M.; Bernstein, Dennis S.

1991-01-01

Lyapunov function proofs of sufficient conditions for asymptotic stability are given for feedback interconnections of bounded real and positive real transfer functions. Two cases are considered: (1) a proper bounded real (resp., positive real) transfer function with a bounded real (resp., positive real) time-varying memoryless nonlinearity; and (2) two strictly proper bounded real (resp., positive real) transfer functions. A similar treatment is given for the circle and Popov theorems. Application of these results to robust stability with time-varying bounded real, positive real, and sector-bounded uncertainty is discussed.

Interaction of angiotensin-converting enzyme (ACE) with membrane-bound carboxypeptidase M (CPM) - a new function of ACE.

PubMed

Sun, Xiaoou; Wiesner, Burkhard; Lorenz, Dorothea; Papsdorf, Gisela; Pankow, Kristin; Wang, Po; Dietrich, Nils; Siems, Wolf-Eberhard; Maul, Björn

2008-12-01

Angiotensin-converting enzyme (ACE) demonstrates, besides its typical dipeptidyl-carboxypeptidase activity, several unusual functions. Here, we demonstrate with molecular, biochemical, and cellular techniques that the somatic wild-type murine ACE (mACE), stably transfected in Chinese Hamster Ovary (CHO) or Madin-Darby Canine Kidney (MDCK) cells, interacts with endogenous membranal co-localized carboxypeptidase M (CPM). CPM belongs to the group of glycosylphosphatidylinositol (GPI)-anchored proteins. Here we report that ACE, completely independent of its known dipeptidase activities, has GPI-targeted properties. Our results indicate that the spatial proximity between mACE and the endogenous CPM enables an ACE-evoked release of CPM. These results are discussed with respect to the recently proposed GPI-ase activity and function of sperm-bound ACE.

Effects of Biotin Deficiency on Biotinylated Proteins and Biotin-Related Genes in the Rat Brain.

PubMed

Yuasa, Masahiro; Aoyama, Yuki; Shimada, Ryoko; Sawamura, Hiromi; Ebara, Shuhei; Negoro, Munetaka; Fukui, Toru; Watanabe, Toshiaki

2016-01-01

Biotin is a water-soluble vitamin that functions as a cofactor for biotin-dependent carboxylases. The biochemical and physiological roles of biotin in brain regions have not yet been investigated sufficiently in vivo. Thus, in order to clarify the function of biotin in the brain, we herein examined biotin contents, biotinylated protein expression (e.g. holocarboxylases), and biotin-related gene expression in the brain of biotin-deficient rats. Three-week-old male Wistar rats were divided into a control group, biotin-deficient group, and pair-fed group. Rats were fed experimental diets from 3 wk old for 8 wk, and the cortex, hippocampus, striatum, hypothalamus, and cerebellum were then collected. In the biotin-deficient group, the maintenance of total biotin and holocarboxylases, increases in the bound form of biotin and biotinidase activity, and the expression of an unknown biotinylated protein were observed in the cortex. In other regions, total and free biotin contents decreased, holocarboxylase expression was maintained, and bound biotin and biotinidase activity remained unchanged. Biotin-related gene (pyruvate carboxylase, sodium-dependent multivitamin transporter, holocarboxylase synthetase, and biotinidase) expression in the cortex and hippocampus also remained unchanged among the dietary groups. These results suggest that biotin may be related to cortex functions by binding protein, and the effects of a biotin deficiency and the importance of biotin differ among the different brain regions.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

The Phosphorylation of Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) by Engineered Surfaces with Electrostatically or Covalently Immobilized VEGF

PubMed Central

Anderson, Sean M.; Chen, Tom T.; Iruela-Arispe, M. Luisa; Segura, Tatiana

2010-01-01

Growth factors are a class of signaling proteins that direct cell fate through interaction with cell surface receptors. Although a myriad of possible cell fates stem from a growth factor binding to its receptor, the signaling cascades that result in one fate over another are still being elucidated. One possible mechanism by which nature modulates growth factor signaling is through the method of presentation of the growth factor – soluble or immobilized (matrix bound). Here we present the methodology to study signaling of soluble versus immobilized VEGF through VEGFR-2. We have designed a strategy to covalently immobilize VEGF using its heparin-binding domain to orient the molecule (bind) and a secondary functional group to mediate covalent binding (lock). This bind-and-lock approach aims to allow VEGF to assume a bioactive orientation before covalent immobilization. Surface plasmon resonance (SPR) demonstrated heparin and VEGF binding with surface densities of 60 ng/cm2 and 100 pg/cm2, respectively. ELISA experiments confirmed VEGF surface density and showed that electrostatically bound VEGF releases in cell medium and heparin solutions while covalently bound VEGF remains immobilized. Electrostatically bound VEGF and covalently bound VEGF phosphorylate VEGFR-2 in both VEGFR-2 transfected cells and VEGFR-2 endogenously producing cells. HUVECs plated on VEGF functionalized surfaces showed different morphologies between surface-bound VEGF and soluble VEGF. The surfaces synthesized in these studies allow for the study of VEGF/VEGFR-2 signaling induced by covalently bound, electrostatically bound, and soluble VEGF and may provide further insight into the design of materials for the generation of a mature and stable vasculature. PMID:19540581

Dissecting Orthosteric Contacts for a Reverse-Fragment-Based Ligand Design.

PubMed

Chandramohan, Arun; Tulsian, Nikhil K; Anand, Ganesh S

2017-08-01

Orthosteric sites on proteins are formed typically from noncontiguous interacting sites in three-dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the local secondary structure. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD). In this study, we describe an approach of progressive unfolding of a target protein using a gradient of denaturant urea to reveal the individual energetic contributions of various ligand-functional groups to the affinity of the entire ligand. Through calibrated unfolding of two protein-ligand systems: cAMP-bound regulatory subunit of Protein Kinase A (RIα) and IBMX-bound phosphodiesterase8 (PDE8), monitored by amide hydrogen-deuterium exchange mass spectrometry, we show progressive disruption of individual orthosteric contacts in the ligand binding sites, allowing us to rank the energetic contributions of these individual interactions. In the two cAMP-binding sites of RIα, exocyclic phosphate oxygens of cAMP were identified to mediate stronger interactions than ribose 2'-OH in both the RIα-cAMP binding interfaces. Further, we have also ranked the relative contributions of the different functional groups of IBMX based on their interactions with the orthosteric residues of PDE8. This strategy for deconstruction of individual binding sites and identification of the strongest functional group interaction in enzyme orthosteric sites offers a rational starting point for FBDD.

Evidence of mercury trapping in biofilm-EPS and mer operon-based volatilization of inorganic mercury in a marine bacterium Bacillus cereus BW-201B.

PubMed

Dash, Hirak R; Basu, Subham; Das, Surajit

2017-04-01

Biofilm-forming mercury-resistant marine bacterium Bacillus cereus BW-201B has been explored to evident that the bacterial biofilm-EPS (exopolymers) trap inorganic mercury but subsequently release EPS-bound mercury for induction of mer operon-mediated volatilization of inorganic mercury. The isolate was able to tolerate 50 ppm of mercury and forms biofilm in presence of mercury. mer operon-mediated volatilization was confirmed, and -SH was found to be the key functional group of bacterial EPS responsible for mercury binding. Biofilm-EPS-bound mercury was found to be internalized to the bacterial system as confirmed by reversible conformational change of -SH group and increased expression level of merA gene in a timescale experiment. Biofilm-EPS trapped Hg after 24 h of incubation, and by 96 h, the volatilization process reaches to its optimum confirming the internalization of EPS-bound mercury to the bacterial cells. Biofilm disintegration at the same time corroborates the results.

The preventive effect of the bounding exercise programme on hamstring injuries in amateur soccer players: the design of a randomized controlled trial.

PubMed

Van de Hoef, S; Huisstede, B M A; Brink, M S; de Vries, N; Goedhart, E A; Backx, F J G

2017-08-22

Hamstring injuries are the most common muscle injury in amateur and professional soccer. Most hamstring injuries occur in the late swing phase, when the hamstring undergoes a stretch-shortening cycle and the hamstring does a significant amount of eccentric work. The incidence of these injuries has not decreased despite there being effective injury prevention programmes focusing on improving eccentric hamstring strength. As this might be because of poor compliance, a more functional injury prevention exercise programme that focuses on the stretch-shortening cycle might facilitate compliance. In this study, a bounding exercise programme consisting of functional plyometric exercises is being evaluated. A cluster-randomized controlled trial (RCT). Male amateur soccer teams (players aged 18-45 years) have been randomly allocated to intervention and control groups. Both groups are continuing regular soccer training and the intervention group is additionally performing a 12-week bounding exercise programme (BEP), consisting of a gradual build up and maintenance programme for the entire soccer season. The primary outcome is hamstring injury incidence. Secondary outcome is compliance with the BEP during the soccer season and 3 months thereafter. Despite effective hamstring injury prevention programmes, the incidence of these injuries remains high in soccer. As poor compliance with these programmes may be an issue, a new plyometric exercise programme may encourage long-term compliance and is expected to enhance sprinting and jumping performance besides preventing hamstring injuries. NTR6129 . Retrospectively registered on 1 November 2016.

Determination of copper binding in Pseudomonas putida CZ1 by chemical modifications and X-ray absorption spectroscopy.

PubMed

Chen, XinCai; Shi, JiYan; Chen, YingXu; Xu, XiangHua; Chen, LiTao; Wang, Hui; Hu, TianDou

2007-03-01

Previously performed studies have shown that Pseudomonas putida CZ1 biomass can bind an appreciable amount of Cu(II) and Zn(II) ions from aqueous solutions. The mechanisms of Cu- and Zn-binding by P. putida CZ1 were ascertained by chemical modifications of the biomass followed by Fourier transform infrared and X-ray absorption spectroscopic analyses of the living or nonliving cells. A dramatic decrease in Cu(II)- and Zn(II)-binding resulted after acidic methanol esterification of the nonliving cells, indicating that carboxyl functional groups play an important role in the binding of metal to the biomaterial. X-ray absorption spectroscopy was used to determine the speciation of Cu ions bound by living and nonliving cells, as well as to elucidate which functional groups were involved in binding of the Cu ions. The X-ray absorption near-edge structure spectra analysis showed that the majority of the Cu was bound in both samples as Cu(II). The fitting results of Cu K-edge extended X-ray absorption fine structure spectra showed that N/O ligands dominated in living and nonliving cells. Therefore, by combining different techniques, our results indicate that carboxyl functional groups are the major ligands responsible for the metal binding in P. putida CZ1.

Protonation of carboxyl groups in EuDOTA-tetraamide complexes results in catalytic prototropic exchange and quenching of the CEST signal

NASA Astrophysics Data System (ADS)

Zhang, Lei; Evbuomwan, Osasere M.; Tieu, Michael; Zhao, Piyu; Martins, Andre F.; Sherry, A. Dean

2017-10-01

The CEST properties of EuDOTA-tetraamide complexes bearing pendant carboxylate and carboxyl ethyl esters were measured as a function of pH. The CEST signal from the Eu3+-bound water molecule decreased in intensity between pH 8.5 and 4.5 while the proton exchange rates (kex) increased over this same pH range. In comparison, the CEST signal in the corresponding carboxyl ester derivatives was nearly constant. Both observations are consistent with stepwise protonation of the four carboxylic acid groups over this same pH range. This indicates that negative charges on the carboxyl groups above pH 6 facilitate the formation of a strong hydrogen-bonding network in the coordination second sphere above the single Eu3+-bound water molecule, thereby decreasing prototropic exchange of protons on the bound water molecule with bulk water protons. The percentage of square antiprismatic versus twisted square antiprism coordination isomers also decreased as the appended carboxylic acid groups were positioned further away from the amide. The net effect of lowering the pH was an overall increase in kex and a quenching of the CEST signal. This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.

Ir-Catalyzed, Silyl-Directed, peri-Borylation of C-H Bonds in Fused Polycyclic Arenes and Heteroarenes.

PubMed

Su, Bo; Hartwig, John F

2018-05-20

peri-Disubstituted naphthalenes exhibit interesting physical properties and unique chemical reactivity, due to the parallel arrangement of the bonds to the two peri-disposed substituents. Regioselective installation of a functional group at the position peri to 1-substituted naphthalenes is challenging due to the steric interaction between the existing substituent and the position at which the second one would be installed. We report an iridium-catalyzed borylation of the C-H bond peri to a silyl group in naphthalenes and analogous polyaromatic hydrocarbons. The reaction occurs under mild conditions with wide functional group tolerance. The silyl group and the boryl group in the resulting products are precursors to a range of functional groups bound to the naphthalene ring through C-C, C-O, C-N, C-Br and C-Cl bonds. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-assembling multimeric nucleic acid constructs

DOEpatents

Cantor, Charles R.; Niemeyer, Christof M.; Smith, Cassandra L.; Sano, Takeshi; Hnatowich, Donald J.; Rusckowski, Mary

1999-10-12

The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

Self-assembling multimeric nucleic acid constructs

DOEpatents

Cantor, Charles R.; Niemeyer, Christof M.; Smith, Cassandra L.; Sano, Takeshi; Hnatowich, Donald J.; Rusckowski, Mary

1996-01-01

The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

Self-assembling multimeric nucleic acid constructs

DOEpatents

Cantor, C.R.; Niemeyer, C.M.; Smith, C.L.; Sano, Takeshi; Hnatowich, D.J.; Rusckowski, M.

1996-10-01

The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products. 5 figs.

Research on Bounded Rationality of Fuzzy Choice Functions

PubMed Central

Wu, Xinlin; Zhao, Yong

2014-01-01

The rationality of a fuzzy choice function is a hot research topic in the study of fuzzy choice functions. In this paper, two common fuzzy sets are studied and analyzed in the framework of the Banerjee choice function. The complete rationality and bounded rationality of fuzzy choice functions are defined based on the two fuzzy sets. An assumption is presented to study the fuzzy choice function, and especially the fuzzy choice function with bounded rationality is studied combined with some rationality conditions. Results show that the fuzzy choice function with bounded rationality also satisfies some important rationality conditions, but not vice versa. The research gives supplements to the investigation in the framework of the Banerjee choice function. PMID:24782677

Research on bounded rationality of fuzzy choice functions.

PubMed

Wu, Xinlin; Zhao, Yong

2014-01-01

The rationality of a fuzzy choice function is a hot research topic in the study of fuzzy choice functions. In this paper, two common fuzzy sets are studied and analyzed in the framework of the Banerjee choice function. The complete rationality and bounded rationality of fuzzy choice functions are defined based on the two fuzzy sets. An assumption is presented to study the fuzzy choice function, and especially the fuzzy choice function with bounded rationality is studied combined with some rationality conditions. Results show that the fuzzy choice function with bounded rationality also satisfies some important rationality conditions, but not vice versa. The research gives supplements to the investigation in the framework of the Banerjee choice function.

Molecular evidence for biodegradation of geomacromolecules

NASA Astrophysics Data System (ADS)

Jenisch-Anton, A.; Adam, P.; Michaelis, W.; Connan, J.; Herrmann, D.; Rohmer, M.; Albrecht, P.

2000-10-01

The biodegradability of macromolecular organic structures of geological origin was investigated by performing in vitro studies. Cultures of the common Nocardioides simplex were grown, first, on a high molecular weight, asymmetric thioether (1-(phytanylsulfanyl)-octadecane 1) and then on macromolecular fractions isolated from a sulfur-rich oil. Gross data indicate that bacteria convert macromolecular substances to material of higher polarity by oxidizing the abundant thioethers to sulfones and sulfoxides and by introducing new functionalities, such as carboxylic acid, keto or hydroxyl groups. Furthermore, bacteria remineralize the macromolecular structures. Bacterially induced alterations were also studied on a molecular level after chemical desulfurization of the macromolecular structure. Thus, it could be established that the amounts of linear hydrocarbons in the macromolecular structure are decreased relative to branched and cyclic structures due to a preferential bacterial attack of the linear moieties bound to the macromolecules. This is further supported by the detection of S-bound fatty acids resulting from the bacterial oxidation of S-bound n-alkanes. Moreover, N. simplex also degraded sulfur-bound steranes by oxidation of the steroid side-chain leading to S-bound steroid acids.

The wave function and minimum uncertainty function of the bound quadratic Hamiltonian system

NASA Technical Reports Server (NTRS)

Yeon, Kyu Hwang; Um, Chung IN; George, T. F.

1994-01-01

The bound quadratic Hamiltonian system is analyzed explicitly on the basis of quantum mechanics. We have derived the invariant quantity with an auxiliary equation as the classical equation of motion. With the use of this invariant it can be determined whether or not the system is bound. In bound system we have evaluated the exact eigenfunction and minimum uncertainty function through unitary transformation.

Vapor Grown Carbon Fiber/Hybrid Organic-Inorganic Matrix Composites. Nanometer-sized Silsesquiozane Phase Chemically Bound in a Matrix

DTIC Science & Technology

2006-04-28

for this work included: (1) Polyhedral oligomeric silsesquioxane chemicals (POSS macromers) of three types: those with no polymerizable group, those...Polyhedral oligomeric silsesquioxane chemicals (POSS macromers) of three types: those with no polymerizable group, those with one reactive function and...atoms and ions. Polyhedral Oligomeric Silsesquioxane/Organic Matrix Nanocomposites Major reviews of POSS polymer and copolymer chemistry. The first

Sulfonyl chlorides as an efficient tool for the postsynthetic modification of Cr-MIL-101-SO3H and CAU-1-NH2.

PubMed

Klinkebiel, Arne; Reimer, Nele; Lammert, Martin; Stock, Norbert; Lüning, Ulrich

2014-08-25

Postsynthetic modification can be used to introduce sulfonamide functionalities into MOF frameworks. Using sulfonyl chlorides as reactive intermediates, Cr-MIL-SO3H and CAU-1-NH2 have been further modified to give hitherto unknown functionalized MOFs in which a sulfonamide group is bound to the framework either by its N or its S atom.

Career Development and Personal Functioning Differences between Work-Bound and Non-Work Bound Students

ERIC Educational Resources Information Center

Creed, Peter A.; Patton, Wendy; Hood, Michelle

2010-01-01

We surveyed 506 Australian high school students on career development (exploration, planning, job-knowledge, decision-making, indecision), personal functioning (well-being, self-esteem, life satisfaction, school satisfaction) and control variables (parent education, school achievement), and tested differences among work-bound, college-bound and…

Bounds for the Eventual Positivity of Difference Functions of Partitions

NASA Astrophysics Data System (ADS)

Woodford, Roger

2007-01-01

In this paper we specialize work done by Bateman and Erdos concerning difference functions of partition functions. In particular, we are concerned with partitions into fixed powers of the primes. We show that any difference function of these partition functions is eventually increasing, and derive explicit bounds for when it will attain strictly positive values. From these bounds an asymptotic result is derived.

Hybrid microspheres

NASA Technical Reports Server (NTRS)

Yen, Richard C. K. (Inventor); Rembaum, Alan (Inventor)

1985-01-01

Substrates, particularly inert synthetic organic resin beads (10) or sheet (12) such as polystyrene are coated with a covalently bound layer (24) of polyacrolein by irradiation a solution (14) of acrolein or other aldehyde with high intensity radiation. Individual microspheres (22) are formed which attach to the surface to form the aldehyde containing layer (24). The aldehyde groups can be converted to other functional groups by reaction with materials such as hydroxylamine. Adducts of proteins such as antibodies or enzymes can be formed by direct reaction with the surface aldehyde groups.

Transfer Function Bounds for Partial-unit-memory Convolutional Codes Based on Reduced State Diagram

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

The performance of a coding system consisting of a convolutional encoder and a Viterbi decoder is analytically found by the well-known transfer function bounding technique. For the partial-unit-memory byte-oriented convolutional encoder with m sub 0 binary memory cells and (k sub 0 m sub 0) inputs, a state diagram of 2(K) (sub 0) was for the transfer function bound. A reduced state diagram of (2 (m sub 0) +1) is used for easy evaluation of transfer function bounds for partial-unit-memory codes.

A recurrent neural network for nonlinear optimization with a continuously differentiable objective function and bound constraints.

PubMed

Liang, X B; Wang, J

2000-01-01

This paper presents a continuous-time recurrent neural-network model for nonlinear optimization with any continuously differentiable objective function and bound constraints. Quadratic optimization with bound constraints is a special problem which can be solved by the recurrent neural network. The proposed recurrent neural network has the following characteristics. 1) It is regular in the sense that any optimum of the objective function with bound constraints is also an equilibrium point of the neural network. If the objective function to be minimized is convex, then the recurrent neural network is complete in the sense that the set of optima of the function with bound constraints coincides with the set of equilibria of the neural network. 2) The recurrent neural network is primal and quasiconvergent in the sense that its trajectory cannot escape from the feasible region and will converge to the set of equilibria of the neural network for any initial point in the feasible bound region. 3) The recurrent neural network has an attractivity property in the sense that its trajectory will eventually converge to the feasible region for any initial states even at outside of the bounded feasible region. 4) For minimizing any strictly convex quadratic objective function subject to bound constraints, the recurrent neural network is globally exponentially stable for almost any positive network parameters. Simulation results are given to demonstrate the convergence and performance of the proposed recurrent neural network for nonlinear optimization with bound constraints.

Aminopropyl-modified magnesium-phyllosilicates: layered solids with tailored interlayer access and reactivity.

PubMed

Ferreira, Ricardo B; da Silva, César R; Pastore, Heloise O

2008-12-16

Despite its wide application, the synthesis of aminopropyl-modified magnesium-phyllosilicates was known only in the case where every silicon atom bore an organic pending group. This paper shows the preparation of aminopropyl-modified talc where tailored amounts of silicon atoms are bound to an aminopropyl group. The decrease in the concentration of the organoamino group leaves a proportional concentration of interlayer SiOH groups that can be used to react with other silylation agents. The amino group reacts with CO2, forming a carbamate functionality; it seems that the presence of this group avoids delamination in water as performed for the parent compound. Bearing in mind that the aminopropyl group can be changed by other groups, the present synthesis strategy demonstrates ways to produce solids with controlled surface properties with interlayer amino and SiOH groups in variable concentrations, allowing formation of several other interlayer functionalities.

Variational bounds on the temperature distribution

NASA Astrophysics Data System (ADS)

Kalikstein, Kalman; Spruch, Larry; Baider, Alberto

1984-02-01

Upper and lower stationary or variational bounds are obtained for functions which satisfy parabolic linear differential equations. (The error in the bound, that is, the difference between the bound on the function and the function itself, is of second order in the error in the input function, and the error is of known sign.) The method is applicable to a range of functions associated with equalization processes, including heat conduction, mass diffusion, electric conduction, fluid friction, the slowing down of neutrons, and certain limiting forms of the random walk problem, under conditions which are not unduly restrictive: in heat conduction, for example, we do not allow the thermal coefficients or the boundary conditions to depend upon the temperature, but the thermal coefficients can be functions of space and time and the geometry is unrestricted. The variational bounds follow from a maximum principle obeyed by the solutions of these equations.

POLAR ORGANIC OXYGENATES IN PM2.5 AT A SOUTHEASTERN SITE IN THE UNITED STATES

EPA Science Inventory

A field study was undertaken in Research Triangle Park, NC, USA, during the summer of 2000 to identify classes of polar oxygenates in PM2.5 containing carbonyl and/or hydroxyl functional groups and, to the extent possible, determine the individual particle-bound oxygenates that m...

Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1

PubMed Central

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; Ramanathan, Arvind; Zhang, Weixing; Shelat, Anang A.; Zuo, Jian; Kriwacki, Richard W.

2015-01-01

Disordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27Kip1 (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A). PMID:26507530

Stability of proton-bound clusters of alkyl alcohols, aldehydes and ketones in Ion Mobility Spectrometry.

PubMed

Jurado-Campos, Natividad; Garrido-Delgado, Rocío; Martínez-Haya, Bruno; Eiceman, Gary A; Arce, Lourdes

2018-08-01

Significant substances in emerging applications of ion mobility spectrometry such as breath analysis for clinical diagnostics and headspace analysis for food purity include low molar mass alcohols, ketones, aldehydes and esters which produce mobility spectra containing protonated monomers and proton-bound dimers. Spectra for all n- alcohols, aldehydes and ketones from carbon number three to eight exhibited protonated monomers and proton-bound dimers with ion drift times of 6.5-13.3 ms at ambient pressure and from 35° to 80 °C in nitrogen. Only n-alcohols from 1-pentanol to 1-octanol produced proton-bound trimers which were sufficiently stable to be observed at these temperatures and drift times of 12.8-16.3 ms. Polar functional groups were protected in compact structures in ab initio models for proton-bound dimers of alcohols, ketones and aldehydes. Only alcohols formed a V-shaped arrangement for proton-bound trimers strengthening ion stability and lifetime. In contrast, models for proton-bound trimers of aldehydes and ketones showed association of the third neutral through weak, non-specific, long-range interactions consistent with ion dissociation in the ion mobility drift tube before arriving at the detector. Collision cross sections derived from reduced mobility coefficients in nitrogen gas atmosphere support the predicted ion structures and approximate degrees of hydration. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamics of bound water molecules in fullerenol at different hydration levels

NASA Astrophysics Data System (ADS)

Wang, Yilin; Robey, Steven; Reutt-Robey, Janice

Fullerenols, polyhydroxylated fullerenes, are of great interest as promising materials in medical application because of their high water solubility and biocompatibility. Fullerenols are highly responsive to their environment, for example, they readily undergo hydration under ambient conditions. Understanding the dynamics of water molecules bound to fullerenols, and the interplay between water molecules and fullerenols is important in realizing biological function. Here, broadband dielectric spectroscopy (BDS), was performed on a fullerenol with 44 hydroxyl groups, C60(OH)44, between 300 K and 340 K. At room temperature and under ambient conditions, C60(OH)44 is hydrated, releasing bound water molecules with increasing temperature, as quantified by thermal gravimetric analysis (TGA) measurements. At room temperature, a dielectric band due to collective bulk-like dynamics of the bound water molecules is observed. The relaxation peak of the water molecules shifts to higher frequency with increasing of temperature, reflecting the dynamics of bound water. Upon loss of water molecules, either thermally induced or vacuum induced, the relaxation peak shifts to lower frequency. The stoichiometric relationship between the dielectric properties of the hydrated fullerenol and the interplay between the bound water molecules and C60(OH)44 will be discussed. This work was supported by the National Science Foundation (NSF) under Award Number 1310380.

Turning Around along the Cosmic Web

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Yepes, Gustavo

2016-12-01

A bound violation designates a case in which the turnaround radius of a bound object exceeds the upper limit imposed by the spherical collapse model based on the standard ΛCDM paradigm. Given that the turnaround radius of a bound object is a stochastic quantity and that the spherical model overly simplifies the true gravitational collapse, which actually proceeds anisotropically along the cosmic web, the rarity of the occurrence of a bound violation may depend on the web environment. Assuming a Planck cosmology, we numerically construct the bound-zone peculiar velocity profiles along the cosmic web (filaments and sheets) around the isolated groups with virial mass {M}{{v}}≥slant 3× {10}13 {h}-1 {M}⊙ identified in the Small MultiDark Planck simulations and determine the radial distances at which their peculiar velocities equal the Hubble expansion speed as the turnaround radii of the groups. It is found that although the average turnaround radii of the isolated groups are well below the spherical bound limit on all mass scales, the bound violations are not forbidden for individual groups, and the cosmic web has an effect of reducing the rarity of the occurrence of a bound violation. Explaining that the spherical bound limit on the turnaround radius in fact represents the threshold distance up to which the intervention of the external gravitational field in the bound-zone peculiar velocity profiles around the nonisolated groups stays negligible, we discuss the possibility of using the threshold distance scale to constrain locally the equation of state of dark energy.

Verifying the error bound of numerical computation implemented in computer systems

DOEpatents

Sawada, Jun

2013-03-12

A verification tool receives a finite precision definition for an approximation of an infinite precision numerical function implemented in a processor in the form of a polynomial of bounded functions. The verification tool receives a domain for verifying outputs of segments associated with the infinite precision numerical function. The verification tool splits the domain into at least two segments, wherein each segment is non-overlapping with any other segment and converts, for each segment, a polynomial of bounded functions for the segment to a simplified formula comprising a polynomial, an inequality, and a constant for a selected segment. The verification tool calculates upper bounds of the polynomial for the at least two segments, beginning with the selected segment and reports the segments that violate a bounding condition.

Universal bounds on current fluctuations.

PubMed

Pietzonka, Patrick; Barato, Andre C; Seifert, Udo

2016-05-01

For current fluctuations in nonequilibrium steady states of Markovian processes, we derive four different universal bounds valid beyond the Gaussian regime. Different variants of these bounds apply to either the entropy change or any individual current, e.g., the rate of substrate consumption in a chemical reaction or the electron current in an electronic device. The bounds vary with respect to their degree of universality and tightness. A universal parabolic bound on the generating function of an arbitrary current depends solely on the average entropy production. A second, stronger bound requires knowledge both of the thermodynamic forces that drive the system and of the topology of the network of states. These two bounds are conjectures based on extensive numerics. An exponential bound that depends only on the average entropy production and the average number of transitions per time is rigorously proved. This bound has no obvious relation to the parabolic bound but it is typically tighter further away from equilibrium. An asymptotic bound that depends on the specific transition rates and becomes tight for large fluctuations is also derived. This bound allows for the prediction of the asymptotic growth of the generating function. Even though our results are restricted to networks with a finite number of states, we show that the parabolic bound is also valid for three paradigmatic examples of driven diffusive systems for which the generating function can be calculated using the additivity principle. Our bounds provide a general class of constraints for nonequilibrium systems.

Novel Function of the Fanconi Anemia Group J or RECQ1 Helicase to Disrupt Protein-DNA Complexes in a Replication Protein A-stimulated Manner*

PubMed Central

Sommers, Joshua A.; Banerjee, Taraswi; Hinds, Twila; Wan, Bingbing; Wold, Marc S.; Lei, Ming; Brosh, Robert M.

2014-01-01

Understanding how cellular machinery deals with chromosomal genome complexity is an important question because protein bound to DNA may affect various cellular processes of nucleic acid metabolism. DNA helicases are at the forefront of such processes, yet there is only limited knowledge how they remodel protein-DNA complexes and how these mechanisms are regulated. We have determined that representative human RecQ and Fe-S cluster DNA helicases are potently blocked by a protein-DNA interaction. The Fanconi anemia group J (FANCJ) helicase partners with the single-stranded DNA-binding protein replication protein A (RPA) to displace BamHI-E111A bound to duplex DNA in a specific manner. Protein displacement was dependent on the ATPase-driven function of the helicase and unique properties of RPA. Further biochemical studies demonstrated that the shelterin proteins TRF1 and TRF2, which preferentially bind the telomeric repeat found at chromosome ends, effectively block FANCJ from unwinding the forked duplex telomeric substrate. RPA, but not the Escherichia coli single-stranded DNA-binding protein or shelterin factor Pot1, stimulated FANCJ ejection of TRF1 from the telomeric DNA substrate. FANCJ was also able to displace TRF2 from the telomeric substrate in an RPA-dependent manner. The stimulation of helicase-catalyzed protein displacement is also observed with the DNA helicase RECQ1, suggesting a conserved functional interaction of RPA-interacting helicases. These findings suggest that partnerships between RPA and interacting human DNA helicases may greatly enhance their ability to dislodge proteins bound to duplex DNA, an activity that is likely to be highly relevant to their biological roles in DNA metabolism. PMID:24895130

Protective Effect of Free and Bound Polyphenol Extracts from Ginger (Zingiber officinale Roscoe) on the Hepatic Antioxidant and Some Carbohydrate Metabolizing Enzymes of Streptozotocin-Induced Diabetic Rats

PubMed Central

Kazeem, Mutiu Idowu; Akanji, Musbau Adewunmi; Yakubu, Musa Toyin; Ashafa, Anofi Omotayo Tom

2013-01-01

This study investigated the hepatoprotective effects of polyphenols from Zingiber officinale on streptozotocin-induced diabetic rats by assessing liver antioxidant enzymes, carbohydrate-metabolizing enzymes and liver function indices. Initial oral glucose tolerance test was conducted using 125 mg/kg, 250 mg/kg, and 500 mg/kg body weight of both free and bound polyphenols from Z. officinale. 28 day daily oral administration of 500 mg/kg body weight of free and bound polyphenols from Z. officinale to streptozotocin-induced (50 mg/kg) diabetic rats significantly reduced (P < 0.05) the fasting blood glucose compared to control groups. There was significant increase (P < 0.05) in the antioxidant enzymes activities in the animals treated with both polyphenols. Similarly, the polyphenols normalised the activities of some carbohydrate metabolic enzymes (hexokinase and phosphofructokinase) in the liver of the rats treated with it and significantly reduced (P < 0.05) the activities of liver function enzymes. The results from the present study have shown that both free and bound polyphenols from Z. officinale especially the free polyphenol could ameliorate liver disorders caused by diabetes mellitus in rats. This further validates the use of this species as medicinal herb and spice by the larger population of Nigerians. PMID:24367390

Protective Effect of Free and Bound Polyphenol Extracts from Ginger (Zingiber officinale Roscoe) on the Hepatic Antioxidant and Some Carbohydrate Metabolizing Enzymes of Streptozotocin-Induced Diabetic Rats.

PubMed

Kazeem, Mutiu Idowu; Akanji, Musbau Adewunmi; Yakubu, Musa Toyin; Ashafa, Anofi Omotayo Tom

2013-01-01

This study investigated the hepatoprotective effects of polyphenols from Zingiber officinale on streptozotocin-induced diabetic rats by assessing liver antioxidant enzymes, carbohydrate-metabolizing enzymes and liver function indices. Initial oral glucose tolerance test was conducted using 125 mg/kg, 250 mg/kg, and 500 mg/kg body weight of both free and bound polyphenols from Z. officinale. 28 day daily oral administration of 500 mg/kg body weight of free and bound polyphenols from Z. officinale to streptozotocin-induced (50 mg/kg) diabetic rats significantly reduced (P < 0.05) the fasting blood glucose compared to control groups. There was significant increase (P < 0.05) in the antioxidant enzymes activities in the animals treated with both polyphenols. Similarly, the polyphenols normalised the activities of some carbohydrate metabolic enzymes (hexokinase and phosphofructokinase) in the liver of the rats treated with it and significantly reduced (P < 0.05) the activities of liver function enzymes. The results from the present study have shown that both free and bound polyphenols from Z. officinale especially the free polyphenol could ameliorate liver disorders caused by diabetes mellitus in rats. This further validates the use of this species as medicinal herb and spice by the larger population of Nigerians.

Randomness in the network inhibits cooperation based on the bounded rational collective altruistic decision

NASA Astrophysics Data System (ADS)

Ohdaira, Tetsushi

2014-07-01

Previous studies discussing cooperation employ the best decision that every player knows all information regarding the payoff matrix and selects the strategy of the highest payoff. Therefore, they do not discuss cooperation based on the altruistic decision with limited information (bounded rational altruistic decision). In addition, they do not cover the case where every player can submit his/her strategy several times in a match of the game. This paper is based on Ohdaira's reconsideration of the bounded rational altruistic decision, and also employs the framework of the prisoner's dilemma game (PDG) with sequential strategy. The distinction between this study and the Ohdaira's reconsideration is that the former covers the model of multiple groups, but the latter deals with the model of only two groups. Ohdaira's reconsideration shows that the bounded rational altruistic decision facilitates much more cooperation in the PDG with sequential strategy than Ohdaira and Terano's bounded rational second-best decision does. However, the detail of cooperation of multiple groups based on the bounded rational altruistic decision has not been resolved yet. This study, therefore, shows how randomness in the network composed of multiple groups affects the increase of the average frequency of mutual cooperation (cooperation between groups) based on the bounded rational altruistic decision of multiple groups. We also discuss the results of the model in comparison with related studies which employ the best decision.

Intermixed adatom and surface-bound adsorbates in regular self-assembled monolayers of racemic 2-butanethiol on Au(111).

PubMed

Ouyang, Runhai; Yan, Jiawei; Jensen, Palle S; Ascic, Erhad; Gan, Shiyu; Tanner, David; Mao, Bingwei; Niu, Li; Zhang, Jingdong; Tang, Chunguang; Hush, Noel S; Reimers, Jeffrey R; Ulstrup, Jens

2015-04-07

In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30%), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25%) and near that for linear-chain 1-butanethiol (33%). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Renormalization group flow of the Higgs potential

NASA Astrophysics Data System (ADS)

Gies, Holger; Sondenheimer, René

2018-01-01

We summarize results for local and global properties of the effective potential for the Higgs boson obtained from the functional renormalization group, which allows one to describe the effective potential as a function of both scalar field amplitude and renormalization group scale. This sheds light onto the limitations of standard estimates which rely on the identification of the two scales and helps in clarifying the origin of a possible property of meta-stability of the Higgs potential. We demonstrate that the inclusion of higher-dimensional operators induced by an underlying theory at a high scale (GUT or Planck scale) can relax the conventional lower bound on the Higgs mass derived from the criterion of absolute stability. This article is part of the Theo Murphy meeting issue `Higgs cosmology'.

Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox.

PubMed

Kaever, Thomas; Matho, Michael H; Meng, Xiangzhi; Crickard, Lindsay; Schlossman, Andrew; Xiang, Yan; Crotty, Shane; Peters, Bjoern; Zajonc, Dirk M

2016-05-01

Vaccinia virus (VACV) A27 is a target for viral neutralization and part of the Dryvax smallpox vaccine. A27 is one of the three glycosaminoglycan (GAG) adhesion molecules and binds to heparan sulfate. To understand the function of anti-A27 antibodies, especially their protective capacity and their interaction with A27, we generated and subsequently characterized 7 murine monoclonal antibodies (MAbs), which fell into 4 distinct epitope groups (groups I to IV). The MAbs in three groups (groups I, III, and IV) bound to linear peptides, while the MAbs in group II bound only to VACV lysate and recombinant A27, suggesting that they recognized a conformational and discontinuous epitope. Only group I antibodies neutralized the mature virion in a complement-dependent manner and protected against VACV challenge, while a group II MAb partially protected against VACV challenge but did not neutralize the mature virion. The epitope for group I MAbs was mapped to a region adjacent to the GAG binding site, a finding which suggests that group I MAbs could potentially interfere with the cellular adhesion of A27. We further determined the crystal structure of the neutralizing group I MAb 1G6, as well as the nonneutralizing group IV MAb 8E3, bound to the corresponding linear epitope-containing peptides. Both the light and the heavy chains of the antibodies are important in binding to their antigens. For both antibodies, the L1 loop seems to dominate the overall polar interactions with the antigen, while for MAb 8E3, the light chain generally appears to make more contacts with the antigen. Vaccinia virus is a powerful model to study antibody responses upon vaccination, since its use as the smallpox vaccine led to the eradication of one of the world's greatest killers. The immunodominant antigens that elicit the protective antibodies are known, yet for many of these antigens, little information about their precise interaction with antibodies is available. In an attempt to better understand the interplay between the antibodies and their antigens, we generated and functionally characterized a panel of anti-A27 antibodies and studied their interaction with the epitope using X-ray crystallography. We identified one protective antibody that binds adjacent to the heparan sulfate binding site of A27, likely affecting ligand binding. Analysis of the antibody-antigen interaction supports a model in which antibodies that can interfere with the functional activity of the antigen are more likely to confer protection than those that bind at the extremities of the antigen. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Chemoproteomic profiling and discovery of protein electrophiles in human cells

NASA Astrophysics Data System (ADS)

Matthews, Megan L.; He, Lin; Horning, Benjamin D.; Olson, Erika J.; Correia, Bruno E.; Yates, John R.; Dawson, Philip E.; Cravatt, Benjamin F.

2017-03-01

Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells. Using this approach, we demonstrate that the pyruvoyl cofactor of S-adenosyl-L-methionine decarboxylase (AMD1) is dynamically controlled by intracellular methionine concentrations. We also identify a heretofore unknown modification—an N-terminally bound glyoxylyl group—in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells.

Internalization of exogenous ADP-ribosylation factor 6 (Arf6) proteins into cells.

PubMed

Afroze, Syeda H; Uddin, M Nasir; Cao, Xiaobo; Asea, Alexzander; Gizachew, Dawit

2011-08-01

Endogenous Arf6 is a myristoylated protein mainly involved in endosomal membrane traffic and structural organization at the plasma membrane. It has been shown that Arf6 mediates cancer cell invasion and shedding of plasma membrane microvesicles derived from tumor cells. In this article, we determined that Arf6 proteins both in the GDP and GTPγS bound forms can enter cells when simply added in the cell culture medium without requiring the myristoyl group. The GTPγS bound can enter cells at a faster rate than the GDP-bound Arf6. Despite the role of the endogenous Arf6 in endocytosis and membrane trafficking, the internalization of exogenous Arf6 may involve non-endocytic processes. As protein therapeutics is becoming important in medicine, we examined the effect of the uptake of Arf6 proteins on cellular functions and determined that exogenous Arf6 inhibits proliferation, invasion, and migration of cells. Future studies of the internalization of Arf6 mutants will reveal key residues that play a role in the internalization of Arf6 and its interaction and possible structural conformations bound to the plasma membrane.

Estimation of two ordered mean residual lifetime functions.

PubMed

Ebrahimi, N

1993-06-01

In many statistical studies involving failure data, biometric mortality data, and actuarial data, mean residual lifetime (MRL) function is of prime importance. In this paper we introduce the problem of nonparametric estimation of a MRL function on an interval when this function is bounded from below by another such function (known or unknown) on that interval, and derive the corresponding two functional estimators. The first is to be used when there is a known bound, and the second when the bound is another MRL function to be estimated independently. Both estimators are obtained by truncating the empirical estimator discussed by Yang (1978, Annals of Statistics 6, 112-117). In the first case, it is truncated at a known bound; in the second, at a point somewhere between the two empirical estimates. Consistency of both estimators is proved, and a pointwise large-sample distribution theory of the first estimator is derived.

Regularization by Functions of Bounded Variation and Applications to Image Enhancement

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

Casas, E.; Kunisch, K.; Pola, C.

1999-09-15

Optimization problems regularized by bounded variation seminorms are analyzed. The optimality system is obtained and finite-dimensional approximations of bounded variation function spaces as well as of the optimization problems are studied. It is demonstrated that the choice of the vector norm in the definition of the bounded variation seminorm is of special importance for approximating subspaces consisting of piecewise constant functions. Algorithms based on a primal-dual framework that exploit the structure of these nondifferentiable optimization problems are proposed. Numerical examples are given for denoising of blocky images with very high noise.

Impact of managed care on physician organizational behavior.

PubMed

Reece, R L

1999-01-01

This article examines how physicians act, react, and organize when managed care forces them to consolidate into larger groups and business corporations. Physicians have experimented with ownership by hospitals or business corporations to gain capital, management skills, and information systems. Now they're moving toward physician-owned groups with "outsourcing" of administrative and information system functions. The mood, movement, and momentum of physicians, in short, is toward integrated physician organizations bound together by information that amplifies on their core competencies and capacities to deliver care.

Polymer adsorption on silica and wettability of graphene oxide surfaces, experiments and simulations

NASA Astrophysics Data System (ADS)

Mortazavian, Hamid

Among the various classifications of polymer composites, studying polymers adsorbed to a surface such as silica is important due to their numerous applications. Adsorbed polymers usually show different properties than their bulk counterparts due to their interactions with the surface. In this study, we observed tightly- and loosely-bound polymer and mobile components in poly(vinyl acetate) (PVAc) on silica both with temperature-modulated differential scanning calorimetry (TMDSC) experiments and computer simulations. The more-mobile component which correlated to the region of low density at the air interface is reported for the first time using TMDSC thermograms. Pore size distribution and pore volume development of adsorbed PMMA samples showed different behavior below and above the tightly-bound amount of the polymer. The amount of tightly-bound polymer was obtained by a linear regression analysis of the ratio of the area under the two glass transitions. The values obtained vary from 0.52 to 0.86 mg PVAc/m2 silica depending upon the molecular mass for the amounts of PVAc and the specific surface area of fumed silica. Direct comparisons of the thermal properties and intermolecular interactions were performed between PVAc and poly(methyl methacrylate) (PMMA) with similar molecular masses and adsorbed amounts on silica. A larger amount of tightly-bound polymer and a greater change in glass transition were observed for adsorbed PMMA compared to adsorbed PVAc. These observations suggested that the interactions between PMMA and silica were stronger than those between PVAc and silica. Molecular modeling of these surface polymers showed that PMMA associates more strongly with silica than does PVAc through additional hydrogen-bonding interactions. Graphene oxide (GO) material surface characteristics make it easy to functionalize, making it a water repellant surface. To test the effect of chemical makeup and size of attached groups on the surface wettability of GO, we performed experimental water contact angle measurements and molecular modeling investigations on functionalized GO surfaces. Experimental and molecular simulation water contact angle measurements showed quantitative agreement for functionalizing groups with the same chain length at a variety of surface coverages.

Carving out the end of the world or (superconformal bootstrap in six dimensions)

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

Chang, Chi-Ming; Lin, Ying-Hsuan

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

Carving out the end of the world or (superconformal bootstrap in six dimensions)

DOE PAGES

Chang, Chi-Ming; Lin, Ying-Hsuan

2017-08-29

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

A linear programming approach to characterizing norm bounded uncertainty from experimental data

NASA Technical Reports Server (NTRS)

Scheid, R. E.; Bayard, D. S.; Yam, Y.

1991-01-01

The linear programming spectral overbounding and factorization (LPSOF) algorithm, an algorithm for finding a minimum phase transfer function of specified order whose magnitude tightly overbounds a specified nonparametric function of frequency, is introduced. This method has direct application to transforming nonparametric uncertainty bounds (available from system identification experiments) into parametric representations required for modern robust control design software (i.e., a minimum-phase transfer function multiplied by a norm-bounded perturbation).

Influence of the Relative Enamel Abrasivity (REA) of Toothpastes on the Uptake of KOH-soluble and Structurally Bound Fluoride.

PubMed

Elmazi, Valbona; Sener, Beatrice; Attin, Thomas; Imfeld, Thomas; Wegehaupt, Florian J

2015-01-01

To determine the influence of the relative enamel abrasivity (REA) of fluoridated toothpaste on the uptake of KOH-soluble and structurally bound fluoride into enamel. Bovine enamel samples were randomly allocated to 6 groups (n=36 per group). Groups A to C were treated with sodium fluoride (NaF) toothpastes and groups D to F with amine fluoride (AmF) toothpastes (1500 ppm F each). The REA in groups A and D was 2, in groups B and E it was 6 and in groups C and F it was 9. Twice a day, 18 samples of each group were immersed for 2 min in a slurry (toothpaste:artificial saliva=1:3), while the remaining samples were brushed with the respective slurry (2.5 N force; 60 strokes/min; 2 min). All samples were stored at 37°C and 100% humidity. After five days, the amount of KOH-soluble and structurally bound fluoride was determined and statistically compared by Scheffe's post-hoc tests. REA value and mode of application (immersion or brushing) had no significant influence on the amount of either kind of fluoride from NaF toothpastes. Only for the NaF toothpaste with REA 6 was the amount of KOH-soluble fluoride significantly higher after brushing. With AmF toothpastes, KOH-soluble and structurally bound fluoride concentrations were significantly higher when the samples were brushed. Furthermore, in the REA-2 group, the amounts of KOH-soluble fluoride (brushed or immersed) and structurally bound fluoride (brushed) were significantly higher than in the other groups. The REA dependency of KOH-soluble and structurally bound fluoride was found only for the AmF toothpastes. Using AmF toothpaste, the mode of application influenced the uptake of KOH-soluble and structurally bound fluoride into enamel.

Physicist's simple access to protein structures: the computer program WHAT IF

NASA Astrophysics Data System (ADS)

Altenberg-Greulich, Brigitte; Zech, Stephan G.; Stehlik, Dietmar; Vriend, Gert

2001-06-01

We describe the computer program WHAT IF and its application to two physical examples. For the DNA binding protein, OCT-1 (pou domain) the location of amino acids with a sidechain amino group is shown. Such knowledge is required when staining this molecule with a fluorescence dye, which binds chemically to the amino terminus as well as amino groups in sidechains. The program shows that most sidechain amino groups are protected when DNA is bound to OCT-1, allowing selective staining of the amino terminal NH2 group. A protein stained this way can be used in fluorescence spectroscopic studies on function aspects of OCT-1.

Renormalization group flow of the Higgs potential.

PubMed

Gies, Holger; Sondenheimer, René

2018-03-06

We summarize results for local and global properties of the effective potential for the Higgs boson obtained from the functional renormalization group, which allows one to describe the effective potential as a function of both scalar field amplitude and renormalization group scale. This sheds light onto the limitations of standard estimates which rely on the identification of the two scales and helps in clarifying the origin of a possible property of meta-stability of the Higgs potential. We demonstrate that the inclusion of higher-dimensional operators induced by an underlying theory at a high scale (GUT or Planck scale) can relax the conventional lower bound on the Higgs mass derived from the criterion of absolute stability.This article is part of the Theo Murphy meeting issue 'Higgs cosmology'. © 2018 The Author(s).

Phosphorus-31 and carbon-13 nuclear magnetic resonance studies of divalent cation binding to phosphatidylserine membranes. Use of cobalt as a paramagnetic probe

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

McLaughlin, A.C.

1982-01-01

The paramagnetic divalent cation cobalt has large and well-understood effects on NMR signals from ligands bound in the first coordination sphere, i.e., inner-sphere ligands, and the authors have used these effects to identify divalent cation binding sites at the surface of phosphatidylserine membranes. /sup 31/P NMR results show that 13% of the bound cobalt ions are involved in inner-sphere complexes with the phosphodiester group, while /sup 13/C NMR results show that 54% of the bound cobalt ions are involved in unidentate inner sphere complexes with the carboxyl group. No evidence is found for cobalt binding to the carbonyl groups, butmore » proton release studies suggest that 32% of the bound cobalt ions are involved in chelate complexes that contain both the carboxyl and the amine groups. All of the bound cobalt ions can thus be accounted for in terms of inner sphere complexes with the phosphodiester group or the carboxyl group. They suggest that the unidentate inner-sphere complex between cobalt and the carboxyl group of phosphatidylserine and the inner-sphere complex between cobalt and the phosphodiester group of phosphatidylserine provide reasonable models for complexes between alkaline earth cations and phosphatidylserine membranes.« less

Phosphorus-31 and carbon-13 nuclear magnetic resonance studies of divalent cation binding to phosphatidylserine membranes: use of cobalt as a paramagnetic probe

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

McLaughlin, A.C.

1982-09-28

The paramagnetic divalent cation cobalt has large and well-understood effects on NMR signals from ligands bound in the first coordination sphere, i.e., inner-sphere ligands, and we have used these effects to identify divalent cation binding sites at the surface of phosphatidylserine membranes. /sup 31/P NMR results show that 13% of the bound cobalt ions are involved in inner-sphere complexes with the phosphodiester group, while /sup 13/C NMR results show that 54% of the bound cobalt ions are involved in unidentate inner sphere complexes with the carboxyl group. No evidence is found for cobalt binding to the carbonyl groups, but protonmore » release studies suggest that 32% of the bound cobalt ions are involved in chelate complexes that contain both the carboxyl and the amine groups. All (i.e., 13% + 54% + 32% = 99%) of the bound cobalt ions can thus be accounted for in terms of inner sphere complexes with the phosphodiester group or the carboxyl group. We suggest that the unidentate inner-sphere complex between cobalt and the carboxyl group of phosphatidylserine and the inner-sphere complex between cobalt and the phosphodiester group of phosphatidylserine provide reasonable models for complexes between alkaline earth cations and phosphatidylserine membranes.« less

Synthesis and characterization of covalently bound benzocaine graphite oxide derivative

NASA Astrophysics Data System (ADS)

Kabbani, Ahmad; Kabbani, Mohamad; Safadi, Khadija

2015-09-01

Graphite oxide (GO) derived materials include chemically functionalize or reduced graphene oxide (exfoliated from GO) sheets, assembled paper-like forms , and graphene-based composites GO consists of intact graphitic regions interspersed with sp3-hybridized carbons containing hydroxyl and epoxide functional groups on the top and bottom surfaces of each sheet and sp2-hybridized carbons containing carboxyl and carbonyl groups mostly at the sheet edges. Hence, GO is hydrophilic and readily disperses in water to form stable colloidal suspensions Due to the attached oxygen functional groups, GO was used to prepare different derivatives which result in some physical and chemical properties that are dramatically different from their bulk counterparts .The present work discusses the covalent cross linking of graphite oxide to benzocaine or ethyl ester of para-aminobenzoic acid,structure I,used in many over-the-counter ointment drug.Synthesis is done via diazotization of the amino group.The product is characterized via IR,Raman, X-ray photoelectron spectroscopy as well as electron microscopy.

Thiol Versus Hydroxamate as Zinc Binding Group In HDAC Inhibition: An Ab Initio QM/MM Molecular Dynamics Study

PubMed Central

Gong, Wenjing; Wu, Ruibo; Zhang, Yingkai

2015-01-01

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding towards class IIa HDACs. PMID:26452222

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study.

PubMed

Gong, Wenjing; Wu, Ruibo; Zhang, Yingkai

2015-11-15

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs. © 2015 Wiley Periodicals, Inc.

Circulating HMGB1 and RAGE as Clinical Biomarkers in Malignant and Autoimmune Diseases

PubMed Central

Pilzweger, Christin; Holdenrieder, Stefan

2015-01-01

High molecular group box 1 (HMGB1) is a highly conserved member of the HMG-box-family; abundantly expressed in almost all human cells and released in apoptosis; necrosis or by activated immune cells. Once in the extracellular space, HMGB1 can act as a danger associated molecular pattern (DAMP), thus stimulating or inhibiting certain functions of the immune system; depending on the “combinatorial cocktail” of the surrounding milieu. HMGB1 exerts its various functions through binding to a multitude of membrane-bound receptors such as TLR-2; -4 and -9; IL-1 and RAGE (receptor for advanced glycation end products); partly complex-bound with intracellular fragments like nucleosomes. Soluble RAGE in the extracellular space, however, acts as a decoy receptor by binding to HMGB1 and inhibiting its effects. This review aims to outline today’s knowledge of structure, intra- and extracellular functions including mechanisms of release and finally the clinical relevance of HMGB1 and RAGE as clinical biomarkers in therapy monitoring, prediction and prognosis of malignant and autoimmune disease. PMID:26854151

On the perturbation of the group generalized inverse for a class of bounded operators in Banach spaces

NASA Astrophysics Data System (ADS)

Castro-González, N.; Vélez-Cerrada, J. Y.

2008-05-01

Given a bounded operator A on a Banach space X with Drazin inverse AD and index r, we study the class of group invertible bounded operators B such that I+AD(B-A) is invertible and . We show that they can be written with respect to the decomposition as a matrix operator, , where B1 and are invertible. Several characterizations of the perturbed operators are established, extending matrix results. We analyze the perturbation of the Drazin inverse and we provide explicit upper bounds of ||B#-AD|| and ||BB#-ADA||. We obtain a result on the continuity of the group inverse for operators on Banach spaces.

Functional analysis of a missense mutation in the serine protease inhibitor SPINT2 associated with congenital sodium diarrhea.

PubMed

Faller, Nicolas; Gautschi, Ivan; Schild, Laurent

2014-01-01

Membrane-bound serine proteases play important roles in different biological processes. Their regulation by endogenous inhibitors is poorly understood. A Y163C mutation in the SPINT2 gene encoding the serine protease inhibitor Hepatocyte Growth Factor Inhibitor HAI-2 is associated with a congenital sodium diarrhea. The functional consequences of this mutation on HAI-2 activity and its physiological targets are unknown. We established a cellular assay in Xenopus laevis oocytes to study functional interactions between HAI-2 and candidate membrane-bound serine proteases expressed in the gastro-intestinal tract. We found that the wild-type form of HAI-2 is a potent inhibitor of nine gastro-intestinal serine proteases. The Y163C mutation in the second Kunitz domain of HAI-2 resulted in a complete loss of inhibitory activity on two intestinal proteases, prostasin and tmprss13. The effect of the mutation of the homologous Y68C in the first Kunitz domain of HAI-2 is consistent with a differential contribution of the two Kunitz domains of HAI-2 in the inhibition of serine proteases. By contrast to the Tyr to Cys, the Tyr to Ser substitution did not change the inhibitory potency of HAI-2, indicating that the thiol-group of the cysteine rather than the Tyr deletion is responsible for the HAI-2 loss of function. Our functional assay allowed us to identify membrane-bound serine proteases as cellular target for inhibition by HAI-2 wild type and mutants, and to better define the role of the Tyr in the second Kunitz domain in the inhibitory activity of HAI-2.

