Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz.

PubMed Central

Heerschap, A; Haasnoot, C A; Hilbers, C W

1983-01-01

Resonances of the water exchangeable iminoprotons of the T and anticodon stem of yeast tRNAPhe were assigned by means of Nuclear Overhauser Effects (NOE's). Together with our previous assignments of iminoproton resonances from the acceptor and D stem (A. Heerschap, C.A.G. Haasnoot and C.W. Hilbers (1982) Nucleic Acids Res. 10, 6981-7000) the present results constitute a complete assignment of all resonances of iminoprotons involved in the secondary structure of yeast tRNAPhe with a reliability and spectral resolution not reached heretofore. Separate identification of the methylprotons in m5C40 and m5C49 was also possible due to specific NOE patterns in the lowfield part of the spectrum. Our experiments indicate that in solution the psi 39 residue in the anticodon stem is orientated in a syn conformation in contrast to the normally observed anti orientation of the uracil base in AU basepairs. Evidence is presented that in solution the acceptor stem is stacked upon the T stem. Furthermore, it turns out that in a similar way the anticodon stem forms a continuous stack with the D stem, but here the m2(2)G26 residue is located between the latter two stems (as is found in the X-ray crystal structure). The stacking of these stems is not strictly dependent on the presence of magnesium ions. NOE experiments show that these structural features are preserved when proceeding from a buffer with magnesium ions to a buffer without magnesium ions although differences in chemical shifts and NOE intensities indicate changes in the conformation of the tRNA. PMID:6346268

NMR resonance assignments of a hypoallergenic isoform of the major birch pollen allergen Bet v 1.

PubMed

Ahammer, Linda; Grutsch, Sarina; Wallner, Michael; Ferreira, Fatima; Tollinger, Martin

2017-10-01

In Northern America and Europe a great number of people are suffering from birch pollen allergy and pollen related food allergies. The trigger for these immunological reactions is the 17.5 kDa major birch pollen allergen Bet v 1, which belongs to the family of PR-10 (pathogenesis-related) proteins. In nature, Bet v 1 occurs as a mixture of various isoforms that possess different immunological properties despite their high sequence identities. Bet v 1.0102 (Bet v 1d), which is investigated here, is a hypoallergenic isoform of Bet v 1 and a potential candidate for allergen-specific immunotherapy. We assigned the backbone and side chain 1 H, 13 C and 15 N resonances of this protein and predicted its secondary structure. The NMR-chemical shift data indicate that Bet v 1.0102 is composed of three α-helices and a seven stranded β-sheet, in agreement with the known structure of the hyperallergenic isoform Bet v 1.0101 (Bet v 1a). Our resonance assignments create the foundation for detailed characterization of the dynamic properties of Bet v 1 isoforms by NMR relaxation measurements.

Bone quantitative susceptibility mapping using a chemical species-specific R2* signal model with ultrashort and conventional echo data.

PubMed

Dimov, Alexey V; Liu, Zhe; Spincemaille, Pascal; Prince, Martin R; Du, Jiang; Wang, Yi

2018-01-01

To develop quantitative susceptibility mapping (QSM) of bone using an ultrashort echo time (UTE) gradient echo (GRE) sequence for signal acquisition and a bone-specific effective transverse relaxation rate ( R2*) to model water-fat MR signals for field mapping. Three-dimensional radial UTE data (echo times ≥ 40 μs) was acquired on a 3 Tesla scanner and fitted with a bone-specific signal model to map the chemical species and susceptibility field. Experiments were performed ex vivo on a porcine hoof and in vivo on healthy human subjects (n = 7). For water-fat separation, a bone-specific model assigning R2* decay mostly to water was compared with the standard models that assigned the same decay for both fat and water. In the ex vivo experiment, bone QSM was correlated with CT. Compared with standard models, the bone-specific R2* method significantly reduced errors in the fat fraction within the cortical bone in all tested data sets, leading to reduced artifacts in QSM. Good correlation was found between bone CT and QSM values in the porcine hoof (R 2  = 0.77). Bone QSM was successfully generated in all subjects. The QSM of bone is feasible using UTE with a conventional echo time GRE acquisition and a bone-specific R2* signal model. Magn Reson Med 79:121-128, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming.

PubMed

Abbas, Ahmed; Guo, Xianrong; Jing, Bing-Yi; Gao, Xin

2014-06-01

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on 'slices', which are one-dimensional vectors in three-dimensional spectra that correspond to certain ([Formula: see text]) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin.

PubMed

Gagné, Donald; Narayanan, Chitra; Bafna, Khushboo; Charest, Laurie-Anne; Agarwal, Pratul K; Doucet, Nicolas

2017-10-01

Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1 H, 13 C and 15 N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.

NMR resonance assignments of the lantibiotic immunity protein NisI from Lactococcus lactis.

PubMed

Hacker, Carolin; Christ, Nina Alexandra; Duchardt-Ferner, Elke; Korn, Sophie; Berninger, Lucija; Kötter, Peter; Entian, Karl-Dieter; Wöhnert, Jens

2015-10-01

The lantibiotic nisin is a small antimicrobial peptide which acts against a wide range of Gram-positive bacteria. Nisin-producing Lactococcus lactis strains express four genes for self-protection against their own antimicrobial compound. This immunity system consists of the lipoprotein NisI and the ABC transporter NisFEG. NisI is attached to the outside of the cytoplasmic membrane via a covalently linked diacylglycerol anchor. Both the lipoprotein and the ABC transporter are needed for full immunity but the exact immunity mechanism is still unclear. To gain insights into the highly specific immunity mechanism of nisin producing strains on a structural level we present here the backbone resonance assignment of NisI (25.8 kDa) as well as the virtually complete (1)H,(15)N,(13)C chemical shift assignments for the isolated 12.7 kDa N-terminal and 14.6 kDa C-terminal domains of NisI.

Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

PubMed

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of (1)H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as (13)C or (15)N. In this method, after the initial preparation of proton magnetization and cross-polarization to (13)C nuclei, transverse magnetization of desired (13)C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific (13)C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of (1)H-(1)H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

Towards Automated Structure-Based NMR Resonance Assignment

NASA Astrophysics Data System (ADS)

Jang, Richard; Gao, Xin; Li, Ming

We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

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

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

Selective excitation enables assignment of proton resonances and {sup 1}H-{sup 1}H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

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

Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of {sup 1}H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as {sup 13}C or {sup 15}N. In this method, after the initial preparation of proton magnetization and cross-polarization to {sup 13}C nuclei, transverse magnetization of desired {sup 13}C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferredmore » to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific {sup 13}C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of {sup 1}H-{sup 1}H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.« less

Multiple-step relayed correlation spectroscopy: sequential resonance assignments in oligosaccharides.

PubMed Central

Homans, S W; Dwek, R A; Fernandes, D L; Rademacher, T W

1984-01-01

A general property of the high-resolution proton NMR spectra of oligosaccharides is the appearance of low-field well-resolved resonances corresponding to the anomeric (H1) and H2 protons. The remaining skeletal protons resonate in the region 3-4 ppm, giving rise to an envelope of poorly resolved resonances. Assignments can be made from the H1 and H2 protons to their J-coupled neighbors (H2 and H3) within this main envelope by using 1H-1H correlated spectroscopy. However, the tight coupling (J congruent to delta) between further protons results in poor spectral dispersion with consequent assignment ambiguities. We describe here three-step two-dimensional relayed correlation spectroscopy and show how it can be used to correlate the resolved anomeric (H1) and H2 protons with remote (H4, H5) protons directly through a linear network of couplings using sequential magnetization transfer around the oligosaccharide rings. Resonance assignments are then obtained by inspection of cross-peaks that appear in well-resolved regions of the two-dimensional spectrum. This offers a general solution to the assignment problem in oligosaccharides and, importantly, these assignments will subsequently allow for the three-dimensional solution conformation to be determined by using one-dimensional and two-dimensional nuclear Overhauser experiments. PMID:6593701

Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2002-06-01

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.

PubMed

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

2017-02-01

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H δ21 and H ε21 , respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

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

Darbon, H.; Weber, C.; Braun, W.

1991-02-19

Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includesmore » two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.« less

Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins.

PubMed

Mas, Guillaume; Crublet, Elodie; Hamelin, Olivier; Gans, Pierre; Boisbouvier, Jérôme

2013-11-01

The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D2O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d10. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

PubMed

Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

2015-02-01

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

1H, 15N, 13C resonance assignment of folded and 8 M urea-denatured state of SUMO from Drosophila melanogaster.

PubMed

Kumar, Dinesh; Kumar, Ashutosh; Misra, Jyoti Ranjan; Chugh, Jeetender; Sharma, Shilpy; Hosur, Ramakrishna V

2008-06-01

SUMO, an important post-translational modifier of variety of substrate proteins, regulates different cellular functions. Here, we report the NMR resonance assignment of the folded and 8 M urea-denatured state of SUMO from Drosophila melanogaster (dsmt3).

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

PubMed

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

PubMed Central

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

NMR assignment of a PDZ domain in complex with a HPV51 E6 derived N-terminally pyroglutamic acid modified peptide.

PubMed

Mischo, André; Ohlenschläger, Oliver; Ramachandran, Ramadurai; Görlach, Matthias

2013-04-01

The resonance assignment of an amino-terminal pyroglutamic acid containing peptide derived from the E6 protein of human papillomavirus (HPV) type 51 in complex with PDZ domain 2 of hDlg/SAP-97 is reported. The assignments include (1)H, (13)C and (15)N resonances for the protein and peptide in the complex and all of the peptide's pyroglutamic acid nuclei.

Nanoimaging of resonating hyperbolic polaritons in linear boron nitride antennas

PubMed Central

Alfaro-Mozaz, F. J.; Alonso-González, P.; Vélez, S.; Dolado, I.; Autore, M.; Mastel, S.; Casanova, F.; Hueso, L. E.; Li, P.; Nikitin, A. Y.; Hillenbrand, R.

2017-01-01

Polaritons in layered materials—including van der Waals materials—exhibit hyperbolic dispersion and strong field confinement, which makes them highly attractive for applications including optical nanofocusing, sensing and control of spontaneous emission. Here we report a near-field study of polaritonic Fabry–Perot resonances in linear antennas made of a hyperbolic material. Specifically, we study hyperbolic phonon–polaritons in rectangular waveguide antennas made of hexagonal boron nitride (h-BN, a prototypical van der Waals crystal). Infrared nanospectroscopy and nanoimaging experiments reveal sharp resonances with large quality factors around 100, exhibiting atypical modal near-field patterns that have no analogue in conventional linear antennas. By performing a detailed mode analysis, we can assign the antenna resonances to a single waveguide mode originating from the hybridization of hyperbolic surface phonon–polaritons (Dyakonov polaritons) that propagate along the edges of the h-BN waveguide. Our work establishes the basis for the understanding and design of linear waveguides, resonators, sensors and metasurface elements based on hyperbolic materials and metamaterials. PMID:28589941

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

Neutron Resonance Spin Determination Using Multi-Segmented Detector DANCE

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

Baramsai, B.; Mitchell, G. E.; Chyzh, A.

2011-06-01

A sensitive method to determine the spin of neutron resonances is introduced based on the statistical pattern recognition technique. The new method was used to assign the spins of s-wave resonances in {sup 155}Gd. The experimental neutron capture data for these nuclei were measured with the DANCE (Detector for Advanced Neutron Capture Experiment) calorimeter at the Los Alamos Neutron Science Center. The highly segmented calorimeter provided detailed multiplicity distributions of the capture {gamma}-rays. Using this information, the spins of the neutron capture resonances were determined. With these new spin assignments, level spacings are determined separately for s-wave resonances with J{supmore » {pi}} = 1{sup -} and 2{sup -}.« less

Simple and robust referencing system enables identification of dissolved-phase xenon spectral frequencies.

PubMed

Antonacci, Michael A; Zhang, Le; Burant, Alex; McCallister, Drew; Branca, Rosa T

2018-08-01

To assess the effect of macroscopic susceptibility gradients on the gas-phase referenced dissolved-phase 129 Xe (DPXe) chemical shift (CS) and to establish the robustness of a water-based referencing system for in vivo DPXe spectra. Frequency shifts induced by spatially varying magnetic susceptibility are calculated by finite-element analysis for the human head and chest. Their effect on traditional gas-phase referenced DPXe CS is then assessed theoretically and experimentally. A water-based referencing system for the DPXe resonances that uses the local water protons as reference is proposed and demonstrated in vivo in rats. Across the human brain, macroscopic susceptibility gradients can induce an apparent variation in the DPXe CS of up to 2.5 ppm. An additional frequency shift as large as 6.5 ppm can exist between DPXe and gas-phase resonances. By using nearby water protons as reference for the DPXe CS, the effect of macroscopic susceptibility gradients is eliminated and consistent CS values are obtained in vivo, regardless of shimming conditions, region of interest analyzed, animal orientation, or lung inflation. Combining in vitro and in vivo spectroscopic measurements finally enables confident assignment of some of the DPXe peaks observed in vivo. To use hyperpolarized xenon as a biological probe in tissues, the DPXe CS in specific organs/tissues must be reliably measured. When the gas-phase is used as reference, variable CS values are obtained for DPXe resonances. Reliable peak assignments in DPXe spectra can be obtained by using local water protons as reference. Magn Reson Med 80:431-441, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Backbone resonance assignments of the PRYSPRY domain of TRIM25.

PubMed

Kong, Chen; Penumutchu, Srinivasa R; Hung, Kuo-Wei; Huang, Huiying; Lin, Tianwei; Yu, Chin

2015-10-01

TRIM25 is a member of the tripartite motif (TRIM) family and has been implicated in the regulation of innate immune signaling via the RIG-I (retinoic acid-inducible gene-I) pathway for antiviral defense. As the essential first step towards the structural and functional characterization of the TRIM25/RIG-I interaction, the backbone resonance of the PRYSPRY domain of TRIM25 is assigned here based on triple-resonance experiments using uniformly [(2)H, (13)C, (15)N]-labeled protein.

Franck-Condon fingerprinting of vibration-tunneling spectra.

PubMed

Berrios, Eduardo; Sundaradevan, Praveen; Gruebele, Martin

2013-08-15

We introduce Franck-Condon fingerprinting as a method for assigning complex vibration-tunneling spectra. The B̃ state of thiophosgene (SCCl2) serves as our prototype. Despite several attempts, assignment of its excitation spectrum has proved difficult because of near-degenerate vibrational frequencies, Fermi resonance between the C-Cl stretching mode and the Cl-C-Cl bending mode, and large tunneling splittings due to the out-of-plane umbrella mode. Hence, the spectrum has never been fitted to an effective Hamiltonian. Our assignment approach replaces precise frequency information with intensity information, eliminating the need for double resonance spectroscopy or combination differences, neither of which have yielded a full assignment thus far. The dispersed fluorescence spectrum of each unknown vibration-tunneling state images its character onto known vibrational progressions in the ground state. By using this Franck-Condon fingerprint, we were able to determine the predominant character of several vibration-tunneling states and assign them; in other cases, the fingerprinting revealed that the states are strongly mixed and cannot be characterized with a simple normal mode assignment. The assigned transitions from vibration-tunneling wave functions that were not too strongly mixed could be fitted within measurement uncertainty by an effective vibration-tunneling Hamiltonian. A fit of all observed vibration-tunneling states will require a full resonance-tunneling Hamiltonian.

Raman spectra of ruthenium and tantalum trimers in argon matrices

NASA Astrophysics Data System (ADS)

Fang, Li; Shen, Xiaole; Chen, Xiaoyu; Lombardi, John R.

2000-12-01

The resonance Raman spectra of ruthenium trimers (Ru 3) in argon matrices have been obtained. Three resonance Raman transitions were observed between 570 and 590 nm. Two of them (303.4 and 603.7 cm -1) are assigned to the totally symmetric vibrational progression, giving k e=1.86 mdyne/ Å. The line at 581.5 cm-1 is assigned as the origin of a low-lying electronic state. We also report on the observation of a resonance Raman spectrum of tantalum trimers (Ta 3). Observed lines include 251.2 and 501.9 cm-1 which we assign to the fundamental and the first overtone of the symmetric stretch in Ta 3. This gives k e=2.25 mdyne/ Å.

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor.

PubMed Central

Fairbrother, W. J.; Champe, M. A.; Christinger, H. W.; Keyt, B. A.; Starovasnik, M. A.

1997-01-01

Nearly complete sequence-specific 1H, 13C, and 15N resonance assignments are reported for the backbone atoms of the receptor-binding domain of vascular endothelial growth factor (VEGF), a 23-kDa homodimeric protein that is a major regulator of both normal and pathological angiogenesis. The assignment strategy relied on the use of seven 3D triple-resonance experiments [HN(CO)CA, HNCA, HNCO, (HCA)CONH, HN(COCA)HA, HN(CA)HA, and CBCA-(CO)NH] and a 3D 15N-TOCSY-HSQC experiment recorded on a 0.5 mM (12 mg/mL) sample at 500 MHz, pH 7.0, 45 degrees C. Under these conditions, 15N relaxation data show that the protein has a rotational correlation time of 15.0 ns. Despite this unusually long correlation time, assignments were obtained for 94 of the 99 residues; 8 residues lack amide 1H and 15N assignments, presumably due to rapid exchange of the amide 1H with solvent under the experimental conditions used. The secondary structure of the protein was deduced from the chemical shift indices of the 1H alpha, 13C alpha, 13C beta, and 13CO nuclei, and from analysis of backbone NOEs observed in a 3D 15N-NOESY-HSQC spectrum. Two helices and a significant amount of beta-sheet structure were identified, in general agreement with the secondary structure found in a recently determined crystal structure of a similar VEGF construct [Muller YA et al., 1997, Proc Natl Acad Sci USA 94:7192-7197]. PMID:9336848

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

PubMed

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to uncover large consistent sets of interactions. Our algorithm has been implemented in the platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

Advances in stable isotope assisted labeling strategies with information science.

PubMed

Kigawa, Takanori

2017-08-15

Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets. Various combinatorial selective labeling schemes have been developed as more sophisticated labeling strategies. In these strategies, amino acids are represented by combinations of SI labeled samples, rather than simply assigning one amino acid to one SI labeled sample as in the case of conventional amino acid-selective labeling. These strategies have proven to be useful for NMR analyses of difficult proteins, such as those in large complex systems, in living cells, attached or integrated into membranes, or with poor solubility. In this review, recent advances in stable isotope assisted labeling strategies will be discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

NASA Astrophysics Data System (ADS)

Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

2012-05-01

The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

Total angular momenta of high-lying odd levels of U I at ∼ 4 eV using resonance ionization laser polarization spectroscopy

NASA Astrophysics Data System (ADS)

Rath, Asawari D.; Kundu, S.; Ray, A. K.

2018-02-01

Laser induced photoionization of atoms shows significant dependence on the choice of polarizations of lasers. In multi-step, multi-photon excitation and subsequent ionization of atoms different polarization combinations of the exciting lasers lead to distinctly different ion yields. This fact is exploited in this work to determine total angular momenta of odd-parity energy levels of U I lying at ∼ 4 eV from its ground level using resonance ionization laser polarization spectroscopy in time of flight mass spectrometer. These levels are populated by two-step resonant excitation using two pulsed dye lasers with preset polarizations of choice followed by nonresonant ionization by third laser. The dependence of ionization yield on specific polarizations of the first two lasers is studied experimentally for each level under consideration. This dependence when compared to simulations makes possible unambiguous assignment of J angular momenta to these levels.

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

Astrof, Nathan S.; Lyon, Charles E.; Griffin, Robert G.

2001-10-01

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CON CA experiment establishes the correlation of 13Ci-1 to 13Cαi and 15Ni by simultaneously encoding the 13COi-1 and 15Ni chemical shifts. The CAN COCA experiment establishes the correlation 13Cai and 15COi to 13Cαi-1 and 15Ni-1 within a single experiment by simultaneous encoding of the 13Cαi and 15Ni chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

Practical aspects of NMR signal assignment in larger and challenging proteins

PubMed Central

Frueh, Dominique P.

2014-01-01

NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model.

PubMed

Hao, Jie; Astle, William; De Iorio, Maria; Ebbels, Timothy M D

2012-08-01

Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject to human error. Conversely, alignment and binning can introduce artefacts and limit immediate biological interpretation of models. We present the Bayesian automated metabolite analyser for NMR spectra (BATMAN), an R package that deconvolutes peaks from one-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples. It applies a Markov chain Monte Carlo algorithm to sample from a joint posterior distribution of the model parameters and obtains concentration estimates with reduced error compared with conventional numerical integration and comparable to manual deconvolution by experienced spectroscopists. http://www1.imperial.ac.uk/medicine/people/t.ebbels/ t.ebbels@imperial.ac.uk.

Sequential /sup 1/H NMR assignments and secondary structure of hen egg white lysozyme in solution

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

Redfield, C.; Dobson, C.M.

Assignments of /sup 1/H NMR resonances of 121 of the 129 residues of hen egg white lysozyme have been obtained by sequence-specific methods. Spin systems were identified with phase-sensitive two-dimensional (2-D) correlated spectroscopy and single and double relayed coherence transfer spectroscopy. For key types of amino acid residues, particularly alanine, threonine, valine, and glycine, complete spin systems were identified. For other residues a less complete definition of the spin system was found to be adequate for the purpose of sequential assignment. Sequence-specific assignments were achieved by phase-sensitive 2-D nuclear Overhauser enhancement spectroscopy (NOESY). Exploitation of the wide range of hydrogenmore » exchange rates found in lysozyme was a useful approach to overcoming the problem of spectral overlap. The sequential assignment was built up from 21 peptide segments ranging in length from 2 to 13 residues. The NOESY spectra were also used to provide information about the secondary structure of the protein in solution. Three helical regions and two regions of ..beta..-sheet were identified from the NOESY data; these regions are identical with those found in the X-ray structure of hen lysozyme. Slowly exchanging amides are generally correlated with hydrogen bonding identified in the X-ray structure; a number of exceptions to this general trend were, however, found. The results presented in this paper indicate that highly detailed information can be obtained from 2-D NMR spectra of a protein that is significantly larger than those studies previously.« less

Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction

NASA Astrophysics Data System (ADS)

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-05-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.

Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction

PubMed Central

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-01-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 – 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. PMID:25863893

Direct assignment of the cysteinyl, the slowly exchangeable, and the aromatic ring H nuclear magnetic resonances in clostridial-type ferredoxins. [Clostridium acidi-urici, C. pasteurianum, C. perfringens, Peptococcus aerogenes

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

Packer, E.L.; Sweeney, W.V.; Rabinowitz, J.C.

1977-04-10

We have directly assigned the /sup 1/H NMR corresponding to the cysteinyl protons, the slowly exchangeable protons, and the aromatic ring protons in the /sup 1/H NMR spectrum of Clostridium acidi-urici ferredoxin by isotopic labeling and /sup 13/C NMR decoupling techniques. We also show that the resonance pattern in the 8- to 20-ppM (from 2,2-dimethyl-2-sialapentanesulfonic acid) region of the /sup 1/H NMR spectra of oxidized Clostridium acidi-urici, Clostridium pasteurianum, Clostridium perfringens, and Peptococcus aerogenes ferredoxins are very similar, and we assign the resonances in this region by analogy with the spectrum of C. acidi-urici ferredoxin. The /sup 1/H NMR spectramore » of the ..beta.. protons of the cysteinyl residues of these ferredoxins differ, however, from the /sup 1/H NMR spectra of equivalent ..beta.. protons of the methylene carbon atoms bonded via a sulfur atom to (4Fe-4S) clusters in synthetic inorganic analogues. In the spectra of the synthetic compounds, the ..beta.. protons appear as a single resonance shifted 10 ppM from its unbonded reference position. In the spectra of oxidized clostridial ferredoxins, the cysteinyl ..beta.. protons appear as a series of at least eight resolved resonances with shifts that range from 6 to 14 ppM, relative to the free amino acid resonance position.« less

QPO observations related to neutron star equations of state

NASA Astrophysics Data System (ADS)

Stuchlik, Zdenek; Urbanec, Martin; Török, Gabriel; Bakala, Pavel; Cermak, Petr

We apply a genetic algorithm method for selection of neutron star models relating them to the resonant models of the twin peak quasiperiodic oscillations observed in the X-ray neutron star binary systems. It was suggested that pairs of kilo-hertz peaks in the X-ray Fourier power density spectra of some neutron stars reflect a non-linear resonance between two modes of accretion disk oscillations. We investigate this concept for a specific neutron star source. Each neutron star model is characterized by the equation of state (EOS), rotation frequency Ω and central energy density ρc . These determine the spacetime structure governing geodesic motion and position dependent radial and vertical epicyclic oscillations related to the stable circular geodesics. Particular kinds of resonances (KR) between the oscillations with epicyclic frequencies, or the frequencies derived from them, can take place at special positions assigned ambiguously to the spacetime structure. The pairs of resonant eigenfrequencies relevant to those positions are therefore fully given by KR,ρc , Ω, EOS and can be compared to the observationally determined pairs of eigenfrequencies in order to eliminate the unsatisfactory sets (KR,ρc , Ω, EOS). For the elimination we use the advanced genetic algorithm. Genetic algorithm comes out from the method of natural selection when subjects with the best adaptation to assigned conditions have most chances to survive. The chosen genetic algorithm with sexual reproduction contains one chromosome with restricted lifetime, uniform crossing and genes of type 3/3/5. For encryption of physical description (KR,ρ, Ω, EOS) into chromosome we used Gray code. As a fitness function we use correspondence between the observed and calculated pairs of eigenfrequencies.

Neutron star equation of state and QPO observations

NASA Astrophysics Data System (ADS)

Urbanec, Martin; Stuchlík, Zdeněk; Török, Gabriel; Bakala, Pavel; Čermák, Petr

2007-12-01

Assuming a resonant origin of the twin peak quasiperiodic oscillations observed in the X-ray neutron star binary systems, we apply a genetic algorithm method for selection of neutron star models. It was suggested that pairs of kilohertz peaks in the X-ray Fourier power density spectra of some neutron stars reflect a non-linear resonance between two modes of accretion disk oscillations. We investigate this concept for a specific neutron star source. Each neutron star model is characterized by the equation of state (EOS), rotation frequency Ω and central energy density rho_{c}. These determine the spacetime structure governing geodesic motion and position dependent radial and vertical epicyclic oscillations related to the stable circular geodesics. Particular kinds of resonances (KR) between the oscillations with epicyclic frequencies, or the frequencies derived from them, can take place at special positions assigned ambiguously to the spacetime structure. The pairs of resonant eigenfrequencies relevant to those positions are therefore fully given by KR, rho_{c}, Ω, EOS and can be compared to the observationally determined pairs of eigenfrequencies in order to eliminate the unsatisfactory sets (KR, rho_{c}, Ω, EOS). For the elimination we use the advanced genetic algorithm. Genetic algorithm comes out from the method of natural selection when subjects with the best adaptation to assigned conditions have most chances to survive. The chosen genetic algorithm with sexual reproduction contains one chromosome with restricted lifetime, uniform crossing and genes of type 3/3/5. For encryption of physical description (KR, rho_{c}, Ω, EOS) into the chromosome we use the Gray code. As a fitness function we use correspondence between the observed and calculated pairs of eigenfrequencies.

Is a neutral expression also a neutral stimulus? A study with functional magnetic resonance.

PubMed

Carvajal, Fernando; Rubio, Sandra; Serrano, Juan M; Ríos-Lago, Marcos; Alvarez-Linera, Juan; Pacheco, Lara; Martín, Pilar

2013-08-01

Although neutral faces do not initially convey an explicit emotional message, it has been found that individuals tend to assign them an affective content. Moreover, previous research has shown that affective judgments are mediated by the task they have to perform. Using functional magnetic resonance imaging in 21 healthy participants, we focus this study on the cerebral activity patterns triggered by neutral and emotional faces in two different tasks (social or gender judgments). Results obtained, using conjunction analyses, indicated that viewing both emotional and neutral faces evokes activity in several similar brain areas indicating a common neural substrate. Moreover, neutral faces specifically elicit activation of cerebellum, frontal and temporal areas, while emotional faces involve the cuneus, anterior cingulated gyrus, medial orbitofrontal cortex, posterior superior temporal gyrus, precentral/postcentral gyrus and insula. The task selected was also found to influence brain activity, in that the social task recruited frontal areas while the gender task involved the posterior cingulated, inferior parietal lobule and middle temporal gyrus to a greater extent. Specifically, in the social task viewing neutral faces was associated with longer reaction times and increased activity of left dorsolateral frontal cortex compared with viewing facial expressions of emotions. In contrast, in the same task emotional expressions distinctively activated the left amygdale. The results are discussed taking into consideration the fact that, like other facial expressions, neutral expressions are usually assigned some emotional significance. However, neutral faces evoke a greater activation of circuits probably involved in more elaborate cognitive processing.

Novel selective TOCSY method enables NMR spectral elucidation of metabolomic mixtures

NASA Astrophysics Data System (ADS)

MacKinnon, Neil; While, Peter T.; Korvink, Jan G.

2016-11-01

Complex mixture analysis is routinely encountered in NMR-based investigations. With the aim of component identification, spectral complexity may be addressed chromatographically or spectroscopically, the latter being favored to reduce sample handling requirements. An attractive experiment is selective total correlation spectroscopy (sel-TOCSY), which is capable of providing tremendous spectral simplification and thereby enhancing assignment capability. Unfortunately, isolating a well resolved resonance is increasingly difficult as the complexity of the mixture increases and the assumption of single spin system excitation is no longer robust. We present TOCSY optimized mixture elucidation (TOOMIXED), a technique capable of performing spectral assignment particularly in the case where the assumption of single spin system excitation is relaxed. Key to the technique is the collection of a series of 1D sel-TOCSY experiments as a function of the isotropic mixing time (τm), resulting in a series of resonance intensities indicative of the underlying molecular structure. By comparing these τm -dependent intensity patterns with a library of pre-determined component spectra, one is able to regain assignment capability. After consideration of the technique's robustness, we tested TOOMIXED firstly on a model mixture. As a benchmark we were able to assign a molecule with high confidence in the case of selectively exciting an isolated resonance. Assignment confidence was not compromised when performing TOOMIXED on a resonance known to contain multiple overlapping signals, and in the worst case the method suggested a follow-up sel-TOCSY experiment to confirm an ambiguous assignment. TOOMIXED was then demonstrated on two realistic samples (whisky and urine), where under our conditions an approximate limit of detection of 0.6 mM was determined. Taking into account literature reports for the sel-TOCSY limit of detection, the technique should reach on the order of 10 μ M sensitivity. We anticipate this technique will be highly attractive to various analytical fields facing mixture analysis, including metabolomics, foodstuff analysis, pharmaceutical analysis, and forensics.

Neutron Capture Measurements on 97Mo with the DANCE Array

NASA Astrophysics Data System (ADS)

Walker, Carrie L.

Neutron capture is a process that is crucial to understanding nucleosynthesis, reactors, and nuclear weapons. Precise knowledge of neutron capture cross-sections and level densities is necessary in order to model these high-flux environments. High-confidence spin and parity assignments for neutron resonances are of critical importance to this end. For nuclei in the A=100 mass region, the p-wave neutron strength function is at a maximum, and the s-wave strength function is at a minimum, producing up to six possible Jpi combinations. Parity determination becomes important to assigning spins in this mass region, and the large number of spin groups adds complexity to the problem. In this work, spins and parities for 97Mo resonances are assigned, and best fit models for photon strength function and level density are determined. The neutron capture-cross section for 97Mo is also determined, as are resonance parameters for neutron energies ranging from 16 eV to 2 keV.

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Systematic assignment of Feshbach resonances via an asymptotic bound state model

NASA Astrophysics Data System (ADS)

Goosen, Maikel; Kokkelmans, Servaas

2008-05-01

We present an Asymptotic Bound state Model (ABM), which is useful to predict Feshbach resonances. The model utilizes asymptotic properties of the interaction potentials to represent coupled molecular wavefunctions. The bound states of this system give rise to Feshbach resonances, localized at the magnetic fields of intersection of these bound states with the scattering threshold. This model was very successful to assign measured Feshbach resonances in an ultra cold mixture of ^6Li and ^40K atomsootnotetextE. Wille, F.M. Spiegelhalder, G. Kerner, D. Naik, A. Trenkwalder, G. Hendl, F. Schreck, R. Grimm, T.G. Tiecke, J.T.M. Walraven, S.J.J.M.F. Kokkelmans, E. Tiesinga, P.S. Julienne, arXiv:0711.2916. For this system, the accuracy of the determined scattering lengths is comparable to full coupled channels results. However, it was not possible to predict the width of the resonances. We discuss how an incorporation of threshold effects will improve the model, and we apply it to a mixture of ^87Rb and ^133Cs atoms, where recently Feshbach resonances have been measured.

1H, 13C, and 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica

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

Rossi, Paolo; Ramelot, Theresa A.; Xiao, Rong

2005-11-01

The product of gene locus BB0938 from Bordetella bronchiseptica (Swiss-Prot ID: Q7WNU7-BORBR; NESG target ID: BoR11; Wunderlich et al., 2004; Pfam ID: PF03476) is a 128-residue protein of unknown function. This broadly conserved protein family is found in eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 98% of backbone and 94% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a b topology with a seven-residue helical insert, ??????????. BMRB deposit with accession number 6693. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family

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

Aramini, James M.; Swapna, G.V.T.; Huang, Yuanpeng

2005-11-01

Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

Reward Activates Stimulus-Specific and Task-Dependent Representations in Visual Association Cortices

PubMed Central

Muller, Timothy; Yeung, Nick; Waszak, Florian

2014-01-01

Humans reliably learn which actions lead to rewards. One prominent question is how credit is assigned to environmental stimuli that are acted upon. Recent functional magnetic resonance imaging (fMRI) studies have provided evidence that representations of rewarded stimuli are activated upon reward delivery, providing possible eligibility traces for credit assignment. Our study sought evidence of postreward activation in sensory cortices satisfying two conditions of instrumental learning: postreward activity should reflect the stimulus category that preceded reward (stimulus specificity), and should occur only if the stimulus was acted on to obtain reward (task dependency). Our experiment implemented two tasks in the fMRI scanner. The first was a perceptual decision-making task on degraded face and house stimuli. Stimulus specificity was evident as rewards activated the sensory cortices associated with face versus house perception more strongly after face versus house decisions, respectively, particularly in the fusiform face area. Stimulus specificity was further evident in a psychophysiological interaction analysis wherein face-sensitive areas correlated with nucleus accumbens activity after face-decision rewards, whereas house-sensitive areas correlated with nucleus accumbens activity after house-decision rewards. The second task required participants to make an instructed response. The criterion of task dependency was fulfilled as rewards after face versus house responses activated the respective association cortices to a larger degree when faces and houses were relevant to the performed task. Our study is the first to show that postreward sensory cortex activity meets these two key criteria of credit assignment, and does so independently from bottom-up perceptual processing. PMID:25411489

Millimeter-wave optical double resonance schemes for rapid assignment of perturbed spectra, with applications to the C{sup ~} {sup 1}B{sub 2} state of SO{sub 2}

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

Park, G. Barratt, E-mail: barratt@mit.edu, E-mail: barratt.park@gmail.com; Womack, Caroline C.; Jiang, Jun

2015-04-14

Millimeter-wave detected, millimeter-wave optical double resonance (mmODR) spectroscopy is a powerful tool for the analysis of dense, complicated regions in the optical spectra of small molecules. The availability of cavity-free microwave and millimeter wave spectrometers with frequency-agile generation and detection of radiation (required for chirped-pulse Fourier-transform spectroscopy) opens up new schemes for double resonance experiments. We demonstrate a multiplexed population labeling scheme for rapid acquisition of double resonance spectra, probing multiple rotational transitions simultaneously. We also demonstrate a millimeter-wave implementation of the coherence-converted population transfer scheme for background-free mmODR, which provides a ∼10-fold sensitivity improvement over the population labeling scheme.more » We analyze perturbations in the C{sup ~} state of SO{sub 2}, and we rotationally assign a b{sub 2} vibrational level at 45 328 cm{sup −1} that borrows intensity via a c-axis Coriolis interaction. We also demonstrate the effectiveness of our multiplexed mmODR scheme for rapid acquisition and assignment of three predissociated vibrational levels of the C{sup ~} state of SO{sub 2} between 46 800 and 47 650 cm{sup −1}.« less

A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment

PubMed Central

Mobli, Mehdi; Stern, Alan S.; Bermel, Wolfgang; King, Glenn F.; Hoch, Jeffrey C.

2010-01-01

One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives. PMID:20299257

Impact of Lesion Visibility on Transrectal Ultrasound on the Prediction of Clinically Significant Prostate Cancer (Gleason Score 3 + 4 or Greater) with Transrectal Ultrasound-Magnetic Resonance Imaging Fusion Biopsy.