Simultaneous LC/MS/MS determination of thiols and disulfides in urine samples based on differential labeling with ferrocene-based maleimides.

PubMed

Seiwert, Bettina; Karst, Uwe

2007-09-15

A method for the simultaneous determination of a series of thiols and disulfides in urine samples has been developed based on the sequential labeling of free and bound thiol functionalities with two ferrocene-based maleimide reagents. The sample is first exposed to N-(2-ferroceneethyl)maleimide, thus leading to the derivatization of free thiol groups in the sample. After quantitative reaction and subsequent reduction of the disulfide-bound thiols by tris(2-carboxyethyl)phosphine, the newly formed thiol functionalities are reacted with ferrocenecarboxylic acid-(2-maleimidoyl)ethylamide. The reaction products are determined by LC/MS/MS in the multiple reaction mode, and precursor ion scan as well as neutral loss scan is applied to detect unknown further thiols. The method was successfully applied to the analysis of free and disulfide-bound thiols in urine samples. Limits of detection are 30 to 110 nM, and the linear range comprises two decades of concentration, thus covering the relevant concentration range of thiols in urine samples. The thiol and disulfide concentrations were referred to the creatinine content to compensate for different sample volumes. As some calibration standards for the disulfides are not commercially available, they were synthesized in an electrochemical flow-through cell. This allowed the synthesis of hetero- and homodimeric disulfides.

Computing an upper bound on contact stress with surrogate duality

NASA Astrophysics Data System (ADS)

Xuan, Zhaocheng; Papadopoulos, Panayiotis

2016-07-01

We present a method for computing an upper bound on the contact stress of elastic bodies. The continuum model of elastic bodies with contact is first modeled as a constrained optimization problem by using finite elements. An explicit formulation of the total contact force, a fraction function with the numerator as a linear function and the denominator as a quadratic convex function, is derived with only the normalized nodal contact forces as the constrained variables in a standard simplex. Then two bounds are obtained for the sum of the nodal contact forces. The first is an explicit formulation of matrices of the finite element model, derived by maximizing the fraction function under the constraint that the sum of the normalized nodal contact forces is one. The second bound is solved by first maximizing the fraction function subject to the standard simplex and then using Dinkelbach's algorithm for fractional programming to find the maximum—since the fraction function is pseudo concave in a neighborhood of the solution. These two bounds are solved with the problem dimensions being only the number of contact nodes or node pairs, which are much smaller than the dimension for the original problem, namely, the number of degrees of freedom. Next, a scheme for constructing an upper bound on the contact stress is proposed that uses the bounds on the sum of the nodal contact forces obtained on a fine finite element mesh and the nodal contact forces obtained on a coarse finite element mesh, which are problems that can be solved at a lower computational cost. Finally, the proposed method is verified through some examples concerning both frictionless and frictional contact to demonstrate the method's feasibility, efficiency, and robustness.

Self-organized fluorescent nanosensors for ratiometric Pb2+ detection.

PubMed

Arduini, Maria; Mancin, Fabrizio; Tecilla, Paolo; Tonellato, Umberto

2007-07-31

Silica nanoparticles (60 nm diameter) doped with fluorescent dyes and functionalized on the surface with thiol groups have been proved to be efficient fluorescent chemosensors for Pb2+ ions. The particles can detect a 1 microM metal ion concentration with a good selectivity, suffering only interference from Cu2+ ions. Analyte binding sites are provided by the simple grafting of the thiol groups on the nanoparticles. Once bound to the particles surface, the Pb2+ ions quench the emission of the reporting dyes embedded. Sensor performances can be improved by taking advantage of the ease of production of multishell silica particles. On one hand, signaling units can be concentrated in the external shells, allowing a closer interaction with the surface-bound analyte. On the other, a second dye can be buried in the particle core, far enough from the surface to be unaffected by the Pb2+ ions, thus producing a reference signal. In this way, a ratiometric system is easily prepared by simple self-organization of the particle components.

Asymptotic safety of gravity-matter systems

NASA Astrophysics Data System (ADS)

Meibohm, J.; Pawlowski, J. M.; Reichert, M.

2016-04-01

We study the ultraviolet stability of gravity-matter systems for general numbers of minimally coupled scalars and fermions. This is done within the functional renormalization group setup put forward in [N. Christiansen, B. Knorr, J. Meibohm, J. M. Pawlowski, and M. Reichert, Phys. Rev. D 92, 121501 (2015).] for pure gravity. It includes full dynamical propagators and a genuine dynamical Newton's coupling, which is extracted from the graviton three-point function. We find ultraviolet stability of general gravity-fermion systems. Gravity-scalar systems are also found to be ultraviolet stable within validity bounds for the chosen generic class of regulators, based on the size of the anomalous dimension. Remarkably, the ultraviolet fixed points for the dynamical couplings are found to be significantly different from those of their associated background counterparts, once matter fields are included. In summary, the asymptotic safety scenario does not put constraints on the matter content of the theory within the validity bounds for the chosen generic class of regulators.

Alkyl group substitution by oxime-bound palladium(II) (the Shaw reaction): Alkly group selectivity and deuterium isotope effects

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

Wells, A.P.; Kitching, W.

1992-08-01

This report provides information regarding the selectivity of alkyl groups and the nature of the transition state for C-H palladation by oxime-bound palladium(II) (the Shaw reaction). The kinetic deuterium isotope effects are also presented. 21 refs.

Serum pentosidine as an indicator of Alzheimer's disease.

PubMed

Meli, M; Perier, C; Ferron, C; Parssegny, F; Denis, C; Gonthier, R; Laurent, B; Reynaud, E; Frey, J; Chamson, A

2002-04-01

Pentosidine, an advanced glycation end product (AGE), was assayed by HPLC in serum proteins from patients with Alzheimer type dementia (AD), patients with diabetes mellitus (D), and healthy (C) age-matched old subjects (mean age from each group = 84 years). Serum pentosidine was significantly different between the three groups despite similar renal function (serum creatinine < 160 micromol/L). In all groups of patients, pentosidine was independent of glycated hemoglobin (HbA1C) and the early glycation marker fructosamine and appeared to be an independent marker, mainly bound to serum albumin. Pentosidine could be an important factor useful for the diagnosis of Alzheimer's disease.

Structure Functions of Bound Neutrons

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

Sebastian Kuhn

2005-04-01

We describe an experiment measuring electron scattering on a neutron bound in deuterium with coincident detection of a fast, backward-going spectator proton. Our data map out the relative importance of the pure PWIA spectator mechanism and final state interactions in various kinematic regions, and give a first glimpse of the modification of the structure function of a bound neutron as a function of its off-shell mass. We also discuss a new experimental program to study the structure of a free neutron by extending the same technique to much lower spectator momenta.

Coexistence of bounded and unbounded motions in a bouncing ball model

NASA Astrophysics Data System (ADS)

Marò, Stefano

2013-05-01

We consider the model describing the vertical motion of a ball falling with constant acceleration on a wall and elastically reflected. The wall is supposed to move in the vertical direction according to a given periodic function f. We apply the Aubry-Mather theory to the generating function in order to prove the existence of bounded motions with prescribed mean time between the bounces. As the existence of unbounded motions is known, it is possible to find a class of functions f that allow both bounded and unbounded motions.

The Laughlin liquid in an external potential

NASA Astrophysics Data System (ADS)

Rougerie, Nicolas; Yngvason, Jakob

2018-04-01

We study natural perturbations of the Laughlin state arising from the effects of trapping and disorder. These are N-particle wave functions that have the form of a product of Laughlin states and analytic functions of the N variables. We derive an upper bound to the ground state energy in a confining external potential, matching exactly a recently derived lower bound in the large N limit. Irrespective of the shape of the confining potential, this sharp upper bound can be achieved through a modification of the Laughlin function by suitably arranged quasi-holes.

Socially Coherent Negotiation for Cooperative Multiagent Systems

DTIC Science & Technology

2008-07-16

of altruism by substituting the preferences of others for one’s own. • It is assumed that each member will...approximation) — it is not a species of bounded rationality. (c) It naturally extends to the multi-agent case, thereby providing a natural frame- work...are mass functions, permits a natural way to aggregate the preference orderings of the individuals to form a group preference ordering. As is well

A Preliminary Investigation of Ego Stage and Leadership Effectiveness.

DTIC Science & Technology

1988-03-01

traits are not necessarily linked to observable0! behavior. For example, an individual may refrain from sexual harassment because he is legally bound...are given value as a function of their worth to the child. Bodily impulses, such as sexual and aggressive im- pulses, appropriate to the particular...potentialities in various circumstances. Conscientiousness of oneself transmutes group standards of conduct and appearance. No longer does the person see one

Transglutaminases in Dysbiosis As Potential Environmental Drivers of Autoimmunity

PubMed Central

Lerner, Aaron; Aminov, Rustam; Matthias, Torsten

2017-01-01

Protein-glutamine γ-glutamyltransferases (transglutaminases, Tgs) belong to the class of transferases. They catalyze the formation of an isopeptide bond between the acyl group at the end of the side chain of protein- or peptide-bound glutamine residues and the first order 𝜀-amine groups of protein- or peptide-bound lysine. The Tgs are considered to be universal protein cross-linkers, and they play an essential role in a number of human diseases. In this review, we discuss mainly the bacterial Tgs in terms of the functionality of the enzymes and a potential role they may play in bacterial survival. Since microbial transglutaminases (mTgs) are functionally similar to the human homologs, they may be involved in the human disease provocation. We suggest here a potential involvement of Tgs in the pathologies such as autoimmune diseases. In this hypothesis, the endogenous mTgs that are secreted by the gut microbiota, especially in a dysbiotic configuration, are potential drivers of systemic autoimmunity, via the enzymatic posttranslational modification of peptides in the gut lumen. These mTg activities directed toward cross-linking of naïve proteins can potentially generate neo-epitopes that are not only immunogenic but may also activate some immune response cascades leading to the pathological autoimmune processes. PMID:28174571

Error bounds of adaptive dynamic programming algorithms for solving undiscounted optimal control problems.

PubMed

Liu, Derong; Li, Hongliang; Wang, Ding

2015-06-01

In this paper, we establish error bounds of adaptive dynamic programming algorithms for solving undiscounted infinite-horizon optimal control problems of discrete-time deterministic nonlinear systems. We consider approximation errors in the update equations of both value function and control policy. We utilize a new assumption instead of the contraction assumption in discounted optimal control problems. We establish the error bounds for approximate value iteration based on a new error condition. Furthermore, we also establish the error bounds for approximate policy iteration and approximate optimistic policy iteration algorithms. It is shown that the iterative approximate value function can converge to a finite neighborhood of the optimal value function under some conditions. To implement the developed algorithms, critic and action neural networks are used to approximate the value function and control policy, respectively. Finally, a simulation example is given to demonstrate the effectiveness of the developed algorithms.

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

PubMed Central

2013-01-01

Background The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results and discussion Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread co-localization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes. PMID:23442797

Optimal bounds and extremal trajectories for time averages in dynamical systems

NASA Astrophysics Data System (ADS)

Tobasco, Ian; Goluskin, David; Doering, Charles

2017-11-01

For systems governed by differential equations it is natural to seek extremal solution trajectories, maximizing or minimizing the long-time average of a given quantity of interest. A priori bounds on optima can be proved by constructing auxiliary functions satisfying certain point-wise inequalities, the verification of which does not require solving the underlying equations. We prove that for any bounded autonomous ODE, the problems of finding extremal trajectories on the one hand and optimal auxiliary functions on the other are strongly dual in the sense of convex duality. As a result, auxiliary functions provide arbitrarily sharp bounds on optimal time averages. Furthermore, nearly optimal auxiliary functions provide volumes in phase space where maximal and nearly maximal trajectories must lie. For polynomial systems, such functions can be constructed by semidefinite programming. We illustrate these ideas using the Lorenz system, producing explicit volumes in phase space where extremal trajectories are guaranteed to reside. Supported by NSF Award DMS-1515161, Van Loo Postdoctoral Fellowships, and the John Simon Guggenheim Foundation.

Exact results for the finite time thermodynamic uncertainty relation

NASA Astrophysics Data System (ADS)

Manikandan, Sreekanth K.; Krishnamurthy, Supriya

2018-03-01

We obtain exact results for the recently discovered finite-time thermodynamic uncertainty relation, for the dissipated work W d , in a stochastically driven system with non-Gaussian work statistics, both in the steady state and transient regimes, by obtaining exact expressions for any moment of W d at arbitrary times. The uncertainty function (the Fano factor of W d ) is bounded from below by 2k_BT as expected, for all times τ, in both steady state and transient regimes. The lower bound is reached at τ=0 as well as when certain system parameters vanish (corresponding to an equilibrium state). Surprisingly, we find that the uncertainty function also reaches a constant value at large τ for all the cases we have looked at. For a system starting and remaining in steady state, the uncertainty function increases monotonically, as a function of τ as well as other system parameters, implying that the large τ value is also an upper bound. For the same system in the transient regime, however, we find that the uncertainty function can have a local minimum at an accessible time τm , for a range of parameter values. The large τ value for the uncertainty function is hence not a bound in this case. The non-monotonicity suggests, rather counter-intuitively, that there might be an optimal time for the working of microscopic machines, as well as an optimal configuration in the phase space of parameter values. Our solutions show that the ratios of higher moments of the dissipated work are also bounded from below by 2k_BT . For another model, also solvable by our methods, which never reaches a steady state, the uncertainty function, is in some cases, bounded from below by a value less than 2k_BT .

Optimal bounds and extremal trajectories for time averages in nonlinear dynamical systems

NASA Astrophysics Data System (ADS)

Tobasco, Ian; Goluskin, David; Doering, Charles R.

2018-02-01

For any quantity of interest in a system governed by ordinary differential equations, it is natural to seek the largest (or smallest) long-time average among solution trajectories, as well as the extremal trajectories themselves. Upper bounds on time averages can be proved a priori using auxiliary functions, the optimal choice of which is a convex optimization problem. We prove that the problems of finding maximal trajectories and minimal auxiliary functions are strongly dual. Thus, auxiliary functions provide arbitrarily sharp upper bounds on time averages. Moreover, any nearly minimal auxiliary function provides phase space volumes in which all nearly maximal trajectories are guaranteed to lie. For polynomial equations, auxiliary functions can be constructed by semidefinite programming, which we illustrate using the Lorenz system.

Implementing and Bounding a Cascade Heuristic for Large-Scale Optimization

DTIC Science & Technology

2017-06-01

solving the monolith, we develop a method for producing lower bounds to the optimal objective function value. To do this, we solve a new integer...as developing and analyzing methods for producing lower bounds to the optimal objective function value of the seminal problem monolith, which this...length of the window decreases, the end effects of the model typically increase (Zerr, 2016). There are four primary methods for correcting end

Large deviation function for a driven underdamped particle in a periodic potential

NASA Astrophysics Data System (ADS)

Fischer, Lukas P.; Pietzonka, Patrick; Seifert, Udo

2018-02-01

Employing large deviation theory, we explore current fluctuations of underdamped Brownian motion for the paradigmatic example of a single particle in a one-dimensional periodic potential. Two different approaches to the large deviation function of the particle current are presented. First, we derive an explicit expression for the large deviation functional of the empirical phase space density, which replaces the level 2.5 functional used for overdamped dynamics. Using this approach, we obtain several bounds on the large deviation function of the particle current. We compare these to bounds for overdamped dynamics that have recently been derived, motivated by the thermodynamic uncertainty relation. Second, we provide a method to calculate the large deviation function via the cumulant generating function. We use this method to assess the tightness of the bounds in a numerical case study for a cosine potential.

New upper bounds on the rate of a code via the Delsarte-MacWilliams inequalities

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Rodemich, E. R.; Rumsey, H., Jr.; Welch, L. R.

1977-01-01

An upper bound on the rate of a binary code as a function of minimum code distance (using a Hamming code metric) is arrived at from Delsarte-MacWilliams inequalities. The upper bound so found is asymptotically less than Levenshtein's bound, and a fortiori less than Elias' bound. Appendices review properties of Krawtchouk polynomials and Q-polynomials utilized in the rigorous proofs.

Rational design and synthesis of androgen receptor-targeted nonsteroidal anti-androgen ligands for the tumor-specific delivery of a doxorubicin-formaldehyde conjugate.

PubMed

Cogan, Peter S; Koch, Tad H

2003-11-20

The synthesis and preliminary evaluation of a doxorubicin-formaldehyde conjugate tethered to the nonsteroidal antiandrogen, cyanonilutamide (RU 56279), for the treatment of prostate cancer are reported. The relative ability of the targeting group to bind to the human androgen receptor was studied as a function of tether. The tether served to attach the antiandrogen to the doxorubicin-formaldehyde conjugate via an N-Mannich base of a salicylamide derivative. The salicylamide was selected to serve as a trigger release mechanism to separate the doxorubicin-formaldehyde conjugate from the targeting group after it has bound to the androgen receptor. The remaining part of the tether consisted of a linear group that spanned from the 5-position of the salicylamide to the 3'-position of cyanonilutamide. The structures explored for the linear region of the tether were derivatives of di(ethylene glycol), tri(ethylene glycol), N,N'-disubstituted-piperazine, and 2-butyne-1,4-diol. Relative binding affinity of the tethers bound to the targeting group for human androgen receptor were measured using a (3)H-Mibolerone competition assay and varied from 18% of nilutamide binding for the butynediol-based linear region to less than 1% for one of the piperazine derivatives. The complete targeted drug with the butynediol-based linear region has a relative binding affinity of 10%. This relative binding affinity is encouraging in light of the cocrystal structure of human androgen receptor ligand binding domain bound to the steroid Metribolone which predicts very limited space for a tether connecting the antiandrogen on the inside to the cytotoxin on the outside.

Polymeric Coatings that Mimic the Endothelium: Combining Nitric Oxide Release with Surface-Bound Active Thrombomodulin and Heparin

PubMed Central

Wu, Biyun; Gerlitz, Bruce; Grinnell, Brian W.; Meyerhoff, Mark E.

2007-01-01

Multi-functional bilayer polymeric coatings are prepared with both controlled nitric oxide (NO) release and surface-bound active thrombomodulin (TM) alone or in combination with immobilized heparin. The outer-layer is made of CarboSil, a commercially available copolymer of silicone rubber (SR) and polyurethane (PU). The CarboSil is either carboxylated or aminated via an allophanate reaction with a diisocyanate compound followed by a urea-forming reaction between the generated isocyanate group of the polymer and the amine group of an amino acid (glycine), an oligopeptide (triglycine) or a diamine. The carboxylated CarboSil can then be used to immobilize TM through the formation of an amide bond between the surface carboxylic acid groups and the lysine residues of TM. Aminated CarboSil can also be employed to initially couple heparin to the surface, and then the carboxylic acid groups on heparin can be further used to anchor TM. Both surface-bound TM and heparin’s activity are evaluated by chromogenic assays and found to be at clinically significant levels. The underlying NO release layer is made with another commercial SR-PU copolymer (PurSil) mixed with a lipophilic NO donor (N-diazeniumdiolated dibutylhexanediamine (DBHD/N2O2)). The NO release rate can be tuned by changing the thickness of top coatings, and the duration of NO release at physiologically relevant levels can be as long as 2 weeks. The combination of controlled NO release as well as immobilized active TM and heparin from/on the same polymeric surface mimics the highly thromboresistant endothelium layer. Hence, such multifunctional polymer coatings should provide more blood-compatible surfaces for biomedical devices. PMID:17597201

Multivariate Lipschitz optimization: Survey and computational comparison

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

Hansen, P.; Gourdin, E.; Jaumard, B.

1994-12-31

Many methods have been proposed to minimize a multivariate Lipschitz function on a box. They pertain the three approaches: (i) reduction to the univariate case by projection (Pijavskii) or by using a space-filling curve (Strongin); (ii) construction and refinement of a single upper bounding function (Pijavskii, Mladineo, Mayne and Polak, Jaumard Hermann and Ribault, Wood...); (iii) branch and bound with local upper bounding functions (Galperin, Pint{acute e}r, Meewella and Mayne, the present authors). A survey is made, stressing similarities of algorithms, expressed when possible within a unified framework. Moreover, an extensive computational comparison is reported on.

Diagnostics and Robust Estimation When Transforming the Regression Model and the Response.

DTIC Science & Technology

1986-10-01

Bounded-influence estimators place a bound on the influence function of each observation. Bounded-influence regression estimators have been proposed by...Hampel et al. (1986, chapter 4) for further details. First we note that the influence function of 9 satisfying (14) is IF -)8""’IF.(yi,.9) B -.(Y. ,9...where 1 1.1-1 Page 21 B - N-I N T B N IZ NVT O(Y0]1=1 1 1iY~). This definition of the influence function is conditional on x .. XN but coincides with

Evaluation of Adsorption Characteristics of a Fibrous Adsorbent Containing Zwitter-Ionic Functional Group, Targeting Organic Acids.

PubMed

Nakazawa, Akira; Tang, Ning; Inoue, Yoshinori; Kamichatani, Waka; Katoh, Toshifumi; Saito, Mitsuru; Obara, Kenji; Toriba, Akira; Hayakawa, Kazuichi

2017-01-01

Diallylamine-maleic acid copolymer (DAM)-nonwoven fabric (DAM-f), a fibrous adsorbent, contains DAM with zwitter-ionic functional groups and forms a hydration layer on the surface. The aim of this report was to evaluate the adsorption selectivity of DAM-f to semi-volatile organic acid (C1-C5). In the aqueous phase, formic acid dissolved in the hydration layer bound to the imino group of DAM-f due to anion exchange interaction. In the gas phase, the adsorption amounts of organic acids increased with the exposure time. Moreover, the adsorption rate constants correlated with the air/water partition coefficients (log K aw ) for formic acid, propionic acid, butyric acid, valeric acid and isovaleric acid, except for acetic acid. These results indicate that DAM-f is highly selective to hydrophilic compounds which easily move from the air to the hydration layer of DAM-f.

Coated particles for lithium battery cathodes

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

Singh, Mohit; Eitouni, Hany Basam; Pratt, Russell Clayton

Particles of cathodic materials are coated with polymer to prevent direct contact between the particles and the surrounding electrolyte. The polymers are held in place either by a) growing the polymers from initiators covalently bound to the particle, b) attachment of the already-formed polymers by covalently linking to functional groups attached to the particle, or c) electrostatic interactions resulting from incorporation of cationic or anionic groups in the polymer chain. Carbon or ceramic coatings may first be formed on the surfaces of the particles before the particles are coated with polymer. The polymer coating is both electronically and ionically conductive.

GTP- and GDP-Dependent Rab27a Effectors in Pancreatic Beta-Cells.

PubMed

Yamaoka, Mami; Ishizaki, Toshimasa; Kimura, Toshihide

2015-01-01

Small guanosine triphosphatases (GTPases) participate in a wide variety of cellular functions including proliferation, differentiation, adhesion, and intracellular transport. Conventionally, only the guanosine 5'-triphosphate (GTP)-bound small GTPase interacts with effector proteins, and the resulting downstream signals control specific cellular functions. Therefore, the GTP-bound form is regarded as active, and the focus has been on searching for proteins that bind the GTP form to look for their effectors. The Rab family small GTPase Rab27a is highly expressed in some secretory cells and is involved in the control of membrane traffic. The present study reviews recent progress in our understanding of the roles of Rab27a and its effectors in pancreatic beta-cells. In the basal state, GTP-bound Rab27a controls insulin secretion at pre-exocytic stages via its GTP-dependent effectors. We previously identified novel guanosine 5'-diphosphate (GDP)-bound Rab27-interacting proteins. Interestingly, GDP-bound Rab27a controls endocytosis of the secretory membrane via its interaction with these proteins. We also demonstrated that the insulin secretagogue glucose converts Rab27a from its GTP- to GDP-bound forms. Thus, GTP- and GDP-bound Rab27a regulate pre-exocytic and endocytic stages in membrane traffic, respectively. Since the physiological importance of GDP-bound GTPases has been largely overlooked, we consider that the investigation of GDP-dependent effectors for other GTPases is necessary for further understanding of cellular function.

The Function of Neuroendocrine Cells in Prostate Cancer

DTIC Science & Technology

2012-04-01

high profile article describing the technology developed by our group (Goldstein et al. Nat Protoc. 2011; 6:656-67). We explored the utility of...UGSM cells and transplanted in vivo into immune-deficient mice. We utilize an activated form of AKT (myristoylated rendering it membrane-bound) which... utilized for research can vary greatly. The second possibility is that the SV40 T-antigen is toxic to naïve benign primary human prostate cells when

Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

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

Pathuri, P.; Nguyen, E.T.; Svard, S.G.

2007-07-12

Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutivemore » over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower-symmetry space group with four molecules in the asymmetric unit. Vesicle-binding studies suggest that alpha-11 giardin, unlike most other annexins, does not bind to vesicles composed of acidic phospholipids in a calcium-dependent manner.« less

Bounded-Influence Inference in Regression.

DTIC Science & Technology

1984-02-01

be viewed as generalization of the classical F-test. By means of the influence function their robustness properties are investigated and optimally...robust tests that maximize the asymptotic power within each class, under the side condition of a bounded influence function , are constructed. Finally, an

Ochratoxin A Dietary Exposure of Ten Population Groups in the Czech Republic: Comparison with Data over the World.

PubMed

Ostry, Vladimir; Malir, Frantisek; Dofkova, Marcela; Skarkova, Jarmila; Pfohl-Leszkowicz, Annie; Ruprich, Jiri

2015-09-10

Ochratoxin A is a nephrotoxic and renal carcinogenic mycotoxin and is a common contaminant of various food commodities. Eighty six kinds of foodstuffs (1032 food samples) were collected in 2011-2013. High-performance liquid chromatography with fluorescence detection was used for ochratoxin A determination. Limit of quantification of the method varied between 0.01-0.2 μg/kg depending on the food matrices. The most exposed population is children aged 4-6 years old. Globally for this group, the maximum ochratoxin A dietary exposure for "average consumer" was estimated at 3.3 ng/kg bw/day (lower bound, considering the analytical values below the limit of quantification as 0) and 3.9 ng/kg bw/day (middle bound, considering the analytical values below the limit of quantification as 1/2 limit of quantification). Important sources of exposure for this latter group include grain-based products, confectionery, meat products and fruit juice. The dietary intake for "high consumers" in the group 4-6 years old was estimated from grains and grain-based products at 19.8 ng/kg bw/day (middle bound), from tea at 12.0 ng/kg bw/day (middle bound) and from confectionery at 6.5 ng/kg bw/day (middle bound). For men aged 18-59 years old beer was the main contributor with an intake of 2.60 ng/kg bw/day ("high consumers", middle bound). Tea and grain-based products were identified to be the main contributors for dietary exposure in women aged 18-59 years old. Coffee and wine were identified as a higher contributor of the OTA intake in the population group of women aged 18-59 years old compared to the other population groups.

Investigating the mechanisms of surface-bound functional groups in overcoming kinetic barriers to the precipitation of ordered dolomite at low temperature (Invited)

NASA Astrophysics Data System (ADS)

Kenward, P. A.; Roberts, J.; Fowle, D.; Goldstein, R.; Moore, D.; Gonzalez, L. A.

2013-12-01

The mineral dolomite, while abundant in the geologic record, is scarce in modern environments and limited to specific environments, due to kinetic barriers at low temperature (< 50°C). The microbial mediation of dolomite has been extensively studied using numerous microorganisms and disordered dolomite has been synthesized under abiotic conditions. However these studies either yielded disordered dolomite or failed to elucidate the specific mechanism(s) necessary to achieve the precipitation ordered phases of dolomite. Our work [1,2] demonstrates laboratory synthesis of dolomite at 25 °C using microcosms composed of either microbial biomass or abiotic carboxylated polystyrene micro-spheres and fluids with a range of marine-type compositions. We identify the density of surface-bound carboxyl-groups of organic matter as a primary control in ordered dolomite formation at low temperatures under the conditions studied. We hypothesize that surface-bound carboxyl-groups, such as those associated with organic matter or microbial biomass, overcome slow reaction kinetics for dolomite precipitation by dehydrating Mg2+ in an energetically favorable reaction. The precipitation of solid carbonate phases remains the most effective means of permanently sequestering CO2 from the atmosphere. As such, an increased understanding of dolomite kinetics at low temperature affords us the opportunity to apply this mechanism to engineered systems designed to enhance carbon sequestration in environments which do not kinetically favor the formation of carbonate mineral phases. [1] Kenward et al. (2013) AAPG, in press. [2] Roberts et al. (2013) PNAS, in press.

Theoretical and computational studies of excitons in conjugated polymers

NASA Astrophysics Data System (ADS)

Barford, William; Bursill, Robert J.; Smith, Richard W.

2002-09-01

We present a theoretical and computational analysis of excitons in conjugated polymers. We use a tight-binding model of π-conjugated electrons, with 1/r interactions for large r. In both the weak-coupling limit (defined by W>>U) and the strong-coupling limit (defined by W<

Beneficial influence of ellagic acid on biochemical indexes associated with experimentally induced colon carcinogenesis.

PubMed

Syed, Umesalma; Ganapasam, Sudhandiran

2017-01-01

To elucidate the key biochemical indexes associated with 1, 2-dimethylhydrazine (DMH)-induced colon carcinogenesis and the modulatory efficacy of a dietary polyphenol, ellagic acid (EA). Wistar rats were chosen to study objective, and were divided into 4 groups; Group 1-control rats; Group 2-rats received EA (60 mg/kg body weight/day, orally); rats in Group 3-induced with DMH (20 mg/kg body weight) subcutaneously for 15 weeks; DMH-induced Group 4 rats were initiated with EA treatment. We examined key citric acid cycle enzymes such as isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, succinate dehydrogenase, malate dehydrogenase and the activities of respiratory chain enzymes NADH dehydrogenase and Cytochrome-C-oxidase and membrane-bound enzyme profiles (Na +/K + ATPase, Ca 2+ ATPase and Mg 2+ ATPase), activities of lysosomal proteases such as β-D-glucuronidase, β-galactosidase and N-acety-β-D-glucosaminidase and cellular thiols (oxidized glutathione, protein thiols, and total thiols). It was found that administration of DMH to rats decreased both mitochondrial and membrane-bound enzymes activities, increased activities of lysosomal enzymes and further modulates cellular thiols levels. Treatment with EA significantly restored the mitochondrial and ATPases levels and further reduced lysosomal enzymes to near normalcy thereby restoring harmful effects induced by DMH. EA treatment was able to effectively restore the detrimental effects induced by DMH, which proves the chemoprotective function of EA against DMH-induced experimental colon carcinogenesis.

Techniques for active passivation

DOEpatents

Roscioli, Joseph R.; Herndon, Scott C.; Nelson, Jr., David D.

2016-12-20

In one embodiment, active (continuous or intermittent) passivation may be employed to prevent interaction of sticky molecules with interfaces inside of an instrument (e.g., an infrared absorption spectrometer) and thereby improve response time. A passivation species may be continuously or intermittently applied to an inlet of the instrument while a sample gas stream is being applied. The passivation species may have a highly polar functional group that strongly binds to either water or polar groups of the interfaces, and once bound presents a non-polar group to the gas phase in order to prevent further binding of polar molecules. The instrument may be actively used to detect the sticky molecules while the passivation species is being applied.

A modular, energy-based approach to the development of nickel containing molecular electrocatalysts for hydrogen production and oxidation.

PubMed

Shaw, Wendy J; Helm, Monte L; DuBois, Daniel L

2013-01-01

This review discusses the development of molecular electrocatalysts for H2 production and oxidation based on nickel. A modular approach is used in which the structure of the catalyst is divided into first, second, and outer coordination spheres. The first coordination sphere consists of the ligands bound directly to the metal center, and this coordination sphere can be used to control such factors as the presence or absence of vacant coordination sites, redox potentials, hydride donor abilities and other important thermodynamic parameters. The second coordination sphere includes functional groups such as pendent acids or bases that can interact with bound substrates such as H2 molecules and hydride ligands, but that do not form strong bonds with the metal center. These functional groups can play diverse roles such as assisting the heterolytic cleavage of H2, controlling intra- and intermolecular proton transfer reactions, and providing a physical pathway for coupling proton and electron transfer reactions. By controlling both the hydride donor ability of the catalysts using the first coordination sphere and the proton donor abilities of the functional groups in the second coordination sphere, catalysts can be designed that are biased toward H2 production, oxidation, or bidirectional (catalyzing both H2 oxidation and production). The outer coordination sphere is defined as that portion of the catalytic system that is beyond the second coordination sphere. This coordination sphere can assist in the delivery of protons and electrons to and from the catalytically active site, thereby adding another important avenue for controlling catalytic activity. Many features of these simple catalytic systems are good models for enzymes, and these simple systems provide insights into enzyme function and reactivity that may be difficult to probe in enzymes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Pattern Genes Suggest Functional Connectivity of Organs

NASA Astrophysics Data System (ADS)

Qin, Yangmei; Pan, Jianbo; Cai, Meichun; Yao, Lixia; Ji, Zhiliang

2016-05-01

Human organ, as the basic structural and functional unit in human body, is made of a large community of different cell types that organically bound together. Each organ usually exerts highly specified physiological function; while several related organs work smartly together to perform complicated body functions. In this study, we present a computational effort to understand the roles of genes in building functional connection between organs. More specifically, we mined multiple transcriptome datasets sampled from 36 human organs and tissues, and quantitatively identified 3,149 genes whose expressions showed consensus modularly patterns: specific to one organ/tissue, selectively expressed in several functionally related tissues and ubiquitously expressed. These pattern genes imply intrinsic connections between organs. According to the expression abundance of the 766 selective genes, we consistently cluster the 36 human organs/tissues into seven functional groups: adipose & gland, brain, muscle, immune, metabolism, mucoid and nerve conduction. The organs and tissues in each group either work together to form organ systems or coordinate to perform particular body functions. The particular roles of specific genes and selective genes suggest that they could not only be used to mechanistically explore organ functions, but also be designed for selective biomarkers and therapeutic targets.

Period Integrals, L--Functions, and Applications to Subconvexity Bound and Mass Equidistribution

NASA Astrophysics Data System (ADS)

Hu, Yueke

In this thesis we first study a period integral which gives the cuspidal part of a restricted Eisenstein series defined over a quadratic extension. This integral can be thought of as a complementary case to the well-known Rankin-Selberg integral and Triple product formula. We shall show the L-functions it represents and compute local integrals with ramifications. In the second part we will give explicit formula or bound for Triple product integral with very general ramifications. Such results can be applied to prove the subconvexity bound of triple product L--function and Mass equidistribution problems, greatly generalizing previous works.

Cytoskeleton and Cytoskeleton-Bound RNA Visualization in Frog and Insect Oocytes.

PubMed

Kloc, Malgorzata; Bilinski, Szczepan; Kubiak, Jacek Z

2016-01-01

The majority of oocyte functions involves and depends on the cytoskeletal elements, which include microtubules and actin and cytokeratin filaments. Various structures and molecules are temporarily or permanently bound to the cytoskeletal elements and their functions rely on cytoskeleton integrity and its timely assembly. Thus the accurate visualization of cytoskeleton is often crucial for studies and analyses of oocyte structure and functions. Here we describe several reliable methods for microtubule and/or microfilaments preservation and visualization in Xenopus oocyte extracts, and in situ in live and fixed insect and frog (Xenopus) oocytes. In addition, we describe visualization of cytoskeleton-bound RNAs using molecular beacons in live Xenopus oocytes.

Photochemically modified diamond-like carbon surfaces for neural interfaces.

PubMed

Hopper, A P; Dugan, J M; Gill, A A; Regan, E M; Haycock, J W; Kelly, S; May, P W; Claeyssens, F

2016-01-01

Diamond-like carbon (DLC) was modified using a UV functionalization method to introduce surface-bound amine and aldehyde groups. The functionalization process rendered the DLC more hydrophilic and significantly increased the viability of neurons seeded to the surface. The amine functionalized DLC promoted adhesion of neurons and fostered neurite outgrowth to a degree indistinguishable from positive control substrates (glass coated with poly-L-lysine). The aldehyde-functionalized surfaces performed comparably to the amine functionalized surfaces and both additionally supported the adhesion and growth of primary rat Schwann cells. DLC has many properties that are desirable in biomaterials. With the UV functionalization method demonstrated here it may be possible to harness these properties for the development of implantable devices to interface with the nervous system. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Synthesis and Late-Stage Functionalization of Complex Molecules through C–H Fluorination and Nucleophilic Aromatic Substitution

PubMed Central

2015-01-01

We report the late-stage functionalization of multisubstituted pyridines and diazines at the position α to nitrogen. By this process, a series of functional groups and substituents bound to the ring through nitrogen, oxygen, sulfur, or carbon are installed. This functionalization is accomplished by a combination of fluorination and nucleophilic aromatic substitution of the installed fluoride. A diverse array of functionalities can be installed because of the mild reaction conditions revealed for nucleophilic aromatic substitutions (SNAr) of the 2-fluoroheteroarenes. An evaluation of the rates for substitution versus the rates for competitive processes provides a framework for planning this functionalization sequence. This process is illustrated by the modification of a series of medicinally important compounds, as well as the increase in efficiency of synthesis of several existing pharmaceuticals. PMID:24918484

High-Throughput Genetic Identification of Functionally Important Regions of the Yeast DEAD-Box Protein Mss116p

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

Mohr, Georg; Del Campo, Mark; Turner, Kathryn G.

The Saccharomyces cerevisiae DEAD-box protein Mss116p is a general RNA chaperone that functions in splicing mitochondrial group I and group II introns. Recent X-ray crystal structures of Mss116p in complex with ATP analogs and single-stranded RNA show that the helicase core induces a bend in the bound RNA, as in other DEAD-box proteins, while a C-terminal extension (CTE) induces a second bend, resulting in RNA crimping. Here, we illuminate these structures by using high-throughput genetic selections, unigenic evolution, and analyses of in vivo splicing activity to comprehensively identify functionally important regions and permissible amino acid substitutions throughout Mss116p. The functionallymore » important regions include those containing conserved sequence motifs involved in ATP and RNA binding or interdomain interactions, as well as previously unidentified regions, including surface loops that may function in protein-protein interactions. The genetic selections recapitulate major features of the conserved helicase motifs seen in other DEAD-box proteins but also show surprising variations, including multiple novel variants of motif III (SAT). Patterns of amino acid substitutions indicate that the RNA bend induced by the helicase core depends on ionic and hydrogen-bonding interactions with the bound RNA; identify a subset of critically interacting residues; and indicate that the bend induced by the CTE results primarily from a steric block. Finally, we identified two conserved regions - one the previously noted post II region in the helicase core and the other in the CTE - that may help displace or sequester the opposite RNA strand during RNA unwinding.« less

Ab-initio Study of the Electron Mobility in a Functionalized UiO-66 Metal Organic Framework

NASA Astrophysics Data System (ADS)

Musho, Terence D.; Yasin, Alhassan S.

2018-03-01

This study leverages density functional theory accompanied with Boltzmann transport equation approaches to investigate the electronic mobility as a function of inorganic substitution and functionalization in a thermally stable UiO-66 metal-organic framework (MOF). The MOFs investigated are based on Zr-UiO-66 MOF with three functionalization groups of benzene dicarboxylate (BDC), BDC functionalized with an amino group (BDC + NH_2 ) and a nitro group (BDC + NO_2 ). The design space of this study is bound by UiO-66(M)-R, [M=Zr , Ti, Hf; R=BDC , BDC+NO_2 , BDC+NH_2 ]. The elastic modulus was not found to vary significantly over the structural modification of the design space for either functionalization or inorganic substitution. However, the electron-phonon scattering potential was found to be controllable by up to 30% through controlled inorganic substitution in the metal clusters of the MOF structure. The highest electron mobility was predicted for a UiO-66(Hf_5Zr_1 ) achieving a value of approximately 1.4× 10^{-3} cm^2 /V s. It was determined that functionalization provides a controlled method of modulating the charge density, while inorganic substitution provides a controlled method of modulating the electronic mobility. Within the proposed design space the electrical conductivity was able to be increased by approximately three times the base conductivity through a combination of inorganic substitution and functionalization.

Ab-initio Study of the Electron Mobility in a Functionalized UiO-66 Metal Organic Framework

NASA Astrophysics Data System (ADS)

Musho, Terence D.; Yasin, Alhassan S.

2018-07-01

This study leverages density functional theory accompanied with Boltzmann transport equation approaches to investigate the electronic mobility as a function of inorganic substitution and functionalization in a thermally stable UiO-66 metal-organic framework (MOF). The MOFs investigated are based on Zr-UiO-66 MOF with three functionalization groups of benzene dicarboxylate (BDC), BDC functionalized with an amino group (BDC + NH_2) and a nitro group (BDC + NO_2). The design space of this study is bound by UiO-66(M)-R, [M=Zr, Ti, Hf; R=BDC, BDC+NO_2, BDC+NH_2]. The elastic modulus was not found to vary significantly over the structural modification of the design space for either functionalization or inorganic substitution. However, the electron-phonon scattering potential was found to be controllable by up to 30% through controlled inorganic substitution in the metal clusters of the MOF structure. The highest electron mobility was predicted for a UiO-66(Hf_5Zr_1) achieving a value of approximately 1.4× 10^{-3} cm^2/V s. It was determined that functionalization provides a controlled method of modulating the charge density, while inorganic substitution provides a controlled method of modulating the electronic mobility. Within the proposed design space the electrical conductivity was able to be increased by approximately three times the base conductivity through a combination of inorganic substitution and functionalization.

Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin.

PubMed

Broco, Manuela; Soares, Cláudio M; Oliveira, Solange; Mayhew, Stephen G; Rodrigues-Pousada, Claudina

2007-09-18

Flavoredoxin participates in Desulfovibrio gigas thiosulfate reduction pathway. Its 3-dimensional model was generated allowing the oxidized riboflavin-5'-phosphate (FMN) site to be predicted. Residues likely to be involved in FMN-binding were identified (N29, W35, T56, K92, H131 and F164) and mutated to alanine. Fluorescence titration with apoprotein showed that FMN is strongly bound in the wild-type protein. Comparison of K(d) values for mutants suggests that interactions with the phosphate group of FMN, contribute more to binding than the interactions with the isoalloxazine ring. The redox potential of bound FMN determined for wild-type and mutants revealed shifts to less negative values. These findings were correlated with the protein structure in order to contribute to a better understanding of the structure-function relationships in flavoredoxin.

Moral satisficing: rethinking moral behavior as bounded rationality.

PubMed

Gigerenzer, Gerd

2010-07-01

What is the nature of moral behavior? According to the study of bounded rationality, it results not from character traits or rational deliberation alone, but from the interplay between mind and environment. In this view, moral behavior is based on pragmatic social heuristics rather than moral rules or maximization principles. These social heuristics are not good or bad per se, but solely in relation to the environments in which they are used. This has methodological implications for the study of morality: Behavior needs to be studied in social groups as well as in isolation, in natural environments as well as in labs. It also has implications for moral policy: Only by accepting the fact that behavior is a function of both mind and environmental structures can realistic prescriptive means of achieving moral goals be developed. Copyright © 2010 Cognitive Science Society, Inc.

Structure and Dynamics of Water/Methanol Mixtures at Hydroxylated Silica Interfaces Relevant to Chromatography.

PubMed

Gupta, Prashant Kumar; Meuwly, Markus

2016-09-19

The spectroscopy and dynamics of water/methanol (MeOH) mixtures at hydroxylated silica surfaces is investigated from atomistic simulations. The particular focus is on how the structural dynamics of MeOH changes when comparing surface-bound and MeOH in the bulk. From analyzing the frequency frequency correlation functions it is found that the dynamics on the picosecond time scale differs by almost a factor of two. While the relaxation time is 2.0 ps for MeOH in the bulk solvent it is considerably slowed-down to 3.5 ps for surface-bound MeOH. Surface-adsorbed MeOH molecules reside there for several nanoseconds and their H-bonds are strongly oriented towards the surface-OH groups. These results are of particular relevance for chromatographic systems where the solvent may play a central role in their function. The present simulations suggest that surface-sensitive spectroscopic techniques should be useful in better characterizing such heterogeneous systems and provide detailed insight into solvent dynamics and structure relevant in chromatographic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Eu(III) sorption to TiO2 (anatase and rutile): batch, XPS, and EXAFS studies.

PubMed

Tan, Xiaoli; Fan, Qiaohui; Wang, Xiangke; Grambow, Bernd

2009-05-01

The sorption of Eu(III) on anatase and rutile was studied as a function of ionic strength, humic acid (HA, 7.5 mg/L), and electrolyte anions over a large range of pH (2-12). The presence of HA significantly affected Eu(III) sorption to anatase and rutile. The sorption of Eu(III) on anatase and rutile was independent of ionic strength. Results of an X-ray photoelectron spectroscopy (XPS) analysis showed that Eu(III) was chemically present within the near-surface of TiO2 due to the formation of triple bond SOEu and triple bond SOHAEu complexes. An extended X-ray absorption fine structure (EXAFS) technique was applied to characterize the local structural environment of the adsorbed Eu(III), and the results indicated that Eu(III) was bound to about seven or eight O atoms at a distance of about 2.40 A. The functional groups of surface-bound HA were expected to be involved in the sorption process. The measured Eu-Ti distance confirmed the formation of inner-sphere sorption complexes on a TiO2 surface.

Discovery of Small Molecules that Inhibit the Disordered Protein, p27 Kip1

DOE PAGES

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; ...

2015-10-28

In disordered proteins we see that they are highly prevalent in biological systems. They control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27 Kip1 (p27). Moreover, two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groupsmore » of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule: disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of- principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).« less

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

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha

In disordered proteins we see that they are highly prevalent in biological systems. They control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27 Kip1 (p27). Moreover, two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groupsmore » of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule: disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of- principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).« less

[The effect of emotional stressors on thyroid gland function].

PubMed

Pastukhov, N A

1975-01-01

Response of the normal and goiterous thyroid gland to the information on the forthcoming operation was studied in 12 patients with varicose veins of the lower limbs and in 67 patients with thyrotoxicosis; this was done by determination of protein-bound iodine (PBI). PBI proved to increase before the operation in both groups of the patients. Due to undesirable hyperfunction of the thyroid gland prior to the operation in thyrotoxicosis, the psychodepressive premedication component should be increased.

Adsorbent catalytic nanoparticles and methods of using the same

DOEpatents

Slowing, Igor Ivan; Kandel, Kapil

2017-01-31

The present invention provides an adsorbent catalytic nanoparticle including a mesoporous silica nanoparticle having at least one adsorbent functional group bound thereto. The adsorbent catalytic nanoparticle also includes at least one catalytic material. In various embodiments, the present invention provides methods of using and making the adsorbent catalytic nanoparticles. In some examples, the adsorbent catalytic nanoparticles can be used to selectively remove fatty acids from feedstocks for biodiesel, and to hydrotreat the separated fatty acids.

K4[Fe(CN)6] immobilized anion sensitive protonated amine functionalized polysilsesquioxane films for ultra-low electrochemical detection of dsDNA.

PubMed

Silambarasan, Krishnamoorthy; Narendra Kumar, Alam Venugopal; Joseph, James

2016-03-14

Charge transport in polymeric films bound by redox reagents is a topic of current interest. The dynamics of electroinactive ions across the interface is studied by immobilizing ferrocyanide anion in a polysilsesquioxanes (PSQs) modified electrode. Redox reagents can stay in the polymeric film by either physical forces or electrostatic binding. The present work describes the immobilization of ferro/ferricyanide redox couples in PSQ films possessing protonated amine functional groups by electrostatic interactions. Charge transport in [Fe(CN)6](4-)-PSQs film was found to be anion dependent, and its formal potential value varied with the relative hydrophilic or hydrophobic nature of the anion used in the supporting electrolyte, unlike the observed dependence on solution cation for electrodes modified with metal hexacyanoferrates (Prussian Blue analogues). The [Fe(CN)6](4-) bound PSQs films were extensively characterized by varying different supporting electrolytes anions using cyclic voltammetry. The redox peak currents were linearly proportional to the square root of the scan rate, implying that the transport of charge carriers is accompanied with redox ion diffusion and electron hopping in a confined space. dsDNA molecules were found to interact with this polymer matrix through anionic phosphate groups. Both voltammetry and A.C. impedance spectroscopy studies revealed that these interactions could be exploited for the determination of ultra-low level (0.5 attomolar) of dsDNA present in aqueous solution.

Outward Bound in the Professional Education of Teachers. A Study of an Experimental Component in Field Experiences.

ERIC Educational Resources Information Center

Smathers, Keener M.

In an effort to measure the impact of Outward Bound (OB) education on teacher candidates, an 18-day stress experience was arranged for 12 Appalachian State University students and then compared with the effects of the normal 11-week student teacher experiences of two other groups. The OB group underwent a series of individual and group wilderness…

Communication: An exact bound on the bridge function in integral equation theories.

PubMed

Kast, Stefan M; Tomazic, Daniel

2012-11-07

We show that the formal solution of the general closure relation occurring in Ornstein-Zernike-type integral equation theories in terms of the Lambert W function leads to an exact relation between the bridge function and correlation functions, most notably to an inequality that bounds possible bridge values. The analytical results are illustrated on the example of the Lennard-Jones fluid for which the exact bridge function is known from computer simulations under various conditions. The inequality has consequences for the development of bridge function models and rationalizes numerical convergence issues.

The Scl1 protein of M6-type group A Streptococcus binds the human complement regulatory protein, factor H, and inhibits the alternative pathway of complement.

PubMed

Caswell, Clayton C; Han, Runlin; Hovis, Kelley M; Ciborowski, Pawel; Keene, Douglas R; Marconi, Richard T; Lukomski, Slawomir

2008-02-01

Non-specific activation of the complement system is regulated by the plasma glycoprotein factor H (FH). Bacteria can avoid complement-mediated opsonization and phagocytosis through acquiring FH to the cell surface. Here, we characterize an interaction between the streptococcal collagen-like protein Scl1.6 of M6-type group A Streptococcus (GAS) and FH. Using affinity chromatography with immobilized recombinant Scl1.6 protein, we co-eluted human plasma proteins with molecular weight of 155 kDa, 43 kDa and 38 kDa. Mass spectrometry identified the 155 kDa band as FH and two other bands as isoforms of the FH-related protein-1. The identities of all three bands were confirmed by Western immunoblotting with specific antibodies. Structure-function relation studies determined that the globular domain of the Scl1.6 variant specifically binds FH while fused to collagenous tails of various lengths. This binding is not restricted to Scl1.6 as the phylogenetically linked Scl1.55 variant also binds FH. Functional analyses demonstrated the cofactor activity of the rScl1.6-bound FH for factor I-mediated cleavage of C3b. Finally, purified FH bound to the Scl1.6 protein present in the cell wall material obtained from M6-type GAS. In conclusion, we have identified a functional interaction between Scl1 and plasma FH, which may contribute to GAS evasion of complement-mediated opsonization and phagocytosis.

Development of dialyzer with immobilized glycoconjugate polymers for removal of Shiga-toxin.

PubMed

Miyagawa, Atsushi; Watanabe, Miho; Igai, Katsura; Kasuya, Maria Carmelita Z; Natori, Yasuhiro; Nishikawa, Kiyotaka; Hatanaka, Kenichi

2006-06-01

The dialyzer for Shiga-toxin elimination was developed and its performance was established. The dialyzer was prepared by immobilization of multivalent ligands. Glycoconjugate polymers having oligosaccharides and amino groups were synthesized to function as Shiga-toxin adsorbents. The amino group was utilized to immobilize the polymer inside the cellulose hollow fiber of the dialyzer. Cellulose hollow fibers packed in the dialyzer were carboxymethylated under moderate conditions. The glycoconjugate polymers were bound covalently to the hollow fibers of the dialyzer by condensation reaction between the amino group of the polymer and the carboxyl group of the cellulose hollow fiber. Shiga-toxin eliminabilities of the prepared dialyzers were evaluated at various conditions. Even at high concentration of protein such as FCS, the dialyzer showed an excellent performance for Shiga-toxin adsorption.

Optical soliton solutions, periodic wave solutions and complexitons of the cubic Schrödinger equation with a bounded potential

NASA Astrophysics Data System (ADS)

Yan, Xue-Wei; Tian, Shou-Fu; Dong, Min-Jie; Zou, Li

2018-01-01

In this paper, we consider the cubic Schrödinger equation with a bounded potential, which describes the propagation properties of optical soliton solutions. By employing an ansatz method, we precisely derive the bright and dark soliton solutions of the equation. Moreover, we obtain three classes of analytic periodic wave solutions expressed in terms of the Jacobi's elliptic functions including cn ,sn and dn functions. Finally, by using a tanh function method, its complexitons solutions are derived in a very natural way. It is hoped that our results can enrich the nonlinear dynamical behaviors of the cubic Schrödinger equation with a bounded potential.

Uniform sparse bounds for discrete quadratic phase Hilbert transforms

NASA Astrophysics Data System (ADS)

Kesler, Robert; Arias, Darío Mena

2017-09-01

For each α \\in T consider the discrete quadratic phase Hilbert transform acting on finitely supported functions f : Z → C according to H^{α }f(n):= \\sum _{m ≠ 0} e^{iα m^2} f(n - m)/m. We prove that, uniformly in α \\in T , there is a sparse bound for the bilinear form < H^{α } f , g > for every pair of finitely supported functions f,g : Z→ C . The sparse bound implies several mapping properties such as weighted inequalities in an intersection of Muckenhoupt and reverse Hölder classes.

Interfacing nanostructures to biological cells

DOEpatents

Chen, Xing; Bertozzi, Carolyn R.; Zettl, Alexander K.

2012-09-04

Disclosed herein are methods and materials by which nanostructures such as carbon nanotubes, nanorods, etc. are bound to lectins and/or polysaccharides and prepared for administration to cells. Also disclosed are complexes comprising glycosylated nanostructures, which bind selectively to cells expressing glycosylated surface molecules recognized by the lectin. Exemplified is a complex comprising a carbon nanotube functionalized with a lipid-like alkane, linked to a polymer bearing repeated .alpha.-N-acetylgalactosamine sugar groups. This complex is shown to selectively adhere to the surface of living cells, without toxicity. In the exemplified embodiment, adherence is mediated by a multivalent lectin, which binds both to the cells and the .alpha.-N-acetylgalactosamine groups on the nanostructure.

Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.

PubMed

Townley, Robert; Shapiro, Lawrence

2007-03-23

The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.

Fitting Curves by Fractal Interpolation: AN Application to the Quantification of Cognitive Brain Processes

NASA Astrophysics Data System (ADS)

Navascues, M. A.; Sebastian, M. V.

Fractal interpolants of Barnsley are defined for any continuous function defined on a real compact interval. The uniform distance between the function and its approximant is bounded in terms of the vertical scale factors. As a general result, the density of the affine fractal interpolation functions of Barnsley in the space of continuous functions in a compact interval is proved. A method of data fitting by means of fractal interpolation functions is proposed. The procedure is applied to the quantification of cognitive brain processes. In particular, the increase in the complexity of the electroencephalographic signal produced by the execution of a test of visual attention is studied. The experiment was performed on two types of children: a healthy control group and a set of children diagnosed with an attention deficit disorder.

What Information Theory Says About Best Response and About Binding Contracts

NASA Technical Reports Server (NTRS)

Wolpert, David H.

2004-01-01

Product Distribution (PD) theory is the information-theoretic extension of conventional full- rationality game theory to bounded rational games. Here PD theory is used to investigate games in which the players use bounded rational best-response strategies. This investigation illuminates how to determine the optimal organization chart for a corporation, or more generally how to order the sequence of moves of the players / employees so as to optimize an overall objective function. It is then shown that in the continuum-time limit, bounded rational best response games result in a variant of the replicator dynamics of evolutionary game theory. This variant is then investigated for team games, in which the players share the same utility function, by showing that such continuum- limit bounded rational best response is identical to Newton-Raphson iterative optimization of the shared utility function. Next PD theory is used to investigate changing the coordinate system of the game, i.e., changing the mapping from the joint move of the players to the arguments in the utility functions. Such a change couples those arguments, essentially by making each players move be an offered binding contract.

Estimates on Functional Integrals of Quantum Mechanics and Non-relativistic Quantum Field Theory

NASA Astrophysics Data System (ADS)

Bley, Gonzalo A.; Thomas, Lawrence E.