PubMed

Garcia-Reyes, Kirema; Nguyen, Hao G; Zagoria, Ronald J; Shinohara, Katsuto; Carroll, Peter R; Behr, Spencer C; Westphalen, Antonio C

2017-09-20

The purpose of this study was to estimate the impact of lesion visibility with transrectal ultrasound on the prediction of clinically significant prostate cancer with transrectal ultrasound-magnetic resonance imaging fusion biopsy. This HIPAA (Health Insurance Portability and Accountability Act) compliant, institutional review board approved, retrospective study was performed in 178 men who were 64.7 years old with prostate specific antigen 8.9 ng/ml. They underwent transrectal ultrasound-magnetic resonance imaging fusion biopsy from January 2013 to September 2016. Visible lesions on magnetic resonance imaging were assigned a PI-RADS™ (Prostate Imaging Reporting and Data System), version 2 score of 3 or greater. Transrectal ultrasound was positive when a hypoechoic lesion was identified. We used a 3-level, mixed effects logistic regression model to determine how transrectal ultrasound-magnetic resonance imaging concordance predicted the presence of clinically significant prostate cancer. The diagnostic performance of the 2 methods was estimated using ROC curves. A total of 1,331 sextants were targeted by transrectal ultrasound-magnetic resonance imaging fusion or systematic biopsies, of which 1,037 were negative, 183 were Gleason score 3 + 3 and 111 were Gleason score 3 + 4 or greater. Clinically significant prostate cancer was diagnosed by transrectal ultrasound and magnetic resonance imaging alone at 20.5% and 19.7% of these locations, respectively. Men with positive imaging had higher odds of clinically significant prostate cancer than men without visible lesions regardless of modality (transrectal ultrasound OR 14.75, 95% CI 5.22-41.69, magnetic resonance imaging OR 12.27, 95% CI 6.39-23.58 and the 2 modalities OR 28.68, 95% CI 14.45-56.89, all p <0.001). The ROC AUC to detect clinically significant prostate cancer using the 2 methods (0.85, 95% CI 0.81-0.89) was statistically greater than that of transrectal ultrasound alone (0.80, 95% CI 0.76-0.85, p = 0.001) and magnetic resonance imaging alone (0.83, 95% CI 0.79-0.87, p = 0.04). The sensitivity and specificity of transrectal ultrasound were 42.3% and 91.6%, and the sensitivity and specificity of magnetic resonance imaging were 62.2% and 84.1%, respectively. Lesion visibility on magnetic resonance imaging or transrectal ultrasound denotes a similar probability of clinically significant prostate cancer. This probability is greater when each examination is positive. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin.

PubMed

D'Angelo, Paola; Lucarelli, Debora; della Longa, Stefano; Benfatto, Maurizio; Hazemann, Jean Louis; Feis, Alessandro; Smulevich, Giulietta; Ilari, Andrea; Bonamore, Alessandra; Boffi, Alberto

2004-06-01

Escherichia coli flavohemoglobin is endowed with the notable property of binding specifically unsaturated and/or cyclopropanated fatty acids both as free acids or incorporated into a phospholipid molecule. Unsaturated or cyclopropanated fatty acid binding to the ferric heme results in a spectral change observed in the visible absorption, resonance Raman, extended x-ray absorption fine spectroscopy (EXAFS), and x-ray absorption near edge spectroscopy (XANES) spectra. Resonance Raman spectra, measured on the flavohemoglobin heme domain, demonstrate that the lipid (linoleic acid or total lipid extracts)-induced spectral signals correspond to a transition from a five-coordinated (typical of the ligand-free protein) to a hexacoordinated, high spin heme iron. EXAFS and XANES measurements have been carried out both on the lipid-free and on the lipid-bound protein to assign the nature of ligand in the sixth coordination position of the ferric heme iron. EXAFS data analysis is consistent with the presence of a couple of atoms in the sixth coordination position at 2.7 A in the lipid-bound derivative (bonding interaction), whereas a contribution at 3.54 A (nonbonding interaction) can be singled out in the lipid-free protein. This last contribution is assigned to the CD1 carbon atoms of the distal LeuE11, in full agreement with crystallographic data on the lipid-free protein at 1.6 A resolution obtained in the present work. Thus, the contributions at 2.7 A distance from the heme iron are assigned to a couple of carbon atoms of the lipid acyl chain, possibly corresponding to the unsaturated carbons of the linoleic acid.

Evidence for two interconverting protein isomers in the methotrexate complex of dihydrofolate reductase from Escherichia coli

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

Falzone, C.J.; Benkovic, S.J.; Wright, P.E.

1991-02-26

Two-dimensional {sup 1}H NMR methods and a knowledge of the X-ray crystal structure have been used to make resonance assignments for the amino acid side chains of dihydrofolate reductase from Escherichia coli complexed with methotrexate. The H7 proton on the pteridine ring of methotrexate was found to have NOEs to the methyl protons of Leu-28 which were assigned by using the L28F mutant. These NOEs indicated that the orientation of the methotrexate pteridine ring is similar in both solution and crystal structures. During the initial assignment process, it became evident that many of the resonances in this complex, unlike thosemore » of the folate complex, are severally broadened or doubled. The observation of two distinct sets of resonances in a ratio of approximately 2:1 was attributed to the presence of two protein isomers. Many of the side chains with clearly doubled resonances were located in the {beta}-sheet and the active site. Preliminary studies on the apoprotein also revealed doubled resonances in the absence of the inhibitor, indicating the existence of the protein isomers prior to methotrexate binding. In contrast to the methotrexate complex, the binary complex with folate and the ternary MTX-NADPH-DHFR complex presented a single enzyme form. These results are proposed to reflect the ability of folate and NADPH to bind predominantly to one protein isomer.« less

Complete structure of the polysaccharide from Streptococcus sanguis J22

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

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1990-01-09

The cell wall polysaccharides of certain oral streptococci such as Streptococcus sanguis strains 34 and J22, although immunologically distinct, act as receptors for the fimbrial lectins of Actinomyces viscosus T14V. The authors report the complete covalent structure of the polysaccharide from S. sanguis J22 which is composed of a heptasaccharide subunit linked by phosphodiester bonds. The repeating subunit, which contains {alpha}-GalNAc, {alpha}-rhamnose, {beta}-rhamnose, {beta}-glucose, and {beta}-galactose all in the pyranoside form and {beta}-galactofuranose, is compared with the previously published structure of the polysaccharide from strain 34. The structure has been determined almost exclusively by high-resolution nuclear magnetic resonance methods. Themore » {sup 1}H and {sup 13}C NMR spectra of the polysaccharides from both strains 34 and J22 have been completely assigned. The stereochemistry of pyranosides was assigned from J{sub H-H} values determined from phase-sensitive COSY spectra, and acetamido sugars were assigned by correlation of the resonances of the amide {sup 1}H with the sugar ring protons. The {sup 13}C spectra were assigned by {sup 1}H-detected multiple-quantum correlation (HMQC) spectra, and the assignments were confirmed by {sup 1}H-detected multiple-bond correlation (HMBC) spectra. The positions of the glycosidic linkages were assigned by detection of three-bond {sup 1}H-{sup 13}C correlation across the glycosidic linkage in the HMBC spectra. The positions of the phosphodiester linkages were determined by splittings observed in the {sup 13}C resonances due to {sup 31}P coupling and also by {sup 1}H-detected {sup 31}P correlation spectroscopy.« less

Intervalley double resonance processes in MoS2

NASA Astrophysics Data System (ADS)

Wang, Yuanxi; Carvalho, Bruno; Malard, Leandro; Fantini, Cristiano; Crespi, Vincent; Pimenta, Marcos

Intervalley scattering plays a significant role in electronic energy dissipation in semiconductors. We investigate the intervalley scattering of monolayer and few-layer MoS2, by combining density functional theory calculations and resonant Raman spectroscopy probed by up to 20 laser excitation energies. We observe that two Raman peaks within 420-460 cm-1 are dispersive over a small range of laser energy, a clear signature of second-order processes involving intervalley scattering. Both modes involve LA and TA phonons at or near the K point. A third Raman peak at 466 cm-1 shows a strong intensity dependence on the layer number and is assigned 2LA(M). Our results invalidate previous Raman peak assignment proposals and open up a better understanding of double resonance processes in transition metal dichalcogenides.

Low-energy-electron scattering by CH3CN

NASA Astrophysics Data System (ADS)

Maioli, Leticia S.; Bettega, Márcio H. F.

2017-12-01

We report integral and differential cross sections for the elastic scattering of low-energy electrons by methyl cyanide (CH3CN), also known as acetonitrile. The cross sections were computed using the Schwinger multichannel method implemented with pseudopotentials. The fixed-nuclei scattering calculations were performed in the static-exchange and static-exchange plus polarization approximations for energies up to 15 eV. In our calculations with polarization effects, we found a π* shape resonance at around 2.22 eV and a broad structure associated to a σ* shape resonance at around 7 eV. The low-lying resonance was assigned to the electron capture by the two-fold degenerate π* orbital of the E symmetry of C3v group; the second was assigned to a σ* shape resonance in the A1 symmetry. We compared our cross sections with theoretical results and experimental data available in the literature, and in general we found good agreement for the positions of the two resonances. Contribution to the Topical Issue: "Low Energy Positron and Electron Interactions", edited by James Sullivan, Ron White, Michael Bromley, Ilya Fabrikant, and David Cassidy.

Assignments of /sup 1/H nuclear magnetic resonances of the cystyl, asparaginyl, and aromatic residues of arginine vasopressin in D/sub 2/O. A comparison with lysine vasopressin and oxytocin in terms of solution conformation

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

Wyssbrod, H.R.; Fischman, A.J.; Live, D.H.

1979-07-18

The resonances of the C/sup ..cap alpha../ and C/sup ..beta../ protons of the cystyl, asparaginyl, and aromatic residues of (8-arginine)vasopressin (AVP) in D/sub 2/O at pD 3.8 and 20/sup 0/C were assigned in a rigorous manner by the use of isotopic isomers of AVP that contain specific replacements of protons by deuterons and by comparison of /sup 1/H NMR characteristics of AVP to those of (8-lysine)vasopressin (LVP) and oxytocin (OT). Although there is extensive overlap of resonances of C/sup ..beta../ protons even at 360 MHz, all of the chemical shifts of these protons and most of the couplings between themmore » and their vicinal C/sup ..cap alpha../ protons could be determined, at least to a first approximation. It was concluded that the cyclic moieties (residues 1-6) of AVP, LVP, and OT possess essentially the same overall backbone conformation, and that the side-chain conformation - or rotamer populations - about the C/sup ..cap alpha../-C/sup ..beta../ bonds of the cystyl residue (positions 1 and 6), the tyrosyl residue (position 2), and the asparaginyl residue (position 5) are similar. This study indicates that selective replacements of C/sup ..beta../ protons by deuterons are necessary to improve the accuracy of coupling constants extracted from 360-MHz spectra of a AVP for use in conformational analysis.« less

Empirical Equation Based Chirality (n, m) Assignment of Semiconducting Single Wall Carbon Nanotubes from Resonant Raman Scattering Data

PubMed Central

Arefin, Md Shamsul

2012-01-01

This work presents a technique for the chirality (n, m) assignment of semiconducting single wall carbon nanotubes by solving a set of empirical equations of the tight binding model parameters. The empirical equations of the nearest neighbor hopping parameters, relating the term (2n− m) with the first and second optical transition energies of the semiconducting single wall carbon nanotubes, are also proposed. They provide almost the same level of accuracy for lower and higher diameter nanotubes. An algorithm is presented to determine the chiral index (n, m) of any unknown semiconducting tube by solving these empirical equations using values of radial breathing mode frequency and the first or second optical transition energy from resonant Raman spectroscopy. In this paper, the chirality of 55 semiconducting nanotubes is assigned using the first and second optical transition energies. Unlike the existing methods of chirality assignment, this technique does not require graphical comparison or pattern recognition between existing experimental and theoretical Kataura plot. PMID:28348319

CHARACTERIZATION OF METABOLITES IN SMALL FISH BIOFLUIDS AND TISSUES BY NMR SPECTROSCOPY

EPA Science Inventory

Nuclear magnetic resonance (NMR) spectroscopy has been utilized for assessing ecotoxicity in small fish models by means of metabolomics. Two fundamental challenges of NMR-based metabolomics are the detection limit and characterization of metabolites (or NMR resonance assignments...

Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

PubMed

Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

2015-10-01

Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous.

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

Characterization of active phosphorus surface sites at synthetic carbonate-free fluorapatite using single-pulse 1H, 31P, and 31P CP MAS NMR.

PubMed

Jarlbring, Mathias; Sandström, Dan E; Antzutkin, Oleg N; Forsling, Willis

2006-05-09

The chemically active phosphorus surface sites defined as PO(x), PO(x)H, and PO(x)H2, where x = 1, 2, or 3, and the bulk phosphorus groups of PO4(3-) at synthetic carbonate-free fluorapatite (Ca5(PO4)3F) have been studied by means of single-pulse 1H,31P, and 31P CP MAS NMR. The changes in composition and relative amounts of each surface species are evaluated as a function of pH. By combining spectra from single-pulse 1H and 31P MAS NMR and data from 31P CP MAS NMR experiments at varying contact times in the range 0.2-3.0 ms, it has been possible to distinguish between resonance lines in the NMR spectra originating from active surface sites and bulk phosphorus groups and also to assign the peaks in the NMR spectra to the specific phosphorus species. In the 31P CP MAS NMR experiments, the spinning frequency was set to 4.2 kHz; in the single-pulse 1H MAS NMR experiments, the spinning frequency was 10 kHz. The 31P CP MAS NMR spectrum of fluorapatite at pH 5.9 showed one dominating resonance line at 2.9 ppm assigned to originate from PO4(3-) groups and two weaker shoulder peaks at 5.4 and 0.8 ppm which were assigned to the unprotonated PO(x) (PO, PO2-, and PO3(2-)) and protonated PO(x)H (PO2H and PO3H-) surface sites. At pH 12.7, the intensity of the peak representing unprotonated PO(x) surface sites has increased 1.7% relative to the bulk peak, while the intensity of the peaks of the protonated species PO(x)H have decreased 1.4% relative to the bulk peak. At pH 3.5, a resonance peak at -4.5 ppm has appeared in the 31P CP MAS NMR spectrum assigned to the surface species PO(x)H2 (PO3H2). The results from the 1H MAS and 31P CP MAS NMR measurements indicated that H+, OH-, and physisorbed H2O at the surface were released during the drying process at 200 degrees C.

Bridge over troubled proline: assignment of intrinsically disordered proteins using (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H experiments concomitantly with HNCO and i(HCA)CO(CA)NH.

PubMed

Hellman, Maarit; Piirainen, Henni; Jaakola, Veli-Pekka; Permi, Perttu

2014-01-01

NMR spectroscopy is by far the most versatile and information rich technique to study intrinsically disordered proteins (IDPs). While NMR is able to offer residue level information on structure and dynamics, assignment of chemical shift resonances in IDPs is not a straightforward process. Consequently, numerous pulse sequences and assignment protocols have been developed during past several years, targeted especially for the assignment of IDPs, including experiments that employ H(N), H(α) or (13)C detection combined with two to six indirectly detected dimensions. Here we propose two new HN-detection based pulse sequences, (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H, that provide correlations with (1)H(N)(i - 1), (13)C'(i - 1) and (15)N(i), and (1)H(N)(i + 1), (13)C'(i) and (15)N(i) frequencies, respectively. Most importantly, they offer sequential links across the proline bridges and enable filling the single proline gaps during the assignment. We show that the novel experiments can efficiently complement the information available from existing HNCO and intraresidual i(HCA)CO(CA)NH pulse sequences and their concomitant usage enabled >95 % assignment of backbone resonances in cytoplasmic tail of adenosine receptor A2A in comparison to 73 % complete assignment using the HNCO/i(HCA)CO(CA)NH data alone.

3μm - 1.6μm Double Resonance Spectroscopy of CH_4

NASA Astrophysics Data System (ADS)

Schwartz, George; Belaas, Erik; Yang, Shaoyue; Lehmann, Kevin

2016-06-01

The Near-IR Spectrum of CH_4 is dense with many overlapping bands that perturb each other by vibrational and ro-vibrational interactions. Assignments of the individual lines are needed in order to simulate the spectrum as a function of pressure and temperature, as needed in the search for CH_4 in extrasolar planets. Both the group at the University College, London^1 and that at the University of Reins^2 have produced theoretical spectra that allows simulation up to the high temperatures expected on ``Hot Jupiters''. The accuracy of these theoretical spectra need to be further tested. Because CH_4 is a light spherical top, assignment of its perturbed spectra is a formable challenge as none of the lines allowed in the rigid rotor approximation have ground vibrational state combination differences. We are using IR-IR double resonance to observe modulation in the strength of near-IR absorption caused by a modulation of a 3 μm OPO beam that is tuned to a particular transition in the C-H stretching fundamental of CH_4. This produces V-type double resonance transitions (which share the lower state with the pump transition), which provides firm assignments for lines normally observed in absorption in the near-IR. We also observe sequential double resonance which reveals transitions that have a known rotational level of the ν_3 fundamental as the lower state and reaches final states in the 9000 cm-1 spectral region. These are states of A, E, F_1 vibrational symmetries which are forbidden in transitions from the ground vibrational state. These 3 level double resonance transitions are Doppler Free and have a linewidth of ˜10 MHz due to a combination of near-IR laser jitter and power broadening of the mid-IR transition. We also observed many 4-level double resonance transitions that we have tentatively assigned as arising from the ν_4 fundamental level. These are distinguished from the 3-level double resonance transitions by they being Doppler broadened and having a large phase shift relative to the intensity modulation. 1. S.N. Yurchenko, PNAS 111 9379-83 (2014); 2. M. Rey, JQSRT 18, 207-220 (2015), PCCP 18, 176-189 (2016)

(1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

PubMed

Moro, Sean L; Cocco, Melanie J

2015-10-01

The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.

PubMed

Nakabayashi, Ryo; Sawada, Yuji; Yamada, Yutaka; Suzuki, Makoto; Hirai, Masami Yokota; Sakurai, Tetsuya; Saito, Kazuki

2013-02-05

Phytochemicals containing heteroatoms (N, O, S, and halogens) often have biological activities that are beneficial to humans. Although targeted profiling methods for such phytochemicals are expected to contribute to rapid chemical assignments, thus making phytochemical genomics and crop breeding much more efficient, there are few profiling methods for the metabolites. Here, as an ultrahigh performance approach, we propose a practical profiling method for S-containing metabolites (S-omics) using onions (Allium cepa) as a representative species and (12)C- and (13)C-based mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses by liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FTICR-MS). Use of the ultrahigh quality data from FTICR-MS enabled simplifying the previous methods to determine specific elemental compositions. MS analysis with a resolution of >250,000 full width at half-maximum and a mass accuracy of <1 ppm can distinguish S-containing monoisotopic ions from other ions on the basis of the natural abundance of (32)S and (34)S and the mass differences among the S isotopes. Comprehensive peak picking using the theoretical mass difference (1.99579 Da) between (32)S-containing monoisotopic ions and their (34)S-substituted counterparts led to the assignment of 67 S-containing monoisotopic ions from the (12)C-based MS spectra, which contained 4693 chromatographic ions. The unambiguous elemental composition of 22 ions was identified through comparative analysis of the (12)C- and (13)C-based MS spectra. Finally, of these, six ions were found to be derived from S-alk(en)ylcysteine sulfoxides and glutathione derivatives. This S-atom-driven approach afforded an efficient chemical assignment of S-containing metabolites, suggesting its potential application for screening not only S but also other heteroatom-containing metabolites in MS-based metabolomics.

(n,{gamma}) Experiments on tin isotopes

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

Baramsai, B.; Mitchell, G. E.; Walker, C. L.

2013-04-19

Neutron capture experiments on highly enriched {sup 117,119}Sn isotopes were performed with the DANCE detector array located at the Los Alamos Neutron Science Center. The DANCE detector provides detailed information about the multi-step {gamma}-ray cascade following neutron capture. Analysis of the experimental data provides important information to improve understanding of the neutron capture reaction, including a test of the statistical model, the assignment of spins and parities of neutron resonances, and information concerning the Photon Strength Function (PSF) and Level Density (LD) below the neutron separation energy. Preliminary results for the (n,{gamma}) reaction on {sup 117,119}Sn are presented. Resonance spinsmore » of the odd-A tin isotopes were almost completely unknown. Resonance spins and parities have been assigned via analysis of the multi-step {gamma}-ray spectra and directional correlations.« less

Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Basire, Marie; Mouhat, Félix; Fraux, Guillaume; Bordage, Amélie; Hazemann, Jean-Louis; Louvel, Marion; Spezia, Riccardo; Bonella, Sara; Vuilleumier, Rodolphe

2017-04-01

Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them.

Covariance NMR Processing and Analysis for Protein Assignment.

PubMed

Harden, Bradley J; Frueh, Dominique P

2018-01-01

During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

Conformation-selective resonant photoelectron imaging from dipole-bound states of cold 3-hydroxyphenoxide

NASA Astrophysics Data System (ADS)

Zhu, Guo-Zhu; Huang, Dao-Ling; Wang, Lai-Sheng

2017-07-01

We report a photoelectron imaging and photodetachment study of cryogenically cooled 3-hydroxyphenoxide (3HOP) anions, m-HO(C6H4)O-. In a previous preliminary study, two conformations of the cold 3HOP anions with different dipole bound states were observed [D. L. Huang et al., J. Phys. Chem. Lett. 6, 2153 (2015)]. Five near-threshold vibrational resonances were revealed in the photodetachment spectrum from the dipole-bound excited states of the two conformations. Here, we report a more extensive investigation of the two conformers with observation of thirty above-threshold vibrational resonances in a wide spectral range between 18 850 and 19 920 cm-1 (˜1000 cm-1 above the detachment thresholds). By tuning the detachment laser to the vibrational resonances in the photodetachment spectrum, high-resolution conformation-selective resonant photoelectron images are obtained. Using information of the autodetachment channels and theoretical vibrational frequencies, we are able to assign the resonant peaks in the photodetachment spectrum: seventeen are assigned to vibrational levels of anti-3HOP, eight to syn-3HOP, and five to overlapping vibrational levels of both conformers. From the photodetachment spectrum and the conformation-selective resonant photoelectron spectra, we have obtained fourteen fundamental vibrational frequencies for the neutral syn- and anti-m-HO(C6H4)Oṡ radicals. The possibility to produce conformation-selected neutral beams using resonant photodetachment via dipole-bound excited states of anions is discussed.

Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states of bromobenzene and the S{sub 0} and D{sub 0}{sup +} states of iodobenzene

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

Andrejeva, Anna; Tuttle, William D.; Harris, Joe P.

2015-12-28

We report vibrationally resolved spectra of the S{sub 1}←S{sub 0} transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h{sub 5} as well as its perdeuterated isotopologue, bromobenzene-d{sub 5}. The form of the vibrational modes between the isotopologues and also between the S{sub 0} and S{sub 1} electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S{sub 1} spectra are discussed. Additionally, themore » vibrations in the ground state cation, D{sub 0}{sup +}, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S{sub 0} and D{sub 0}{sup +} states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states, gaining insight into vibrational activity and vibrational couplings.« less

Fingerprinting analysis of Saposhnikovia divaricata using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography.

PubMed

Xin, Yue-Yang; Deng, An-Jun; Du, Guan-Hua; Zhang, Jin-Lan; Qin, Hai-Lin

2010-09-01

The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar and polar extracts (control substance for plant drug [CSPD] A and B) from the roots of 12 specimens of Saposhnikovia divaricata (Turcz.) Schischk were achieved with Fourier Transform (FT)-NMR spectrometer and assigned by comparison to each other and to the (1)H NMR spectra of the isolated individual compounds. These fingerprints were found to be uniform in terms of the specificity for the implication of all 12 specimens being systematically of the same origin. The uniformity was further affirmed by high performance liquid chromatography (HPLC), which also revealed exactly identical specificity for the identified S. divaricata species with the (1)H NMR appearances of corresponding CSPD on the part of the composition of characteristic constituents when comparing to corresponding individual compounds. This investigation unambiguously shows that the specific signals from the chemotaxonomically significant compounds of chromones and coumarins in S. divaricata are exhibited distinctively in the composite features of both (1)H NMR fingerprints and HPLC profiles. The (1)H NMR and HPLC profiles established can successfully be used as reference for the authentication of the origin of S. divaricata species as well as for chemotaxonomic studies.

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

PubMed

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

Vibrational Spectroscopy of BENZENE-(WATER)_N Clusters with N=6,7

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Kusaka, Ryoji; Walsh, Patrick S.; Zwier, Timothy S.

2015-06-01

The investigation of benzene-water clusters (Bz-(H_2O)_n) provides insight into the relative importance π-hydrogen bond interactions in cluster formation. Taking advantage of the higher resolution of current IR sources, isomer-specific resonant ion-dip infrared (RIDIR) spectra were recorded in the OH stretch region (3000-3750 cm-1). A local mode Hamiltonian for describing the OH stretch vibrations of water clusters is applied to Bz-(H_2O)_6 and Bz-(H_2O)_7 and compared with the RIDIR spectra. These clusters are the smallest water clusters in which three-dimensional H-bonded networks containing three-coordinate water molecules begin to be formed, and are therefore particularly susceptible to re-ordering or re-shaping in response to the presence of a benzene molecule. The spectrum of Bz-(H_2O)_6 is assigned to an inverted book structure while the major conformer of Bz-(H_2O)_7 is assigned to an S_4-derived inserted cubic structure in which the benzene occupies one corner of the cube. The local mode model is used to extract monomer Hamiltonians for individual water molecules, including stretch-bend Fermi resonance and intra-monomer couplings. The monomer Hamiltonians divide into sub-groups based on their local H-bonding architecture (DA, DDA, DAA) and the nature of their interaction with benzene.

Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry.

PubMed

Nakabayashi, Ryo; Sawada, Yuji; Aoyagi, Morihiro; Yamada, Yutaka; Hirai, Masami Yokota; Sakurai, Tetsuya; Kamoi, Takahiro; Rowan, Daryl D; Saito, Kazuki

2016-02-01

The chemical assignment of metabolites is crucial to understanding the relation between food composition and biological activity. This study was designed to detect and chemically assign sulfur-containing metabolites by using LC-Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) in Allium plants. Ultrahigh resolution (>250,000 full width at half-maximum) and mass accuracy (<1 mDa) by FTICR-MS allowed us to distinguish ions containing sulfur isotopes ((32)S and (34)S). Putative 69 S-containing monoisotopic ions (S-ions) were extracted from the metabolome data of onion (Allium cepa), green onion (Allium fistulosum), and garlic (Allium sativum) on the basis of theoretical mass differences between (32)S-ions and their (34)S-substituted counterparts and on the natural abundance of (34)S. Eight S-ions were chemically assigned by using the reference data according to the guidelines of the Metabolomics Standards Initiative. Three ions detected in garlic were assigned as derived from the isomers γ-glutamyl-S-1-propenylcysteine and γ-glutamyl-S-2-propenylcysteine and as S-2-propenylmercaptoglutathione on the basis of differences in key product ions identified in reference tandem MS spectra. The ability to discriminate between such geometric isomers will be extremely useful for the chemical assignment of unknown metabolites in MS-based metabolomics. © 2016 American Society for Nutrition.

Hyperpolarized [U-(2) H, U-(13) C]Glucose reports on glycolytic and pentose phosphate pathway activity in EL4 tumors and glycolytic activity in yeast cells.

PubMed

Timm, Kerstin N; Hartl, Johannes; Keller, Markus A; Hu, De-En; Kettunen, Mikko I; Rodrigues, Tiago B; Ralser, Markus; Brindle, Kevin M

2015-12-01

A resonance at ∼181 ppm in the (13) C spectra of tumors injected with hyperpolarized [U-(2) H, U-(13) C]glucose was assigned to 6-phosphogluconate (6PG), as in previous studies in yeast, whereas in breast cancer cells in vitro this resonance was assigned to 3-phosphoglycerate (3PG). These peak assignments were investigated here using measurements of 6PG and 3PG (13) C-labeling using liquid chromatography tandem mass spectrometry (LC-MS/MS) METHODS: Tumor-bearing mice were injected with (13) C6 glucose and the (13) C-labeled and total 6PG and 3PG concentrations measured. (13) C MR spectra of glucose-6-phosphate dehydrogenase deficient (zwf1Δ) and wild-type yeast were acquired following addition of hyperpolarized [U-(2) H, U-(13) C]glucose and again (13) C-labeled and total 6PG and 3PG were measured by LC-MS/MS RESULTS: Tumor (13) C-6PG was more abundant than (13) C-2PG/3PG and the resonance at ∼181 ppm matched more closely that of 6PG. (13) C MR spectra of wild-type and zwf1Δ yeast cells showed a resonance at ∼181 ppm after labeling with hyperpolarized [U-(2) H, U-(13) C]glucose, however, there was no 6PG in zwf1Δ cells. In the wild-type cells 3PG was approximately four-fold more abundant than 6PG CONCLUSION: The resonance at ∼181 ppm in (13) C MR spectra following injection of hyperpolarized [U-(2) H, U-(13) C]glucose originates predominantly from 6PG in EL4 tumors and 3PG in yeast cells. © 2014 Wiley Periodicals, Inc.

Laser-polarized xenon-129 magnetic resonance spectroscopy and imaging. The development of a method for in vivo perfusion measurement

NASA Astrophysics Data System (ADS)

Rosen, Matthew Scot

2001-07-01

This thesis presents in vivo nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) studies with laser-polarized 129Xe delivered to living rats by inhalation and transported to tissue via blood flow. The results presented herein include the observation, assignment, and dynamic measurement of 129Xe resonances in the brain and body, the first one- and two-dimensional chemical-shift-resolved images of 129Xe in blood, tissue, and gas in the thorax, and the first images of 129Xe in brain tissue. These results establish that laser-polarized 129Xe can be used as a magnetic resonance tracer in vivo. NMR resonances at 0, 191, 198, and 209 ppm relative to the 129 Xe gas resonance are observed in the rat thorax and assigned to 129Xe in gas, fat, tissue, and blood respectively. Resonances at 189, 192, 195, 198, and 209 ppm are observed in the brain, and the 195 and 209 ppm resonances are assigned to 129Xe in grey matter, and blood, respectively. The design and construction of a laser-polarized 129Xe production and delivery system is described. This system produces liter-volumes of laser- polarized 129Xe by spin-exchange optical- pumping. It represented an order of magnitude increase over previously reported production volumes of polarized 129Xe. At approximately 3-7% polarization, 157 cc-atm of xenon is produced and stored as ice every 5 minutes. This reliable, effective, and simple production method for large volumes of 129Xe can be applied to other areas of research involving the use of laser-polarized noble gases. A model of the in vivo transport of laser polarized 129Xe to tissue under realistic experimental NMR conditions is described. Appropriate control of the NMR parameters is shown to allow tissue perfasion and 129Xe tissue T1 to be extracted from measurement of the steady-state 129Xe tissue signal. In vivo rodent 129Xe NMR results are used to estimate the signal-to-noise ratio of this technique, and an inhaled 30% xenon/70% O2 mixture polarized to 5% is estimated to provide sufficient SNR in rodent grey matter. Application to the measurement of regional cerebral blood flow and neuronal activation is discussed.

Prostate Postbrachytherapy Seed Distribution: Comparison of High-Resolution, Contrast-Enhanced, T1- and T2-Weighted Endorectal Magnetic Resonance Imaging Versus Computed Tomography: Initial Experience

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

Bloch, B. Nicolas; Department of Radiology, General Hospital Vienna, Medical University Vienna, Vienna; Lenkinski, Robert E.

2007-09-01

Purpose: To compare contrast-enhanced, T1-weighted, three-dimensional magnetic resonance imaging (CEMR) and T2-weighted magnetic resonance imaging (T2MR) with computed tomography (CT) for prostate brachytherapy seed location for dosimetric calculations. Methods and Materials: Postbrachytherapy prostate MRI was performed on a 1.5 Tesla unit with combined surface and endorectal coils in 13 patients. Both CEMR and T2MR used a section thickness of 3 mm. Spiral CT used a section thickness of 5 mm with a pitch factor of 1.5. All images were obtained in the transverse plane. Two readers using CT and MR imaging assessed brachytherapy seed distribution independently. The dependency of datamore » read by both readers for a specific subject was assessed with a linear mixed effects model. Results: The mean percentage ({+-} standard deviation) values of the readers for seed detection and location are presented. Of 1205 implanted seeds, CEMR, T2MR, and CT detected 91.5% {+-} 4.8%, 78.5% {+-} 8.5%, and 96.1% {+-} 2.3%, respectively, with 11.8% {+-} 4.5%, 8.5% {+-} 3.5%, 1.9% {+-} 1.0% extracapsular, respectively. Assignment to periprostatic structures was not possible with CT. Periprostatic seed assignments for CEMR and T2MR, respectively, were as follows: neurovascular bundle, 3.5% {+-} 1.6% and 2.1% {+-} 0.9%; seminal vesicles, 0.9% {+-} 1.8% and 0.3% {+-} 0.7%; periurethral, 7.1% {+-} 3.3% and 5.8% {+-} 2.9%; penile bulb, 0.6% {+-} 0.8% and 0.3% {+-} 0.6%; Denonvillier's Fascia/rectal wall, 0.5% {+-} 0.6% and 0%; and urinary bladder, 0.1% {+-} 0.3% and 0%. Data dependency analysis showed statistical significance for the type of imaging but not for reader identification. Conclusion: Both enumeration and localization of implanted seeds are readily accomplished with CEMR. Calculations with MRI dosimetry do not require CT data. Dose determinations to specific extracapsular sites can be obtained with MRI but not with CT.« less

Study of inelastic decay amplitudes in /sup 51/Mn

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

Whatley, K.M.

1982-01-01

Detailed angular distribution measurments on inelastically scattered protons and de-excitation ..gamma..-rays in the /sup 50/Cr(p,p') and /sup 50/Cr(p,p'..gamma..) reactions were performed for 107 resonances in /sup 51/Mn in the proton energy range 3.0-4.4 MeV. An overall resolution of 425 eV was obtained with the tandem Van de Graaff accelerator and the high resolution system at the Triangle Universities Nuclear Laboratory. Spin and parity assignments for the 107 resonances studied were as follows: 1/2/sup +/ (4); 1/2/sup -/ (6); 3/2/sup -/ (30); 3/2/sup +/ (20); 5/2/sup +/ (38); 5/2/sup -/ (7); 7/2/sup +/ (1); and 9/2/sup +/ (1). Mixing ratios formore » the inelastic decay amplitudes were uniquely determined for all resonances except those assigned J/sup ..pi../ = 1/2/sup +/, 1/2/sup -/, or 3/2/sup +/. For 1/2/sup +/ and 1/2/sup -/ resonances there is only one open decay channel. For 3/2/sup +/ resonances, insufficient information is obtained from this experiment to determine a unique solution for the mixing ratios. Statistical studies were performed on the set of 3/2/sup -/ resonances and on the set of 5/2/sup +/ resonances. Strong channel-channel correlations were observed in the distributions of the reduced widths and the reduced width amplitudes for 5/2/sup +/ resonances. The existence of such correlations is a violation of the extreme statistical model. The present results agree with the reduced width amplitude distribution of Krieger and Porter which includes channel-channel correlations.« less

Structure of 10 N in 9 C+p resonance scattering

DOE PAGES

Hooker, J.; Rogachev, G. V.; Goldberg, V. Z.; ...

2017-03-17

We studied the structure of exotic nucleus 10N using 9C+p resonance scattering. Two ℓ=0 resonances were found to be the lowest states in 10N. Furthermore, the ground state of 10N is unbound with respect to proton decay by 2.2(2) or 1.9(2) MeV depending on the 2 -or 1 -spin-parity assignment, and the first excited state is unbound by 2.8(2) MeV.

Anion states of η4-polyene iron tricarbonyl complexes

NASA Astrophysics Data System (ADS)

Olthoff, J. K.; Moore, J. H.; Tossell, J. A.; Giordan, J. C.; Baerends, E. J.

1987-12-01

Attachment energies of low energy electrons to Fe(CO)5 and to η4 complexes of 1,3-butadiene, 1,3-cyclohexadiene, cyclooctatetraene, and cyclobutadiene with Fe(CO3) have been determined by electron transmission spectroscopy. The spectrum of Fe(CO)5 is similar to that of Cr(CO)6, showing an anion resonance near threshold assigned to predominantly Fe3d orbitals and two resonances between 1 and 3 eV assigned to predominantly COπ* orbitals.The diene complexes show threshold features similar to Fe(CO)5, COπ* resonances around 2 eV, and one or more diene π* resonances. The resonances from the lowest π* orbitals of butadiene, cyclohexadiene, and cyclooctatetraene are little different in the free dienes and the complexes, but higher π* orbitals are substantially destabilized in the complexes, consistent with qualitative symmetry arguments. In the cyclobutadiene complex the π*3 orbital of cyclobutadiene is strongly destabilized by interaction with the Fe3d, giving a resonant feature at 1.2 eV. Dissociative attachment of electrons by the iron tricarbonyl complexes has been observed mass spectrometrically. The phenomenon is observed for electrons of energy less than 2 eV and results primarily in the loss of CO. For the cyclobutadiene complex, however, the attachment of 0 eV electrons results in a complex chemical process leading to the ejection of C2.

MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

PubMed

MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

2013-01-01

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

Probing cis-trans isomerization in the S{sub 1} state of C{sub 2}H{sub 2} via H-atom action and hot band-pumped IR-UV double resonance spectroscopies

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

Changala, P. Bryan; Baraban, Joshua H.; Field, Robert W., E-mail: rwfield@mit.edu

2015-08-28

We report novel experimental strategies that should prove instrumental in extending the vibrational and rotational assignments of the S{sub 1} state of acetylene, C{sub 2}H{sub 2}, in the region of the cis-trans isomerization barrier. At present, the assignments are essentially complete up to ∼500 cm{sup −1} below the barrier. Two difficulties arise when the assignments are continued to higher energies. One is that predissociation into C{sub 2}H + H sets in roughly 1100 cm{sup −1} below the barrier; the resulting quenching of laser-induced fluorescence (LIF) reduces its value for recording spectra in this region. The other difficulty is that tunnelingmore » through the barrier causes a staggering in the K-rotational structure of isomerizing vibrational levels. The assignment of these levels requires data for K values up to at least 3. Given the rotational selection rule K′ − ℓ{sup ′′} = ± 1, such data must be obtained via excited vibrational levels of the ground state with ℓ{sup ′′} > 0. In this paper, high resolution H-atom resonance-enhanced multiphoton ionization spectra are demonstrated to contain predissociated bands which are almost invisible in LIF spectra, while preliminary data using a hyperthermal pulsed nozzle show that ℓ{sup ′′} = 2 states can be selectively populated in a jet, giving access to K′ = 3 states in IR-UV double resonance.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE PAGES

Zinke, Maximilian; Fricke, Pascal; Samson, Camille; ...

2017-07-07

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

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

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Nuclear magnetic resonance spectroscopy in the structure elucidation and biosynthesis of natural products

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

Meksuriyen, D.

1988-01-01

Examination of a chloroform extract of Dracaena loureiri Gagnep (Agavaceae), a Thia medicinal plant possessing antibacterial activity, has led to the isolation of fifteen flavenoids. The biogenic relationships among these flavenoids isolated were briefly discussed. Definition of the skeleton and the unambiguous assignment of all of the protons of the isolates was achieved through extensive 2D-homonuclear chemical shift correlation, nuclear Overhauser effect (NOE) difference spectroscopy and 2D-NOE experiments. The {sup 1}H and {sup 13}C NMR spectra of staurosporine, a potent biologically active agent from Streptomyces staurosporeus, were unambiguously assigned by using 2D homonuclear chemical shift correlation, NOE, {sup 1}H-detected heteronuclearmore » multiple-quantum coherence via direct coupling and via multiple-bond coupling for resonance assignments of protonated and nonprotonated carbons, respectively. S. Staurosporeus was found to utilize endogenous and exogenous D- and L-isomers of trytophan in the production of staurosporine. The biosynthesis of staurosporine was examined by employing carbon-14, tritium, and carbon-13 labeled precursors.« less

Quantum coherence selective 2D Raman–2D electronic spectroscopy

PubMed Central

Spencer, Austin P.; Hutson, William O.; Harel, Elad

2017-01-01

Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

Resonant photoluminescence studies of carrier localisation in c-plane InGaN/GaN quantum well structures

NASA Astrophysics Data System (ADS)

Blenkhorn, W. E.; Schulz, S.; Tanner, D. S. P.; Oliver, R. A.; Kappers, M. J.; Humphreys, C. J.; Dawson, P.

2018-05-01

In this paper we report on changes in the form of the low temperature (12 K) photoluminescence spectra of an InGaN/GaN quantum well structure as a function of excitation photon energy. As the photon energy is progressively reduced we observe at a critical energy a change in the form of the spectra from one which is determined by the occupation of the complete distribution of hole localisation centres to one which is determined by the resonant excitation of specific localisation sites. This change is governed by an effective mobility edge whereby the photo-excited holes remain localised at their initial energy and are prevented from scattering to other localisation sites. This assignment is confirmed by the results of atomistic tight binding calculations which show that the wave function overlap of the lowest lying localised holes with other hole states is low compared with the overlap of higher lying hole states with other higher lying hole states.

Chemical characterization of a prominent phosphomonoester resonance from mammalian brain. 31P and 1H NMR analysis at 4.7 and 14.1 tesla

NASA Astrophysics Data System (ADS)

Pettegrew, J. W.; Kopp, S. J.; Dadok, J.; Minshew, N. J.; Feliksik, J. M.; Glonek, T.; Cohen, M. M.

A prominent 31P NMR resonance at 3.84 ppm in mammalian brain has been identified as ethanolamine phosphate. The identification was based on 1H and 31P NMR findings (including pH titrations) at 4.7 and 14.1 T, as well as thin-layer chromatography studies. We previously incorrectly assigned the 3.84 ppm resonance to ribose-5-phosphate. The incorrect assignment occurred because the two compounds have very similar 31P chemical shifts, and because we did not carefully consider the effects of counter ions and ionic strengths when interpreting the 31P chemical shifts. In separate preliminary studies we have demonstrated ethanolamine phosphate to be high in immature developing brain and in the degenerating brain of Alzheimer's and Huntington's disease patients. Ethanolamine phosphate may therefore serve as a sensitive marker of membrane phospholipid turnover for both in vitro and in vivo31P NMR studies.

Double cross-polarization MAS NMR in the assignment of abundant-spin resonances: ¹⁹F-{²⁹Si}-¹⁹F FBCP/MAS NMR of fluoride ions incorporated in calcium silicate hydrate (C-S-H) phases.

PubMed

Tran, Thuan T; Bildsøe, Henrik; Jakobsen, Hans J; Skibsted, Jørgen

2012-08-01

A new version of the double cross-polarization MAS NMR experiment, which transfers polarization Forth and Back (FBCP) between high- and low-γ spin nuclei, is presented. The pulse sequence is demonstrated by ¹⁹F-{²⁹Si}-¹⁹F and ¹⁹F-{¹³C}-¹⁹F FBCP NMR spectra of a mixture of cuspidine (Ca₄Si₂O₇F₂) and Teflon (-CF₂-)(n). The experiment is useful for assignment of the high-γ spin resonances, as demonstrated by ¹⁹F-{²⁹Si}-¹⁹F FBCP NMR of a fluoride-containing calcium-silicate-hydrate (C-S-H) phase, where the ¹⁹F resonance from fluoride ions incorporated in the interlayer structure of the C-S-H phase is identified. Copyright © 2012 Elsevier Inc. All rights reserved.

iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins

NASA Astrophysics Data System (ADS)

Feuerstein, Sophie; Plevin, Michael J.; Willbold, Dieter; Brutscher, Bernhard

2012-01-01

An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the 1H- 15N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.

1H, 15N and 13C backbone and side-chain resonance assignments of a family 32 carbohydrate-binding module from the Clostridium perfringens NagH.

PubMed

Grondin, Julie M; Chitayat, Seth; Ficko-Blean, Elizabeth; Boraston, Alisdair B; Smith, Steven P

2012-10-01

The Gram-positive anaerobe Clostridium perfringens is an opportunistic bacterial pathogen that secretes a battery of enzymes involved in glycan degradation. These glycoside hydrolases are thought to be involved in turnover of mucosal layer glycans, and in the spread of major toxins commonly associated with the development of gastrointestinal diseases and gas gangrene in humans. These enzymes employ multi-modularity and carbohydrate-binding function to degrade extracellular eukaryotic host sugars. Here, we report the full (1)H, (15)N and (13)C chemical shift resonance assignments of the first family 32 carbohydrate-binding module from NagH, a secreted family 84 glycoside hydrolase.

Intensity enhancement and selective detection of proximate solvent molecules by molecular near-field effect in resonance hyper-Raman scattering

NASA Astrophysics Data System (ADS)

Shimada, Rintaro; Kano, Hideaki; Hamaguchi, Hiro-o.

2008-07-01

A new molecular phenomenon associated with resonance hyper-Raman (HR) scattering in solution has been discovered. Resonance HR spectra of all-trans-β-carotene and all-trans-lycopene in various solvents exhibited several extra bands that were not assignable to the solute but were unequivocally assigned to the solvents. Neat solvents did not show detectable HR signals under the same experimental conditions. Similar experiments with all-trans-retinal did not exhibit such enhancement either. All-trans-β-carotene and all-trans-lycopene have thus been shown to induce enhanced HR scattering of solvent molecules through a novel molecular effect that is not associated with all-trans-retinal. We call this new effect the "molecular near-field effect." In order to explain this newly found effect, an extended vibronic theory of resonance HR scattering is developed where the vibronic interaction including the proximate solvent molecule (intermolecular vibronic coupling) is explicitly introduced in the solute hyperpolarizability tensor. The potential of "molecular near-field HR spectroscopy," which selectively detects molecules existing in the close vicinity of a HR probe in complex chemical or biological systems, is discussed.

Photoassociation studies of ultracold NaCs from the Cs 6(2)P(3/2) asymptote.

PubMed

Wakim, A; Zabawa, P; Bigelow, N P

2011-11-14

A combination of pulsed depletion spectroscopy and photoassociation spectroscopy is utilized to assign photoassociation spectra of NaCs. These methods investigate the ab initio Ω = 2 potential energy curve and indicate a previously unknown avoided crossing between the (3)Ω = 1 and (4)Ω = 1 electronic states. We present rotational assignments of deeply bound singlet ground state molecules, an improved C(6) coefficient for the (4)Ω = 1 and assignments for all twenty-three photoassociation resonances detuned from the Cs 6(2)P(3/2) asymptote.

Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions.

PubMed

Castillo, Andrés M; Bernal, Andrés; Patiny, Luc; Wist, Julien

2015-08-01

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self-consistent peak-picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto-assignment routine used is based on branch-and-bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web-based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

PubMed

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a larger number of residues. On the other hand, when there are multiple equally good assignments that are significantly different from each other, the modified NSGA-II is less efficient than MC/SA in finding all the solutions. This problem is solved by a combined NSGA-II/MC algorithm, which appears to have the advantages of both NSGA-II and MC/SA. This combination algorithm is robust for the three most difficult chemical shift datasets examined here and is expected to give the highest-quality de novo assignment of challenging protein NMR spectra.

United States Air Force Summer Faculty Research Program (1983). Program Management Report.

DTIC Science & Technology

1983-12-01

845-5011 Dr. John Eoll Degree: Ph.D., Astrophysics, 1976 Assistant Professor Specialty: Radiaton Transport , Fluid Lernir-Rhyne College Dynamics...Applications Newark, DE 19711 Assigned: RADC (302) 738-8173 Dr. Gregory Jones Degree: Ph.D., Mathematics, 1972 Associate Professor Specialty: Computability...1965 Associate Professor Specialty: Magnetic Resonance, University of Dayton Transport Properties Physics Department Assigned: ML Dayton, OH 45469 5

NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

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

Vourtsis, Dionysios J.; Chasapis, Christos T.; Pairas, George

2014-07-18

Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successfulmore » overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.« less

MEMS-Based Force-Detected Nuclear Magnetic Resonance (FDNMR) Spectrometer

NASA Technical Reports Server (NTRS)

Lee, Choonsup; Butler, Mark C.; Elgammal, Ramez A.; George, Thomas; Hunt, Brian; Weitekamp, Daniel P.

2006-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy allows assignment of molecular structure by acquiring the energy spectrum of nuclear spins in a molecule, and by interpreting the symmetry and positions of resonance lines in the spectrum. As such, NMR has become one of the most versatile and ubiquitous spectroscopic methods. Despite these tremendous successes, NMR experiments suffer from inherent low sensitivity due to the relatively low energy of photons in the radio frequency (rt) region of the electromagnetic spectrum. Here, we describe a high-resolution spectroscopy in samples with diameters in the micron range and below. We have reported design and fabrication of force-detected nuclear magnetic resonance (FDNMR).

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

Monitoring of pistachio (Pistacia Vera) ripening by high field nuclear magnetic resonance spectroscopy.

PubMed

Sciubba, Fabio; Avanzato, Damiano; Vaccaro, Angela; Capuani, Giorgio; Spagnoli, Mariangela; Di Cocco, Maria Enrica; Tzareva, Irina Nikolova; Delfini, Maurizio

2017-04-01

The metabolic profiling of pistachio (Pistacia vera) aqueous extracts from two different cultivars, namely 'Bianca' and 'Gloria', was monitored over the months from May to September employing high field NMR spectroscopy. A large number of water-soluble metabolites were assigned by means of 1D and 2D NMR experiments. The change in the metabolic profiles monitored over time allowed the pistachio development to be investigated. Specific temporal trends of amino acids, sugars, organic acids and other metabolites were observed and analysed by multivariate Partial Least Squares (PLS) analysis. Statistical analysis showed that while in the period from May to September there were few differences between the two cultivars, the ripening rate was different.

Backbone dynamics of a model membrane protein: assignment of the carbonyl carbon /sup 13/C NMR resonances in detergent-solubilized M13 coat protein

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

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

The major coat protein of the filamentous bacteriophage M13 is a 50-residue amphiphilic polypeptide which is inserted, as an integral membrane-spanning protein, in the inner membrane of the Escherichia coli host during infection. /sup 13/C was incorporated biosynthetically into a total of 23 of the peptide carbonyls using labeled amino acids (alanine, glycine, lysine, phenylalanine, and proline). The structure and dynamics of carbonyl-labeled M13 coat protein were monitored by /sup 13/C nuclear magnetic resonance (NMR) spectroscopy. Assignment of many resonances was achieved by using protease digestion, pH titration, or labeling of the peptide bond with both /sup 13/C and /supmore » 15/N. The carbonyl region of the natural-abundance /sup 13/C NMR spectrum of M13 coat protein in sodium dodecyl sulfate solution shows approximately eight backbone carbonyl resonances with line widths much narrower than the rest. Three of these more mobile residues correspond to assigned peaks (glycine-3, lysine-48, and alanine-49) in the individual amino acid spectra, and another almost certainly arises from glutamic acid-2. A ninth residue, alanine-1, also gives rise to a very narrow carbonyl resonance if the pH is well above or below the pK/sub a/ of the terminal amino group. These data suggest that only about four residues at either end of the protein experience large-amplitude spatial fluctuations; the rest of the molecule is essentially rigid on the time scale of the overall rotational tumbling of the protein-detergent complex. The relative exposure of different regions of detergent-bound protein was monitored by limited digestion with proteinase K. Comparable spectra and digestion patterns were obtained when the protein was solubilized in sodium deoxycholate, suggesting that the coat protein binds both amphiphiles in a similar fashion.« less

Observation of new even-parity states of Sm I by resonance ionization mass spectrometry

NASA Astrophysics Data System (ADS)

Jayasekharan, T.; Razvi, M. A. N.; Bhale, G. L.

1996-04-01

Resonance ionization mass spectrometry is applied to investigate high-lying even-parity states of Sm I. Eighty-six even-parity states of Sm I are discovered in the region 32950-36000 cm -1 . Absolute energies of these states are measured with an uncertainty of +/- 0.3 cm -1 , and total angular momenta are uniquely assigned for most of them.

(1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

PubMed

Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

2016-10-01

The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

Investigation of the thermonuclear 18Ne(α,p)21Na reaction rate via resonant elastic scattering of 21Na + p

NASA Astrophysics Data System (ADS)

Zhang, L. Y.; He, J. J.; Parikh, A.; Xu, S. W.; Yamaguchi, H.; Kahl, D.; Kubono, S.; Mohr, P.; Hu, J.; Ma, P.; Chen, S. Z.; Wakabayashi, Y.; Wang, H. W.; Tian, W. D.; Chen, R. F.; Guo, B.; Hashimoto, T.; Togano, Y.; Hayakawa, S.; Teranishi, T.; Iwasa, N.; Yamada, T.; Komatsubara, T.; Zhang, Y. H.; Zhou, X. H.

2014-01-01

The 18Ne(α,p)21Na reaction is thought to be one of the key breakout reactions from the hot CNO cycles to the rp process in type I x-ray bursts. In this work, the resonant properties of the compound nucleus 22Mg have been investigated by measuring the resonant elastic scattering of 21Na + p. An 89-MeV 21Na radioactive beam delivered from the CNS Radioactive Ion Beam Separator bombarded an 8.8 mg/cm2 thick polyethylene (CH2)n target. The 21Na beam intensity was about 2×105 pps, with a purity of about 70% on target. The recoiled protons were measured at the center-of-mass scattering angles of θc.m.≈175.2∘, 152.2∘, and 150.5∘ by three sets of ΔE-E telescopes, respectively. The excitation function was obtained with the thick-target method over energies Ex(22Mg)=5.5-9.2 MeV. In total, 23 states above the proton-threshold in 22Mg were observed, and their resonant parameters were determined via an R-matrix analysis of the excitation functions. We have made several new Jπ assignments and confirmed some tentative assignments made in previous work. The thermonuclear 18Ne(α,p)21Na rate has been recalculated based on our recommended spin-parity assignments. The astrophysical impact of our new rate has been investigated through one-zone postprocessing x-ray burst calculations. We find that the 18Ne(α,p)21Na rate significantly affects the peak nuclear energy generation rate, reaction fluxes, and onset temperature of this breakout reaction in these astrophysical phenomena.

A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: amyloid fibrils of human CA150.WW2.

PubMed

Becker, Johanna; Ferguson, Neil; Flinders, Jeremy; van Rossum, Barth-Jan; Fersht, Alan R; Oschkinat, Hartmut

2008-08-11

The second WW domain (WW2) of CA150, a human transcriptional activator, forms amyloid fibrils in vitro under physiological conditions. Based on experimental constraints from MAS NMR spectroscopy experiments, alanine scanning and electron microscopy, a structural model of CA150.WW2 amyloid fibrils was calculated earlier. Here, the assignment strategy is presented and suggested as a general approach for proteins that show intermediate line width. The (13)C,(13)C correlation experiments were recorded on fully or partially (13)C-labelled fibrils. The earlier (13)C assignment (26 residues) was extended to 34 of the 40 residues by direct (13)C-excitation experiments by using a deuterated sample that showed strongly improved line width. A 3D HNC-TEDOR (transferred-echo double-resonance) experiment with deuterated CA150.WW2 fibrils yielded 14 amide nitrogen and proton resonance assignments. The obtained chemical shifts were compared with the chemical shifts determined with the natively folded WW domain. TALOS (Torsion angle likelihood obtained from shift and sequence similarity) predictions confirmed that, under physiological conditions, the fibrillar form of CA150.WW2 adopts a significantly different beta structure than the native WW-domain fold.

1H, 15N and 13C resonance assignments for free and IEEVD peptide-bound forms of the tetratricopeptide repeat domain from the human E3 ubiquitin ligase CHIP.

PubMed

Zhang, Huaqun; McGlone, Cameron; Mannion, Matthew M; Page, Richard C

2017-04-01

The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the 1 H, 13 C, and 15 N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.

The BG21 isoform of Golli myelin basic protein is intrinsically disordered with a highly flexible amino-terminal domain.

PubMed

Ahmed, Mumdooh A M; Bamm, Vladimir V; Harauz, George; Ladizhansky, Vladimir

2007-08-28

The genes of the oligodendrocyte lineage (Golli) encode a family of developmentally regulated isoforms of myelin basic protein. The "classic" MBP isoforms arise from transcription start site 3, whereas Golli-specific isoforms arise from transcription start site 1, and comprise both Golli-specific and classic MBP sequences. The Golli isoform BG21 has been suggested to play roles in myelination and T cell activation pathways. It is an intrinsically disordered protein, thereby presenting a large effective surface area for interaction with other proteins such as Golli-interacting protein. We have used multidimensional heteronuclear NMR spectroscopy to achieve sequence-specific resonance assignments of the recombinant murine BG21 in physiologically relevant buffer, to analyze its secondary structure using chemical shift indexing (CSI), and to investigate its backbone dynamics using 15N spin relaxation measurements. We have assigned 184 out of 199 residues unambiguously. The CSI analysis revealed little ordered secondary structure under these conditions, with only some small fragments having a slight tendency toward alpha-helicity, which may represent putative recognition motifs. The 15N relaxation and NOE measurements confirmed the general behavior of the protein as an extended polypeptide chain, with the N-terminal Golli-specific portion (residues S5-T69) being exceptionally flexible, even in comparison to other intrinsically disordered proteins that have been studied this way. The high degree of flexibility of this N-terminal region may be to provide additional plasticity, or conformational adaptability, in protein-protein interactions. Another highly mobile segment, A126-S127-G128-G129, may function as a hinge.

Application of phase correction to improve the interpretation of crude oil spectra obtained using 7 T Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Cho, Yunju; Qi, Yulin; O'Connor, Peter B; Barrow, Mark P; Kim, Sunghwan

2014-01-01

In this study, a phase-correction technique was applied to the study of crude oil spectra obtained using a 7 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). 7 T FT-ICR MS had not been widely used for oil analysis due to the lower resolving power compared with high field FT-ICR MS. For low field instruments, usage of data that has not been phase-corrected results in an inability to resolve critical mass splits of C3 and SH4 (3.4 mDa), and (13)C and CH (4.5 mDa). This results in incorrect assignments of molecular formulae, and discontinuous double bond equivalents (DBE) and carbon number distributions of S1, S2, and hydrocarbon classes are obtained. Application of phase correction to the same data, however, improves the reliability of assignments and produces continuous DBE and carbon number distributions. Therefore, this study clearly demonstrates that phase correction improves data analysis and the reliability of assignments of molecular formulae in crude oil anlayses.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba 2In 2O 4(OH) 2 Structure and Dynamics

DOE PAGES

Dervisoglu, Riza; Middlemiss, Derek S.; Blanc, Frederic; ...

2015-05-01

Here, a structural characterization of the hydrated form of the brownmillerite-type phase Ba 2In 2O 5, Ba 2In 2O 4(OH) 2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics 2004, 170, 25–32) using X-ray and neutron studies. Calculationsmore » of possible proton arrangements within the partially occupied layer of Ba 2In 2O 4(OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H– 17O double resonance experiments.« less

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2015-06-09

A structural characterization of the hydrated form of the brownmillerite-type phase Ba 2 In 2 O 5 , Ba 2 In 2 O 4 (OH) 2 , is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2 O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25-32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba 2 In 2 O 4 (OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1 H and 17 O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1 H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1 H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17 O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1 H- 17 O double resonance experiments.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

PubMed Central

2015-01-01

A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

Pleomorphic copper coordination by Alzheimer's disease amyloid-beta peptide.

PubMed

Drew, Simon C; Noble, Christopher J; Masters, Colin L; Hanson, Graeme R; Barnham, Kevin J

2009-01-28

Numerous conflicting models have been proposed regarding the nature of the Cu(2+) coordination environment of the amyloid beta (Abeta) peptide, the causative agent of Alzheimer's disease. This study used multifrequency CW-EPR spectroscopy to directly resolve the superhyperfine interactions between Cu(2+) and the ligand nuclei of Abeta, thereby avoiding ambiguities associated with introducing point mutations. Using a library of Abeta16 analogues with site-specific (15)N-labeling at Asp1, His6, His13, and His14, numerical simulations of the superhyperfine resonances delineated two independent 3N1O Cu(2+) coordination modes, {N(a)(D1), O, N(epsilon)(H6), N(epsilon)(H13)} (component Ia) and {N(a)(D1), O, N(epsilon)(H6), N(epsilon)(H14)} (component Ib), between pH 6-7. A third coordination mode (component II) was identified at pH 8.0, and simulation of the superhyperfine resonances indicated a 3N1O coordination sphere involving nitrogen ligation by His6, His13, and His14. No differences were observed upon (17)O-labeling of the phenolic oxygen of Tyr10, confirming it is not a key oxygen ligand in the physiological pH range. Hyperfine sublevel correlation (HYSCORE) spectroscopy, in conjunction with site-specific (15)N-labeling, provided additional support for the common role of His6 in components Ia and Ib, and for the assignment of a {O, N(epsilon)(H6), N(epsilon)(H13), N(epsilon)(H14)} coordination sphere to component II. HYSCORE studies of a peptide analogue with selective (13)C-labeling of Asp1 revealed (13)C cross-peaks characteristic of equatorial coordination by the carboxylate oxygen of Asp1 in component Ia/b coordination. The direct resolution of Cu(2+) ligand interactions, together with the key finding that component I is composed of two distinct coordination modes, provides valuable insight into a range of conflicting ligand assignments and highlights the complexity of Cu(2+)/Abeta interactions.

The 700-1500 cm{sup −1} region of the S{sub 1} (A{sup ~1}B{sub 2}) state of toluene studied with resonance-enhanced multiphoton ionization (REMPI), zero-kinetic-energy (ZEKE) spectroscopy, and time-resolved slow-electron velocity-map imaging (tr-SEVI) spectroscopy

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

Gardner, Adrian M.; Green, Alistair M.; Tamé-Reyes, Victor M.

We report (nanosecond) resonance-enhanced multiphoton ionization (REMPI), (nanosecond) zero-kinetic-energy (ZEKE) and (picosecond) time-resolved slow-electron velocity map imaging (tr-SEVI) spectra of fully hydrogenated toluene (Tol-h{sub 8}) and the deuterated-methyl group isotopologue (α{sub 3}-Tol-d{sub 3}). Vibrational assignments are made making use of the activity observed in the ZEKE and tr-SEVI spectra, together with the results from quantum chemical and previous experimental results. Here, we examine the 700–1500 cm{sup −1} region of the REMPI spectrum, extending our previous work on the region ≤700 cm{sup −1}. We provide assignments for the majority of the S{sub 1} and cation bands observed, and in particular wemore » gain insight regarding a number of regions where vibrations are coupled via Fermi resonance. We also gain insight into intramolecular vibrational redistribution in this molecule.« less

A simple resonance enhanced laser ionization scheme for CO via the A1Π state

NASA Astrophysics Data System (ADS)

Sun, Z. F.; von Zastrow, A. D.; Parker, D. H.

2017-07-01

We investigate the laser ionization process taking place when the CO molecule is exposed to vacuum ultraviolet (VUV) radiation resonant with the CO A1Π (v = 0) ← X1Σ+ (v = 0) transition around 154 nm, along with the ultraviolet (UV) and visible (Red) radiation used to generate VUV by four-wave difference-frequency mixing. By measuring the CO+ ion recoil and a room temperature gas spectrum, it is possible to assign the ionization process as 1 + 1' + 1'' REMPI where the one-photon steps refer to the VUV, UV, and Red radiation, respectively. Resonance enhanced ionization of rotational states around J = 12 arise due to the overlap of the fixed wavelength UV (˜250 nm) with the R band-head of a transition assigned to CO E1Π (v = 6) ← A1Π (v = 0) with a term value of 104 787.5 cm-1. The REMPI process is efficient and polarization sensitive and should be useful in a wide range of studies involving nascent CO.

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

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

Extrinsic Tryptophans as NMR Probes of Allosteric Coupling in Membrane Proteins: Application to the A2A Adenosine Receptor.

PubMed

Eddy, Matthew T; Gao, Zhan-Guo; Mannes, Philip; Patel, Nilkanth; Jacobson, Kenneth A; Katritch, Vsevolod; Stevens, Raymond C; Wüthrich, Kurt

2018-06-20

Tryptophan indole 15 N- 1 H signals are well separated in nuclear magnetic resonance (NMR) spectra of proteins. Assignment of the indole 15 N- 1 H signals therefore enables one to obtain site-specific information on complex proteins in supramacromolecular systems, even when extensive assignment of backbone 15 N- 1 H resonances is challenging. Here we exploit the unique indole 15 N- 1 H chemical shift by introducing extrinsic tryptophan reporter residues at judiciously chosen locations in a membrane protein for increased coverage of structure and function by NMR. We demonstrate this approach with three variants of the human A 2A adenosine receptor (A 2A AR), a class A G protein-coupled receptor, each containing a single extrinsic tryptophan near the receptor intracellular surface, in helix V, VI, or VII, respectively. We show that the native A 2A AR global protein fold and ligand binding activity are preserved in these A 2A AR variants. The indole 15 N- 1 H signals from the extrinsic tryptophan reporter residues show different responses to variable efficacy of drugs bound to the receptor orthosteric cavity, and the indole 15 N- 1 H chemical shift of the tryptophan introduced at the intracellular end of helix VI is sensitive to conformational changes resulting from interactions with a polypeptide from the carboxy terminus of the Gα S intracellular partner protein. Introducing extrinsic tryptophans into proteins in complex supramolecular systems thus opens new avenues for NMR investigations in solution.

1H, 13C, and 15N resonance assignments of an enzymatically active domain from the catalytic component (CDTa, residues 216-420) of a binary toxin from Clostridium difficile.

PubMed

Roth, Braden M; Godoy-Ruiz, Raquel; Varney, Kristen M; Rustandi, Richard R; Weber, David J

2016-04-01

Clostridium difficile is a bacterial pathogen and is the most commonly reported source of nosocomial infection in industrialized nations. Symptoms of C. difficile infection (CDI) include antibiotic-associated diarrhea, pseudomembranous colitis, sepsis and death. Over the last decade, rates and severity of hospital infections in North America and Europe have increased dramatically and correlate with the emergence of a hypervirulent strain of C. difficile characterized by the presence of a binary toxin, CDT (C. difficile toxin). The binary toxin consists of an enzymatic component (CDTa) and a cellular binding component (CDTb) that together form the active binary toxin complex. CDTa harbors a pair of structurally similar but functionally distinct domains, an N-terminal domain (residues 1-215; (1-215)CDTa) that interacts with CDTb and a C-terminal domain (residues 216-420; (216-420)CDTa) that harbors the intact ADP-ribosyltransferase (ART) active site. Reported here are the (1)H, (13)C, and (15)N backbone resonance assignments of the 23 kDa, 205 amino acid C-terminal enzymatic domain of CDTa, termed (216-420)CDTa. These NMR resonance assignments for (216-420)CDTa represent the first for a family of ART binary toxins and provide the framework for detailed characterization of the solution-state protein structure determination, dynamic studies of this domain, as well as NMR-based drug discovery efforts.

NMR studies on the structure and dynamics of lac operator DNA

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

Lee, S.C.

Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with amore » maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.« less

CP/MAS /sup 13/C NMR spectroscopic study of chlorophyll a in the solid state

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

Brown, C.E.; Spencer, R.B.; Burger, V.T.

1983-09-01

Solid-state cross-polarization, magic-angle sample spinning carbon-13 nuclear magnetic resonance spectra have been recorded on chlorophyll a- water aggregates, methyl pyrochlorophyllide a and methyl pyropheophorbide a (derivatives that lack a phytyl chain). Spectra have also been collected under a decoupling regime in which resonances of certain hydrogen-bearing carbon atoms are suppressed. These observations are used to assign the solid state spectra.

Conformation and Complexation of Tannins: NMR Spectra and Molecular Search Modeling of Flavan-3-ols

Treesearch

Richard W. Hemingway; Fred L. Tohiason; G. Wayne McGraw; Jan P. Steynberg

1996-01-01

Studies offlavan-3-01sin their biologically significant phenolic form show that both H-6 and C-6 resonances are downfield from H-8 and C-8. Therefore, assignments for the H atoms of the A-ring are inverse to those commonly reported. By contrast, in the methyl ether and methyl ether acetate derivatives, both H-8 and C-8 are downfield from H-6 and C-6 and assignments...

PICKY: a novel SVD-based NMR spectra peak picking method.

PubMed

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-06-15

Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 A. PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

Suppressing the crosstalk between racetrack resonators by grating assisted couplers for WDM sensing

NASA Astrophysics Data System (ADS)

Zhang, Xuezhi; Jiang, Junfeng; Liu, Kun; Yu, Zhe; Feng, Ming; Chen, Wenjie; Liu, Tiegen

2017-12-01

We proposed a uniform racetrack resonators based sensor for bio-chemical WDM sensing. The sensing channels are assigned by grating assisted contra-directional couplers. Each resonator only occupies one sensing channel. The crosstalk between sensing channels can be suppressed by aligning the center coupling wavelength of one resonator with the weak coupling wavelength of the others. Based on the simulation results obtained from transfer matrix method, the sensing channel gap can be reduced down to 2 FSRs (˜1.5 nm) of the resonator. The total crosstalk can be as low as 2.5 × 10-2 dB in a sensor with 23 channels covering the whole C band. This sensor with high throughput will be very important for analyzing a wide range of analytes, such as organic compounds or biological materials.

Metallated DNA Aptamers for Prostate Cancer Treatment

DTIC Science & Technology

2013-03-01

minor groove while the new 320 nm maxima reflect the binding of N-methyl pyrrole moieties of netropsin in the minor groove of 3’FdU.(Zimmer, Marck...resonance assignment and those consistent with the pyrrole 1 H resonances of netropsin (Fig. 3). NOESY crosspeaks from FdU imino 1 H to putative...computational chemistry data from our laboratory and with netropsin binding in the minor groove based upon NOE data from pyrrole 1 H of netropsin and

NMR 1H,13C, 15N backbone and 13C side chain resonance assignment of the G12C mutant of human K-Ras bound to GDP.

PubMed

Sharma, Alok K; Lee, Seung-Joo; Rigby, Alan C; Townson, Sharon A

2018-05-02

K-Ras is a key driver of oncogenesis, accounting for approximately 80% of Ras-driven human cancers. The small GTPase cycles between an inactive, GDP-bound and an active, GTP-bound state, regulated by guanine nucleotide exchange factors and GTPase activating proteins, respectively. Activated K-Ras regulates cell proliferation, differentiation and survival by signaling through several effector pathways, including Raf-MAPK. Oncogenic mutations that impair the GTPase activity of K-Ras result in a hyperactivated state, leading to uncontrolled cellular proliferation and tumorogenesis. A cysteine mutation at glycine 12 is commonly found in K-Ras associated cancers, and has become a recent focus for therapeutic intervention. We report here 1 H N, 15 N, and 13 C resonance assignments for the 19.3 kDa (aa 1-169) human K-Ras protein harboring an oncogenic G12C mutation in the GDP-bound form (K-RAS G12C-GDP ), using heteronuclear, multidimensional NMR spectroscopy. Backbone 1 H- 15 N correlations have been assigned for all non-proline residues, except for the first methionine residue.

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

PubMed

Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

2014-05-01

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase.

PubMed

Yamanoi, Takashi; Oda, Yoshiki; Katsuraya, Kaname; Inazu, Toshiyuki; Yamamoto, Kenji

2016-06-02

This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through (1)H- and (13)C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1. Copyright © 2016 Elsevier Ltd. All rights reserved.

1H, 15N, 13C resonance assignment of human GAP-43.

PubMed

Flamm, Andrea Gabriele; Żerko, Szymon; Zawadzka-Kazimierczuk, Anna; Koźmiński, Wiktor; Konrat, Robert; Coudevylle, Nicolas

2016-04-01

GAP-43 is a 25 kDa neuronal intrinsically disordered protein, highly abundant in the neuronal growth cone during development and regeneration. The exact molecular function(s) of GAP-43 remains unclear but it appears to be involved in growth cone guidance and actin cytoskeleton organization. Therefore, GAP-43 seems to play an important role in neurotransmitter vesicle fusion and recycling, long-term potentiation, spatial memory formation and learning. Here we report the nearly complete assignment of recombinant human GAP-43.

Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study

DOE PAGES

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; ...

2015-07-29

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

SUGGEL: A Program Suggesting the Orbital Angular Momentum of a Neutron Resonance from the Magnitude of its Neutron Width

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

Oh, S.Y.

2001-02-02

The SUGGEL computer code has been developed to suggest a value for the orbital angular momentum of a neutron resonance that is consistent with the magnitude of its neutron width. The suggestion is based on the probability that a resonance having a certain value of g{Gamma}{sub n} is an l-wave resonance. The probability is calculated by using Bayes' theorem on the conditional probability. The probability density functions (pdf's) of g{Gamma}{sub n} for up to d-wave (l=2) have been derived from the {chi}{sup 2} distribution of Porter and Thomas. The pdf's take two possible channel spins into account. This code ismore » a tool which evaluators will use to construct resonance parameters and help to assign resonance spin. The use of this tool is expected to reduce time and effort in the evaluation procedure, since the number of repeated runs of the fitting code (e.g., SAMMY) may be reduced.« less

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

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

Lee, Andrew Loyd

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ patternmore » of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T 1, T 2, and 15N/ 1H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.« less

Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.

PubMed Central

Wiltscheck, R.; Kammerer, R. A.; Dames, S. A.; Schulthess, T.; Blommers, M. J.; Engel, J.; Alexandrescu, A. T.

1997-01-01

The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

PICKY: a novel SVD-based NMR spectra peak picking method

PubMed Central

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-01-01

Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 Å. Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking. Contact: mli@uwaterloo.ca PMID:19477998

MRI-based IMRT planning for MR-linac: comparison between CT- and MRI-based plans for pancreatic and prostate cancers

NASA Astrophysics Data System (ADS)

Prior, Phil; Chen, Xinfeng; Botros, Maikel; Paulson, Eric S.; Lawton, Colleen; Erickson, Beth; Li, X. Allen

2016-05-01

The treatment planning in radiation therapy (RT) can be arranged to combine benefits of computed tomography (CT) and magnetic resonance imaging (MRI) together to maintain dose calculation accuracy and improved target delineation. Our aim is study the dosimetric impact of uniform relative electron density assignment on IMRT treatment planning with additional consideration given to the effect of a 1.5 T transverse magnetic field (TMF) in MR-Linac. A series of intensity modulated RT (IMRT) plans were generated for two representative tumor sites, pancreas and prostate, using CT and MRI datasets. Representative CT-based IMRT plans were generated to assess the impact of different electron density (ED) assignment on plan quality using CT without the presence of a 1.5 T TMF. The relative ED (rED) values used were taken from the ICRU report 46. Four types of rED assignment in the organs at risk (OARs), the planning target volumes (PTV) and in the non-specified tissue (NST) were considered. Dose was recalculated (no optimization) using a Monaco 5.09.07a research planning system employing Monte Carlo calculations with an option to include TMF. To investigate the dosimetric effect of different rED assignment, the dose-volume parameters (DVPs) obtained from these specific rED plans were compared to those obtained from the original plans based on CT. Overall, we found that uniform rED assignment results in differences in DVPs within 3% for the PTV and 5% for OAR. The presence of 1.5 T TMF on IMRT DVPs resulted in differences that were generally within 3% of the Gold St for both the pancreas and prostate. The combination of uniform rED assignment and TMF produced differences in DVPs that were within 4-5% of the Gold St. Larger differences in DVPs were observed for OARs on T2-based plans. The effects of using different rED assignments and the presence of 1.5 T TMF for pancreas and prostate IMRT plans are generally within 3% and 5% of PTV and OAR Gold St values. There are noticeable dosimetric differences between the CT- and MRI-based IMRT plans caused by a combination of anatomical changes between the two image acquisition times, uniform rED assignment and 1.5 T TMF. This work was present in part at the 2014 ASTRO annual meeting.