2017-01-01

We provide a unified method for obtaining upper bounds for certain functional integrals appearing in quantum mechanics and non-relativistic quantum field theory, functionals of the form {E[{exp}(A_T)]} , the (effective) action {A_T} being a function of particle trajectories up to time T. The estimates in turn yield rigorous lower bounds for ground state energies, via the Feynman-Kac formula. The upper bounds are obtained by writing the action for these functional integrals in terms of stochastic integrals. The method is illustrated in familiar quantum mechanical settings: for the hydrogen atom, for a Schrödinger operator with {1/|x|^2} potential with small coupling, and, with a modest adaptation of the method, for the harmonic oscillator. We then present our principal applications of the method, in the settings of non-relativistic quantum field theories for particles moving in a quantized Bose field, including the optical polaron and Nelson models.

A note on bound constraints handling for the IEEE CEC'05 benchmark function suite.

PubMed

Liao, Tianjun; Molina, Daniel; de Oca, Marco A Montes; Stützle, Thomas

2014-01-01

The benchmark functions and some of the algorithms proposed for the special session on real parameter optimization of the 2005 IEEE Congress on Evolutionary Computation (CEC'05) have played and still play an important role in the assessment of the state of the art in continuous optimization. In this article, we show that if bound constraints are not enforced for the final reported solutions, state-of-the-art algorithms produce infeasible best candidate solutions for the majority of functions of the IEEE CEC'05 benchmark function suite. This occurs even though the optima of the CEC'05 functions are within the specified bounds. This phenomenon has important implications on algorithm comparisons, and therefore on algorithm designs. This article's goal is to draw the attention of the community to the fact that some authors might have drawn wrong conclusions from experiments using the CEC'05 problems.

Lieb-Robinson bounds for spin-boson lattice models and trapped ions.

PubMed

Jünemann, J; Cadarso, A; Pérez-García, D; Bermudez, A; García-Ripoll, J J

2013-12-06

We derive a Lieb-Robinson bound for the propagation of spin correlations in a model of spins interacting through a bosonic lattice field, which satisfies a Lieb-Robinson bound in the absence of spin-boson couplings. We apply these bounds to a system of trapped ions and find that the propagation of spin correlations, as mediated by the phonons of the ion crystal, can be faster than the regimes currently explored in experiments. We propose a scheme to test the bounds by measuring retarded correlation functions via the crystal fluorescence.

Lieb-Robinson bounds on n -partite connected correlation functions

NASA Astrophysics Data System (ADS)

Tran, Minh Cong; Garrison, James R.; Gong, Zhe-Xuan; Gorshkov, Alexey V.

2017-11-01

Lieb and Robinson provided bounds on how fast bipartite connected correlations can arise in systems with only short-range interactions. We generalize Lieb-Robinson bounds on bipartite connected correlators to multipartite connected correlators. The bounds imply that an n -partite connected correlator can reach unit value in constant time. Remarkably, the bounds also allow for an n -partite connected correlator to reach a value that is exponentially large with system size in constant time, a feature which stands in contrast to bipartite connected correlations. We provide explicit examples of such systems.

An Inserted α/β Subdomain Shapes the Catalytic Pocket of Lactobacillus johnsonii Cinnamoyl Esterase

PubMed Central

Vu, Clara; Xu, Xiaohui; Cui, Hong; Molloy, Sara; Savchenko, Alexei; Yakunin, Alexander; Gonzalez, Claudio F.

2011-01-01

Background Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. Methodology/Principal Findings We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical α/β fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser106, His225, and Asp197, while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted α/β subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. Conclusions The binding mechanism characterized (involving the inserted α/β subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases. PMID:21876742

An inserted α/β subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase.

PubMed

Lai, Kin-Kwan; Stogios, Peter J; Vu, Clara; Xu, Xiaohui; Cui, Hong; Molloy, Sara; Savchenko, Alexei; Yakunin, Alexander; Gonzalez, Claudio F

2011-01-01

Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical α/β fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser(106), His(225), and Asp(197), while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted α/β subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. The binding mechanism characterized (involving the inserted α/β subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases.

Ochratoxin A Dietary Exposure of Ten Population Groups in the Czech Republic: Comparison with Data over the World

PubMed Central

Ostry, Vladimir; Malir, Frantisek; Dofkova, Marcela; Skarkova, Jarmila; Pfohl-Leszkowicz, Annie; Ruprich, Jiri

2015-01-01

Ochratoxin A is a nephrotoxic and renal carcinogenic mycotoxin and is a common contaminant of various food commodities. Eighty six kinds of foodstuffs (1032 food samples) were collected in 2011–2013. High-performance liquid chromatography with fluorescence detection was used for ochratoxin A determination. Limit of quantification of the method varied between 0.01–0.2 μg/kg depending on the food matrices. The most exposed population is children aged 4–6 years old. Globally for this group, the maximum ochratoxin A dietary exposure for “average consumer” was estimated at 3.3 ng/kg bw/day (lower bound, considering the analytical values below the limit of quantification as 0) and 3.9 ng/kg bw/day (middle bound, considering the analytical values below the limit of quantification as 1/2 limit of quantification). Important sources of exposure for this latter group include grain-based products, confectionery, meat products and fruit juice. The dietary intake for “high consumers” in the group 4–6 years old was estimated from grains and grain-based products at 19.8 ng/kg bw/day (middle bound), from tea at 12.0 ng/kg bw/day (middle bound) and from confectionery at 6.5 ng/kg bw/day (middle bound). For men aged 18–59 years old beer was the main contributor with an intake of 2.60 ng/kg bw/day (“high consumers”, middle bound). Tea and grain-based products were identified to be the main contributors for dietary exposure in women aged 18–59 years old. Coffee and wine were identified as a higher contributor of the OTA intake in the population group of women aged 18–59 years old compared to the other population groups. PMID:26378578

Bounds on the cross-correlation functions of state m-sequences

NASA Astrophysics Data System (ADS)

Woodcock, C. F.; Davies, Phillip A.; Shaar, Ahmed A.

1987-03-01

Lower and upper bounds on the peaks of the periodic Hamming cross-correlation function for state m-sequences, which are often used in frequency-hopped spread-spectrum systems, are derived. The state position mapped (SPM) sequences of the state m-sequences are described. The use of SPM sequences for OR-channel code division multiplexing is studied. The relation between the Hamming cross-correlation function and the correlation function of SPM sequence is examined. Numerical results which support the theoretical data are presented.

Cooperation between bound waters and hydroxyls in controlling isotope-exchange rates

NASA Astrophysics Data System (ADS)

Panasci, Adele F.; McAlpin, J. Gregory; Ohlin, C. André; Christensen, Shauna; Fettinger, James C.; Britt, R. David; Rustad, James R.; Casey, William H.

2012-02-01

Mineral oxides differ from aqueous ions in that the bound water molecules are usually attached to different metal centers, or vicinal, and thus separated from one another. In contrast, for most monomeric ions used to establish kinetic reactivity trends, such as octahedral aquo ions (e.g., Al(H 2O) 63+), the bound waters are closely packed, or geminal. Because of this structural difference, the existing literature about ligand substitution in monomer ions may be a poor guide to the reactions of geochemical interest. To understand how coordination of the reactive functional groups might affect the rates of simple water-exchange reactions, we synthesized two structurally similar Rh(III) complexes, [Rh(phen) 2(H 2O) 2] 3+ [ 1] and [Rh(phen) 2(H 2O)Cl] 2+ [ 2] where (phen) = 1,10-phenanthroline. Complex [ 1] has two adjacent, geminal, bound waters in the inner-coordination sphere and [ 2] has a single bound water adjacent to a bound chloride ion. We employed Rh(III) as a trivalent metal rather than a more geochemically relevant metal like Fe(III) or Al(III) to slow the rate of reaction, which makes possible measurement of the rates of isotopic substitution by simple mass spectrometry. We prepared isotopically pure versions of the molecules, dissolved them into isotopically dissimilar water, and measured the rates of exchange from the extents of 18O and 16O exchange at the bound waters. The pH dependency of rates differ enormously between the two complexes. Pseudo-first-order rate coefficients at 298 K for water exchanges from the fully protonated molecules are close: k0298 = 5 × 10 -8(±0.5 × 10 -8) s -1 for [ 1] and k0298 = 2.5 × 10 -9(±1 × 10 -9) for [ 2]. Enthalpy and entropy activation parameters (Δ H‡ and Δ S‡) were measured to be 119(±3) kJ mol -1, and 14(±1) J mol -1 K -1, respectively for [ 1]. The corresponding parameters for the mono-aquo complex, [ 2], are 132(±3) kJ mol -1 and 41.5(±2) J mol -1 K -1. Rates increase by many orders of magnitude upon deprotonation of one of the bound waters in complex [ 1] because of the close proximity of a transferable proton that can convert the bound hydroxyl to a bound water. This interconversion allows the oxygen to exchange as a bound water, rather than as a bound hydroxyl, which is slow at near-neutral pH conditions.

Prebiotic replicase evolution in a surface-bound metabolic system: parasites as a source of adaptive evolution

PubMed Central

2008-01-01

Background The remarkable potential of recent forms of life for reliably passing on genetic information through many generations now depends on the coordinated action of thousands of specialized biochemical "machines" (enzymes) that were obviously absent in prebiotic times. Thus the question how a complicated system like the living cell could have assembled on Earth seems puzzling. In seeking for a scientific explanation one has to search for step-by-step evolutionary changes from prebiotic chemistry to the emergence of the first proto-cell. Results We try to sketch a plausible scenario for the first steps of prebiotic evolution by exploring the ecological feasibility of a mineral surface-bound replicator system that facilitates a primitive metabolism. Metabolism is a hypothetical network of simple chemical reactions producing monomers for the template-copying of RNA-like replicators, which in turn catalyse metabolic reactions. Using stochastic cellular automata (SCA) simulations we show that the surface-bound metabolic replicator system is viable despite internal competition among the genes and that it also maintains a set of mild "parasitic" sequences which occasionally evolve functions such as that of a replicase. Conclusion Replicase activity is shown to increase even at the expense of slowing down the replication of the evolving ribozyme itself, due to indirect mutualistic benefits in a diffuse form of group selection among neighbouring replicators. We suggest possible paths for further evolutionary changes in the metabolic replicator system leading to increased metabolic efficiency, improved replicase functionality, and membrane production. PMID:18826645

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

PubMed Central

Camilloni, Carlo; Sahakyan, Aleksandr B.; Holliday, Michael J.; Isern, Nancy G.; Zhang, Fengli; Eisenmesser, Elan Z.; Vendruscolo, Michele

2014-01-01

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as “peptidyl-prolyl isomerases” (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes. PMID:24982184

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism.

PubMed

Camilloni, Carlo; Sahakyan, Aleksandr B; Holliday, Michael J; Isern, Nancy G; Zhang, Fengli; Eisenmesser, Elan Z; Vendruscolo, Michele

2014-07-15

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as "peptidyl-prolyl isomerases" (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes.

Japanese Culture-Bound Disorders: The Relationship between "Taijin Kyofusho, Hikikomori," and Shame

ERIC Educational Resources Information Center

Cole, Levi Edward

2013-01-01

First conceptualized in the 1960s, the term culture-bound disorders refers to a classification of mental disorders or syndromes that are considered specific or closely related to cultural factors and or particular ethnocultural groups. In Japan, two culture-bound disorders, "taijin kyofusho" and "hikikomori," have seized the…

Upward Bound Math-Science: Program Description and Interim Impact Estimates

ERIC Educational Resources Information Center

Olsen, Robert; Seftor, Neil; Silva, Tim; Myers, David; DesRoches, David; Young, Julie

2007-01-01

To help address continuing disparities in academic achievement and under-representation of disadvantaged groups in math and science majors and careers, the U.S. Department of Education (ED) established a math and science initiative in 1990 within Upward Bound, a federal grant program known as Upward Bound Math-Science (UBMS) designed to provide…

Highly porous ceramic oxide aerogels having improved flexibility

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Nguyen, Baochau N. (Inventor)

2012-01-01

Ceramic oxide aerogels incorporating periodically dispersed flexible linkages are provided. The flexible linkages impart greater flexibility than the native aerogels without those linkages, and have been shown to reduce or eliminate the need for supercritical CO.sub.2-mediated drying of the corresponding wet gels. The gels may also be polymer cross-linked via organic polymer chains that are attached to and extend from surface-bound functional groups provided or present over the internal surfaces of a mesoporous ceramic oxide particle network via appropriate chemical reactions.

Bounds on Herglotz functions and fundamental limits of broadband passive quasistatic cloaking

NASA Astrophysics Data System (ADS)

Cassier, Maxence; Milton, Graeme W.

2017-07-01

Using a sum rule, we derive new bounds on Herglotz functions that generalize those given in Bernland et al. [J. Phys. A: Math. Theor. 44(14), 145205 (2011)] and Gustafsson and Sjöberg [New J. Phys. 12(4), 043046 (2010)]. These bounds apply to a wide class of linear passive systems such as electromagnetic passive materials. Among these bounds, we describe the optimal ones and also discuss their meaning in various physical situations like in the case of a transparency window, where we exhibit sharp bounds. Then, we apply these bounds in the context of broadband passive cloaking in the quasistatic regime to refute the following challenging question: is it possible to construct a passive cloaking device that cloaks an object over a whole frequency band? Our rigorous approach, although limited to quasistatics, gives quantitative limitations on the cloaking effect over a finite frequency range by providing inequalities on the polarizability tensor associated with the cloaking device. We emphasize that our results hold for a cloak or object of any geometrical shape.

Upper bounds on superpartner masses from upper bounds on the Higgs boson mass.

PubMed

Cabrera, M E; Casas, J A; Delgado, A

2012-01-13

The LHC is putting bounds on the Higgs boson mass. In this Letter we use those bounds to constrain the minimal supersymmetric standard model (MSSM) parameter space using the fact that, in supersymmetry, the Higgs mass is a function of the masses of sparticles, and therefore an upper bound on the Higgs mass translates into an upper bound for the masses for superpartners. We show that, although current bounds do not constrain the MSSM parameter space from above, once the Higgs mass bound improves big regions of this parameter space will be excluded, putting upper bounds on supersymmetry (SUSY) masses. On the other hand, for the case of split-SUSY we show that, for moderate or large tanβ, the present bounds on the Higgs mass imply that the common mass for scalars cannot be greater than 10(11)  GeV. We show how these bounds will evolve as LHC continues to improve the limits on the Higgs mass.

Process and composition for drying of gaseous hydrogen halides

DOEpatents

Tom, Glenn M.; Brown, Duncan W.

1989-08-01

A process for drying a gaseous hydrogen halide of the formula HX, wherein X is selected from the group consisting of bromine, chlorine, fluorine, and iodine, to remove water impurity therefrom, comprising: contacting the water impurity-containing gaseous hydrogen halide with a scavenger including a support having associated therewith one or more members of the group consisting of: (a) an active scavenging moiety selected from one or more members of the group consisting of: (i) metal halide compounds dispersed in the support, of the formula MX.sub.y ; and (ii) metal halide pendant functional groups of the formula -MX.sub.y-1 covalently bonded to the support, wherein M is a y-valent metal, and y is an integer whose value is from 1 to 3; (b) corresponding partially or fully alkylated compounds and/or pendant functional groups, of the metal halide compounds and/or pendant functional groups of (a); wherein the alkylated compounds and/or pendant functional groups, when present, are reactive with the gaseous hydrogen halide to form the corresponding halide compounds and/or pendant functional groups of (a); and M being selected such that the heat of formation, .DELTA.H.sub.f of its hydrated halide, MX.sub.y.(H.sub.2 O).sub.n, is governed by the relationship: .DELTA.H.sub.f .gtoreq.n.times.10.1 kilocalories/mole of such hydrated halide compound wherein n is the number of water molecules bound to the metal halide in the metal halide hydrate. Also disclosed is an appertaining scavenger composition and a contacting apparatus wherein the scavenger is deployed in a bed for contacting with the water impurity-containing gaseous hydrogen halide.

A first-principles study of methyl lactate adsorption on the chiral Cu (643) surface

NASA Astrophysics Data System (ADS)

Yuk, Simuck F.; Asthagiri, Aravind

2014-11-01

We used dispersion-corrected density function theory (DFT) to investigate the enantiospecific adsorption of R- and S-methyl lactate on the chiral Cu (643)R surface. Initial study of methyl lactate adsorbed on the Cu (111) surface revealed that the most strongly bound states are associated with interaction of the hydroxyl and alkoxide group with the surface. Using dispersion-corrected DFT-derived pre-factors and desorption energies within the Redhead analysis predicts peak temperatures that are in relatively good agreement with experimental values for molecular methyl lactate desorption from both the Cu (111) and Cu (643)R surface. The global minimum of S-methyl lactate is more firmly bound by 9.5 kJ/mol over its enantiomer on the Cu (643)R surface, with a peak temperature difference of 25 K versus an experimental value of 12 K.

Creation of Rydberg Polarons in a Bose Gas

NASA Astrophysics Data System (ADS)

Schmidt, Richard

2017-04-01

In this talk we review the theory of various types of Bose polarons that can be realized in ultracold atomic systems. We then report the spectroscopic observation of Rydberg polarons in a Bose gas which is in excellent agreement with theoretical predictions. This novel type of polaron is created by excitation of Rydberg atoms in a strontium Bose-Einstein condensate and it is distinguished by the occupation of a large number bound molecular states. The cross-over from few-body bound molecular oligomers to many-body polaron features is described with a functional determinant theory that solves an extended Froehlich Hamiltonian for an impurity in a Bose gas. The detailed analysis of the red-detuned tail of the excitation spectrum describes the contribution from the region of highest density in the condensate and provides a clear signature of Rydberg polarons. This work has been performed in collaboration with groups at Rice University, Harvard University, and the TU Vienna.

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

PubMed

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Optimized synthesis of phosphorothioate oligodeoxyribonucleotides substituted with a 5′-protected thiol function and a 3′-amino group

PubMed Central

Aubert, Yves; Bourgerie, Sylvain; Meunier, Laurent; Mayer, Roger; Roche, Annie-Claude; Monsigny, Michel; Thuong, Nguyen T.; Asseline, Ulysse

2000-01-01

A new deprotection procedure enables a medium scale preparation of phosphodiester and phosphorothioate oligonucleotides substituted with a protected thiol function at their 5′-ends and an amino group at their 3′-ends in good yield (up to 72 OD units/µmol for a 19mer phosphorothioate). Syntheses of 3′-amino-substituted oligonucleotides were carried out on a modified support. A linker containing the thioacetyl moiety was manually coupled in two steps by first adding its phosphoramidite derivative in the presence of tetrazole followed by either oxidation or sulfurization to afford the bis-derivatized oligonucleotide bound to the support. Deprotection was achieved by treating the fully protected oligonucleotide with a mixture of 2,2′-dithiodipyridine and concentrated aqueous ammonia in the presence of phenol and methanol. This procedure enables (i) cleavage of the oligonucleotide from the support, releasing the oligonucleotide with a free amino group at its 3′-end, (ii) deprotection of the phosphate groups and the amino functions of the nucleic bases, as well as (iii) transformation of the 5′-terminal S-acetyl function into a dithiopyridyl group. The bis-derivatized phosphorothioate oligomer was further substituted through a two-step procedure: first, the 3′-amino group was reacted with fluorescein isothiocyanate to yield a fluoresceinylated oligonucleotide; the 5′-dithiopyridyl group was then quantitatively reduced to give a free thiol group which was then substituted by reaction with an Nα-bromoacetyl derivative of a signal peptide containing a KDEL sequence to afford a fluoresceinylated peptide–oligonucleotide conjugate. PMID:10637335

Locating the Discontinuities of a Bounded Function by the Partial Sums of its Fourier Series I: Periodical Case

NASA Technical Reports Server (NTRS)

Kvernadze, George; Hagstrom,Thomas; Shapiro, Henry

1997-01-01

A key step for some methods dealing with the reconstruction of a function with jump discontinuities is the accurate approximation of the jumps and their locations. Various methods have been suggested in the literature to obtain this valuable information. In the present paper, we develop an algorithm based on identities which determine the jumps of a 2(pi)-periodic bounded not-too-highly oscillating function by the partial sums of its differentiated Fourier series. The algorithm enables one to approximate the locations of discontinuities and the magnitudes of jumps of a bounded function. We study the accuracy of approximation and establish asymptotic expansions for the approximations of a 27(pi)-periodic piecewise smooth function with one discontinuity. By an appropriate linear combination, obtained via derivatives of different order, we significantly improve the accuracy. Next, we use Richardson's extrapolation method to enhance the accuracy even more. For a function with multiple discontinuities we establish simple formulae which "eliminate" all discontinuities of the function but one. Then we treat the function as if it had one singularity following the method described above.

Photo-oxidative doping in π-conjugated zig-zag chain of carbon atoms with sulfur-functional group

NASA Astrophysics Data System (ADS)

Ikeura-Sekiguchi, Hiromi; Sekiguchi, Tetsuhiro

2017-12-01

Photo-oxidative doping processes were studied for the trans-polyacetylene backbone with the -SCH3 side group as a chemically representative of the precisely controlled S-functionalized zig-zag graphene nanoribbon edge. Sulfur K-edge X-ray absorption near edge structure (XANES) spectroscopy indicates that photochemical reaction of S-CH3 with atmospheric O2 forms selectively oxidized products such as -S(O)CH3 and -SO3- bound to the polyacetylene (PA) backbone. Using the correlation between the oxidation states of sulfur and the XANES peak positions, the partial charge distribution of CH3Sδ+-PAδ- has been estimated. Such positively charged sulfur atoms can attract higher electronegative oxygen atoms and expect to enhance the photooxidization capabilities. The formation of the -SO3- side group is evidently responsible for hole doping into the PA backbone. The results can provide some strategy for area-selective and controllable doping processes of atomic-scale molecular systems with the assistance of UV light.

The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family

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

Bade-Döding, Christina; Theodossis, Alex; Gras, Stephanie

2011-09-28

Polymorphic differences between human leukocyte antigen (HLA) molecules affect the specificity and conformation of their bound peptides and lead to differential selection of the T-cell repertoire. Mismatching during allogeneic transplantation can, therefore, lead to immunological reactions. We investigated the structure-function relationships of six members of the HLA-B*41 allelic group that differ by six polymorphic amino acids, including positions 80, 95, 97 and 114 within the antigen-binding cleft. Peptide-binding motifs for B*41:01, *41:02, *41:03, *41:04, *41:05 and *41:06 were determined by sequencing self-peptides from recombinant B*41 molecules by electrospray ionization tandem mass spectrometry. The crystal structures of HLA-B*41:03 bound to amore » natural 16-mer self-ligand (AEMYGSVTEHPSPSPL) and HLA-B*41:04 bound to a natural 11-mer self-ligand (HEEAVSVDRVL) were solved. Peptide analysis revealed that all B*41 alleles have an identical anchor motif at peptide position 2 (glutamic acid), but differ in their choice of C-terminal p{Omega} anchor (proline, valine, leucine). Additionally, B*41:04 displayed a greater preference for long peptides (>10 residues) when compared to the other B*41 allomorphs, while the longest peptide to be eluted from the allelic group (a 16mer) was obtained from B*41:03. The crystal structures of HLA-B*41:03 and HLA-B*41:04 revealed that both alleles interact in a highly conserved manner with the terminal regions of their respective ligands, while micropolymorphism-induced changes in the steric and electrostatic properties of the antigen-binding cleft account for differences in peptide repertoire and auxiliary anchoring. Differences in peptide repertoire, and peptide length specificity reflect the significant functional evolution of these closely related allotypes and signal their importance in allogeneic transplantation, especially B*41:03 and B*41:04, which accommodate longer peptides, creating structurally distinct peptide-HLA complexes.« less

A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts.

PubMed

Asakura, Yukari; Barkan, Alice

2007-12-01

The CRM domain is a recently recognized RNA binding domain found in three group II intron splicing factors in chloroplasts, in a bacterial protein that associates with ribosome precursors, and in a family of uncharacterized proteins in plants. To elucidate the functional repertoire of proteins with CRM domains, we studied CFM2 (for CRM Family Member 2), which harbors four CRM domains. RNA coimmunoprecipitation assays showed that CFM2 in maize (Zea mays) chloroplasts is associated with the group I intron in pre-trnL-UAA and group II introns in the ndhA and ycf3 pre-mRNAs. T-DNA insertions in the Arabidopsis thaliana ortholog condition a defective-seed phenotype (strong allele) or chlorophyll-deficient seedlings with impaired splicing of the trnL group I intron and the ndhA, ycf3-int1, and clpP-int2 group II introns (weak alleles). CFM2 and two previously described CRM proteins are bound simultaneously to the ndhA and ycf3-int1 introns and act in a nonredundant fashion to promote their splicing. With these findings, CRM domain proteins are implicated in the activities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.

Bounding the Failure Probability Range of Polynomial Systems Subject to P-box Uncertainties

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Kenny, Sean P.; Giesy, Daniel P.

2012-01-01

This paper proposes a reliability analysis framework for systems subject to multiple design requirements that depend polynomially on the uncertainty. Uncertainty is prescribed by probability boxes, also known as p-boxes, whose distribution functions have free or fixed functional forms. An approach based on the Bernstein expansion of polynomials and optimization is proposed. In particular, we search for the elements of a multi-dimensional p-box that minimize (i.e., the best-case) and maximize (i.e., the worst-case) the probability of inner and outer bounding sets of the failure domain. This technique yields intervals that bound the range of failure probabilities. The offset between this bounding interval and the actual failure probability range can be made arbitrarily tight with additional computational effort.

Bounds on OPE coefficients from interference effects in the conformal collider

NASA Astrophysics Data System (ADS)

Córdova, Clay; Maldacena, Juan; Turiaci, Gustavo J.

2017-11-01

We apply the average null energy condition to obtain upper bounds on the three-point function coefficients of stress tensors and a scalar operator, < TTOi>, in general CFTs. We also constrain the gravitational anomaly of U(1) currents in four-dimensional CFTs, which are encoded in three-point functions of the form 〈 T T J 〉. In theories with a large N AdS dual we translate these bounds into constraints on the coefficient of a higher derivative bulk term of the form ∫ϕ W 2. We speculate that these bounds also apply in de-Sitter. In this case our results constrain inflationary observables, such as the amplitude for chiral gravity waves that originate from higher derivative terms in the Lagrangian of the form ϕ W W ∗.

Majorana bound states in the finite-length chain

NASA Astrophysics Data System (ADS)

Zvyagin, A. A.

2015-08-01

Recent experiments investigating edge states in ferromagnetic atomic chains on superconducting substrate are analyzed. In particular, finite size effects are considered. It is shown how the energy of the Majorana bound state depends on the length of the chain, as well as on the parameters of the model. Oscillations of the energy of the bound edge state in the chain as a function of the length of the chain, and as a function of the applied voltage (or the chemical potential) are studied. In particular, it has been shown that oscillations can exist only for some values of the effective potential.

Thomson scattering in the average-atom approximation.

PubMed

Johnson, W R; Nilsen, J; Cheng, K T

2012-09-01

The average-atom model is applied to study Thomson scattering of x-rays from warm dense matter with emphasis on scattering by bound electrons. Parameters needed to evaluate the dynamic structure function (chemical potential, average ionic charge, free electron density, bound and continuum wave functions, and occupation numbers) are obtained from the average-atom model. The resulting analysis provides a relatively simple diagnostic for use in connection with x-ray scattering measurements. Applications are given to dense hydrogen, beryllium, aluminum, and titanium plasmas. In the case of titanium, bound states are predicted to modify the spectrum significantly.

Minimum-error quantum distinguishability bounds from matrix monotone functions: A comment on 'Two-sided estimates of minimum-error distinguishability of mixed quantum states via generalized Holevo-Curlander bounds' [J. Math. Phys. 50, 032106 (2009)

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

Tyson, Jon

2009-06-15

Matrix monotonicity is used to obtain upper bounds on minimum-error distinguishability of arbitrary ensembles of mixed quantum states. This generalizes one direction of a two-sided bound recently obtained by the author [J. Tyson, J. Math. Phys. 50, 032106 (2009)]. It is shown that the previously obtained special case has unique properties.

Bounds on the performance of a class of digital communication systems

NASA Technical Reports Server (NTRS)

Polk, D. R.; Gupta, S. C.; Cohn, D. L.

1973-01-01

Bounds on the capacity of a class of digital communication channels are derived. Equating the bounds on capacity to rate-distortion functions of (typical) sources in turn produces bounds on the performance of a class of digital communication systems. For ratios of squared quantization level to noise variance much less than one, the power requirements for this class of digital communication systems are shown to be within approximately 3 dB of the theoretical optimum.

Effects of PDGF-BB delivery from heparinized collagen sutures on the healing of lacerated chicken flexor tendon in vivo.

PubMed

Younesi, Mousa; Knapik, Derrick M; Cumsky, Jameson; Donmez, Baris Ozgur; He, Ping; Islam, Anowarul; Learn, Greg; McClellan, Philip; Bohl, Michael; Gillespie, Robert J; Akkus, Ozan

2017-11-01

Flexor tendon lacerations are traditionally repaired by using non-absorbable monofilament sutures. Recent investigations have explored to improve the healing process by growth factor delivery from the sutures. However, it is difficult to conjugate growth factors to nylon or other synthetic sutures. This study explores the performance of a novel electrochemically aligned collagen suture in a flexor tendon repair model with and without platelet derived growth factor following complete tendon laceration in vivo. Collagen suture was fabricated via electrochemical alignment process. Heparin was covalently bound to electrochemically aligned collagen sutures (ELAS) to facilitate affinity bound delivery of platelet-derived growth factor-BB (PDGF-BB). Complete laceration of the flexor digitorum profundus in the third digit of the foot was performed in 36 skeletally mature White Leghorn chickens. The left foot was used as the positive control. Animals were randomly divided into three groups: control specimens treated with standard nylon suture (n=12), specimens repaired with heparinated ELAS suture without PDGF-BB (n=12) and specimens repaired with heparinated ELAS suture with affinity bound PDGF-BB (n=12). Specimens were harvested at either 4weeks or 12weeks following tendon repair. Differences between groups were evaluated by the degree of gross tendon excursion, failure load/stress, stiffness/modulus, absorbed energy at failure, elongation/strain at failure. Quantitative histological scoring was performed to assess cellularity and vascularity. Closed flexion angle measurements demonstrated no significant differences in tendon excursion between the study groups at 4 or 12weeks. Biomechanical testing showed that the group treated with PDGF-BB bound heparinated ELAS suture had significantly higher stiffness and failure load (p<0.05) at 12-weeks relative to both heparinated ELAS suture and nylon suture. Similarly, the group treated with PDGF-BB bound suture had significantly higher ultimate tensile strength and Young's modulus (p<0.05) at 12-weeks relative to both ELAS suture and nylon suture. Compared to nylon controls, heparinized ELAS with PDGF-BB improved biomechanics and vascularity during tendon healing by 12-weeks following primary repair. The ability of ELAS to deliver PDGF-BB to the lacerated area of tendon presents investigators with a functional bioinductive platform to improve repair outcomes following flexor tendon repair. A high strength aligned collagen suture was fabricated via linear electrocompaction and heparinized for prolonged delivery of PDFG-BB. When it was used to suture a complete lacerated flexor tendon in a chicken model controlled release of the PDGF-BB improved the strength of treated tendon after 12 weeks compared to tendon sutured with commercial nylon suture. Furthermore, Collagen suture with affinity bound PDGF-BB enhanced the vascularization and remodeling of lacerated tendon when it compare to synthetic nylon suture. Overall, electrocompacted collagen sutures holds potential to improve repair outcome in flexor tendon surgeries by improving repair strength and stiffness, vascularity, and remodeling via sustained delivery of the PDGF-BB. The bioinductive collagen suture introduces a platform for sustained delivery of other growth factors for a wide-array of applications. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Dynamical error bounds for continuum discretisation via Gauss quadrature rules—A Lieb-Robinson bound approach

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

Woods, M. P.; Centre for Quantum Technologies, National University of Singapore; QuTech, Delft University of Technology, Lorentzweg 1, 2611 CJ Delft

2016-02-15

Instances of discrete quantum systems coupled to a continuum of oscillators are ubiquitous in physics. Often the continua are approximated by a discrete set of modes. We derive error bounds on expectation values of system observables that have been time evolved under such discretised Hamiltonians. These bounds take on the form of a function of time and the number of discrete modes, where the discrete modes are chosen according to Gauss quadrature rules. The derivation makes use of tools from the field of Lieb-Robinson bounds and the theory of orthonormal polynomials.

Identification of symptom and functional domains that fibromyalgia patients would like to see improved: a cluster analysis.

PubMed

Bennett, Robert M; Russell, Jon; Cappelleri, Joseph C; Bushmakin, Andrew G; Zlateva, Gergana; Sadosky, Alesia

2010-06-28

The purpose of this study was to determine whether some of the clinical features of fibromyalgia (FM) that patients would like to see improved aggregate into definable clusters. Seven hundred and eighty-eight patients with clinically confirmed FM and baseline pain > or =40 mm on a 100 mm visual analogue scale ranked 5 FM clinical features that the subjects would most like to see improved after treatment (one for each priority quintile) from a list of 20 developed during focus groups. For each subject, clinical features were transformed into vectors with rankings assigned values 1-5 (lowest to highest ranking). Logistic analysis was used to create a distance matrix and hierarchical cluster analysis was applied to identify cluster structure. The frequency of cluster selection was determined, and cluster importance was ranked using cluster scores derived from rankings of the clinical features. Multidimensional scaling was used to visualize and conceptualize cluster relationships. Six clinical features clusters were identified and named based on their key characteristics. In order of selection frequency, the clusters were Pain (90%; 4 clinical features), Fatigue (89%; 4 clinical features), Domestic (42%; 4 clinical features), Impairment (29%; 3 functions), Affective (21%; 3 clinical features), and Social (9%; 2 functional). The "Pain Cluster" was ranked of greatest importance by 54% of subjects, followed by Fatigue, which was given the highest ranking by 28% of subjects. Multidimensional scaling mapped these clusters to two dimensions: Status (bounded by Physical and Emotional domains), and Setting (bounded by Individual and Group interactions). Common clinical features of FM could be grouped into 6 clusters (Pain, Fatigue, Domestic, Impairment, Affective, and Social) based on patient perception of relevance to treatment. Furthermore, these 6 clusters could be charted in the 2 dimensions of Status and Setting, thus providing a unique perspective for interpretation of FM symptomatology.

Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.

PubMed

Stafford, Amy J; Ensign, Daniel L; Webb, Lauren J

2010-11-25

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

Kodiak: An Implementation Framework for Branch and Bound Algorithms

NASA Technical Reports Server (NTRS)

Smith, Andrew P.; Munoz, Cesar A.; Narkawicz, Anthony J.; Markevicius, Mantas

2015-01-01

Recursive branch and bound algorithms are often used to refine and isolate solutions to several classes of global optimization problems. A rigorous computation framework for the solution of systems of equations and inequalities involving nonlinear real arithmetic over hyper-rectangular variable and parameter domains is presented. It is derived from a generic branch and bound algorithm that has been formally verified, and utilizes self-validating enclosure methods, namely interval arithmetic and, for polynomials and rational functions, Bernstein expansion. Since bounds computed by these enclosure methods are sound, this approach may be used reliably in software verification tools. Advantage is taken of the partial derivatives of the constraint functions involved in the system, firstly to reduce the branching factor by the use of bisection heuristics and secondly to permit the computation of bifurcation sets for systems of ordinary differential equations. The associated software development, Kodiak, is presented, along with examples of three different branch and bound problem types it implements.

Imaginary-frequency polarizability and van der Waals force constants of two-electron atoms, with rigorous bounds

NASA Technical Reports Server (NTRS)

Glover, R. M.; Weinhold, F.

1977-01-01

Variational functionals of Braunn and Rebane (1972) for the imagery-frequency polarizability (IFP) have been generalized by the method of Gramian inequalities to give rigorous upper and lower bounds, valid even when the true (but unknown) unperturbed wavefunction must be represented by a variational approximation. Using these formulas in conjunction with flexible variational trial functions, tight error bounds are computed for the IFP and the associated two- and three-body van der Waals interaction constants of the ground 1(1S) and metastable 2(1,3S) states of He and Li(+). These bounds generally establish the ground-state properties to within a fraction of a per cent and metastable properties to within a few per cent, permitting a comparative assessment of competing theoretical methods at this level of accuracy. Unlike previous 'error bounds' for these properties, the present results have a completely a priori theoretical character, with no empirical input data.

On Nonlinear Functionals of Random Spherical Eigenfunctions

NASA Astrophysics Data System (ADS)

Marinucci, Domenico; Wigman, Igor

2014-05-01

We prove central limit theorems and Stein-like bounds for the asymptotic behaviour of nonlinear functionals of spherical Gaussian eigenfunctions. Our investigation combines asymptotic analysis of higher order moments for Legendre polynomials and, in addition, recent results on Malliavin calculus and total variation bounds for Gaussian subordinated fields. We discuss applications to geometric functionals like the defect and invariant statistics, e.g., polyspectra of isotropic spherical random fields. Both of these have relevance for applications, especially in an astrophysical environment.

Equation for the Nakanishi Weight Function Using the Inverse Stieltjes Transform

NASA Astrophysics Data System (ADS)

Karmanov, V. A.; Carbonell, J.; Frederico, T.

2018-05-01

The bound state Bethe-Salpeter amplitude was expressed by Nakanishi in terms of a smooth weight function g. By using the generalized Stieltjes transform, we derive an integral equation for the Nakanishi function g for a bound state case. It has the standard form g= \\hat{V} g, where \\hat{V} is a two-dimensional integral operator. The prescription for obtaining the kernel V starting with the kernel K of the Bethe-Salpeter equation is given.

Coulomb bound states of strongly interacting photons

DOE PAGES

Maghrebi, M. F.; Gullans, Michael J.; Bienias, P.; ...

2015-09-16

We show that two photons coupled to Rydberg states via electromagnetically induced transparency (EIT) can interact via an effective Coulomb potential. The interaction then gives rise to a continuum of two-body bound states. Within the continuum, metastable bound states are distinguished in analogy with quasi-bound states tunneling through a potential barrier. We find multiple branches of metastable bound states whose energy spectrum is governed by the Coulomb problem, thus obtaining a photonic analogue of the hydrogen atom. These states propagate with a negative group velocity in the medium, which allows for a simple preparation and detection scheme, before they slowlymore » decay to pairs of bound Rydberg atoms. As a result, we verify the metastability and backward propagation of these Coulomb bound states with exact numerical simulations.« less

Group IV nanocrystals with ion-exchangeable surface ligands and methods of making the same

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

Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.

Methods are described that include reacting a starting nanocrystal that includes a starting nanocrystal core and a covalently bound surface species to create an ion-exchangeable (IE) nanocrystal that includes a surface charge and a first ion-exchangeable (IE) surface ligand ionically bound to the surface charge, where the starting nanocrystal core includes a group IV element.

City Kids in the Wilderness: A Pilot-Test of Outward Bound for Foster Care Group Home Youth.

ERIC Educational Resources Information Center

Fischer, Robert L.; Attah, E. B.

2001-01-01

A study examined perceptions of a 7-day Outward Bound program among 23 urban youths, foster parents, and foster care workers from group homes in Atlanta (Georgia). Foster parents reported improved self-esteem and behavior among the teens, but foster care workers reported worse behavior. Negative program impressions lessened among male youths but…

Improving the Lieb-Robinson Bound for Long-Range Interactions

NASA Astrophysics Data System (ADS)

Matsuta, Takuro; Koma, Tohru; Nakamura, Shu

2017-02-01

We improve the Lieb-Robinson bound for a wide class of quantum many-body systems with long-range interactions decaying by power law. As an application, we show that the group velocity of information propagation grows by power law in time for such systems, whereas systems with short-range interactions exhibit a finite group velocity as shown by Lieb and Robinson.

Exploring the Origin of Blue and Ultraviolet Fluorescence in Graphene Oxide.

PubMed

Kozawa, Daichi; Miyauchi, Yuhei; Mouri, Shinichiro; Matsuda, Kazunari

2013-06-20

We studied the fluorescence (FL) properties of highly exfoliated graphene oxide (GO) in aqueous solution using continuous-wave and time-resolved FL spectroscopy. The FL spectra of highly exfoliated GO showed two distinct peaks at ∼440 (blue) and ∼300 nm [ultraviolet (UV)]. The FL of GO in the UV region at ∼300 nm was observed for the first time. The average FL lifetimes of the emission peaks at ∼440 and ∼300 nm are 8-13 and 6-8 ns, respectively. The experimentally observed peak wavelengths of pH-dependent FL, FL excitation spectra, and the FL lifetimes are nearly coincident with those of aromatic compounds bound with oxygen functional groups, which suggests that the FL comes from sp(2) fragments consisting of small numbers of aromatic rings with oxygen functional groups acting as FL centers in the GO.

Supramolecular gating of ion transport in nanochannels.

PubMed

Kumar, B V V S Pavan; Rao, K Venkata; Sampath, S; George, Subi J; Eswaramoorthy, Muthusamy

2014-11-24

Several covalent strategies towards surface charge-reversal in nanochannels have been reported with the purpose of manipulating ion transport. However, covalent routes lack dynamism, modularity and post-synthetic flexibility, and hence restrict their applicability in different environments. Here, we introduce a facile non-covalent approach towards charge-reversal in nanochannels (<10 nm) using strong charge-transfer interactions between dicationic viologen (acceptor) and trianionic pyranine (donor). The polarity of ion transport was switched from anion selective to ambipolar to cation selective by controlling the extent of viologen bound to the pyranine. We could also regulate the ion transport with respect to pH by selecting a donor with pH-responsive functional groups. The modularity of this approach further allows facile integration of various functional groups capable of responding to stimuli such as light and temperature to modulate the transport of ions as well as molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Froissart bound and self-similarity based models of proton structure functions

NASA Astrophysics Data System (ADS)

Choudhury, D. K.; Saikia, Baishali

2018-03-01

Froissart bound implies that the total proton-proton cross-section (or equivalently proton structure function) cannot rise faster than log2s ˜log2 1 x. Compatibility of such behavior with the notion of self-similarity in proton structure function was suggested by us sometime back. In the present work, we generalize and improve it further by considering more recent self-similarity based models of proton structure functions and compare with recent data as well as with the model of Block, Durand, Ha and McKay.

Variation of preserving organic matter bound in interlayer of montmorillonite induced by microbial metabolic process.

PubMed

Zhao, Yulian; Dong, Faqin; Dai, Qunwei; Li, Gang; Ma, Jie

2017-07-25

This paper aimed to investigate the variation of preserving organic matter bound in the interlayer space of montmorillonite (Mt) induced by a microbe metabolic process. We selected Bacillus pumilus as the common soil native bacteria. The alteration of d 001 value, functional group, and C,N organic matter contents caused by bacteria were analyzed by XRD, FTIR, and elementary analyzer, respectively. XRD results showed that the d 001 value of montmorillonite increased with the concentration decreasing and decreased with the culture time increasing after interacting with bacteria indicating the interlayer space of montmorillonite was connected with the organic matter. The findings of long-term interaction by resetting culture conditions implied that the montmorillonite buffered the organic matter when the nutrition was enough and released again when the nutrition was lacking. The results of the elementary analyzer declared the content of organic matter was according to the d 001 value of montmorillonite and N organic matter which played a major impact. FTIR results confirmed that the Si-O stretching vibrations of Mt were affected by the functional group of organic matter. Our results showed that the montmorillonite under the influence of soil bacteria has a strong buffering capacity for preserving organic matter into the interlayer space in a short-term. It might provide critical implications for understanding the evolution process and the preservation of fertilization which was in the over-fertilization or less-fertilization conditions on farmland.

Bacterial cell surface properties: role of loosely bound extracellular polymeric substances (LB-EPS).

PubMed

Zhao, Wenqiang; Yang, Shanshan; Huang, Qiaoyun; Cai, Peng

2015-04-01

This study investigated the effect of loosely bound extracellular polymeric substances (LB-EPS) on the comprehensive surface properties of four bacteria (Bacillus subtilis, Streptococcus suis, Escherichia coli and Pseudomonas putida). The removal of LB-EPS from bacterial surfaces by high-speed centrifugation (12,000×g) was confirmed by SEM images. Viability tests showed that the percentages of viable cells ranged from 95.9% to 98.0%, and no significant difference was found after treatment (P>0.05). FTIR spectra revealed the presence of phosphodiester, carboxylic, phosphate, and amino functional groups on bacteria surfaces, and the removal of LB-EPS did not alter the types of cell surface functional groups. Potentiometric titration results suggested the total site concentrations on the intact bacteria were higher than those on LB-EPS free bacteria. Most of the acidity constants (pKa) were almost identical, except the increased pKa values of phosphodiester groups on LB-EPS free S. suis and E. coli surfaces. The electrophoretic mobilities and hydrodynamic diameters of the intact and LB-EPS free bacteria were statistically unchanged (P>0.05), indicating LB-EPS had no influence on the net surface charges and size distribution of bacteria. However, LB-ESP could enhance cell aggregation processes. The four LB-EPS free bacteria all exhibited fewer hydrophobicity values (26.1-65.0%) as compared to the intact cells (47.4-69.3%), suggesting the removal of uncharged nonpolar compounds (e.g., carbohydrates) in LB-EPS. These findings improve our understanding of the changes in cell surface characterizations induced by LB-EPS, and have important implications for assessing the role of LB-EPS in bacterial adhesion and transport behaviors. Copyright © 2015 Elsevier B.V. All rights reserved.

N-METHYL GROUPS IN BACTERIAL LIPIDS

PubMed Central

Goldfine, Howard; Ellis, Martha E.

1964-01-01

Goldfine, Howard (Harvard Medical School, Boston, Mass.), and Martha E. Ellis. N-methyl groups in bacterial lipids. J. Bacteriol. 87:8–15. 1964.—The ability of bacteria to synthesize lecithin was examined by measuring the incorporation of the methyl group of methionine into the water-soluble moieties obtained on acid hydrolysis of bacterial lipids. Of 21 species examined, mostly of the order Eubacteriales, only 2, Agrobacterium radiobacter and A. rhizogenes, incorporated the methyl group of methionine into lipid-bound choline. Evidence was also obtained for the formation of lipid-bound N-methylethanolamine and N,N′-dimethylethanolamine in these two organisms. Two other species, Clostridium butyricum and Proteus vulgaris, incorporated the methyl group of methionine into lipid-bound N-methylethanolamine, but did not appear to be able to further methylate these lipids to form lecithin. The results of this study lend further strength to the generalization that bacteria, with the exception of the genus Agrobacterium, are unable to synthesize lecithin. PMID:14102879

An upper bound on the radius of a highly electrically conducting lunar core

NASA Technical Reports Server (NTRS)

Hobbs, B. A.; Hood, L. L.; Herbert, F.; Sonett, C. P.

1983-01-01

Parker's (1980) nonlinear inverse theory for the electromagnetic sounding problem is converted to a form suitable for analysis of lunar day-side transfer function data by: (1) transforming the solution in plane geometry to that in spherical geometry; and (2) transforming the theoretical lunar transfer function in the dipole limit to an apparent resistivity function. The theory is applied to the revised lunar transfer function data set of Hood et al. (1982), which extends in frequency from 10 to the -5th to 10 to the -3rd Hz. On the assumption that an iron-rich lunar core, whether molten or solid, can be represented by a perfect conductor at the minimum sampled frequency, an upper bound of 435 km on the maximum radius of such a core is calculated. This bound is somewhat larger than values of 360-375 km previously estimated from the same data set via forward model calculations because the prior work did not consider all possible mantle conductivity functions.

Assigning uncertainties in the inversion of NMR relaxation data.

PubMed

Parker, Robert L; Song, Yi-Qaio

2005-06-01

Recovering the relaxation-time density function (or distribution) from NMR decay records requires inverting a Laplace transform based on noisy data, an ill-posed inverse problem. An important objective in the face of the consequent ambiguity in the solutions is to establish what reliable information is contained in the measurements. To this end we describe how upper and lower bounds on linear functionals of the density function, and ratios of linear functionals, can be calculated using optimization theory. Those bounded quantities cover most of those commonly used in the geophysical NMR, such as porosity, T(2) log-mean, and bound fluid volume fraction, and include averages over any finite interval of the density function itself. In the theory presented statistical considerations enter to account for the presence of significant noise in the signal, but not in a prior characterization of density models. Our characterization of the uncertainties is conservative and informative; it will have wide application in geophysical NMR and elsewhere.

Semilocal density functional obeying a strongly tightened bound for exchange

PubMed Central

Sun, Jianwei; Perdew, John P.; Ruzsinszky, Adrienn

2015-01-01

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb–Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic “meta-GGA made very simple” (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew–Burke–Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules. PMID:25561554

Semilocal density functional obeying a strongly tightened bound for exchange.

PubMed

Sun, Jianwei; Perdew, John P; Ruzsinszky, Adrienn

2015-01-20

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb-Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic "meta-GGA made very simple" (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew-Burke-Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules.

Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

PubMed

Liu, Liyan; Zhang, Ruifeng; Liu, Ying; Tan, Wei; Zhu, Guorui

2018-05-28

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

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

Wilson, E.B. Jr.

Various methods for the calculation of lower bounds for eigenvalues are examined, including those of Weinstein, Temple, Bazley and Fox, Gay, and Miller. It is shown how all of these can be derived in a unified manner by the projection technique. The alternate forms obtained for the Gay formula show how a considerably improved method can be readily obtained. Applied to the ground state of the helium atom with a simple screened hydrogenic trial function, this new method gives a lower bound closer to the true energy than the best upper bound obtained with this form of trial function. Possiblemore » routes to further improved methods are suggested.« less

Upper Bounds on the Expected Value of a Convex Function Using Gradient and Conjugate Function Information.

DTIC Science & Technology

1987-08-01

of the absolute difference between the random variable and its mean.Gassmann and Ziemba 119861 provide a weaker bound that does not require...2.8284, and EX4tV) -12 EX’iX) = -42. Hence C = -2 -€t* i-4’]= I-- . 1213. £1 2 5 COMPARISONS OF BOUNDS IN IIn Gassmann and Ziemba 11986) extend an idea...solution of the foLLowing Linear program: (see Gassmann, Ziemba (1986),Theorem 1) m m m-GZ=max(XT(vi) I: z. 1=1,Z vo=x io (5.1hk i-l i=i i=1 I I where 0

The isolation limits of stochastic vibration

NASA Technical Reports Server (NTRS)

Knopse, C. R.; Allaire, P. E.

1993-01-01

The vibration isolation problem is formulated as a 1D kinematic problem. The geometry of the stochastic wall trajectories arising from the stroke constraint is defined in terms of their significant extrema. An optimal control solution for the minimum acceleration return path determines a lower bound on platform mean square acceleration. This bound is expressed in terms of the probability density function on the significant maxima and the conditional fourth moment of the first passage time inverse. The first of these is found analytically while the second is found using a Monte Carlo simulation. The rms acceleration lower bound as a function of available space is then determined through numerical quadrature.

Asymptotic expansions of solutions of the heat conduction equation in internally bounded cylindrical geometry

USGS Publications Warehouse

Ritchie, R.H.; Sakakura, A.Y.

1956-01-01

The formal solutions of problems involving transient heat conduction in infinite internally bounded cylindrical solids may be obtained by the Laplace transform method. Asymptotic series representing the solutions for large values of time are given in terms of functions related to the derivatives of the reciprocal gamma function. The results are applied to the case of the internally bounded infinite cylindrical medium with, (a) the boundary held at constant temperature; (b) with constant heat flow over the boundary; and (c) with the "radiation" boundary condition. A problem in the flow of gas through a porous medium is considered in detail.

A complex ligase ribozyme evolved in vitro from a group I ribozyme domain

NASA Technical Reports Server (NTRS)

Jaeger, L.; Wright, M. C.; Joyce, G. F.; Bada, J. L. (Principal Investigator)

1999-01-01

Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.

Bound states in string nets

NASA Astrophysics Data System (ADS)

Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien

2016-11-01

We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

What Information Theory Says about Bounded Rational Best Response

NASA Technical Reports Server (NTRS)

Wolpert, David H.

2005-01-01

Probability Collectives (PC) provides the information-theoretic extension of conventional full-rationality game theory to bounded rational games. Here an explicit solution to the equations giving the bounded rationality equilibrium of a game is presented. Then PC is used to investigate games in which the players use bounded rational best-response strategies. Next it is shown that in the continuum-time limit, bounded rational best response games result in a variant of the replicator dynamics of evolutionary game theory. It is then shown that for team (shared-payoff) games, this variant of replicator dynamics is identical to Newton-Raphson iterative optimization of the shared utility function.

Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

PubMed

Zhang, Changzhe; Bu, Yuxiang

2016-09-14

Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

Effectiveness of Qigong in promoting the health of wheelchair-bound older adults in long-term care facilities.

PubMed

Kuan, Shu-Chien; Chen, Kuei-Min; Wang, Chi

2012-04-01

Institutional wheelchair-bound older adults often do not get regular exercise and are prone to health problems. The aim of this study was to test the effects of a 12-week qigong exercise program on the physiological and psychological health of wheelchair-bound older adults in long-term care facilities. Study design was quasi-experimental, pre-post test, nonequivalent control group. Participants comprised a convenience sample of 72 wheelchair-bound older adults (qigong = 34; control = 38). The qigong group exercised 35 min/day, 5 days/week for 12 weeks. Measures for physical health (blood pressure, heart rate variability, and distal skin temperature) and psychological health (Brief Symptom Rating Scale-5) were collected before and during study Weeks 4, 8, and 12. The qigong group participants' blood pressure, distal skin temperature, and psychological health were significantly improved (all p < .001). These findings suggest that qigong exercise is a suitable daily activity for elderly residents in long-term care facilities and may help in the control of blood pressure among older adults.

Pre-Mission Communication And Awareness Stratgies For Positive Group Functioning And Development: Analysis Of A Crew At The Mars Desert Research Station (MDRS) In Utah, USA

NASA Astrophysics Data System (ADS)

Allner, Matthew; Bishop, Sheryl; Gushin, Vadim; McKay, Chris; Rygalov, Vadim; Allner, Matthew

Introduction: Psychosocial group functioning has become an increased international focus of many space faring nations due to the recent shift in focus of colonizing the Moon and then preparing to travel to Mars and beyond. Purpose: This study investigates the effects of pre-mission communication and awareness strategies for positive group functioning in extreme environments as well as suggestive countermeasures to maintain positive group dynamic development in isolated and confined extreme (ICE) environments. The study is supported by both preand intra-mission management efforts, which included crewmember assessments at various mission phases (pre-, intra-, and end-mission). Methods: A six person heterogeneous American crew conducted a Mars simulation mission at the Mars Society's Mars Desert Research Station in Utah, USA in 2006 as part of a new NASA training program called Spaceward Bound. Participants were administered assessments of personality, personal and group identity/functioning, subjective stress, coping, and subjective motivation. All participants were also provided information (pre-mission) regarding past research and tendencies of group functioning, stressors, cognitive functioning, and mission mistakes from a mission phase analysis approach, to see if this would be a factor in positive group dynamic development. Results: Data collected and obtained by both assessment and journaling methods were both consistent and indicative of positive personalities desirable of expedition crews. Assessment data further indicated positive group cohesion and group interactions, along with supportive and strong leadership, all which led to positive personal and group experiences for crewmembers. Crewmembers all displayed low levels of competition while still reporting high motivation and satisfaction for the group dynamic development and the mission objectives that were completed. Journals kept by the crew psychologist indicated that crewmembers all felt that the pre-mission awareness of group dynamic development tendencies of past expedition crews was integral in maintaining crew cohesiveness throughout the mission. Crewmembers felt that raising the level of awareness, both preand intra-mission, served as a positive factor in the overall positive group dynamic development of the crew.

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study.

PubMed

Dudev, Todor; Chang, Li-Ying; Lim, Carmay

2005-03-23

Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.

A Langevin dynamics simulation study of the tribology of polymer loop brushes.

PubMed

Yin, Fang; Bedrov, Dmitry; Smith, Grant D; Kilbey, S Michael

2007-08-28

The tribology of surfaces modified with doubly bound polymer chains (loops) has been investigated in good solvent conditions using Langevin dynamics simulations. The density profiles, brush interpenetration, chain inclination, normal forces, and shear forces for two flat substrates modified by doubly bound bead-necklace polymers and equivalent singly bound polymers (twice as many polymer chains of 12 the molecular weight of the loop chains) were determined and compared as a function of surface separation, grafting density, and shear velocity. The doubly bound polymer layers showed less interpenetration with decreasing separation than the equivalent singly bound layers. Surprisingly, this difference in interpenetration between doubly bound polymer and singly bound polymer did not result in decreased friction at high shear velocity possibly due to the decreased ability of the doubly bound chains to deform in response to the applied shear. However, at lower shear velocity, where deformation of the chains in the flow direction is less pronounced and the difference in interpenetration is greater between the doubly bound and singly bound chains, some reduction in friction was observed.

Atomic resolution view into the structure–function relationships of the human myelin peripheral membrane protein P2

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

Ruskamo, Salla; University of Oulu, Oulu; Yadav, Ravi P.

2014-01-01

The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure–function relationships in P2 are emerging. P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structuralmore » analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.« less

Zero-Bounded Limits as a Special Case of the Squeeze Theorem for Evaluating Single-Variable and Multivariable Limits

ERIC Educational Resources Information Center

Gkioulekas, Eleftherios

2013-01-01

Many limits, typically taught as examples of applying the "squeeze" theorem, can be evaluated more easily using the proposed zero-bounded limit theorem. The theorem applies to functions defined as a product of a factor going to zero and a factor that remains bounded in some neighborhood of the limit. This technique is immensely useful…

Biosensor platform based on carbon nanotubes covalently modified with aptamers

NASA Astrophysics Data System (ADS)

Komarov, I. A.; Rubtsova, E. I.; Golovin, A. V.; Bobrinetskiy, I. I.

2016-12-01

We developed a new platform for biosensing applications. Aptamers as sensitive agents have a great potential and gives us possibility to have highest possible selectivity among other sensing agents like enzymes or antibodies. We covalently bound aptamers to the functional groups of c-CNTs and then put this system on the surface of polymer substrate. Thus we got high sensitive flexible transparent biological sensors. We also suggest that by varying aptamer type we can make set of biosensors for disease detection which can be integrated into self-healthcare systems and gadgets.

Finite-Time Attitude Tracking Control for Spacecraft Using Terminal Sliding Mode and Chebyshev Neural Network.

PubMed

An-Min Zou; Kumar, K D; Zeng-Guang Hou; Xi Liu

2011-08-01

A finite-time attitude tracking control scheme is proposed for spacecraft using terminal sliding mode and Chebyshev neural network (NN) (CNN). The four-parameter representations (quaternion) are used to describe the spacecraft attitude for global representation without singularities. The attitude state (i.e., attitude and velocity) error dynamics is transformed to a double integrator dynamics with a constraint on the spacecraft attitude. With consideration of this constraint, a novel terminal sliding manifold is proposed for the spacecraft. In order to guarantee that the output of the NN used in the controller is bounded by the corresponding bound of the approximated unknown function, a switch function is applied to generate a switching between the adaptive NN control and the robust controller. Meanwhile, a CNN, whose basis functions are implemented using only desired signals, is introduced to approximate the desired nonlinear function and bounded external disturbances online, and the robust term based on the hyperbolic tangent function is applied to counteract NN approximation errors in the adaptive neural control scheme. Most importantly, the finite-time stability in both the reaching phase and the sliding phase can be guaranteed by a Lyapunov-based approach. Finally, numerical simulations on the attitude tracking control of spacecraft in the presence of an unknown mass moment of inertia matrix, bounded external disturbances, and control input constraints are presented to demonstrate the performance of the proposed controller.

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

DOE PAGES

Isaacs, Eric B.; Wolverton, Chris

2018-06-22

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

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

Isaacs, Eric B.; Wolverton, Chris

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Resin-Bound Crypto-Thioester for Native Chemical Ligation.

PubMed

Naruse, Naoto; Ohkawachi, Kento; Inokuma, Tsubasa; Shigenaga, Akira; Otaka, Akira

2018-04-20

The resin-bound N-sulfanylethylanilide (SEAlide) peptide was found to function as a crypto-thioester peptide. Exposure of the peptide resin to an aqueous solution under neutral conditions in the presence of thiols affords thioesters without accompanying racemization of C-terminal amino acids. Furthermore, the resin-bound SEAlide peptides react with N-terminal cysteinyl peptides in the absence of phosphate salts to afford ligated products, whereas soluble SEAlide peptides do not. This unexpected difference in reactivity of the SEAlide peptides allows for a one-pot/three-fragment ligation using resin-bound and unbound peptides.

Comonotonic bounds on the survival probabilities in the Lee-Carter model for mortality projection

NASA Astrophysics Data System (ADS)

Denuit, Michel; Dhaene, Jan

2007-06-01

In the Lee-Carter framework, future survival probabilities are random variables with an intricate distribution function. In large homogeneous portfolios of life annuities, value-at-risk or conditional tail expectation of the total yearly payout of the company are approximately equal to the corresponding quantities involving random survival probabilities. This paper aims to derive some bounds in the increasing convex (or stop-loss) sense on these random survival probabilities. These bounds are obtained with the help of comonotonic upper and lower bounds on sums of correlated random variables.

Synthesis of surface bound silver nanoparticles on cellulose fibers using lignin as multi-functional agent.

PubMed

Hu, Sixiao; Hsieh, You-Lo

2015-10-20

Lignin has proven to be highly effective "green" multi-functional binding, complexing and reducing agents for silver cations as well as capping agents for the synthesis of silver nanoparticles on ultra-fine cellulose fibrous membranes. Silver nanoparticles could be synthesized in 10min to be densely distributed and stably bound on the cellulose fiber surfaces at up to 2.9% in mass. Silver nanoparticle increased in sizes from 5 to 100nm and became more polydispersed in size distribution on larger fibers and with longer synthesis time. These cellulose fiber bound silver nanoparticles did not agglomerate under elevated temperatures and showed improved thermal stability. The presence of alkali lignin conferred moderate UV absorbing ability in both UV-B and UV-C regions whereas the bound silver nanoparticles exhibited excellent antibacterial activities toward Escherichia coli. Copyright © 2015 Elsevier Ltd. All rights reserved.

Performance bounds for nonlinear systems with a nonlinear ℒ2-gain property

NASA Astrophysics Data System (ADS)

Zhang, Huan; Dower, Peter M.

2012-09-01

Nonlinear ℒ2-gain is a finite gain concept that generalises the notion of conventional (linear) finite ℒ2-gain to admit the application of ℒ2-gain analysis tools of a broader class of nonlinear systems. The computation of tight comparison function bounds for this nonlinear ℒ2-gain property is important in applications such as small gain design. This article presents an approximation framework for these comparison function bounds through the formulation and solution of an optimal control problem. Key to the solution of this problem is the lifting of an ℒ2-norm input constraint, which is facilitated via the introduction of an energy saturation operator. This admits the solution of the optimal control problem of interest via dynamic programming and associated numerical methods, leading to the computation of the proposed bounds. Two examples are presented to demonstrate this approach.

The condition of a finite Markov chain and perturbation bounds for the limiting probabilities

NASA Technical Reports Server (NTRS)

Meyer, C. D., Jr.

1979-01-01

The inequalities bounding the relative error the norm of w- w squiggly/the norm of w are exhibited by a very simple function of E and A. Let T denote the transition matrix of an ergodic chain, C, and let A = I - T. Let E be a perturbation matrix such that T squiggly = T - E is also the transition matrix of an ergodic chain, C squiggly. Let w and w squiggly denote the limiting probability (row) vectors for C and C squiggly. The inequality is the best one possible. This bound can be significant in the numerical determination of the limiting probabilities for an ergodic chain. In addition to presenting a sharp bound for the norm of w-w squiggly/the norm of w an explicit expression for w squiggly will be derived in which w squiggly is given as a function of E, A, w and some other related terms.

Synthesis of feedback systems with large plant ignorance for prescribed time domain tolerances

NASA Technical Reports Server (NTRS)

Horowitz, I. M.; Sidi, M.

1971-01-01

There is given a minimum-phase plant transfer function, with prescribed bounds on its parameter values. The plant is imbedded in a two-degree-of freedom feedback system, which is to be designed such that the system time response to a deterministic input lies within specified boundaries. Subject to the above, the design should be such as to minimize the effect of sensor noise at the input to the plant. This report presents a design procedure for this purpose, based on frequency response concepts. The time-domain tolerances are translated into equivalent frequency response tolerances. The latter lead to bounds on the loop transmission function in the form of continuous curves on the Nichols chart. The properties of the loop transmission function which satisfy these bounds with minimum effect of sensor noise, are derived.

Biomimetic approaches with smart interfaces for bone regeneration.

PubMed

Sailaja, G S; Ramesh, P; Vellappally, Sajith; Anil, Sukumaran; Varma, H K

2016-11-05

A 'smart tissue interface' is a host tissue-biomaterial interface capable of triggering favourable biochemical events inspired by stimuli responsive mechanisms. In other words, biomaterial surface is instrumental in dictating the interface functionality. This review aims to investigate the fundamental and favourable requirements of a 'smart tissue interface' that can positively influence the degree of healing and promote bone tissue regeneration. A biomaterial surface when interacts synergistically with the dynamic extracellular matrix, the healing process become accelerated through development of a smart interface. The interface functionality relies equally on bound functional groups and conjugated molecules belonging to the biomaterial and the biological milieu it interacts with. The essential conditions for such a special biomimetic environment are discussed. We highlight the impending prospects of smart interfaces and trying to relate the design approaches as well as critical factors that determine species-specific functionality with special reference to bone tissue regeneration.

Long-Term Effects of Docosahexaenoic Acid-Bound Phospholipids and the Combination of Docosahexaenoic Acid-Bound Triglyceride and Egg Yolk Phospholipid on Lipid Metabolism in Mice

NASA Astrophysics Data System (ADS)

Che, Hongxia; Cui, Jie; Wen, Min; Xu, Jie; Yanagita, Teruyoshi; Wang, Qi; Xue, Changhu; Wang, Yuming

2018-04-01

The bioavailability of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) depends on their chemical forms. This study investigated the long-term effects of DHA-bound triglyceride (TG-DHA), DHA-bound phospholipid (PL-DHA), and the combination of TG-DHA and egg yolk phospholipid (Egg-PL) on lipid metabolism in mice fed with a high-fat diet (fat levels of 22.5%). Male C57BL/6J mice were fed with different formulations containing 0.5% DHA, including TG-DHA, PL-DHA, and the combination of TG-DHA and Egg-PL, for 6 weeks. Serum, hepatic, and cerebral lipid concentrations and the fatty acid compositions of the liver and brain were determined. The concentrations of serum total triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-c), and hepatic TG in the PL-DHA group and the combination group were significantly lower than those in the high-fat (HF) group ( P < 0.05). Atherogenic index (AI) of the PL-DHA group was significantly lower than that of the combination group ( P < 0.05). Hepatic TC level in the combination group was significantly lower than that in the HF group ( P < 0.05), but no significant difference was observed between the combination group and the PL-DHA group. Both the PL-DHA and the combination groups showed significantly increased DHA levels in the liver compared with the HF group ( P < 0.05). However, there were no obvious increases in the cerebral DHA levels in all DHA diet groups. These results suggest that PL-DHA was superior to the combination of TG-DHA and Egg-PL in decreasing the AI. Long-term dietary supplementation with low amount of DHA (0.5%) may improve hepatic DHA levels, although cerebral DHA levels may not be enhanced.

Computer program for single input-output, single-loop feedback systems

NASA Technical Reports Server (NTRS)

1976-01-01

Additional work is reported on a completely automatic computer program for the design of single input/output, single loop feedback systems with parameter uncertainly, to satisfy time domain bounds on the system response to step commands and disturbances. The inputs to the program are basically the specified time-domain response bounds, the form of the constrained plant transfer function and the ranges of the uncertain parameters of the plant. The program output consists of the transfer functions of the two free compensation networks, in the form of the coefficients of the numerator and denominator polynomials, and the data on the prescribed bounds and the extremes actually obtained for the system response to commands and disturbances.

Bounds of memory strength for power-law series.

PubMed

Guo, Fangjian; Yang, Dan; Yang, Zimo; Zhao, Zhi-Dan; Zhou, Tao

2017-05-01

Many time series produced by complex systems are empirically found to follow power-law distributions with different exponents α. By permuting the independently drawn samples from a power-law distribution, we present nontrivial bounds on the memory strength (first-order autocorrelation) as a function of α, which are markedly different from the ordinary ±1 bounds for Gaussian or uniform distributions. When 1<α≤3, as α grows bigger, the upper bound increases from 0 to +1 while the lower bound remains 0; when α>3, the upper bound remains +1 while the lower bound descends below 0. Theoretical bounds agree well with numerical simulations. Based on the posts on Twitter, ratings of MovieLens, calling records of the mobile operator Orange, and the browsing behavior of Taobao, we find that empirical power-law-distributed data produced by human activities obey such constraints. The present findings explain some observed constraints in bursty time series and scale-free networks and challenge the validity of measures such as autocorrelation and assortativity coefficient in heterogeneous systems.

Bounds of memory strength for power-law series

NASA Astrophysics Data System (ADS)

Guo, Fangjian; Yang, Dan; Yang, Zimo; Zhao, Zhi-Dan; Zhou, Tao

2017-05-01

Many time series produced by complex systems are empirically found to follow power-law distributions with different exponents α . By permuting the independently drawn samples from a power-law distribution, we present nontrivial bounds on the memory strength (first-order autocorrelation) as a function of α , which are markedly different from the ordinary ±1 bounds for Gaussian or uniform distributions. When 1 <α ≤3 , as α grows bigger, the upper bound increases from 0 to +1 while the lower bound remains 0; when α >3 , the upper bound remains +1 while the lower bound descends below 0. Theoretical bounds agree well with numerical simulations. Based on the posts on Twitter, ratings of MovieLens, calling records of the mobile operator Orange, and the browsing behavior of Taobao, we find that empirical power-law-distributed data produced by human activities obey such constraints. The present findings explain some observed constraints in bursty time series and scale-free networks and challenge the validity of measures such as autocorrelation and assortativity coefficient in heterogeneous systems.

Robust inference in the negative binomial regression model with an application to falls data.

PubMed

Aeberhard, William H; Cantoni, Eva; Heritier, Stephane

2014-12-01

A popular way to model overdispersed count data, such as the number of falls reported during intervention studies, is by means of the negative binomial (NB) distribution. Classical estimating methods are well-known to be sensitive to model misspecifications, taking the form of patients falling much more than expected in such intervention studies where the NB regression model is used. We extend in this article two approaches for building robust M-estimators of the regression parameters in the class of generalized linear models to the NB distribution. The first approach achieves robustness in the response by applying a bounded function on the Pearson residuals arising in the maximum likelihood estimating equations, while the second approach achieves robustness by bounding the unscaled deviance components. For both approaches, we explore different choices for the bounding functions. Through a unified notation, we show how close these approaches may actually be as long as the bounding functions are chosen and tuned appropriately, and provide the asymptotic distributions of the resulting estimators. Moreover, we introduce a robust weighted maximum likelihood estimator for the overdispersion parameter, specific to the NB distribution. Simulations under various settings show that redescending bounding functions yield estimates with smaller biases under contamination while keeping high efficiency at the assumed model, and this for both approaches. We present an application to a recent randomized controlled trial measuring the effectiveness of an exercise program at reducing the number of falls among people suffering from Parkinsons disease to illustrate the diagnostic use of such robust procedures and their need for reliable inference. © 2014, The International Biometric Society.

Theoretical derivation of laser-dressed atomic states by using a fractal space

NASA Astrophysics Data System (ADS)

Duchateau, Guillaume

2018-05-01

The derivation of approximate wave functions for an electron submitted to both a Coulomb and a time-dependent laser electric fields, the so-called Coulomb-Volkov (CV) state, is addressed. Despite its derivation for continuum states does not exhibit any particular problem within the framework of the standard theory of quantum mechanics (QM), difficulties arise when considering an initially bound atomic state. Indeed the natural way of translating the unperturbed momentum by the laser vector potential is no longer possible since a bound state does not exhibit a plane wave form explicitly including a momentum. The use of a fractal space permits to naturally define a momentum for a bound wave function. Within this framework, it is shown how the derivation of laser-dressed bound states can be performed. Based on a generalized eikonal approach, a new expression for the laser-dressed states is also derived, fully symmetric relative to the continuum or bound nature of the initial unperturbed wave function. It includes an additional crossed term in the Volkov phase which was not obtained within the standard theory of quantum mechanics. The derivations within this fractal framework have highlighted other possible ways to derive approximate laser-dressed states in QM. After comparing the various obtained wave functions, an application to the prediction of the ionization probability of hydrogen targets by attosecond XUV pulses within the sudden approximation is provided. This approach allows to make predictions in various regimes depending on the laser intensity, going from the non-resonant multiphoton absorption to tunneling and barrier-suppression ionization.

A new upper bound for the norm of interval matrices with application to robust stability analysis of delayed neural networks.

PubMed

Faydasicok, Ozlem; Arik, Sabri

2013-08-01

The main problem with the analysis of robust stability of neural networks is to find the upper bound norm for the intervalized interconnection matrices of neural networks. In the previous literature, the major three upper bound norms for the intervalized interconnection matrices have been reported and they have been successfully applied to derive new sufficient conditions for robust stability of delayed neural networks. One of the main contributions of this paper will be the derivation of a new upper bound for the norm of the intervalized interconnection matrices of neural networks. Then, by exploiting this new upper bound norm of interval matrices and using stability theory of Lyapunov functionals and the theory of homomorphic mapping, we will obtain new sufficient conditions for the existence, uniqueness and global asymptotic stability of the equilibrium point for the class of neural networks with discrete time delays under parameter uncertainties and with respect to continuous and slope-bounded activation functions. The results obtained in this paper will be shown to be new and they can be considered alternative results to previously published corresponding results. We also give some illustrative and comparative numerical examples to demonstrate the effectiveness and applicability of the proposed robust stability condition. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stochastic analysis of three-dimensional flow in a bounded domain

USGS Publications Warehouse

Naff, R.L.; Vecchia, A.V.

1986-01-01

A commonly accepted first-order approximation of the equation for steady state flow in a fully saturated spatially random medium has the form of Poisson's equation. This form allows for the advantageous use of Green's functions to solve for the random output (hydraulic heads) in terms of a convolution over the random input (the logarithm of hydraulic conductivity). A solution for steady state three- dimensional flow in an aquifer bounded above and below is presented; consideration of these boundaries is made possible by use of Green's functions to solve Poisson's equation. Within the bounded domain the medium hydraulic conductivity is assumed to be a second-order stationary random process as represented by a simple three-dimensional covariance function. Upper and lower boundaries are taken to be no-flow boundaries; the mean flow vector lies entirely in the horizontal dimensions. The resulting hydraulic head covariance function exhibits nonstationary effects resulting from the imposition of boundary conditions. Comparisons are made with existing infinite domain solutions.

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

Branch and bound algorithm for accurate estimation of analytical isotropic bidirectional reflectance distribution function models.

PubMed

Yu, Chanki; Lee, Sang Wook

2016-05-20

We present a reliable and accurate global optimization framework for estimating parameters of isotropic analytical bidirectional reflectance distribution function (BRDF) models. This approach is based on a branch and bound strategy with linear programming and interval analysis. Conventional local optimization is often very inefficient for BRDF estimation since its fitting quality is highly dependent on initial guesses due to the nonlinearity of analytical BRDF models. The algorithm presented in this paper employs L₁-norm error minimization to estimate BRDF parameters in a globally optimal way and interval arithmetic to derive our feasibility problem and lower bounding function. Our method is developed for the Cook-Torrance model but with several normal distribution functions such as the Beckmann, Berry, and GGX functions. Experiments have been carried out to validate the presented method using 100 isotropic materials from the MERL BRDF database, and our experimental results demonstrate that the L₁-norm minimization provides a more accurate and reliable solution than the L₂-norm minimization.

Entanglement on linked boundaries in Chern-Simons theory with generic gauge groups

NASA Astrophysics Data System (ADS)

Dwivedi, Siddharth; Singh, Vivek Kumar; Dhara, Saswati; Ramadevi, P.; Zhou, Yang; Joshi, Lata Kh

2018-02-01

We study the entanglement for a state on linked torus boundaries in 3 d Chern-Simons theory with a generic gauge group and present the asymptotic bounds of Rényi entropy at two different limits: (i) large Chern-Simons coupling k, and (ii) large rank r of the gauge group. These results show that the Rényi entropies cannot diverge faster than ln k and ln r, respectively. We focus on torus links T (2 , 2 n) with topological linking number n. The Rényi entropy for these links shows a periodic structure in n and vanishes whenever n = 0 (mod p), where the integer p is a function of coupling k and rank r. We highlight that the refined Chern-Simons link invariants can remove such a periodic structure in n.

A study of planar anchor groups for graphene-based single-molecule electronics.

PubMed

Bailey, Steven; Visontai, David; Lambert, Colin J; Bryce, Martin R; Frampton, Harry; Chappell, David

2014-02-07

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

Mechanism of nucleotide sensing in group II chaperonins.

PubMed

Pereira, Jose H; Ralston, Corie Y; Douglas, Nicholai R; Kumar, Ramya; Lopez, Tom; McAndrew, Ryan P; Knee, Kelly M; King, Jonathan A; Frydman, Judith; Adams, Paul D

2012-02-01

Group II chaperonins mediate protein folding in an ATP-dependent manner in eukaryotes and archaea. The binding of ATP and subsequent hydrolysis promotes the closure of the multi-subunit rings where protein folding occurs. The mechanism by which local changes in the nucleotide-binding site are communicated between individual subunits is unknown. The crystal structure of the archaeal chaperonin from Methanococcus maripaludis in several nucleotides bound states reveals the local conformational changes associated with ATP hydrolysis. Residue Lys-161, which is extremely conserved among group II chaperonins, forms interactions with the γ-phosphate of ATP but shows a different orientation in the presence of ADP. The loss of the ATP γ-phosphate interaction with Lys-161 in the ADP state promotes a significant rearrangement of a loop consisting of residues 160-169. We propose that Lys-161 functions as an ATP sensor and that 160-169 constitutes a nucleotide-sensing loop (NSL) that monitors the presence of the γ-phosphate. Functional analysis using NSL mutants shows a significant decrease in ATPase activity, suggesting that the NSL is involved in timing of the protein folding cycle.

A study of planar anchor groups for graphene-based single-molecule electronics

NASA Astrophysics Data System (ADS)

Bailey, Steven; Visontai, David; Lambert, Colin J.; Bryce, Martin R.; Frampton, Harry; Chappell, David

2014-02-01

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

Adsorption of Pb(II) and Cd(II) by Squid Ommastrephes bartrami Melanin

PubMed Central

Chen, Shiguo; Xue, Changhu; Wang, Jingfeng; Feng, Hui; Wang, Yuming; Ma, Qin; Wang, Dongfeng

2009-01-01

The adsorption of Cd(II) and Pb(II) by squid melanin was investigated. At a metal ion concentration of 2 mM/L, the biosorption efficiency of melanin reached 95% for Cd(II) and Pb(II). The maximum content of bound Cd(II) and Pb(II) was 0.93 mM/g and 0.65 mM/g, respectively. Temperature had no obvious effect on the adsorption of the metals, and in a pH range of 4.0–7.0, the adsorption yield was high and stable. Macrosalts such as NaCl, MgCl2, and CaCl2 had no obvious effect on the binding of Pb(II) but greatly diminished the adsorption of Cd(II), which indicated that different functional groups in squid melanin are responsible for their adsorption. IR analysis of metal ion-enriched squid melanin demonstrated that the possible functional groups responsible for metal binding were phenolic hydroxyl (OH), carboxyl (COOH), and amine groups (NH). This study reports a new material for the removal of heavy metals from low-strength wastewater. PMID:20148082

Nobiletin: a citrus flavonoid displaying potent physiological activity.

PubMed

Noguchi, Shuji; Atsumi, Haruka; Iwao, Yasunori; Kan, Toshiyuki; Itai, Shigeru

2016-02-01

Nobiletin [systematic name: 2-(3,4-dimethoxyphenyl)-5,6,7,8-tetramethoxy-4H-chromen-4-one; C21H22O8] is a flavonoid found in citrus peels, and has been reported to show a wide range of physiological properties, including anti-inflammatory, anticancer and antidementia activities. We have solved the crystal structure of nobiletin, which revealed that the chromene and arene rings of its flavone moiety, as well as the two methoxy groups bound to its arene ring, were coplanar. In contrast, the C atoms of the four methoxy groups bound to the chromene ring are out of the plane, making the molecule conformationally chiral. A comparison of the crystal structures of nobiletin revealed that it could adopt a variety of different conformations through rotation of the covalent bond between the chromene and arene rings, and the orientations of methoxy groups bound to the chromene ring.

Piper betle-mediated green synthesis of biocompatible gold nanoparticles

NASA Astrophysics Data System (ADS)

Punuri, Jayasekhar Babu; Sharma, Pragya; Sibyala, Saranya; Tamuli, Ranjan; Bora, Utpal

2012-08-01

Here, we report the novel use of the ethonolic leaf extract of Piper betle for gold nanoparticle (AuNP) synthesis. The successful formation of AuNPs was confirmed by UV-visible spectroscopy, and different parameters such as leaf extract concentration (2%), gold salt concentration (0.5 mM), and time (18 s) were optimized. The synthesized AuNPs were characterized with different biophysical techniques such as transmission electron microscopy (TEM), Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), and energy-dispersive X-ray spectroscopy (EDX). TEM experiments showed that nanoparticles were of various shapes and sizes ranging from 10 to 35 nm. FT-IR spectroscopy revealed that AuNPs were functionalized with biomolecules that have primary amine group -NH2, carbonyl group, -OH groups, and other stabilizing functional groups. EDX showed the presence of the elements on the surface of the AuNPs. FT-IR and EDX together confirmed the presence of biomolecules bounded on the AuNPs. Cytotoxicity of the AuNPs was tested on HeLa and MCF-7 cancer cell lines, and they were found to be nontoxic, indicating their biocompatibility. Thus, synthesized AuNPs have potential for use in various biomedical applications.

Nature of a single doped hole in two-leg Hubbard and t - J ladders

DOE PAGES

Liu, Shenxiu; Jiang, Hong -Chen; Devereaux, Thomas P.

2016-10-15

In this study, we have systematically studied the single-hole problem in two-leg Hubbard and t–J ladders by large-scale density-matrix renormalization-group calculations. We found that the doped holes in both models behave similarly, while the three-site correlated hopping term is not important in determining the ground-state properties. For more insights, we have also calculated the elementary excitations, i.e., the energy gaps to the excited states of the system. In the strong-rung limit, we found that the doped hole behaves as a Bloch quasiparticle in both systems where the spin and charge of the doped hole are tightly bound together. In themore » isotropic limit, while the hole still behaves like a quasiparticle in the long-wavelength limit, our results show that its spin and charge components are only loosely bound together inside the quasiparticle, whose internal structure can lead to a visible residual effect which dramatically changes the local structure of the ground-state wave function.« less

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

Liu, Shenxiu; Jiang, Hong -Chen; Devereaux, Thomas P.

In this study, we have systematically studied the single-hole problem in two-leg Hubbard and t–J ladders by large-scale density-matrix renormalization-group calculations. We found that the doped holes in both models behave similarly, while the three-site correlated hopping term is not important in determining the ground-state properties. For more insights, we have also calculated the elementary excitations, i.e., the energy gaps to the excited states of the system. In the strong-rung limit, we found that the doped hole behaves as a Bloch quasiparticle in both systems where the spin and charge of the doped hole are tightly bound together. In themore » isotropic limit, while the hole still behaves like a quasiparticle in the long-wavelength limit, our results show that its spin and charge components are only loosely bound together inside the quasiparticle, whose internal structure can lead to a visible residual effect which dramatically changes the local structure of the ground-state wave function.« less

Hash Functions and Information Theoretic Security

NASA Astrophysics Data System (ADS)

Bagheri, Nasour; Knudsen, Lars R.; Naderi, Majid; Thomsen, Søren S.

Information theoretic security is an important security notion in cryptography as it provides a true lower bound for attack complexities. However, in practice attacks often have a higher cost than the information theoretic bound. In this paper we study the relationship between information theoretic attack costs and real costs. We show that in the information theoretic model, many well-known and commonly used hash functions such as MD5 and SHA-256 fail to be preimage resistant.

Adaptive dynamic programming for finite-horizon optimal control of discrete-time nonlinear systems with ε-error bound.

PubMed

Wang, Fei-Yue; Jin, Ning; Liu, Derong; Wei, Qinglai

2011-01-01

In this paper, we study the finite-horizon optimal control problem for discrete-time nonlinear systems using the adaptive dynamic programming (ADP) approach. The idea is to use an iterative ADP algorithm to obtain the optimal control law which makes the performance index function close to the greatest lower bound of all performance indices within an ε-error bound. The optimal number of control steps can also be obtained by the proposed ADP algorithms. A convergence analysis of the proposed ADP algorithms in terms of performance index function and control policy is made. In order to facilitate the implementation of the iterative ADP algorithms, neural networks are used for approximating the performance index function, computing the optimal control policy, and modeling the nonlinear system. Finally, two simulation examples are employed to illustrate the applicability of the proposed method.

Structural Changes and Proapoptotic Peroxidase Activity of Cardiolipin-Bound Mitochondrial Cytochrome c

PubMed Central

Mandal, Abhishek; Hoop, Cody L.; DeLucia, Maria; Kodali, Ravindra; Kagan, Valerian E.; Ahn, Jinwoo; van der Wel, Patrick C.A.

2015-01-01

The cellular process of intrinsic apoptosis relies on the peroxidation of mitochondrial lipids as a critical molecular signal. Lipid peroxidation is connected to increases in mitochondrial reactive oxygen species, but there is also a required role for mitochondrial cytochrome c (cyt-c). In apoptotic mitochondria, cyt-c gains a new function as a lipid peroxidase that catalyzes the reactive oxygen species-mediated chemical modification of the mitochondrial lipid cardiolipin (CL). This peroxidase activity is caused by a conformational change in the protein, resulting from interactions between cyt-c and CL. The nature of the conformational change and how it causes this gain-of-function remain uncertain. Via a combination of functional, structural, and biophysical experiments we investigate the structure and peroxidase activity of cyt-c in its membrane-bound state. We reconstituted cyt-c with CL-containing lipid vesicles, and determined the increase in peroxidase activity resulting from membrane binding. We combined these assays of CL-induced proapoptotic activity with structural and dynamic studies of the membrane-bound protein via solid-state NMR and optical spectroscopy. Multidimensional magic angle spinning (MAS) solid-state NMR of uniformly 13C,15N-labeled protein was used to detect site-specific conformational changes in oxidized and reduced horse heart cyt-c bound to CL-containing lipid bilayers. MAS NMR and Fourier transform infrared measurements show that the peripherally membrane-bound cyt-c experiences significant dynamics, but also retains most or all of its secondary structure. Moreover, in two-dimensional and three-dimensional MAS NMR spectra the CL-bound cyt-c displays a spectral resolution, and thus structural homogeneity, that is inconsistent with extensive membrane-induced unfolding. Cyt-c is found to interact primarily with the membrane interface, without significantly disrupting the lipid bilayer. Thus, membrane binding results in cyt-c gaining the increased peroxidase activity that represents its pivotal proapoptotic function, but we do not observe evidence for large-scale unfolding or penetration into the membrane core. PMID:26536264

Transmutation of a heme protein.

PubMed Central

Barker, P D; Ferrer, J C; Mylrajan, M; Loehr, T M; Feng, R; Konishi, Y; Funk, W D; MacGillivray, R T; Mauk, A G

1993-01-01

Residue Asn57 of bovine liver cytochrome b5 has been replaced with a cysteine residue, and the resulting variant has been isolated from recombinant Escherichia coli as a mixture of four major species: A, BI, BII, and C. A combination of electronic spectroscopy, 1H NMR spectroscopy, resonance Raman spectroscopy, electrospray mass spectrometry, and direct electrochemistry has been used to characterize these four major cytochrome derivatives. The red form A (E(m) = -19 mV) is found to possess a heme group bound covalently through a thioether linkage involving Cys57 and the alpha carbon of the heme 4-vinyl group. Form BI has a covalently bound heme group coupled through a thioether linkage involving the beta carbon of the heme 4-vinyl group. Form BII is similar to BI except that the sulfur involved in the thioether linkage is oxidized to a sulfoxide. The green form C (E(m) = 175 mV) possesses a noncovalently bound prosthetic group with spectroscopic properties characteristic of a chlorin. A mechanism is proposed for the generation of these derivatives, and the implications of these observations for the biosynthesis of cytochrome c and naturally occurring chlorin prosthetic groups are discussed. PMID:8341666

Response of discrete linear systems to forcing functions with inequality constraints.

NASA Technical Reports Server (NTRS)

Michalopoulos, C. D.; Riley, T. A.

1972-01-01

An analysis is made of the maximum response of discrete, linear mechanical systems to arbitrary forcing functions which lie within specified bounds. Primary attention is focused on the complete determination of the forcing function which will engender maximum displacement to any particular mass element of a multi-degree-of-freedom system. In general, the desired forcing function is found to be a bang-bang type function, i.e., a function which switches from the maximum to the minimum bound and vice-versa at certain instants of time. Examples of two-degree-of-freedom systems, with and without damping, are presented in detail. Conclusions are drawn concerning the effect of damping on the switching times and the general procedure for finding these times is discussed.

Transient response of multidegree-of-freedom linear systems to forcing functions with inequality constraints

NASA Technical Reports Server (NTRS)

Michalopoulos, C. D.

1974-01-01

Optimal control theory is applied to analyze the transient response of discrete linear systems to forcing functions with unknown time dependence but having known bounds. Particular attention is given to forcing functions which include: (1) maximum displacement of any given mass element, (2) maximum relative displacement of any two adjacent masses, and (3) maximum acceleration of a given mass. Linear mechanical systems with an arbitrary number of degrees of freedom and only one forcing function acting are considered. In the general case, the desired forcing function is found to be a function that switches from the upper-to-lower bound and vice-versa at certain moments of time. A general procedure for finding such switching times is set forth.

Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

PubMed Central

Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

2010-01-01

Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10–20% nucleotide deviation from the canonical ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. PMID:20047966

Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.

PubMed

Mason, Christopher E; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M; Kallen, Roland G; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B

2010-04-01

Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10-20% nucleotide deviation from the canonical ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.

A derivation of the Cramer-Rao lower bound of euclidean parameters under equality constraints via score function

NASA Astrophysics Data System (ADS)

Susyanto, Nanang

2017-12-01

We propose a simple derivation of the Cramer-Rao Lower Bound (CRLB) of parameters under equality constraints from the CRLB without constraints in regular parametric models. When a regular parametric model and an equality constraint of the parameter are given, a parametric submodel can be defined by restricting the parameter under that constraint. The tangent space of this submodel is then computed with the help of the implicit function theorem. Finally, the score function of the restricted parameter is obtained by projecting the efficient influence function of the unrestricted parameter on the appropriate inner product spaces.

On the Convergence Analysis of the Optimized Gradient Method.

PubMed

Kim, Donghwan; Fessler, Jeffrey A

2017-01-01

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

On the Convergence Analysis of the Optimized Gradient Method

PubMed Central

Kim, Donghwan; Fessler, Jeffrey A.

2016-01-01

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

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.

PubMed

Méndez, Raúl; Leplae, Raphaël; Lensink, Marc F; Wodak, Shoshana J

2005-08-01

The current status of docking procedures for predicting protein-protein interactions starting from their three-dimensional (3D) structure is reassessed by evaluating blind predictions, performed during 2003-2004 as part of Rounds 3-5 of the community-wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Ten newly determined structures of protein-protein complexes were used as targets for these rounds. They comprised 2 enzyme-inhibitor complexes, 2 antigen-antibody complexes, 2 complexes involved in cellular signaling, 2 homo-oligomers, and a complex between 2 components of the bacterial cellulosome. For most targets, the predictors were given the experimental structures of 1 unbound and 1 bound component, with the latter in a random orientation. For some, the structure of the free component was derived from that of a related protein, requiring the use of homology modeling. In some of the targets, significant differences in conformation were displayed between the bound and unbound components, representing a major challenge for the docking procedures. For 1 target, predictions could not go to completion. In total, 1866 predictions submitted by 30 groups were evaluated. Over one-third of these groups applied completely novel docking algorithms and scoring functions, with several of them specifically addressing the challenge of dealing with side-chain and backbone flexibility. The quality of the predicted interactions was evaluated by comparison to the experimental structures of the targets, made available for the evaluation, using the well-agreed-upon criteria used previously. Twenty-four groups, which for the first time included an automatic Web server, produced predictions ranking from acceptable to highly accurate for all targets, including those where the structures of the bound and unbound forms differed substantially. These results and a brief survey of the methods used by participants of CAPRI Rounds 3-5 suggest that genuine progress in the performance of docking methods is being achieved, with CAPRI acting as the catalyst.

Communication complexity and information complexity

NASA Astrophysics Data System (ADS)

Pankratov, Denis

Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information complexity of two of the most studied functions in the communication complexity literature: Gap Hamming Distance (GHD) and Inner Product mod 2 (IP). In our first result we affirm the conjecture that the information complexity of GHD is linear even under the uniform distribution. This strengthens the O(n) bound shown by Kerenidis et al. (2012) and answers an open problem by Chakrabarti et al. (2012). We also prove that the information complexity of IP is arbitrarily close to the trivial upper bound n as the permitted error tends to zero, again strengthening the O(n) lower bound proved by Braverman and Weinstein (2011). More importantly, our proofs demonstrate that self-reducibility makes the connection between information complexity and communication complexity lower bounds a two-way connection. Whereas numerous results in the past used information complexity techniques to derive new communication complexity lower bounds, we explore a generic way, in which communication complexity lower bounds imply information complexity lower bounds in a black-box manner. In the third contribution we consider the roles that private and public randomness play in the definition of information complexity. In communication complexity, private randomness can be trivially simulated by public randomness. Moreover, the communication cost of simulating public randomness with private randomness is well understood due to Newman's theorem (1991). In information complexity, the roles of public and private randomness are reversed: public randomness can be trivially simulated by private randomness. However, the information cost of simulating private randomness with public randomness is not understood. We show that protocols that use only public randomness admit a rather strong compression. In particular, efficient simulation of private randomness by public randomness would imply a version of a direct sum theorem in the setting of communication complexity. This establishes a yet another connection between the two areas. (Abstract shortened by UMI.).

Bohr effect of human hemoglobin: Separation of tertiary and quaternary contributions based on the Wyman equation.

PubMed

Okonjo, Kehinde Onwochei

2017-09-01

As a prelude to separating tertiary from quaternary structure contributions to the Bohr effect, we employed the Wyman equation to analyze Bohr data for human hemoglobin to which 2,3-bisphosphoglycerate, 2,3-BPG, is bound. Changes in the pK a s of the histidine Bohr groups result in a net reduction of their contributions to the Bohr effect at pH 7.4 compared to their contributions in stripped hemoglobin. The non-histidine 2,3-BPG binding groups - the β-chain terminal amino group and Lys82β - make negative and positive contributions, respectively, to the Bohr effect. The final result is that the Bohr effect at physiological pH is higher for 2,3-BPG bound compared to stripped hemoglobin. Contributions linked to His2β, His77β and His143β enable us to separate tertiary from quaternary Bohr contributions in stripped and in 2,3-BPG bound hemoglobin. Both contributions serve to make the Bohr effect for 2,3-BPG bound hemoglobin higher than for stripped hemoglobin at physiological pH. Copyright © 2017 Elsevier B.V. All rights reserved.

Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

PubMed Central

Raman, E. Prabhu; Yu, Wenbo; Guvench, Olgun; MacKerell, Alexander D.

2011-01-01

The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility towards specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design. PMID:21456594

Protein-protein binding before and after photo-modification of albumin

NASA Astrophysics Data System (ADS)

Rozinek, Sarah C.; Glickman, Randolph D.; Thomas, Robert J.; Brancaleon, Lorenzo

2016-03-01

Bioeffects of directed-optical-energy encompass a wide range of applications. One aspect of photochemical interactions involves irradiating a photosensitizer with visible light in order to induce protein unfolding and consequent changes in function. In the past, irradiation of several dye-protein combinations has revealed effects on protein structure. Beta lactoglobulin, human serum albumin (HSA) and tubulin have all been photo-modified with meso-tetrakis(4- sulfonatophenyl)porphyrin (TSPP) bound, but only in the case of tubulin has binding caused a verified loss of biological function (loss of ability to form microtubules) as a result of this light-induced structural change. The current work questions if the photo-induced structural changes that occur to HSA, are sufficient to disable its biological function of binding to osteonectin. The albumin-binding protein, osteonectin, is about half the molecular weight of HSA, so the two proteins and their bound product can be separated and quantified by size exclusion high performance liquid chromatography. TSPP was first bound to HSA and irradiated, photo-modifying the structure of HSA. Then native HSA or photo-modified HSA (both with TSPP bound) were compared, to assess loss in HSA's innate binding ability as a result of light-induced structure modification.

“Local” Dark Energy Outflows Around Galaxy Groups and Rich Clusters

NASA Astrophysics Data System (ADS)

Byrd, Gene G.; Chernin, A. D.; Teerikorpi, P.; Dolgachev, V. P.; Kanter, A. A.; Domozhilova, L. M.; Valtonen, M.

2013-01-01

First detected at large Gpc distances, dark energy is a vacuum energy formulated as Einstein's cosmological constant, Λ. We have found its effects on “small” 1-3 Mpc scales in our Local Group. We have now found these effects in other nearby groups using member Doppler shifts and 3D distances from group centers (Cen A-M83; M81-M82; CV I). For the larger 20-30 Mpc Virgo and Fornax clusters, we now have found similar effects. Observationally, for both groups and clusters, gravity dominates a bound central system. The system gravitation and dark energy create a “zero-gravity” radius (R_{ZG}) from the center where the two balance. Smaller members bound inside R_{ZG} may be pulled out along with the less bound members which recede farther. A linear increase of recession with distance results which approaches a linear global Hubble law. These outflows are seen around groups in cosmological simulations which include galaxies as small as ~10^{-4} of the group mass. Scaled plots of asymptotic recessional velocity, V/(H(R_{ZG})), versus distance/ R_{ZG} of the outer galaxies are very similar for both the small groups and large clusters. This similarity on 1-30 Mpc scales suggests that a quasi-stationary bound central component and an expanding outflow applies to a wide range of groups and clusters due to small scale action of dark energy. Our new text book: Byrd, G., Chernin, A., Terrikorpi, P. and Valtonen, M. 2012, "Paths to Dark Energy: Theory and Observation," de Gruyter, Berlin/Boston, contains background and cosmological simulation plots. Group data and scaled plots are in our new article: A. D. Chernin, P. Teerikorpi, V. P. Dolgachev, A. A. Kanter, L. M. Domozhilova, M. J. Valtonen, and G. G. Byrd, 2012, Astronomy Reports, Vol. 56 , p. 653-669.

Functional Adaptation of the Calcaneus in Historical Foot Binding

PubMed Central

Reznikov, Natalie; Phillips, Carina; Cooke, Martyn; Garbout, Amin; Ahmed, Farah

2017-01-01

ABSTRACT The normal structure of human feet is optimized for shock dampening during walking and running. Foot binding was a historical practice in China aimed at restricting the growth of female feet for aesthetic reasons. In a bound foot the shock‐dampening function normally facilitated by the foot arches is withdrawn, resulting in the foot functioning as a rigid extension of the lower leg. An interesting question inspiring this study regards the nature of adaptation of the heel bone to this nonphysiological function using the parameters of cancellous bone anisotropy and 3D fabric topology and a novel intertrabecular angle (ITA) analysis. We found that the trabecular microarchitecture of the normal heel bone, but not of the bound foot, adapts to function by increased anisotropy and preferred orientation of trabeculae. The anisotropic texture in the normal heel bone consistently follows the physiological stress trajectories. However, in the bound foot heel bone the characteristic anisotropy pattern fails to develop, reflecting the lack of a normal biomechanical input. Moreover, the basic topological blueprint of cancellous bone investigated by the ITA method is nearly invariant in both normal and bound foot. These findings suggest that the anisotropic cancellous bone texture is an acquired characteristic that reflects recurrent loading conditions; conversely, an inadequate biomechanical input precludes the formation of anisotropic texture. This opens a long‐sought‐after possibility to reconstruct bone function from its form. The conserved topological parameters characterize the generic 3D fabric of cancellous bone, which is to a large extent independent of its adaptation to recurrent loading and perhaps determines the mechanical competence of trabecular bone regardless of its functional adaptation. © 2017 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals Inc. PMID:28561380

Functional Adaptation of the Calcaneus in Historical Foot Binding.

PubMed

Reznikov, Natalie; Phillips, Carina; Cooke, Martyn; Garbout, Amin; Ahmed, Farah; Stevens, Molly M

2017-09-01

The normal structure of human feet is optimized for shock dampening during walking and running. Foot binding was a historical practice in China aimed at restricting the growth of female feet for aesthetic reasons. In a bound foot the shock-dampening function normally facilitated by the foot arches is withdrawn, resulting in the foot functioning as a rigid extension of the lower leg. An interesting question inspiring this study regards the nature of adaptation of the heel bone to this nonphysiological function using the parameters of cancellous bone anisotropy and 3D fabric topology and a novel intertrabecular angle (ITA) analysis. We found that the trabecular microarchitecture of the normal heel bone, but not of the bound foot, adapts to function by increased anisotropy and preferred orientation of trabeculae. The anisotropic texture in the normal heel bone consistently follows the physiological stress trajectories. However, in the bound foot heel bone the characteristic anisotropy pattern fails to develop, reflecting the lack of a normal biomechanical input. Moreover, the basic topological blueprint of cancellous bone investigated by the ITA method is nearly invariant in both normal and bound foot. These findings suggest that the anisotropic cancellous bone texture is an acquired characteristic that reflects recurrent loading conditions; conversely, an inadequate biomechanical input precludes the formation of anisotropic texture. This opens a long-sought-after possibility to reconstruct bone function from its form. The conserved topological parameters characterize the generic 3D fabric of cancellous bone, which is to a large extent independent of its adaptation to recurrent loading and perhaps determines the mechanical competence of trabecular bone regardless of its functional adaptation. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

Selenium speciation in paired serum and cerebrospinal fluid samples of sheep.

PubMed

Humann-Ziehank, Esther; Ganter, Martin; Michalke, Bernhard

2016-01-01

This study was performed to characterise selenium (Se) and Se species in cerebrospinal fluid (CSF) of sheep and its relation to the respective Se concentrations in serum. Paired samples from 10 adult sheep were used for the study. Five sheep were fed a diet with a marginal Se concentration of <0.05mg Se/kg diet dry weight (dw, Se(-)), and five animals were fed the same diet supplemented with sodium selenite revealing a concentration of 0.2mg Se/kg diet dw (Se(+)). The feeding strategy was conducted for two years; The results on metabolic effects were published previously. At the end of the feeding period, paired samples of serum and CSF were collected and analysed using ion exchange chromatography inductively coupled plasma-dynamic reaction cell-mass spectrometry (IEC-ICP-DRC-MS) technique for total Se concentration and concentrations of Se species. Albumin concentrations were analysed additionally. The feeding strategy caused significant differences (p<0.01) in serum Se concentrations with 33.1±5.11μg Se/l in the Se(-) group and 96.5±18.3μg Se/l in the Se(+) group, respectively. The corresponding total Se concentrations in CSF were 4.38±1.02μg Se/l and 6.13±1.64μg Se/l in the Se(-) and the Se(+) group, respectively, missing statistical significance (p=0.077). IEC-ICP-DRC-MS technique was able to differentiate the Se species selenoprotein P-bound Se (SePP), selenomethionine, glutathione peroxidase-bound Se (Se-GPx), selenocystine, thioredoxin reductase-bound Se, ovine serum albumin-bound Se (Se-OSA), SeIV and SeVI in ovine serum and CSF. Quantitatively, SePP is the main selenoprotein in ovine serum followed by Se-GPx. The CSF/blood ratio of albumin (QAlbumin) reflected a physiological function of the blood-CSF barrier in all sheep. QSe-species were higher than QAlbumin both feeding groups, supporting the hypothesis of local production of Se species in the brain. Significant positive regression lines for CSF vs. serum were found for albumin and Se-OSA only, suggesting a role of albumin to convey Se across the blood-CSF barrier. The ovine model, together with the IEC-ICP-DRC-MS technique to characterise the Se species, might be a worthwhile model for further studies as repeated sample collection as well as modification of the nutritional status is feasible and effective. Copyright © 2015 Elsevier GmbH. All rights reserved.

Radiative transitions involving the (2p2)(3 Pe) metastable autodetaching of H(-)

NASA Technical Reports Server (NTRS)

Jacobs, V. L.; Bhatia, A. K.; Temkin, A.

1974-01-01

The absorption coefficient for the free-bound transition H (ls) + e(-)+ h omega yields H(-)(2 sq p,(3)P(e)) is calculated (together with the differential emission rate for the inverse process) using ls - 2s - 2p close coupling continuum wave functions and a Hylleraas bound state wave function. A maximum in the absorption and emission spectra is found to occur at a photon wavelength of 1219.5 A, which is 2 A closer to the Lyman alpha line than predicted by the calculations of Drake, and is in closer agreement with the stellar absorption feature identified by Heap and Stecher. The free-bound absorption process appears to be a significant source of continuous ultraviolet opacity.

Pumping‐induced leakage in a bounded aquifer: An example of a scale‐invariant phenomenon

USGS Publications Warehouse

Butler, James J.; Tsou, Ming‐shu

2003-01-01

A new approach is presented for calculation of the volume of pumping‐induced leakage entering an aquifer as a function of time. This approach simplifies the total leakage calculation by extending analytical‐based methods developed for infinite systems to bounded aquifers of any size. The simplification is possible because of the relationship between drawdown and leakage in aquifers laterally bounded by impermeable formations. This relationship produces a scale‐invariant total leakage; i.e., the volume of leakage as a function of time does not change with the size of the aquifer or with the location of the pumping well. Two examples and image well theory are used to demonstrate and prove, respectively, the generality of this interesting phenomenon.

Two-dimensional correlation spectroscopic analysis on the interaction between humic acids and aluminum coagulant.

PubMed

Jin, Pengkang; Song, Jina; Wang, Xiaochang C; Jin, Xin

2018-02-01

In this study, two-dimensional correlation spectroscopy integrated with synchronous fluorescence and infrared absorption spectroscopy was employed to investigate the interaction between humic acids and aluminum coagulant at slightly acidic and neutral pH. Higher fluorescence quenching was produced for fulvic-like and humic-like fractions at pH5. At pH5, the humic-like fractions originating from the carboxylic acid, carboxyl and polysaccharide compounds were bound to aluminum first, followed by the fulvic-like fractions originating from the carboxyl and polysaccharide compounds. This finding also demonstrated that the activated functional groups of HA were involved in forming the Al-HA complex, which was accompanied by the removal of other groups by co-precipitation. Meanwhile, at pH7, almost no fluorescence quenching occurred, and surface complexation was observed to occur, in which the activated functional groups were absorbed on the amorphous Al(OH) 3 . Two-dimensional FT-IR correlation spectroscopy indicated the sequence of HA structural change during coagulation with aluminum, with IR bands affected in the order of COOH>COO - >NH deformation of amide II>aliphatic hydroxyl COH at pH5, and COO - >aliphatic hydroxyl COH at pH7. This study provides a promising pathway for analysis and insight into the priority of functional groups in the interaction between organic matters and metal coagulants. Copyright © 2017. Published by Elsevier B.V.

Linking Thermodynamics to Pollutant Reduction Kinetics by Fe2+ Bound to Iron Oxides.

PubMed

Stewart, Sydney M; Hofstetter, Thomas B; Joshi, Prachi; Gorski, Christopher A

2018-05-15

Numerous studies have reported that pollutant reduction rates by ferrous iron (Fe 2+ ) are substantially enhanced in the presence of an iron (oxyhydr)oxide mineral. Developing a thermodynamic framework to explain this phenomenon has been historically difficult due to challenges in quantifying reduction potential ( E H ) values for oxide-bound Fe 2+ species. Recently, our group demonstrated that E H values for hematite- and goethite-bound Fe 2+ can be accurately calculated using Gibbs free energy of formation values. Here, we tested if calculated E H values for oxide-bound Fe 2+ could be used to develop a free energy relationship capable of describing variations in reduction rate constants of substituted nitrobenzenes, a class of model pollutants that contain reducible aromatic nitro groups, using data collected here and compiled from the literature. All the data could be described by a single linear relationship between the logarithms of the surface-area-normalized rate constant ( k SA ) values and E H and pH values [log( k SA ) = - E H /0.059 V - pH + 3.42]. This framework provides mechanistic insights into how the thermodynamic favorability of electron transfer from oxide-bound Fe 2+ relates to redox reaction kinetics.

Abnormal medial temporal activity for bound information during working memory maintenance in patients with schizophrenia.

PubMed

Luck, David; Danion, Jean-Marie; Marrer, Corrine; Pham, Bich-Tuy; Gounot, Daniel; Foucher, Jack

2010-08-01

Alterations of binding in long-term memory in schizophrenia are well established and occur as a result of aberrant activity in the medial temporal lobe (MTL). In working memory (WM), such a deficit is less clear and the pathophysiological bases remain unstudied. Seventeen patients with schizophrenia and 17 matched healthy controls performed a WM binding task while undergoing functional magnetic resonance imaging. Binding was assessed by contrasting two conditions comprising an equal amount of verbal and spatial information (i.e., three letters and three spatial locations), but differing in the absence or presence of a link between them. In healthy controls, MTL activation was observed for encoding and maintenance of bound information but not for its retrieval. Between-group comparisons revealed that patients with schizophrenia showed MTL hypoactivation during the maintenance phase only. In addition, BOLD signals correlated with behavioral performance in controls but not in patients with schizophrenia. Our results confirm the major role that the MTL plays in the pathophysiology of schizophrenia. Short-term and long-term relational memory deficits in schizophrenia may share common cognitive and functional pathological bases. Our results provide additional information about the episodic buffer that represents an integrative interface between WM and long-term memory. Copyright 2009 Wiley-Liss, Inc.

Sperm DNA Fragmentation Index and Hyaluronan Binding Ability in Men from Infertile Couples and Men with Testicular Germ Cell Tumor

PubMed Central

Filipiak, Eliza; Walczak-Jedrzejowska, Renata; Oszukowska, Elzbieta; Sobkiewicz, Slawomir; Wojt, Malgorzata; Chmiel, Jacek; Kula, Krzysztof; Slowikowska-Hilczer, Jolanta

2016-01-01

Objective. To investigate sperm DNA fragmentation and sperm functional maturity in men from infertile couples (IC) and men with testicular germ cell tumor (TGCT). Materials and Methods. Semen samples were collected from 312 IC men and 23 men with TGCT before unilateral orchiectomy and oncological treatment. The sperm chromatin dispersion test was performed to determine DNA fragmentation index (DFI) and the ability of sperm to bind with hyaluronan (HA) was assessed. Results. In comparison with the IC men, the men with TGCT had a higher percentage of sperm with fragmented DNA (median 28% versus 21%; p < 0.01) and a lower percentage of HA-bound sperm (24% versus 66%; p < 0.001). Normal results of both analyses were observed in 24% of IC men and 4% of men with TGCT. Negative Spearman's correlations were found between DFI and the percentage of HA-bound sperm in the whole group and in IC subjects and those with TGCT analyzed separately. Conclusions. Approximately 76% of IC men and 96% with TGCT awaiting orchiectomy demonstrated DNA fragmentation and/or sperm immaturity. We therefore recommend sperm banking after unilateral orchiectomy, but before irradiation and chemotherapy; the use of such a deposit appears to be a better strategy to obtain functionally efficient sperms. PMID:27999814

A novel fluorescence sensor based on covalent immobilization of 3-amino-9-ethylcarbazole by using silver nanoparticles as bridges and carriers.