Modeling the Conformation-Specific Infrared Spectra of N-Alkylbenzenes

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Hewett, Daniel M.; Korn, Joseph A.; Zwier, Timothy S.

2016-06-01

Conformation-specific UV-IR double resonance spectra are presented for n-alkylbenzenes. With the aid of a local mode Hamiltonian that includes the effects of stretch-bend Fermi coupling, the spectra of ethyl, n-propyl, and n-butylbenzene are assigned to individual conformers. These molecules allow for further development of the work on a first principles method for calculating alkyl stretch spectra. Due to the consistency of the anharmonic couplings from conformer to conformer, construction of the model Hamiltonian for a given conformer only requires a harmonic frequency calculation at the conformer's minimum geometry as an input. The model Hamiltonian can be parameterized with either density functional theory or MP2 electronic structure calculations. The relative strengths and weaknesses of these methods are evaluated, including their predictions of the relative energetics of the conformers. Finally, the IR spectra for conformers that have the alkyl chain bend back and interact with the π cloud of the benzene ring are modeled.

Probing intermolecular interactions in a diethylcarbamazine citrate salt by fast MAS 1H solid-state NMR spectroscopy and GIPAW calculations.

PubMed

Venâncio, Tiago; Oliveira, Lyege Magalhaes; Ellena, Javier; Boechat, Nubia; Brown, Steven P

2017-10-01

Fast magic-angle spinning (MAS) NMR is used to probe intermolecular interactions in a diethylcarbamazine salt, that is widely used as a treatment against adult worms of Wuchereria bancrofti which cause a common disease in tropical countries named filariasis. Specifically, a dihydrogen citrate salt that has improved thermal stability and solubility as compared to the free form is studied. One-dimensional 1 H, 13 C and 15 N and two-dimensional 1 H- 13 C and 14 N- 1 H heteronuclear correlation NMR experiments under moderate and fast MAS together with GIPAW (CASTEP) calculations enable the assignment of the 1 H, 13 C and 14 N/ 15 N resonances. A two-dimensional 1 H- 1 H double-quantum (DQ) -single-quantum (SQ) MAS spectrum recorded with BaBa recoupling at 60kHz MAS identifies specific proton-proton proximities associated with citrate-citrate and citrate-diethylcarbamazine intermolecular interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Bound and resonance states of the dipolar anion of hydrogen cyanide: Competition between threshold effects and rotation in an open quantum system

DOE PAGES

Fossez, K.; Michel, N.; Nazarewicz, W.; ...

2015-01-12

In this paper, bound and resonance states of the dipole-bound anion of hydrogen cyanide HCN – are studied using a nonadiabatic pseudopotential method and the Berggren expansion technique involving bound states, decaying resonant states, and nonresonant scattering continuum. We devise an algorithm to identify the resonant states in the complex energy plane. To characterize spatial distributions of electronic wave functions, we introduce the body-fixed density and use it to assign families of resonant states into collective rotational bands. We find that the nonadiabatic coupling of electronic motion to molecular rotation results in a transition from the strong-coupling to weak-coupling regime.more » In the strong-coupling limit, the electron moving in a subthreshold, spatially extended halo state follows the rotational motion of the molecule. Above the ionization threshold, the electron's motion in a resonance state becomes largely decoupled from molecular rotation. Finally, the widths of resonance-band members depend primarily on the electron orbital angular momentum.« less

The predictive value of magnetic resonance imaging of retinoblastoma for the likelihood of high-risk pathologic features.

PubMed

Hiasat, Jamila G; Saleh, Alaa; Al-Hussaini, Maysa; Al Nawaiseh, Ibrahim; Mehyar, Mustafa; Qandeel, Monther; Mohammad, Mona; Deebajah, Rasha; Sultan, Iyad; Jaradat, Imad; Mansour, Asem; Yousef, Yacoub A

2018-06-01

To evaluate the predictive value of magnetic resonance imaging in retinoblastoma for the likelihood of high-risk pathologic features. A retrospective study of 64 eyes enucleated from 60 retinoblastoma patients. Contrast-enhanced magnetic resonance imaging was performed before enucleation. Main outcome measures included demographics, laterality, accuracy, sensitivity, and specificity of magnetic resonance imaging in detecting high-risk pathologic features. Optic nerve invasion and choroidal invasion were seen microscopically in 34 (53%) and 28 (44%) eyes, respectively, while they were detected in magnetic resonance imaging in 22 (34%) and 15 (23%) eyes, respectively. The accuracy of magnetic resonance imaging in detecting prelaminar invasion was 77% (sensitivity 89%, specificity 98%), 56% for laminar invasion (sensitivity 27%, specificity 94%), 84% for postlaminar invasion (sensitivity 42%, specificity 98%), and 100% for optic cut edge invasion (sensitivity100%, specificity 100%). The accuracy of magnetic resonance imaging in detecting focal choroidal invasion was 48% (sensitivity 33%, specificity 97%), and 84% for massive choroidal invasion (sensitivity 53%, specificity 98%), and the accuracy in detecting extrascleral extension was 96% (sensitivity 67%, specificity 98%). Magnetic resonance imaging should not be the only method to stratify patients at high risk from those who are not, eventhough it can predict with high accuracy extensive postlaminar optic nerve invasion, massive choroidal invasion, and extrascleral tumor extension.

The 18Ne(α,p)21Na breakout reaction in x-ray bursts: Experimental determination of spin-parities for α resonances in 22Mg via resonant elastic scattering of 21Na+p

NASA Astrophysics Data System (ADS)

He, J. J.; Zhang, L. Y.; Parikh, A.; Xu, S. W.; Yamaguchi, H.; Kahl, D.; Kubono, S.; Hu, J.; Ma, P.; Chen, S. Z.; Wakabayashi, Y.; Sun, B. H.; Wang, H. W.; Tian, W. D.; Chen, R. F.; Guo, B.; Hashimoto, T.; Togano, Y.; Hayakawa, S.; Teranishi, T.; Iwasa, N.; Yamada, T.; Komatsubara, T.

2013-07-01

The 18Ne(α,p)21Na reaction provides a pathway for breakout from the hot CNO cycles to the rp process in type-I x-ray bursts. To better determine this astrophysical reaction rate, the resonance parameters of the compound nucleus 22Mg have been investigated by measuring the resonant elastic scattering of 21Na+p. An 89 MeV 21Na radioactive ion beam was produced at the CNS Radioactive Ion Beam Separator and bombarded an 8.8 mg/cm2 thick polyethylene target. The recoiled protons were measured at scattering angles of θc.m.≈175∘ and 152∘ by three ΔE-E silicon telescopes. The excitation function was obtained with a thick-target method over energies Ex(22Mg) = 5.5-9.2 MeV. The resonance parameters have been determined through an R-matrix analysis. For the first time, the Jπ values for ten states above the α threshold in 22Mg have been experimentally determined in a single consistent measurement. We have made three new Jπ assignments and confirmed seven of the ten tentative assignments in the previous work. The 18Ne(α,p)21Na reaction rate has been recalculated, and the astrophysical impact of our new rate has been investigated through one-zone postprocessing x-ray burst calculations. We find that the 18Ne(α,p)21Na rate significantly affects the peak nuclear energy generation rate and the onset temperature of this breakout reaction in these phenomena.

Vibrational spectra and structures of neutral Si(m)C(n) clusters (m + n = 6): sequential doping of silicon clusters with carbon atoms.

PubMed

Savoca, Marco; Lagutschenkov, Anita; Langer, Judith; Harding, Dan J; Fielicke, André; Dopfer, Otto

2013-02-14

Vibrational spectra of mixed silicon carbide clusters Si(m)C(n) with m + n = 6 in the gas phase are obtained by resonant infrared-vacuum-ultraviolet two-color ionization (IR-UV2CI for n ≤ 2) and density functional theory (DFT) calculations. Si(m)C(n) clusters are produced in a laser vaporization source, in which the silicon plasma reacts with methane. Subsequently, they are irradiated with tunable IR light from an IR free electron laser before they are ionized with UV photons from an F(2) laser. Resonant absorption of one or more IR photons leads to an enhanced ionization efficiency for Si(m)C(n) and provides the size-specific IR spectra. IR spectra measured for Si(6), Si(5)C, and Si(4)C(2) are assigned to their most stable isomers by comparison with calculated linear absorption spectra. The preferred Si(m)C(n) structures with m + n = 6 illustrate the systematic transition from chain-like geometries for bare C(6) to three-dimensional structures for bare Si(6). In contrast to bulk SiC, carbon atom segregation is observed already for the smallest n (n = 2).

Spectroscopic and Kinetic Properties of the Molybdenum-containing, NAD+-dependent Formate Dehydrogenase from Ralstonia eutropha*

PubMed Central

Niks, Dimitri; Duvvuru, Jayant; Escalona, Miguel; Hille, Russ

2016-01-01

We have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, NAD+-dependent FdsABG formate dehydrogenase from Ralstonia eutropha. We confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). We have also characterized the electron paramagnetic resonance signal of the molybdenum center in its MoV state and demonstrated the direct transfer of the substrate Cα hydrogen to the molybdenum center in the course of the reaction. Varying temperature, microwave power, and level of enzyme reduction, we are able to clearly identify the electron paramagnetic resonance signals for four of the iron/sulfur clusters of the enzyme and find suggestive evidence for two others; we observe a magnetic interaction between the molybdenum center and one of the iron/sulfur centers, permitting assignment of this signal to a specific iron/sulfur cluster in the enzyme. In light of recent advances in our understanding of the structure of the molybdenum center, we propose a reaction mechanism involving direct hydride transfer from formate to a molybdenum-sulfur group of the molybdenum center. PMID:26553877

Deciphering the fluorescence resonance energy transfer from denatured transport protein to anthracene 1,5 disulphonate in reverse micellar environment

NASA Astrophysics Data System (ADS)

Singharoy, Dipti; Bhattacharya, Subhash Chandra

2017-12-01

Constrained environmental effect inside AOT reverse micellar media has been employed in this work to collect the information about energy transfer efficacy between sodium salt of anthracene 1,5 disulphonate (1,5-AS) with model transport proteins, bovine serum albumin (BSA), and human serum albumin (HSA). Steady state, time-resolved fluorescence and circular dichroism techniques have been used for this purpose and corresponding Fӧrster-type resonance energy transfer (FRET) from tryptophan residues to 1,5-AS indicates that 1,5-AS binds in the vicinity of the tryptophan residue (BSA and HSA) with equal strength. Indication of protein damage from fluorescence data and its confirmation has been measured from CD measurement. Molecular modeling study hereby plays a crucial role to predict the minimum energy docked conformation of the probe inside the protein environment. From the docked conformation the distance between 1,5-AS and tryptophan moiety of BSA/HSA has successfully explained the FRET possibility between them. A comparative modeling study between BSA and HSA with 1,5-AS assigning their binding site within specific amino acids plays a crucial role in support of the FRET study.

The characterization of the concentration of the single-walled carbon nanotubes in aqueous dispersion by UV-Vis-NIR absorption spectroscopy.

PubMed

Yang, Bing; Ren, Lingling; Li, Luming; Tao, Xingfu; Shi, Yunhua; Zheng, Yudong

2013-11-07

Current and future applications of single-wall carbon nanotubes (SWCNTs) depend on the dispersion of the SWCNTs in aqueous solution and their quantitation. The concentration of SWCNTs is an important indicator to evaluate the dispersibility of the surfactant-dispersed SWCNTs suspension. Due to the complexity of the SWCNTs suspension, it is necessary to determine both the total concentration of the dispersed SWCNTs and the concentration of individually dispersed SWCNTs in aqueous suspensions, and these were evaluated through the absorbance and the resonance ratios of UV-Vis-NIR absorption spectra, respectively. However, there is no specific and reliable position assigned for either calculation of the absorbance or the resonance ratio of the UV-Vis-NIR absorption spectrum. In this paper, different ranges of wavelengths for these two parameters were studied. From this, we concluded that the wavelength range between 300 nm and 600 nm should be the most suitable for evaluation of the total concentration of dispersed SWCNTs in the suspension; also, wavelengths below 800 nm should be most suitable for evaluation of the concentration of individually dispersed SWCNTs in the suspension. Moreover, these wavelength ranges are verified by accurate dilution experiments.

Red-excitation resonance Raman analysis of the nu(Fe=O) mode of ferryl-oxo hemoproteins.

PubMed

Ikemura, Kenichiro; Mukai, Masahiro; Shimada, Hideo; Tsukihara, Tomitake; Yamaguchi, Satoru; Shinzawa-Itoh, Kyoko; Yoshikawa, Shinya; Ogura, Takashi

2008-11-05

The Raman excitation profile of the nuFe O mode of horseradish peroxidase compound II exhibits a maximum at 580 nm. This maximum is located within an absorption band with a shoulder assignable to an oxygen-to-iron charge transfer band on the longer wavelength side of the alpha-band. Resonance Raman bands of the nuFe O mode of various ferryl-oxo type hemoproteins measured at 590 nm excitation indicate that many hemoproteins in the ferryl-oxo state have an oxygen-to-iron charge transfer band in the visible region. Since this red-excited resonance Raman technique causes much less photochemical damage in the proteins relative to blue-excited resonance Raman spectroscopy, it produces a higher signal-to-noise ratio and thus represents a powerful tool for investigations of ferryl-oxo intermediates of hemoproteins.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

Correlation of probability scores of placenta accreta on magnetic resonance imaging with hemorrhagic morbidity.

PubMed

Lim, Grace; Horowitz, Jeanne M; Berggruen, Senta; Ernst, Linda M; Linn, Rebecca L; Hewlett, Bradley; Kim, Jennifer; Chalifoux, Laurie A; McCarthy, Robert J

2016-11-01

To evaluate the hypothesis that assigning grades to magnetic resonance imaging (MRI) findings of suspected placenta accreta will correlate with hemorrhagic outcomes. We chose a single-center, retrospective, observational design. Nulliparous or multiparous women who had antenatal placental MRI performed at a tertiary level academic hospital were included. Cases with antenatal placental MRI were included and compared with cases without MRI performed. Two radiologists assigned a probability score for accreta to each study. Estimated blood loss and transfusion requirements were compared among groups by the Kruskal-Wallis H test. Thirty-five cases had placental MRI performed. MRI performance was associated with higher blood loss compared with the non-MRI group (2600 [1400-4500]mL vs 900[600-1500]mL, P<.001). There was no difference in estimated blood loss (P=.31) or transfusion (P=.57) among the MRI probability groups. In cases of suspected placenta accreta, probability scores for antenatal placental MRI may not be associated with increasing degrees of hemorrhage. Continued research is warranted to determine the effectiveness of assigning probability scores for antenatal accreta imaging studies, combined with clinical indices of suspicion, in assisting with antenatal multidisciplinary team planning for operative management of this morbid condition. Copyright © 2016 Elsevier Inc. All rights reserved.

Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

PubMed Central

Lee, Hyeyoung; An, Hyun Joo; Lerno, Larry A.; German, J. Bruce; Lebrilla, Carlito B.

2010-01-01

Gangliosides are anionic glycosphingolipids widely distributed in vertebrate tissues and fluids. Their structural and quantitative expression patterns depend on phylogeny and are distinct down to the species level. In milk, gangliosides are exclusively associated with the milk fat globule membrane. They may participate in diverse biological processes but more specifically to host-pathogen interactions. However, due to the molecular complexities, the analysis needs extensive sample preparation, chromatographic separation, and even chemical reaction, which makes the process very complex and time-consuming. Here, we describe a rapid profiling method for bovine and human milk gangliosides employing matrix-assisted desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Prior to the analyses of biological samples, milk ganglioside standards GM3 and GD3 fractions were first analyzed in order to validate this method. High mass accuracy and high resolution obtained from MALDI FTICR MS allow for the confident assignment of chain length and degree of unsaturation of the ceramide. For the structural elucidation, tandem mass spectrometry (MS/MS), specifically as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) were employed. Complex ganglioside mixtures from bovine and human milk were further analyzed with this method. The samples were prepared by two consecutive chloroform/methanol extraction and solid phase extraction. We observed a number of differences between bovine milk and human milk. The common gangliosides in bovine and human milk are NeuAc-NeuAc-Hex-Hex-Cer (GD3) and NeuAc-Hex-Hex-Cer (GM3); whereas, the ion intensities of ganglioside species are different between two milk samples. Kendrick mass defect plot yields grouping of ganglioside peaks according to their structural similarities. Gangliosides were further probed by tandem MS to confirm the compositional and structural assignments. We found that only in human milk gangliosides was the ceramide carbon always even numbered, which is consistent with the notion that differences in the oligosaccharide and the ceramide moieties confer to their physiological distinctions. PMID:21860602

Raman spectroscopy as a tool in differentiating conjugated polyenes from synthetic and natural sources.

PubMed

Fernandes, Rafaella F; Maia, Lenize F; Couri, Mara R C; Costa, Luiz Antonio S; de Oliveira, Luiz Fernando C

2015-01-05

This work presents the Raman spectroscopic characterization of synthetic analogs of natural conjugated polyenals found in octocorals, focusing the unequivocal identification of the chemical species present in these systems. The synthetic material was produced by the autocondensation reaction of crotonaldehyde, generating a demethylated conjugated polyene containing 11 carbon-carbon double bonds, with just a methyl group on the end of the carbon chain. The resonance Raman spectra of such pigment has shown the existence of enhanced modes assigned to ν₁(CC) and ν₂(CC) modes of the main chain. For the resonance Raman spectra of natural pigments from octocorals collected in the Brazilian coast, besides the previously cited bands, it could be also observed the presence of the ν₄(CCH₃), related to the vibrational mode who describes the vibration of the methyl group of the central carbon chain of carotenoids. Other interesting point is the observation of overtones and combination bands, which for carotenoids involves the presence of the ν₄ mode, whereas for the synthetic polyene this band, besides be seen at a slightly different wavenumber position, does not appear as an enhanced mode and also as a combination, such as for the natural carotenoids. Theoretical molecular orbital analysis of polyenal-11 and lycopene has shown the structural differences which are also responsible for the resonance Raman data, based on the appearance of the (CH3) vibrational mode in the resonant transition only for lycopene. At last, the Raman band at ca. 1010 cm(-1), assigned to the (CH₃) vibrational mode, can be used for attributing the presence of each one of the conjugated polyenes: the resonance Raman spectrum containing the band at ca. 1010 cm(-1) refers to the carotenoid (in this case lycopene), and the absence of such band in resonance conditions refers to the polyenal (in this case the polyenal-11). Copyright © 2014 Elsevier B.V. All rights reserved.

Raman spectroscopy as a tool in differentiating conjugated polyenes from synthetic and natural sources

NASA Astrophysics Data System (ADS)

Fernandes, Rafaella F.; Maia, Lenize F.; Couri, Mara R. C.; Costa, Luiz Antonio S.; de Oliveira, Luiz Fernando C.

2015-01-01

This work presents the Raman spectroscopic characterization of synthetic analogs of natural conjugated polyenals found in octocorals, focusing the unequivocal identification of the chemical species present in these systems. The synthetic material was produced by the autocondensation reaction of crotonaldehyde, generating a demethylated conjugated polyene containing 11 carbon-carbon double bonds, with just a methyl group on the end of the carbon chain. The resonance Raman spectra of such pigment has shown the existence of enhanced modes assigned to ν1(Cdbnd C) and ν2(Csbnd C) modes of the main chain. For the resonance Raman spectra of natural pigments from octocorals collected in the Brazilian coast, besides the previously cited bands, it could be also observed the presence of the ν4(Csbnd CH3), related to the vibrational mode who describes the vibration of the methyl group of the central carbon chain of carotenoids. Other interesting point is the observation of overtones and combination bands, which for carotenoids involves the presence of the ν4 mode, whereas for the synthetic polyene this band, besides be seen at a slightly different wavenumber position, does not appear as an enhanced mode and also as a combination, such as for the natural carotenoids. Theoretical molecular orbital analysis of polyenal-11 and lycopene has shown the structural differences which are also responsible for the resonance Raman data, based on the appearance of the (sbnd CH3) vibrational mode in the resonant transition only for lycopene. At last, the Raman band at ca. 1010 cm-1, assigned to the (sbnd CH3) vibrational mode, can be used for attributing the presence of each one of the conjugated polyenes: the resonance Raman spectrum containing the band at ca. 1010 cm-1 refers to the carotenoid (in this case lycopene), and the absence of such band in resonance conditions refers to the polyenal (in this case the polyenal-11).

NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded β-sheet peptide.

PubMed

Sonti, Rajesh; Rai, Rajkishor; Ragothama, Srinivasarao; Balaram, Padmanabhan

2012-12-13

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel β-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-LFV(D)P(L)PLFV-OMe (peptide 1) favors the β-hairpin conformation nucleated by the type II' β-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded β-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C(α)-C(β)(χ(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Magnetic Resonance Spectroscopy for Evaluating the Effect of Pulsed Electromagnetic Fields on Marrow Adiposity in Postmenopausal Women With Osteopenia.

PubMed

Li, Shaojun; Jiang, Hongning; Wang, Bo; Gu, Mingjun; Bi, Xia; Yin, Ying; Wang, Yu

2018-06-12

Pulsed electromagnetic fields (PEMFs) could promote osteogenic differentiation and suppress adipogenic differentiation in bone mesenchymal stem cells ex vivo. However, data on the effect of PEMF on marrow adiposity in humans remain elusive. We aimed to determine the in vivo effect of PEMF on marrow adiposity in postmenopausal women using magnetic resonance spectroscopy. Sixty-one postmenopausal women with osteopenia, aged 53 to 85 years, were randomly assigned to receive either PEMF treatment or placebo. The session was performed 3 times per week for 6 months. All women received adequate dietary calcium and vitamin D. Bone mineral density (BMD) by dual-energy x-ray absorptiometry, vertebral marrow fat content by magnetic resonance spectroscopy, and serum biomarkers were evaluated before and after 6 months of treatment. A total of 27 (87.1%) and 25 (83.3%) women completed the treatment schedule in the PEMF and placebo groups, respectively. After the 6-month treatment, lumbar spine and hip BMD increased by 1.46% to 2.04%, serum bone-specific alkaline phosphatase increased by 3.23%, and C-terminal telopeptides of type 1 collagen decreased by 9.12% in the PEMF group (P < 0.05), whereas the mean percentage changes in BMD and serum biomarkers were not significant in the placebo group. Pulsed electromagnetic field treatment significantly reduced marrow fat fraction by 4.81%. The treatment difference between the 2 groups was -4.43% (95% confidence interval, -3.70% to -5.65%; P = 0.009). Pulsed electromagnetic field is an effective physiotherapy in postmenopausal women, and this effect may, at least in part, regulate the amount of fat within the bone marrow. Magnetic resonance spectroscopy may serve as a complementary imaging biomarker for monitoring response to therapy in osteoporosis.

Methods Development for Spectral Simplification of Room-Temperature Rotational Spectra

NASA Astrophysics Data System (ADS)

Kent, Erin B.; Shipman, Steven

2014-06-01

Room-temperature rotational spectra are dense and difficult to assign, and so we have been working to develop methods to accelerate this process. We have tested two different methods with our waveguide-based spectrometer, which operates from 8.7 to 26.5 GHz. The first method, based on previous work by Medvedev and De Lucia, was used to estimate lower state energies of transitions by performing relative intensity measurements at a range of temperatures between -20 and +50 °C. The second method employed hundreds of microwave-microwave double resonance measurements to determine level connectivity between rotational transitions. The relative intensity measurements were not particularly successful in this frequency range (the reasons for this will be discussed), but the information gleaned from the double-resonance measurements can be incorporated into other spectral search algorithms (such as autofit or genetic algorithm approaches) via scoring or penalty functions to help with the spectral assignment process. I.R. Medvedev, F.C. De Lucia, Astrophys. J. 656, 621-628 (2007).

EPR, optical and superposition model study of Mn2+ doped L+ glutamic acid

NASA Astrophysics Data System (ADS)

Kripal, Ram; Singh, Manju

2015-12-01

Electron paramagnetic resonance (EPR) study of Mn2+ doped L+ glutamic acid single crystal is done at room temperature. Four interstitial sites are observed and the spin Hamiltonian parameters are calculated with the help of large number of resonant lines for various angular positions of external magnetic field. The optical absorption study is also done at room temperature. The energy values for different orbital levels are calculated, and observed bands are assigned as transitions from 6A1g(s) ground state to various excited states. With the help of these assigned bands, Racah inter-electronic repulsion parameters B = 869 cm-1, C = 2080 cm-1 and cubic crystal field splitting parameter Dq = 730 cm-1 are calculated. Zero field splitting (ZFS) parameters D and E are calculated by the perturbation formulae and crystal field parameters obtained using superposition model. The calculated values of ZFS parameters are in good agreement with the experimental values obtained by EPR.

Assignment of the molecular origins of CEST signals at 2 ppm in rat brain.

PubMed

Zhang, Xiao-Yong; Xie, Jingping; Wang, Feng; Lin, Eugene C; Xu, Junzhong; Gochberg, Daniel F; Gore, John C; Zu, Zhongliang

2017-09-01

Chemical exchange saturation transfer effects at 2 ppm (CEST@2ppm) in brain have previously been interpreted as originating from creatine. However, protein guanidino amine protons may also contribute to CEST@2ppm. This study aims to investigate the molecular origins and specificity of CEST@2ppm in brain. Two experiments were performed: (i) samples containing egg white albumin and creatine were dialyzed using a semipermeable membrane to demonstrate that proteins and creatine can be separated by this method; and (ii) tissue homogenates of rat brain with and without dialysis to remove creatine were studied to measure the relative contributions of proteins and creatine to CEST@2ppm. The experiments indicate that dialysis can successfully remove creatine from proteins. Measurements on tissue homogenates show that, with the removal of creatine via dialysis, CEST@2ppm decreases to approximately 34% of its value before dialysis, which indicates that proteins and creatine have comparable contribution to the CEST@2ppm in brain. However, considering the contribution from peptides and amino acids to CEST@2ppm, creatine may have much less contribution to CEST@2ppm. The contribution of proteins, peptides, and amino acids to CEST@2ppm cannot be neglected. The CEST@2ppm measurements of creatine in rat brain should be interpreted with caution. Magn Reson Med 78:881-887, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

ESR investigations on γ-ray irradiated 3-methyl nylon 3

NASA Astrophysics Data System (ADS)

Catiker, Efkan; Guven, Olgun; Ozarslan, Ozdemir; Chipara, Mircea

2008-06-01

Electron spin resonance spectroscopy investigations on γ irradiated 3-methyl nylon 3 (poly-3-methyl β-alanine) are reported. The resonance spectra (recorded after the irradiation in nitrogen atmosphere has been stopped) have been attributed to the parallel and perpendicular components of a triplet line assigned to the delocalization of the uncoupled electron over an effective nuclear spin 1. It was suggested that this effective spin arises from the fast tunneling/rotation of a proton between two positions. The resonance spectra have been simulated with accuracy by using a simplified spin Hamiltonian and assuming Lorentzian-like resonance line shapes and axial asymmetry of the resonance line due to the trapping of free radicals in randomly oriented crystallites. The time evolution of free radicals in nitrogen atmosphere at room temperature has been analyzed. The decay kinetics of stable free radicals in 3-methyl nylon 3 (under inert atmosphere) has been investigated. It was shown that the radiation-induced radicals in inert atmosphere decay through a unimolecular reaction.

Calculation and measurement of radiation corrections for plasmon resonances in nanoparticles

NASA Astrophysics Data System (ADS)

Hung, L.; Lee, S. Y.; McGovern, O.; Rabin, O.; Mayergoyz, I.

2013-08-01

The problem of plasmon resonances in metallic nanoparticles can be formulated as an eigenvalue problem under the condition that the wavelengths of the incident radiation are much larger than the particle dimensions. As the nanoparticle size increases, the quasistatic condition is no longer valid. For this reason, the accuracy of the electrostatic approximation may be compromised and appropriate radiation corrections for the calculation of resonance permittivities and resonance wavelengths are needed. In this paper, we present the radiation corrections in the framework of the eigenvalue method for plasmon mode analysis and demonstrate that the computational results accurately match analytical solutions (for nanospheres) and experimental data (for nanorings and nanocubes). We also demonstrate that the optical spectra of silver nanocube suspensions can be fully assigned to dipole-type resonance modes when radiation corrections are introduced. Finally, our method is used to predict the resonance wavelengths for face-to-face silver nanocube dimers on glass substrates. These results may be useful for the indirect measurements of the gaps in the dimers from extinction cross-section observations.

Photogenerated radical intermediates of vitamin K 1: a time-resolved resonance Raman study

NASA Astrophysics Data System (ADS)

Balakrishnan, G.; Umapathy, S.

1999-01-01

Quinones play a vital role in the process of electron transfer in bacterial photosynthetic reaction centers. It is of interest to investigate the photochemical reactions involving quinones with a view to elucidating the structure-function relationships in the biological processes. Resonance Raman spectra of radical anions and the time-resolved resonance Raman spectra of vitamin K 1 (model compound for Q A in Rhodopseudomonas viridis, a bacterial photosynthetic reception center) are presented. The photochemical intermediates of vitamin K 1, viz. radical anion, ketyl radical and o-quinone methide have been identified. The vibrational assignments of all these intermediates are made on the basis of comparison with our earlier TR3 studies on radical anions of naphthoquinone and menaquinone.

Coulomb and nuclear excitations of narrow resonances in 17Ne

DOE PAGES

Marganiec, J.; Wamers, F.; Aksouh, F.; ...

2016-05-25

New experimental data for dissociation of relativistic 17Ne projectiles incident on targets of lead, carbon, and polyethylene targets at GSI are presented. Special attention is paid to the excitation and decay of narrow resonant states in 17Ne. Distributions of internal energy in the 15O+p +p three-body system have been determined together with angular and partial-energy correlations between the decay products in different energy regions. The analysis was done using existing experimental data on 17Ne and its mirror nucleus 17N. The isobaric multiplet mass equation is used for assignment of observed resonances and their spins and parities. A combination of datamore » from the heavy and light targets yielded cross sections and transition probabilities for the Coulomb excitations of the narrow resonant states. Finally, the resulting transition probabilities provide information relevant for a better understanding of the 17Ne structure.« less

Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques.

PubMed

Singh, Gurpreet; Mohanty, B P; Saini, G S S

2016-02-15

Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide. Copyright © 2015 Elsevier B.V. All rights reserved.

Study of D J meson decays to D +π-, D 0π+ and D ∗+π- final states in pp collisions

NASA Astrophysics Data System (ADS)