PubMed

Tan, Shu-Zhen; Hu, Yan-Jun; Gong, Fu-Chun; Cao, Zhong; Xia, Jiao-Yun; Zhang, Ling

2009-03-23

A novel technique of covalent immobilization of indicator dyes in the preparation of fluorescence sensors is developed. Silver nanoparticles are used as bridges and carriers for anchoring indicator dyes. 3-amino-9-ethylcarbazole (AEC) was employed as an example of indicator dyes with terminal amino groups and covalently immobilized onto the outmost surface of a quartz glass slide. First, the glass slide was functionalized by (3-mercaptopropyl) trimethoxysilane (MPS) to form a thiol-terminated self-assembled monolayer, where silver nanoparticles were strongly bound to the surface through covalent bonding. Then, 16-mercaptohexadecanoic acid (MHDA) was self-assembled to bring carboxylic groups onto the surface of silver nanoparticles. A further activation by using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) converted the carboxylic groups into succinimide esters. Finally, the active succinimide esters on the surface of silver nanoparticles were reacted with AEC. Thus, AEC was covalently bound to the glass slide and an AEC-immobilized sensor was obtained. The sensor exhibited very satisfactory reproducibility and reversibility, rapid response and no dye-leaching. Rutin can quench the fluorescence intensity of the sensor and be measured by using the sensor. The linear response of the sensor to rutin covers the range from 2.0 x 10(-6) to 1.5 x 10(-4) molL(-1) with a detection limit of 8.0 x 10(-7) molL(-1). The proposed technique may be feasible to the covalent immobilization of other dyes with primary amino groups.

Preparation and Characterization of Fluorescent Derivatives of Chicken Egg White Lysozyme

NASA Technical Reports Server (NTRS)

Sumida, John; Forsythe, Elizabeth; Pusey, Marc

2000-01-01

Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared a number of fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow, cascade blue, and 5-(2-aminoethyl)aminonapthalene-l-sulfonic acid (EDANS) have been attached to the side chain carboxyl of asp101 using a carbodiimide coupling procedure. asp101 lies within the active site cleft, and it is believed that the probes are at least partially "buried" within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive groups have been bound to hisl5, located on the "back side" of the molecule relative to the active site. The fluorescently labeled protein is readily purified from the starting material by cation exchange chromatography. All the derivatives fluoresce in both the solution and the crystalline states. Fluorescence characterization has focused on determining the bound probe quantum yields, lifetimes, absorption and emission spectra, and quenching by added solutes in comparison to the free probe. No appreciable changes are found in the lifetimes of any of the probes except for cascade blue, where Tau(sub free) = 3.52 ns vrs Tau(sub bound) = 2.8 ns. Spectral shifts are found in most cases. Particularly strong quenching upon binding is found in the case of the cascade blue derivative, likely due to probe interactions with the active site cleft. While none of the asp101 bound probes are well quenched by commonly employed solutes, such as potassium and sodium iodide, acrylamide, primuline, the chloride salts of manganese, cesium, and cobalt, trifluoroacetamide, trichloroethanol, and thallium iodide, in those cases where quenching is observed the bound probe is less efficiently quenched relative to the free probe. This indicates that the bound probes are less accessible to the bulk solution, an expected finding for attachment within the active site cleft. Attempts have been made to bind other molecules to these sites, with varying success. Interestingly, all three probes contain one or more sulfonate ((Ar-S03)-) groups. We have not been successful in binding analogous probes without sulfate groups such as pyrene, or with derivatized sulfonate groups such as dansyl type probes, analogous to MANS but where the sulfonate group is derivatized, Ar-S02-N2C2H7. None of the probes is rigidly bound to the protein, i.e., they all have a probe motion superimposed on that of the protein.

A new approach to flow through a region bounded by two ellipses of the same ellipticity

NASA Astrophysics Data System (ADS)

Lal, K.; Chorlton, F.

1981-05-01

A new approach is presented to calculate steady flow of a laminar viscous incompressible fluid through a channel whose cross section is bounded by two ellipses with the same ellipticity. The Milne-Thomas approach avoids the stream function and is similar to the Rayleigh-Ritz approximation process of the calculus of variations in its first satisfying boundary conditions and then adjusting constants or multiplying functions to fit the differential equation.

A Posteriori Bounds for Linear-Functional Outputs of Crouzeix-Raviart Finite Element Discretizations of the Incompressible Stokes Problem

NASA Technical Reports Server (NTRS)

Patera, Anthony T.; Paraschivoiu, Marius

1998-01-01

We present a finite element technique for the efficient generation of lower and upper bounds to outputs which are linear functionals of the solutions to the incompressible Stokes equations in two space dimensions; the finite element discretization is effected by Crouzeix-Raviart elements, the discontinuous pressure approximation of which is central to our approach. The bounds are based upon the construction of an augmented Lagrangian: the objective is a quadratic "energy" reformulation of the desired output; the constraints are the finite element equilibrium equations (including the incompressibility constraint), and the intersubdomain continuity conditions on velocity. Appeal to the dual max-min problem for appropriately chosen candidate Lagrange multipliers then yields inexpensive bounds for the output associated with a fine-mesh discretization; the Lagrange multipliers are generated by exploiting an associated coarse-mesh approximation. In addition to the requisite coarse-mesh calculations, the bound technique requires solution only of local subdomain Stokes problems on the fine-mesh. The method is illustrated for the Stokes equations, in which the outputs of interest are the flowrate past, and the lift force on, a body immersed in a channel.

Quantum dot nanoparticle conjugation, characterization, and applications in neuroscience

NASA Astrophysics Data System (ADS)

Pathak, Smita

Quantum dot are semiconducting nanoparticles that have been used for decades in a variety of applications such as solar cells, LEDs and medical imaging. Their use in the last area, however, has been extremely limited despite their potential as revolutionary new biological labeling tools. Quantum dots are much brighter and more stable than conventional fluorophores, making them optimal for high resolution imaging and long term studies. Prior work in this area involves synthesizing and chemically conjugating quantum dots to molecules of interest in-house. However this method is both time consuming and prone to human error. Additionally, non-specific binding and nanoparticle aggregation currently prevent researchers from utilizing this system to its fullest capacity. Another critical issue that has not been addressed is determining the number of ligands bound to nanoparticles, which is crucial for proper interpretation of results. In this work, methods to label fixed cells using two types of chemically modified quantum dots are studied. Reproducible non-specific artifact labeling is consistently demonstrated if antibody-quantum dot conditions are less than optimal. In order to explain this, antibodies bound to quantum dots were characterized and quantified. While other groups have qualitatively characterized antibody functionalized quantum dots using TEM, AFM, UV spectroscopy and gel electrophoresis, and in some cases have reported calculated estimates of the putative number of total antibodies bound to quantum dots, no quantitative experimental results had been reported prior to this work. The chemical functionalization and characterization of quantum dot nanocrystals achieved in this work elucidates binding mechanisms of ligands to nanoparticles and allows researchers to not only translate our tools to studies in their own areas of interest but also derive quantitative results from these studies. This research brings ease of use and increased reliability to nanoparticles in medical imaging.

The Nonreceptor Protein Tyrosine Phosphatase PTP1B Binds to the Cytoplasmic Domain of N-Cadherin and Regulates the Cadherin–Actin Linkage

PubMed Central

Balsamo, Janne; Arregui, Carlos; Leung, TinChung; Lilien, Jack

1998-01-01

Cadherin-mediated adhesion depends on the association of its cytoplasmic domain with the actin-containing cytoskeleton. This interaction is mediated by a group of cytoplasmic proteins: α-and β- or γ- catenin. Phosphorylation of β-catenin on tyrosine residues plays a role in controlling this association and, therefore, cadherin function. Previous work from our laboratory suggested that a nonreceptor protein tyrosine phosphatase, bound to the cytoplasmic domain of N-cadherin, is responsible for removing tyrosine-bound phosphate residues from β-catenin, thus maintaining the cadherin–actin connection (Balsamo et al., 1996). Here we report the molecular cloning of the cadherin-associated tyrosine phosphatase and identify it as PTP1B. To definitively establish a causal relationship between the function of cadherin-bound PTP1B and cadherin-mediated adhesion, we tested the effect of expressing a catalytically inactive form of PTP1B in L cells constitutively expressing N-cadherin. We find that expression of the catalytically inactive PTP1B results in reduced cadherin-mediated adhesion. Furthermore, cadherin is uncoupled from its association with actin, and β-catenin shows increased phosphorylation on tyrosine residues when compared with parental cells or cells transfected with the wild-type PTP1B. Both the transfected wild-type and the mutant PTP1B are found associated with N-cadherin, and recombinant mutant PTP1B binds to N-cadherin in vitro, indicating that the catalytically inactive form acts as a dominant negative, displacing endogenous PTP1B, and rendering cadherin nonfunctional. Our results demonstrate a role for PTP1B in regulating cadherin-mediated cell adhesion. PMID:9786960

Biochemical Roles for Conserved Residues in the Bacterial Fatty Acid-binding Protein Family*

PubMed Central

Broussard, Tyler C.; Miller, Darcie J.; Jackson, Pamela; Nourse, Amanda; White, Stephen W.; Rock, Charles O.

2016-01-01

Fatty acid kinase (Fak) is a ubiquitous Gram-positive bacterial enzyme consisting of an ATP-binding protein (FakA) that phosphorylates the fatty acid bound to FakB. In Staphylococcus aureus, Fak is a global regulator of virulence factor transcription and is essential for the activation of exogenous fatty acids for incorporation into phospholipids. The 1.2-Å x-ray structure of S. aureus FakB2, activity assays, solution studies, site-directed mutagenesis, and in vivo complementation were used to define the functions of the five conserved residues that define the FakB protein family (Pfam02645). The fatty acid tail is buried within the protein, and the exposed carboxyl group is bound by a Ser-93-fatty acid carboxyl-Thr-61-His-266 hydrogen bond network. The guanidinium of the invariant Arg-170 is positioned to potentially interact with a bound acylphosphate. The reduced thermal denaturation temperatures of the T61A, S93A, and H266A FakB2 mutants illustrate the importance of the hydrogen bond network in protein stability. The FakB2 T61A, S93A, and H266A mutants are 1000-fold less active in the Fak assay, and the R170A mutant is completely inactive. All FakB2 mutants form FakA(FakB2)2 complexes except FakB2(R202A), which is deficient in FakA binding. Allelic replacement shows that strains expressing FakB2 mutants are defective in fatty acid incorporation into phospholipids and virulence gene transcription. These conserved residues are likely to perform the same critical functions in all bacterial fatty acid-binding proteins. PMID:26774272

Tissue-specific expression of transgenic secreted ACE in vasculature can restore normal kidney functions, but not blood pressure, of Ace-/- mice.

PubMed

Chattopadhyay, Saurabh; Kessler, Sean P; Colucci, Juliana Almada; Yamashita, Michifumi; Senanayake, Preenie deS; Sen, Ganes C

2014-01-01

Angiotensin-converting enzyme (ACE) regulates normal blood pressure and fluid homeostasis through its action in the renin-angiotensin-system (RAS). Ace-/- mice are smaller in size, have low blood pressure and defective kidney structure and functions. All of these defects are cured by transgenic expression of somatic ACE (sACE) in vascular endothelial cells of Ace-/- mice. sACE is expressed on the surface of vascular endothelial cells and undergoes a natural cleavage secretion process to generate a soluble form in the body fluids. Both the tissue-bound and the soluble forms of ACE are enzymatically active, and generate the vasoactive octapeptide Angiotensin II (Ang II) with equal efficiency. To assess the relative physiological roles of the secreted and the cell-bound forms of ACE, we expressed, in the vascular endothelial cells of Ace-/- mice, the ectodomain of sACE, which corresponded to only the secreted form of ACE. Our results demonstrated that the secreted form of ACE could normalize kidney functions and RAS integrity, growth and development of Ace-/- mice, but not their blood pressure. This study clearly demonstrates that the secreted form of ACE cannot replace the tissue-bound ACE for maintaining normal blood pressure; a suitable balance between the tissue-bound and the soluble forms of ACE is essential for maintaining all physiological functions of ACE.

Tissue-Specific Expression of Transgenic Secreted ACE in Vasculature Can Restore Normal Kidney Functions, but Not Blood Pressure, of Ace-/- Mice

PubMed Central

Chattopadhyay, Saurabh; Kessler, Sean P.; Colucci, Juliana Almada; Yamashita, Michifumi; Senanayake, Preenie deS; Sen, Ganes C.

2014-01-01

Angiotensin-converting enzyme (ACE) regulates normal blood pressure and fluid homeostasis through its action in the renin-angiotensin-system (RAS). Ace-/- mice are smaller in size, have low blood pressure and defective kidney structure and functions. All of these defects are cured by transgenic expression of somatic ACE (sACE) in vascular endothelial cells of Ace-/- mice. sACE is expressed on the surface of vascular endothelial cells and undergoes a natural cleavage secretion process to generate a soluble form in the body fluids. Both the tissue-bound and the soluble forms of ACE are enzymatically active, and generate the vasoactive octapeptide Angiotensin II (Ang II) with equal efficiency. To assess the relative physiological roles of the secreted and the cell-bound forms of ACE, we expressed, in the vascular endothelial cells of Ace-/- mice, the ectodomain of sACE, which corresponded to only the secreted form of ACE. Our results demonstrated that the secreted form of ACE could normalize kidney functions and RAS integrity, growth and development of Ace-/- mice, but not their blood pressure. This study clearly demonstrates that the secreted form of ACE cannot replace the tissue-bound ACE for maintaining normal blood pressure; a suitable balance between the tissue-bound and the soluble forms of ACE is essential for maintaining all physiological functions of ACE. PMID:24475296

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

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

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard

2008-01-10

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched inmore » bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.« less

Public participation and marginalized groups: the community development model.

PubMed

O'Keefe, Eileen; Hogg, Christine

1999-12-01

OBJECTIVES: To develop ways of reaching house-bound people and enabling them to give their views in planning and monitoring health and social care. STRATEGY: HealthLINK - a project based in a community health council - explored ways of involving older house-bound people in the London Borough of Camden, in planning and monitoring health and social care using community development techniques. RESULTS: HealthLINK set up an infrastructure to enable house-bound people to have access to information and to enable them to give their views. This resulted in access for health and local authorities to the views of house-bound older people and increased the self esteem and quality of life of those who became involved. CONCLUSIONS: Community development approaches that enable an infrastructure to be established may be an effective way of reaching marginalized communities. However, there are tensions in this approach between the different requirements for public involvement of statutory bodies and of users, and between representation of groups and listening to individual voices.

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

PubMed

Bantignies, Frédéric

2013-01-01

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

Subgap in the Surface Bound States Spectrum of Superfluid (3) 3 He-B with Rough Surface

NASA Astrophysics Data System (ADS)

Nagato, Y.; Higashitani, S.; Nagai, K.

2018-03-01

The subgap structure in the surface bound states spectrum of superfluid ^3He-B with rough surface is discussed. The subgap is formed by the level repulsion between the surface bound state and the continuum states in the course of multiple scattering by the surface roughness. We show that the level repulsion is originated from the nature of the wave function of the surface bound state that is now recognized as Majorana fermion. We study the superfluid ^3He-B with a rough surface and in a magnetic field perpendicular to the surface using the quasi-classical Green function together with a random S-matrix model. We calculate the self-consistent order parameters, the spin polarization density and the surface density of states. It is shown that the subgap is found also in a magnetic field perpendicular to the surface. The magnetic field dependence of the transverse acoustic impedance is also discussed.

Computation of convex bounds for present value functions with random payments

NASA Astrophysics Data System (ADS)

Ahcan, Ales; Darkiewicz, Grzegorz; Goovaerts, Marc; Hoedemakers, Tom

2006-02-01

In this contribution we study the distribution of the present value function of a series of random payments in a stochastic financial environment. Such distributions occur naturally in a wide range of applications within fields of insurance and finance. We obtain accurate approximations by developing upper and lower bounds in the convex-order sense for present value functions. Technically speaking, our methodology is an extension of the results of Dhaene et al. [Insur. Math. Econom. 31(1) (2002) 3-33, Insur. Math. Econom. 31(2) (2002) 133-161] to the case of scalar products of mutually independent random vectors.

The light bound states of N=1 supersymmetric SU(3) Yang-Mills theory on the lattice

NASA Astrophysics Data System (ADS)

Ali, Sajid; Bergner, Georg; Gerber, Henning; Giudice, Pietro; Montvay, Istvan; Münster, Gernot; Piemonte, Stefano; Scior, Philipp

2018-03-01

In this article we summarise our results from numerical simulations of N=1 supersymmetric Yang-Mills theory with gauge group SU(3). We use the formulation of Curci and Veneziano with clover-improved Wilson fermions. The masses of various bound states have been obtained at different values of the gluino mass and gauge coupling. Extrapolations to the limit of vanishing gluino mass indicate that the bound states form mass-degenerate supermultiplets.

Foot Loading Characteristics of Chinese Bound Feet Women: A Comparative Analysis

PubMed Central

Gu, Yaodong; Mei, Qichang; Fernandez, Justin; Li, Jianshe; Ren, Xuejun; Feng, Neng

2015-01-01

The custom of bound feet among Chinese women has existed for almost a century. This practice has influenced the daily life of Chinese women, especially during everyday locomotion. The primary aim of this study is to analyze the loading patterns of bound feet. Specifically, the plantar pressure and center of pressure were analyzed for peak pressure, contact area, force time integral, center of pressure displacement velocity and trajectory in the anterior-posterior direction via a comparison with normal feet. The key outcomes from this work were that the forefoot and rearfoot of bound feet bear the whole loading during stance phase. The center of pressure displacement velocity of bound feet was also greatly reduced with the shortening of trajectories. This suggests that the proprioceptive system adjusts motor function to adapt to new loading patterns while maintaining locomotive stability. A biomechanical understanding of bound feet may assist with prevention, treatment and rehabilitation of bound feet disorders. PMID:25884982

Virial Expansion Bounds

NASA Astrophysics Data System (ADS)

Tate, Stephen James

2013-10-01

In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

Bounds on the attractor dimension for magnetohydrodynamic channel flow with parallel magnetic field at low magnetic Reynolds number.

PubMed

Low, R; Pothérat, A

2015-05-01

We investigate aspects of low-magnetic-Reynolds-number flow between two parallel, perfectly insulating walls in the presence of an imposed magnetic field parallel to the bounding walls. We find a functional basis to describe the flow, well adapted to the problem of finding the attractor dimension and which is also used in subsequent direct numerical simulation of these flows. For given Reynolds and Hartmann numbers, we obtain an upper bound for the dimension of the attractor by means of known bounds on the nonlinear inertial term and this functional basis for the flow. Three distinct flow regimes emerge: a quasi-isotropic three-dimensional (3D) flow, a nonisotropic 3D flow, and a 2D flow. We find the transition curves between these regimes in the space parametrized by Hartmann number Ha and attractor dimension d(att). We find how the attractor dimension scales as a function of Reynolds and Hartmann numbers (Re and Ha) in each regime. We also investigate the thickness of the boundary layer along the bounding wall and find that in all regimes this scales as 1/Re, independently of the value of Ha, unlike Hartmann boundary layers found when the field is normal to the channel. The structure of the set of least dissipative modes is indeed quite different between these two cases but the properties of turbulence far from the walls (smallest scales and number of degrees of freedom) are found to be very similar.

Seasonal variations and source apportionment of atmospheric PM2.5-bound polycyclic aromatic hydrocarbons in a mixed multi-function area of Hangzhou, China.

PubMed

Lu, Hao; Wang, Shengsheng; Li, Yun; Gong, Hui; Han, Jingyi; Wu, Zuliang; Yao, Shuiliang; Zhang, Xuming; Tang, Xiujuan; Jiang, Boqiong

2017-07-01

To reveal the seasonal variations and sources of PM 2.5 -bound polycyclic aromatic hydrocarbons (PAHs) during haze and non-haze episodes, daily PM 2.5 samples were collected from March 2015 to February 2016 in a mixed multi-function area in Hangzhou, China. Ambient concentrations of 16 priority-controlled PAHs were determined. The sums of PM 2.5 -bound PAH concentrations during the haze episodes were 4.52 ± 3.32 and 13.6 ± 6.29 ng m -3 in warm and cold seasons, respectively, which were 1.99 and 1.49 times those during the non-haze episodes. Four PAH sources were identified using the positive matrix factorization model and conditional probability function, which were vehicular emissions (45%), heavy oil combustion (23%), coal and natural gas combustion (22%), and biomass combustion (10%). The four source concentrations of PAHs consistently showed higher levels in the cold season, compared with those in the warm season. Vehicular emissions were the most considerable sources that result in the increase of PM 2.5 -bound PAH levels during the haze episodes, and heavy oil combustion played an important role in the aggravation of haze pollution. The analysis of air mass back trajectories indicated that air mass transport had an influence on the PM 2.5 -bound PAH pollution, especially on the increased contributions from coal combustion and vehicular emissions in the cold season.

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

PubMed

Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

2015-12-11

Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Skin friction measurements of systematically-varied roughness: Probing the role of roughness amplitude and skewness

NASA Astrophysics Data System (ADS)

Barros, Julio; Flack, Karen; Schultz, Michael

2017-11-01

Real-world engineering systems which feature either external or internal wall-bounded turbulent flow are routinely affected by surface roughness. This gives rise to performance degradation in the form of increased drag or head loss. However, at present there is no reliable means to predict these performance losses based upon the roughness topography alone. This work takes a systematic approach by generating random surface roughness in which the surface statistics are closely controlled. Skin friction and roughness function results will be presented for two groups of these rough surfaces. The first group is Gaussian (i.e. zero skewness) in which the root-mean-square roughness height (krms) is varied. The second group has a fixed krms, and the skewness is varied from approximately -1 to +1. The effect of the roughness amplitude and skewness on the skin friction will be discussed. Particular attention will be paid to the effect of these parameters on the roughness function in the transitionally-rough flow regime. For example, the role these parameters play in the monotonic or inflectional nature of the roughness function will be addressed. Future research into the details of the turbulence structure over these rough surfaces will also be outlined. Research funded by U.S. Office of Naval Research (ONR).

Influence of Al(III) on biofilm and its extracellular polymeric substances in sequencing batch biofilm reactors.

PubMed

Hu, Xuewei; Yang, Lei; Lai, Xinke; Yao, Qi; Chen, Kai

2017-10-03

This paper presented the influence of Al(III) on biodegradability, micromorphology, composition and functional groups characteristics of the biofilm extracellular polymeric substances (EPS) during different growth phases. The sequencing batch biofilm reactors were developed to cultivate biofilms under different Al(III) dosages. The results elucidated that Al(III) affected biofilm development adversely at the beginning of biofilm growth, but promoted the biofilm mass and improved the biofilm activity with the growth of the biofilm. The micromorphological observation indicated that Al(III) led to a reduction of the filaments and promotion of the EPS secretion in growth phases of the biofilm, also Al(III) could promote microorganisms to form larger colonies for mature biofilm. Then, the analysis of EPS contents and components suggested that Al(III) could increase the protein (PN) of tightly bound EPS (TB-EPS) which alleviated the metal toxicity inhibition on the biofilm during the initial phases of biofilm growth. The biofilm could gradually adapt to the inhibition caused by Al(III) at the biofilm maturation moment. Finally, through the Fourier transform infrared spectroscopy, it was found that Al(III) was beneficial for the proliferation and secretion of TB-EPS functional groups, especially the functional groups of protein and polysaccharides.

Reductive electrografting of benzene (p-bisdiazonium hexafluorophosphate): a simple and effective protocol for creating diazonium-functionalized thin films.

PubMed

Marshall, Nicholas; Locklin, Jason

2011-11-01

In this Article, we describe a protocol for surface functionalization of benzenediazonium hexafluorophosphate monolayers by in situ electrochemical reduction of bis(benzenediazonium) hexafluorophosphate. Due to the considerable difference in potential between the first and second reduction of this species, it is possible to form a high density of surface-bound diazonium groups by use of a mild potential which selectively reduces only one diazonium group per ring. The resulting diazonium-containing monolayer reacts readily with solutions of electron-rich aromatic compounds. The reaction with ferrocene produces a dense (2.7 × 10(-10) mol/cm(2)) ferrocene-containing monolayer through a Gomberg-Bachmann type arylation. The resulting ferrocene group exhibits relatively rapid electron transfer to the electrode due to the conjugated linker layer as measured by alternating current voltammetry (ACV) and cyclic voltammetry. Aromatic systems with π-donor substitutents (N,N-dimethylaniline, N,N,N',N'-tetramethyldiaminobenzophenone, and hydroquinone) react through an azo-coupling to form monolayers linked to the surface through an azobenzene moiety. The redox properties of these electron-rich species tethered to the surface were observed and quantified using cyclic voltammetry. This simple and versatile functionalization procedure has a wide variety of potential applications in surface science and materials research.

Two-polariton bound states in the Jaynes-Cummings-Hubbard model

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

Wong, Max T. C.; Law, C. K.

2011-05-15

We examine the eigenstates of the one-dimensional Jaynes-Cummings-Hubbard model in the two-excitation subspace. We discover that two-excitation bound states emerge when the ratio of vacuum Rabi frequency to the tunneling rate between cavities exceeds a critical value. We determine the critical value as a function of the quasimomentum quantum number, and indicate that the bound states carry a strong correlation in which the two polaritons appear to be spatially confined together.

A Posteriori Finite Element Bounds for Sensitivity Derivatives of Partial-Differential-Equation Outputs. Revised

NASA Technical Reports Server (NTRS)

Lewis, Robert Michael; Patera, Anthony T.; Peraire, Jaume

1998-01-01

We present a Neumann-subproblem a posteriori finite element procedure for the efficient and accurate calculation of rigorous, 'constant-free' upper and lower bounds for sensitivity derivatives of functionals of the solutions of partial differential equations. The design motivation for sensitivity derivative error control is discussed; the a posteriori finite element procedure is described; the asymptotic bounding properties and computational complexity of the method are summarized; and illustrative numerical results are presented.

Enzyme-modified electrolyte-gated organic field-effect transistors

NASA Astrophysics Data System (ADS)

Buth, Felix; Donner, Andreas; Stutzmann, Martin; Garrido, Jose A.

2012-10-01

Organic solution-gated field-effect transistors (SGFETs) can be operated at low voltages in aqueous environments, paving the way to the use of organic semiconductors in bio-sensing applications. However, it has been shown that these devices exhibit only a rather weak sensitivity to standard electrolyte parameters such as pH and ionic strength. In order to increase the sensitivity and to add specificity towards a given analyte, the covalent attachment of functional groups and enzymes to the device surface would be desirable. In this contribution we demonstrate that enzyme modified organic SGFETs can be used for the in-situ detection of penicillin in the low μM regime. In a first step, silane molecules with amine terminal groups are grafted to α-sexithiophene-based thin film transistors. Surface characterization techniques like X-ray photoemission confirm the modification of the surface with these functional groups, which are stable in standard aqueous electrolytes. We show that the presence of surface-bound amphoteric groups (e.g. amino or carboxylic moieties) increases the pH-sensitivity of the organic SGFETs. In addition, these groups serve as anchoring sites for the attachment of the enzyme penicillinase. The resulting enzyme-FETs are used for the detection of penicillin, enabling the study of the influence of the buffer strength and the pH of the electrolyte on the enzyme kinetics. The functionalization of the organic FETs shown here can be extended to a large variety of enzymes, allowing the specific detection of different chemical and biochemical analytes.

Real-Time Counting People in Crowded Areas by Using Local Empirical Templates and Density Ratios

NASA Astrophysics Data System (ADS)

Hung, Dao-Huu; Hsu, Gee-Sern; Chung, Sheng-Luen; Saito, Hideo

In this paper, a fast and automated method of counting pedestrians in crowded areas is proposed along with three contributions. We firstly propose Local Empirical Templates (LET), which are able to outline the foregrounds, typically made by single pedestrians in a scene. LET are extracted by clustering foregrounds of single pedestrians with similar features in silhouettes. This process is done automatically for unknown scenes. Secondly, comparing the size of group foreground made by a group of pedestrians to that of appropriate LET captured in the same image patch with the group foreground produces the density ratio. Because of the local scale normalization between sizes, the density ratio appears to have a bound closely related to the number of pedestrians who induce the group foreground. Finally, to extract the bounds of density ratios for groups of different number of pedestrians, we propose a 3D human models based simulation in which camera viewpoints and pedestrians' proximity are easily manipulated. We collect hundreds of typical occluded-people patterns with distinct degrees of human proximity and under a variety of camera viewpoints. Distributions of density ratios with respect to the number of pedestrians are built based on the computed density ratios of these patterns for extracting density ratio bounds. The simulation is performed in the offline learning phase to extract the bounds from the distributions, which are used to count pedestrians in online settings. We reveal that the bounds seem to be invariant to camera viewpoints and humans' proximity. The performance of our proposed method is evaluated with our collected videos and PETS 2009's datasets. For our collected videos with the resolution of 320x240, our method runs in real-time with good accuracy and frame rate of around 30 fps, and consumes a small amount of computing resources. For PETS 2009's datasets, our proposed method achieves competitive results with other methods tested on the same datasets [1], [2].

Development and characterization of methacrylate-based hydrazide monoliths for oriented immobilization of antibodies.

PubMed

Brne, P; Lim, Y-P; Podgornik, A; Barut, M; Pihlar, B; Strancar, A

2009-03-27

Convective interaction media (CIM; BIA Separations) monoliths are attractive stationary phases for use in affinity chromatography because they enable fast affinity binding, which is a consequence of convectively enhanced mass transport. This work focuses on the development of novel CIM hydrazide (HZ) monoliths for the oriented immobilization of antibodies. Adipic acid dihydrazide (AADH) was covalently bound to CIM epoxy monoliths to gain hydrazide groups on the monolith surface. Two different antibodies were afterwards immobilized to hydrazide functionalized monolithic columns and prepared columns were tested for their selectivity. One column was further tested for the dynamic binding capacity.

Colorado Outward Bound School Rafting Manual.

ERIC Educational Resources Information Center

Brown, Al

River rafting trips at the Colorado Outward Bound School (COBS) present participants with an opportunity for developing self-confidence, self-awareness, and concern for others through challenging and adventuresome group effort, combined with a program of instruction in rafting skills, safety consciousness, and awareness of the natural environment.…

Dependence in probabilistic modeling Dempster-Shafer theory and probability bounds analysis

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

Ferson, Scott; Nelsen, Roger B.; Hajagos, Janos

2015-05-01

This report summarizes methods to incorporate information (or lack of information) about inter-variable dependence into risk assessments that use Dempster-Shafer theory or probability bounds analysis to address epistemic and aleatory uncertainty. The report reviews techniques for simulating correlated variates for a given correlation measure and dependence model, computation of bounds on distribution functions under a specified dependence model, formulation of parametric and empirical dependence models, and bounding approaches that can be used when information about the intervariable dependence is incomplete. The report also reviews several of the most pervasive and dangerous myths among risk analysts about dependence in probabilistic models.

An analytic study on bounds for the associated Legendre functions. [for truncation of geopotential series in spherical harmonics in orbital analyses

NASA Technical Reports Server (NTRS)

Payne, M. H.

1973-01-01

The bounds for the normalized associated Legendre functions P sub nm were studied to provide a rational basis for the truncation of the geopotential series in spherical harmonics in various orbital analyses. The conjecture is made that the largest maximum of the normalized associated Legendre function lies in the interval which indicates the greatest integer function. A procedure is developed for verifying this conjecture. An on-line algebraic manipulator, IAM, is used to implement the procedure and the verification is carried out for all n equal to or less than 2m, for m = 1 through 6. A rigorous proof of the conjecture is not available.

Quantum mechanics without potential function

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

Alhaidari, A. D., E-mail: haidari@sctp.org.sa; Ismail, M. E. H.

2015-07-15

In the standard formulation of quantum mechanics, one starts by proposing a potential function that models the physical system. The potential is then inserted into the Schrödinger equation, which is solved for the wavefunction, bound states energy spectrum, and/or scattering phase shift. In this work, however, we propose an alternative formulation in which the potential function does not appear. The aim is to obtain a set of analytically realizable systems, which is larger than in the standard formulation and may or may not be associated with any given or previously known potential functions. We start with the wavefunction, which ismore » written as a bounded infinite sum of elements of a complete basis with polynomial coefficients that are orthogonal on an appropriate domain in the energy space. Using the asymptotic properties of these polynomials, we obtain the scattering phase shift, bound states, and resonances. This formulation enables one to handle not only the well-known quantum systems but also previously untreated ones. Illustrative examples are given for two- and three-parameter systems.« less

Existence and uniqueness of weak solutions of the compressible spherically symmetric Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Huang, Xiangdi

2017-02-01

One of the most influential fundamental tools in harmonic analysis is the Riesz transforms. It maps Lp functions to Lp functions for any p ∈ (1 , ∞) which plays an important role in singular operators. As an application in fluid dynamics, the norm equivalence between ‖∇u‖Lp and ‖ div u ‖ Lp +‖ curl u ‖ Lp is well established for p ∈ (1 , ∞). However, since Riesz operators sent bounded functions only to BMO functions, there is no hope to bound ‖∇u‖L∞ in terms of ‖ div u ‖ L∞ +‖ curl u ‖ L∞. As pointed out by Hoff (2006) [11], this is the main obstacle to obtain uniqueness of weak solutions for isentropic compressible flows. Fortunately, based on new observations, see Lemma 2.2, we derive an exact estimate for ‖∇u‖L∞ ≤ (2 + 1 / N)‖ div u ‖ L∞ for any N-dimensional radially symmetric vector functions u. As a direct application, we give an affirmative answer to the open problem of uniqueness of some weak solutions to the compressible spherically symmetric flows in a bounded ball.

Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.

PubMed

Werner, Tomás

2015-07-01

Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings.

Exciton binding energy in a pyramidal quantum dot

NASA Astrophysics Data System (ADS)

Anitha, A.; Arulmozhi, M.

2018-05-01

The effects of spatially dependent effective mass, non-parabolicity of the conduction band and dielectric screening function on exciton binding energy in a pyramid-shaped quantum dot of GaAs have been investigated by variational method as a function of base width of the pyramid. We have assumed that the pyramid has a square base with area a× a and height of the pyramid H=a/2. The trial wave function of the exciton has been chosen according to the even mirror boundary condition, i.e. the wave function of the exciton at the boundary could be non-zero. The results show that (i) the non-parabolicity of the conduction band affects the light hole (lh) and heavy hole (hh) excitons to be more bound than that with parabolicity of the conduction band, (ii) the dielectric screening function (DSF) affects the lh and hh excitons to be more bound than that without the DSF and (iii) the spatially dependent effective mass (SDEM) affects the lh and hh excitons to be less bound than that without the SDEM. The combined effects of DSF and SDEM on exciton binding energy have also been calculated. The results are compared with those available in the literature.

All-inorganic Germanium nanocrystal films by cationic ligand exchange

DOE PAGES

Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.; ...

2016-01-21

In this study, we introduce a new paradigm for group IV nanocrystal surface chemistry based on room temperature surface activation that enables ionic ligand exchange. Germanium nanocrystals synthesized in a gas-phase plasma reactor are functionalized with labile, cationic alkylammonium ligands rather than with traditional covalently bound groups. We employ Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies to demonstrate the alkylammonium ligands are freely exchanged on the germanium nanocrystal surface with a variety of cationic ligands, including short inorganic ligands such as ammonium and alkali metal cations. This ionic ligand exchange chemistry is used to demonstrate enhanced transport inmore » germanium nanocrystal films following ligand exchange as well as the first photovoltaic device based on an all-inorganic germanium nanocrystal absorber layer cast from solution. This new ligand chemistry should accelerate progress in utilizing germanium and other group IV nanocrystals for optoelectronic applications.« less

Method of producing catalytic material for fabricating nanostructures

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

Seals, Roland D.; Menchhofer, Paul A.; Howe, Jane Y.

Methods of fabricating nano-catalysts are described. In some embodiments the nano-catalyst is formed from a powder-based substrate material and is some embodiments the nano-catalyst is formed from a solid-based substrate material. In some embodiments the substrate material may include metal, ceramic, or silicon or another metalloid. The nano-catalysts typically have metal nanoparticles disposed adjacent the surface of the substrate material. The methods typically include functionalizing the surface of the substrate material with a chelating agent, such as a chemical having dissociated carboxyl functional groups (--COO), that provides an enhanced affinity for metal ions. The functionalized substrate surface may then bemore » exposed to a chemical solution that contains metal ions. The metal ions are then bound to the substrate material and may then be reduced, such as by a stream of gas that includes hydrogen, to form metal nanoparticles adjacent the surface of the substrate.« less

Modeling of the gate-controlled Kondo effect at carbon point defects in graphene

NASA Astrophysics Data System (ADS)

May, Daniel; Lo, Po-Wei; Deltenre, Kira; Henke, Anika; Mao, Jinhai; Jiang, Yuhang; Li, Guohong; Andrei, Eva Y.; Guo, Guang-Yu; Anders, Frithjof B.

2018-04-01

We study the magnetic properties in the vicinity of a single carbon defect in a monolayer of graphene. We include the unbound σ orbital and the vacancy-induced bound π state in an effective two-orbital single-impurity model. The local magnetic moments are stabilized by the Coulomb interaction as well as a significant ferromagnetic Hund's rule coupling between the orbitals predicted by a density functional theory calculation. A hybridization between the orbitals and the Dirac fermions is generated by the curvature of the graphene sheet in the vicinity of the vacancy. We present results for the local spectral function calculated using Wilson's numerical renormalization group approach for a realistic graphene band structure and find three different regimes depending on the filling, the controlling chemical potential, and the hybridization strength. These different regions are characterized by different magnetic properties. The calculated spectral functions qualitatively agree with recent scanning tunneling spectra on graphene vacancies.

Method of producing catalytic materials for fabricating nanostructures

DOEpatents

Seals, Roland D; Menchhofer, Paul A; Howe, Jane Y; Wang, Wei

2013-02-19

Methods of fabricating nano-catalysts are described. In some embodiments the nano-catalyst is formed from a powder-based substrate material and is some embodiments the nano-catalyst is formed from a solid-based substrate material. In some embodiments the substrate material may include metal, ceramic, or silicon or another metalloid. The nano-catalysts typically have metal nanoparticles disposed adjacent the surface of the substrate material. The methods typically include functionalizing the surface of the substrate material with a chelating agent, such as a chemical having dissociated carboxyl functional groups (--COO), that provides an enhanced affinity for metal ions. The functionalized substrate surface may then be exposed to a chemical solution that contains metal ions. The metal ions are then bound to the substrate material and may then be reduced, such as by a stream of gas that includes hydrogen, to form metal nanoparticles adjacent the surface of the substrate.

Using State Merging and State Pruning to Address the Path Explosion Problem Faced by Symbolic Execution

DTIC Science & Technology

2014-06-19

urgent and compelling. Recent efforts in this area automate program analysis techniques using model checking and symbolic execution [2, 5–7]. These...bounded model checking tool for x86 binary programs developed at the Air Force Institute of Technology (AFIT). Jiseki creates a bit-vector logic model based...assume there are n different paths through the function foo . The program could potentially call the function foo a bound number of times, resulting in n

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes.

PubMed

Koshy, Seena S; Eyles, Stephen J; Weis, Robert M; Thompson, Lynmarie K

2013-12-10

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.

Hydrogen Exchange Mass Spectrometry of Functional Membrane-bound Chemotaxis Receptor Complexes

PubMed Central

Koshy, Seena S.; Eyles, Stephen J.; Weis, Robert M.; Thompson, Lynmarie K.

2014-01-01

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (~2 Å) piston displacement of one helix of the periplasmic and transmembrane domains towards the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen exchange mass spectrometry (HDX-MS) measurements of global exchange of CF demonstrate that CF exhibits significantly slower exchange in functional complexes than in solution. Since the exchange rates in functional complexes are comparable to that of other proteins of similar structure, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements, by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system. PMID:24274333

A Randomized Controlled Trial to Evaluate the Safety and Efficacy of Cardiac Contractility Modulation.

PubMed

Abraham, William T; Kuck, Karl-Heinz; Goldsmith, Rochelle L; Lindenfeld, JoAnn; Reddy, Vivek Y; Carson, Peter E; Mann, Douglas L; Saville, Benjamin; Parise, Helen; Chan, Rodrigo; Wiegn, Phi; Hastings, Jeffrey L; Kaplan, Andrew J; Edelmann, Frank; Luthje, Lars; Kahwash, Rami; Tomassoni, Gery F; Gutterman, David D; Stagg, Angela; Burkhoff, Daniel; Hasenfuß, Gerd

2018-05-05

The authors sought to confirm a subgroup analysis of the prior FIX-HF-5 (Evaluate Safety and Efficacy of the OPTIMIZER System in Subjects With Moderate-to-Severe Heart Failure) study showing that cardiac contractility modulation (CCM) improved exercise tolerance (ET) and quality of life in patients with ejection fractions between 25% and 45%. CCM therapy for New York Heart Association (NYHA) functional class III and IV heart failure (HF) patients consists of nonexcitatory electrical signals delivered to the heart during the absolute refractory period. A total of 160 patients with NYHA functional class III or IV symptoms, QRS duration <130 ms, and ejection fraction ≥25% and ≤45% were randomized to continued medical therapy (control, n = 86) or CCM (treatment, n = 74, unblinded) for 24 weeks. Peak VO 2 (primary endpoint), Minnesota Living With Heart Failure questionnaire, NYHA functional class, and 6-min hall walk were measured at baseline and at 12 and 24 weeks. Bayesian repeated measures linear modeling was used for the primary endpoint analysis with 30% borrowing from the FIX-HF-5 subgroup. Safety was assessed by the percentage of patients free of device-related adverse events with a pre-specified lower bound of 70%. The difference in peak VO 2 between groups was 0.84 (95% Bayesian credible interval: 0.123 to 1.552) ml O 2 /kg/min, satisfying the primary endpoint. Minnesota Living With Heart Failure questionnaire (p < 0.001), NYHA functional class (p < 0.001), and 6-min hall walk (p = 0.02) were all better in the treatment versus control group. There were 7 device-related events, yielding a lower bound of 80% of patients free of events, satisfying the primary safety endpoint. The composite of cardiovascular death and HF hospitalizations was reduced from 10.8% to 2.9% (p = 0.048). CCM is safe, improves exercise tolerance and quality of life in the specified group of HF patients, and leads to fewer HF hospitalizations. (Evaluate Safety and Efficacy of the OPTIMIZER System in Subjects With Moderate-to-Severe Heart Failure; NCT01381172). Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Bounds on quantum confinement effects in metal nanoparticles

NASA Astrophysics Data System (ADS)

Blackman, G. Neal; Genov, Dentcho A.

2018-03-01

Quantum size effects on the permittivity of metal nanoparticles are investigated using the quantum box model. Explicit upper and lower bounds are derived for the permittivity and relaxation rates due to quantum confinement effects. These bounds are verified numerically, and the size dependence and frequency dependence of the empirical Drude size parameter is extracted from the model. Results suggest that the common practice of empirically modifying the dielectric function can lead to inaccurate predictions for highly uniform distributions of finite-sized particles.

Bounded Community: Designing and Facilitating Learning Communities in Formal Courses

ERIC Educational Resources Information Center

Wilson, Brent G.; Ludwig-Hardman, Stacey; Thornam, Christine L.; Dunlap, Joanna C.

2004-01-01

Learning communities can emerge spontaneously when people find common learning goals and pursue projects and tasks together in pursuit of those goals. "Bounded" learning communities (BLCs) are groups that form within a structured teaching or training setting, typically a course. Unlike spontaneous communities, BLCs develop in direct response to…

Potential estimates for the p-Laplace system with data in divergence form

NASA Astrophysics Data System (ADS)

Cianchi, A.; Schwarzacher, S.

2018-07-01

A pointwise bound for local weak solutions to the p-Laplace system is established in terms of data on the right-hand side in divergence form. The relevant bound involves a Havin-Maz'ya-Wolff potential of the datum, and is a counterpart for data in divergence form of a classical result of [25], recently extended to systems in [28]. A local bound for oscillations is also provided. These results allow for a unified approach to regularity estimates for broad classes of norms, including Banach function norms (e.g. Lebesgue, Lorentz and Orlicz norms), and norms depending on the oscillation of functions (e.g. Hölder, BMO and, more generally, Campanato type norms). In particular, new regularity properties are exhibited, and well-known results are easily recovered.

Low capping group surface density on zinc oxide nanocrystals.

PubMed

Valdez, Carolyn N; Schimpf, Alina M; Gamelin, Daniel R; Mayer, James M

2014-09-23

The ligand shell of colloidal nanocrystals can dramatically affect their stability and reaction chemistry. We present a methodology to quantify the dodecylamine (DDA) capping shell of colloidal zinc oxide nanocrystals in a nonpolar solvent. Using NMR spectroscopy, three different binding regimes are observed: strongly bound, weakly associated, and free in solution. The surface density of bound DDA is constant over a range of nanocrystal sizes, and is low compared to both predictions of the number of surface cations and maximum coverages of self-assembled monolayers. The density of strongly bound DDA ligands on the as-prepared ZnO NCs is 25% of the most conservative estimate of the maximum surface DDA density. Thus, these NCs do not resemble the common picture of a densely capped surface ligand layer. Annealing the ZnO NCs in molten DDA for 12 h at 160 °C, which is thought to remove surface hydroxide groups, resulted in a decrease of the weakly associated DDA and an increase in the density of strongly bound DDA, to ca. 80% of the estimated density of a self-assembled monolayer on a flat ZnO surface. These findings suggest that as-prepared nanocrystal surfaces contain hydroxide groups (protons on the ZnO surfaces) that inhibit strong binding of DDA.

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum

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

Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen

2011-09-06

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1 {angstrom}, respectively. The apoenzyme crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with twomore » molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4{sub 3} with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.« less

Impact of dia- and catagenesis on sulphur and oxygen sequestration of biomarkers as revealed by artificial maturation of an immature sedimentary rock

USGS Publications Warehouse

Koopmans, M.P.; De Leeuw, J. W.; Lewan, M.D.; Sinninghe, Damste J.S.

1996-01-01

Hydrous pyrolysis of an immature (R(a)??? 0.25%) sulphur-rich marl from the Gessoso-solfifera Formation (Messinian) in the Vena del Gesso Basin was carried out at 160C ??? T ???330 C for 72 h, to study the effect of progressive diagenesis and early catagenesis on the abundance and distribution of sulphur-containing and sulphur- and oxygen-linked carbon skeletons in low-molecular-weight and highmolecular-weight fractions (e.g. kerogen). To this end, compounds in the saturated hydrocarbon fraction, monoaromatic hydrocarbon fraction, polyaromatic hydrocarbon fraction, alkylsulphide fraction and ketone fraction were quantified, as well as compounds released after desulphurisation of the polar fraction and HI/LiAIH4 treatment of the desulphurised polar fraction. Sulphur-bound phytane and (20R)-5??,14??,17??(H) and (20R)-5??,14??,17??(H) C27 C29 steranes in the polar fraction become less abundant with increasing maturation temperature, whereas the amount of their corresponding hydrocarbons increases in the saturated hydrocarbon fraction. Carbon skeletons that are bound in the kerogen by multiple bonds (e.g. C38 n-alkane and isorenieratane) are first released into the polar fraction, and then as free hydrocarbons. These changes occur at relatively low levels of thermal maturity (R(a) <0.6%), as evidenced by the 'immature' values of biomarker maturity parameters such as the ????/(????+ ???? + ????) C35 hopane ratio and the 22S/(22S + 22R)-17??,21??(H) C35 hopane ratio. Sulphur- and oxygen-bound moieties, present in the polar fraction, are not stable with increasing thermal maturation. However, alkylthiophenes, ketones. 1,2-di-n-alkylbenzenes and free n-alkanes seem to be stable thermal degradation products of these sulphur- and oxygen-bound moieties. Thus, apart from free n-alkanes, which are abundantly present in more mature sedimentary rocks and crude oils, alkylthiophenes, 1,2-di-n-alkylbenzenes and ketones can also be expected to occur. The positions of the thiophene moiety and the carbonyl group coincide with the original positions of the functional groups of their precursors. Thus, important information about palaeobiochemicals is retained throughout the sequestration/degradation process.

Performances of One-Round Walks in Linear Congestion Games

NASA Astrophysics Data System (ADS)

Bilò, Vittorio; Fanelli, Angelo; Flammini, Michele; Moscardelli, Luca

We investigate the approximation ratio of the solutions achieved after a one-round walk in linear congestion games. We consider the social functions {Stextsc{um}}, defined as the sum of the players’ costs, and {Mtextsc{ax}}, defined as the maximum cost per player, as a measure of the quality of a given solution. For the social function {Stextsc{um}} and one-round walks starting from the empty strategy profile, we close the gap between the upper bound of 2+sqrt{5}≈ 4.24 given in [8] and the lower bound of 4 derived in [4] by providing a matching lower bound whose construction and analysis require non-trivial arguments. For the social function {Mtextsc{ax}}, for which, to the best of our knowledge, no results were known prior to this work, we show an approximation ratio of Θ(sqrt[4]{n^3}) (resp. Θ(nsqrt{n})), where n is the number of players, for one-round walks starting from the empty (resp. an arbitrary) strategy profile.

A complex guided spectral transform Lanczos method for studying quantum resonance states

DOE PAGES

Yu, Hua-Gen

2014-12-28

A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos (cFOL) polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the originalmore » Hamiltonian in the spectral range of interest. Therefore the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO₂, and compared to previous calculations.« less

Frequency-dependent scaling from mesoscale to macroscale in viscoelastic random composites

PubMed Central

Zhang, Jun

2016-01-01

This paper investigates the scaling from a statistical volume element (SVE; i.e. mesoscale level) to representative volume element (RVE; i.e. macroscale level) of spatially random linear viscoelastic materials, focusing on the quasi-static properties in the frequency domain. Requiring the material statistics to be spatially homogeneous and ergodic, the mesoscale bounds on the RVE response are developed from the Hill–Mandel homogenization condition adapted to viscoelastic materials. The bounds are obtained from two stochastic initial-boundary value problems set up, respectively, under uniform kinematic and traction boundary conditions. The frequency and scale dependencies of mesoscale bounds are obtained through computational mechanics for composites with planar random chessboard microstructures. In general, the frequency-dependent scaling to RVE can be described through a complex-valued scaling function, which generalizes the concept originally developed for linear elastic random composites. This scaling function is shown to apply for all different phase combinations on random chessboards and, essentially, is only a function of the microstructure and mesoscale. PMID:27274689

Enhanced sensitivity of self-assembled-monolayer-based SPR immunosensor for detection of benzaldehyde using a single-step multi-sandwich immunoassay.

PubMed

Gobi, K Vengatajalabathy; Matsumoto, Kiyoshi; Toko, Kiyoshi; Ikezaki, Hidekazu; Miura, Norio

2007-04-01

This paper describes the fabrication and sensing characteristics of a self-assembled monolayer (SAM)-based surface plasmon resonance (SPR) immunosensor for detection of benzaldehyde (BZ). The functional sensing surface was fabricated by the immobilization of a benzaldehyde-ovalbumin conjugate (BZ-OVA) on Au-thiolate SAMs containing carboxyl end groups. Covalent binding of BZ-OVA on SAM was found to be dependent on the composition of the base SAM, and it is improved very much with the use of a mixed monolayer strategy. Based on SPR angle measurements, the functional sensor surface is established as a compact monolayer of BZ-OVA bound on the mixed SAM. The BZ-OVA-bound sensor surface undergoes immunoaffinity binding with anti-benzaldehyde antibody (BZ-Ab) selectively. An indirect inhibition immunoassay principle has been applied, in which analyte benzaldehyde solution was incubated with an optimal concentration of BZ-Ab for 5 min and injected over the sensor chip. Analyte benzaldehyde undergoes immunoreaction with BZ-Ab and makes it inactive for binding to BZ-OVA on the sensor chip. As a result, the SPR angle response decreases with an increase in the concentration of benzaldehyde. The fabricated immunosensor demonstrates a low detection limit (LDL) of 50 ppt (pg mL(-1)) with a response time of 5 min. Antibodies bound to the sensor chip during an immunoassay could be detached by a brief exposure to acidic pepsin. With this surface regeneration, reusability of the same sensor chip for as many as 30 determination cycles has been established. Sensitivity has been enhanced further with the application of an additional single-step multi-sandwich immunoassay step, in which the BZ-Ab bound to the sensor chip was treated with a mixture of biotin-labeled secondary antibody, streptavidin and biotin-bovine serum albumin (Bio-BSA) conjugate. With this approach, the SPR sensor signal increased by ca. 12 times and the low detection limit improved to 5 ppt with a total response time of no more than ca. 10 min. Figure A single-step multi-sandwich immunoassay step increases SPR sensor signal by ca. 12 times affording a low detection limit for benzaldehyde of 5 ppt.

Quadrature formula for evaluating left bounded Hadamard type hypersingular integrals

NASA Astrophysics Data System (ADS)

Bichi, Sirajo Lawan; Eshkuvatov, Z. K.; Nik Long, N. M. A.; Okhunov, Abdurahim

2014-12-01

Left semi-bounded Hadamard type Hypersingular integral (HSI) of the form H(h,x) = 1/π √{1+x/1-x }∫-1 **1√{1-t/1+t }h(t)/(t-x)2 dt,x∈(-1.1), Where h(t) is a smooth function is considered. The automatic quadrature scheme (AQS) is constructed by approximating the density function h(t) by the truncated Chebyshev polynomials of the fourth kind. Numerical results revealed that the proposed AQS is highly accurate when h(t) is choosing to be the polynomial and rational functions. The results are in line with the theoretical findings.

Using new hetero-spectral two-dimensional correlation analyses and synchrotron-radiation-based spectromicroscopy to characterize binding of Cu to soil dissolved organic matter.

PubMed

Sun, Fusheng; Li, Yaqing; Wang, Xiang; Chi, Zhilai; Yu, Guanghui

2017-04-01

Understanding the binding characteristics of copper (Cu) to different functional groups in soil dissolved organic matter (DOM) is important to explore Cu toxicity, bioavailability and ultimate fate in the environment. However, the methods used to explore such binding characteristics are still limited. Here, two-dimensional correlation spectroscopy (2DCOS) integrated with Fourier transform infrared (FTIR), 29 Si nuclear magnetic resonance (NMR), 27 Al NMR, and synchrotron-radiation-based FTIR spectromicroscopy were used to explore the binding characteristics of Cu to soil DOM as part of a long-term (23 years) fertilization experiment. Compared with no fertilization and inorganic fertilization (NPK), long-term pig manure fertilization (M) treatment significantly increased the concentration of total and bioavailable Cu in soils. Furthermore, hetero-spectral 2DCOS analyses demonstrated that the binding characteristics of Cu onto functional groups in soil DOM were modified by fertilization regimes. In the NPK treatment, Cu was bound to aliphatic C, whereas in the manure treatment SiO groups had higher affinity toward Cu than aliphatic C. Also, the sequence of binding of functional groups to Cu was modified by the fertilization treatments. Moreover, synchrotron-radiation-based FTIR spectromicroscopy showed that Cu, clay minerals and sesquioxides, and C functional groups were heterogeneously distributed at the micro-scale. Specifically, clay-OH as well as mineral elements had a distribution pattern similar to Cu, but certain (but not all) C forms showed a distribution pattern inconsistent with that of Cu. The combination of synchrotron radiation spectromicroscopy and 2DCOS is a useful tool in exploring the interactions among heavy metals, minerals and organic components in soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Wavelet-bounded empirical mode decomposition for measured time series analysis

NASA Astrophysics Data System (ADS)

Moore, Keegan J.; Kurt, Mehmet; Eriten, Melih; McFarland, D. Michael; Bergman, Lawrence A.; Vakakis, Alexander F.

2018-01-01

Empirical mode decomposition (EMD) is a powerful technique for separating the transient responses of nonlinear and nonstationary systems into finite sets of nearly orthogonal components, called intrinsic mode functions (IMFs), which represent the dynamics on different characteristic time scales. However, a deficiency of EMD is the mixing of two or more components in a single IMF, which can drastically affect the physical meaning of the empirical decomposition results. In this paper, we present a new approached based on EMD, designated as wavelet-bounded empirical mode decomposition (WBEMD), which is a closed-loop, optimization-based solution to the problem of mode mixing. The optimization routine relies on maximizing the isolation of an IMF around a characteristic frequency. This isolation is measured by fitting a bounding function around the IMF in the frequency domain and computing the area under this function. It follows that a large (small) area corresponds to a poorly (well) separated IMF. An optimization routine is developed based on this result with the objective of minimizing the bounding-function area and with the masking signal parameters serving as free parameters, such that a well-separated IMF is extracted. As examples of application of WBEMD we apply the proposed method, first to a stationary, two-component signal, and then to the numerically simulated response of a cantilever beam with an essentially nonlinear end attachment. We find that WBEMD vastly improves upon EMD and that the extracted sets of IMFs provide insight into the underlying physics of the response of each system.