Aaij, R.; Adeva, B.; Adinolfi, M.; Adrover, C.; Affolder, A.; Ajaltouni, Z.; Albrecht, J.; Alessio, F.; Alexander, M.; Ali, S.; Alkhazov, G.; Cartelle, P. Alvarez; Alves, A. A.; Amato, S.; Amerio, S.; Amhis, Y.; Anderlini, L.; Anderson, J.; Andreassen, R.; Andrews, J. E.; Appleby, R. B.; Gutierrez, O. Aquines; Archilli, F.; Artamonov, A.; Artuso, M.; Aslanides, E.; Auriemma, G.; Baalouch, M.; Bachmann, S.; Back, J. J.; Baesso, C.; Balagura, V.; Baldini, W.; Barlow, R. J.; Barschel, C.; Barsuk, S.; Barter, W.; Bauer, Th.; Bay, A.; Beddow, J.; Bedeschi, F.; Bediaga, I.; Belogurov, S.; Belous, K.; Belyaev, I.; Ben-Haim, E.; Bencivenni, G.; Benson, S.; Benton, J.; Berezhnoy, A.; Bernet, R.; Bettler, M.-O.; van Beuzekom, M.; Bien, A.; Bifani, S.; Bird, T.; Bizzeti, A.; Bjørnstad, P. M.; Blake, T.; Blanc, F.; Blouw, J.; Blusk, S.; Bocci, V.; Bondar, A.; Bondar, N.; Bonivento, W.; Borghi, S.; Borgia, A.; Bowcock, T. J. V.; Bowen, E.; Bozzi, C.; Brambach, T.; van den Brand, J.; Bressieux, J.; Brett, D.; Britsch, M.; Britton, T.; Brook, N. H.; Brown, H.; Burducea, I.; Bursche, A.; Busetto, G.; Buytaert, J.; Cadeddu, S.; Callot, O.; Calvi, M.; Gomez, M. Calvo; Camboni, A.; Campana, P.; Perez, D. Campora; Carbone, A.; Carboni, G.; Cardinale, R.; Cardini, A.; Carranza-Mejia, H.; Carson, L.; Akiba, K. Carvalho; Casse, G.; Garcia, L. Castillo; Cattaneo, M.; Cauet, Ch.; Cenci, R.; Charles, M.; Charpentier, Ph.; Chen, P.; Chiapolini, N.; Chrzaszcz, M.; Ciba, K.; Vidal, X. Cid; Ciezarek, G.; Clarke, P. E. L.; Clemencic, M.; Cliff, H. V.; Closier, J.; Coca, C.; Coco, V.; Cogan, J.; Cogneras, E.; Collins, P.; Comerma-Montells, A.; Contu, A.; Cook, A.; Coombes, M.; Coquereau, S.; Corti, G.; Couturier, B.; Cowan, G. A.; Craik, D. C.; Cunliffe, S.; Currie, R.; D'Ambrosio, C.; David, P.; David, P. N. Y.; Davis, A.; De Bonis, I.; De Bruyn, K.; De Capua, S.; De Cian, M.; De Miranda, J. M.; De Paula, L.; De Silva, W.; De Simone, P.; Decamp, D.; Deckenhoff, M.; Del Buono, L.; Déléage, N.; Derkach, D.; Deschamps, O.; Dettori, F.; Di Canto, A.; Dijkstra, H.; Dogaru, M.; Donleavy, S.; Dordei, F.; Suárez, A. Dosil; Dossett, D.; Dovbnya, A.; Dupertuis, F.; Durante, P.; Dzhelyadin, R.; Dziurda, A.; Dzyuba, A.; Easo, S.; Egede, U.; Egorychev, V.; Eidelman, S.; van Eijk, D.; Eisenhardt, S.; Eitschberger, U.; Ekelhof, R.; Eklund, L.; El Rifai, I.; Elsasser, Ch.; Falabella, A.; Färber, C.; Fardell, G.; Farinelli, C.; Farry, S.; Fave, V.; Ferguson, D.; Albor, V. Fernandez; Rodrigues, F. Ferreira; Ferro-Luzzi, M.; Filippov, S.; Fiore, M.; Fitzpatrick, C.; Fontana, M.; Fontanelli, F.; Forty, R.; Francisco, O.; Frank, M.; Frei, C.; Frosini, M.; Furcas, S.; Furfaro, E.; Torreira, A. Gallas; Galli, D.; Gandelman, M.; Gandini, P.; Gao, Y.; Garofoli, J.; Garosi, P.; Tico, J. Garra; Garrido, L.; Gaspar, C.; Gauld, R.; Gersabeck, E.; Gersabeck, M.; Gershon, T.; Ghez, Ph.; Gibson, V.; Giubega, L.; Gligorov, V. V.; Göbel, C.; Golubkov, D.; Golutvin, A.; Gomes, A.; Gordon, H.; Gándara, M. Grabalosa; Diaz, R. Graciani; Cardoso, L. A. Granado; Graugés, E.; Graziani, G.; Grecu, A.; Greening, E.; Gregson, S.; Griffith, P.; Grünberg, O.; Gui, B.; Gushchin, E.; Guz, Yu.; Gys, T.; Hadjivasiliou, C.; Haefeli, G.; Haen, C.; Haines, S. C.; Hall, S.; Hamilton, B.; Hampson, T.; Hansmann-Menzemer, S.; Harnew, N.; Harnew, S. T.; Harrison, J.; Hartmann, T.; He, J.; Head, T.; Heijne, V.; Hennessy, K.; Henrard, P.; Morata, J. A. Hernando; van Herwijnen, E.; Hicheur, A.; Hicks, E.; Hill, D.; Hoballah, M.; Hombach, C.; Hopchev, P.; Hulsbergen, W.; Hunt, P.; Huse, T.; Hussain, N.; Hutchcroft, D.; Hynds, D.; Iakovenko, V.; Idzik, M.; Ilten, P.; Jacobsson, R.; Jaeger, A.; Jans, E.; Jaton, P.; Jawahery, A.; Jing, F.; John, M.; Johnson, D.; Jones, C. R.; Joram, C.; Jost, B.; Kaballo, M.; Kandybei, S.; Kanso, W.; Karacson, M.; Karbach, T. M.; Kenyon, I. R.; Ketel, T.; Keune, A.; Khanji, B.; Kochebina, O.; Komarov, I.; Koopman, R. F.; Koppenburg, P.; Korolev, M.; Kozlinskiy, A.; Kravchuk, L.; Kreplin, K.; Kreps, M.; Krocker, G.; Krokovny, P.; Kruse, F.; Kucharczyk, M.; Kudryavtsev, V.; Kvaratskheliya, T.; La Thi, V. N.; Lacarrere, D.; Lafferty, G.; Lai, A.; Lambert, D.; Lambert, R. W.; Lanciotti, E.; Lanfranchi, G.; Langenbruch, C.; Latham, T.; Lazzeroni, C.; Le Gac, R.; van Leerdam, J.; Lees, J.-P.; Lefèvre, R.; Leflat, A.; Lefrançois, J.; Leo, S.; Leroy, O.; Lesiak, T.; Leverington, B.; Li, Y.; Gioi, L. Li; Liles, M.; Lindner, R.; Linn, C.; Liu, B.; Liu, G.; Lohn, S.; Longstaff, I.; Lopes, J. H.; Lopez-March, N.; Lu, H.; Lucchesi, D.; Luisier, J.; Luo, H.; Machefert, F.; Machikhiliyan, I. V.; Maciuc, F.; Maev, O.; Malde, S.; Manca, G.; Mancinelli, G.; Maratas, J.; Marconi, U.; Märki, R.; Marks, J.; Martellotti, G.; Martens, A.; Sánchez, A. M´ın; Martinelli, M.; Santos, D. Martinez; Tostes, D. Martins; Massafferri, A.; Matev, R.; Mathe, Z.; Matteuzzi, C.; Maurice, E.; Mazurov, A.; Skelly, B. Mc; McCarthy, J.; McNab, A.; McNulty, R.; Meadows, B.; Meier, F.; Meissner, M.; Merk, M.; Milanes, D. A.; Minard, M.-N.; Rodriguez, J. Molina; Monteil, S.; Moran, D.; Morawski, P.; Mordà, A.; Morello, M. J.; Mountain, R.; Mous, I.; Muheim, F.; Müller, K.; Muresan, R.; Muryn, B.; Muster, B.; Naik, P.; Nakada, T.; Nandakumar, R.; Nasteva, I.; Needham, M.; Neubert, S.; Neufeld, N.; Nguyen, A. D.; Nguyen, T. D.; Nguyen-Mau, C.; Nicol, M.; Niess, V.; Niet, R.; Nikitin, N.; Nikodem, T.; Nomerotski, A.; Novoselov, A.; Oblakowska-Mucha, A.; Obraztsov, V.; Oggero, S.; Ogilvy, S.; Okhrimenko, O.; Oldeman, R.; Orlandea, M.; Goicochea, J. M. Otalora; Owen, P.; Oyanguren, A.; Pal, B. K.; Palano, A.; Palutan, M.; Panman, J.; Papanestis, A.; Pappagallo, M.; Parkes, C.; Parkinson, C. J.; Passaleva, G.; Patel, G. D.; Patel, M.; Patrick, G. N.; Patrignani, C.; Pavel-Nicorescu, C.; Alvarez, A. Pazos; Pellegrino, A.; Penso, G.; Altarelli, M. Pepe; Perazzini, S.; Trigo, E. Perez; Yzquierdo, A. Pérez-Calero; Perret, P.; Perrin-Terrin, M.; Pessina, G.; Petridis, K.; Petrolini, A.; Phan, A.; Olloqui, E. Picatoste; Pietrzyk, B.; Pilař, T.; Pinci, D.; Playfer, S.; Casasus, M. Plo; Polci, F.; Polok, G.; Poluektov, A.; Polycarpo, E.; Popov, A.; Popov, D.; Popovici, B.; Potterat, C.; Powell, A.; Prisciandaro, J.; Pritchard, A.; Prouve, C.; Pugatch, V.; Navarro, A. Puig; Punzi, G.; Qian, W.; Rademacker, J. H.; Rakotomiaramanana, B.; Rangel, M. S.; Raniuk, I.; Rauschmayr, N.; Raven, G.; Redford, S.; Reid, M. M.; dos Reis, A. C.; Ricciardi, S.; Richards, A.; Rinnert, K.; Molina, V. Rives; Romero, D. A. Roa; Robbe, P.; Roberts, D. A.; Rodrigues, E.; Perez, P. Rodriguez; Roiser, S.; Romanovsky, V.; Vidal, A. Romero; Rouvinet, J.; Ruf, T.; Ruffini, F.; Ruiz, H.; Valls, P. Ruiz; Sabatino, G.; Silva, J. J. Saborido; Sagidova, N.; Sail, P.; Saitta, B.; Guimaraes, V. Salustino; Salzmann, C.; Sedes, B. Sanmartin; Sannino, M.; Santacesaria, R.; Rios, C. Santamarina; Santovetti, E.; Sapunov, M.; Sarti, A.; Satriano, C.; Satta, A.; Savrie, M.; Savrina, D.; Schaack, P.; Schiller, M.; Schindler, H.; Schlupp, M.; Schmelling, M.; Schmidt, B.; Schneider, O.; Schopper, A.; Schune, M.-H.; Schwemmer, R.; Sciascia, B.; Sciubba, A.; Seco, M.; Semennikov, A.; Senderowska, K.; Sepp, I.; Serra, N.; Serrano, J.; Seyfert, P.; Shapkin, M.; Shapoval, I.; Shatalov, P.; Shcheglov, Y.; Shears, T.; Shekhtman, L.; Shevchenko, O.; Shevchenko, V.; Shires, A.; Coutinho, R. Silva; Sirendi, M.; Skwarnicki, T.; Smith, N. A.; Smith, E.; Smith, J.; Smith, M.; Sokoloff, M. D.; Soler, F. J. P.; Soomro, F.; Souza, D.; De Paula, B. Souza; Spaan, B.; Sparkes, A.; Spradlin, P.; Stagni, F.; Stahl, S.; Steinkamp, O.; Stevenson, S.; Stoica, S.; Stone, S.; Storaci, B.; Straticiuc, M.; Straumann, U.; Subbiah, V. K.; Sun, L.; Swientek, S.; Syropoulos, V.; Szczekowski, M.; Szczypka, P.; Szumlak, T.; T'Jampens, S.; Teklishyn, M.; Teodorescu, E.; Teubert, F.; Thomas, C.; Thomas, E.; van Tilburg, J.; Tisserand, V.; Tobin, M.; Tolk, S.; Tonelli, D.; Topp-Joergensen, S.; Torr, N.; Tournefier, E.; Tourneur, S.; Tran, M. T.; Tresch, M.; Tsaregorodtsev, A.; Tsopelas, P.; Tuning, N.; Garcia, M. Ubeda; Ukleja, A.; Urner, D.; Ustyuzhanin, A.; Uwer, U.; Vagnoni, V.; Valenti, G.; Vallier, A.; Van Dijk, M.; Gomez, R. Vazquez; Regueiro, P. Vazquez; Sierra, C. Vázquez; Vecchi, S.; Velthuis, J. J.; Veltri, M.; Veneziano, G.; Vesterinen, M.; Viaud, B.; Vieira, D.; Vilasis-Cardona, X.; Vollhardt, A.; Volyanskyy, D.; Voong, D.; Vorobyev, A.; Vorobyev, V.; Voß, C.; Voss, H.; Waldi, R.; Wallace, C.; Wallace, R.; Wandernoth, S.; Wang, J.; Ward, D. R.; Watson, N. K.; Webber, A. D.; Websdale, D.; Whitehead, M.; Wicht, J.; Wiechczynski, J.; Wiedner, D.; Wiggers, L.; Wilkinson, G.; Williams, M. P.; Williams, M.; Wilson, F. F.; Wimberley, J.; Wishahi, J.; Witek, M.; Wotton, S. A.; Wright, S.; Wu, S.; Wyllie, K.; Xie, Y.; Xing, Z.; Yang, Z.; Young, R.; Yuan, X.; Yushchenko, O.; Zangoli, M.; Zavertyaev, M.; Zhang, F.; Zhang, L.; Zhang, W. C.; Zhang, Y.; Zhelezov, A.; Zhokhov, A.; Zhong, L.; Zvyagin, A.

2013-09-01

A study of D +π-, D 0π+ and D ∗+π- final states is performed using pp collision data, corresponding to an integrated luminosity of 1.0 fb-1, collected at a centre-of-mass energy of 7 TeV with the LHCb detector. The D 1(2420)0 resonance is observed in the D ∗+π- final state and the resonance is observed in the D +π-, D 0π+ and D ∗+π- final states. For both resonances, their properties and spin-parity assignments are obtained. In addition, two natural parity and two unnatural parity resonances are observed in the mass region between 2500 and 2800 MeV. Further structures in the region around 3000 MeV are observed in all the D ∗+π-, D +π- and D 0π+ final states. [Figure not available: see fulltext.

Origin of the positive spin- 1 2 photoluminescence-detected magnetic resonance in π-conjugated materials and devices

DOE PAGES

Chen, Ying; Cai, Min; Hellerich, Emily; ...

2015-09-02

The spin-1/2 single-modulation (SM) and double-modulation (DM) photoluminescence (PL) detected magnetic resonance (PLDMR) in poly(2-methoxy-5-(2'-ethyl)–hexoxy-1,4- phenylene vinylene) (MEH-PPV) films and poly(3-hexylthiophene) (P3HT) films is described, analyzed, and discussed. In particular, the models based on spin-dependent recombination of charge pairs (SDR) and triplet-polaron quenching (TPQ) are evaluated. By analyzing the dependence of the resonance amplitude on the microwave chopping (modulation) frequency using rate equations, it is demonstrated that the TPQ model can well explain the observed resonance behavior, while SDR model cannot reproduce the results of the observed DM-PLDMR. As a result, the observed spin-1/2 PLDMR is assigned to TPQ rathermore » than SDR, even though the latter may also be present.« less

Incidental Memory Encoding Assessed with Signal Detection Theory and Functional Magnetic Resonance Imaging (fMRI).

PubMed

Clemens, Benjamin; Regenbogen, Christina; Koch, Kathrin; Backes, Volker; Romanczuk-Seiferth, Nina; Pauly, Katharina; Shah, N Jon; Schneider, Frank; Habel, Ute; Kellermann, Thilo

2015-01-01

In functional magnetic resonance imaging (fMRI) studies that apply a "subsequent memory" approach, successful encoding is indicated by increased fMRI activity during the encoding phase for hits vs. misses, in areas underlying memory encoding such as the hippocampal formation. Signal-detection theory (SDT) can be used to analyze memory-related fMRI activity as a function of the participant's memory trace strength (d(')). The goal of the present study was to use SDT to examine the relationship between fMRI activity during incidental encoding and participants' recognition performance. To implement a new approach, post-experimental group assignment into High- or Low Performers (HP or LP) was based on 29 healthy participants' recognition performance, assessed with SDT. The analyses focused on the interaction between the factors group (HP vs. LP) and recognition performance (hits vs. misses). A whole-brain analysis revealed increased activation for HP vs. LP during incidental encoding for remembered vs. forgotten items (hits > misses) in the insula/temporo-parietal junction (TPJ) and the fusiform gyrus (FFG). Parameter estimates in these regions exhibited a significant positive correlation with d('). As these brain regions are highly relevant for salience detection (insula), stimulus-driven attention (TPJ), and content-specific processing of mnemonic stimuli (FFG), we suggest that HPs' elevated memory performance was associated with enhanced attentional and content-specific sensory processing during the encoding phase. We provide first correlative evidence that encoding-related activity in content-specific sensory areas and content-independent attention and salience detection areas influences memory performance in a task with incidental encoding of facial stimuli. Based on our findings, we discuss whether the aforementioned group differences in brain activity during incidental encoding might constitute the basis of general differences in memory performance between HP and LP.

Photoabsorption and S 2p photoionization of the SF6 molecule: resonances in the excitation energy range of 200-280 eV.

PubMed

Stener, M; Bolognesi, P; Coreno, M; O'Keeffe, P; Feyer, V; Fronzoni, G; Decleva, P; Avaldi, L; Kivimäki, A

2011-05-07

Photoabsorption and S 2p photoionization of the SF(6) molecule have been studied experimentally and theoretically in the excitation energy range up to 100 eV above the S 2p ionization potentials. In addition to the well-known 2t(2g) and 4e(g) shape resonances, the spin-orbit-resolved S 2p photoionization cross sections display two weak resonances between 200 and 210 eV, a wide resonance around 217 eV, a Fano-type resonance around 240 eV, and a second wide resonance around 260 eV. Calculations based on time-dependent density functional theory allow us to assign the 217-eV and 260-eV features to the shape resonances in S 2p photoionization. The Fano resonance is caused by the interference between the direct S 2p photoionization channel and the resonant channel that results from the participator decay of the S 2s(-1)6t(1u) excited state. The weak resonances below 210-eV photon energy, not predicted by theory, are tentatively suggested to originate from the coupling between S 2p shake-up photoionization and S 2p single-hole photoionization. The experimental and calculated angular anisotropy parameters for S 2p photoionization are in good agreement.

Textual and Discoursal Resources Used in the Essay Genre in Sociology and English

ERIC Educational Resources Information Center

Bruce, Ian

2010-01-01

Research that has examined university assignment writing has varied from large-scale, inventorial surveys across disciplines to more specific, finer-grained analyses of the assignment requirements of specific disciplines. However, while such research has involved surveys of the views and expectations of faculty or the analysis of assignment tasks,…

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

PubMed

Tolić, Nikola; Liu, Yina; Liyu, Andrey; Shen, Yufeng; Tfaily, Malak M; Kujawinski, Elizabeth B; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W; Paša-Tolić, Ljiljana; Hess, Nancy J

2017-12-05

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

On performance of cylindrical dipole antenna in diagnostics of wave phenomena in space plasma

NASA Astrophysics Data System (ADS)

Kiraga, A.

Tubular and wire antennas have been employed since an advent of in situ measurements in space. It is generally accepted that they are well suited to recipe electromagnetic radiation from remote sources as well as divers local plasma emissions. Quasi thermal noise spectroscopy provides an example of well documented, both experimentally and theoretically, technique to study solar wind plasma. In many data sets of wave spectra, recorded with use of tubular or wire antennas at all altitudes inside a plasma sphere, there is pronounced, permanent, variable frequency spectral structure, routinely assigned to upper hybrid band (UHR) emissions. On the other hand, spectral structure, which could be assigned to upper hybrid band, is less pronounced and infrequent, in sets of wave spectra recorded in polar region with the use of spherical double probes. These apparently inconsistent observations have not drawn much attention of wave community. Assignment to UHR emission have been bolstered by theoretical plausibility, permanency in data sets, frequency verification with independent techniques and conviction that measurements were performed with good voltmeter with well known properties. It has been recognized that stray capacitance acts as a voltage divider and underestimates real voltage imposed on antenna. But in sufficiently dense and cold main plasma component, even short antenna is inductive in some frequency band below upper hybrid frequency. Stray capacitance and antenna inductance result in circuit resonance, which is very pronounced, if antenna resistance is low and input resistance is high. In such circumstances, a good voltmeter concept is very misleading. In this report we show that good voltmeter concept is not sufficient for interpretation of passive mode spectra recorded with tubular antenna on IK -19, APEX and CORONAS satellites. With orbit inclination of ~80deg and altitude range of 500-3000km, very divers plasmas were encountered, but distinct plasma emission within upper hybrid band do not show up. In equivalent circuit simulations, salient spectral characteristics can be matched and related to specific impedances. Equivalent circuit analysis was enforced by apparent difference between local plasma frequencies derived from onboard topside sounder data and frequencies of adjacent maximum in passive mode spectra. It has been subsequently verified and developed with the aid of impedance measurements, onboard sounder data and analysis of electron beam induced spectra. We show that circuit resonance can be neatly controlled to provide very low interference technique to monitor density of cold plasma. Circuit resonance monitoring, if properly coupled with impedance measurements and electron beam injection may be very useful, low interference tool for diagnostics of highly structured plasmas like those in auroral region.

Basic Vision Events.

DTIC Science & Technology

1982-08-01

6 4 Resonance Raman Spectrum of Astaxanthin .............................. 8 5 Excitation Profile of CC1 4...Solution of Astaxanthin ........................ 9 LIST OF TABLES Table Page I Suggested Vibrational Assignments Frequencies (cm- 1...past year. These measurements on the carotenoid, astaxanthin , showed an alteration in the C=C stretching vibration from 1517 cm ŕ , under the action

Solution structure of a lipid transfer protein extracted from rice seeds. Comparison with homologous proteins.

PubMed

Poznanski, J; Sodano, P; Suh, S W; Lee, J Y; Ptak, M; Vovelle, F

1999-02-01

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the three dimensional structure of rice nonspecific lipid transfer protein (ns-LTP), a 91 amino acid residue protein belonging to the broad family of plant ns-LTP. Sequence specific assignment was obtained for all but three HN backbone 1H resonances and for more than 95% of the 1H side-chain resonances using a combination of 1H 2D NOESY; TOCSY and COSY experiments at 293 K. The structure was calculated on the basis of four disulfide bridge restraints, 1259 distance constraints derived from 1H-1H Overhauser effects, 72 phi angle restraints and 32 hydrogen-bond restraints. The final solution structure involves four helices (H1: Cys3-Arg18, H2: Ala25-Ala37, H3: Thr41-Ala54 and H4: Ala66-Cys73) followed by a long C-terminal tail (T) with no observable regular structure. N-capping residues (Thr2, Ser24, Thr40), whose side-chain oxygen atoms are involved in hydrogen bonds with i + 3 amide proton additionally stabilize the N termini of the first three helices. The fourth helix involving Pro residues display a mixture of alpha and 3(10) conformation. The rms deviation of 14 final structures with respect to the average structure is 1.14 +/- 0.16 A for all heavy atoms (C, N, O and S) and 0.72 +/- 0.01 A for the backbone atoms. The global fold of rice ns-LTP is close to the previously published structures of wheat, barley and maize ns-LTPs exhibiting nearly identical pattern of the numerous sequence specific interactions. As reported previously for different four-helix topology proteins, hydrophobic, hydrogen bonding and electrostatic mechanisms of fold stabilization were found for the rice ns-LTP. The sequential alignment of 36 ns-LTP primary structures strongly suggests that there is a uniform pattern of specific long-range interactions (in terms of sequence), which stabilize the fold of all plant ns-LTPs.

Evaluation of Automatically Assigned Job-Specific Interview Modules

PubMed Central

Friesen, Melissa C.; Lan, Qing; Ge, Calvin; Locke, Sarah J.; Hosgood, Dean; Fritschi, Lin; Sadkowsky, Troy; Chen, Yu-Cheng; Wei, Hu; Xu, Jun; Lam, Tai Hing; Kwong, Yok Lam; Chen, Kexin; Xu, Caigang; Su, Yu-Chieh; Chiu, Brian C. H.; Ip, Kai Ming Dennis; Purdue, Mark P.; Bassig, Bryan A.; Rothman, Nat; Vermeulen, Roel

2016-01-01

Objective: In community-based epidemiological studies, job- and industry-specific ‘modules’ are often used to systematically obtain details about the subject’s work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the correct module. We evaluated, in the context of a case–control study of lymphoid neoplasms in Asia (‘AsiaLymph’), the performance of an algorithm that provided automatic, real-time module assignment during a computer-assisted personal interview. Methods: AsiaLymph’s occupational component began with a lifetime occupational history questionnaire with free-text responses and three solvent exposure screening questions. To assign each job to one of 23 study-specific modules, an algorithm automatically searched the free-text responses to the questions ‘job title’ and ‘product made or services provided by employer’ using a list of module-specific keywords, comprising over 5800 keywords in English, Traditional and Simplified Chinese. Hierarchical decision rules were used when the keyword match triggered multiple modules. If no keyword match was identified, a generic solvent module was assigned if the subject responded ‘yes’ to any of the three solvent screening questions. If these question responses were all ‘no’, a work location module was assigned, which redirected the subject to the farming, teaching, health professional, solvent, or industry solvent modules or ended the questions for that job, depending on the location response. We conducted a reliability assessment that compared the algorithm-assigned modules to consensus module assignments made by two industrial hygienists for a subset of 1251 (of 11409) jobs selected using a stratified random selection procedure using module-specific strata. Discordant assignments between the algorithm and consensus assignments (483 jobs) were qualitatively reviewed by the hygienists to evaluate the potential information lost from missed questions with using the algorithm-assigned module (none, low, medium, high). Results: The most frequently assigned modules were the work location (33%), solvent (20%), farming and food industry (19%), and dry cleaning and textile industry (6.4%) modules. In the reliability subset, the algorithm assignment had an exact match to the expert consensus-assigned module for 722 (57.7%) of the 1251 jobs. Overall, adjusted for the proportion of jobs in each stratum, we estimated that 86% of the algorithm-assigned modules would result in no information loss, 2% would have low information loss, and 12% would have medium to high information loss. Medium to high information loss occurred for <10% of the jobs assigned the generic solvent module and for 21, 32, and 31% of the jobs assigned the work location module with location responses of ‘someplace else’, ‘factory’, and ‘don’t know’, respectively. Other work location responses had ≤8% with medium to high information loss because of redirections to other modules. Medium to high information loss occurred more frequently when a job description matched with multiple keywords pointing to different modules (29–69%, depending on the triggered assignment rule). Conclusions: These evaluations demonstrated that automatically assigned modules can reliably reproduce an expert’s module assignment without the direct involvement of an industrial hygienist or interviewer. The feasibility of adapting this framework to other studies will be language- and exposure-specific. PMID:27250109

Evaluation of Automatically Assigned Job-Specific Interview Modules.

PubMed

Friesen, Melissa C; Lan, Qing; Ge, Calvin; Locke, Sarah J; Hosgood, Dean; Fritschi, Lin; Sadkowsky, Troy; Chen, Yu-Cheng; Wei, Hu; Xu, Jun; Lam, Tai Hing; Kwong, Yok Lam; Chen, Kexin; Xu, Caigang; Su, Yu-Chieh; Chiu, Brian C H; Ip, Kai Ming Dennis; Purdue, Mark P; Bassig, Bryan A; Rothman, Nat; Vermeulen, Roel

2016-08-01

In community-based epidemiological studies, job- and industry-specific 'modules' are often used to systematically obtain details about the subject's work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the correct module. We evaluated, in the context of a case-control study of lymphoid neoplasms in Asia ('AsiaLymph'), the performance of an algorithm that provided automatic, real-time module assignment during a computer-assisted personal interview. AsiaLymph's occupational component began with a lifetime occupational history questionnaire with free-text responses and three solvent exposure screening questions. To assign each job to one of 23 study-specific modules, an algorithm automatically searched the free-text responses to the questions 'job title' and 'product made or services provided by employer' using a list of module-specific keywords, comprising over 5800 keywords in English, Traditional and Simplified Chinese. Hierarchical decision rules were used when the keyword match triggered multiple modules. If no keyword match was identified, a generic solvent module was assigned if the subject responded 'yes' to any of the three solvent screening questions. If these question responses were all 'no', a work location module was assigned, which redirected the subject to the farming, teaching, health professional, solvent, or industry solvent modules or ended the questions for that job, depending on the location response. We conducted a reliability assessment that compared the algorithm-assigned modules to consensus module assignments made by two industrial hygienists for a subset of 1251 (of 11409) jobs selected using a stratified random selection procedure using module-specific strata. Discordant assignments between the algorithm and consensus assignments (483 jobs) were qualitatively reviewed by the hygienists to evaluate the potential information lost from missed questions with using the algorithm-assigned module (none, low, medium, high). The most frequently assigned modules were the work location (33%), solvent (20%), farming and food industry (19%), and dry cleaning and textile industry (6.4%) modules. In the reliability subset, the algorithm assignment had an exact match to the expert consensus-assigned module for 722 (57.7%) of the 1251 jobs. Overall, adjusted for the proportion of jobs in each stratum, we estimated that 86% of the algorithm-assigned modules would result in no information loss, 2% would have low information loss, and 12% would have medium to high information loss. Medium to high information loss occurred for <10% of the jobs assigned the generic solvent module and for 21, 32, and 31% of the jobs assigned the work location module with location responses of 'someplace else', 'factory', and 'don't know', respectively. Other work location responses had ≤8% with medium to high information loss because of redirections to other modules. Medium to high information loss occurred more frequently when a job description matched with multiple keywords pointing to different modules (29-69%, depending on the triggered assignment rule). These evaluations demonstrated that automatically assigned modules can reliably reproduce an expert's module assignment without the direct involvement of an industrial hygienist or interviewer. The feasibility of adapting this framework to other studies will be language- and exposure-specific. Published by Oxford University Press on behalf of the British Occupational Hygiene Society 2016.

Predictive models in the diagnosis and treatment of autoimmune epilepsy.

PubMed

Dubey, Divyanshu; Singh, Jaysingh; Britton, Jeffrey W; Pittock, Sean J; Flanagan, Eoin P; Lennon, Vanda A; Tillema, Jan-Mendelt; Wirrell, Elaine; Shin, Cheolsu; So, Elson; Cascino, Gregory D; Wingerchuk, Dean M; Hoerth, Matthew T; Shih, Jerry J; Nickels, Katherine C; McKeon, Andrew

2017-07-01

To validate predictive models for neural antibody positivity and immunotherapy response in epilepsy. We conducted a retrospective study of epilepsy cases at Mayo Clinic (Rochester-MN; Scottsdale-AZ, and Jacksonville-FL) in whom autoimmune encephalopathy/epilepsy/dementia autoantibody testing profiles were requested (06/30/2014-06/30/2016). An Antibody Prevalence in Epilepsy (APE) score, based on clinical characteristics, was assigned to each patient. Among patients who received immunotherapy, a Response to Immunotherapy in Epilepsy (RITE) score was assigned. Favorable seizure outcome was defined as >50% reduction of seizure frequency at the first follow-up. Serum and cerebrospinal fluid (CSF) from 1,736 patients were sent to the Mayo Clinic Neuroimmunology Laboratory for neural autoantibody evaluation. Three hundred eighty-seven of these patients met the diagnostic criteria for epilepsy. Central nervous system (CNS)-specific antibodies were detected in 44 patients. Certain clinical features such as new-onset epilepsy, autonomic dysfunction, viral prodrome, faciobrachial dystonic seizures/oral dyskinesia, inflammatory CSF profile, and mesial temporal magnetic resonance imaging (MRI) abnormalities had a significant association with positive antibody results. A significantly higher proportion of antibody-positive patients had an APE score ≥4 (97.7% vs. 21.6%, p < 0.01). Sensitivity and specificity of an APE score ≥4 to predict presence of specific neural auto-antibody were 97.7% and 77.9%, respectively. In the subset of patients who received immunotherapy (77), autonomic dysfunction, faciobrachial dystonic seizures/oral dyskinesia, early initiation of immunotherapy, and presence of antibodies targeting plasma membrane proteins (cell-surface antigens) were associated with favorable seizure outcome. Sensitivity and specificity of a RITE score ≥7 to predict favorable seizure outcome were 87.5% and 83.8%, respectively. APE and RITE scores can aid diagnosis, treatment, and prognostication of autoimmune epilepsy. A PowerPoint slide summarizing this article is available for download in the Supporting Information section here. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

H6+ in irradiated solid para-hydrogen and its decay dynamics: reinvestigation of quartet electron paramagnetic resonance lines assigned to H2-.

PubMed

Kumada, Takayuki; Tachikawa, Hiroto; Takayanagi, Toshiyuki

2005-03-07

The quartet electron paramagnetic resonance (EPR) lines observed in gamma- and X-ray irradiated solid para-H2, which have previously been assigned to H2-, are reinvestigated. We have reassigned the quartet lines to H6 rather than H2- mainly due to comparison of experimentally obtained EPR parameters to theoretical results. Based on the new assignment, trapping site, rotation, ortho-para conversion, quantum diffusion and isotope effect of H+ have been reinterpreted by the precise reanalysis as follows. The H6+ ion is composed of the collinearly aligned H2+ core at the center and two H2 rotors at both ends, occupies a single substitutional site, and has a precession motion around a crystalline axis with the angle of approximately 57 degrees. The ortho-para conversion of H2+ core of H6+ is completed within the time-scale of hours, whereas ortho-H2 molecules near H6+ convert much faster. H6+ diffuses quantum mechanically by the repetition of H6+ + H2 --> H2 + H6+ reaction. The diffusion terminates by the reaction, H6(+) + HD --> H5D(+) + H2, with a HD impurity contained in the para-H2 sample at natural abundance. Finally, we will propose a possible reason why H6+ is produced instead of H3+ in the irradiated solid H2.

"Miss! I'm Done!" Finishing Craft Assignments as a Situated Activity System in Preschool

ERIC Educational Resources Information Center

Deunk, Marjolein; Berenst, Jan; de Glopper, Kees

2010-01-01

We describe the Situated Activity System of finishing craft assignments in preschool: the specific, routinized way that child and teacher jointly close the child's craft assignment, employing a specific discourse pattern. We analyzed the interactions of 14 Dutch children between 2.1 and 3.10 years old while they were finishing their craft…

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

Castillo, Andrés M; Bernal, Andrés; Dieden, Reiner; Patiny, Luc; Wist, Julien

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

Elastic alpha-particle resonances as evidence of clustering at high excitation in 40Ca

NASA Astrophysics Data System (ADS)

Norrby, M.; Lönnroth, T.; Goldberg, V. Z.; Rogachev, G. V.; Golovkov, M. S.; Källman, K.-M.; Lattuada, M.; Perov, S. V.; Romano, S.; Skorodumov, B. B.; Tiourin, G. P.; Trzaska, W. H.; Tumino, A.; Vorontsov, A. N.

2011-08-01

The elastic-scattering reaction 36Ar + α was studied using the Thick Target Inverse Kinematics technique. Data were taken at a beam energy of 150 MeV in a reaction chamber filled with 4He gas, corresponding to the excitation region of 12-20 MeV in 40Ca. Using a simplified R -matrix method of analysis energies, widths and spin assignments were obtained for 137 resonances. The structure is discussed within the concept of α-cluster structure in the quasi-continuum of 40Ca and is compared to other nuclei in the same mass region.

Transition of lasing modes in polymeric opal photonic crystal resonating cavity.

PubMed

Shi, Lan-Ting; Zheng, Mei-Ling; Jin, Feng; Dong, Xian-Zi; Chen, Wei-Qiang; Zhao, Zhen-Sheng; Duan, Xuan-Ming

2016-06-10

We demonstrate the transition of lasing modes in the resonating cavity constructed by polystyrene opal photonic crystals and 7 wt. % tert-butyl Rhodamine B doped polymer film. Both single mode and multiple mode lasing emission are observed from the resonating cavity. The lasing threshold is determined to be 0.81  μJ/pulse for single mode lasing emission and 2.25  μJ/pulse for multiple mode lasing emission. The single mode lasing emission is attributed to photonic lasing resulting from the photonic bandgap effect of the opal photonic crystals, while the multiple mode lasing emission is assigned to random lasing due to the defects in the photonic crystals. The result would benefit the development of low threshold polymeric solid state photonic crystal lasers.

Identification of the Ga interstitial in Al(x)Ga(1-x)As by optically detected magnetic resonance

NASA Technical Reports Server (NTRS)

Kennedy, T. A.; Spencer, M. G.

1986-01-01

A new optically detected magnetic resonance spectrum in Al(x)Ga(1-x)As is reported and assigned to native Ga interstitials. Luminescence-quenching signals were observed over the energy region from 0.75 to 1.1 eV. The optically detected magnetic resonance is nearly isotropic, with spin-Hamiltonian parameters g = 2.025 + or - 0.006, central hyperfine splitting A(Ga-69) = 0.050 + or - 0.001/cm, and A(Ga-71) = 0.064 + or - 0.001/cm for H near the 001 line. The strong hyperfine coupling denotes an electronic state of A1 symmetry, which current theories predict for the Ga interstitial but not the Ga antisite. The slight anisotropy probably indicates that the Ga(i) is paired with a second, unknown defect.

Scissors Mode of 162 Dy Studied from Resonance Neutron Capture

DOE PAGES

Baramsai, B.; Bečvář, F.; Bredeweg, T. A.; ...

2015-05-28

Multi-step cascade γ-ray spectra from the neutron capture at isolated resonances of 161Dy nucleus were measured at the LANSCE/DANCE time-of-flight facility in Los Alamos National Laboratory. The objectives of this experiment were to confirm and possibly extend the spin assignment of s-wave neutron resonances and get new information on photon strength functions with emphasis on the role of the M1 scissors mode vibration. The preliminary results show that the scissors mode plays a significant role in all transitions between accessible states of the studied nucleus. The photon strength functions describing well our data are compared to results from 3He-induced reactions,more » (n,γ) experiments on Gd isotopes, and (γ,γ’) reactions.« less

Nonlinear resonance ultrasonic vibrations in Czochralski-silicon wafers

NASA Astrophysics Data System (ADS)

Ostapenko, S.; Tarasov, I.

2000-04-01

A resonance effect of generation of subharmonic acoustic vibrations is observed in as-grown, oxidized, and epitaxial silicon wafers. Ultrasonic vibrations were generated into a standard 200 mm Czochralski-silicon (Cz-Si) wafer using a circular ultrasound transducer with major frequency of the radial vibrations at about 26 kHz. By tuning frequency (f) of the transducer within a resonance curve, we observed a generation of intense f/2 subharmonic acoustic mode assigned as a "whistle." The whistle mode has a threshold amplitude behavior and narrow frequency band. The whistle is attributed to a nonlinear acoustic vibration of a silicon plate. It is demonstrated that characteristics of the whistle mode are sensitive to internal stress and can be used for quality control and in-line diagnostics of oxidized and epitaxial Cz-Si wafers.

Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems

NASA Astrophysics Data System (ADS)

Singh, Amrinder; Dubey, Abhinav; Adiga, Satish K.; Atreya, Hanudatta S.

2018-01-01

We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide.

PubMed

Sardo, Mariana; Siegel, Renée; Santos, Sérgio M; Rocha, João; Gomes, José R B; Mafra, Luis

2012-06-28

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.

Novel NMR tools to study structure and dynamics of biomembranes.

PubMed

Gawrisch, Klaus; Eldho, Nadukkudy V; Polozov, Ivan V

2002-06-01

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

The Reduction of a Nitrile (CN) Group by Sodium Borohydride. The Preparation of Phosphine--Amine and Phosphine--Iimidate Complesex of Tungsten Carbonyl.

ERIC Educational Resources Information Center

Faust, Kristen E.; Storhoff, Bruce N.

1989-01-01

Describes an experiment for advanced-level undergraduate students for extending student experiences involving recording and interpreting infrared (IR) and nuclear magnetic resonance (NMR) spectra from reactions of organometallic compounds. Experimental procedures, analyses and structural assignments, and suggestions for extension and modification…

NMR spectra of 3β-hydroxy-5α-cholane derivatives, zymosterol synthesis intermediates

NASA Astrophysics Data System (ADS)

Baranovsky, A. V.; Bolotin, A. A.; Kiselev, V. P.

2011-05-01

Proton and carbon resonances in NMR spectra of a number of derivatives of 3β-hydroxy-5α-cholanes, zymosterol synthesis intermediates, have been completely assigned using 2D NMR spectroscopy methods. The stereochemistry of the chiral centers and the structures of the molecules have been confirmed.

A general system for automatic biomedical image segmentation using intensity neighborhoods.

PubMed

Chen, Cheng; Ozolek, John A; Wang, Wei; Rohde, Gustavo K

2011-01-01

Image segmentation is important with applications to several problems in biology and medicine. While extensively researched, generally, current segmentation methods perform adequately in the applications for which they were designed, but often require extensive modifications or calibrations before being used in a different application. We describe an approach that, with few modifications, can be used in a variety of image segmentation problems. The approach is based on a supervised learning strategy that utilizes intensity neighborhoods to assign each pixel in a test image its correct class based on training data. We describe methods for modeling rotations and variations in scales as well as a subset selection for training the classifiers. We show that the performance of our approach in tissue segmentation tasks in magnetic resonance and histopathology microscopy images, as well as nuclei segmentation from fluorescence microscopy images, is similar to or better than several algorithms specifically designed for each of these applications.

Discursive Deployments: Mobilizing Support for Municipal and Community Wireless Networks in the U.S.

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

Alvarez, Rosio; Rodriguez, Juana Maria

2008-08-16

This paper examines Municipal Wireless (MW) deployments in the United States. In particular, the interest is in understanding how discourse has worked to mobilize widespread support for MW networks. We explore how local governments discursively deploy the language of social movements to create a shared understanding of the networking needs of communities. Through the process of"framing" local governments assign meaning to the MW networks in ways intended to mobilize support anddemobilize opposition. The mobilizing potential of a frame varies and is dependent on its centrality and cultural resonance. We examine the framing efforts of MW networks by using a samplemore » of Request for Proposals for community wireless networks, semi-structured interviews and local media sources. Prominent values that are central to a majority of the projects and others that are culturally specific are identified and analyzed for their mobilizing potency.« less

The neural substrates of in-group bias: a functional magnetic resonance imaging investigation.

PubMed

Van Bavel, Jay J; Packer, Dominic J; Cunningham, William A

2008-11-01

Classic minimal-group studies found that people arbitrarily assigned to a novel group quickly display a range of perceptual, affective, and behavioral in-group biases. We randomly assigned participants to a mixed-race team and used functional magnetic resonance imaging to identify brain regions involved in processing novel in-group and out-group members independently of preexisting attitudes, stereotypes, or familiarity. Whereas previous research on intergroup perception found amygdala activity--typically interpreted as negativity--in response to stigmatized social groups, we found greater activity in the amygdala, fusiform gyri, orbitofrontal cortex, and dorsal striatum when participants viewed novel in-group faces than when they viewed novel out-group faces. Moreover, activity in orbitofrontal cortex mediated the in-group bias in self-reported liking for the faces. These in-group biases in neural activity were not moderated by race or by whether participants explicitly attended to team membership or race, a finding suggesting that they may occur automatically. This study helps clarify the role of neural substrates involved in perceptual and affective in-group biases.

The {sup 17}F(p,{gamma}){sup 18}Ne3{sup +} resonance state studied with the {sup 16}O({sup 3}He,n){sup 18}Ne reaction

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

Parpottas, Y.; Grimes, S.M.; Brune, C.R.

2005-08-01

The astrophysically important 3{sup +} resonance of the {sup 17}F(p,{gamma}){sup 18}Ne reaction has been studied with the {sup 16}O({sup 3}He,n){sup 18}Ne reaction. High-resolution measurements were carried out for three different kinematic configurations. We find an excitation energy of 4527(4) keV and a proton width of 17(4) keV for the 3{sup +} state. Measured differential cross sections were compared with Hauser-Feshbach predictions to assign the spin of the 4527-keV state and confirm the spin assignments of the two known levels in this region. Our results differ from the earlier {sup 16}O({sup 3}He,n){sup 18}Ne findings of Garcia et al. [Phys. Rev. Cmore » 43, 2012 (1991)], but they agree well with the {sup 17}F(p,p){sup 17}F measurements of Bardayan et al. [Phys. Rev. C 62, 055804 (2002)].« less

A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT.

PubMed

Latosińska, Jolanta N; Seliger, Janez; Zagar, Veselko; Burchardt, Dorota V

2012-01-01

A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on (14)N were detected at 180 K and assigned to particular nitrogen sites (-NH(2), -N=, and -NH-) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds.

Establishment of the purity values of carbohydrate certified reference materials using quantitative nuclear magnetic resonance and mass balance approach.

PubMed

Quan, Can

2014-06-15

This work described the assignment of purity values to six carbohydrate certified reference materials, including glucose, fructose, galactose, lactose, xylose and sucrose, according to the ISO Guides 34 and 35. The CRMs' purity values were assigned based on the weighted average of quantitative nuclear magnetic resonance method and mass balance approach with high resolution liquid chromatography - evaporative light scattering detection. All the six CRMs with following value amount fractions: glucose (GBW10062) at a certified purity P ± U (k=2) of (0.99 ± 0.005)%; fructose (GBW10063) at (0.99 ± 0.005)%; galactose (GBW10064) at (0.99 ± 0.007)%; lactose (GBW10065) at (0.99 ± 0.008)%; xylose (GBW10066) at (0.99 ± 0.007)% and sucrose (GBW10067) at (0.99 ± 0.008)%, respectively were certified. The homogeneity of the CRMs was determined by an in-house validated liquid chromatographic method. Potential degradation during storage was also investigated and a shelf-life based on this value was established. Copyright © 2013 Elsevier Ltd. All rights reserved.

Distribution functions for resonantly trapped orbits in the Galactic disc

NASA Astrophysics Data System (ADS)

Monari, Giacomo; Famaey, Benoit; Fouvry, Jean-Baptiste; Binney, James

2017-11-01

The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment, however, leads to singularities at resonances, which prevent quantitative comparisons with data. Here, we manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. We then follow the prescription of Binney, assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits depends only on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of DFs in action space.

Impact of Clinical History on Maximum PI-RADS Version 2 Score: A Six-Reader 120-Case Sham History Retrospective Evaluation.

PubMed

Shankar, Prasad R; Kaza, Ravi K; Al-Hawary, Mahmoud M; Masch, William R; Curci, Nicole E; Mendiratta-Lala, Mishal; Sakala, Michelle D; Johnson, Timothy D; Davenport, Matthew S

2018-04-17

Purpose To assess the impact of clinical history on the maximum Prostate Imaging Recording and Data System (PI-RADS) version 2 (v2) score assigned to multiparametric magnetic resonance (MR) imaging of the prostate. Materials and Methods This retrospective cohort study included 120 consecutively selected multiparametric prostate MR imaging studies performed between November 1, 2016, and December 31, 2016. Sham clinical data in four domains (digital rectal examination, prostate-specific antigen level, plan for biopsy, prior prostate cancer history) were randomly assigned to each case by using a balanced orthogonal design. Six fellowship-trained abdominal radiologists independently reviewed the sham data, actual patient age, and each examination while they were blinded to interreader scoring, true clinical data, and histologic findings. Readers were told the constant sham histories were true, believed the study to be primarily investigating interrater agreement, and were asked to assign a maximum PI-RADS v2 score to each case. Linear regression was performed to assess the association between clinical variables and maximum PI-RADS v2 score designation. Intraclass correlation coefficients (ICCs) were obtained to compare interreader scoring. Results Clinical information had no significant effect on maximum PI-RADS v2 scoring for any of the six readers (P = .09-.99, 42 reader-variable pairs). Distributions of maximum PI-RADS v2 scores in the research context were similar to the distribution of the scores assigned clinically and had fair-to-excellent pairwise interrater agreement (ICC range: 0.53-0.76). Overall interrater agreement was good (ICC: 0.64; 95% confidence interval: 0.57, 0.71). Conclusion Clinical history does not appear to be a substantial bias in maximum PI-RADS v2 score assignment. This is potentially important for clinical nomograms that plan to incorporate PI-RADS v2 score and clinical data into their algorithms (ie, PI-RADS v2 scoring is not confounded by clinical data). © RSNA, 2018 Online supplemental material is available for this article.

Validation of organ procurement and transplant network (OPTN)/united network for organ sharing (UNOS) criteria for imaging diagnosis of hepatocellular carcinoma.

PubMed

Fowler, Kathryn J; Karimova, E Jane; Arauz, Anthony R; Saad, Nael E; Brunt, Elizabeth M; Chapman, William C; Heiken, Jay P

2013-06-27

Imaging diagnosis of hepatocellular carcinoma (HCC) presents an important pathway for transplant exception points and priority for cirrhotic patients. The purpose of this retrospective study is to evaluate the validity of the new Organ Procurement and Transplant Network (OPTN) classification system on patients undergoing transplantation for HCC. One hundred twenty-nine patients underwent transplantation for HCC from April 14, 2006 to April 18, 2011; a total of 263 lesions were reported as suspicious for HCC on pretransplantation magnetic resonance imaging. Magnetic resonance imaging examinations were reviewed independently by two experienced radiologists, blinded to final pathology. Reviewers identified major imaging features and an OPTN classification was assigned to each lesion. Final proof of diagnosis was pathology on explant or necrosis along with imaging findings of ablation after transarterial chemoembolization. Application of OPTN imaging criteria in our population resulted in high specificity for the diagnosis of HCC. Sensitivity in diagnosis of small lesions (≥1 and <2 cm) was low (range, 26%-34%). Use of the OPTN system would have resulted in different management in 17% of our population who had received automatic exception points for HCC based on preoperative imaging but would not have met criteria under the new system. Eleven percent of the patients not meeting OPTN criteria were found to have T2 stage tumor burden on pathology. The OPTN imaging policy introduces a high level of specificity for HCC but may decrease sensitivity for small lesions. Management may be impacted in a number of patients, potentially requiring longer surveillance periods or biopsy to confirm diagnosis.

Vibrational spectrum of the K-590 intermediate in the bacteriorhodopsin photocycle at room temperature: picosecond time-resolved resonance coherent anti-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Ujj, L.; Jäger, F.; Popp, A.; Atkinson, G. H.

1996-12-01

The vibrational spectrum of the K-590 intermediate, thought to contribute significantly to the energy storage and transduction mechanism in the bacteriorhodopsin (BR) photocycle, is measured at room temperature using picosecond time-resolved resonance coherent anti-Stokes Raman scattering (PTR/CARS). The room-temperature BR photocycle is initiated by the 3 ps, 570 nm excitation of the ground-state species, BR-570, prepared in both H 2O and D 2O suspensions of BR. PTR/CARS data, recorded 50 ps after BR-570 excitation, at which time only BR-570 and K-590 are present, have an excellent S/N which provides a significantly more detailed view of the K-590 vibrational degrees of freedom than previously available. Two picosecond (6 ps FWHM) laser pulses, ω1 (633.4 nm) and ωS (675-700 nm), are used to record PTR/CARS data via electronic resonance enhancement in both BR-570 and K-590, each of which contains a distinct retinal structure (assigned as 13- rans, 15- anti, 13- cis, respectively). To obtain the vibrational spectrum of K-590 separately, the PTR/CARS spectra from the mixture of isomeric retinals is quantitatively analyzed in terms of third-order susceptibility ( η(3)) relationships. PTR/CARS spectra of K-590 recorded from both H 2O and D 2O suspensions of BR are compared with the analogous vibrational data obtained via spontaneous resonance Raman (RR) scattering at both low (77 K) and room temperature. Analyses of these vibrational spectra identify temperature-dependent effects and changes assignable to the substitution of deuterium at the Schiff-base nitrogen not previously reported.

Detection of hydrogen dissolved in acrylonitrile butadiene rubber by 1H nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Nishimura, Shin; Fujiwara, Hirotada

2012-01-01

Rubber materials, which are used for hydrogen gas seal, can dissolve hydrogen during exposure in high-pressure hydrogen gas. Dissolved hydrogen molecules were detected by solid state 1H NMR of the unfilled vulcanized acrylonitrile butadiene rubber. Two signals were observed at 4.5 ppm and 4.8 ppm, which were assignable to dissolved hydrogen, in the 1H NMR spectrum of NBR after being exposed 100 MPa hydrogen gas for 24 h at room temperature. These signals were shifted from that of gaseous hydrogen molecules. Assignment of the signals was confirmed by quantitative estimation of dissolved hydrogen and peak area of the signals.

Jet-cooled laser-induced fluorescence spectroscopy of ScH: Observation of an Ω‧=2-Ω″=1 transition

NASA Astrophysics Data System (ADS)

Mukund, Sheo; Bhattacharyya, Soumen; Nakhate, S. G.

2014-11-01

New bands of scandium monohydride at origins 17,914.5 and 17,942.3 cm-1 have been observed in a jet-cooled beam with laser-induced fluorescence spectroscopy. Mass-selected resonant photoionization spectroscopy also confirmed the carrier of the band as ScH. The rotational analysis indicated that both transitions at 17,914.5 and 17,942.3 cm-1 are of Ω‧=2-Ω″=1 type with vibrational assignments (0,0) and (1,1) respectively. The assigned g3Φ2-a3Δ1 excitation is the first observed triplet-triplet transition in ScH.

3D Motions of Iron in Six-Coordinate {FeNO} 7 Hemes by Nuclear Resonance Vibration Spectroscopy [3-D Motions of Iron in Six-coordinate {FeNO} 7 Hemes by NRVS

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

Peng, Qian; Pavlik, Jeffrey W.; Silvernail, Nathan J.

The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(T pFPP)(1-MeIm)(NO)] (T pFPP = tetra- para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicularmore » to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v 50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X= N, C, and O) complexes is correlated with the Fe XO bond lengths. The nature of highest frequency band at ≈560 cm -1 has also been examined in two additional new derivatives. Previously assigned as the Fe NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. In conclusion, the results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.« less

3D Motions of Iron in Six-Coordinate {FeNO} 7 Hemes by Nuclear Resonance Vibration Spectroscopy [3-D Motions of Iron in Six-coordinate {FeNO} 7 Hemes by NRVS

DOE PAGES

Peng, Qian; Pavlik, Jeffrey W.; Silvernail, Nathan J.; ...

2016-03-21

The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(T pFPP)(1-MeIm)(NO)] (T pFPP = tetra- para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicularmore » to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v 50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X= N, C, and O) complexes is correlated with the Fe XO bond lengths. The nature of highest frequency band at ≈560 cm -1 has also been examined in two additional new derivatives. Previously assigned as the Fe NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. In conclusion, the results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.« less

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

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

Tolić, Nikola; Liu, Yina; Liyu, Andrey

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenatedmore » organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.« less

Measurement of radiative proton capture on F 18 and implications for oxygen-neon novae reexamined

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

Akers, C.; Laird, A. M.; Fulton, B. R.

The rate of the F-18(p, gamma)Ne-19 reaction affects the final abundance of the gamma-ray observable radioisotope F-18, produced in novae. However, no successful measurement of this reaction exists and the rate used is calculated from incomplete information on the contributing resonances. Of the two resonances thought to play a significant role, one has a radiative width estimated from the assumed analogue state in the mirror nucleus, F-19. The second does not have an analogue state assignment at all, resulting in an arbitrary radiative width being assumed. Here, we report the first successful direct measurement of the F-18(p, gamma)Ne-19 reaction. Themore » strength of the 665 keV resonance (E-x = 7.076 MeV) is found to be over an order of magnitude weaker than currently assumed in nova models. Reaction rate calculations show that this resonance therefore plays no significant role in the destruction of F-18 at any astrophysical energy.« less

Meta-cognitive student reflections

NASA Astrophysics Data System (ADS)

Barquist, Britt; Stewart, Jim

2009-05-01

We have recently concluded a project testing the effectiveness of a weekly assignment designed to encourage awareness and improvement of meta-cognitive skills. The project is based on the idea that successful problem solvers implement a meta-cognitive process in which they identify the specific concept they are struggling with, and then identify what they understand, what they don't understand, and what they need to know in order to resolve their problem. The assignment required the students to write an email assessing the level of completion of a weekly workbook assignment and to examine in detail their experiences regarding a specific topic they struggled with. The assignment guidelines were designed to coach them through this meta-cognitive process. We responded to most emails with advice for next week's assignment. Our data follow 12 students through a quarter consisting of 11 email assignments which were scored using a rubric based on the assignment guidelines. We found no correlation between rubric scores and final grades. We do have anecdotal evidence that the assignment was beneficial.

Resonant Raman spectra of diindenoperylene thin films

NASA Astrophysics Data System (ADS)

Scholz, R.; Gisslén, L.; Schuster, B.-E.; Casu, M. B.; Chassé, T.; Heinemeyer, U.; Schreiber, F.

2011-01-01

Resonant and preresonant Raman spectra obtained on diindenoperylene (DIP) thin films are interpreted with calculations of the deformation of a relaxed excited molecule with density functional theory (DFT). The comparison of excited state geometries based on time-dependent DFT or on a constrained DFT scheme with observed absorption spectra of dissolved DIP reveals that the deformation pattern deduced from constrained DFT is more reliable. Most observed Raman peaks can be assigned to calculated A_g-symmetric breathing modes of DIP or their combinations. As the position of one of the laser lines used falls into a highly structured absorption band, we have carefully analyzed the Raman excitation profile arising from the frequency dependence of the dielectric tensor. This procedure gives Raman cross sections in good agreement with the observed relative intensities, both in the fully resonant and in the preresonant case.

Resonant Raman spectra of diindenoperylene thin films.

PubMed

Scholz, R; Gisslén, L; Schuster, B-E; Casu, M B; Chassé, T; Heinemeyer, U; Schreiber, F

2011-01-07

Resonant and preresonant Raman spectra obtained on diindenoperylene (DIP) thin films are interpreted with calculations of the deformation of a relaxed excited molecule with density functional theory (DFT). The comparison of excited state geometries based on time-dependent DFT or on a constrained DFT scheme with observed absorption spectra of dissolved DIP reveals that the deformation pattern deduced from constrained DFT is more reliable. Most observed Raman peaks can be assigned to calculated A(g)-symmetric breathing modes of DIP or their combinations. As the position of one of the laser lines used falls into a highly structured absorption band, we have carefully analyzed the Raman excitation profile arising from the frequency dependence of the dielectric tensor. This procedure gives Raman cross sections in good agreement with the observed relative intensities, both in the fully resonant and in the preresonant case.

1H, 15N, and 13C resonance assignments of the third domain from the S. aureus innate immune evasion protein Eap.

PubMed

Herrera, Alvaro I; Ploscariu, Nicoleta T; Geisbrecht, Brian V; Prakash, Om

2018-04-01

Staphylococcus aureus is a widespread and persistent pathogen of humans and livestock. The bacterium expresses a wide variety of virulence proteins, many of which serve to disrupt the host's innate immune system from recognizing and clearing bacteria with optimal efficiency. The extracellular adherence protein (Eap) is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement system (Woehl et al in J Immunol 193:6161-6171, 2014) and Neutrophil Serine Proteases (NSPs) (Stapels et al in Proc Natl Acad Sci USA 111:13187-13192, 2014). The third domain of Eap, Eap3, is an ~ 11 kDa protein that was recently shown to bind complement component C4b (Woehl et al in Protein Sci 26:1595-1608, 2017) and therefore play an essential role in inhibiting the classical and lectin pathways of complement (Woehl et al in J Immunol 193:6161-6171, 2014). Since structural characterization of Eap3 is still incomplete, we acquired a series of 2D and 3D NMR spectra of Eap3 in solution. Here we report the backbone and side-chain 1 H, 15 N, and 13 C resonance assignments of Eap3 and its predicted secondary structure via the TALOS-N server. The assignment data have been deposited in the BMRB data bank under accession number 27087.

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

Pratt, S. T.; Chemistry

The photoelectron spectrum following resonant two-photon ionization of 1,4-diazabicyclo[2.2.2]octane (DABCO) was recorded with the laser tuned to the origin band of the S{sub 2}{l_arrow}S{sub 0} transition. The spectrum is consistent with the rapid radiationless transition from the S2 state into high vibrational levels of the S1 state, as proposed by Smith et al. Features in the double-resonance spectrum of Smith et al. that were previously assigned to photoionization of S(-) 3s(-){sup 1}A'{sub 2} vibrational levels populated by a radiationless transition from the S2 state are reinterpreted, with the conclusion that the S(-) state has yet to be observed.

Identification of a new low energy 1u state in dicopper with resonant four-wave mixing.

PubMed

Visser, B; Beck, M; Bornhauser, P; Knopp, G; van Bokhoven, J A; Marquardt, R; Gourlaouen, C; Radi, P P

2017-12-07

The low energy electronic structure of the copper dimer has been re-investigated using non-linear four-wave mixing spectroscopy and high level ab initio calculations. In addition to the measurement of the previously reported A, B, and C electronic states, a new state denoted A' is identified with T 0 = 20 100.4090(16) cm -1 ( 63 Cu 2 ). Rotational analysis of the A'-X (0,0) and (1,0) transitions leads to the assignment of A' 1 u . Ab initio calculations present the first theoretical description of the low energy states of the copper dimer in Hund's case (c) and confirm the experimental assignment. The discovery of this new low energy excited state emphasizes that spin-orbit coupling is significant in states with d-hole electronic configurations and resolves a decades-long mystery in the initial assignment of the A state.

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

Pease, J.H.

The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometrymore » calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.« less

Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

PubMed

Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

2015-10-01

Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data.

PubMed

Benigni, Paolo; Marin, Rebecca; Fernandez-Lima, Francisco

2015-10-01

With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MS n and IMS n measurements for faster and more accurate tridimensional structural assignment.

Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra

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

Bernal, Andrés; Patiny, Luc; Castillo, Andrés M.

2015-02-21

Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruningmore » of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems.« less

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

USGS Publications Warehouse

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

Use of Genetic Data to Infer Population-Specific Ecological and Phenotypic Traits from Mixed Aggregations

PubMed Central

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions. PMID:24905464

Infrared resonance Raman, and excitation profile studies of Os/sub 2/(O/sub 2/CCH/sub 3/)/sub 4/Cl/sub 2/ and Os/sub 2/(O/sub 2/CCD/sub 3/)/sub 4/Cl/sub 2/. The assignment of the osmium-osmium stretching vibration for a complex involving an osmium-osmium multiple bond

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

Clark, R.J.H.; Hempleman, A.J.; Tocher, D.A.

1988-08-31

Extensive Raman studies (1525-40 cm/sup /minus/1/) of Os/sub 2/(O/sub 2/CCH/sub 3/)/sub 4/Cl/sub 2/ have led to the identification of the three strong bands, /nu//sub 1/, /nu//sub 2/, and /nu//sub 3/, at 229, 393, and 292 cm/sup /minus/1/ to the key skeletal stretching modes, /nu/(OsOs), /nu/(OsO), and /nu/(OsCl), respectively. Raman spectra of the complex at resonance with the intense electronic band at /lambda//sub max/ = 383 nm lead to the development of a six-membered overtone progression in /nu//sub 1/ as well as combination band progressions in /nu//sub 1/ based upon one quantum of either /nu//sub 2/ or /nu//sub 3/. This indicatesmore » that the principal structural change attendant upon excitation to the resonant state is along the OsOs coordinate. Fourier transform infrared spectra (3500-40 cm/sup /minus/1/) have also been obtained. Acetate deuteriation provides conclusive evidence for many of the infrared and Raman band assignments. The study provides the first firm identification of /nu/(OsOs) for a multiply bonded species.« less

Resonance Raman spectroscopy of 2H-labelled spheroidenes in petroleum ether and in the Rhodobacter sphaeroides reaction centre.

PubMed

Kok, P; Köhler, J; Groenen, E J; Gebhard, R; van der Hoef, I; Lugtenburg, J; Farhoosh, R; Frank, H A

1997-03-01

As a step towards the structural analysis of the carotenoid spheroidene in the Rhodobacter sphaeroides reaction centre, we present the resonance Raman spectra of 14-2H, 15-2H, 15'-2H, 14'-2H, 14,15'-2H2 and 15-15'-2H2 spheroidenes in petroleum ether and, except for 14,15'-2H2 spheroidene, in the Rb. sphaeroides R26 reaction center (RC). Analysis of the spectral changes upon isotopic substitution allows a qualitative assignment of most of the vibrational bands to be made. For the all-trans spheroidenes in solution the resonance enhancement of the Raman bands is determined by the participation of carbon carbon stretching modes in the centre of the conjugated chain, the C9 to C15' region. For the RC-bound 15,15'-cis spheroidenes, enhancement is determined by the participation of carbon-carbon stretching modes in the centre of the molecule, the C13 to C13' region. Comparison of the spectra in solution and in the RC reveals evidence for an out-of-plane distortion of the RC-bound spheroidene in the central C14 to C14' region of the carotenoid. The characteristic 1240 cm-1 band in the spectrum of the RC-bound spheroidene has been assigned to a normal mode that contains the coupled C12-C13 and C13'-C12' stretch vibrations.

28 CFR 100.13 - Directly assignable costs.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., COMMUNICATIONS ASSISTANCE FOR LAW ENFORCEMENT ACT OF 1994 § 100.13 Directly assignable costs. (a) A cost is directly assignable to the CALEA compliance effort if it is a plant cost incurred specifically to meet the...

Rotational Spectroscopy and Conformational Studies of 4-PENTYNENITRILE, 4-PENTENENITRILE, and Glutaronitrile

NASA Astrophysics Data System (ADS)

Hays, Brian M.; Mehta-Hurt, Deepali; Jawad, Khadija M.; Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Zhang, Di; Zwier, Timothy S.

2017-06-01

The pure rotational spectra of 4-pentynenitrile, 4-pentenenitrile, and glutaronitrile were acquired using chirped pulse Fouirer transform microwave spectroscopy. 4-pentynenitrile and 4-pentenenitrile are the recombination products of two resonance stabilized radicals, propargyl + cyanomethyl or allyl + cyanomethyl, respectively, and are thus anticipated to be significant among the more complex nitriles in Titan's atmosphere. Indeed, these partially unsaturated alkyl cyanides have been found in laboratory analogs of tholins and are also expected to have interesting photochemistry. The optimized structures of all conformers below predicted energies of 500 \\wn were calculated for each molecule. Both of the conformers, trans and gauche, for 4-pentynenitrile have been identified and assigned. Five conformers were assigned in 4-pentenenitrile. The eclipsed conformers, with respect to the vinyl group, dominate the spectrum but some population was found in the syn conformers including the syn-gauche conformer, calculated to be 324 \\wn above the global minimum. The glutaronitrile spectrum contained only the two conformers below 500 \\wn, with reduced amount of the gauche trans conformer. The assigned spectra and structural assignments will be presented.

Vibrational normal modes of diazo-dimedone: A comparative study by Fourier infrared/Raman spectroscopies and conformational analysis by MM/QM

NASA Astrophysics Data System (ADS)

Téllez Soto, C. A.; Ramos, J. M.; Rianelli, R. S.; de Souza, M. C. B. V.; Ferreira, V. F.

2007-07-01

The 2-diazo-5,5-dimethyl-cyclohexane-1,3-dione ( 3) was synthesized and the FT-IR/Raman spectra were measured with the purpose of obtain a full assignment of the vibrational modes. Singular aspects concerning the -C dbnd N dbnd N oscillator are discussed in view of two strong bands observed in the region of 2300-2100 cm -1 in both, Infrared and Raman spectra. The density functional theory (DFT) was used to obtain the geometrical structure and for assisting in the vibrational assignment joint to the traditional normal coordinate analysis (NCA). The observed wavenumbers at 2145 (IR), 2144(R) are assigned as the coupled ν(N dbnd N) + ν(C dbnd N) vibrational mode with higher participation of the N dbnd N stretching. A 2188 cm -1 (IR) and at 2186 cm -1 (R) can be assigned as a overtone of one of ν(CC) normal mode or to a combination band of the fundamentals δ(CCH) found at 1169 cm -1 and the δ (CC dbnd N) found at 1017 cm -1 enhanced by Fermi resonance.

Reflection spectra of bio-organic materials in the 2.5-4 micron region and the interpretation of the infrared spectrum of Mars.

PubMed

Rea, D G; Belsky, T; Calvin, M

1964-01-01

The nature and assignment of the Martian spectral features observed by W. M. Sinton in the 3-4 micron region have been re-examined. It is shown that it is not possible to state unequivocally that there are absorption bands at 2710 (3.69 microns), 2790 (3.58 microns) and 2900 (3.45 microns) cm-1. Rather the possibility of the presence of true reflection features complicates the issue and enables only a wide range to be specified for the corresponding resonant frequencies. To clarify the assignment of these a large number of pure organic and inorganic solids, together with a selection of biological samples, have been recorded in reflection. The assignment of the features to organic matter, implying the presence of life on the Martian maria, is found to be improbable. While inorganic carbonates have bands in this region, they also do not provide a satisfactory explanation of the observations. The assignment of these Martian spectral features is then an open question.

13C-13C dipolar recoupling under very fast magic angle spinning in solid-state nuclear magnetic resonance: Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

A technique is presented to recouple homonuclear dipolar couplings between dilute spin pairs such as 13C-13C systems under very fast magic angle spinning (MAS) in solid-state nuclear magnetic resonance (NMR) spectroscopy. The presented technique, finite pulse rf driven recoupling (fpRFDR), restores homonuclear dipolar interactions based on constructive usage of finite pulse-width effects in a phase- and symmetry-cycled π-pulse train in which a rotor-synchronous π pulse is applied every rotation period. The restored effective dipolar interaction has the form of a zero-quantum dipolar Hamiltonian for static solids, whose symmetry in spin space is different from that obtained by conventional rf driven recoupling (RFDR) techniques. It is demonstrated that the efficiency of recoupling by fpRFDR is not strongly dependent on chemical shift differences or resonance offsets in contrast to previous recoupling methods under very fast MAS. To realize distance measurements without effects of spin relaxation, a constant-time version of fpRFDR (CT-fpRFDR) is introduced, in which the effective evolution period is varied by refocusing dipolar evolution with a rotor-synchronized solid echo while the total recoupling period is kept constant. From CT-fpRFDR experiments at a spinning speed of 30.3 kHz in a field of 17.6 T, the 13C-13C distance of [1-13C]Ala-[1-13C]Gly-Gly was determined to be 3.27 Å, which agrees well with the value of 3.20 Å obtained by x-ray diffraction. Also, two-dimensional (2D) 13C/13C chemical-shift correlation NMR spectrum in a field of 9.4 T was obtained with fpRFDR for fibrils of the segmentally 13C- and 15N-labeled Alzheimer's β-Amyloid fragments, Aβ16-22 (residues 16-22 taken from the 40-residue Aβ peptide) in which Leu-17 through Ala-21 are uniformly 13C- and 15N-labeled. Most 13C resonances for the main chain as well as for the side chains are assigned based on 2D 13C/13C chemical-shift correlation patterns specific to amino-acid types. Examination of the obtained 13C chemical shifts revealed the formation of β-strand across the entire molecule of Aβ16-22. Possibility of high throughput determination of global main-chain structures based on 13C shifts obtained from 2D 13C/13C chemical-shift correlation under very fast MAS is also discussed for uniformly/segmentally 13C-labeled protein/peptide samples.

Complete structure of the cell surface polysaccharide of Streptococcus oralis C104: A 600-MHz NMR study

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

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1991-09-03

Specific lectin-carbohydrate interactions between certain oral streptococci and actinomyces contribute to the microbial colonization of teeth. The receptor molecules of Streptococcus oralis, 34, ATCC 10557, and Streptococcus mitis J22 for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii are antigenically distinct polysaccharides, each formed by a different phosphodiester-linked oligosaccharide repeating unit. Receptor polysaccharide was isolated form S. oralis C104 cells and was shown to contain galactose, N-acetylgalactosamine, ribitol, and phosphate with molar ratios of 4:1:1:1. The {sup 1}H NMR spectrum of the polysaccharide shows that it contains a repeating structure. The individual sugars in themore » repeating unit were identified by {sup 1}H coupling constants observed in E-COSY and DQF-COSY spectra. NMR methods included complete resonance assignments ({sup 1}H and {sup 13}C) by various homonuclear and heteronuclear correlation experiments that utilize scalar couplings. Sequence and linkage assignments were obtained from the heteronuclear multiple-bond correlation (HMBC) spectrum. This analysis shows that the receptor polysaccharide of S. oralis C104 is a ribitol teichoic acid polymer composed of a linear hexasaccharide repeating unit containing two residues each of galactopyranose and galactofuranose and a residue each of GalNAc and ribitol joined end to end by phosphodiester linkages.« less

The Tandem of Full Spin Analysis and qHNMR for the Quality Control of Botanicals Exemplified with Ginkgo biloba

PubMed Central

Napolitano, José G.; Gödecke, Tanja; Rodríguez-Brasco, María F.; Jaki, Birgit U.; Chen, Shao-Nong; Lankin, David C.; Pauli, GuidoF.

2012-01-01

Botanical dietary supplements and herbal remedies are widely used for health promotion and disease prevention. Due to the high chemical complexity of these natural products, it is essential to develop new analytical strategies to guarantee their quality and consistency. In particular, the precise characterization of multiple botanical markers remains a challenge. This study demonstrates how a combination of computer-aided spectral analysis and 1D quantitative 1H NMR spectroscopy (qHNMR) generates the analytical foundation for innovative means of simultaneously identifying and quantifying botanical markers in complex mixtures. First, comprehensive 1H NMR profiles (fingerprints) of selected botanical markers were generated via 1H iterative Full Spin Analysis (HiFSA) with PERCH. Next, the 1H fingerprints were used to assign specific 1H resonances in the NMR spectra of reference materials, enriched fractions and crude extracts of Ginkgo biloba leaves. These 1H fingerprints were then used to verify the assignments by 2D NMR. Subsequently, a complete purity and composition assessment by means of 1D qHNMR was conducted. As its major strengths, this tandem approach enables the simultaneous quantification of multiple constituents without the need for identical reference materials, the semi-quantitative determination of particular sub-classes of components, and the detection of impurities and adulterants. PMID:22332915

Generative adversarial networks for brain lesion detection

NASA Astrophysics Data System (ADS)

Alex, Varghese; Safwan, K. P. Mohammed; Chennamsetty, Sai Saketh; Krishnamurthi, Ganapathy

2017-02-01

Manual segmentation of brain lesions from Magnetic Resonance Images (MRI) is cumbersome and introduces errors due to inter-rater variability. This paper introduces a semi-supervised technique for detection of brain lesion from MRI using Generative Adversarial Networks (GANs). GANs comprises of a Generator network and a Discriminator network which are trained simultaneously with the objective of one bettering the other. The networks were trained using non lesion patches (n=13,000) from 4 different MR sequences. The network was trained on BraTS dataset and patches were extracted from regions excluding tumor region. The Generator network generates data by modeling the underlying probability distribution of the training data, (PData). The Discriminator learns the posterior probability P (Label Data) by classifying training data and generated data as "Real" or "Fake" respectively. The Generator upon learning the joint distribution, produces images/patches such that the performance of the Discriminator on them are random, i.e. P (Label Data = GeneratedData) = 0.5. During testing, the Discriminator assigns posterior probability values close to 0.5 for patches from non lesion regions, while patches centered on lesion arise from a different distribution (PLesion) and hence are assigned lower posterior probability value by the Discriminator. On the test set (n=14), the proposed technique achieves whole tumor dice score of 0.69, sensitivity of 91% and specificity of 59%. Additionally the generator network was capable of generating non lesion patches from various MR sequences.

Dual Outcomes of Psychology Assignments: Perceived Learning and Feelings of Prideful Accomplishment

ERIC Educational Resources Information Center

Pines, Harvey A.; Larkin, Judith E.; Murray, Molly P.

2016-01-01

Two studies explored properties of psychology assignments from an atypical perspective: students' own perceptions of what they learned and their emotional reactions to the assignments, specifically feelings of pride in their work. Study 1 showed that assignments vary in their likelihood of generating prideful accomplishment and identified three…

38 CFR 21.4146 - Assignments of benefits prohibited.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Administration of Educational Assistance Programs Payments; Educational Assistance Allowance § 21.4146 Assignments of benefits prohibited. (a) General... authorized by law. No law specifically authorizes assignments of educational assistance allowances payable...

38 CFR 21.4146 - Assignments of benefits prohibited.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Administration of Educational Assistance Programs Payments; Educational Assistance Allowance § 21.4146 Assignments of benefits prohibited. (a) General... authorized by law. No law specifically authorizes assignments of educational assistance allowances payable...

Occupational exposures and chronic obstructive pulmonary disease (COPD): comparison of a COPD-specific job exposure matrix and expert-evaluated occupational exposures

PubMed Central

Kurth, Laura; Doney, Brent; Weinmann, Sheila

2017-01-01

Objectives To compare the occupational exposure levels assigned by our National Institute for Occupational Safety and Health chronic obstructive pulmonary disease-specific job exposure matrix (NIOSH COPD JEM) and by expert evaluation of detailed occupational information for various jobs held by members of an integrated health plan in the Northwest USA. Methods We analysed data from a prior study examining COPD and occupational exposures. Jobs were assigned exposure levels using 2 methods: (1) the COPD JEM and (2) expert evaluation. Agreement (Cohen’s κ coefficients), sensitivity and specificity were calculated to compare exposure levels assigned by the 2 methods for 8 exposure categories. Results κ indicated slight to moderate agreement (0.19–0.51) between the 2 methods and was highest for organic dust and overall exposure. Sensitivity of the matrix ranged from 33.9% to 68.5% and was highest for sensitisers, diesel exhaust and overall exposure. Specificity ranged from 74.7% to 97.1% and was highest for fumes, organic dust and mineral dust. Conclusions This COPD JEM was compared with exposures assigned by experts and offers a generalisable approach to assigning occupational exposure. PMID:27777373

Interference effect as resonance killer of newly observed charmoniumlike states Y(4320) and Y(4390)

NASA Astrophysics Data System (ADS)

Chen, Dian-Yong; Liu, Xiang; Matsuki, Takayuki

2018-02-01

In this letter, we decode the newly observed charmoniumlike states, Y(4320) and Y(4390), by introducing interference effect between ψ (4160) and ψ (4415), which plays a role of resonance killer for Y(4320) and Y(4390). It means that two newly reported charmoniumlike states are not genuine resonances, according to which we can naturally explain why two well-established charmonia ψ (4160) and ψ (4415) are missing in the cross sections of e^+e^- → π ^+ π ^- J/ψ and π ^+ π ^- h_c simultaneously. To well describe the detailed data of these cross sections around √{s}=4.2 GeV, our study further illustrates that a charmoniumlike structure Y(4220) must be introduced. As a charmonium, Y(4220) should dominantly decay into its open-charm channel e^+e^- → D^0 π ^+ D^{*-}, which provides an extra support to ψ (4S) assignment to Y(4220). In fact, this interference effect introduced to explain Y(4320) and Y(4390) gives a typical example of non-resonant explanations to the observed XYZ states, which should be paid more attention especially before identifying the observed XYZ states as genuine resonances.