Thyroid function and obesity.

PubMed

Laurberg, Peter; Knudsen, Nils; Andersen, Stig; Carlé, Allan; Pedersen, Inge Bülow; Karmisholt, Jesper

2012-10-01

Important interaction exists between thyroid function, weight control, and obesity. Several mechanisms seem to be involved, and in studies of groups of people the pattern of thyroid function tests depends on the balance of obesity and underlying thyroid disease in the cohort studied. Obese people with a normal thyroid gland tend to have activation of the hypothalamic-pituitary-thyroid axis with higher serum TSH and thyroid hormones in serum. On the other hand, small differences in thyroid function are associated with up to 5 kg difference in body weight. The weight loss after therapy of overt hypothyroidism is caused by excretion of water bound in tissues (myxoedema). Many patients treated for hyperthyroidism experience a gain of more weight than they lost during the active phase of the disease. The mechanism for this excessive weight gain has not been fully elucidated. New studies on the relation between L-T3 therapy and weight control are discussed. The interaction between weight control and therapy of thyroid disease is important to many patients and it should be studied in more detail.

Near-field limits on the role of faint galaxies in cosmic reionization

NASA Astrophysics Data System (ADS)

Boylan-Kolchin, Michael; Bullock, James S.; Garrison-Kimmel, Shea

2014-09-01

Reionizing the Universe with galaxies appears to require significant star formation in low-mass haloes at early times, while local dwarf galaxy counts tell us that star formation has been minimal in small haloes around us today. Using simple models and the ELVIS simulation suite, we show that reionization scenarios requiring appreciable star formation in haloes with Mvir ≈ 108 M⊙ at z = 8 are in serious tension with galaxy counts in the Local Group. This tension originates from the seemingly inescapable conclusion that 30-60 haloes with Mvir > 108 M⊙ at z = 8 will survive to be distinct bound satellites of the Milky Way at z = 0. Reionization models requiring star formation in such haloes will produce dozens of bound galaxies in the Milky Way's virial volume today (and 100-200 throughout the Local Group), each with ≳105 M⊙ of old stars (≳13 Gyr). This exceeds the stellar mass function of classical Milky Way satellites today, even without allowing for the (significant) post-reionization star formation observed in these galaxies. One possible implication of these findings is that star formation became sharply inefficient in haloes smaller than ˜109 M⊙ at early times, implying that the high-z luminosity function must break at magnitudes brighter than is often assumed (at MUV ≃ -14). Our results suggest that the James Webb Space Telescope (and possibly even the Hubble Space Telescope with the Frontier Fields) may realistically detect the faintest galaxies that drive reionization. It remains to be seen how these results can be reconciled with the most sophisticated simulations of early galaxy formation at present, which predict substantial star formation in Mvir ˜ 108 M⊙ haloes during the epoch of reionization.

Photon-assisted tunneling through a topological superconductor with Majorana bound states

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

Tang, Han-Zhao; Zhang, Ying-Tao, E-mail: zhangyt@mail.hebtu.edu.cn; Liu, Jian-Jun, E-mail: liujj@mail.hebtu.edu.cn

Employing the Keldysh Nonequilibrium Green’s function method, we investigate time-dependent transport through a topological superconductor with Majorana bound states in the presence of a high frequency microwave field. It is found that Majorana bound states driven by photon-assisted tunneling can absorb(emit) photons and the resulting photon-assisted tunneling side band peaks can split the Majorana bound state that then appears at non-zero bias. This splitting breaks from the current opinion that Majorana bound states appear only at zero bias and thus provides a new experimental method for detecting Majorana bound states in the Non-zero-energy mode. We not only demonstrate that themore » photon-assisted tunneling side band peaks are due to Non-zero-energy Majorana bound states, but also that the height of the photon-assisted tunneling side band peaks is related to the intensity of the microwave field. It is further shown that the time-varying conductance induced by the Majorana bound states shows negative values for a certain period of time, which corresponds to a manifestation of the phase coherent time-varying behavior in mesoscopic systems.« less

The structures and properties of proton- and alkali-bound cysteine dimers.

PubMed

Ieritano, Christian; Carr, Patrick J J; Hasan, Moaraj; Burt, Michael; Marta, Rick A; Steinmetz, Vincent; Fillion, Eric; McMahon, Terrance B; Scott Hopkins, W

2016-02-14

The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm(-1) region show that protonation is localized on an amine group, and that intermolecular hydrogen bonding occurs between the protonated amine and the carbonyl oxygen of the neutral Cys moiety. Alkali-bound dimers adopt structures reminiscent of those observed for the monomeric Cys·Li(+) and Cys·Na(+) species. Calculations of the heavier Cys2·M(+) (M = K, Rb or Cs) species suggest that these are significantly less strongly bound than the lighter (M = H, Li, or Na) dimers.

Comparing hard and soft prior bounds in geophysical inverse problems

NASA Technical Reports Server (NTRS)

Backus, George E.

1988-01-01

In linear inversion of a finite-dimensional data vector y to estimate a finite-dimensional prediction vector z, prior information about X sub E is essential if y is to supply useful limits for z. The one exception occurs when all the prediction functionals are linear combinations of the data functionals. Two forms of prior information are compared: a soft bound on X sub E is a probability distribution p sub x on X which describes the observer's opinion about where X sub E is likely to be in X; a hard bound on X sub E is an inequality Q sub x(X sub E, X sub E) is equal to or less than 1, where Q sub x is a positive definite quadratic form on X. A hard bound Q sub x can be softened to many different probability distributions p sub x, but all these p sub x's carry much new information about X sub E which is absent from Q sub x, and some information which contradicts Q sub x. Both stochastic inversion (SI) and Bayesian inference (BI) estimate z from y and a soft prior bound p sub x. If that probability distribution was obtained by softening a hard prior bound Q sub x, rather than by objective statistical inference independent of y, then p sub x contains so much unsupported new information absent from Q sub x that conclusions about z obtained with SI or BI would seen to be suspect.

Comparing hard and soft prior bounds in geophysical inverse problems

NASA Technical Reports Server (NTRS)

Backus, George E.

1987-01-01

In linear inversion of a finite-dimensional data vector y to estimate a finite-dimensional prediction vector z, prior information about X sub E is essential if y is to supply useful limits for z. The one exception occurs when all the prediction functionals are linear combinations of the data functionals. Two forms of prior information are compared: a soft bound on X sub E is a probability distribution p sub x on X which describeds the observer's opinion about where X sub E is likely to be in X; a hard bound on X sub E is an inequality Q sub x(X sub E, X sub E) is equal to or less than 1, where Q sub x is a positive definite quadratic form on X. A hard bound Q sub x can be softened to many different probability distributions p sub x, but all these p sub x's carry much new information about X sub E which is absent from Q sub x, and some information which contradicts Q sub x. Both stochastic inversion (SI) and Bayesian inference (BI) estimate z from y and a soft prior bound p sub x. If that probability distribution was obtained by softening a hard prior bound Q sub x, rather than by objective statistical inference independent of y, then p sub x contains so much unsupported new information absent from Q sub x that conclusions about z obtained with SI or BI would seen to be suspect.

1-norm support vector novelty detection and its sparseness.

PubMed

Zhang, Li; Zhou, WeiDa

2013-12-01

This paper proposes a 1-norm support vector novelty detection (SVND) method and discusses its sparseness. 1-norm SVND is formulated as a linear programming problem and uses two techniques for inducing sparseness, or the 1-norm regularization and the hinge loss function. We also find two upper bounds on the sparseness of 1-norm SVND, or exact support vector (ESV) and kernel Gram matrix rank bounds. The ESV bound indicates that 1-norm SVND has a sparser representation model than SVND. The kernel Gram matrix rank bound can loosely estimate the sparseness of 1-norm SVND. Experimental results show that 1-norm SVND is feasible and effective. Copyright © 2013 Elsevier Ltd. All rights reserved.

Oviductal epithelial cells selected boar sperm according to their functional characteristics

PubMed Central

López-Úbeda, Rebeca; García-Vázquez, Francisco A; Gadea, Joaquín; Matás, Carmen

2017-01-01

The interaction of oviductal epithelial cells (OECs) with the spermatozoa has beneficial effects on the sperm functions. The aim of this study is to evaluate the in vitro fertilizing capacity of incubating spermatozoa previously selected by density gradient in OEC and determinate some sperm characteristics that could explain the results obtained. In this study, we assessed in vitro fertilization (IVF), tyrosine phosphorylation, phosphatidylserine translocation, nuclear DNA fragmentation, and chromatin decondensation. Three experimental sperm groups, previously selected by Percoll gradient, were established according to the origin of the sperm used for IVF: (i) W30 group: spermatozoa were incubated with oocytes in the absence of OEC; (ii) NB group: after sperm incubation in OEC, the unbound spermatozoa were incubated with oocytes, in the absence of OEC; and (iii) B group: after sperm incubation with OEC, the bound spermatozoa were incubated with oocytes in the OEC plates. The results showed that sperm from the NB group led to a lower IVF yield, accompanied by low penetration rates (NB: 19.6%, B: 94.9%, and W30: 62.9%; P < 0.001) and problems of nuclear decondensation. Moreover, higher levels of tyrosine phosphorylation were observed in the NB group compared with the W30 and B groups (NB: 58.7%, B: 2.5%, and W30: 4.5%; P < 0.01). A similar trend was observed in phosphatidylserine translocation (NB: 93.7%, B: 5.7%, and W30: 44.2%; P < 0.01). These results demonstrate that the OEC exerts a rigorous degree of sperm selection, even within an already highly selected population of spermatozoa, and can capture the best functional spermatozoa for fertilization. PMID:27232850

Density Large Deviations for Multidimensional Stochastic Hyperbolic Conservation Laws

NASA Astrophysics Data System (ADS)

Barré, J.; Bernardin, C.; Chetrite, R.

2018-02-01

We investigate the density large deviation function for a multidimensional conservation law in the vanishing viscosity limit, when the probability concentrates on weak solutions of a hyperbolic conservation law. When the mobility and diffusivity matrices are proportional, i.e. an Einstein-like relation is satisfied, the problem has been solved in Bellettini and Mariani (Bull Greek Math Soc 57:31-45, 2010). When this proportionality does not hold, we compute explicitly the large deviation function for a step-like density profile, and we show that the associated optimal current has a non trivial structure. We also derive a lower bound for the large deviation function, valid for a more general weak solution, and leave the general large deviation function upper bound as a conjecture.

PIXE-electrophoresis shows starving collembolan reallocates protein-bound metals.

PubMed

Bengtsson, Göran; Pallon, Jan; Nilsson, Christina; Triebskorn, Rita; Köhler, Heinz-R

2016-01-01

One of multiple functions of metalloproteins is to provide detoxification to excess metal levels in organisms. Here we address the induction and persistence of a range of low to high molecular weight copper- and zinc binding proteins in the collembolan species Tetrodontophora bielanensis exposed to copper- and zinc-enriched food, followed by a period of recovery from metal exposure, in absence and presence of food. After 10 days of feeding copper and zinc contaminated yeast, specimens were either moved to ample of leaf litter material from their woodland stand of origin or starved (no food offered). The molecular weight distribution of metal binding proteins was determined by native polyacryl gel electrophoresis. One gel was stained with Comassie brilliant blue and a duplicate gel dried and scanned for the amount of copper and zinc by particle-induced X-ray emission. Specimens exposed to copper and recovered from it with ample of food had copper bound to two groups of rather low molecular weight proteins (40-50 kDa) and two of intermediate size (70-80 kDa). Most zinc in specimens from the woodland stand was bound to two large proteins of about 104 and 106 kDa. The same proteins were holding some zinc in metal-exposed specimens, but most zinc was found in proteins <40 kDa in size. Specimens recovered from metal exposure in presence of ample of food had the same distribution pattern of zinc binding proteins, whereas starved specimens had zinc as well as copper mainly bound to two proteins of 8 and 10 kDa in size. Thus, the induction and distribution of copper- and zinc-binding proteins depend on exposure conditions, and the presence of low molecular weight binding proteins, characteristic of metallothioneins, was mainly limited to starving conditions.

On a method for generating inequalities for the zeros of certain functions

NASA Astrophysics Data System (ADS)

Gatteschi, Luigi; Giordano, Carla

2007-10-01

In this paper we describe a general procedure which yields inequalities satisfied by the zeros of a given function. The method requires the knowledge of a two-term approximation of the function with bound for the error term. The method was successfully applied many years ago [L. Gatteschi, On the zeros of certain functions with application to Bessel functions, Nederl. Akad. Wetensch. Proc. Ser. 55(3)(1952), Indag. Math. 14(1952) 224-229] and more recently too [L. Gatteschi and C. Giordano, Error bounds for McMahon's asymptotic approximations of the zeros of the Bessel functions, Integral Transform Special Functions, 10(2000) 41-56], to the zeros of the Bessel functions of the first kind. Here, we present the results of the application of the method to get inequalities satisfied by the zeros of the derivative of the function . This function plays an important role in the asymptotic study of the stationary points of the solutions of certain differential equations.

Bounds on the conductivity of a suspension of random impenetrable spheres

NASA Astrophysics Data System (ADS)

Beasley, J. D.; Torquato, S.

1986-11-01

We compare the general Beran bounds on the effective electrical conductivity of a two-phase composite to the bounds derived by Torquato for the specific model of spheres distributed throughout a matrix phase. For the case of impenetrable spheres, these bounds are shown to be identical and to depend on the microstructure through the sphere volume fraction φ2 and a three-point parameter ζ2, which is an integral over a three-point correlation function. We evaluate ζ2 exactly through third order in φ2 for distributions of impenetrable spheres. This expansion is compared to the analogous results of Felderhof and of Torquato and Lado, all of whom employed the superposition approximation for the three-particle distribution function involved in ζ2. The results indicate that the exact ζ2 will be greater than the value calculated under the superposition approximation. For reasons of mathematical analogy, the results obtained here apply as well to the determination of the thermal conductivity, dielectric constant, and magnetic permeability of composite media and the diffusion coefficient of porous media.

Matrix algorithms for solving (in)homogeneous bound state equations

PubMed Central

Blank, M.; Krassnigg, A.

2011-01-01

In the functional approach to quantum chromodynamics, the properties of hadronic bound states are accessible via covariant integral equations, e.g. the Bethe–Salpeter equation for mesons. In particular, one has to deal with linear, homogeneous integral equations which, in sophisticated model setups, use numerical representations of the solutions of other integral equations as part of their input. Analogously, inhomogeneous equations can be constructed to obtain off-shell information in addition to bound-state masses and other properties obtained from the covariant analogue to a wave function of the bound state. These can be solved very efficiently using well-known matrix algorithms for eigenvalues (in the homogeneous case) and the solution of linear systems (in the inhomogeneous case). We demonstrate this by solving the homogeneous and inhomogeneous Bethe–Salpeter equations and find, e.g. that for the calculation of the mass spectrum it is as efficient or even advantageous to use the inhomogeneous equation as compared to the homogeneous. This is valuable insight, in particular for the study of baryons in a three-quark setup and more involved systems. PMID:21760640

Application of the N-quantum approximation to the proton radius problem

NASA Astrophysics Data System (ADS)

Cowen, Steven

This thesis is organized into three parts: 1. Introduction and bound state calculations of electronic and muonic hydrogen, 2. Bound states in motion, and 3.Treatment of soft photons. In the first part, we apply the N-Quantum Approximation (NQA) to electronic and muonic hydrogen and search for any new corrections to energy levels that could account for the 0.31 meV discrepancy of the proton radius problem. We derive a bound state equation and compare our numerical solutions and wave functions to those of the Dirac equation. We find NQA Lamb shift diagrams and calculate the associated energy shift contributions. We do not find any new corrections large enough to account for the discrepancy. In part 2, we discuss the effects of motion on bound states using the NQA. We find classical Lorentz contraction of the lowest order NQA wave function. Finally, in part 3, we develop a clothing transformation for interacting fields in order to produce the correct asymptotic limits. We find the clothing eliminates a trilinear interacting Hamiltonian term and produces a quadrilinear soft photon interaction term.

Interactions between macromolecule-bound antioxidants and Trolox during liposome autoxidation: A multivariate approach.

PubMed

Çelik, Ecem Evrim; Rubio, Jose Manuel Amigo; Andersen, Mogens L; Gökmen, Vural

2017-12-15

The interactions between free and macromolecule-bound antioxidants were investigated in order to evaluate their combined effects on the antioxidant environment. Dietary fiber (DF), protein and lipid-bound antioxidants, obtained from whole wheat, soybean and olive oil products, respectively and Trolox were used for this purpose. Experimental studies were carried out in autoxidizing liposome medium by monitoring the development of fluorescent products formed by lipid oxidation. Chemometric methods were used both at experimental design and multivariate data analysis stages. Comparison of the simple addition effects of Trolox and bound antioxidants with measured values on lipid oxidation revealed synergetic interactions for DF and refined olive oil-bound antioxidants, and antagonistic interactions for protein and extra virgin olive oil-bound antioxidants with Trolox. A generalized version of logistic function was successfully used for modelling the oxidation curve of liposomes. Principal component analysis revealed two separate phases of liposome autoxidation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Robust passivity analysis for discrete-time recurrent neural networks with mixed delays

NASA Astrophysics Data System (ADS)

Huang, Chuan-Kuei; Shu, Yu-Jeng; Chang, Koan-Yuh; Shou, Ho-Nien; Lu, Chien-Yu

2015-02-01

This article considers the robust passivity analysis for a class of discrete-time recurrent neural networks (DRNNs) with mixed time-delays and uncertain parameters. The mixed time-delays that consist of both the discrete time-varying and distributed time-delays in a given range are presented, and the uncertain parameters are norm-bounded. The activation functions are assumed to be globally Lipschitz continuous. Based on new bounding technique and appropriate type of Lyapunov functional, a sufficient condition is investigated to guarantee the existence of the desired robust passivity condition for the DRNNs, which can be derived in terms of a family of linear matrix inequality (LMI). Some free-weighting matrices are introduced to reduce the conservatism of the criterion by using the bounding technique. A numerical example is given to illustrate the effectiveness and applicability.

Searching for an Axis-Parallel Shoreline

NASA Astrophysics Data System (ADS)

Langetepe, Elmar

We are searching for an unknown horizontal or vertical line in the plane under the competitive framework. We design a framework for lower bounds on all cyclic and monotone strategies that result in two-sequence functionals. For optimizing such functionals we apply a method that combines two main paradigms. The given solution shows that the combination method is of general interest. Finally, we obtain the current best strategy and can prove that this is the best strategy among all cyclic and monotone strategies which is a main step toward a lower bound construction.

Bayesian inference based on dual generalized order statistics from the exponentiated Weibull model

NASA Astrophysics Data System (ADS)

Al Sobhi, Mashail M.

2015-02-01

Bayesian estimation for the two parameters and the reliability function of the exponentiated Weibull model are obtained based on dual generalized order statistics (DGOS). Also, Bayesian prediction bounds for future DGOS from exponentiated Weibull model are obtained. The symmetric and asymmetric loss functions are considered for Bayesian computations. The Markov chain Monte Carlo (MCMC) methods are used for computing the Bayes estimates and prediction bounds. The results have been specialized to the lower record values. Comparisons are made between Bayesian and maximum likelihood estimators via Monte Carlo simulation.

Sleep quality and depression of nursing home older adults in wheelchairs after exercises.

PubMed

Chen, Kuei-Min; Huang, Hsin-Ting; Cheng, Yin-Yin; Li, Chun-Huw; Chang, Ya-Hui

2015-01-01

Sleep disturbances and depression are costly and potentially disabling conditions that affect a considerable proportion of older adults. The purpose of this study was to test the effectiveness of 6 months of elastic band exercises on sleep quality and depression of wheelchair-bound older adults in nursing homes. One hundred twenty-seven older adults from 10 nursing homes participated in this cluster randomized controlled trial, and 114 completed the study. Participants were randomly assigned to two groups: experimental group (five nursing homes, n = 59) and control group (five nursing homes, n = 55). A 40-minute wheelchair-bound senior elastic band exercise program was implemented 3 times per week for 6 months. Sleep quality and depression of the participants were examined at baseline, after 3 months, and at the end of the 6-month study. Participants in the experimental group had longer sleep durations, better habitual sleep efficiencies, and less depression than the control group at 3 months of the study and maintained them throughout the rest of the 6-month study. Nursing home directors could recruit volunteers to learn the program and lead the elderly residents in wheelchairs in practicing the wheelchair-bound senior elastic band exercises regularly in the facilities. Copyright © 2015 Elsevier Inc. All rights reserved.

Group Variable Selection Via Convex Log-Exp-Sum Penalty with Application to a Breast Cancer Survivor Study

PubMed Central

Geng, Zhigeng; Wang, Sijian; Yu, Menggang; Monahan, Patrick O.; Champion, Victoria; Wahba, Grace

2017-01-01

Summary In many scientific and engineering applications, covariates are naturally grouped. When the group structures are available among covariates, people are usually interested in identifying both important groups and important variables within the selected groups. Among existing successful group variable selection methods, some methods fail to conduct the within group selection. Some methods are able to conduct both group and within group selection, but the corresponding objective functions are non-convex. Such a non-convexity may require extra numerical effort. In this article, we propose a novel Log-Exp-Sum(LES) penalty for group variable selection. The LES penalty is strictly convex. It can identify important groups as well as select important variables within the group. We develop an efficient group-level coordinate descent algorithm to fit the model. We also derive non-asymptotic error bounds and asymptotic group selection consistency for our method in the high-dimensional setting where the number of covariates can be much larger than the sample size. Numerical results demonstrate the good performance of our method in both variable selection and prediction. We applied the proposed method to an American Cancer Society breast cancer survivor dataset. The findings are clinically meaningful and may help design intervention programs to improve the qualify of life for breast cancer survivors. PMID:25257196

A lower bound on the Milky Way mass from general phase-space distribution function models

NASA Astrophysics Data System (ADS)

Bratek, Łukasz; Sikora, Szymon; Jałocha, Joanna; Kutschera, Marek

2014-02-01

We model the phase-space distribution of the kinematic tracers using general, smooth distribution functions to derive a conservative lower bound on the total mass within ≈150-200 kpc. By approximating the potential as Keplerian, the phase-space distribution can be simplified to that of a smooth distribution of energies and eccentricities. Our approach naturally allows for calculating moments of the distribution function, such as the radial profile of the orbital anisotropy. We systematically construct a family of phase-space functions with the resulting radial velocity dispersion overlapping with the one obtained using data on radial motions of distant kinematic tracers, while making no assumptions about the density of the tracers and the velocity anisotropy parameter β regarded as a function of the radial variable. While there is no apparent upper bound for the Milky Way mass, at least as long as only the radial motions are concerned, we find a sharp lower bound for the mass that is small. In particular, a mass value of 2.4 × 1011 M⊙, obtained in the past for lower and intermediate radii, is still consistent with the dispersion profile at larger radii. Compared with much greater mass values in the literature, this result shows that determining the Milky Way mass is strongly model-dependent. We expect a similar reduction of mass estimates in models assuming more realistic mass profiles. Full Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/562/A134

[Development of long-term post-tetanic potentiation and changes in S-100 protein contents in hippocampal slices of rats in different functional states].

PubMed

Baĭdo, A I; Shiriaeva, N V; Khichenko, V I; Liuboslavskaia, P N; Starostina, M V

1992-06-01

Male rats of the strains with low (LE) high excitability (HE) of the nervous system have been used in this study. Half of the animals of each strain were neurotized in accordance with the Hecht's scheme. In the hippocampal slices of the non-neurotized LE rats there was a significant increase of the populational spike amplitude during development of LTP as compared with the opposite group of the animals. The LTP formation in the LE strain of rats caused a decrease in the S-100 protein content in the water-soluble, and an increase in the membrane-bound fraction of the protein. Similar results we have observed with the non-inbred Wistar rats but not with the HE strain of the animals. The levels of the water-soluble S-100 protein fraction were also higher in the hippocampuses and entorenal cortices, but not in the cerebellae of the LE strain, as compared with the HE strain of the rats. No differences have been found in the membrane-bound fraction of S-100 protein.

The role of free and bound water in irradiation preservation: Free radical damage as a function of the physical state of water

USGS Publications Warehouse

Wedemeyer, Gary; Dollar, A.M.

1964-01-01

English sole fillets previously equilibrated with aqueous 0.1% cysteine were dehydrated by three methods to moisture levels ranging from 2 to 72%. Model systems using cellulose to replace the fish tissue were also used. The samples were irradiated at 1 Mrad in an air, nitrogen, or oxygen atmosphere. The destruction of −SH groups was measured and related to the amount and physical state of the tissue water. As free water was removed, destruction steadily increased, reaching a maximum at about 20% moisture. Destruction decreased markedly at moisture levels below 10%, and calorimetric measurements confirmed that 10% moisture was about the level of bound water in this species. These data suggest that dehydration favors the reaction of solute molecules with free radicals formed in the free water of muscle cells. At moisture levels greater than about 20%, simple free radical recombination is more likely than reaction with solute molecules, while below 20% moisture the reverse is true. The calculated α values support this conclusion, as do the results from model systems using cellulose.

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

Oberkampf, William Louis; Tucker, W. Troy; Zhang, Jianzhong

This report summarizes methods to incorporate information (or lack of information) about inter-variable dependence into risk assessments that use Dempster-Shafer theory or probability bounds analysis to address epistemic and aleatory uncertainty. The report reviews techniques for simulating correlated variates for a given correlation measure and dependence model, computation of bounds on distribution functions under a specified dependence model, formulation of parametric and empirical dependence models, and bounding approaches that can be used when information about the intervariable dependence is incomplete. The report also reviews several of the most pervasive and dangerous myths among risk analysts about dependence in probabilistic models.

Upper and lower bounds for semi-Markov reliability models of reconfigurable systems

NASA Technical Reports Server (NTRS)

White, A. L.

1984-01-01

This paper determines the information required about system recovery to compute the reliability of a class of reconfigurable systems. Upper and lower bounds are derived for these systems. The class consists of those systems that satisfy five assumptions: the components fail independently at a low constant rate, fault occurrence and system reconfiguration are independent processes, the reliability model is semi-Markov, the recovery functions which describe system configuration have small means and variances, and the system is well designed. The bounds are easy to compute, and examples are included.

Tunneling spectroscopy of quasiparticle bound states in a spinful Josephson junction.

PubMed

Chang, W; Manucharyan, V E; Jespersen, T S; Nygård, J; Marcus, C M

2013-05-24

The spectrum of a segment of InAs nanowire, confined between two superconducting leads, was measured as function of gate voltage and superconducting phase difference using a third normal-metal tunnel probe. Subgap resonances for odd electron occupancy-interpreted as bound states involving a confined electron and a quasiparticle from the superconducting leads, reminiscent of Yu-Shiba-Rusinov states-evolve into Kondo-related resonances at higher magnetic fields. An additional zero-bias peak of unknown origin is observed to coexist with the quasiparticle bound states.

Protein immobilization onto various surfaces using a polymer-bound isocyanate

NASA Astrophysics Data System (ADS)

Kang, Hyun-Jin; Cha, Eun Ji; Park, Hee-Deung

2015-01-01

Silane coupling agents have been widely used for immobilizing proteins onto inorganic surfaces. However, the immobilization method using silane coupling agents requires several treatment steps, and its application is limited to only surfaces containing hydroxyl groups. The aim of this study was to develop a novel method to overcome the limitations of the silane-based immobilization method using a polymer-bound isocyanate. Initially, polymer-bound isocyanate was dissolved in organic solvent and then was used to dip-coat inorganic surfaces. Proteins were then immobilized onto the dip-coated surfaces by the formation of urea bonds between the isocyanate groups of the polymer and the amine groups of the protein. The reaction was verified by FT-IR in which NCO stretching peaks disappeared, and CO and NH stretching peaks appeared after immobilization. The immobilization efficiency of the newly developed method was insensitive to reaction temperatures (4-50 °C), but the efficiency increased with reaction time and reached a maximum after 4 h. Furthermore, the method showed comparable immobilization efficiency to the silane-based immobilization method and was applicable to surfaces that cannot form hydroxyl groups. Taken together, the newly developed method provides a simple and efficient platform for immobilizing proteins onto surfaces.

Respiratory muscle weakness and respiratory muscle training in severely disabled multiple sclerosis patients.

PubMed

Gosselink, R; Kovacs, L; Ketelaer, P; Carton, H; Decramer, M

2000-06-01

To evaluate the contribution of respiratory muscle weakness (part 1) and respiratory muscle training (part 2) to pulmonary function, cough efficacy, and functional status in patients with advanced multiple sclerosis (MS). Survey (part 1) and randomized controlled trial (part 2). Rehabilitation center for MS. Twenty-eight bedridden or wheelchair-bound MS patients (part 1); 18 patients were randomly assigned to a training group (n = 9) or a control group (n = 9) (part 2). The training group (part 2) performed three series of 15 contractions against an expiratory resistance (60% maximum expiratory pressure [PEmax]) two times a day, whereas the control group performed breathing exercises to enhance maximal inspirations. Forced vital capacity (FVC), inspiratory, and expiratory muscle strength (PImax and PEmax), neck flexion force (NFF), cough efficacy by means of the Pulmonary Index (PI), and functional status by means of the Extended Disability Status Scale (EDSS). Part 1 revealed a significantly reduced FVC (43% +/- 26% predicted), PEmax (18% +/- 8% predicted), and PImax (27% +/- 11% predicted), whereas NFF was only mildly reduced (93% +/- 26% predicted). The PI (median score, 10) and EDSS (median score, 8.5) were severely reduced. PEmax was significantly correlated to FVC, EDSS, and PI (r = .77, -.79, and -.47, respectively). In stepwise multiple regression analysis. PEmax was the only factor contributing to the explained variance in FVC (R2 = .60), whereas body weight (R2 = .41) was the only factor for the PI. In part 2, changes in PImax and PEmax tended to be higher in the training group (p = .06 and p = .07, respectively). The PI was significantly improved after 3 months of training compared with the control group (p < .05). After 6 months, the PI remained significantly better in the training group. Expiratory muscle strength was significantly reduced and related to FVC, cough efficacy, and functional status. Expiratory muscle training tended to enhance inspiratory and expiratory muscle strength. In addition, subjectively and objectively rated cough efficacy improved significantly and lasted for 3 months after training cessation.

A Numerical Comparison of Barrier and Modified Barrier Methods for Large-Scale Bound-Constrained Optimization

NASA Technical Reports Server (NTRS)

Nash, Stephen G.; Polyak, R.; Sofer, Ariela

1994-01-01

When a classical barrier method is applied to the solution of a nonlinear programming problem with inequality constraints, the Hessian matrix of the barrier function becomes increasingly ill-conditioned as the solution is approached. As a result, it may be desirable to consider alternative numerical algorithms. We compare the performance of two methods motivated by barrier functions. The first is a stabilized form of the classical barrier method, where a numerically stable approximation to the Newton direction is used when the barrier parameter is small. The second is a modified barrier method where a barrier function is applied to a shifted form of the problem, and the resulting barrier terms are scaled by estimates of the optimal Lagrange multipliers. The condition number of the Hessian matrix of the resulting modified barrier function remains bounded as the solution to the constrained optimization problem is approached. Both of these techniques can be used in the context of a truncated-Newton method, and hence can be applied to large problems, as well as on parallel computers. In this paper, both techniques are applied to problems with bound constraints and we compare their practical behavior.

Lower bound for LCD image quality

NASA Astrophysics Data System (ADS)

Olson, William P.; Balram, Nikhil

1996-03-01

The paper presents an objective lower bound for the discrimination of patterns and fine detail in images on a monochrome LCD. In applications such as medical imaging and military avionics the information of interest is often at the highest frequencies in the image. Since LCDs are sampled data systems, their output modulation is dependent on the phase between the input signal and the sampling points. This phase dependence becomes particularly significant at high spatial frequencies. In order to use an LCD for applications such as those mentioned above it is essential to have a lower (worst case) bound on the performance of the display. We address this problem by providing a mathematical model for the worst case output modulation of an LCD in response to a sine wave input. This function can be interpreted as a worst case modulation transfer function (MTF). The intersection of the worst case MTF with the contrast threshold function (CTF) of the human visual system defines the highest spatial frequency that will always be detectable. In addition to providing the worst case limiting resolution, this MTF is combined with the CTF to produce objective worst case image quality values using the modulation transfer function area (MTFA) metric.

Constraints on parity violating conformal field theories in d = 3

NASA Astrophysics Data System (ADS)

Chowdhury, Subham Dutta; David, Justin R.; Prakash, Shiroman

2017-11-01

We derive constraints on three-point functions involving the stress tensor, T, and a conserved U(1) current, j, in 2+1 dimensional conformal field theories that violate parity, using conformal collider bounds introduced by Hofman and Maldacena. Conformal invariance allows parity-odd tensor-structures for the 〈 T T T〉 and 〈 jjT〉 correlation functions which are unique to three space-time dimensions. Let the parameters which determine the 〈 T T T〉 correlation function be t 4 and α T , where α T is the parity-violating contribution. Similarly let the parameters which determine 〈 jjT〉 correlation function be a 2, and α J , where α J is the parity-violating contribution. We show that the parameters ( t 4, α T ) and (a2, α J ) are bounded to lie inside a disc at the origin of the t 4 - α T plane and the a 2 - α J plane respectively. We then show that large N Chern-Simons theories coupled to a fundamental fermion/boson lie on the circle which bounds these discs. The `t Hooft coupling determines the location of these theories on the boundary circles.

Synthesis, surface modifications, and size-sorting of mixed nickel-zinc ferrite colloidal magnetic nanoparticles.

PubMed

Majewski, P; Krysiński, P

2008-01-01

We report on the spontaneous covalent growth of monomolecular adlayers on mixed nickel-zinc nanoferrite colloidal suspensions (ferrofluids). Synthesized nanoparticles were subjected to surface modification by means of acid chloride chemistry, leading to the formation of covalent bonds between the hydroxy groups at the nanoparticle surface and the acid chloride molecules. This procedure can be easily tailored to allow for the formation of adlayers containing both hydrophobic and hydrophilic regions stacked at predetermined distances from the magnetic core, and also providing the nanoferrites with functional carboxy groups capable of further modifications with, for example, drug molecules. Here, fluorophore aminopyrene molecules were bound to such modified nanoferrites through amide bonds. We also used the same chemistry to modify the surface with covalently bound long-chain palmitoyl moieties, and for comparison we also modified the nanoferrite surface by simple adsorption of oleic acid. Both procedures made the surface highly hydrophobic. These hydrophobic colloids were subsequently spread on an aqueous surface to form Langmuir monolayers with different characteristics. Moreover, since uniformity of size is crucial in a number of applications, we propose an efficient way of sorting the magnetic nanoparticles by size in their colloidal suspension. The suspension is centrifuged at increasing rotational speed and the fractions are collected after each run. The mean size of nanoferrite in each fraction was measured by the powder X-ray diffraction (PXRD) technique.

Trithorax complex component Menin controls differentiation and maintenance of T helper 17 cells

PubMed Central

Watanabe, Yukiko; Onodera, Atsushi; Kanai, Urara; Ichikawa, Tomomi; Obata-Ninomiya, Kazushige; Wada, Tomoko; Kiuchi, Masahiro; Iwamura, Chiaki; Tumes, Damon J.; Shinoda, Kenta; Yagi, Ryoji; Motohashi, Shinichiro; Hirahara, Kiyoshi; Nakayama, Toshinori

2014-01-01

Epigenetic modifications, such as posttranslational modifications of histones, play an important role in gene expression and regulation. These modifications are in part mediated by the Trithorax group (TrxG) complex and the Polycomb group (PcG) complex, which activate and repress transcription, respectively. We herein investigate the role of Menin, a component of the TrxG complex in T helper (Th) cell differentiation and show a critical role for Menin in differentiation and maintenance of Th17 cells. Menin−/− T cells do not efficiently differentiate into Th17 cells, leaving Th1 and Th2 cell differentiation intact in in vitro cultures. Menin deficiency resulted in the attenuation of Th17-induced airway inflammation. In differentiating Th17 cells, Menin directly bound to the Il17a gene locus and was required for the deposition of permissive histone modifications and recruitment of the RNA polymerase II transcriptional complex. Interestingly, although Menin bound to the Rorc locus, Menin was dispensable for the induction of Rorc expression and permissive histone modifications in differentiating Th17 cells. In contrast, Menin was required to maintain expression of Rorc in differentiated Th17 cells, indicating that Menin is essential to stabilize expression of the Rorc gene. Thus, Menin orchestrates Th17 cell differentiation and function by regulating both the induction and maintenance of target gene expression. PMID:25136117

Receptor Expression in Rat Skeletal Muscle Cell Cultures

NASA Technical Reports Server (NTRS)

Young, Ronald B.

1996-01-01

One on the most persistent problems with long-term space flight is atrophy of skeletal muscles. Skeletal muscle is unique as a tissue in the body in that its ability to undergo atrophy or hypertrophy is controlled exclusively by cues from the extracellular environment. The mechanism of communication between muscle cells and their environment is through a group of membrane-bound and soluble receptors, each of which carries out unique, but often interrelated, functions. The primary receptors include acetyl choline receptors, beta-adrenergic receptors, glucocorticoid receptors, insulin receptors, growth hormone (i.e., somatotropin) receptors, insulin-like growth factor receptors, and steroid receptors. This project has been initiated to develop an integrated approach toward muscle atrophy and hypertrophy that takes into account information on the populations of the entire group of receptors (and their respective hormone concentrations), and it is hypothesized that this information can form the basis for a predictive computer model for muscle atrophy and hypertrophy. The conceptual basis for this project is illustrated in the figure below. The individual receptors are shown as membrane-bound, with the exception of the glucocorticoid receptor which is a soluble intracellular receptor. Each of these receptors has an extracellular signalling component (e.g., innervation, glucocorticoids, epinephrine, etc.), and following the interaction of the extracellular component with the receptor itself, an intracellular signal is generated. Each of these intracellular signals is unique in its own way; however, they are often interrelated.

Rab proteins: The key regulators of intracellular vesicle transport

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

Bhuin, Tanmay; Roy, Jagat Kumar, E-mail: jkroy@bhu.ac.in

2014-10-15

Vesicular/membrane trafficking essentially regulates the compartmentalization and abundance of proteins within the cells and contributes in many signalling pathways. This membrane transport in eukaryotic cells is a complex process regulated by a large and diverse array of proteins. A large group of monomeric small GTPases; the Rabs are essential components of this membrane trafficking route. Most of the Rabs are ubiquitously expressed proteins and have been implicated in vesicle formation, vesicle motility/delivery along cytoskeleton elements and docking/fusion at target membranes through the recruitment of effectors. Functional impairments of Rabs affecting transport pathways manifest different diseases. Rab functions are accompanied bymore » cyclical activation and inactivation of GTP-bound and GDP-bound forms between the cytosol and membranes which is regulated by upstream regulators. Rab proteins are characterized by their distinct sub-cellular localization and regulate a wide variety of endocytic, transcytic and exocytic transport pathways. Mutations of Rabs affect cell growth, motility and other biological processes. - Highlights: • Rab proteins regulate different signalling pathways. • Deregulation of Rabs is the fundamental causes of a variety of human diseases. • This paper gives potential directions in developing therapeutic targets. • This paper also gives ample directions for modulating pathways central to normal physiology. • These are the huge challenges for drug discovery and delivery in near future.« less

More N =4 superconformal bootstrap

NASA Astrophysics Data System (ADS)

Beem, Christopher; Rastelli, Leonardo; van Rees, Balt C.

2017-08-01

In this long overdue second installment, we continue to develop the conformal bootstrap program for N =4 superconformal field theories (SCFTs) in four dimensions via an analysis of the correlation function of four stress-tensor supermultiplets. We review analytic results for this correlator and make contact with the SCFT/chiral algebra correspondence of Beem et al. [Commun. Math. Phys. 336, 1359 (2015), 10.1007/s00220-014-2272-x]. We demonstrate that the constraints of unitarity and crossing symmetry require the central charge c to be greater than or equal to 3 /4 in any interacting N =4 SCFT. We apply numerical bootstrap methods to derive upper bounds on scaling dimensions and operator product expansion coefficients for several low-lying, unprotected operators as a function of the central charge. We interpret our bounds in the context of N =4 super Yang-Mills theories, formulating a series of conjectures regarding the embedding of the conformal manifold—parametrized by the complexified gauge coupling—into the space of scaling dimensions and operator product expansion coefficients. Our conjectures assign a distinguished role to points on the conformal manifold that are self-dual under a subgroup of the S -duality group. This paper contains a more detailed exposition of a number of results previously reported in Beem et al. [Phys. Rev. Lett. 111, 071601 (2013), 10.1103/PhysRevLett.111.071601] in addition to new results.

Boundaries for algebras of holomorphic functions on Marcinkiewicz sequence spaces

NASA Astrophysics Data System (ADS)

Choi, Yun Sung; Han, Kwang Hee

2006-11-01

Let be the Banach algebra of all complex-valued bounded continuous functions on the closed unit ball BE of a complex Banach space E and holomorphic in the interior of BE and let be the closed subalgebra of those functions which are uniformly continuous on BE. For the case whose bidual is a Marcinkiewicz sequence space Mw, we describe some sufficient conditions for a set to be a boundary of either or . Moreover, we consider some analogous problems on to those which were studied on the Gowers space Gp of characteristic p by Grados and Moraes [L.R. Grados, L.A. Moraes, Boundaries for algebras of holomorphic functions, J. Math. Anal. Appl. 281 (2003) 575-586; L.R. Grados, L.A. Moraes, Boundaries for an algebra of bounded holomorphic functions, J. Korean Math. Soc. 41 (1) (2004) 231-242].

Conformation-dependent DNA attraction

NASA Astrophysics Data System (ADS)

Li, Weifeng; Nordenskiöld, Lars; Zhou, Ruhong; Mu, Yuguang

2014-05-01

Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03235c

Effect of Fermentation and Cooking on Soluble and Bound Phenolic Profiles of Finger Millet Sour Porridge.

PubMed

Gabaza, Molly; Shumoy, Habtu; Muchuweti, Maud; Vandamme, Peter; Raes, Katleen

2016-10-12

The aim of this study was to evaluate the soluble and bound phenolic content of finger millet and the impact of process induced changes on phenolic profiles of their sour porridge. Finger millet porridge and intermediate products were collected from four groups of households in the Hwedza communal area, Zimbabwe, after which soluble and bound phenolic compounds (PC) including condensed tannins (CT) were quantified. Bound PC and CT contributed 95% of the total PC and CT. The CT were only detected in the red varieties. Major individual PC identified were catechin occurring in the soluble fraction only, while ferulic, sinapic, and salicylic acid were mainly present in the bound fraction. Fermentation and cooking caused a more than 2-fold increase in soluble PC, CT, and individual PC. Improved traditional processing techniques optimized for improved bioavailability and health benefits of phenolics are highly relevant for the low income populations.

Bounding entanglement spreading after a local quench

NASA Astrophysics Data System (ADS)

Drumond, Raphael C.; Móller, Natália S.

2017-06-01

We consider the variation of von Neumann entropy of subsystem reduced states of general many-body lattice spin systems due to local quantum quenches. We obtain Lieb-Robinson-like bounds that are independent of the subsystem volume. The main assumptions are that the Hamiltonian satisfies a Lieb-Robinson bound and that the volume of spheres on the lattice grows at most exponentially with their radius. More specifically, the bound exponentially increases with time but exponentially decreases with the distance between the subsystem and the region where the quench takes place. The fact that the bound is independent of the subsystem volume leads to stronger constraints (than previously known) on the propagation of information throughout many-body systems. In particular, it shows that bipartite entanglement satisfies an effective "light cone," regardless of system size. Further implications to t density-matrix renormalization-group simulations of quantum spin chains and limitations to the propagation of information are discussed.

Cysteine-containing peptide tag for site-specific conjugation of proteins

DOEpatents

Backer, Marina V.; Backer, Joseph M.

2008-04-08

The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety bound to the targeting moiety; the biological conjugate having a covalent bond between the thiol group of SEQ ID NO:2 and a functional group in the binding moiety. The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety that comprises an adapter protein, the adapter protein having a thiol group; the biological conjugate having a disulfide bond between the thiol group of SEQ ID NO:2 and the thiol group of the adapter protein. The present invention is also directed to biological sequences employed in the above biological conjugates, as well as pharmaceutical preparations and methods using the above biological conjugates.

Cysteine-containing peptide tag for site-specific conjugation of proteins

DOEpatents

Backer, Marina V.; Backer, Joseph M.

2010-10-05

The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety bound to the targeting moiety; the biological conjugate having a covalent bond between the thiol group of SEQ ID NO:2 and a functional group in the binding moiety. The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety that comprises an adapter protein, the adapter protein having a thiol group; the biological conjugate having a disulfide bond between the thiol group of SEQ ID NO:2 and the thiol group of the adapter protein. The present invention is also directed to biological sequences employed in the above biological conjugates, as well as pharmaceutical preparations and methods using the above biological conjugates.

The Structure of the Human Centrin 2-Xeroderma Pigmentosum Group C Protein Complex

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

Thompson,J.; Ryan, Z.; Salisbury, J.

2006-01-01

Human centrin-2 plays a key role in centrosome function and stimulates nucleotide excision repair by binding to the xeroderma pigmentosum group C protein. To determine the structure of human centrin-2 and to develop an understanding of molecular interactions between centrin and xeroderma pigmentosum group C protein, we characterized the crystal structure of calcium-loaded full-length centrin-2 complexed with a xeroderma pigmentosum group C peptide. Our structure shows that the carboxyl-terminal domain of centrin-2 binds this peptide and two calcium atoms, whereas the amino-terminal lobe is in a closed conformation positioned distantly by an ordered {alpha}-helical linker. A stretch of the amino-terminalmore » domain unique to centrins appears disordered. Two xeroderma pigmentosum group C peptides both bound to centrin-2 also interact to form an {alpha}-helical coiled-coil. The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin.« less

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.

PubMed

Adrian, Michael; Winnerdy, Fernaldo Richtia; Heddi, Brahim; Phan, Anh Tuân

2017-08-22

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

$$ \\mathcal{N} $$ = 4 superconformal bootstrap of the K 3 CFT

DOE PAGES

Lin, Ying-Hsuan; Shao, Shu-Heng; Simmons-Duffin, David; ...

2017-05-23

We study two-dimensional (4; 4) superconformal eld theories of central charge c = 6, corresponding to nonlinear sigma models on K3 surfaces, using the superconformal bootstrap. This is made possible through a surprising relation between the BPS N = 4 superconformal blocks with c = 6 and bosonic Virasoro conformal blocks with c = 28, and an exact result on the moduli dependence of a certain integrated BPS 4-point function. Nontrivial bounds on the non-BPS spectrum in the K3 CFT are obtained as functions of the CFT moduli, that interpolate between the free orbifold points and singular CFT points. Wemore » observe directly from the CFT perspective the signature of a continuous spectrum above a gap at the singular moduli, and fi nd numerically an upper bound on this gap that is saturated by the A1 N = 4 cigar CFT. We also derive an analytic upper bound on the fi rst nonzero eigenvalue of the scalar Laplacian on K3 in the large volume regime, that depends on the K3 moduli data. As two byproducts, we find an exact equivalence between a class of BPS N = 2 superconformal blocks and Virasoro conformal blocks in two dimensions, and an upper bound on the four-point functions of operators of sufficiently low scaling dimension in three and four dimensional CFTs.« less

$$ \\mathcal{N} $$ = 4 superconformal bootstrap of the K 3 CFT

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

Lin, Ying-Hsuan; Shao, Shu-Heng; Simmons-Duffin, David

We study two-dimensional (4; 4) superconformal eld theories of central charge c = 6, corresponding to nonlinear sigma models on K3 surfaces, using the superconformal bootstrap. This is made possible through a surprising relation between the BPS N = 4 superconformal blocks with c = 6 and bosonic Virasoro conformal blocks with c = 28, and an exact result on the moduli dependence of a certain integrated BPS 4-point function. Nontrivial bounds on the non-BPS spectrum in the K3 CFT are obtained as functions of the CFT moduli, that interpolate between the free orbifold points and singular CFT points. Wemore » observe directly from the CFT perspective the signature of a continuous spectrum above a gap at the singular moduli, and fi nd numerically an upper bound on this gap that is saturated by the A1 N = 4 cigar CFT. We also derive an analytic upper bound on the fi rst nonzero eigenvalue of the scalar Laplacian on K3 in the large volume regime, that depends on the K3 moduli data. As two byproducts, we find an exact equivalence between a class of BPS N = 2 superconformal blocks and Virasoro conformal blocks in two dimensions, and an upper bound on the four-point functions of operators of sufficiently low scaling dimension in three and four dimensional CFTs.« less

Disadvantaged Older Jobseekers and the Concept of Bounded Agency

ERIC Educational Resources Information Center

Meyers, Rebecca

2017-01-01

This article uses the concept of bounded agency to interpret the findings of a study that explored the training and job-seeking activities of a group of older adults. A qualitative, phenomenological approach was used to obtain personal and nuanced accounts of their experiences. A series of semi-structured interviews was conducted with eight adults…

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site.

PubMed

DeChancie, Jason; Houk, K N

2007-05-02

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.

Equivalence principle and bound kinetic energy.

PubMed

Hohensee, Michael A; Müller, Holger; Wiringa, R B

2013-10-11

We consider the role of the internal kinetic energy of bound systems of matter in tests of the Einstein equivalence principle. Using the gravitational sector of the standard model extension, we show that stringent limits on equivalence principle violations in antimatter can be indirectly obtained from tests using bound systems of normal matter. We estimate the bound kinetic energy of nucleons in a range of light atomic species using Green's function Monte Carlo calculations, and for heavier species using a Woods-Saxon model. We survey the sensitivities of existing and planned experimental tests of the equivalence principle, and report new constraints at the level of between a few parts in 10(6) and parts in 10(8) on violations of the equivalence principle for matter and antimatter.

Explicit asymmetric bounds for robust stability of continuous and discrete-time systems

NASA Technical Reports Server (NTRS)

Gao, Zhiqiang; Antsaklis, Panos J.

1993-01-01

The problem of robust stability in linear systems with parametric uncertainties is considered. Explicit stability bounds on uncertain parameters are derived and expressed in terms of linear inequalities for continuous systems, and inequalities with quadratic terms for discrete-times systems. Cases where system parameters are nonlinear functions of an uncertainty are also examined.

Choosing the Number of Clusters in K-Means Clustering

ERIC Educational Resources Information Center

Steinley, Douglas; Brusco, Michael J.

2011-01-01

Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

Frequency dependence of sensitivities in second-order RC active filters

NASA Astrophysics Data System (ADS)

Kunieda, T.; Hiramatsu, Y.; Fukui, A.

1980-02-01

This paper presents that gain and phase sensitivities to some element in biquadratic filters approximately constitute a circle on the complex sensitivity plane, provided that the quality factor Q of the circuit is appreciably larger than unity. Moreover, the group delay sensitivity is represented by the imaginary part of a cardioid. Using these results, bounds of maximum values of gain, phase, and group delay sensitivities are obtained. Further, it is proved that the maximum values of these sensitivities can be simultaneously minimized by minimizing the absolute value of the transfer function sensitivity at the center frequency provided that w(0)-sensitivities are constant and do not contain design parameters. Next, a statistical variability measure for the optimal-filter design is proposed. Finally, the relation between some variability measures proposed to the present time is made clear.

Series of structural and functional models for the ES (enzyme-substrate) complex of the Co(II)-containing quercetin 2,3-dioxygenase.

PubMed

Sun, Ying-Ji; Huang, Qian-Qian; Zhang, Jian-Jun

2014-03-17

A series of mononuclear Co(II)-flavonolate complexes [Co(II)L(R)(fla)] (L(R)H = 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-p/m-R-benzoic acid; R = p-OMe (1), p-Me (2), m-Br (4), and m-NO2 (5); fla = flavonolate) were designed and synthesized as structural and functional models for the ES (enzyme-substrate) complexes to mimic the active site of the Co(II)-containing quercetin 2,3-dioxygenase (Co-2,3-QD). The metal center Co(II) ion in each complex shows a similar distorted octahedral geometry. The model complexes display high enzyme-type dioxygenation reactivity (oxidative O-heterocyclic ring opening of the coordinated substrate flavonolate) at low temperature, presumably due to the attached carboxylate group in the ligands. The reactivity exhibits a substituent group dependent order of -OMe (1) > -Me (2) > -H (3)14b > -Br (4) > -NO2 (5), and the Hammett plot is linear (ρ = -0.78). This can be explained as the electronic nature of the substituent group in the ligands may influence the conformation and redox potential of the bound flavonolate and finally bring different reactivity. The structures, properties, and reactivity of the model complexes show some dependence on the substituent group in the supporting model ligands, and there is some relationship among them. This study is the first example of a series of structural and functional ES models of Co-2,3-QD, with focus on the effects of the electronic nature of substituted groups and the carboxylate group of the ligands to the dioxygenation reactivity, that will provide important insights into the structure-property-reactivity relationship and the catalytic role of Co-2,3-QD.

Structural and dynamical properties of recombining ultracold neutral plasma

NASA Astrophysics Data System (ADS)

Tiwari, Sanat Kumar; Shaffer, Nathaniel R.; Baalrud, Scott D.

2017-10-01

An ultracold plasma (UCP) is an evolving collection of free charges and bound charges (Rydberg atoms). Over time, bound species concentration increases due to recombination. We present the structural and dynamical properties of an evolving UCP using classical molecular dynamics simulation. Coulomb collapse is avoided using a repulsive core with the attractive Coulomb potential. The repulsive core size controls the concentration of bound states, as it determines the depth of the potential well between opposite charges. We vary the repulsive core size to emulate the quasi-static state of plasma at different time during the evolution. Binary, chain and ring-like bound states are observed in the simulation carried out at different coupling strengths and repulsive core size. The effect of bound states can be seen as molecular peaks in the radial distribution function (RDF). The thermodynamic properties associated with the free charges can be analyzed from RDF by separating free from bound states. These bound states also change the dynamical properties of the plasma. The electron velocity auto-correlation displays oscillations due to the orbital motion in bound states. These bound states act like a neutral species, damping electron plasmon modes and broadening the ion acoustic mode. This work is supported by AFOSR Grant Number FA9550-16-1-0221. It used computational resources by XSEDE, which is supported by NSF Grant Number ACI-1053575.

Versatile On-Resin Synthesis of High Mannose Glycosylated Asparagine with Functional Handles

PubMed Central

Chen, Rui; Pawlicki, Mark A.; Tolbert, Thomas J.

2013-01-01

Here we present a synthetic route for solid phase synthesis of N-linked glycoconjugates containing high mannose oligosaccharides which allows the incorporation of useful functional handles on the N-terminus of asparagine. In this strategy, the C-terminus of an Fmoc protected aspartic acid residue is first attached to a solid phase support. The side chain of aspartic acid is protected by a 2-phenylisopropyl protecting group, which allows selective deprotection for the introduction of glycosylation. By using a convergent on-resin glycosylamine coupling strategy, an N-glycosidic linkage is successfully formed on the free side chain of the resin bound aspartic acid with a large high mannose oligosaccharide, Man8GlcNAc2, to yield N-linked high mannose glycosylated asparagine. The use of on-resin glycosylamine coupling provides excellent glycosylation yield, can be applied to couple other types of oligosaccharides, and also makes it possible to recover excess oligosaccharides conveniently after the on-resin coupling reaction. Useful functional handles including an alkene (p-vinylbenzoic acid), an alkyne (4-pentynoic acid), biotin, and 5-carboxyfluorescein are then conjugated onto the N-terminal amine of asparagine on-resin after the removal of the Fmoc protecting group. In this way, useful functional handles are introduced onto the glycosylated asparagine while maintaining the structural integrity of the reducing end of the oligosaccharide. The asparagine side chain also serves as a linker between the glycan and the functional group and preserves the native presentation of N-linked glycan which may aid in biochemical and structural studies. As an example of a biochemical study using functionalized high mannose glycosylated asparagine, a fluorescence polarization assay has been utilized to study the binding of the lectin Concanavalin A (ConA) using 5-carboxyfluorescein labeled high mannose glycosylated asparagine. PMID:24326091

Reflections on conformal spectra

DOE PAGES

Kim, Hyungrok; Kravchuk, Petr; Ooguri, Hirosi

2016-04-29

Here, we use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ 0 of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ 0 as well as for large Δ 0.more » We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.« less

Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

PubMed Central

Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

2013-01-01

Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit. PMID:24106279

Nano-anisotropic surface coating based on drug immobilized pendant polymer to suppress macrophage adhesion response.