Distribution functions for orbits trapped at the resonances in the Galactic disc

NASA Astrophysics Data System (ADS)

Monari, G.

2017-12-01

The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment however leads to singularities at resonances, which prevent quantitative comparisons with data. Monari et al. manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. They then follow the prescription of Binney (2016), assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits only depends on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of distribution functions in action space.

Determination of the shear impedance of viscoelastic liquids using cylindrical piezoceramic resonators.

PubMed

Kiełczyński, Piotr; Pajewski, Wincenty; Szalewski, Marek

2003-03-01

In this paper, a new method for determining the rheological parameters of viscoelastic liquids is presented. To this end, we used the perturbation method applied to shear vibrations of cylindrical piezoceramic resonators. The resonator was viscoelastically loaded on the outer cylindrical surface. Due to this loading, the resonant frequency and quality factor of the resonator changed. According to the perturbation method, the change in the complex resonant frequency deltaomega = deltaomega(re) + jdeltaomega(im) is directly proportional to the specific acoustic impedance for cylindrical waves Zc of a viscoelastic liquid surrounding the resonator, i.e., deltaomega is approximately equal to jZc, where j = (-1)1/2. Hence, the measurement of the real and imaginary parts of the complex resonant frequency deltaomega determines the real part, Rc, and imaginary part, Xc, of the complex acoustic impedance for cylindrical waves Zc of an investigated liquid. Furthermore, the specific impedance ZL for plane waves was related to the specific impedance Zc for cylindrical waves. Using theoretical formulas established and the results of the experiments performed, the shear storage modulus mu and the viscosity eta for various liquids (e.g., epoxy resins) were determined. Moreover, the authors derived for cylindrical resonators a formula that relates the shift in resonant frequency to the viscosity of the liquid. This formula is analogous to the Kanazawa-Gordon formula that was derived for planar resonators and Newtonian liquids.

Nuclear Resonance Vibrational Spectra of Five-Coordinate Imidazole-ligated Iron(II) Porphyrinates

PubMed Central

Hu, Chuanjiang; Barabanschikov, Alexander; Ellison, Mary K.; Zhao, Jiyong; Alp, E. Ercan; Sturhahn, Wolfgang; Zgierski, Marek Z.; Sage, J. Timothy; Scheidt, W. Robert

2012-01-01

Nuclear resonance vibrational spectra have been obtained for six five-coordinate imidazole-ligated iron(II) porphyrinates, [Fe(Por)(L)] (Por = tetraphenylporphyrinate, octaethylporphyrinate, tetratolylporphyrinate or protoporphyrinate IX and L = 2-methylimidazole or 1,2-dimethylimidazole). Measurements have been made on both powder and oriented crystal samples. The spectra are dominated by strong signals around 200–300 cm−1. Although the in-plane and out-of-plane vibrations are seriously overlapped, oriented crystal spectra allow their deconvolution. Thus, oriented crystal experimental data, along with DFT calculations, enable the assignment of key vibrations in the spectra. Molecular dynamics are also discussed. The nature of the Fe–NIm vibrations has been elaborated further than was possible from resonance Raman studies. Our study suggests that the Fe motions are coupled with the porphyrin core and peripheral groups motions. Both peripheral groups and their conformations have significant influence on the vibrational spectra (position and shape). PMID:22243131

Evaluation of resonances above the proton threshold in 26Si

NASA Astrophysics Data System (ADS)

Chipps, K. A.

2016-09-01

26Al remains an intriguing target for observational gamma-ray astronomy, thanks to its characteristic decay. The 25Al(p, γ)26Si reaction is the crucial link in a sequence that bypasses the production of the observable 26Alg . s . in favor of the isomeric state, and as such has been the focus of many studies. Considerable confusion in this regard has arisen from the use of outdated excitation energies and masses in reaction studies and rate evaluations. Recalibration of existing data from the literature has resulted in updated excitation and resonance energies, but open questions remain, particularly with regard to spin assignments and partial widths/resonance strengths. A discussion of the levels just above the proton threshold in 26Si relevant to the astrophysical 25Al(p, γ)26Si reaction rate will be presented. This work is funded by the US Department of Energy, Office of Science, Office of Nuclear Physics.

High-Resolution Triple Resonance Autoionization of Uranium Isotopes

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

Schumann, Philipp G.; Wendt, K; Bushaw, Bruce A.

2005-11-01

The near-threshold autoionization (AI) spectrum of uranium has been investigated by triple-resonance excitation with single-mode continuous lasers. Spectra were recorded over the first {approx}30 cm-1 above the first ionization limit at a resolution of 3x10-4 cm 1 using intermediate states with different J values (6, 7, 8) to assign AI level total angular momentum JAI = 5 to 9. Resonances with widths ranging from 8 MHz to 30 GHz were observed; the strongest ones have JAI = 9 and widths of {approx} 60 MHz. Hyperfine structures for 235U and isotope shifts for 234,235U have been measured in the two intermediatemore » levels and in the final AI level for the most favorable excitation path. These measurements were performed using aqueous samples containing sub-milligram quantities of uranium at natural isotopic abundances, indicating the potential of this approach for trace isotope ratio determinations.« less

Impact of field strength and iron oxide nanoparticle concentration on the linearity and diagnostic accuracy of off-resonance imaging.

PubMed

Farrar, Christian T; Dai, Guangping; Novikov, Mikhail; Rosenzweig, Anthony; Weissleder, Ralph; Rosen, Bruce R; Sosnovik, David E

2008-06-01

Off-resonance imaging (ORI) techniques are being increasingly used to image iron oxide imaging agents such as monocrystalline iron oxide nanoparticles (MION). However, the diagnostic accuracy, linearity, and field dependence of ORI have not been fully characterized. In this study, the sensitivity, specificity, and linearity of ORI were thus examined as a function of both MION concentration and magnetic field strength (4.7 and 14 T). MION phantoms with and without an air interface as well as MION uptake in a mouse model of healing myocardial infarction were imaged. MION-induced resonance shifts were shown to increase linearly with MION concentration. In contrast, the ORI signal/sensitivity was highly non-linear, initially increasing with MION concentration until T2 became comparable to the TE and decreasing thereafter. The specificity of ORI to distinguish MION-induced resonance shifts from on-resonance water was found to decrease with increasing field because of the increased on-resonance water linewidths (15 Hz at 4.7 T versus 45 Hz at 14 T). Large resonance shifts ( approximately 300 Hz) were observed at air interfaces at 4.7 T, both in vitro and in vivo, and led to poor ORI specificity for MION concentrations less than 150 microg Fe/mL. The in vivo ORI sensitivity was sufficient to detect the accumulation of MION in macrophages infiltrating healing myocardial infarcts, but the specificity was limited by non-specific areas of positive contrast at the air/tissue interfaces of the thoracic wall and the descending aorta. Improved specificity and linearity can, however, be expected at lower fields where decreased on-resonance water linewidths, reduced air-induced resonance shifts, and longer T2 relaxation times are observed. The optimal performance of ORI will thus likely be seen at low fields, with moderate MION concentrations and with sequences containing very short TEs. Copyright (c) 2007 John Wiley & Sons, Ltd.

Quality of pharmacy-specific Medical Subject Headings (MeSH) assignment in pharmacy journals indexed in MEDLINE.

PubMed

Minguet, Fernando; Salgado, Teresa M; van den Boogerd, Lucienne; Fernandez-Llimos, Fernando

2015-01-01

The Medical Subject Headings (MeSH) is the National Library of Medicine (NLM) controlled vocabulary for indexing articles. Inaccuracies in the MeSH thesaurus have been reported for several areas including pharmacy. To assess the quality of pharmacy-specific MeSH assignment to articles indexed in pharmacy journals. The 10 journals containing the highest number of articles published in 2012 indexed under the MeSH 'Pharmacists' were identified. All articles published over a 5-year period (2008-2012) in the 10 previously selected journals were retrieved from PubMed. MeSH terms used to index these articles were extracted and pharmacy-specific MeSH terms were identified. The frequency of use of pharmacy-specific MeSH terms was calculated across journals. A total of 6989 articles were retrieved from the 10 pharmacy journals, of which 328 (4.7%) were articles not fully indexed and therefore did not contain any MeSH terms assigned. Among the 6661 articles fully indexed, the mean number of MeSH terms was 10.1 (SD = 4.0), being 1.0 (SD = 1.3) considered as Major MeSH. Both values significantly varied across journals. The mean number of pharmacy-specific MeSH terms per article was 0.9 (SD = 1.2). A total of 3490 (52.4%) of the 6661 articles were indexed in pharmacy journals without a single pharmacy-specific MeSH. Of the total 67193 MeSH terms assigned to articles, on average 10.5% (SD = 13.9) were pharmacy-specific MeSH. A statistically significant different pattern of pharmacy-specific MeSH assignment was identified across journals (Kruskal-Wallis P < 0.001). The quality of assignment of the existing pharmacy-specific MeSH terms to articles indexed in pharmacy journals can be improved to further enhance evidence gathering in pharmacy. Over half of the articles published in the top-10 journals publishing pharmacy literature were indexed without a single pharmacy-specific MeSH. Copyright © 2015 Elsevier Inc. All rights reserved.

Magnetic Resonance Imaging

MedlinePlus

... specific information about your own examination. What is magnetic resonance imaging (MRI)? What is MRI used for? How safe ... What is the MRI examination like? What is magnetic resonance imaging (MRI)? MRI, or magnetic resonance imaging, is a ...

Backbone resonance assignment of an insect arylalkylamine N-acetyltransferase from Bombyx mori reveals conformational heterogeneity.

PubMed

Aboalroub, Adam A; Zhang, Ziming; Keramisanou, Dimitra; Gelis, Ioannis

2017-04-01

Arylalkylamine N-acetyltransferases (AANATs) catalyze the transfer of an acetyl group from the acetyl-group donor, acetyl-CoA, to an arylalkylamine acceptor. Although a single AANAT has been identified in mammals, insects utilize multiple AANATs in a diverse array of biological processes. AANATs belong to the GCN5-related acetyltransferase (GNAT) superfamily of enzymes, which despite their overall very low sequence homology, are characterized by a well conserved catalytic core domain. The structural properties of many GNATs have been extensively studied by X-ray crystallography that revealed common features during the catalytic cycle. Here we report the 1 H, 13 C and 15 N backbone NMR resonance assignment of the 24 kDa AANAT3 from Bombyx mori (bmAANAT3) as a first step towards understanding the role of protein dynamics in the catalytic properties of AANATs. Our preliminary solution NMR studies reveal that bmAANAT3 is well-folded in solution. The P-loop, which is responsible for cofactor binding, is flexible in the free-state, while a large region of the enzyme interconverts between two distinct conformations in the slow exchange regime.

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

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

Holliday, Michael; Zhang, Fengli; Isern, Nancy G.

2014-04-01

Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerizationmore » reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.« less

Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

PubMed

Abraham, Anuji; Crull, George

2014-10-06

A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

Identification of the altered pyrrole in the isomeric sulfmyoglobins: hyperfine shift patterns as indicators of ring saturation in ferric chlorins.

PubMed

Chatfield, M J; La Mar, G N; Smith, K M; Leung, H K; Pandey, R K

1988-03-08

Analysis of the 1H NMR hyperfine shift patterns of isomeric sulfmyoglobins is carried out in the met-aquo and met-cyano states to determine the site of saturation in each protein. The utility of the patterns for structure elucidation is established by specific deuterium labeling of the heme methyls of the terminal base product. On the basis of the known saturation of ring B in this isomer [Chatfield, M.J., La Mar, G.N., Lecomte, J.T.J., Balch, A.L., Smith, K.M., & Langry, K.C. (1986) J. Am. Chem. Soc. 108, 7108-7110], the methyl resonance of the saturated ring is found to have strongly attenuated contact shift. Thus, the heme methyl contact shift pattern is diagnostic for the saturated pyrrole in the high-spin state. This rationale is then applied to analyze the assigned NMR spectra of the initial and terminal acid sulfmyoglobin products, revealing that the same ring B is saturated in each isomer. In contrast, the heme methyl contact shift pattern in low-spin ferric complexes reveals that the methyls both on the affected pyrrole and on the trans pyrrole are influenced similarly on sulfmyoglobin formation, precluding the use of this methyl shift pattern as a unique indicator of the site of saturation. Identification of exchangeable proximal histidine resonances for met-aquo sulfmyoglobin complexes with shifts similar to that in native myoglobin dictates inconsequential axial alterations in the sulfmyoglobins, while location of downfield meso proton resonances analogous to those of the native protein demonstrates the retention of the coordinate water in the active site of met-sulfmyoglobin.

Impact of the integration of proton magnetic resonance imaging spectroscopy to PI-RADS 2 for prediction of high grade and high stage prostate cancer.

PubMed

Leapman, Michael S; Wang, Zhen J; Behr, Spencer C; Kurhanewicz, John; Zagoria, Ronald J; Carroll, Peter R; Westphalen, Antonio C

2017-01-01

To compare the predictions of dominant Gleason pattern ≥ 4 or non-organ confined disease with Prostate Imaging Reporting and Data System (PI-RADS v2) with or without proton magnetic resonance spectroscopic imaging ( 1 H-MRSI). Thirty-nine men underwent 3-tesla endorectal multiparametric MRI including 1 H-MRSI and prostatectomy. Two radiologists assigned PI-RADS v2 and 1 H-MRSI scores to index lesions. Statistical analyses used logistic regressions, receiver operating characteristic (ROC) curves, and 2x2 tables for diagnostic accuracies. The sensitivity and specificity of 1 H-MRSI and PI-RADS v2 for high-grade prostate cancer (PCa) were 85.7% (57.1%) and 92.9% (100%), and 56% (68.0%) and 24.0% (24.0%). The sensitivity and specificity of 1 H-MRSI and PI-RADS v2 for extra-prostatic extension (EPE) were 64.0% (40%) and 20.0% (48%), and 50.0% (57.1%) and 71.4% (64.3%). The area under the ROC curves (AUC) for prediction of high-grade prostate cancer were 0.65 and 0.61 for PI-RADS v2 and 0.72 and 0.70 when combined with 1 H-MRSI (readers 1 and 2, p = 0.04 and 0.21). For prediction of EPE the AUC were 0.54 and 0.60 for PI-RADS v2 and 0.55 and 0.61 when combined with 1 H-MRSI ( p > 0.05). 1 H-MRSI might improve the discrimination of high-grade prostate cancer when combined to PI-RADS v2, particularly for PI-RADS v2 score 4 lesions, but it does not affect the prediction of EPE.

1H NMR studies of the 5-(hydroxymethyl)-2'-deoxyuridine containing TF1 binding site.

PubMed

Pasternack, L B; Bramham, J; Mayol, L; Galeone, A; Jia, X; Kearns, D R

1996-07-15

The pyrimidine base 5-(hydroxymethyl)-2'-deoxyuridine (HmU) is a common nucleotide in SPO1 phage DNA. Numerous transcriptional proteins bind HmU-containing DNA preferentially implicating a regulatory function of HmU. We have investigated the conformation and dynamics of d-(5'-CHmUCHmUACACGHmUGHmUAGAG-OH-3')2 (HmU-DNA). This oligonucleotide mimics the consensus sequence of Transcription Factor 1 (TF1). The HmU-DNA was compared to the thymine-containing oligonucleotide. NOESY and DQF COSY spectroscopy provided resonance assignments of nonexchangeable and exchangeable protons, intranucleotide, internucleotide and intrastrand proton-proton distances, and dihedral angle constraints. Methylene protons of the hydroxymethyl group are nonequivalent protons and the hydroxymethyl group is not freely rotating. The hydroxymethyl group adopts a specific orientation with the OH group oriented on the 3' side of the plane of the base. Analysis of imino proton resonances and NOEs indicates additional end base pair fraying and a temperature-induced transition to a conformation in which the internal HmU-A base pairs are disrupted or have reduced lifetimes. Orientation of the hydroxymethyl group indicates the presence of internucleotide intrastrand hydrogen bonding between the HmU12C5 hydroxyl group and A13. All sugars in both DNAs show a C2'endo conformation (typical of B-DNA).

PVT Degradation Studies: NMR Analysis

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

Cho, Herman M.; Kouzes, Richard T.

Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity ismore » contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.« less

Assessment of Prospectively Assigned Likert Scores for Targeted Magnetic Resonance Imaging-Transrectal Ultrasound Fusion Biopsies in Patients with Suspected Prostate Cancer.

PubMed

Costa, Daniel N; Lotan, Yair; Rofsky, Neil M; Roehrborn, Claus; Liu, Alexander; Hornberger, Brad; Xi, Yin; Francis, Franto; Pedrosa, Ivan

2016-01-01

We assess the performance of prospectively assigned magnetic resonance imaging based Likert scale scores for the detection of clinically significant prostate cancer, and analyze the pre-biopsy imaging variables associated with increased cancer detection using targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy. In this retrospective review of prospectively generated data including men with abnormal multiparametric prostate magnetic resonance imaging (at least 1 Likert score 3 or greater lesion) who underwent subsequent targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy, we determined the association between different imaging variables (Likert score, lesion size, lesion location, prostate volume, radiologist experience) and targeted biopsy positivity rate. We also compared the detection of clinically significant cancer according to Likert scale scores. Tumors with high volume (50% or more of any core) Gleason score 3+4 or any tumor with greater Gleason score were considered clinically significant. Each lesion served as the elementary unit for analysis. We used logistic regression for univariate and multivariate (stepwise selection) analysis to assess for an association between targeted biopsy positivity rate and each tested variable. The relationship between Likert scale and Gleason score was evaluated using the Spearman correlation coefficient. A total of 161 men with 244 lesions met the study eligibility criteria. Targeted biopsies diagnosed cancer in 41% (66 of 161) of the men and 41% (99 of 244) of the lesions. The Likert score was the strongest predictor of targeted biopsy positivity (OR 3.7, p <0.0001). Other imaging findings associated with a higher targeted biopsy positivity rate included smaller prostate volume (OR 0.7, p <0.01), larger lesion size (OR 2.2, p <0.001) and anterior location (OR 2.0, p=0.01). On multiple logistic regression analysis Likert score, lesion size and prostate volume were significant predictors of targeted biopsy positivity. Higher Likert scores were also associated with increased detection of clinically significant tumors (p <0.0001). The Likert scale score used to convey the degree of suspicion on multiparametric magnetic resonance imaging is the strongest predictor of targeted biopsy positivity and of the presence of clinically significant tumor. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

An Updated Scheme for Categorizing Foods Implicated in Foodborne Disease Outbreaks: A Tri-Agency Collaboration.

PubMed

Richardson, LaTonia Clay; Bazaco, Michael C; Parker, Cary Chen; Dewey-Mattia, Daniel; Golden, Neal; Jones, Karen; Klontz, Karl; Travis, Curtis; Kufel, Joanna Zablotsky; Cole, Dana

2017-12-01

Foodborne disease data collected during outbreak investigations are used to estimate the percentage of foodborne illnesses attributable to specific food categories. Current food categories do not reflect whether or how the food has been processed and exclude many multiple-ingredient foods. Representatives from three federal agencies worked collaboratively in the Interagency Food Safety Analytics Collaboration (IFSAC) to develop a hierarchical scheme for categorizing foods implicated in outbreaks, which accounts for the type of processing and provides more specific food categories for regulatory purposes. IFSAC also developed standard assumptions for assigning foods to specific food categories, including some multiple-ingredient foods. The number and percentage of outbreaks assignable to each level of the hierarchy were summarized. The IFSAC scheme is a five-level hierarchy for categorizing implicated foods with increasingly specific subcategories at each level, resulting in a total of 234 food categories. Subcategories allow distinguishing features of implicated foods to be reported, such as pasteurized versus unpasteurized fluid milk, shell eggs versus liquid egg products, ready-to-eat versus raw meats, and five different varieties of fruit categories. Twenty-four aggregate food categories contained a sufficient number of outbreaks for source attribution analyses. Among 9791 outbreaks reported from 1998 to 2014 with an identified food vehicle, 4607 (47%) were assignable to food categories using this scheme. Among these, 4218 (92%) were assigned to one of the 24 aggregate food categories, and 840 (18%) were assigned to the most specific category possible. Updates to the food categorization scheme and new methods for assigning implicated foods to specific food categories can help increase the number of outbreaks attributed to a single food category. The increased specificity of food categories in this scheme may help improve source attribution analyses, eventually leading to improved foodborne illness source attribution estimates and enhanced food safety and regulatory efforts.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Devine, Jessalyn A.; Babin, Mark C.; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M.

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH3OH → HF + CH3O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH3OHF- anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy.

PubMed

Weichman, Marissa L; DeVine, Jessalyn A; Babin, Mark C; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH 3 OH → HF + CH 3 O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH 3 OHF - anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Comprehensive analysis of oil sands processed water by direct-infusion Fourier-transform ion cyclotron resonance mass spectrometry with and without offline UHPLC sample prefractionation.

PubMed

Nyakas, Adrien; Han, Jun; Peru, Kerry M; Headley, John V; Borchers, Christoph H

2013-05-07

Oil sands processed water (OSPW) is the main byproduct of the large-scale bitumen extraction activity in the Athabasca oil sands region (Alberta, Canada). We have investigated the acid-extractable fraction (AEF) of OSPW by extraction-only (EO) direct infusion (DI) negative-ion mode electrospray ionization (ESI) on a 12T-Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS), as well as by offline ultrahigh performance liquid chromatography (UHPLC) followed by DI-FTICR-MS. A preliminary offline UHPLC separation into 8 fractions using a reversed-phase C4 column led to approximately twice as many detected peaks and identified compounds (973 peaks versus 2231 peaks, of which 856 and 1734 peaks, respectively, could be assigned to chemical formulas based on accurate mass measurements). Conversion of these masses to the Kendrick mass scale allowed the straightforward recognition of homologues. Naphthenic (CnH2n+zO2) and oxy-naphthenic (CnH2n+zOx) acids represented the largest group of molecules with assigned formulas (64%), followed by sulfur-containing compounds (23%) and nitrogen-containing compounds (8%). Pooling of corresponding fractions from two consecutive offline UHPLC runs prior to MS analysis resulted in ~50% more assignments than a single injection, resulting in 3-fold increase of identifications compared to EO-DI-FTICR-MS using the same volume of starting material. Liquid-liquid extraction followed by offline UHPLC fractionation thus holds enormous potential for a more comprehensive profiling of OSPW, which may provide a deeper understanding of its chemical nature and environmental impact.

Vibrational Spectroscopy of CO2- Radical Anion in Water

NASA Astrophysics Data System (ADS)

Janik, Ireneusz; Tripathi, G. N. R.

2016-06-01

The reductive conversion of CO2 into industrial products (e.g., oxalic acid, formic acid, and methanol) can occur via aqueous CO2- as a transient intermediate. While the formation, structure and reaction pathways of this radical anion have been modelled for decades using various spectroscopic and theoretical approaches, we present here, for the first time, a vibrational spectroscopic investigation in liquid water, using pulse radiolysis time-resolved resonance Raman spectroscopy for its preparation and observation. Excitation of the radical in resonance with its 235 nm absorption displays a transient Raman band at 1298 wn, attributed to the symmetric CO stretch, which is at 45 wn higher frequency than in inert matrices. Isotopic substitution at C (13CO2-) shifts the frequency downwards by 22 wn which confirms its origin and the assignment. A Raman band of moderate intensity compared to the stronger 1298 wn band also appears at 742 wn, and is assignable to the OCO bending mode. A reasonable resonance enhancement of this mode is possible only in a bent CO2-(C2v/Cs) geometry. These resonance Raman features suggest a strong solute-solvent interaction, the water molecules acting as constituents of the radical structure, rather than exerting a minor solvent perturbation. However, there is no evidence of the non-equivalence (Cs) of the two CO bonds. A surprising resonance Raman feature is the lack of overtones of the symmetric CO stretch, which we interpret due to the detachment of the electron from the CO2- moiety towards the solvation shell. Electron detachment occurs at the energies of 0.28+/-0.03 eV or higher with respect to the zero point energy of the ground electronic state. The issue of acid-base equilibrium of the radical which has been in contention for decades, as reflected in a wide variation in the reported pKa (-0.2 to 3.9), has been resolved. A value of 3.4+/-0.2 measured in this work is consistent with the vibrational properties, bond structure and charge distribution in aqueous CO2-.

Joint experimental and computational 17O solid state NMR study of Brownmillerite Ba2In2O5.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Holmes, Lesley A; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2014-02-14

Structural characterization of Brownmillerite Ba2In2O5 was achieved by an approach combining experimental solid-state NMR spectroscopy, density functional theory (DFT) energetics, and GIPAW NMR calculations. While in the previous study of Ba2In2O5 by Adler et al. (S. B. Adler, J. A. Reimer, J. Baltisberger and U. Werner, J. Am. Chem. Soc., 1994, 116, 675-681), three oxygen resonances were observed in the (17)O NMR spectra and assigned to the three crystallographically unique O sites, the present high resolution (17)O NMR measurements under magic angle spinning (MAS) find only two resonances. The resonances have been assigned using first principles (17)O GIPAW NMR calculations to the combination of the O ions connecting the InO4 tetrahedra and the O ions in equatorial sites in octahedral InO6 coordination, and to the axial O ions linking the four- and six-fold coordinated In(3+) ions. Possible structural disorder was investigated in two ways: firstly, by inclusion of the high-energy structure also previously studied by Mohn et al. (C. E. Mohn, N. L. Allan, C. L. Freeman, P. Ravindran and S. Stølen, J. Solid State Chem., 2005, 178, 346-355), where the structural O vacancies are stacked rather than staggered as in Brownmillerite and, secondly, by exploring structures derived from the ground-state structure but with randomly perturbed atomic positions. There is no noticeable NMR evidence for any substantial occupancy of the high-energy structure at room temperature.

Three-Body Nature of N* and Δ* Resonances from Sequential Decay Chains

NASA Astrophysics Data System (ADS)

Thiel, A.; Sokhoyan, V.; Gutz, E.; van Pee, H.; Anisovich, A. V.; Bacelar, J. C. S.; Bantes, B.; Bartholomy, O.; Bayadilov, D.; Beck, R.; Beloglazov, Yu.; Castelijns, R.; Crede, V.; Dutz, H.; Elsner, D.; Ewald, R.; Frommberger, F.; Fuchs, M.; Funke, Ch.; Gregor, R.; Gridnev, A.; Hillert, W.; Hoffmeister, Ph.; Horn, I.; Jaegle, I.; Junkersfeld, J.; Kalinowsky, H.; Kammer, S.; Kleber, V.; Klein, Frank; Klein, Friedrich; Klempt, E.; Kotulla, M.; Krusche, B.; Lang, M.; Löhner, H.; Lopatin, I.; Lugert, S.; Mertens, T.; Messchendorp, J. G.; Metag, V.; Metsch, B.; Nanova, M.; Nikonov, V.; Novinski, D.; Novotny, R.; Ostrick, M.; Pant, L.; Pfeiffer, M.; Piontek, D.; Roy, A.; Sarantsev, A. V.; Schmidt, Ch.; Schmieden, H.; Shende, S.; Süle, A.; Sumachev, V. V.; Szczepanek, T.; Thoma, U.; Trnka, D.; Varma, R.; Walther, D.; Wendel, Ch.; Wilson, A.; Cbelsa/Taps Collaboration

2015-03-01

The N π0π0 decays of positive-parity N* and Δ* resonances at about 2 GeV are studied at ELSA by photoproduction of two neutral pions off protons. The data reveal clear evidence for several intermediate resonances: Δ (1232 ) , N (1520 )3 /2- , and N (1680 )5 /2+ , with spin parities JP=3 /2+ , 3 /2- , and 5 /2+. The partial wave analysis (within the Bonn-Gatchina approach) identifies N (1440 )1 /2+ and the N (π π )S wave (abbreviated as N σ here) as further isobars and assigns the final states to the formation of nucleon and Δ resonances and to nonresonant contributions. We observe the known Δ (1232 )π decays of Δ (1910 )1 /2+ , Δ (1920 )3 /2+, Δ (1905 )5 /2+, Δ (1950 )7 /2+, and of the corresponding spin-parity series in the nucleon sector, N (1880 )1 /2+, N (1900 )3 /2+, N (2000 )5 /2+, and N (1990 )7 /2+ . For the nucleon resonances, these decay modes are reported here for the first time. Further new decay modes proceed via N (1440 )1 /2+π , N (1520 )3 /2-π , N (1680 )5 /2+π , and N σ . The latter decay modes are observed in the decay of N* resonances and at most weakly in Δ* decays. It is argued that these decay modes provide evidence for a 3-quark nature of N* resonances rather than a quark-diquark structure.

Autoionization structure of nitric oxide (NO) at the first ionization limit

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

Miescher, E.; Lee, Y.T.; Guertler, P.

1978-03-15

A new and more detailed interpretation is given to the fine structure in the photoionization curve of cold NO observed by Ng, Mahan, and Lee. Resonances are assigned to autoionizing np and nddelta Rydberg levels which give prominent diffuse absorption bands in a spectrum recorded with the synchrotron radiation continuum. ..delta nu..<-1transitions in the vibrational autoionization process are substantiated.

Conformational isomerism of phenolic procyanidins: preferred conformations in organic solvents and water

Treesearch

Tsutomu Hatano; Richard W. Hemingway

1997-01-01

NMR studies of catechin-{4α→8)-epicatechin (I) and catechin-{4α→8)-catechin (2) provided complete assignment of the proton and carbon resonances for both the more extended and compact conformers in the free phenolic form. When 1 is in organic solvents, the more extended rotamer is preferred over the more compact rotamer (10:7), but...

Monoterpene Unknowns Identified Using IR, [to the first power]H-NMR, [to the thirteenth power]C-NMR, DEPT, COSY, and HETCOR

ERIC Educational Resources Information Center

Alty, Lisa T.

2005-01-01

A study identifies a compound from a set of monoterpenes using infrared (IR) and one-dimensional (1D) nuclear magnetic resonance (NMR) techniques. After identifying the unknown, each carbon and proton signal can be interpreted and assigned to the structure using the information in the two-dimensional (2D) NMR spectra, correlation spectroscopy…

FTIR (Fourier Transform Infrared) and FTNMR (Fourier Transform Nuclear Magnetic Resonance) Study of Organophosphorus Surface Reactions

DTIC Science & Technology

1987-09-01

broad band centered about 1140 cm - , (assigned to v(A1-F), 3 (b) no observable v(P=O), 0 (c) a new band at 1082 cm-f (assigned to J P "’i, and also O O...the growth of hydrolysis product can be followed by using either v((P)-G-C) at 999 cm -’ or vs(P0 2 ) at 1082 cm - , but the v(P-F) at about 870 cm-1 is...1180(m)1139(w) v(AI-F) -iI40(br) l!43(vw) 1109(vw) va(P 0 2 ) 1082 (m) 1103(w) 1026 v((P)-O-C) 1011 950(sh) 917 due to subtraction of silica band 900

The excited J = 01 Σu+ levels of D2: Measurements and ab initio quantum defect study

NASA Astrophysics Data System (ADS)

Glass-Maujean, M.; Jungen, Ch.; Dickenson, G. D.; de Oliveira, N.; Ubachs, W.

2016-02-01

The DESIRS beamline of the SOLEIL synchrotron facility, equipped with a vacuum ultraviolet Fourier-transform spectrometer has been used to measure P (N″ = 1) (N -N″ = - 1) absorption transitions of the D2 molecule. Some 44 P-lines were assigned and their transition frequencies determined up to excitation energies of 134,000 cm-1 above the ground state, thereby extending the earlier work by various authors, and considerably improving the spectral accuracy (<0.1 cm-1). The assignments have been aided by first principles multichannel quantum defect theory (MQDT) calculations. These calculations also provide predictions of the autoionization widths of the upper levels which agree well with the observed resonance widths.

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

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Spectroscopic study of jet-cooled indole-3-carbinol by laser desorption technique: Franck-Condon simulations and anharmonic calculations

NASA Astrophysics Data System (ADS)

Ahn, Ahreum; Min, Ahreum; Moon, Cheol Joo; Lee, Ji Hoon; Lee, Seung Jun; Warashina, Taichi; Ishiuchi, Shun-ichi; Fujii, Masaaki; Choi, Myong Yong

2015-10-01

The conformational structure of indole-3-carbinol (I3C) has been investigated in the gas phase for the first time using a laser desorption technique. A UV-UV hole-burning technique revealed the presence of a single conformer of I3C in the mass-selected resonant two-photon ionization spectrum. The assignment of the observed IR spectrum of I3C is inconclusive due to almost identically predicted IR frequencies of the two lowest energy conformers from harmonic calculations. A conclusive assignment for the conformer of I3C has been reported with an aid of performing anharmonic calculations and Franck-Condon simulations on the two lowest-energy conformers.

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

Effortless assignment with 4D covariance sequential correlation maps.

PubMed

Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

Effortless assignment with 4D covariance sequential correlation maps

NASA Astrophysics Data System (ADS)

Harden, Bradley J.; Mishra, Subrata H.; Frueh, Dominique P.

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.

Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation

NASA Astrophysics Data System (ADS)

Sajid, A.; Reimers, Jeffrey R.; Ford, Michael J.

2018-02-01

Key properties of nine possible defect sites in hexagonal boron nitride (h-BN), VN,VN -1,CN,VNO2 B,VNNB,VNCB,VBCN,VBCNS iN , and VNCBS iB , are predicted using density-functional theory and are corrected by applying results from high-level ab initio calculations. Observed h-BN electron-paramagnetic resonance signals at 22.4, 20.83, and 352.70 MHz are assigned to VN,CN, and VNO2 B , respectively, while the observed photoemission at 1.95 eV is assigned to VNCB . Detailed consideration of the available excited states, allowed spin-orbit couplings, zero-field splitting, and optical transitions is made for the two related defects VNCB and VBCN . VNCB is proposed for realizing long-lived quantum memory in h-BN. VBCN is predicted to have a triplet ground state, implying that spin initialization by optical means is feasible and suitable optical excitations are identified, making this defect of interest for possible quantum-qubit operations.

Spectroscopic evidence for gas-phase formation of successive beta-turns in a three-residue peptide chain.

PubMed

Chin, Wutharath; Compagnon, Isabelle; Dognon, Jean-Pierre; Canuel, Clélia; Piuzzi, François; Dimicoli, Iliana; von Helden, Gert; Meijer, Gerard; Mons, Michel

2005-02-09

We report the first gas-phase spectroscopic study of a three-residue model of a peptide chain, Ac-Phe-Gly-Gly-NH2 (Ac = acetyl), using the IR/UV double resonance technique. The existence of at least five different conformers under supersonic expansion conditions is established, most of them exhibiting rather strong intramolecular H-bonds. One of the most populated conformers, however, exhibits a different H-bonding network characterized by two weak H-bonds. Comparison of the amide A and I/II experimental data with density functional theory calculations carried out on a series of selected conformations enables us to assign this conformer to two successive beta-turns along the peptide chain, the two H-bonds being of C10 type, i.e., each of them closing a 10-atom ring in the molecule. The corresponding form is found to be more stable than the 310 helix secondary structure (not observed), presumably because of specific effects due to the glycine residues.

Combining Fourier phase encoding and broadband inversion toward J-edited spectra

NASA Astrophysics Data System (ADS)

Lin, Yulan; Guan, Quanshuai; Su, Jianwei; Chen, Zhong

2018-06-01

Nuclear magnetic resonance (NMR) spectra are often utilized for gathering accurate information relevant to molecular structures and composition assignments. In this study, we develop a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks, and combine it with a pure shift experiments (PSYCHE) based J-modulated scheme, providing simple 2D J-edited spectra for accurate measurement of scalar coupling networks. Chemical shifts and J coupling constants of protons coupled to the specific protons are demonstrated along the F2 and F1 dimensions, respectively. Polychromatic pulses by Fourier phase encoding were performed to simultaneously detect several coupling networks. Proton-proton scalar couplings are chosen by a polychromatic pulse and a PSYCHE element. Axis peaks and unwanted couplings are complete eradicated by incorporating a selective COSY block as a preparation period. The theoretical principles and the signal processing procedure are laid out, and experimental observations are rationalized on the basis of theoretical analyses.

Electronic and geometric structure of thin CoO(100) films studied by angle-resolved photoemission spectroscopy and Auger electron diffraction

NASA Astrophysics Data System (ADS)

Heiler, M.; Chassé, A.; Schindler, K.-M.; Hollering, M.; Neddermeyer, H.

2000-05-01

We have prepared ordered thin films of CoO by evaporating cobalt in an O 2 atmosphere on to a heated (500 K) Ag(100) substrate. The geometric and electronic structure of the films was characterized by means of Auger electron diffraction (AED) and angle-resolved photoemission spectroscopy (ARUPS), respectively. The experimental AED results were compared with simulated data, which showed that the film grows in (100) orientation on the Ag(100) substrate. Synchrotron-radiation-induced photoemission investigations were performed in the photon energy range from 25 eV to 67 eV. The dispersion of the transitions was found to be similar to that of previous results on a single-crystal CoO(100) surface. The resonance behaviour of the photoemission lines in the valence-band region was investigated by constant-initial-state (CIS) spectroscopy. The implications of this behaviour for assignment of the photoemission lines to specific electronic transitions is discussed and compared with published theoretical models of the electronic structure.