PubMed

Kaladhar, K; Renz, H; Sharma, C P

2015-04-01

Exploring drug molecules for material design, to harness concepts of nano-anisotropy and ligand-receptor interactions, are rather elusive. The aim of this study is to demonstrate the bottom-up design of a single-step and bio-interactive polymeric surface coating, based on drug based pendant polymer. This can be applied on to polystyrene (PS) substrates, to suppress macrophage adhesion and spreading. The drug molecule is used in this coating for two purposes. The first one is drug as a "pendant" group, to produce nano-anisotropic properties that can enable adhesion of the coatings to the substrate. The second purpose is to use the drug as a "ligand", to produce ligand-receptor interaction, between the bound ligand and receptors of albumin, to develop a self-albumin coat over the surface, by the preferential binding of albumin in biological environment, to reduce macrophage adhesion. Our in silico studies show that, diclofenac (DIC) is an ideal drug based "ligand" for albumin. This can also act as a "pendant" group with planar aryl groups. The combination of these two factors can help to harness, both nano-anisotropic properties and biological functions to the polymeric coating. Further, the drug, diclofenac (DIC) is immobilized to the polyvinyl alcohol (PVA), to develop the pendant polymer (PVA-DIC). The interaction of bound DIC with the albumin is a ligand-receptor based interaction, as per the studies by circular dichroism, differential scanning calorimetry, and SDS-PAGE. The non-polar π-π* interactions are regulating; the interactions between PVA bound DIC-DIC interactions, leading to "nano-anisotropic condensation" to form distinct "nano-anisotropic segments" inside the polymeric coating. This is evident from, the thermo-responsiveness and uniform size of nanoparticles, as well as regular roughness in the surface coating, with similar properties as that of nanoparticles. In addition, the hydrophobic DIC-polystyrene (PS) interactions, between the PVA-DIC coating and PS-substrate produce improved coating stability. Subsequently, the PVA-DIC coated substrate has the maximum capacity to suppress the macrophage (RAW 264.7 cell line) adhesion and spreading, which is partly due to wavy-surface topography of hydrophilic PVA and preferential albumin binding capacity of PVA bound DIC. Our result shows that, such surfaces suppress the macrophages, even under stimulation with lipopolysaccharide (LPS). The modified tissue culture plates can be used as an in vitro tool, to study the macrophage response under low spatial cues. Copyright © 2015 Elsevier B.V. All rights reserved.

Stability of Nonlinear Systems with Unknown Time-varying Feedback Delay

NASA Astrophysics Data System (ADS)

Chunodkar, Apurva A.; Akella, Maruthi R.

2013-12-01

This paper considers the problem of stabilizing a class of nonlinear systems with unknown bounded delayed feedback wherein the time-varying delay is 1) piecewise constant 2) continuous with a bounded rate. We also consider application of these results to the stabilization of rigid-body attitude dynamics. In the first case, the time-delay in feedback is modeled specifically as a switch among an arbitrarily large set of unknown constant values with a known strict upper bound. The feedback is a linear function of the delayed states. In the case of linear systems with switched delay feedback, a new sufficiency condition for average dwell time result is presented using a complete type Lyapunov-Krasovskii (L-K) functional approach. Further, the corresponding switched system with nonlinear perturbations is proven to be exponentially stable inside a well characterized region of attraction for an appropriately chosen average dwell time. In the second case, the concept of the complete type L-K functional is extended to a class of nonlinear time-delay systems with unknown time-varying time-delay. This extension ensures stability robustness to time-delay in the control design for all values of time-delay less than the known upper bound. Model-transformation is used in order to partition the nonlinear system into a nominal linear part that is exponentially stable with a bounded perturbation. We obtain sufficient conditions which ensure exponential stability inside a region of attraction estimate. A constructive method to evaluate the sufficient conditions is presented together with comparison with the corresponding constant and piecewise constant delay. Numerical simulations are performed to illustrate the theoretical results of this paper.

On the multiple zeros of a real analytic function with applications to the averaging theory of differential equations

NASA Astrophysics Data System (ADS)

García, Isaac A.; Llibre, Jaume; Maza, Susanna

2018-06-01

In this work we consider real analytic functions , where , Ω is a bounded open subset of , is an interval containing the origin, are parameters, and ε is a small parameter. We study the branching of the zero-set of at multiple points when the parameter ε varies. We apply the obtained results to improve the classical averaging theory for computing T-periodic solutions of λ-families of analytic T-periodic ordinary differential equations defined on , using the displacement functions defined by these equations. We call the coefficients in the Taylor expansion of in powers of ε the averaged functions. The main contribution consists in analyzing the role that have the multiple zeros of the first non-zero averaged function. The outcome is that these multiple zeros can be of two different classes depending on whether the zeros belong or not to the analytic set defined by the real variety associated to the ideal generated by the averaged functions in the Noetheriang ring of all the real analytic functions at . We bound the maximum number of branches of isolated zeros that can bifurcate from each multiple zero z 0. Sometimes these bounds depend on the cardinalities of minimal bases of the former ideal. Several examples illustrate our results and they are compared with the classical theory, branching theory and also under the light of singularity theory of smooth maps. The examples range from polynomial vector fields to Abel differential equations and perturbed linear centers.

UV-Visible Spectroscopy-Based Quantification of Unlabeled DNA Bound to Gold Nanoparticles.

PubMed

Baldock, Brandi L; Hutchison, James E

2016-12-20

DNA-functionalized gold nanoparticles have been increasingly applied as sensitive and selective analytical probes and biosensors. The DNA ligands bound to a nanoparticle dictate its reactivity, making it essential to know the type and number of DNA strands bound to the nanoparticle surface. Existing methods used to determine the number of DNA strands per gold nanoparticle (AuNP) require that the sequences be fluorophore-labeled, which may affect the DNA surface coverage and reactivity of the nanoparticle and/or require specialized equipment and other fluorophore-containing reagents. We report a UV-visible-based method to conveniently and inexpensively determine the number of DNA strands attached to AuNPs of different core sizes. When this method is used in tandem with a fluorescence dye assay, it is possible to determine the ratio of two unlabeled sequences of different lengths bound to AuNPs. Two sizes of citrate-stabilized AuNPs (5 and 12 nm) were functionalized with mixtures of short (5 base) and long (32 base) disulfide-terminated DNA sequences, and the ratios of sequences bound to the AuNPs were determined using the new method. The long DNA sequence was present as a lower proportion of the ligand shell than in the ligand exchange mixture, suggesting it had a lower propensity to bind the AuNPs than the short DNA sequence. The ratio of DNA sequences bound to the AuNPs was not the same for the large and small AuNPs, which suggests that the radius of curvature had a significant influence on the assembly of DNA strands onto the AuNPs.

Metal-dependent function of a mammalian acireductone dioxygenase

PubMed Central

Deshpande, Aditi R.; Wagenpfeil, Karina; Pochapsky, Thomas C.; Petsko, Gregory A.; Ringe, Dagmar

2017-01-01

The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella oxytoca are the only known pair of naturally occurring metalloenzymes with distinct chemical and physical properties determined solely by the identity of the divalent transition metal ion (Fe2+ or Ni2+) in the active site. We now show that this dual chemistry can also occur in mammals. ARD from Mus musculus (MmARD) was studied to relate metal ion identity and three-dimensional structure to enzyme function. The iron-containing isozyme catalyzes the cleavage of 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, the penultimate step in methionine salvage. The nickel bound form of ARD catalyzes an off-pathway reaction resulting in formate, carbon monoxide (CO) and 5-(thiomethyl) propionate. Recombinant MmARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. The Fe2+ bound protein, which shows about ten-fold higher activity than others, catalyzes on-pathway chemistry, whereas the Ni2+, Co2+ or Mn2+ forms exhibit off-pathway chemistry, as has been seen with ARD from Klebsiella. Thermal stability of the isozymes is strongly affected by metal ion identity, with Ni2+ bound MmARD being the most stable followed by Co2+ and Fe2+, and Mn2+-bound ARD being the least stable. Ni2+ and Co2+ bound MmARD were crystallized and the structures of the two proteins found to be similar. Enzyme-ligand complexes provide insight into substrate binding, metal coordination and catalytic mechanism. PMID:26858196

Low energy theorems and the unitarity bounds in the extra U(1) superstring inspired E{sub 6} models

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

Sharma, N.K.; Saxena, Pranav; Nagawat, Ashok K.

2005-11-01

The conventional method using low energy theorems derived by Chanowitz et al. [Phys. Rev. Lett. 57, 2344 (1986);] does not seem to lead to an explicit unitarity limit in the scattering processes of longitudinally polarized gauge bosons for the high energy case in the extra U(1) superstring inspired models, commonly known as {eta} model, emanating from E{sub 6} group of superstring theory. We have made use of an alternative procedure given by Durand and Lopez [Phys. Lett. B 217, 463 (1989);], which is applicable to supersymmetric grand unified theories. Explicit unitarity bounds on the superpotential couplings (identified as Yukawa couplings)more » are obtained from both using unitarity constraints as well as using renormalization group equations (RGE) analysis at one-loop level utilizing critical couplings concepts implying divergence of scalar coupling at M{sub G}. These are found to be consistent with finiteness over the entire range M{sub Z}{<=}{radical}(s){<=}M{sub G} i.e. from grand unification scale to weak scale. For completeness, the similar approach has been made use of in other models i.e., {chi}, {psi}, and {nu} models emanating from E{sub 6} and it has been noticed that at weak scale, the unitarity bounds on Yukawa couplings do not differ among E{sub 6} extra U(1) models significantly except for the case of {chi} model in 16 representations. For the case of the E{sub 6}-{eta} model ({beta}{sub E} congruent with 9.64), the analysis using the unitarity constraints leads to the following bounds on various parameters: {lambda}{sub t(max.)}(M{sub Z})=1.294, {lambda}{sub b(max.)}(M{sub Z})=1.278, {lambda}{sub H(max.)}(M{sub Z})=0.955, {lambda}{sub D(max.)}(M{sub Z})=1.312. The analytical analysis of RGE at the one-loop level provides the following critical bounds on superpotential couplings: {lambda}{sub t,c}(M{sub Z}) congruent with 1.295, {lambda}{sub b,c}(M{sub Z}) congruent with 1.279, {lambda}{sub H,c}(M{sub Z}) congruent with 0.968, {lambda}{sub D,c}(M{sub Z}) congruent with 1.315. Thus superpotential coupling values obtained by both the approaches are in good agreement. Theoretically we have obtained bounds on physical mass parameters using the unitarity constrained superpotential couplings. The bounds are as follows: (i) Absolute upper bound on top quark mass m{sub t}{<=}225 GeV (ii) the upper bound on the lightest neutral Higgs boson mass at the tree level is m{sub H{sub 2}{sup 0}}{sup tree}{<=}169 GeV, and after the inclusion of the one-loop radiative correction it is m{sub H{sub 2}{sup 0}}{<=}229 GeV when {lambda}{sub t}{ne}{lambda}{sub b} at the grand unified theory scale. On the other hand, these are m{sub H{sub 2}{sup 0}}{sup tree}{<=}159 GeV, m{sub H{sub 2}{sup 0}}{<=}222 GeV, respectively, when {lambda}{sub t}={lambda}{sub b} at the grand unified theory scale. A plausible range on D-quark mass as a function of mass scale M{sub Z{sub 2}} is m{sub D}{approx_equal}O(3 TeV) for M{sub Z{sub 2}}{approx_equal}O(1 TeV) for the favored values of tan{beta}{<=}1. The bounds on aforesaid physical parameters in the case of {chi}, {psi}, and {nu} models in the 27 representation are almost identical with those of {eta} model and are consistent with the present day experimental precision measurements.« less

A model for the generation of two-dimensional surf beat

USGS Publications Warehouse

List, Jeffrey H.

1992-01-01

A finite difference model predicting group-forced long waves in the nearshore is constructed with two interacting parts: an incident wave model providing time-varying radiation stress gradients across the nearshore, and a long-wave model which solves the equations of motion for the forcing imposed by the incident waves. Both shallow water group-bound long waves and long waves generated by a time-varying breakpoint are simulated. Model-generated time series are used to calculate the cross correlation between wave groups and long waves through the surf zone. The cross-correlation signal first observed by Tucker (1950) is well predicted. For the first time, this signal is decomposed into the contributions from the two mechanisms of leaky mode forcing. Results show that the cross-correlation signal can be explained by bound long waves which are amplified, though strongly modified, through the surf zone before reflection from the shoreline. The breakpoint-forced long waves are added to the bound long waves at a phase of pi/2 and are a secondary contribution owing to their relatively small size.

The binding of sodium dodecyl sulphate to various proteins

PubMed Central

Pitt-Rivers, Rosalind; Impiombato, F. S. Ambesi

1968-01-01

1. The binding of sodium dodecyl sulphate to proteins by equilibrium dialysis was investigated. 2. Most of the proteins studied bound 90–100% of their weight of sodium dodecyl sulphate. 3. The glycoproteins studied bound 70–100% of their weight of sodium dodecyl sulphate, calculated in terms of the polypeptide moiety of the molecule. 4. Proteins not containing S·S groups bound about 140% of their weight of sodium dodecyl sulphate. 5. Reduction of four proteins containing S·S groups caused a rise in sodium dodecyl sulphate binding to 140% of the weight of protein. 6. The apparent micellar molecular weights of the protein–sodium dodecyl sulphate complexes were measured by the dye-solubilization method; they were all found to have approximately the same micellar molecular weight (34000–41000) irrespective of the molecular weight of the protein to which they were attached. PMID:4177067

Ensemble-based characterization of unbound and bound states on protein energy landscape

PubMed Central

Ruvinsky, Anatoly M; Kirys, Tatsiana; Tuzikov, Alexander V; Vakser, Ilya A

2013-01-01

Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping produces a discrete representation of the landscape, further called energy spectrum. We compiled and characterized ensembles of bound and unbound conformations of six small proteins and explored their spectra in implicit solvent. First, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four proteins. Second, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the root mean square deviation (RMSD) between the bound and unbound conformational ensembles. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states. Fourth, the exhaustively long minimization, making small intrarotamer adjustments (all-atom RMSD ≤ 0.7 Å), dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8–4.6 and 3.5–10.5 kcal/mol for the unbound and bound states correspondingly. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the interstate transitions, including the unbound-to-bound ones. PMID:23526684

Gedanken densities and exact constraints in density functional theory.

PubMed

Perdew, John P; Ruzsinszky, Adrienn; Sun, Jianwei; Burke, Kieron

2014-05-14

Approximations to the exact density functional for the exchange-correlation energy of a many-electron ground state can be constructed by satisfying constraints that are universal, i.e., valid for all electron densities. Gedanken densities are designed for the purpose of this construction, but need not be realistic. The uniform electron gas is an old gedanken density. Here, we propose a spherical two-electron gedanken density in which the dimensionless density gradient can be an arbitrary positive constant wherever the density is non-zero. The Lieb-Oxford lower bound on the exchange energy can be satisfied within a generalized gradient approximation (GGA) by bounding its enhancement factor or simplest GGA exchange-energy density. This enhancement-factor bound is well known to be sufficient, but our gedanken density shows that it is also necessary. The conventional exact exchange-energy density satisfies no such local bound, but energy densities are not unique, and the simplest GGA exchange-energy density is not an approximation to it. We further derive a strongly and optimally tightened bound on the exchange enhancement factor of a two-electron density, which is satisfied by the local density approximation but is violated by all published GGA's or meta-GGA's. Finally, some consequences of the non-uniform density-scaling behavior for the asymptotics of the exchange enhancement factor of a GGA or meta-GGA are given.

Maximum and minimum entropy states yielding local continuity bounds

NASA Astrophysics Data System (ADS)

Hanson, Eric P.; Datta, Nilanjana

2018-04-01

Given an arbitrary quantum state (σ), we obtain an explicit construction of a state ρɛ * ( σ ) [respectively, ρ * , ɛ ( σ ) ] which has the maximum (respectively, minimum) entropy among all states which lie in a specified neighborhood (ɛ-ball) of σ. Computing the entropy of these states leads to a local strengthening of the continuity bound of the von Neumann entropy, i.e., the Audenaert-Fannes inequality. Our bound is local in the sense that it depends on the spectrum of σ. The states ρɛ * ( σ ) and ρ * , ɛ (σ) depend only on the geometry of the ɛ-ball and are in fact optimizers for a larger class of entropies. These include the Rényi entropy and the minimum- and maximum-entropies, providing explicit formulas for certain smoothed quantities. This allows us to obtain local continuity bounds for these quantities as well. In obtaining this bound, we first derive a more general result which may be of independent interest, namely, a necessary and sufficient condition under which a state maximizes a concave and Gâteaux-differentiable function in an ɛ-ball around a given state σ. Examples of such a function include the von Neumann entropy and the conditional entropy of bipartite states. Our proofs employ tools from the theory of convex optimization under non-differentiable constraints, in particular Fermat's rule, and majorization theory.

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

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A {sm_bullet} U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg{sup 2+} ions, which in turn are octahedrallymore » coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.« less

Data-based fault-tolerant control for affine nonlinear systems with actuator faults.

PubMed

Xie, Chun-Hua; Yang, Guang-Hong

2016-09-01

This paper investigates the fault-tolerant control (FTC) problem for unknown nonlinear systems with actuator faults including stuck, outage, bias and loss of effectiveness. The upper bounds of stuck faults, bias faults and loss of effectiveness faults are unknown. A new data-based FTC scheme is proposed. It consists of the online estimations of the bounds and a state-dependent function. The estimations are adjusted online to compensate automatically the actuator faults. The state-dependent function solved by using real system data helps to stabilize the system. Furthermore, all signals in the resulting closed-loop system are uniformly bounded and the states converge asymptotically to zero. Compared with the existing results, the proposed approach is data-based. Finally, two simulation examples are provided to show the effectiveness of the proposed approach. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Stability of coefficients in the Kronecker product of a hook and a rectangle

NASA Astrophysics Data System (ADS)

Ballantine, Cristina M.; Hallahan, William T.

2016-02-01

We use recent work of Jonah Blasiak (2012 arXiv:1209.2018) to prove a stability result for the coefficients in the Kronecker product of two Schur functions: one indexed by a hook partition and one indexed by a rectangle partition. We also give nearly sharp bounds for the size of the partition starting with which the Kronecker coefficients are stable. Moreover, we show that once the bound is reached, no new Schur functions appear in the decomposition of Kronecker product. We call this property superstability. Thus, one can recover the Schur decomposition of the Kronecker product from the smallest case in which the superstability holds. The bound for superstability is sharp. Our study of this particular case of the Kronecker product is motivated by its usefulness for the understanding of the quantum Hall effect (Scharf T et al 1994 J. Phys. A: Math. Gen 27 4211-9).

Synchronization Control of Neural Networks With State-Dependent Coefficient Matrices.

PubMed

Zhang, Junfeng; Zhao, Xudong; Huang, Jun

2016-11-01

This brief is concerned with synchronization control of a class of neural networks with state-dependent coefficient matrices. Being different from the existing drive-response neural networks in the literature, a novel model of drive-response neural networks is established. The concepts of uniformly ultimately bounded (UUB) synchronization and convex hull Lyapunov function are introduced. Then, by using the convex hull Lyapunov function approach, the UUB synchronization design of the drive-response neural networks is proposed, and a delay-independent control law guaranteeing the bounded synchronization of the neural networks is constructed. All present conditions are formulated in terms of bilinear matrix inequalities. By comparison, it is shown that the neural networks obtained in this brief are less conservative than those ones in the literature, and the bounded synchronization is suitable for the novel drive-response neural networks. Finally, an illustrative example is given to verify the validity of the obtained results.

Dwell time-based stabilisation of switched delay systems using free-weighting matrices

NASA Astrophysics Data System (ADS)

Koru, Ahmet Taha; Delibaşı, Akın; Özbay, Hitay

2018-01-01

In this paper, we present a quasi-convex optimisation method to minimise an upper bound of the dwell time for stability of switched delay systems. Piecewise Lyapunov-Krasovskii functionals are introduced and the upper bound for the derivative of Lyapunov functionals is estimated by free-weighting matrices method to investigate non-switching stability of each candidate subsystems. Then, a sufficient condition for the dwell time is derived to guarantee the asymptotic stability of the switched delay system. Once these conditions are represented by a set of linear matrix inequalities , dwell time optimisation problem can be formulated as a standard quasi-convex optimisation problem. Numerical examples are given to illustrate the improvements over previously obtained dwell time bounds. Using the results obtained in the stability case, we present a nonlinear minimisation algorithm to synthesise the dwell time minimiser controllers. The algorithm solves the problem with successive linearisation of nonlinear conditions.

Global optimization algorithm for heat exchanger networks

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

Quesada, I.; Grossmann, I.E.

This paper deals with the global optimization of heat exchanger networks with fixed topology. It is shown that if linear area cost functions are assumed, as well as arithmetic mean driving force temperature differences in networks with isothermal mixing, the corresponding nonlinear programming (NLP) optimization problem involves linear constraints and a sum of linear fractional functions in the objective which are nonconvex. A rigorous algorithm is proposed that is based on a convex NLP underestimator that involves linear and nonlinear estimators for fractional and bilinear terms which provide a tight lower bound to the global optimum. This NLP problem ismore » used within a spatial branch and bound method for which branching rules are given. Basic properties of the proposed method are presented, and its application is illustrated with several example problems. The results show that the proposed method only requires few nodes in the branch and bound search.« less

Relativistic bound-state problem in the light-front Yukawa model

NASA Astrophysics Data System (ADS)

Głazek, Stanisław; Harindranath, Avaroth; Pinsky, Stephen; Shigemitsu, Junko; Wilson, Kenneth

1993-02-01

We study the renormalization problem on the light front for the two-fermion bound state in the (3+1)-dimensional Yukawa model, working within the lowest-order Tamm-Dancoff approximation. In addition to traditional mass and wave-function renormalization, new types of counterterms are required. These are nonlocal and involve arbitrary functions of the longitudinal momenta. Their appearance is consistent with general power-counting arguments on the light front. We estimate the ``arbitrary function'' in two ways: (1) by using perturbation theory as a guide and (2) by considering the asymptotic large transverse momentum behavior of the kernel in the bound-state equations. The latter method, as it is currently implemented, is applicable only to the helicity-zero sector of the theory. Because of triviality, in the Yukawa model one must retain a finite cutoff Λ in order to have a nonvanishing renormalized coupling. For the range of renormalized couplings (and cutoffs) allowed by triviality, one finds that the perturbative counterterm does a good job in eliminating cutoff dependence in the low-energy spectrum (masses <<Λ).

Analytical transition-matrix treatment of electric multipole polarizabilities of hydrogen-like atoms

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

Kharchenko, V.F., E-mail: vkharchenko@bitp.kiev.ua

2015-04-15

The direct transition-matrix approach to the description of the electric polarization of the quantum bound system of particles is used to determine the electric multipole polarizabilities of the hydrogen-like atoms. It is shown that in the case of the bound system formed by the Coulomb interaction the corresponding inhomogeneous integral equation determining an off-shell scattering function, which consistently describes virtual multiple scattering, can be solved exactly analytically for all electric multipole polarizabilities. Our method allows to reproduce the known Dalgarno–Lewis formula for electric multipole polarizabilities of the hydrogen atom in the ground state and can also be applied to determinemore » the polarizability of the atom in excited bound states. - Highlights: • A new description for electric polarization of hydrogen-like atoms. • Expression for multipole polarizabilities in terms of off-shell scattering functions. • Derivation of integral equation determining the off-shell scattering function. • Rigorous analytic solving the integral equations both for ground and excited states. • Study of contributions of virtual multiple scattering to electric polarizabilities.« less

The Reconstruction Problem Revisited

NASA Technical Reports Server (NTRS)

Suresh, Ambaby

1999-01-01

The role of reconstruction in avoiding oscillations in upwind schemes is reexamined, with the aim of providing simple, concise proofs. In one dimension, it is shown that if the reconstruction is any arbitrary function bounded by neighboring cell averages and increasing within a cell for increasing data, the resulting scheme is monotonicity preserving, even though the reconstructed function may have overshoots and undershoots at the cell edges and is in general not a monotone function. In the special case of linear reconstruction, it is shown that merely bounding the reconstruction between neighboring cell averages is sufficient to obtain a monotonicity preservinc,y scheme. In two dimensions, it is shown that some ID TVD limiters applied in each direction result in schemes that are not positivity preserving, i.e. do not give positive updates when the data are positive. A simple proof is given to show that if the reconstruction inside the cell is bounded by the neighboring cell averages (including corner neighbors), then the scheme is positivity preserving. A new limiter that enforces this condition but is not as dissipative as the Minmod limiter is also presented.

Decay dynamics of nascent acetonitrile and nitromethane dipole-bound anions produced by intracluster charge-transfer

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

Yandell, Margaret A.; King, Sarah B.; Neumark, Daniel M., E-mail: dneumark@berkeley.edu

2014-05-14

Decay dynamics of nascent dipole bound states of acetonitrile and nitromethane are examined using time-resolved photoelectron imaging of iodide-acetonitrile (I{sup −}·CH{sub 3}CN) and iodide-nitromethane (I{sup −}·CH{sub 3}NO{sub 2}) complexes. Dipole-bound anions are created by UV-initiated electron transfer to the molecule of interest from the associated iodide ion at energies just below the vertical detachment energy of the halide-molecule complex. The acetonitrile anion is observed to decay biexponentially with time constants in the range of 4–900 ps. In contrast, the dipole bound state of nitromethane decays rapidly over 400 fs to form the valence bound anion. The nitromethane valence anion speciesmore » then decays biexponentially with time constants of 2 ps and 1200 ps. The biexponential decay dynamics in acetonitrile are interpreted as iodine atom loss and autodetachment from the excited dipole-bound anion, followed by slower autodetachment of the relaxed metastable ion, while the dynamics of the nitromethane system suggest that a dipole-bound anion to valence anion transition proceeds via intramolecular vibrational energy redistribution to nitro group modes in the vicinity of the iodine atom.« less

Decay dynamics of nascent acetonitrile and nitromethane dipole-bound anions produced by intracluster charge-transfer.

PubMed

Yandell, Margaret A; King, Sarah B; Neumark, Daniel M

2014-05-14

Decay dynamics of nascent dipole bound states of acetonitrile and nitromethane are examined using time-resolved photoelectron imaging of iodide-acetonitrile (I(-)·CH3CN) and iodide-nitromethane (I(-)·CH3NO2) complexes. Dipole-bound anions are created by UV-initiated electron transfer to the molecule of interest from the associated iodide ion at energies just below the vertical detachment energy of the halide-molecule complex. The acetonitrile anion is observed to decay biexponentially with time constants in the range of 4-900 ps. In contrast, the dipole bound state of nitromethane decays rapidly over 400 fs to form the valence bound anion. The nitromethane valence anion species then decays biexponentially with time constants of 2 ps and 1200 ps. The biexponential decay dynamics in acetonitrile are interpreted as iodine atom loss and autodetachment from the excited dipole-bound anion, followed by slower autodetachment of the relaxed metastable ion, while the dynamics of the nitromethane system suggest that a dipole-bound anion to valence anion transition proceeds via intramolecular vibrational energy redistribution to nitro group modes in the vicinity of the iodine atom.

Rhenium and technetium complexes that bind to amyloid-β plaques.

PubMed

Hayne, David J; North, Andrea J; Fodero-Tavoletti, Michelle; White, Jonathan M; Hung, Lin W; Rigopoulos, Angela; McLean, Catriona A; Adlard, Paul A; Ackermann, Uwe; Tochon-Danguy, Henri; Villemagne, Victor L; Barnham, Kevin J; Donnelly, Paul S

2015-03-21

Alzheimer's disease is associated with the presence of insoluble protein deposits in the brain called amyloid plaques. The major constituent of these deposits is aggregated amyloid-β peptide. Technetium-99m complexes that bind to amyloid-β plaques could provide important diagnostic information on amyloid-β plaque burden using Single Photon Emission Computed Tomography (SPECT). Tridentate ligands with a stilbene functional group were used to form complexes with the fac-[M(I)(CO)3](+) (M = Re or (99m)Tc) core. The rhenium carbonyl complexes with tridentate co-ligands that included a stilbene functional group and a dimethylamino substituent bound to amyloid-β present in human frontal cortex brain tissue from subjects with Alzheimer's disease. This chemistry was extended to make the analogous [(99m)Tc(I)(CO)3](+) complexes and the complexes were sufficiently stable in human serum. Whilst the lipophilicity (log D7.4) of the technetium complexes appeared ideally suited for penetration of the blood-brain barrier, preliminary biodistribution studies in an AD mouse model (APP/PS1) revealed relatively low brain uptake (0.24% ID g(-1) at 2 min post injection).

In Vitro and In Vivo Evaluation of a Novel Ferrocyanide Functionalized Nanopourous Silica Decorporation Agent for Cesium (Cs) in Rats

PubMed Central

Timchalk, Charles; Creim, Jeffrey A; Sukwarotwat, Vichaya; Wiacek, Robert; Addleman, R Shane; Fryxell, Glen E; Yantasee, Wassana

2009-01-01

Novel decorporation agents are being developed to protect against radiological terrorist attacks. These sorbents, known as the self-assembled monolayer on mesoporous supports (SAMMS™), are hybrid materials where differing organic moieties are grafted onto mesoporous silica (SiO2). In vitro experiments focused on the evaluation, and optimization of SAMMS for capturing radiocesium (137Cs); therefore based on these studies, a ferrocyanide copper (FC-Cu-EDA)-SAMMS was advanced for in vivo evaluation. In vivo experiments were conducted comparing the performance of the SAMMS vs. insoluble Prussian blue. Groups of jugular cannulated rats (4/treatment) were evaluated. Animals in group I were administered 137Cs chloride (~40 μg/kg) by intravenous (iv) injection or oral gavage; Group II animals were administered pre-bound 137Cs- SAMMS or sequential 137Cs chloride + SAMMS (~61 ng/kg) by oral gavage; and Group III was orally administered 137Cs chloride (~61 ng/kg) followed by either 0.1 g of SAMMS or Prussian blue. Following dosing, the rats were maintained in metabolism cages for 72 hour and blood, urine and fecal samples were collected for 137Cs analysis (gamma counting). Rats were then humanely euthanized, and selected tissues analyzed. Orally administered 137Cs chloride was rapidly and well absorbed (~100% relative to iv dose), and the pharmacokinetics (blood, urine, feces & tissues) were very comparable to the iv dose group. For both exposures the urine and feces accounted for 20 and 3% of the dose, respectively. The prebound 137Cs-SAMMS was retained primarily within the feces (72% of the dose), with ~1.4% detected in the urine, suggesting that the 137Cs remained tightly bound to SAMMS. SAMMS & Prussian blue both effectively captured available 137Cs in the gut with feces accounting for 80–88% of the administered dose, while less than 2% was detected in the urine. This study suggests that the functionalized SAMMS outperforms Prussian blue in vitro at low pH, but demonstrates comparable in vivo sequestration efficacy at low exposure concentrations. The comparable response may be the result of the low 137Cs chloride dose and high sorbent dosage that was utilized. Future studies are planned to optimize SAMMS in vivo performance over a broader range of doses and conditions. PMID:20699707

In Vitro and In Vivo Evaluation of a Novel Ferrocyanide Functionalized Nanopourous Silica Decorporation Agent for Cesium in Rats

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

Timchalk, Charles; Creim, Jeffrey A.; Sukwarotwat, Vichaya

2010-09-01

Novel decorporation agents are being developed to protect against radiological terrorist attacks. These sorbents, known as the self-assembled monolayer on mesoporous supports (SAMMS™), are hybrid materials where differing organic moieties are grafted onto mesoporous silica (SiO2). In vitro experiments focused on the evaluation, and optimization of SAMMS for capturing radiocesium (137Cs); based on these studies, a ferrocyanide copper (FC-Cu-EDA)-SAMMS was advanced for in vivo evaluation. In vivo experiments were conducted comparing the performance of the SAMMS vs. insoluble Prussian blue. Groups of jugular cannulated rats (4/treatment) were evaluated. Group I was administered 137Cs (~40 μgeq/kg) by intravenous (iv) injection andmore » oral gavage; Group II was administered pre-bound 137Cs-SAMMS and sequential 137Cs + SAMMS (~61 ngeq/kg) by oral gavage; and Group III evaluated orally administered 137Cs (~0.06 μgeq/kg) followed by 0.1 g of either SAMMS or Prussian blue. Following dosing the rats were maintained in metabolism cages for 72 hour and blood, urine and fecal samples were collected for 137Cs analysis (gamma counting). Rats were then humanely euthanized, and selected tissues analyzed. Orally administered 137Cs was rapidly and well absorbed (~100% relative to iv dose), and the pharmacokinetics (blood, urine, feces & tissues) were very comparable to the iv dose group. For both exposures the urine and feces accounted for 20 and 3% of the dose, respectively. The prebound 137Cs-SAMMS was retained primarily within the feces (72% of the dose), with ~1.4% detected in the urine, suggesting that the 137Cs remained tightly bound to SAMMS. SAMMS & Prussian blue both effectively captured available 137Cs in the gut with feces accounting for 80-88% of the administered dose, while less than 2% was detected in the urine. This study suggests that the functionalized SAMMS out performs Prussian blue in vitro at low pH, but demonstrates comparable in vivo sequestration efficacy at low exposure concentrations. The comparable response may be the result of the low 137Cs dose and high sorbent dosage that was utilized. Future studies are planned to optimize SAMMS in vivo performance over a broader range of doses and conditions.« less

The Design, Synthesis, and Characterization of Open Sites on Metal Clusters

NASA Astrophysics Data System (ADS)

Nigra, Michael Mark

Coordinatively unsaturated corner and edge atoms have been hypothesized to have the highest activity of sites responsible for many catalytic reactions on a metal surface. Recent studies have validated this hypothesis in varied reaction systems. However, quantification of different types of coordinatively unsaturated sites, and elucidation of their individual catalytic rates has remained a largely unresolved challenge when understanding catalysis on metal surfaces. Yet such structure-function knowledge would be invaluable to the design of more active and selective metal-surface catalysts in the future. I investigated the catalytic contributions of undercoordinated sites such as corner and edge atoms are investigated in a model reaction system using organic ligands bound to the gold nanoparticle surface. The catalyst consisted of 4 nm gold nanoparticles on a metal oxide support, using resazurin to resorufin as a model reaction system. My results demonstrate that in this system, corner atom sites are the most undercoordinated sites, and are over an order of magnitude more active when compared to undercoordinated edge atom sites, while terrace sites remain catalytically inactive for the reduction reaction of resazurin to resorufin. Catalytic activity has been also demonstrated for calixarene-bound gold nanoparticles using the reduction of 4-nitrophenol. With the 4-nitrophenol reduction reaction, a comparative study was undertaken to compare calixarene phosphine and calixarene thiol bound 4 nm gold particles. The results of the study suggested that a leached site was responsible for catalysis and not sites on the original gold nanoparticles. Future experiments with calixarene bound gold clusters could investigate ligand effects in reactions where the active site is not a leached or aggregated gold species, possibly in oxidation reactions, where electron-rich gold is hypothesized to be a good catalyst. The results that emphasize the enhanced catalytic activity of undercoordinated sites led me to synthesize small gold clusters consisting of a high fraction of coordinatively unsaturated open sites. This was enabled through an approach that utilized bulky calix[4]arene ligands that are bound to a gold core. Since the size of the calix[4]arene ligand is commensurate with the size of the gold cluster core, the calix[4]arene ligand does not pack closely together on the gold cluster surface. This in turn results in areas of accessible gold atom sites between ligands. Additionally, these calix[4]arene ligands prevent cluster aggregation and electronically tune the gold core in a manner conceptually similar to enzymes affecting reactivity through organic side-chains acting as ligands. I quantified the number of open sites that result from this packing problem on the gold cluster surface, using fluorescence probe chemisorption experiments. The results of these chemisorption measurements support the mechanical model of accessibility whereby accessibility is not dependent on the identity of the functional group, whether it be calixarene phosphines or N-heterocyclic carbenes, bound to the gold surface, but rather to the relative radii of curvature of bound ligands and the gold cluster core. Additional materials characterization was completed with transmission electron microscopy in both bright-field imaging of zeolites, in MCM-22 and delaminated ITQ-2 and UCB-1 materials, and in dark field imaging of glucan coatings on oxide particles. These materials could prove to be interesting materials as to use as supports for the calixarene-bound metal clusters described above or for other metal clusters.

Resistance training alters skeletal muscle structure and function in human heart failure: effects at the tissue, cellular and molecular levels

PubMed Central

Toth, Michael J; Miller, Mark S; VanBuren, Peter; Bedrin, Nicholas G; LeWinter, Martin M; Ades, Philip A; Palmer, Bradley M

2012-01-01

Reduced skeletal muscle function in heart failure (HF) patients may be partially explained by altered myofilament protein content and function. Resistance training increases muscle function, although whether these improvements are achieved by correction of myofilament deficits is not known. To address this question, we examined 10 HF patients and 14 controls prior to and following an 18 week high-intensity resistance training programme. Evaluations of whole muscle size and strength, single muscle fibre size, ultrastructure and tension and myosin–actin cross-bridge mechanics and kinetics were performed. Training improved whole muscle isometric torque in both groups, although there were no alterations in whole muscle size or single fibre cross-sectional area or isometric tension. Unexpectedly, training reduced the myofibril fractional area of muscle fibres in both groups. This structural change manifested functionally as a reduction in the number of strongly bound myosin–actin cross-bridges during Ca2+ activation. When post-training single fibre tension data were corrected for the loss of myofibril fractional area, we observed an increase in tension with resistance training. Additionally, training corrected alterations in cross-bridge kinetics (e.g. myosin attachment time) in HF patients back to levels observed in untrained controls. Collectively, our results indicate that improvements in myofilament function in sedentary elderly with and without HF may contribute to increased whole muscle function with resistance training. More broadly, these data highlight novel cellular and molecular adaptations in muscle structure and function that contribute to the resistance-trained phenotype. PMID:22199163

Management Of Competition And Besting Among Crew Members: A Study At The Mars Desert Research Station (MDRS) In Utah, USA

NASA Astrophysics Data System (ADS)

Allner, Matthew; Bishop, Sheryl; Gushin, Vadim; McKay, Chris; Rygalov, Vadim; Allner, Matthew

Introduction: Psychosocial group functioning has become an increased international focus of many space faring nations due to the recent shift in focus of colonizing the Moon and then preparing to travel to Mars and beyond. Purpose: This study investigates the effects of competition and besting among crewmembers in isolated and confined extreme (ICE) environments. Furthermore, the study investigates the effects associated with both preand intra-mission management efforts, which included crewmember assessments at various mission phases (pre-, intra-, and end-mission). Suggestions on how to manage competition and besting within a crew were investigated by implementing preand intra-mission awareness strategies as well as group participation in the development and implementation of countermeasures to manage crewmember tendency towards competition and besting to promote the development of positive group functioning. Methods: A six person heterogeneous American crew conducted a Mars simulation mission at the Mars Society's Mars Desert Research Station in Utah, USA in 2006 as part of a new NASA training program called Spaceward Bound. Participants were administered assessments of personality, personal and group identity/functioning, subjective stress, and subjective motivation. All participants were also provided information (pre-mission) regarding past research findings and tendencies of group functioning, stressors, cognitive functioning, and competition and besting. Results: Anecdotal data obtained from personal interviews with crewmembers strongly showed that pre-mission discussions regarding competition and besting provided awareness that allowed crewmembers to continually self-assess to prevent this tendency from surfacing during the mission. The assessment data results showed support for recorded diary materials which indicated crewmembers felt strongly that continual reminders of the besting concept, along with being allowed to participate in the development and implementation of countermeasures to manage competition and besting, was a key component in preventing it from entering the group dynamic development. Assessment data and diary materials further support the premise that competition and besting was never the cause of any crew conflict during the mission, and successful avoidance of this group fission factor was therefore maintained throughout the duration of the two-week mission.

The evaluation of serum total sialic acid and lipid-bound sialic acid levels in chronically exposed rats to 7,12-dimethylbenz(a)anthracene and fluoride

NASA Astrophysics Data System (ADS)

Oto, Gokhan; Ekin, Suat; Uyar, Hasan; Ozdemir, Hulya; Yıldız, Damla; Karakuş, Yagmur

2017-04-01

In this study, changes in serum total sialic acid (TSA) and lipid-bound sialic acid (LSA) levels were examined in chronically exposed rats to 7,12-dimethylbenz(a)anthracene (DMBA) and fluoride. This study demonstrated that the TSA, LSA levels increased more in DMBA-treated groups compared to the fluoride treated groups. The result obtained has shown that the harmful effect of DMBA which is also causing more cell membrane damage on human and animal health should be taken into consideration.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Trace of totally positive algebraic integers and integer transfinite diameter

NASA Astrophysics Data System (ADS)

Flammang, V.

2009-06-01

Explicit auxiliary functions can be used in the ``Schur-Siegel- Smyth trace problem''. In the previous works, these functions were constructed only with polynomials having all their roots positive. Here, we use several polynomials with complex roots, which are found with Wu's algorithm, and we improve the known lower bounds for the absolute trace of totally positive algebraic integers. This improvement has a consequence for the search of Salem numbers that have a negative trace. The same method also gives a small improvement of the upper bound for the integer transfinite diameter of [0,1].

A generalized modal shock spectra method for spacecraft loads analysis

NASA Technical Reports Server (NTRS)

Trubert, M.; Salama, M.

1979-01-01

Unlike the traditional shock spectra approach, the generalization presented in this paper permits elastic interaction between the spacecraft and launch vehicle in order to obtain accurate bounds on the spacecraft response and structural loads. In addition, the modal response from a previous launch vehicle transient analysis - with or without a dummy spacecraft - is exploited in order to define a modal impulse as a simple idealization of the actual forcing function. The idealized modal forcing function is then used to derive explicit expressions for an estimate of the bound on the spacecraft structural response and forces.

Random walks on combs

NASA Astrophysics Data System (ADS)

Durhuus, Bergfinnur; Jonsson, Thordur; Wheater, John F.

2006-02-01

We develop techniques to obtain rigorous bounds on the behaviour of random walks on combs. Using these bounds, we calculate exactly the spectral dimension of random combs with infinite teeth at random positions or teeth with random but finite length. We also calculate exactly the spectral dimension of some fixed non-translationally invariant combs. We relate the spectral dimension to the critical exponent of the mass of the two-point function for random walks on random combs, and compute mean displacements as a function of walk duration. We prove that the mean first passage time is generally infinite for combs with anomalous spectral dimension.

VizieR Online Data Catalog: Thermodynamic quantities of molecular hydrogen (Popovas+, 2016)

NASA Astrophysics Data System (ADS)

Popovas, A.; Jorgensen, U. G.

2016-07-01

New partition functions for equilibrium, normal, and ortho and para hydrogen are calculated and thermodynamic quantities are reported for the temperature range 1-20000K. Our results are compared to previous estimates in the literature. The calculations are not limited to the ground electronic state, but include all bound and quasi-bound levels of excited electronic states. Dunham coefficients of these states of H2 are also reported. Reported internal partition functions and thermodynamic quantities in the present work are shown to be more accurate than previously available data. (4 data files).

Bootstrapping 3D fermions

DOE PAGES

Iliesiu, Luca; Kos, Filip; Poland, David; ...

2016-03-17

We study the conformal bootstrap for a 4-point function of fermions in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

Search for a hidden strange baryon-meson bound state from ϕ production in a nuclear medium

NASA Astrophysics Data System (ADS)

Gao, Haiyan; Huang, Hongxia; Liu, Tianbo; Ping, Jialun; Wang, Fan; Zhao, Zhiwen

2017-05-01

We investigate the hidden strange light baryon-meson system. With the resonating-group method, two bound states, η'-N and ϕ -N , are found in the quark delocalization color screening model. Focusing on the ϕ -N bound state around 1950 MeV, we obtain the total decay width of about 4 MeV by calculating the phase shifts in the resonance scattering processes. To study the feasibility of an experimental search for the ϕ -N bound state, we perform a Monte Carlo simulation of the bound state production with an electron beam and a gold target. In the simulation, we use the CLAS12 detector with the Forward Tagger and the BONUS12 detector in Hall B at Jefferson Lab. Both the signal and the background channels are estimated. We demonstrate that the signal events can be separated from the background with some momentum cuts. Therefore it is feasible to experimentally search for the ϕ -N bound state through the near threshold ϕ meson production from heavy nuclei.

Experiences of Leaders in One Texas School District Integrating Social Media as a Communication Medium: Bounded Phenomenological Case Study

ERIC Educational Resources Information Center

Lewis, Bradley D.

2017-01-01

The purpose of this bounded phenomenological case study was to investigate the experiences of leaders in one Texas school district integrating social media into communication practices. The participants in this study were twelve campus leaders, four district level leaders, and the superintendent of schools. The focus groups consisted of three…

Ke Kuhikuhi Alaka'I (A Guiding Gesture). Operations Manual. Hawaii Bound.

ERIC Educational Resources Information Center

Hale, Alan N.

The Hawaii Bound School seeks to provide a significant physical and emotional wilderness experience to those participating in its course. For 24 days a group of 12 students live together and are exposed to a wide variety of wilderness experiences. Among the places visited are the Kohala Mountains, Mauna Loa, Ka'u Desert, and the ocean itself.…

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions.

PubMed

Albihlal, Waleed S; Obomighie, Irabonosi; Blein, Thomas; Persad, Ramona; Chernukhin, Igor; Crespi, Martin; Bechtold, Ulrike; Mullineaux, Philip M

2018-05-19

In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide targets (ChIP-seq) and its impact on the transcriptome (RNA-seq) under non-stress (NS), heat stress (HS) in the wild type, and in HSFA1b-overexpressing plants under NS. A total of 952 differentially expressed HSFA1b-targeted genes were identified, of which at least 85 are development associated and were bound predominantly under NS. A further 1780 genes were differentially expressed but not bound by HSFA1b, of which 281 were classified as having development-associated functions. These genes are indirectly regulated through a hierarchical network of 27 transcription factors (TFs). Furthermore, we identified 480 natural antisense non-coding RNA (cisNAT) genes bound by HSFA1b, defining a further mode of indirect regulation. Finally, HSFA1b-targeted genomic features not only harboured heat shock elements, but also MADS box, LEAFY, and G-Box promoter motifs. This revealed that HSFA1b is one of eight TFs that target a common group of stress defence and developmental genes. We propose that HSFA1b transduces environmental cues to many stress tolerance and developmental genes to allow plants to adjust their growth and development continually in a varying environment.

Empirically Estimable Classification Bounds Based on a Nonparametric Divergence Measure

PubMed Central

Berisha, Visar; Wisler, Alan; Hero, Alfred O.; Spanias, Andreas

2015-01-01

Information divergence functions play a critical role in statistics and information theory. In this paper we show that a non-parametric f-divergence measure can be used to provide improved bounds on the minimum binary classification probability of error for the case when the training and test data are drawn from the same distribution and for the case where there exists some mismatch between training and test distributions. We confirm the theoretical results by designing feature selection algorithms using the criteria from these bounds and by evaluating the algorithms on a series of pathological speech classification tasks. PMID:26807014

Relativistic bound states in three space-time dimensions in Minkowski space

NASA Astrophysics Data System (ADS)

Gutierrez, C.; Gigante, V.; Frederico, T.; Tomio, Lauro

2016-01-01

With the aim to derive a workable framework for bound states in Minkowski space, we have investigated the Nakanishi perturbative integral representation of the Bethe-Salpeter (BS) amplitude in two-dimensions (2D) in space and time (2+1). The homogeneous BS amplitude, projected onto the light-front plane, is used to derive an equation for the Nakanishi weight function. The formal development is illustrated in detail and applied to the bound system composed by two scalar particles interacting through the exchange of a massive scalar. The explicit forms of the integral equations are obtained in ladder approximation.

Rotational relaxation of molecular hydrogen at moderate temperatures

NASA Technical Reports Server (NTRS)

Sharma, S. P.

1994-01-01

Using a coupled rotation-vibration-dissociation model the rotational relaxation times for molecular hydrogen as a function of final temperature (500-5000 K), in a hypothetical scenario of sudden compression, are computed. The theoretical model is based on a master equation solver. The bound-bound and bound-free transition rates have been computed using a quasiclassical trajectory method. A review of the available experimental data on the rotational relaxation of hydrogen is presented, with a critical overview of the method of measurements and data reduction, including the sources of errors. These experimental data are then compared with the computed results.

Determining relative error bounds for the CVBEM

USGS Publications Warehouse

Hromadka, T.V.

1985-01-01

The Complex Variable Boundary Element Methods provides a measure of relative error which can be utilized to subsequently reduce the error or provide information for further modeling analysis. By maximizing the relative error norm on each boundary element, a bound on the total relative error for each boundary element can be evaluated. This bound can be utilized to test CVBEM convergence, to analyze the effects of additional boundary nodal points in reducing the modeling error, and to evaluate the sensitivity of resulting modeling error within a boundary element from the error produced in another boundary element as a function of geometric distance. ?? 1985.

On increasing stability in the two dimensional inverse source scattering problem with many frequencies

NASA Astrophysics Data System (ADS)

Entekhabi, Mozhgan Nora; Isakov, Victor

2018-05-01

In this paper, we will study the increasing stability in the inverse source problem for the Helmholtz equation in the plane when the source term is assumed to be compactly supported in a bounded domain Ω with a sufficiently smooth boundary. Using the Fourier transform in the frequency domain, bounds for the Hankel functions and for scattering solutions in the complex plane, improving bounds for the analytic continuation, and the exact observability for the wave equation led us to our goals which are a sharp uniqueness and increasing stability estimate when the wave number interval is growing.

A duality approach for solving bounded linear programming problems with fuzzy variables based on ranking functions and its application in bounded transportation problems

NASA Astrophysics Data System (ADS)

Ebrahimnejad, Ali

2015-08-01

There are several methods, in the literature, for solving fuzzy variable linear programming problems (fuzzy linear programming in which the right-hand-side vectors and decision variables are represented by trapezoidal fuzzy numbers). In this paper, the shortcomings of some existing methods are pointed out and to overcome these shortcomings a new method based on the bounded dual simplex method is proposed to determine the fuzzy optimal solution of that kind of fuzzy variable linear programming problems in which some or all variables are restricted to lie within lower and upper bounds. To illustrate the proposed method, an application example is solved and the obtained results are given. The advantages of the proposed method over existing methods are discussed. Also, one application of this algorithm in solving bounded transportation problems with fuzzy supplies and demands is dealt with. The proposed method is easy to understand and to apply for determining the fuzzy optimal solution of bounded fuzzy variable linear programming problems occurring in real-life situations.

Nutrition Risk in Home-Bound Older Adults: Using Dietician-Trained and Supervised Nutrition Volunteers for Screening and Intervention

ERIC Educational Resources Information Center

Laforest, Sophie; Goldin, Benita; Nour, Kareen; Roy, Marie-Andree; Payette, Helene

2007-01-01

Nutrition screening and early intervention in home-bound older adults are key to preventing unfavourable health outcomes and functional decline. This pilot study's objectives were (a) to test the reliability of the Elderly Nutrition Screening Tool (ENS [C]) when administered by dietician-trained and supervised nutrition volunteers, and (b) to…

A fluorescent nucleic acid nanodevice quantitatively images elevated cyclic adenosine monophosphate in membrane-bound compartments.

PubMed

Sharma, Suruchi; Zaveri, Anisha; Visweswariah, Sandhya S; Krishnan, Yamuna

2014-11-12

cAMPhor: In the presence of cAMP, cAMPhor folds into a structure that binds DFHBI (green), increasing its fluorescence, while Alexa 647 (red) functions as a normalizing dye. It can thus be used to spatially image cAMP quantitatively in membrane-bound compartments. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chromatin-bound RNA and the neurobiology of psychiatric disease.

PubMed

Tushir, J S; Akbarian, S

2014-04-04

A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

Skew information in the XY model with staggered Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Qiu, Liang; Quan, Dongxiao; Pan, Fei; Liu, Zhi

2017-06-01

We study the performance of the lower bound of skew information in the vicinity of transition point for the anisotropic spin-1/2 XY chain with staggered Dzyaloshinskii-Moriya interaction by use of quantum renormalization-group method. For a fixed value of the Dzyaloshinskii-Moriya interaction, there are two saturated values for the lower bound of skew information corresponding to the spin-fluid and Néel phases, respectively. The scaling exponent of the lower bound of skew information closely relates to the correlation length of the model and the Dzyaloshinskii-Moriya interaction shifts the factorization point. Our results show that the lower bound of skew information can be a good candidate to detect the critical point of XY spin chain with staggered Dzyaloshinskii-Moriya interaction.

Energy bounds in designer gravity

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

Amsel, Aaron J.; Marolf, Donald

We consider asymptotically anti-de Sitter gravity coupled to tachyonic scalar fields with mass at or slightly above the Breitenlohner-Freedman bound in d{>=}4 spacetime dimensions. The boundary conditions in these ''designer gravity'' theories are defined in terms of an arbitrary function W. We give a general argument that the Hamiltonian generators of asymptotic symmetries for such systems will be finite, and proceed to construct these generators using the covariant phase space method. The direct calculation confirms that the generators are finite and shows that they take the form of the pure gravity result plus additional contributions from the scalar fields. Bymore » comparing the generators to the spinor charge, we derive a lower bound on the gravitational energy when W has a global minimum and the Breitenlohner-Freedman bound is not saturated.« less

Observation of three-photon bound states in a quantum nonlinear medium

NASA Astrophysics Data System (ADS)

Liang, Qi-Yu; Venkatramani, Aditya V.; Cantu, Sergio H.; Nicholson, Travis L.; Gullans, Michael J.; Gorshkov, Alexey V.; Thompson, Jeff D.; Chin, Cheng; Lukin, Mikhail D.; Vuletić, Vladan

2018-02-01

Bound states of massive particles, such as nuclei, atoms, or molecules, constitute the bulk of the visible world around us. By contrast, photons typically only interact weakly. We report the observation of traveling three-photon bound states in a quantum nonlinear medium where the interactions between photons are mediated by atomic Rydberg states. Photon correlation and conditional phase measurements reveal the distinct bunching and phase features associated with three-photon and two-photon bound states. Such photonic trimers and dimers possess shape-preserving wave functions that depend on the constituent photon number. The observed bunching and strongly nonlinear optical phase are described by an effective field theory of Rydberg-induced photon-photon interactions. These observations demonstrate the ability to realize and control strongly interacting quantum many-body states of light.

Reduced conservatism in stability robustness bounds by state transformation

NASA Technical Reports Server (NTRS)

Yedavalli, R. K.; Liang, Z.

1986-01-01

This note addresses the issue of 'conservatism' in the time domain stability robustness bounds obtained by the Liapunov approach. A state transformation is employed to improve the upper bounds on the linear time-varying perturbation of an asymptotically stable linear time-invariant system for robust stability. This improvement is due to the variance of the conservatism of the Liapunov approach with respect to the basis of the vector space in which the Liapunov function is constructed. Improved bounds are obtained, using a transformation, on elemental and vector norms of perturbations (i.e., structured perturbations) as well as on a matrix norm of perturbations (i.e., unstructured perturbations). For the case of a diagonal transformation, an algorithm is proposed to find the 'optimal' transformation. Several examples are presented to illustrate the proposed analysis.

Adsorption of Pb(II) ions onto biomass from Trifolium resupinatum: equilibrium and kinetic studies

NASA Astrophysics Data System (ADS)

Athar, Makshoof; Farooq, Umar; Aslam, Muhammad; Salman, M.

2013-09-01

The present study provides information about the binding of Pb(II) ions on an eco-friendly and easily available biodegradable biomass Trifolium resupinatum. The powdered biomass was characterized by FTIR, potentiometric titration and surface area analyses. The FTIR spectrum showed the presence of hydroxyl, carbonyl and amino functional groups and Pb(II) ions bound with the oxygen- and nitrogen-containing sites (hydroxyl and amino groups). The acidic groups were also confirmed by titrations. Effects of various environmental parameters (time, pH and concentration) have been studied. The biosorption process achieved equilibrium in a very short period of time (25 min). Non-linear approach for Langmuir and Freundlich models was used to study equilibrium process and root mean-square error was used as an indicator to decide the fitness of the mathematical model. The biosorption process was found to follow pseudo-second-order kinetics and was very fast. Thus, the biomass can be cost-effectively used for the binding of Pb(II) ions from aqueous solutions.

Hydroxamate anchors for improved photoconversion in dye-sensitized solar cells.

PubMed

Brewster, Timothy P; Konezny, Steven J; Sheehan, Stafford W; Martini, Lauren A; Schmuttenmaer, Charles A; Batista, Victor S; Crabtree, Robert H

2013-06-03

We present the first analysis of performance of hydroxamate linkers as compared to carboxylate and phosphonate groups when anchoring ruthenium-polypyridyl dyes to TiO2 surfaces in dye-sensitized solar cells (DSSCs). The study provides fundamental insight into structure/function relationships that are critical for cell performance. Our DSSCs have been produced by using newly synthesized dye molecules and characterized by combining measurements and simulations of experimental current density-voltage (J-V) characteristic curves. We show that the choice of anchoring group has a direct effect on the overall sunlight-to-electricity conversion efficiency (η), with hydroxamate anchors showing the best performance. Solar cells based on the pyridyl-hydroxamate complex exhibit higher efficiency since they suppress electron transfer from the photoanode to the electrolyte and have superior photoinjection characteristics. These findings suggest that hydroxamate anchoring groups should be particularly valuable in DSSCs and photocatalytic applications based on molecular adsorbates covalently bound to semiconductor surfaces. In contrast, analogous acetylacetonate anchors might undergo decomposition under similar conditions suggesting limited potential in future applications.

Bounded extremum seeking with discontinuous dithers

DOE PAGES

Scheinker, Alexander; Scheinker, David

2016-03-21

The analysis of discontinuous extremum seeking (ES) controllers, e.g. those applicable to digital systems, has historically been more complicated than that of continuous controllers. We establish a simple and general extension of a recently developed bounded form of ES to a general class of oscillatory functions, including functions discontinuous with respect to time, such as triangle or square waves with dead time. We establish our main results by combining a novel idea for oscillatory control with an extension of functional analytic techniques originally utilized by Kurzweil, Jarnik, Sussmann, and Liu in the late 80s and early 90s and recently studiedmore » by Durr et al. Lastly, we demonstrate the value of the result with an application to inverter switching control.« less

A one-dimensional model of solid-earth electrical resistivity beneath Florida

USGS Publications Warehouse

Blum, Cletus; Love, Jeffrey J.; Pedrie, Kolby; Bedrosian, Paul A.; Rigler, E. Joshua

2015-11-19

An estimated one-dimensional layered model of electrical resistivity beneath Florida was developed from published geological and geophysical information. The resistivity of each layer is represented by plausible upper and lower bounds as well as a geometric mean resistivity. Corresponding impedance transfer functions, Schmucker-Weidelt transfer functions, apparent resistivity, and phase responses are calculated for inducing geomagnetic frequencies ranging from 10−5 to 100 hertz. The resulting one-dimensional model and response functions can be used to make general estimates of time-varying electric fields associated with geomagnetic storms such as might represent induction hazards for electric-power grid operation. The plausible upper- and lower-bound resistivity structures show the uncertainty, giving a wide range of plausible time-varying electric fields.

Robust Control of Uncertain Systems via Dissipative LQG-Type Controllers

NASA Technical Reports Server (NTRS)

Joshi, Suresh M.

2000-01-01

Optimal controller design is addressed for a class of linear, time-invariant systems which are dissipative with respect to a quadratic power function. The system matrices are assumed to be affine functions of uncertain parameters confined to a convex polytopic region in the parameter space. For such systems, a method is developed for designing a controller which is dissipative with respect to a given power function, and is simultaneously optimal in the linear-quadratic-Gaussian (LQG) sense. The resulting controller provides robust stability as well as optimal performance. Three important special cases, namely, passive, norm-bounded, and sector-bounded controllers, which are also LQG-optimal, are presented. The results give new methods for robust controller design in the presence of parametric uncertainties.

MWCNT-MnFe2O4 nanocomposite for efficient hyperthermia applications

NASA Astrophysics Data System (ADS)

Seal, Papori; Hazarika, Monalisa; Paul, Nibedita; Borah, J. P.

2018-04-01

In this work we present synthesis of multi-walled carbon nanotube (MWCNT)-Manganese ferrite (MnFe2O4) nanocomposite and its probable application in hyperthermia. MnFe2O4 nanoparticles were synthesized by co-precipitation method. X ray diffractogram (XRD) confirms the formation of cubic phase of MnFe2O4 with preferred crystallographic orientation along (311) plane. High resolution electron microscope (HRTEM) image of the composites confirms the presence of MnFe2O4 spherical nanoparticles on the surface of CNT which are bound strongly to the surface. MWCNT-MnFe2O4 nanocomposite were prepared after acid functionalization of MWCNT. Vibrational features of the synthesized samples were confirmed through Fourier transformed infra-red spectroscopy (FTIR). FTIR spectra of acid functionalized MWCNT shows a peak positioned at ˜1620cm-1 which corresponds to C=O functional group of carboxylic acid. Prepared MnFe2O4 nanoparticles and MWCNT-MnFe2O4 nanocomposites were subjected to hyperthermia studies.

Explaining compact groups as change alignments

NASA Technical Reports Server (NTRS)

Mamon, Gary A.

1990-01-01

The physical nature of the apparently densest groups of galaxies, known as compact groups is a topic of some recent controversy, despite the detailed observations of a well-defined catalog of 100 isolated compact groups compiled by Hickson (1982). Whereas many authors have espoused the view that compact groups are bound systems, typically as dense as they appear in projection on the sky (e.g., Williams & Rood 1987; Sulentic 1987; Hickson & Rood 1988), others see them as the result of chance configurations within larger systems, either in 1D (chance alignments: Mamon 1986; Walke & Mamon 1989), or in 3D (transient cores: Rose 1979). As outlined in the companion review to this contribution (Mamon, in these proceedings), the implication of Hickson's compact groups (HCGs) being dense bound systems is that they would then constitute the densest isolated systems of galaxies in the Universe and the privileged site for galaxy interactions. In a previous paper (Mamon 1986), the author reviewed the arguments given for the different theories of compact groups. Since then, a dozen papers have been published on the subject, including a thorough and perceptive review by White (1990), thus more than doubling the amount written on the subject. Here, the author first enumerates the arguments that he brought up in 1986 substantiating the chance alignment hypothesis, then he reviews the current status of the numerous recent arguments arguing against chance alignments and/or for the bound dense group hypothesis (both for the majority of HCGs but not all of them), and finally he reconsiders each one of these anti-chance alignment arguments and shows that, rather than being discredited, the chance alignment hypothesis remains a fully consistent explanation for the nature of compact groups.

Relativistic effects in the double S- and P-wave charmonium production in e{sup +}e{sup -} annihilation

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

Elekina, E. N.; Martynenko, A. P.

2010-03-01

On the basis of perturbative QCD and the relativistic quark model we calculate relativistic and bound state corrections in the pair production of S-wave and P-wave charmonium states. Relativistic factors in the production amplitude connected with the relative motion of heavy quarks and the transformation law of the bound state wave function to the reference frame of the moving S- and P-wave mesons are taken into account. For the gluon and quark propagators entering the production vertex function we use a truncated expansion in the ratio of the relative quark momenta to the center-of-mass energy {radical}(s) up to the secondmore » order. The relativistic treatment of the wave functions makes all such second order terms convergent, thus allowing the reliable calculation of their contributions to the production cross section. Relativistic corrections to the quark bound state wave functions in the rest frame are considered by means of the QCD generalization of the standard Breit potential. It turns out that the examined effects change essentially the nonrelativistic results of the cross section for the reaction e{sup +}+e{sup -{yields}}J/{Psi}({eta}{sub c})+{chi}{sub cJ}(h{sub c}) at the center-of-mass energy {radical}(s)=10.6 GeV.« less

Age differences in change-of-direction performance and its subelements in female football players.

PubMed

Hirose, Norikazu; Nakahori, Chikako

2015-05-01

To describe cross-sectional age differences in change-of-direction performance (CODp) in female football players and investigate the relationship between CODp and linear-sprint speed, muscle power, and body size. A sample of 135 well-trained female football players was divided into 8 age groups. Anthropometry (height, body mass, and lean body mass) and athletic performance (10-m sprint speed, 10-m×5-CODp, and 5-step bounding distance) were compared to determine interage differences using ANOVA. Then, the participants were divided into 3 age groups: 12- to 14-y-olds, 15- to 17-y-olds, and ≥18 y-olds. Simple- and multiple-regression analyses were conducted to determine the correlation between CODp and the other measurement variables in each age group. Age-related differences were found for CODp (F=10.41, P<.01), sprint speed (F=3.27, P<.01), and bounding distance (F=4.20, P<.01). Post hoc analysis revealed that the CODp of 17-y-old players was faster than that of 16-y-old players (P<.01), with no interage differences in sprint speed and bounding distance. Sprint speed and bounding distance were weakly correlated with CODp in 15- to ≥18-y-old players, but only sprint speed was correlated with CODp in 12- to 14-y-old players. CODp improves from 16 to 17 y of age in female players. Linear-sprint speed, muscle power, and body size were weakly correlated with the age differences in CODp.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands.

PubMed

Carroll, Gerard M; Limpens, Rens; Neale, Nathan R

2018-05-09

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups-alkyls, amides, and alkoxides-on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative to alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands-not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals-are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. These results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands

DOE PAGES

Carroll, Gerard M.; Limpens, Rens; Neale, Nathan R.

2018-04-16

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups - alkyls, amides, and alkoxides - on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative tomore » alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands - not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals - are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. Furthermore, these results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.« less

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

Neale, Nathan R; Carroll, Gerard; Limpens, Rens

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups - alkyls, amides, and alkoxides - on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative tomore » alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands - not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals - are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. These results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.« less

Chemical and functional properties of cell wall polymers from two cherry varieties at two developmental stages.

PubMed

Basanta, María F; de Escalada Plá, Marina F; Stortz, Carlos A; Rojas, Ana M

2013-01-30

The cell wall polysaccharides of Regina and Sunburst cherry varieties at two developmental stages were extracted sequentially, and their changes in monosaccharide composition and functional properties were studied. The loosely-attached pectins presented a lower d-galacturonic acid/rhamnose ratio than ionically-bound pectins, as well as lower thickening effects of their respective 2% aqueous solution: the lowest Newtonian viscosity and shear rate dependence during the pseudoplastic phase. The main constituents of the cell wall matrix were covalently bound pectins (probably through diferulate cross-linkings), with long arabinan side chains at the RG-I cores. This pectin domain was also anchored into the XG-cellulose elastic network. Ripening occurred with a decrease in the proportion of HGs, water extractable GGM and xylogalacturonan, and with a concomitant increase in neutral sugars. Ripening was also associated with higher viscosities and thickening effects, and to larger distribution of molecular weights. The highest firmness and compactness of Regina cherry may be associated with its higher proportion of calcium-bound HGs localized in the middle lamellae of cell walls, as well as to some higher molar proportion of NS (Rha and Ara) in covalently bound pectins. These pectins showed significantly better hydration properties than hemicellulose and cellulose network. Chemical composition and functional properties of cell wall polymers were dependent on cherry variety and ripening stage, and helped explain the contrasting firmness of Regina and Sunburst varieties. Copyright © 2012 Elsevier Ltd. All rights reserved.

Visualizing water molecules in transmembrane proteins using radiolytic labeling methods†

PubMed Central

Orban, Tivadar; Gupta, Sayan; Palczewski, Krzysztof; Chance, Mark R.

2010-01-01

Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often co-localize with strategically placed polar or charged groups critical for protein function. Yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of ‘ordered’ waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern and thus the observed waters likely represent a subset of tightly-bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, owing to advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins. PMID:20047303

Hg tolerance and biouptake of an isolated pigmentation yeast Rhodotorula mucilaginosa.

PubMed

Liu, Bing; Wang, Chaogang; Liu, Danxia; He, Ning; Deng, Xu

2017-01-01

A pigmented yeast R1 with strong tolerance to Hg2+ was isolated. Phylogenetic identification based on the analysis of 26S rDNA and ITS revealed R1 is a Rhodotorula mucilaginosa species. R1 was able to grow in the presence of 80 mg/L Hg2+, but the lag phase was much prolonged compared to its growth in the absence of Hg2+. The maximum Hg2+ binding capacity of R1 was 69.9 mg/g, and dead cells could bind 15% more Hg2+ than living cells. Presence of organic substances drastically reduced bioavailability of Hg2+ and subsequently decreased Hg2+ removal ratio from aqueous solution, but this adverse effect could be remarkably alleviated by the simultaneous process of cell propagation and Hg2+ biouptake with actively growing R1. Furthermore, among the functional groups involved in Hg2+ binding, carboxyl group contributed the most, followed by amino & hydroxyl group and phosphate group. XPS analysis disclosed the mercury species bound on yeast cells was HgCl2 rather than HgO or Hg0.

Hg tolerance and biouptake of an isolated pigmentation yeast Rhodotorula mucilaginosa

PubMed Central

Liu, Bing; Wang, Chaogang; Liu, Danxia; He, Ning; Deng, Xu

2017-01-01

A pigmented yeast R1 with strong tolerance to Hg2+ was isolated. Phylogenetic identification based on the analysis of 26S rDNA and ITS revealed R1 is a Rhodotorula mucilaginosa species. R1 was able to grow in the presence of 80 mg/L Hg2+, but the lag phase was much prolonged compared to its growth in the absence of Hg2+. The maximum Hg2+ binding capacity of R1 was 69.9 mg/g, and dead cells could bind 15% more Hg2+ than living cells. Presence of organic substances drastically reduced bioavailability of Hg2+ and subsequently decreased Hg2+ removal ratio from aqueous solution, but this adverse effect could be remarkably alleviated by the simultaneous process of cell propagation and Hg2+ biouptake with actively growing R1. Furthermore, among the functional groups involved in Hg2+ binding, carboxyl group contributed the most, followed by amino & hydroxyl group and phosphate group. XPS analysis disclosed the mercury species bound on yeast cells was HgCl2 rather than HgO or Hg0. PMID:28253367

STATIC QUARK ANTI-QUARK FREE AND INTERNAL ENERGY IN 2-FLAVOR QCD AND BOUND STATES IN THE QGP.

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

ZANTOW, F.; KACZMAREK, O.

2005-07-25

We present results on heavy quark free energies in 2-flavour QCD. The temperature dependence of the interaction between static quark anti-quark pairs will be analyzed in terms of temperature dependent screening radii, which give a first estimate on the medium modification of (heavy quark) bound states in the quark gluon plasma. Comparing those radii to the (zero temperature) mean squared charge radii of chasmonium states indicates that the J/{Psi} may survive the phase transition as a bound state, while {chi}{sub c} and {Psi}{prime} are expected to show significant thermal modifications at temperatures close to the transition. Furthermore we will analyzemore » the relation between heavy quark free energies, entropy contributions and internal energy and discuss their relation to potential models used to analyze the melting of heavy quark bound states above the deconfinement temperature. Results of different groups and various potential models for bound states in the deconfined phase of QCD are compared.« less

Thyroid Function and Obesity

PubMed Central

Laurberg, Peter; Knudsen, Nils; Andersen, Stig; Carlé, Allan; Pedersen, Inge Bülow; Karmisholt, Jesper

2012-01-01

Important interaction exists between thyroid function, weight control, and obesity. Several mechanisms seem to be involved, and in studies of groups of people the pattern of thyroid function tests depends on the balance of obesity and underlying thyroid disease in the cohort studied. Obese people with a normal thyroid gland tend to have activation of the hypothalamic-pituitary-thyroid axis with higher serum TSH and thyroid hormones in serum. On the other hand, small differences in thyroid function are associated with up to 5 kg difference in body weight. The weight loss after therapy of overt hypothyroidism is caused by excretion of water bound in tissues (myxoedema). Many patients treated for hyperthyroidism experience a gain of more weight than they lost during the active phase of the disease. The mechanism for this excessive weight gain has not been fully elucidated. New studies on the relation between L-T3 therapy and weight control are discussed. The interaction between weight control and therapy of thyroid disease is important to many patients and it should be studied in more detail. PMID:24783015

Focusing Your E-Recruitment Efforts to Meet the Expectations of College-Bound Students. E-Expectations 2010

ERIC Educational Resources Information Center

Noel-Levitz, Inc, 2010

2010-01-01

Early in 2010, the E-Expectations research group surveyed more than 1,000 college-bound high school students, polling them on their online behaviors and expectations, as well as other key enrollment-related topics. Highlights of the study include: (1) 1 in 4 students reported removing a school from their prospective list because of a bad…

Nilsson diagrams for light neutron-rich nuclei with weakly-bound neutrons

NASA Astrophysics Data System (ADS)

Hamamoto, Ikuko

2007-11-01

Using Woods-Saxon potentials and the eigenphase formalism for one-particle resonances, one-particle bound and resonant levels for neutrons as a function of quadrupole deformation are presented, which are supposed to be useful for the interpretation of spectroscopic properties of some light neutron-rich nuclei with weakly bound neutrons. Compared with Nilsson diagrams in textbooks that are constructed using modified oscillator potentials, we point out a systematic change of the shell structure in connection with both weakly bound and resonant one-particle levels related to small orbital angular momenta ℓ. Then, it is seen that weakly bound neutrons in nuclei such as C15-19 and Mg33-37 may prefer being deformed as a result of the Jahn-Teller effect, due to the near degeneracy of the 1d5/2-2s1/2 levels and the 1f7/2-2p3/2 levels in the spherical potential, respectively. Furthermore, the absence of some one-particle resonant levels compared with the Nilsson diagrams in textbooks is illustrated.

The Estimation of the IRT Reliability Coefficient and Its Lower and Upper Bounds, with Comparisons to CTT Reliability Statistics

ERIC Educational Resources Information Center

Kim, Seonghoon; Feldt, Leonard S.

2010-01-01

The primary purpose of this study is to investigate the mathematical characteristics of the test reliability coefficient rho[subscript XX'] as a function of item response theory (IRT) parameters and present the lower and upper bounds of the coefficient. Another purpose is to examine relative performances of the IRT reliability statistics and two…

Control of valence and conduction band energies in layered transition metal phosphates via surface functionalization

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

Lentz, Levi C.; Kolb, Brian; Kolpak, Alexie M.

Layered transition metal phosphates and phosphites (TMPs) are a class of 2D materials bound togetherviavan der Waals interactions. Through simple functionalization, band energies can be systematically controlled.

A distinct class of dominant negative Ras mutants: cytosolic GTP-bound Ras effector domain mutants that inhibit Ras signaling and transformation and enhance cell adhesion.

PubMed

Fiordalisi, James J; Holly, Stephen P; Johnson, Ronald L; Parise, Leslie V; Cox, Adrienne D

2002-03-29

Cytosolic GTP-bound Ras has been shown to act as a dominant negative (DN) inhibitor of Ras by sequestering Raf in non-productive cytosolic complexes. Nevertheless, this distinct class of DN mutants has been neither well characterized nor extensively used to analyze Ras signaling. In contrast, DN Ras17N, which functions by blocking Ras guanine nucleotide exchange factors, has been well characterized and is widely used. Cytosolic GTP-bound Ras mutants could be used to inhibit particular Ras effectors by introducing additional mutations (T35S, E37G or Y40C) that permit them to associate selectively with and inhibit Raf, RalGDS, or phosphoinositide 3-kinase, respectively. When the wild-type Ras effector binding region is used, cytosolic Ras should associate with all Ras effectors, even those that are not yet identified, making these DN Ras mutants effective inhibitors of multiple Ras functions. We generated cytosolic GTP-bound H-, N-, and K-Ras, and we assessed their ability to inhibit Ras-induced phenotypes. In fibroblasts, cytosolic H-, N-, and K-Ras inhibited Ras-induced Elk-1 activation and focus formation, induced a flattened cell morphology, and increased adhesion to fibronectin through modulation of a beta(1)-subunit-containing integrin, thereby demonstrating that DN activity is not limited to a subset of Ras isoforms. We also generated cytosolic GTP-bound Ras effector domain mutants (EDMs), each of which reduced the ability of cytosolic GTP-bound Ras proteins to inhibit Elk-1 activation and to induce cell flattening, implicating multiple pathways in these phenotypes. In contrast, Ras-induced focus formation, platelet-derived growth factor (PDGF)-, or Ras-induced phospho-Akt levels and cell adhesion to fibronectin were affected by T35S and Y40C EDMs, whereas PDGF- or Ras-induced phospho-Erk levels were affected only by the T35S EDM, implying that a more limited set of Ras-mediated pathways participate in these phenotypes. These data constitute the first extensive characterization of this functionally distinct class of DN Ras inhibitor proteins.

Protons migrate along interfacial water without significant contributions from jumps between ionizable groups on the membrane surface

PubMed Central

Springer, Andreas; Hagen, Volker; Cherepanov, Dmitry A.; Antonenko, Yuri N.; Pohl, Peter

2011-01-01

Proton diffusion along membrane surfaces is thought to be essential for many cellular processes such as energy transduction. Commonly, it is treated as a succession of jumps between membrane-anchored proton-binding sites. Our experiments provide evidence for an alternative model. We released membrane-bound caged protons by UV flashes and monitored their arrival at distant sites by fluorescence measurements. The kinetics of the arrival is probed as a function of distance for different membranes and for different water isotopes. We found that proton diffusion along the membrane is fast even in the absence of ionizable groups in the membrane, and it decreases strongly in D2O as compared to H2O. We conclude that the fast proton transport along the membrane is dominated by diffusion via interfacial water, and not via ionizable lipid moieties. PMID:21859952

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

PubMed

Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

2013-01-01

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

Exploring the mental health effects of political trauma with newly arrived refugees.

PubMed

Shannon, Patricia J; Wieling, Elizabeth; McCleary, Jennifer Simmelink; Becher, Emily

2015-04-01

We explored the mental health effects of war trauma and torture as described by 111 refugees newly arrived in the United States. We used ethnocultural methodologies to inform 13 culture-specific focus groups with refugees from Bhutan (34), Burma (23), Ethiopia (27), and Somalia (27). Contrary to the belief that stigma prevents refugees from discussing mental health distress, participants readily described complex conceptualizations of degrees of mental health distress informed by political context, observation of symptoms, cultural idioms, and functional impairment. Recommendations for health care providers include assessment processes that inquire about symptoms in their political context, the degree of distress as it is culturally conceptualized, and its effect on functioning. Findings confirm the cross-cultural recognition of symptoms associated with posttraumatic stress disorder; however, refugees described significant cultural variation in expressions of distress, indicating the need for more research on culture-bound disorders and idioms of distress. © The Author(s) 2014.

Evolutionary game analysis and regulatory strategies for online group-buying based on system dynamics

NASA Astrophysics Data System (ADS)

Jiang, Zhong-Zhong; He, Na; Qin, Xuwei; Ip, W. H.; Wu, C. H.; Yung, K. L.

2018-07-01

The emergence of online group-buying provides a new consumption pattern for consumers in e-commerce era. However, many consumers realize that their own interests sometimes can't be guaranteed in the group-buying market due to the lack of being regulated. This paper aims to develop effective regulation strategies for online group-buying market. To the best of our knowledge, most existing studies assume that three parties in online group-buying market, i.e. the retailer, the group-buying platform and the consumer, are perfectly rational. To better understand the decision process, in this paper, we incorporate the concept of bounded rationality into consideration. Firstly, a three-parties evolutionary game model is established to study each player's game strategy based on bounded rationality. Secondly, the game model is simulated as a whole by adopting system dynamics to analyze its stability. Finally, theoretical analysis and extensive computational experiments are conducted to obtain the managerial insights and regulation strategies for online group-buying market. Our results clearly demonstrate that a suitable bonus-penalty measure can promote the healthy development of online group-buying market.

Effects of DHA-phospholipids, melatonin and tryptophan supplementation on erythrocyte membrane physico-chemical properties in elderly patients suffering from mild cognitive impairment.

PubMed

Cazzola, Roberta; Rondanelli, Mariangela; Faliva, Milena; Cestaro, Benvenuto

2012-12-01

A randomized, double-blind placebo-controlled clinical trial was carried out to assess the efficacy of a docosahexenoic acid (DHA)-phospholipids, melatonin and tryptophan supplemented diet in improving the erythrocyte oxidative stress, membrane fluidity and membrane-bound enzyme activities of elderly subjects suffering from mild cognitive impairment (MCI). These subjects were randomly assigned to the supplement group (11 subjects, 9F and 2M; age 85.3±5.3y) or placebo group (14-matched subjects, 11F and 3M; 86.1±6.5). The duration of the treatment was 12weeks. The placebo group showed no significant changes in erythrocyte membrane composition and function. The erythrocyte membranes of the supplement group showed a significant increase in eicosapentenoic acid, docosapentenoic acid and DHA concentrations and a significant decrease in arachidonic acid, malondialdehyde and lipofuscin levels. These changes in membrane composition resulted in an increase in the unsaturation index, membrane fluidity and acetylcholine esterase activity. Moreover, a significant increase in the ratio between reduced and oxidized glutathione was observed in the erythrocyte of the supplement group. Although this study is a preliminary investigation, we believe these findings to be of great speculative and interpretative interest to better understand the complex and multi-factorial mechanisms behind the possible links between diets, their functional components and possible molecular processes that contribute to increasing the risk of developing MCI and Alzheimer's. Copyright © 2012 Elsevier Inc. All rights reserved.

A new class of finite-time nonlinear consensus protocols for multi-agent systems

NASA Astrophysics Data System (ADS)

Zuo, Zongyu; Tie, Lin

2014-02-01

This paper is devoted to investigating the finite-time consensus problem for a multi-agent system in networks with undirected topology. A new class of global continuous time-invariant consensus protocols is constructed for each single-integrator agent dynamics with the aid of Lyapunov functions. In particular, it is shown that the settling time of the proposed new class of finite-time consensus protocols is upper bounded for arbitrary initial conditions. This makes it possible for network consensus problems that the convergence time is designed and estimated offline for a given undirected information flow and a group volume of agents. Finally, a numerical simulation example is presented as a proof of concept.

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

Rice, T. Maurice; Robinson, Neil J.; Tsvelik, Alexei M.

Here, the high-temperature normal state of the unconventional cuprate superconductors has resistivity linear in temperature T, which persists to values well beyond the Mott-Ioffe-Regel upper bound. At low temperatures, within the pseudogap phase, the resistivity is instead quadratic in T, as would be expected from Fermi liquid theory. Developing an understanding of these normal phases of the cuprates is crucial to explain the unconventional superconductivity. We present a simple explanation for this behavior, in terms of the umklapp scattering of electrons. This fits within the general picture emerging from functional renormalization group calculations that spurred the Yang-Rice-Zhang ansatz: Umklapp scatteringmore » is at the heart of the behavior in the normal phase.« less

NKG2D Ligands in Tumor Immunity: Two Sides of a Coin.

PubMed

Zhang, Jinyu; Basher, Fahmin; Wu, Jennifer D

2015-01-01

The activating/co-stimulatory receptor NKG2D (natural-killer group 2, member D) is expressed on the surface of all human NK, NKT, CD8(+) T, and subsets of γδ(+) T cells. The significance of NKG2D function in tumor immunity has been well demonstrated in experimental animal models. However, the role of human NKG2D ligands in regulating tumor immunity and cancer prognosis had been controversial in the literature. In this review, we summarize the latest advancement, discuss the controversies, and present evidence that membrane-bound and soluble NKG2D ligands oppositely regulate tumor immunity. We also discuss new perspectives of targeting NKG2D ligands for cancer immunotherapy.

Spectroscopic and electrochemical characterization of interfacial biomimetic assemblies on electrochemically generated gold oxide surfaces.

PubMed

Krysiński, Paweł; Blanchard, G J

2005-04-01

We report on the formation of a gold oxide layer and the reaction of this oxide with an acid chloride to form a stable, relatively complete monolayer bound through an ester-like bond to the gold oxide surface. We have used cyclic voltammetry, FTIR and optical ellipsometry to characterize this novel monolayer structure. The exposed functional groups of this monolayer can participate in subsequent surface reactions, opening the door to the use of oxide-based surface attachment chemistry on metallic substrates. This chemistry will allow for the formation of films tailored to contain both hydrophobic and hydrophilic regions, stacked at predetermined distances from the substrate that may serve as biomembrane mimetic assemblies.

Survival analysis of the high energy channel of BATSE

NASA Astrophysics Data System (ADS)

Balázs, L. G.; Bagoly, Z.; Horváth, I.; Mészáros, A.

2004-06-01

We used Kaplan-Meier (KM) survival analysis to study the true distribution of high energy (F4) fluences on BATSE. The measured values were divided into two classes: A. if F4 exceeded the 3σ of the noise level we accepted the measured value as 'true event'. B. We treated 3σ as an upper bound if F4 did not exceeded it and identified those data as 'censored'. KM analysis were made for short (t90 < 2 s) and long (t90 > 2 s) bursts, separately. Comparison of the calculated probability distribution functions of the two groups indicated about an order of magnitude difference in the > 300 keV part of the energies released.

Parochial cooperation in nested intergroup dilemmas is reduced when it harms out-groups.

PubMed

Aaldering, Hillie; Ten Velden, Femke S; van Kleef, Gerben A; De Dreu, Carsten K W

2018-06-01

In intergroup settings, humans often contribute to their in-group at a personal cost. Such parochial cooperation benefits the in-group and creates and fuels intergroup conflict when it simultaneously hurts out-groups. Here, we introduce a new game paradigm in which individuals can display universal cooperation (which benefits both in- and out-group) as well as parochial cooperation that does, versus does not hurt the out-group. Using this set-up, we test hypotheses derived from group selection theory, social identity, and bounded generalized reciprocity theory. Across three experiments we find, first, that individuals choose parochial over universal cooperation. Second, there was no evidence for a motive to maximize differences between in- and out-group, which is central to both group selection and social identity theory. However, fitting bounded generalized reciprocity theory, we find that individuals with a prosocial value orientation display parochial cooperation, provided that this does not harm the out-group; individualists, in contrast, display parochialism whether or not nut it hurts the out-group. Our findings were insensitive to cognitive taxation (Experiments 2-3), and emerged even when universal cooperation served social welfare more than parochialism (Experiment 3). (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Bound states for magic state distillation in fault-tolerant quantum computation.

PubMed

Campbell, Earl T; Browne, Dan E

2010-01-22

Magic state distillation is an important primitive in fault-tolerant quantum computation. The magic states are pure nonstabilizer states which can be distilled from certain mixed nonstabilizer states via Clifford group operations alone. Because of the Gottesman-Knill theorem, mixtures of Pauli eigenstates are not expected to be magic state distillable, but it has been an open question whether all mixed states outside this set may be distilled. In this Letter we show that, when resources are finitely limited, nondistillable states exist outside the stabilizer octahedron. In analogy with the bound entangled states, which arise in entanglement theory, we call such states bound states for magic state distillation.

Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding

PubMed Central

Nile, Aaron H.; Mukund, Susmith; Stanger, Karen; Wang, Weiru; Hannoush, Rami N.

2017-01-01

Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt–FZD receptor interactions, the molecular basis for recognition of Wnt cis-unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis-Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis-unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt–FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function. PMID:28377511

A Convex Approach to Fault Tolerant Control

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Cox, David E.; Bauer, Frank (Technical Monitor)

2002-01-01

The design of control laws for dynamic systems with the potential for actuator failures is considered in this work. The use of Linear Matrix Inequalities allows more freedom in controller design criteria than typically available with robust control. This work proposes an extension of fault-scheduled control design techniques that can find a fixed controller with provable performance over a set of plants. Through convexity of the objective function, performance bounds on this set of plants implies performance bounds on a range of systems defined by a convex hull. This is used to incorporate performance bounds for a variety of soft and hard failures into the control design problem.

Remarks on High Reynolds Numbers Hydrodynamics and the Inviscid Limit

NASA Astrophysics Data System (ADS)

Constantin, Peter; Vicol, Vlad

2018-04-01

We prove that any weak space-time L^2 vanishing viscosity limit of a sequence of strong solutions of Navier-Stokes equations in a bounded domain of R^2 satisfies the Euler equation if the solutions' local enstrophies are uniformly bounded. We also prove that t-a.e. weak L^2 inviscid limits of solutions of 3D Navier-Stokes equations in bounded domains are weak solutions of the Euler equation if they locally satisfy a scaling property of their second-order structure function. The conditions imposed are far away from boundaries, and wild solutions of Euler equations are not a priori excluded in the limit.

Kinetic balance and variational bounds failure in the solution of the Dirac equation in a finite Gaussian basis set

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Faegri, Knut, Jr.

1990-01-01

The paper investigates bounds failure in calculations using Gaussian basis sets for the solution of the one-electron Dirac equation for the 2p1/2 state of Hg(79+). It is shown that bounds failure indicates inadequacies in the basis set, both in terms of the exponent range and the number of functions. It is also shown that overrepresentation of the small component space may lead to unphysical results. It is concluded that it is important to use matched large and small component basis sets with an adequate size and exponent range.

Forbidden regimes in the distribution of bipartite quantum correlations due to multiparty entanglement

NASA Astrophysics Data System (ADS)

Kumar, Asutosh; Dhar, Himadri Shekhar; Prabhu, R.; Sen(De), Aditi; Sen, Ujjwal

2017-05-01

Monogamy is a nonclassical property that limits the distribution of quantum correlation among subparts of a multiparty system. We show that monogamy scores for different quantum correlation measures are bounded above by functions of genuine multipartite entanglement for a large majority of pure multiqubit states. The bound is universal for all three-qubit pure states. We derive necessary conditions to characterize the states that violate the bound, which can also be observed by numerical simulation for a small set of states, generated Haar uniformly. The results indicate that genuine multipartite entanglement restricts the distribution of bipartite quantum correlations in a multiparty system.

Achieving unequal error protection with convolutional codes

NASA Technical Reports Server (NTRS)

Mills, D. G.; Costello, D. J., Jr.; Palazzo, R., Jr.

1994-01-01

This paper examines the unequal error protection capabilities of convolutional codes. Both time-invariant and periodically time-varying convolutional encoders are examined. The effective free distance vector is defined and is shown to be useful in determining the unequal error protection (UEP) capabilities of convolutional codes. A modified transfer function is used to determine an upper bound on the bit error probabilities for individual input bit positions in a convolutional encoder. The bound is heavily dependent on the individual effective free distance of the input bit position. A bound relating two individual effective free distances is presented. The bound is a useful tool in determining the maximum possible disparity in individual effective free distances of encoders of specified rate and memory distribution. The unequal error protection capabilities of convolutional encoders of several rates and memory distributions are determined and discussed.

Highly stabilized gadolinium chelates functionalized on metal nanoparticles as magnetic resonance imaging contrast agent

NASA Astrophysics Data System (ADS)

Siddiqui, Talha S.

Magnetic resonance imaging (MRI) is a non-invasive method for imaging and diagnosing tissue damage, organ function and the vascular system. Magnevist(TM) a complex of diethylenetriaminepentaacetic acid (DTPA) and Gd3+ is a clinically approved contrast agent for MRI. A derivative of DTPA was formed by the addition of two cysteine groups (DTPA-L-Cys) through amide linkage. The Gd complex of this ligand bonds with the silver surfaces through the cysteine thiols. GdDTPA-L-Cys was bound to ˜10nm diameter Ag nanoparticles for use as a multifunctional MRI contrast agent. The ligand and complex were characterized by 1H and 13C NMR, ESI-MS and IR spectroscopy. The silver construct was characterized by TEM, TGA and UV-Vis absorption spectra. The per metal complex r1 relaxivity of GdDTPA-L-Cys{Ag} greater than that of Magnavist(TM) with the same molarity for both compounds. The synthesis of a DTPA derivative is described that allows it to bind to silver or gold nanoparticles through a single thiol linkage (DTPASH). The resulting Gd complex, GdDTPASH, was bound to Ag nanoparticles to create a single monolayer on the surface. The construct was further stabilized in buffered solution with the addition of a thiolated PEG chain. The highly stabilized nanoparticle construct delivers a high payload of Gd compelex and is an effective T1 brightening agent. The production of this type of construct opens the way for engineered multimodal MRI contrast agents.

Efficient CO2 capture by functionalized graphene oxide nanosheets as fillers to fabricate multi-permselective mixed matrix membranes.

PubMed

Li, Xueqin; Cheng, Youdong; Zhang, Haiyang; Wang, Shaofei; Jiang, Zhongyi; Guo, Ruili; Wu, Hong

2015-03-11

A novel multi-permselective mixed matrix membrane (MP-MMM) is developed by incorporating versatile fillers functionalized with ethylene oxide (EO) groups and an amine carrier into a polymer matrix. The as-prepared MP-MMMs can separate CO2 efficiently because of the simultaneous enhancement of diffusivity selectivity, solubility selectivity, and reactivity selectivity. To be specific, MP-MMMs were fabricated by incorporating polyethylene glycol- and polyethylenimine-functionalized graphene oxide nanosheets (PEG-PEI-GO) into a commercial low-cost Pebax matrix. The PEG-PEI-GO plays multiple roles in enhancing membrane performance. First, the high-aspect ratio GO nanosheets in a polymer matrix increase the length of the tortuous path of gas diffusion and generate a rigidified interface between the polymer matrix and fillers, enhancing the diffusivity selectivity. Second, PEG consisting of EO groups has excellent affinity for CO2 to enhance the solubility selectivity. Third, PEI with abundant primary, secondary, and tertiary amine groups reacts reversibly with CO2 to enhance reactivity selectivity. Thus, the as-prepared MP-MMMs exhibit excellent CO2 permeability and CO2/gas selectivity. The MP-MMM doped with 10 wt % PEG-PEI-GO displays optimal gas separation performance with a CO2 permeability of 1330 Barrer, a CO2/CH4 selectivity of 45, and a CO2/N2 selectivity of 120, surpassing the upper bound lines of the Robeson study of 2008 (1 Barrer = 10(-10) cm(3) (STP) cm(-2) s(-1) cm(-1) Hg).

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

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

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew

2012-02-07

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

Twisted sigma-model solitons on the quantum projective line

NASA Astrophysics Data System (ADS)

Landi, Giovanni

2018-04-01

On the configuration space of projections in a noncommutative algebra, and for an automorphism of the algebra, we use a twisted Hochschild cocycle for an action functional and a twisted cyclic cocycle for a topological term. The latter is Hochschild-cohomologous to the former and positivity in twisted Hochschild cohomology results into a lower bound for the action functional. While the equations for the critical points are rather involved, the use of the positivity and the bound by the topological term lead to self-duality equations (thus yielding twisted noncommutative sigma-model solitons, or instantons). We present explicit nontrivial solutions on the quantum projective line.

Model-free nuclear magnetic resonance study of intermolecular free energy landscapes in liquids with paramagnetic Ln3+ spotlights: theory and application to Arg-Gly-Asp.

PubMed

Fries, Pascal H

2012-01-28

We propose an easily applicable method for investigating the pair distribution function of a lanthanide Ln(3+) complex LnL (L = ligand) with respect to any solvent or solute molecule A carrying observable nuclear spins. Let r be the distance of Ln(3+) to the observed nuclear spin I. We derive a simple expression of the experimental value of the configurational average of 1/r(6) in terms of longitudinal paramagnetic relaxation (rate) enhancements (PREs) of the spin I measured on a standard high-resolution NMR spectrometer and due to well-chosen concentrations of LnL complexes in which Ln(3+) is a fast-relaxing paramagnetic lanthanide or the slowly-relaxing gadolinium Gd(3+). The derivation is justified in the general case of a molecule A which is by turns in a bound state where it follows the complex and a free state where it moves independently. It rests on the expression of the underlying PRE theory in terms of the angle-dependent pair distribution function of LnL and A. The simplifications of this theory in the high-field regime and under the condition of fast exchange between bound and free states are carefully discussed. We also show that original information on the angle dependence of the molecular pair distribution function can be gained from the measured paramagnetic dipolar shifts induced by complexed fast-relaxing Ln(3+) ions. The method is illustrated by the case study of the anionic Lnttha(3-) = [Ln(3+)(ttha)](3-) (ttha(6-) = triethylene tetraamine hexacetate) complex interacting with the biologically important tripeptide Arg-Gly-Asp (RGD) which carries peripheral ionic groups. The usefulness of an auxiliary reference outer sphere probe solute is emphasized. © 2012 American Institute of Physics

Implicit postural control strategies in older hemodialysis patients: an objective hallmark feature for clinical balance assessment.

PubMed

Magnard, Justine; Hristea, Dan; Lefrancois, Gaëlle; Testa, Angelo; Paris, Anne; Deschamps, Thibault

2014-09-01

Elderly patients with end stage renal diseases (ESRD) undergoing hemodialyis (HD) present poorer physical function and higher accident falls than healthy elderly population. Therefore, the aim of this study was to examine the HD-related changes in postural sway in ESRD patients, as an objective hallmark of their functional abilities. We hypothesized that the ESRD symptoms (i.e. uremic syndrome) and the HD therapy affected the postural control, evidenced by higher bounding limits of center-of-pressure (COP) velocity dynamics. Fifty-five participants, including 28 HD patients and 27 age, body mass index and gender-matched healthy participants HS (70.42 ± 13.69 years; 23.46 ± 4.67 kg/m(2); 35.7% women vs. 73.62 ± 6.59 years; 25.09 ± 3.54 kg/m(2); 37% women), were asked to maintain quiet stance on force platform, with eyes open and eyes closed. COP parameters were mean and standard deviation (SD) of position, velocity and average absolute maximal velocity (AAMV) in antero-posterior and medio-lateral directions. The results revealed a significant main effect of group on velocity-based variables, highlighting that mean velocity, SD velocity and AAMV (p<0.01) were higher for HD as compared to HS. These findings identified the bounding limits of COP velocity as an objective hallmark feature of HD-related changes in postural sway. The clinical assessment of this active control of COP velocity dynamics could be useful to examine the effects of targeted intradialytic exercise programs on functional performances and for early detection of increased fall risk in HD patients. Copyright © 2014 Elsevier B.V. All rights reserved.

Bacterial iron transport: coordination properties of azotobactin, the highly fluorescent siderophore of Azotobacter vinelandii.

PubMed

Palanché, Tania; Blanc, Sylvie; Hennard, Christophe; Abdallah, Mohamed A; Albrecht-Gary, Anne-Marie

2004-02-09

Azotobacter vinelandii, a nitrogen-fixing soil bacterium, secretes in iron deficiency azotobactin delta, a highly fluorescent pyoverdin-like chromopeptidic hexadentate siderophore. The chromophore, derived from 2,3-diamino-6,7 dihydroxyquinoline, is bound to a peptide chain of 10 amino acids: (L)-Asp-(D)-Ser-(L)-Hse-Gly-(D)-beta-threo-HOAsp-(L)-Ser-(D)-Cit-(L)-Hse-(L)-Hse lactone-(D)-N(delta)-Acetyl, N(delta)-HOOrn. Azotobactin delta has three different iron(III) binding sites which are one hydroxamate group at the C-terminal end of the peptidic chain (N(delta)-Acetyl, N(delta)-HOOrn), one alpha-hydroxycarboxylic function in the middle of the chain (beta-threo-hydroxyaspartic acid), and one catechol group on the chromophore. The coordination properties of its iron(III) and iron(II) complexes were measured by spectrophotometry, potentiometry, and voltammetry after the determination of the acid-base functions of the uncomplexed free siderophore. Strongly negatively charged ferric species were observed at neutral p[H]'s corresponding to a predominant absolute configuration Lambda of the ferric complex in solution as deduced from CD measurements. The presence of an alpha-hydroxycarboxylic chelating group does not decrease the stability of the iron(III) complex when compared to the main trishydroxamate siderophores or to pyoverdins. The value of the redox potential of ferric azotobactin is highly consistent with a reductive step by physiological reductants for the iron release. Formation and dissociation kinetics of the azotobactin delta ferric complex point out that both ends of this long siderophore chain get coordinated to Fe(III) before the middle. The most striking result provided by fluorescence measurements is the lasting quenching of the fluorophore in the course of the protonation of the ferric azotobactin delta complex. Despite the release of the hydroxyacid and of the catechol, the fluorescence remains indeed quenched, when iron(III) is bound only to the hydroxamic acid, suggesting a folded conformation at this stage, around the metal ion, in contrast to the unfolded species observed for other siderophores such as ferrioxamine or pyoverdin PaA.

Magnesium and Calcium in Isolated Cell Nuclei

PubMed Central

Naora, H.; Naora, H.; Mirsky, A. E.; Allfrey, V. G.

1961-01-01

The calcium and magnesium contents of thymus nuclei have been determined and the nuclear sites of attachment of these two elements have been studied. The nuclei used for these purposes were isolated in non-aqueous media and in sucrose solutions. Non-aqueous nuclei contain 0.024 per cent calcium and 0.115 per cent magnesium. Calcium and magnesium are held at different sites. The greater part of the magnesium is bound to DNA, probably to its phosphate groups. Evidence is presented that the magnesium atoms combined with the phosphate groups of DNA are also attached to mononucleotides. There is reason to believe that those DNA-phosphate groups to which magnesium is bound, less than 1/10th of the total, are metabolically active, while those to which histones are attached seem to be inactive. PMID:13727745

Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function.

PubMed

Reimann, Michael W; Nolte, Max; Scolamiero, Martina; Turner, Katharine; Perin, Rodrigo; Chindemi, Giuseppe; Dłotko, Paweł; Levi, Ran; Hess, Kathryn; Markram, Henry

2017-01-01

The lack of a formal link between neural network structure and its emergent function has hampered our understanding of how the brain processes information. We have now come closer to describing such a link by taking the direction of synaptic transmission into account, constructing graphs of a network that reflect the direction of information flow, and analyzing these directed graphs using algebraic topology. Applying this approach to a local network of neurons in the neocortex revealed a remarkably intricate and previously unseen topology of synaptic connectivity. The synaptic network contains an abundance of cliques of neurons bound into cavities that guide the emergence of correlated activity. In response to stimuli, correlated activity binds synaptically connected neurons into functional cliques and cavities that evolve in a stereotypical sequence toward peak complexity. We propose that the brain processes stimuli by forming increasingly complex functional cliques and cavities.

Conformational heterogeneity within the Michaelis complex of lactate dehydrogenase†

PubMed Central

Deng, Hua; Vu, Dung V.; Clinch, Keith; Desamero, Ruel; Dyer, R. Brian; Callender, Robert

2011-01-01

A series of isotope edited IR measurements, both static as well as temperature jump relaxation spectroscopy, are performed on lactate dehydrogenase (LDH) to determine the ensemble of structures available to its Michaelis complex. There clearly has been a substantial reduction in the number of states available to the pyruvate substrate (as modeled by the substrate mimic, oxamate) and NADH when bound to protein compared to dissolved in solution, as determined by the bandwidths and positions of the critical C2=O band of bound substrate mimic and the C4-H stretch of NADH reduced nicotinamide group. Moreover, it is found that a strong ionic bond (characterized by a signature IR band discovered in this study) is formed between the carboxyl group of bound pyruvate with (presumably) Arg171, forming a strong ‘anchor’ within the protein matrix. However, conformational heterogeneity within the Michaelis complex is found that has an impact on both catalytic efficiency and thermodynamics of the enzyme. PMID:21568287

New derivation of soliton solutions to the AKNS2 system via dressing transformation methods

NASA Astrophysics Data System (ADS)

Assunção, A. de O.; Blas, H.; da Silva, M. J. B. F.

2012-03-01

We consider certain boundary conditions supporting soliton solutions in the generalized nonlinear Schrödinger equation (AKNSr) (r = 1, 2). Using the dressing transformation (DT) method and the related tau functions, we study the AKNSr system for the vanishing, (constant) non-vanishing and the mixed boundary conditions, and their associated bright, dark and bright-dark N-soliton solutions, respectively. Moreover, we introduce a modified DT related to the dressing group in order to consider the free-field boundary condition and derive generalized N dark-dark solitons. As a reduced submodel of the AKNSr system, we study the properties of the focusing, defocusing and mixed focusing-defocusing versions of the so-called coupled nonlinear Schrödinger equation (r-CNLS), which has recently been considered in many physical applications. We have shown that two-dark-dark-soliton bound states exist in the AKNS2 system, and three- and higher-dark-dark-soliton bound states cannot exist. The AKNSr (r ⩾ 3) extension is briefly discussed in this approach. The properties and calculations of some matrix elements using level-one vertex operators are outlined. Dedicated to the memory of S S Costa

Microburger Biochemistry: Extraction and Spectral Characterization of Myoglyobin from Hamburger

NASA Astrophysics Data System (ADS)

Bylkas, Sheri A.; Andersson, Laura A.

1997-04-01

This experiment provides a demonstration of useful biochemical methods at a Basic or Advanced Level, depending upon the available spectrophotometric equipment. The protocol combines protein extraction, ox-i-dation and reduction, and simple spectroscopic analysis, as well as gel filtration chromatography and generation/analysis of spectral scans. Mammalian myoglobin (Mb) is a monomeric O2-binding protein that functions in muscle to store oxygen. The single iron protoporphyrin IX (heme) group is bound to protein by the amino acid Histidine93. The common, stable forms, Met-Mb and Oxy-Mb are studied because in a non-living system, red Oxy-Mb is converted to brown Met-Mb as bound O2 molecule is released. Mb is easily extracted from steak, to illustrate and address why fresh meat is red and aged meat is brown; the protein has unique spectral properties that are diagnostic for characterization of sample identity. After application of heme redox chemical methods, the MetMb or OxyMb samples can be studied spectroscopically. The color change between Oxy-Mb and Met-Mb is dramatic (illustrating bright red fresh meat vs. brown older meat), and method(s) used in this laboratory are simple, inexpensive, and non-harmful to the student.

Matrin 3 binds and stabilizes mRNA.

PubMed

Salton, Maayan; Elkon, Ran; Borodina, Tatiana; Davydov, Aleksey; Yaspo, Marie-Laure; Halperin, Eran; Shiloh, Yosef

2011-01-01

Matrin 3 (MATR3) is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM), whose function is largely unknown. Recently we found MATR3 to be phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Here, we show that MATR3 interacts in an RNA-dependent manner with several proteins with established roles in RNA processing, and maintains its interaction with RNA via its RRM2 domain. Deep sequencing of the bound RNA (RIP-seq) identified several small noncoding RNA species. Using microarray analysis to explore MATR3's role in transcription, we identified 77 transcripts whose amounts depended on the presence of MATR3. We validated this finding with nine transcripts which were also bound to the MATR3 complex. Finally, we demonstrated the importance of MATR3 for maintaining the stability of several of these mRNA species and conclude that it has a role in mRNA stabilization. The data suggest that the cellular level of MATR3, known to be highly regulated, modulates the stability of a group of gene transcripts.

Matrin 3 Binds and Stabilizes mRNA

PubMed Central

Salton, Maayan; Elkon, Ran; Borodina, Tatiana; Davydov, Aleksey; Yaspo, Marie-Laure; Halperin, Eran; Shiloh, Yosef

2011-01-01

Matrin 3 (MATR3) is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM), whose function is largely unknown. Recently we found MATR3 to be phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Here, we show that MATR3 interacts in an RNA-dependent manner with several proteins with established roles in RNA processing, and maintains its interaction with RNA via its RRM2 domain. Deep sequencing of the bound RNA (RIP-seq) identified several small noncoding RNA species. Using microarray analysis to explore MATR3′s role in transcription, we identified 77 transcripts whose amounts depended on the presence of MATR3. We validated this finding with nine transcripts which were also bound to the MATR3 complex. Finally, we demonstrated the importance of MATR3 for maintaining the stability of several of these mRNA species and conclude that it has a role in mRNA stabilization. The data suggest that the cellular level of MATR3, known to be highly regulated, modulates the stability of a group of gene transcripts. PMID:21858232

Generalized Scalar-on-Image Regression Models via Total Variation.

PubMed

Wang, Xiao; Zhu, Hongtu

2017-01-01

The use of imaging markers to predict clinical outcomes can have a great impact in public health. The aim of this paper is to develop a class of generalized scalar-on-image regression models via total variation (GSIRM-TV), in the sense of generalized linear models, for scalar response and imaging predictor with the presence of scalar covariates. A key novelty of GSIRM-TV is that it is assumed that the slope function (or image) of GSIRM-TV belongs to the space of bounded total variation in order to explicitly account for the piecewise smooth nature of most imaging data. We develop an efficient penalized total variation optimization to estimate the unknown slope function and other parameters. We also establish nonasymptotic error bounds on the excess risk. These bounds are explicitly specified in terms of sample size, image size, and image smoothness. Our simulations demonstrate a superior performance of GSIRM-TV against many existing approaches. We apply GSIRM-TV to the analysis of hippocampus data obtained from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset.

Fluoride ion encapsulation by Mg2+ and phosphates in a fluoride riboswitch

PubMed Central

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

2012-01-01

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswicthes, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg2+ ions, which in turn are octahedrally coordinated to waters and five inwardly-pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state defines how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch most likely functions in gene regulation through a transcription termination mechanism. PMID:22678284

Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication.

PubMed

Ren, Xiaodi; Siegel, Rachael; Kim, Unkyu; Roeder, Robert G

2011-05-06

B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in Igh promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated Igh promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3' enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3' enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism. Copyright © 2011 Elsevier Inc. All rights reserved.

Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication

PubMed Central

Ren, Xiaodi; Siegel, Rachael; Kim, Unkyu; Roeder, Robert G.

2011-01-01

Summary B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in IgH promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated IgH promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3′enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3′enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism. PMID:21549311

A Very Efficient Transfer Function Bounding Technique on Bit Error Rate for Viterbi Decoded, Rate 1/N Convolutional Codes

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

For rate 1/N convolutional codes, a recursive algorithm for finding the transfer function bound on bit error rate (BER) at the output of a Viterbi decoder is described. This technique is very fast and requires very little storage since all the unnecessary operations are eliminated. Using this technique, we find and plot bounds on the BER performance of known codes of rate 1/2 with K 18, rate 1/3 with K 14. When more than one reported code with the same parameter is known, we select the code that minimizes the required signal to noise ratio for a desired bit error rate of 0.000001. This criterion of determining goodness of a code had previously been found to be more useful than the maximum free distance criterion and was used in the code search procedures of very short constraint length codes. This very efficient technique can also be used for searches of longer constraint length codes.

Conformational phases of membrane bound cytoskeletal filaments

NASA Astrophysics Data System (ADS)

Quint, David A.; Grason, Gregory; Gopinathan, Ajay

2013-03-01

Membrane bound cytoskeletal filaments found in living cells are employed to carry out many types of activities including cellular division, rigidity and transport. When these biopolymers are bound to a membrane surface they may take on highly non-trivial conformations as compared to when they are not bound. This leads to the natural question; What are the important interactions which drive these polymers to particular conformations when they are bound to a surface? Assuming that there are binding domains along the polymer which follow a periodic helical structure set by the natural monomeric handedness, these bound conformations must arise from the interplay of the intrinsic monomeric helicity and membrane binding. To probe this question, we study a continuous model of an elastic filament with intrinsic helicity and map out the conformational phases of this filament for various mechanical and structural parameters in our model, such as elastic stiffness and intrinsic twist of the filament. Our model allows us to gain insight into the possible mechanisms which drive real biopolymers such as actin and tubulin in eukaryotes and their prokaryotic cousins MreB and FtsZ to take on their functional conformations within living cells.

Bionic Control of Cheetah Bounding with a Segmented Spine.

PubMed

Wang, Chunlei; Wang, Shigang

2016-01-01

A cheetah model is built to mimic real cheetah and its mechanical and dimensional parameters are derived from the real cheetah. In particular, two joints in spine and four joints in a leg are used to realize the motion of segmented spine and segmented legs which are the key properties of the cheetah bounding. For actuating and stabilizing the bounding gait of cheetah, we present a bioinspired controller based on the state-machine. The controller mainly mimics the function of the cerebellum to plan the locomotion and keep the body balance. The haptic sensor and proprioception system are used to detect the trigger of the phase transition. Besides, the vestibular modulation could perceive the pitching angle of the trunk. At last, the cerebellum acts as the CPU to operate the information from the biological sensors. In addition, the calculated results are transmitted to the low-level controller to actuate and stabilize the cheetah bounding. Moreover, the delay feedback control method is employed to plan the motion of the leg joints to stabilize the pitching motion of trunk with the stability criterion. Finally, the cyclic cheetah bounding with biological properties is realized. Meanwhile, the stability and dynamic properties of the cheetah bounding gait are analyzed elaborately.