Effects of strain and quantum confinement in optically pumped nuclear magnetic resonance in GaAs: Interpretation guided by spin-dependent band structure calculations

DOE PAGES

Wood, R. M.; Saha, D.; McCarthy, L. A.; ...

2014-10-29

A combined experimental-theoretical study of optically pumped NMR (OPNMR) has been performed in a GaAs/Al 0.1Ga 0.9As quantum well film with thermally induced biaxial strain. The photon energy dependence of the Ga-71 OPNMR signal was recorded at magnetic fields of 4.9 and 9.4 T at a temperature of 4.8-5.4 K. The data were compared to the nuclear spin polarization calculated from differential absorption to spin-up and spin-down states of the conduction band using a modified Pidgeon Brown model. Reasonable agreement between theory and experiment is obtained, facilitating assignment of features in the OPNMR energy dependence to specific interband transitions. Despitemore » the approximations made in the quantum-mechanical model and the inexact correspondence between the experimental and calculated observables, the results provide insight into how effects of strain and quantum confinement are manifested in OPNMR signals« less

Correlation distance dependence of the resonance frequency of intermolecular zero quantum coherences and its implication for MR thermometry.

PubMed

Zhang, Le; McCallister, Andrew; Koshlap, Karl M; Branca, Rosa Tamara

2018-03-01

Because the resonance frequency of water-fat intermolecular zero-quantum coherences (iZQCs) reflects the water-fat frequency separation at the microscopic scale, these frequencies have been proposed and used as a mean to obtain more accurate temperature information. The purpose of this work was to investigate the dependence of the water-fat iZQC resonance frequency on sample microstructure and on the specific choice of the correlation distance. The effect of water-fat susceptibility gradients on the water-methylene iZQC resonance frequency was first computed and then measured for different water-fat emulsions and for a mixture of porcine muscle and fat. Similar measurements were also performed for mixed heteronuclear spin systems. A strong dependence of the iZQC resonance frequency on the sample microstructure and on the specific choice of the correlation distance was found for spin systems like water and fat that do not mix, but not for spin systems that mix at the molecular level. Because water and fat spins do not mix at the molecular level, the water-fat iZQC resonance frequency and its temperature coefficient are not only affected by sample microstructure but also by the specific choice of the correlation distance. Magn Reson Med 79:1429-1438, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Prostate Specific Membrane Antigen Positron Emission Tomography May Improve the Diagnostic Accuracy of Multiparametric Magnetic Resonance Imaging in Localized Prostate Cancer.

PubMed

Rhee, H; Thomas, P; Shepherd, B; Gustafson, S; Vela, I; Russell, P J; Nelson, C; Chung, E; Wood, G; Malone, G; Wood, S; Heathcote, P

2016-10-01

Positron emission tomography using ligands targeting prostate specific membrane antigen has recently been introduced. Positron emission tomography imaging with (68)Ga-PSMA-HBED-CC has been shown to detect metastatic prostate cancer lesions at a high rate. In this study we compare multiparametric magnetic resonance imaging and prostate specific membrane antigen positron emission tomography of the prostate with whole mount ex vivo prostate histopathology to determine the true sensitivity and specificity of these imaging modalities for detecting and locating tumor foci within the prostate. In a prospective clinical trial setting 20 patients with localized prostate cancer and a planned radical prostatectomy were recruited. All patients underwent multiparametric magnetic resonance imaging and positron emission tomography before surgery, and whole mount histopathology slides were directly compared to the images. European Society of Urogenital Radiology guidelines for reporting magnetic resonance imaging were used as a template for regional units of analysis. The uropathologist and radiologists were blinded to individual components of the study, and the final correlation was performed by visual and deformable registration analysis. A total of 50 clinically significant lesions were identified from the whole mount histopathological analysis. Based on regional analysis the sensitivity, specificity, positive predictive value and negative predictive value for multiparametric magnetic resonance imaging were 44%, 94%, 81% and 76%, respectively. With prostate specific membrane antigen positron emission tomography the sensitivity, specificity, positive predictive value and negative predictive value were 49%, 95%, 85% and 88%, respectively. Prostate specific membrane antigen positron emission tomography yielded a higher specificity and positive predictive value. A significant proportion of cancers are potentially missed and underestimated by both imaging modalities. Prostate specific membrane antigen positron emission tomography may be used in addition to multiparametric magnetic resonance imaging to help improve local staging in those patients undergoing retropubic radical prostatectomy. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Detecting prostate cancer and prostatic calcifications using advanced magnetic resonance imaging

PubMed Central

Dou, Shewei; Bai, Yan; Shandil, Ankit; Ding, Degang; Shi, Dapeng; Haacke, E Mark; Wang, Meiyun

2017-01-01

Prostate cancer and prostatic calcifications have a high incidence in elderly men. We aimed to investigate the diagnostic capabilities of susceptibility-weighted imaging in detecting prostate cancer and prostatic calcifications. A total number of 156 men, including 34 with prostate cancer and 122 with benign prostate were enrolled in this study. Computed tomography, conventional magnetic resonance imaging, diffusion-weighted imaging, and susceptibility-weighted imaging were performed on all the patients. One hundred and twelve prostatic calcifications were detected in 87 patients. The sensitivities and specificities of the conventional magnetic resonance imaging, apparent diffusion coefficient, and susceptibility-filtered phase images in detecting prostate cancer and prostatic calcifications were calculated. McNemar's Chi-square test was used to compare the differences in sensitivities and specificities between the techniques. The results showed that the sensitivity and specificity of susceptibility-filtered phase images in detecting prostatic cancer were greater than that of conventional magnetic resonance imaging and apparent diffusion coefficient (P < 0.05). In addition, the sensitivity and specificity of susceptibility-filtered phase images in detecting prostatic calcifications were comparable to that of computed tomography and greater than that of conventional magnetic resonance imaging and apparent diffusion coefficient (P < 0.05). Given the high incidence of susceptibility-weighted imaging (SWI) abnormality in prostate cancer, we conclude that susceptibility-weighted imaging is more sensitive and specific than conventional magnetic resonance imaging, diffusion-weighted imaging, and computed tomography in detecting prostate cancer. Furthermore, susceptibility-weighted imaging can identify prostatic calcifications similar to computed tomography, and it is much better than conventional magnetic resonance imaging and diffusion-weighted imaging. PMID:27004542

Detecting prostate cancer and prostatic calcifications using advanced magnetic resonance imaging.

PubMed

Dou, Shewei; Bai, Yan; Shandil, Ankit; Ding, Degang; Shi, Dapeng; Haacke, E Mark; Wang, Meiyun

2017-01-01

Prostate cancer and prostatic calcifications have a high incidence in elderly men. We aimed to investigate the diagnostic capabilities of susceptibility-weighted imaging in detecting prostate cancer and prostatic calcifications. A total number of 156 men, including 34 with prostate cancer and 122 with benign prostate were enrolled in this study. Computed tomography, conventional magnetic resonance imaging, diffusion-weighted imaging, and susceptibility-weighted imaging were performed on all the patients. One hundred and twelve prostatic calcifications were detected in 87 patients. The sensitivities and specificities of the conventional magnetic resonance imaging, apparent diffusion coefficient, and susceptibility-filtered phase images in detecting prostate cancer and prostatic calcifications were calculated. McNemar's Chi-square test was used to compare the differences in sensitivities and specificities between the techniques. The results showed that the sensitivity and specificity of susceptibility-filtered phase images in detecting prostatic cancer were greater than that of conventional magnetic resonance imaging and apparent diffusion coefficient (P < 0.05). In addition, the sensitivity and specificity of susceptibility-filtered phase images in detecting prostatic calcifications were comparable to that of computed tomography and greater than that of conventional magnetic resonance imaging and apparent diffusion coefficient (P < 0.05). Given the high incidence of susceptibility-weighted imaging (SWI) abnormality in prostate cancer, we conclude that susceptibility-weighted imaging is more sensitive and specific than conventional magnetic resonance imaging, diffusion-weighted imaging, and computed tomography in detecting prostate cancer. Furthermore, susceptibility-weighted imaging can identify prostatic calcifications similar to computed tomography, and it is much better than conventional magnetic resonance imaging and diffusion-weighted imaging.

The performance of magnetic resonance imaging in the detection of triangular fibrocartilage complex injury: a meta-analysis.

PubMed

Wang, Z X; Chen, S L; Wang, Q Q; Liu, B; Zhu, J; Shen, J

2015-06-01

The aim of this study was to evaluate the accuracy of magnetic resonance imaging in the detection of triangular fibrocartilage complex injury through a meta-analysis. A comprehensive literature search was conducted before 1 April 2014. All studies comparing magnetic resonance imaging results with arthroscopy or open surgery findings were reviewed, and 25 studies that satisfied the eligibility criteria were included. Data were pooled to yield pooled sensitivity and specificity, which were respectively 0.83 and 0.82. In detection of central and peripheral tears, magnetic resonance imaging had respectively a pooled sensitivity of 0.90 and 0.88 and a pooled specificity of 0.97 and 0.97. Six high-quality studies using Ringler's recommended magnetic resonance imaging parameters were selected for analysis to determine whether optimal imaging protocols yielded better results. The pooled sensitivity and specificity of these six studies were 0.92 and 0.82, respectively. The overall accuracy of magnetic resonance imaging was acceptable. For peripheral tears, the pooled data showed a relatively high accuracy. Magnetic resonance imaging with appropriate parameters are an ideal method for diagnosing different types of triangular fibrocartilage complex tears. © The Author(s) 2015.

The Biomes of Homewood: Interactive Map Software

ERIC Educational Resources Information Center

Shingles, Richard; Feist, Theron; Brosnan, Rae

2005-01-01

To build a learning community, the General Biology faculty at Johns Hopkins University conducted collaborative, problem-based learning assignments outside of class in which students are assigned to specific areas on campus, and gather and report data about their area. To overcome the logistics challenges presented by conducting such assignments in…

47 CFR 90.509 - Frequencies available for assignment.

Code of Federal Regulations, 2012 CFR

2012-10-01

... assignment. Stations engaged in developmental operation may be authorized to use a frequency or frequencies available in the service in which they propose to operate. The number of channels assigned will depend upon the specific requirements of the developmental program and the number of frequencies available in the...

47 CFR 90.509 - Frequencies available for assignment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... assignment. Stations engaged in developmental operation may be authorized to use a frequency or frequencies available in the service in which they propose to operate. The number of channels assigned will depend upon the specific requirements of the developmental program and the number of frequencies available in the...

47 CFR 90.509 - Frequencies available for assignment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... assignment. Stations engaged in developmental operation may be authorized to use a frequency or frequencies available in the service in which they propose to operate. The number of channels assigned will depend upon the specific requirements of the developmental program and the number of frequencies available in the...

Prospective evaluation of magnetic resonance imaging guided in-bore prostate biopsy versus systematic transrectal ultrasound guided prostate biopsy in biopsy naïve men with elevated prostate specific antigen.

PubMed

Quentin, Michael; Blondin, Dirk; Arsov, Christian; Schimmöller, Lars; Hiester, Andreas; Godehardt, Erhard; Albers, Peter; Antoch, Gerald; Rabenalt, Robert

2014-11-01

Magnetic resonance imaging guided biopsy is increasingly performed to diagnose prostate cancer. However, there is a lack of well controlled, prospective trials to support this treatment method. We prospectively compared magnetic resonance imaging guided in-bore biopsy with standard systematic transrectal ultrasound guided biopsy in biopsy naïve men with increased prostate specific antigen. We performed a prospective study in 132 biopsy naïve men with increased prostate specific antigen (greater than 4 ng/ml). After 3 Tesla functional multiparametric magnetic resonance imaging patients were referred for magnetic resonance imaging guided in-bore biopsy of prostate lesions (maximum 3) followed by standard systematic transrectal ultrasound guided biopsy (12 cores). We analyzed the detection rates of prostate cancer and significant prostate cancer (greater than 5 mm total cancer length or any Gleason pattern greater than 3). A total of 128 patients with a mean ± SD age of 66.1 ± 8.1 years met all study requirements. Median prostate specific antigen was 6.7 ng/ml (IQR 5.1-9.0). Transrectal ultrasound and magnetic resonance imaging guided biopsies provided the same 53.1% detection rate, including 79.4% and 85.3%, respectively, for significant prostate cancer. Magnetic resonance imaging and transrectal ultrasound guided biopsies missed 7.8% and 9.4% of clinically significant prostate cancers, respectively. Magnetic resonance imaging biopsy required significantly fewer cores and revealed a higher percent of cancer involvement per biopsy core (each p <0.01). Combining the 2 methods provided a 60.9% detection rate with an 82.1% rate for significant prostate cancer. Magnetic resonance imaging guided in-bore and systematic transrectal ultrasound guided biopsies achieved equally high detection rates in biopsy naïve patients with increased prostate specific antigen. Magnetic resonance imaging guided in-bore biopsies required significantly fewer cores and revealed a significantly higher percent of cancer involvement per biopsy core. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Resonances above the proton threshold in 26Si

DOE PAGES

Chipps, Kelly A.

2016-03-06

26Al remains an intriguing target for observational gamma-ray astronomy, thanks to its characteristic decay. The 25Al(p, )26Si reaction is part of a chain that bypasses the production of the observable 26Alg in favor of the isomeric state; its rate at novae temperatures is dominated by a resonance around 400 keV, the precise location and J assignment of which has been hotly debated. Considerable confusion in this regard has arisen from the use of outdated excitation energies and masses. Here, a reanalysis of previous work is completed to first, elucidate the confusion regarding the level structure just above the proton threshold,more » and second, provide focus to future studies.« less

Correlations of π N partial waves for multireaction analyses

DOE PAGES

Doring, M.; Revier, J.; Ronchen, D.; ...

2016-06-15

In the search for missing baryonic resonances, many analyses include data from a variety of pion- and photon-induced reactions. For elastic πN scattering, however, usually the partial waves of the SAID (Scattering Analysis Interactive Database) or other groups are fitted, instead of data. We provide the partial-wave covariance matrices needed to perform correlated χ 2 fits, in which the obtained χ 2 equals the actual χ 2 up to nonlinear and normalization corrections. For any analysis relying on partial waves extracted from elastic pion scattering, this is a prerequisite to assess the significance of resonance signals and to assign anymore » uncertainty on results. Lastly, the influence of systematic errors is also considered.« less

Multiobjective optimization of cartilage stress for non-invasive, patient-specific recommendations of high tibial osteotomy correction angle - a novel method to investigate alignment correction.

PubMed

Zheng, Keke; Scholes, Corey J; Chen, Junning; Parker, David; Li, Qing

2017-04-01

Medial opening wedge high tibial osteotomy (MOWHTO) is a surgical procedure to treat knee osteoarthritis associated with varus deformity. However, the ideal final alignment of the Hip-Knee-Ankle (HKA) angle in the frontal plane, that maximizes procedural success and post-operative knee function, remains controversial. Therefore, the purpose of this study was to introduce a subject-specific modeling procedure in determining the biomechanical effects of MOWHTO alignment on tibiofemoral cartilage stress distribution. A 3D finite element knee model derived from magnetic resonance imaging of a healthy participant was manipulated in-silico to simulate a range of final HKA angles (i.e. 0.2°, 2.7°, 3.9° and 6.6° valgus). Loading and boundary conditions were assigned based on subject-specific kinematic and kinetic data from gait analysis. Multiobjective optimization was used to identify the final alignment that balanced compressive and shear forces between medial and lateral knee compartments. Peak stresses decreased in the medial and increased in the lateral compartment as the HKA was shifted into valgus, with balanced loading occurring at angles of 4.3° and 2.9° valgus for the femoral and tibial cartilage respectively. The concept introduced here provides a platform for non-invasive, patient-specific preoperative planning of the osteotomy for medial compartment knee osteoarthritis. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

PubMed

Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

2011-06-15

PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

Clinically Practical Magnetic Resonance Protocol for Improved Specificity in Breast Cancer Diagnosis

DTIC Science & Technology

2007-06-01

Protocol for Improved Specificity in Breast Cancer Diagnosis PRINCIPAL INVESTIGATOR: Luminita Alina Tudorica, Ph.D. CONTRACTING...TITLE AND SUBTITLE 5a. CONTRACT NUMBER Clinically Practical Magnetic Resonance Protocol for Improved Specificity in Breast Cancer Diagnosis 5b... breast cancer study in a clinical setting. This study aims to improve specificity of breast cancer detection by using a combined MRI/MRS protocol. In

A Comparison of the Long-Term Learning Effects of Comprehensive and Topic-Specific Practice Set Assignments

ERIC Educational Resources Information Center

Fatemi, Darius; Marley, Robert; Marquis, Linda M.

2015-01-01

The authors examined the long-term learning effects of two different practice set assignment approaches on business students' long-term learning: a comprehensive, multiple-period practice set and a topic-specific practice set. Student learning was measured longitudinally across semesters. The authors found evidence that students using a…

Occupational exposures and chronic obstructive pulmonary disease (COPD): comparison of a COPD-specific job exposure matrix and expert-evaluated occupational exposures.

PubMed

Kurth, Laura; Doney, Brent; Weinmann, Sheila

2017-03-01

To compare the occupational exposure levels assigned by our National Institute for Occupational Safety and Health chronic obstructive pulmonary disease-specific job exposure matrix (NIOSH COPD JEM) and by expert evaluation of detailed occupational information for various jobs held by members of an integrated health plan in the Northwest USA. We analysed data from a prior study examining COPD and occupational exposures. Jobs were assigned exposure levels using 2 methods: (1) the COPD JEM and (2) expert evaluation. Agreement (Cohen's κ coefficients), sensitivity and specificity were calculated to compare exposure levels assigned by the 2 methods for 8 exposure categories. κ indicated slight to moderate agreement (0.19-0.51) between the 2 methods and was highest for organic dust and overall exposure. Sensitivity of the matrix ranged from 33.9% to 68.5% and was highest for sensitisers, diesel exhaust and overall exposure. Specificity ranged from 74.7% to 97.1% and was highest for fumes, organic dust and mineral dust. This COPD JEM was compared with exposures assigned by experts and offers a generalisable approach to assigning occupational exposure. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A Latin-cross-shaped integrated resonant cantilever with second torsion-mode resonance for ultra-resoluble bio-mass sensing

NASA Astrophysics Data System (ADS)

Xia, Xiaoyuan; Zhang, Zhixiang; Li, Xinxin

2008-03-01

Second torsion-mode resonance is proposed for microcantilever biosensors for ultra-high mass-weighing sensitivity and resolution. By increasing both the resonant frequency and Q-factor, the higher mode torsional resonance is favorable for improving the mass-sensing performance. For the first time, a Latin-cross-shaped second-mode resonant cantilever is constructed and optimally designed for both signal-readout and resonance-exciting elements. The cantilever sensor is fabricated by using silicon micromachining techniques. The transverse piezoresistive sensing element and the specific-shaped resonance-exciting loop are successfully integrated in the cantilever. Alpha-fetoprotein (AFP) antibody-antigen specific binding is implemented for the sensing experiment. The proposed cantilever sensor is designed with significantly superior sensitivity to the previously reported first torsion-mode one. After analysis with an Allan variance algorithm, which can be easily embedded in the sensing system, the Latin-cross-shaped second torsion-mode resonant cantilever is evaluated with ultra-high mass resolution. Therefore, the high-performance integrated micro-sensor is promising for on-the-spot bio-molecule detection.

Precise ro-vibrational analysis of molecular bands forbidden in absorption: The ν8 +ν10 band of the 12C2H4 molecule

NASA Astrophysics Data System (ADS)

Ulenikov, O. N.; Gromova, O. V.; Bekhtereva, E. S.; Kashirina, N. V.; Bauerecker, S.; Horneman, V.-M.

2015-07-01

The highly accurate (experimental accuracy in line positions ∼ (1 - 2) ×10-4 cm-1) ro-vibrational spectrum of the ν8 +ν10 band of the 12C2H4 molecule was recorded for the first time with high resolution Fourier transform spectrometry and analyzed in the region of 1650-1950 cm-1 using the Hamiltonian model which takes into account Coriolis resonance interactions between the studied ν8 +ν10 band, which is forbidden in absorption, and the bands ν4 +ν8 and ν7 +ν8 . About 1570 transitions belonging to the ν8 +ν10 band were assigned in the experimental spectra with the maximum values of quantum numbers Jmax. = 35 and Kamax . = 18 . On that basis, a set of 38 vibrational, rotational, centrifugal distortion, and resonance interaction parameters was obtained from the fit. They reproduce values of 598 initial "experimental" ro-vibrational energy levels (positions of about 1570 experimentally recorded and assigned transitions) with the rms error drms = 0.00045 cm-1 (drms = 0.00028 cm-1 when upper ro-vibrational energies obtained from blended and very weak transitions were deleted from the fit).

Improved in-cell structure determination of proteins at near-physiological concentration

PubMed Central

Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Güntert, Peter; Ito, Yutaka

2016-01-01

Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells. PMID:27910948

Anharmonic Resonances among Low-Lying Vibrational Levels of Methyl Iso-Cyanide (H_3CNC)

NASA Astrophysics Data System (ADS)

Pracna, P.; Urban, J.; Urban, V. S.; Varga, J.; Horneman, V.-M.

2010-06-01

Vibrational levels up to 1000 wn of H_3C-N≡C are currently studied in FTIR spectra together with rotational transitions within these levels. This investigation comprises the low-lying excited vibrational levels of the CNC doubly degenerate bending vibration v8=1^± 1 (267.3 wn), v8=20,± 2 (524.6 wn (A), 545.3 wn (E)), and v8=3^± 1,± 3 (792.5 wn (A1+A2), 833.9 wn (E)), respectively, and the next higher fundamental level of the C-N valence vibration v4=1 (945 wn). All these vibrational levels exhibit cubic and quartic anharmonic resonances localized to moderate values of the rotational quantum number K≤10. Therefore the system of rovibrational levels has to be treated as a global polyad in order to describe all the available data quantitatively. The ground state constants have been improved considerably by extending the assignments to higher J/K rotational states both in the purely rotational spectra recorded in the ground vibrational level and in the ground state combination differences generated from the wavenumbers assigned in the fundamental ν_4 band. Similarities and differences with respect to isoelectronic molecules CH_3CN and CH_3CCH are discussed.

1H, 15N and 13C resonance assignments of the J-domain of co-chaperone Sis1 from Saccharomyces cerevisiae.

PubMed

Pinheiro, Glaucia M S; Amorim, Gisele C; Iqbal, Anwar; Ramos, C H I; Almeida, Fabio C L

2018-04-30

Protein folding in the cell is usually aided by molecular chaperones, from which the Hsp70 (Hsp = heat shock protein) family has many important roles, such as aiding nascent folding and participating in translocation. Hsp70 has ATPase activity which is stimulated by binding to the J-domain present in co-chaperones from the Hsp40 family. Hsp40s have many functions, as for instance the binding to partially folded proteins to be delivered to Hsp70. However, the presence of the J-domain characterizes Hsp40s or, by this reason, as J-proteins. The J-domain alone can stimulate Hsp70 ATPase activity. Apparently, it also maintains the same conformation as in the whole protein although structural information on full J-proteins is still missing. This work reports the 1 H, 15 N and 13 C resonance assignments of the J-domain of a Hsp40 from Saccharomyces cerevisiae, named Sis1. Secondary structure and order parameter prediction from chemical shifts are also reported. Altogether, the data show that Sis1 J-domain is highly structured and predominantly formed by α-helices, results that are in very good agreement with those previously reported for the crystallographic structure.

Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

NASA Astrophysics Data System (ADS)

Macleod, Neil A.; Simons, John P.

2002-10-01

The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water 'droplet' forms on the end of the alcohol side-chain.

Re-Visiting the Electronic Energy Map of the Copper Dimer by Double-Resonant Four-Wave Mixing

NASA Astrophysics Data System (ADS)

Visser, Bradley; Bornhauser, Peter; Beck, Martin; Knopp, Gregor; Marquardt, Roberto; Gourlaouen, Christophe; van Bokhoven, Jeroen A.; Radi, Peter

2017-06-01

The copper dimer is one of the most studied transition metal (TM) diatomics due to its alkali-metal like electronic shell structure, strongly bound ground state and chemical reactivity. The high electronic promotion energy in the copper atom yields numerous low-lying electronic states compared to TM dimers with d)-hole electronic configurations. Thus, through extensive study the excited electronic structure of Cu_2 is relatively well known, however in practice few excited states have been investigated with rotational resolution or even assigned term symbols or dissociation limits. The spectroscopic methods that have been used to investigate the copper dimer until now have not possessed sufficient spectral selectivity, which has complicated the analysis of the often overlapping transitions. Resonant four-wave mixing is a non-linear absorption based spectroscopic method. In favorable cases, the two-color version (TC-RFWM) enables purely optical mass selective spectral measurements in a mixed molecular beam. Additionally, by labelling individual rotational levels in the common intermediate state the spectra are dramatically simplified. In this work, we report on the rotationally resolved characterization of low-lying electronic states of dicopper. Several term symbols have been assigned unambiguously. De-perturbation studies performed shed light on the complex electronic structure of the molecule. Furthermore, a new low-lying electronic state of Cu_2 is discovered and has important implications for the high-level theoretical structure calculations performed in parallel. In fact, the ab initio methods applied yield relative energies among the electronic levels that are almost quantitative and allow assignment of the newly observed state that is governed by spin-orbit interacting levels.

Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

PubMed

Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2014-10-01

Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

CW and pulsed electrically detected magnetic resonance spectroscopy at 263 GHz/12 T on operating amorphous silicon solar cells

NASA Astrophysics Data System (ADS)

Akhtar, W.; Schnegg, A.; Veber, S.; Meier, C.; Fehr, M.; Lips, K.

2015-08-01

Here we describe a new high frequency/high field continuous wave and pulsed electrically detected magnetic resonance (CW EDMR and pEDMR) setup, operating at 263 GHz and resonance fields between 0 and 12 T. Spin dependent transport in illuminated hydrogenated amorphous silicon p-i-n solar cells at 5 K and 90 K was studied by in operando 263 GHz CW and pEDMR alongside complementary X-band CW EDMR. Benefiting from the superior resolution at 263 GHz, we were able to better resolve EDMR signals originating from spin dependent hopping and recombination processes. 5 K EDMR spectra were found to be dominated by conduction and valence band tail states involved in spin dependent hopping, with additional contributions from triplet exciton states. 90 K EDMR spectra could be assigned to spin pair recombination involving conduction band tail states and dangling bonds as the dominating spin dependent transport process, with additional contributions from valence band tail and triplet exciton states.

Resonance-enhanced two-photon excitation of CaI

NASA Astrophysics Data System (ADS)

Casero-Junquera, Elena; Lawruszczuk, Rafal; Rostas, Joëlle; Taieb, Guy

1994-07-01

Induced fluorescence following visible (620-655 nm) laser excitation of the CaI radical has been detected not only in the same region (B, A-X transitions), but also in the UV (315-330 nm). The UV two-photon excitation spectrum consists of narrow bands appearing at laser frequencies located within certain bands of the Δ v = 1, 0 sequences of the B 2Σ +-X 2Σ + and A 2Π 1/2-X 2Σ + systems. The main peaks are tentatively assigned to resonance-enhanced excitation of a single vibrational level of the lowest Rydberg D 2Σ + state from successive vibrational levels of the ground state. The excitation process is a one-color two-photon optical—optical-double-resonance via B 2Σ + and A 2Π 1/2 intermediate levels. This analysis is supported by the absorption spectrum observed long ago by Walters and Barratt. The absorption and laser excitation complementary data have been used to derive approximate molecular constants for the D state.

Single-spin stochastic optical reconstruction microscopy

PubMed Central

Pfender, Matthias; Aslam, Nabeel; Waldherr, Gerald; Neumann, Philipp; Wrachtrup, Jörg

2014-01-01

We experimentally demonstrate precision addressing of single-quantum emitters by combined optical microscopy and spin resonance techniques. To this end, we use nitrogen vacancy (NV) color centers in diamond confined within a few ten nanometers as individually resolvable quantum systems. By developing a stochastic optical reconstruction microscopy (STORM) technique for NV centers, we are able to simultaneously perform sub–diffraction-limit imaging and optically detected spin resonance (ODMR) measurements on NV spins. This allows the assignment of spin resonance spectra to individual NV center locations with nanometer-scale resolution and thus further improves spatial discrimination. For example, we resolved formerly indistinguishable emitters by their spectra. Furthermore, ODMR spectra contain metrology information allowing for sub–diffraction-limit sensing of, for instance, magnetic or electric fields with inherently parallel data acquisition. As an example, we have detected nuclear spins with nanometer-scale precision. Finally, we give prospects of how this technique can evolve into a fully parallel quantum sensor for nanometer resolution imaging of delocalized quantum correlations. PMID:25267655

Fingerprinting analysis of Rhizoma chuanxiong of commercial types using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography method.

PubMed

Qin, Hai-Lin; Deng, An-Jun; Du, Guan-Hua; Wang, Peng; Zhang, Jin-Lan; Li, Zhi-Hong

2009-06-01

The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar extracts (control substance for a plant drug (CSPD) A) from Rhizoma chuanxiong, the rhizomes of Ligusticum chuanxiong Hort., of seven specimens from different sources were measured on Fourier Transform (FT)-NMR spectrometer and assigned by comparing them with the (1)H NMR spectra of the isolated pure compounds. The (1)H NMR fingerprints showed exclusively characteristic resonance signals of the major special constituents of the plant. Although the differences in the relative intensity of the (1)H NMR signals due to a discrepancy in the ratio of the major constituents among these samples could be confirmed by high performance liquid chromatography analysis, the general features of the (1)H NMR fingerprint established for an authentic sample of the rhizomes of L. chuanxiong exhibited exclusive data from those special compounds and can be used for authenticating L. Chuanxiong species.

Resonance Raman study on the structure of the active sites of microsomal cytochrome P-450 isozymes LM2 and LM4.

PubMed

Hildebrandt, P; Greinert, R; Stier, A; Taniguchi, H

1989-12-08

The isozymes 2 and 4 of rabbit microsomal cytochrome P-450 (LM2, LM4) have been studied by resonance Raman spectroscopy. Based on high quality spectra, a vibrational assignment of the porphyrin modes in the frequency range between 100-1700 cm-1 is presented for different ferric states of cytochrome P-450 LM2 and LM4. The resonance Raman spectra are interpreted in terms of the spin and ligation state of the heme iron and of heme-protein interactions. While in cytochrome P-450 LM2 the six-coordinated low-spin configuration is predominantly occupied, in the isozyme LM4 the five-coordinated high-spin form is the most stable state. The different stability of these two spin configurations in LM2 and LM4 can be attributed to the structures of the active sites. In the low-spin form of the isozymes LM4 the protein matrix forces the heme into a more rigid conformation than in LM2. These steric constraints are removed upon dissociation of the sixth ligand leading to a more flexible structure of the active site in the high-spin form of the isozyme LM4. The vibrational modes of the vinyl groups were found to be characteristic markers for the specific structures of the heme pockets in both isozymes. They also respond sensitively to type-I substrate binding. While in cytochrome P-450 LM4 the occupation of the substrate-binding pocket induces conformational changes of the vinyl groups, as reflected by frequency shifts of the vinyl modes, in the LM2 isozyme the ground-state conformation of these substituents remain unaffected, suggesting that the more flexible heme pocket can accommodate substrates without imposing steric constraints on the porphyrin. The resonance Raman technique makes structural changes visible which are induced by substrate binding in addition and independent of the changes associated with the shift of the spin state equilibrium: the high-spin states in the substrate-bound and substrate-free enzyme are structurally different. The formation of the inactive form, P-420, involves a severe structural rearrangement in the heme binding pocket leading to drastic changes of the vinyl group conformations. The conformational differences of the active sites in cytochromes P-450 LM2 and LM4 observed in this work contribute to the understanding of the structural basis accounting for substrate and product specificity of cytochrome P-450 isozymes.

Understanding Course Content through Letter Writing: Do Informal Writing Assignments Improve Grades?

ERIC Educational Resources Information Center

Bersamin, Melina; Zamboanga, Byron L.; Orsak-Neff, Natalie

2013-01-01

Using an experimental study design (N = 41), we examined whether participation in an informal writing assignment, specifically writing a letter to a friend about course content, improved exam scores in an undergraduate child development course. Findings indicated that participating in the writing assignment significantly improved scores on an exam…

Magnetic resonance imaging in local staging of endometrial carcinoma: diagnostic performance, pitfalls, and literature review.

PubMed

Zandrino, Franco; La Paglia, Ernesto; Musante, Francesco

2010-01-01

To assess the diagnostic accuracy of magnetic resonance imaging in local staging of endometrial carcinoma, and to review the results and pitfalls described in the literature. Thirty women with a histological diagnosis of endometrial carcinoma underwent magnetic resonance imaging. Unenhanced T2-weighted and dynamic contrast-enhanced Ti-weighted sequences were obtained. Hysterectomy and salpingo-oophorectomy was performed in all patients. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were calculated for the detection of deep myometrial and cervical infiltration. For deep myometrial infiltration T2-weighted sequences reached a sensitivity of 85%, specificity of 76%, PPV of 73%, NVP of 87%, and accuracy of 80%, while contrast-enhanced scans reached a sensitivity of 90%, specificity of 80%, PPV of 82%, NPV of 89%, and accuracy of 85%. For cervical infiltration T2-weighted sequences reached a sensitivity of 75%, specificity of 88%, PPV of 50%, NPV of 96%, and accuracy of 87%, while contrast-enhanced scans reached a sensitivity of 100%, specificity of 94%, PPV of 75%, NPV of 100%, and accuracy of 95%. Unenhanced and dynamic gadolinium-enhanced magnetic resonance allows accurate assessment of myometrial and cervical infiltration. Information provided by magnetic resonance imaging can define prognosis and management.

Charmonium resonances in the 3.9 GeV/c2 energy region and the X(3915)/X(3930) puzzle

NASA Astrophysics Data System (ADS)

Ortega, Pablo G.; Segovia, Jorge; Entem, David R.; Fernández, Francisco

2018-03-01

An interesting controversy has emerged challenging the widely accepted nature of the X (3915) and the X (3930) resonances, which had initially been assigned to the χc0 (2 P) and χc2 (2 P) c c bar states, respectively. To unveil their inner structure, the properties of the JPC =0++ and JPC =2++ charmonium states in the energy region of these resonances are analyzed in the framework of a constituent quark model. Together with the bare q q bar states, threshold effects due to the opening of nearby meson-meson channels are included in a coupled-channels scheme calculation. We find that the structure of both states is dominantly molecular with a probability of bare q q bar states lower than 45%. Our results favor the hypothesis that X (3915) and X (3930) resonances arise as different decay mechanisms of the same JPC =2++ state. Moreover we find an explanation for the recently discovered M = 3860MeV /c2 as a JPC =0++ 2P state and rediscover the lost Y (3940) as an additional state in the JPC =0++ family.

Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations.

PubMed

Webber, Amy L; Elena, Bénédicte; Griffin, John M; Yates, Jonathan R; Pham, Tran N; Mauri, Francesco; Pickard, Chris J; Gil, Ana M; Stein, Robin; Lesage, Anne; Emsley, Lyndon; Brown, Steven P

2010-07-14

A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.

Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance.

PubMed

Sugiki, Toshihiko; Furuita, Kyoko; Fujiwara, Toshimichi; Kojima, Chojiro

2018-06-20

Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15 N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13 C atoms experience less isotope scrambling than the main-chain 15 N atoms do. However, little is known about the side-chain 13 C atoms. Here, the 13 C scrambling profiles of the Cα and side-chain carbons were investigated for 15 N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13 Cα and 13 C side-chain labeling than in 15 N labeling. We utilized this reduced scrambling-prone character of 13 C as a simple and efficient method for amino acid selective 13 C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13 C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1 H- 15 N heteronuclear single-quantum coherence signals of the 15 N scrambling-prone amino acid were also easily filtered using 15 N-{ 13 Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.

NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 3 in apo state and in complex with inhibitor PD173074.

PubMed

Sanfelice, Domenico; Koss, Hans; Bunney, Tom D; Thompson, Gary S; Farrell, Brendan; Katan, Matilda; Breeze, Alexander L

2018-03-26

Fibroblast growth factors receptors (FGFR) are transmembrane protein tyrosine kinases involved in many cellular process, including growth, differentiation and angiogenesis. Dysregulation of FGFR enzymatic activity is associated with developmental disorders and cancers; therefore FGFRs have become attractive targets for drug discovery, with a number of agents in late-stage clinical trials. Here, we present the backbone resonance assignments of FGFR3 tyrosine kinase domain in the ligand-free form and in complex with the canonical FGFR kinase inhibitor PD173074. Analysis of chemical shift changes upon inhibitor binding highlights a characteristic pattern of allosteric network perturbations that is of relevance for future drug discovery activities aimed at development of conformationally-selective FGFR inhibitors.

ConfChem Conference on Select 2016 BCCE Presentations: Specifications Grading in the Flipped Organic Classroom

ERIC Educational Resources Information Center

Ring, Joshua

2017-01-01

Specifications Grading is a system of course-long student assessment based on the division of learning objectives into clearly defined skill tests or assignments. Each skill is evaluated at a mastery level, with opportunities for students to learn from their mistakes and then be re-evaluated for skill tests, or resubmit assignments. Specifications…

Dynamic Spectrum Management for Military Wireless Networks

DTIC Science & Technology

2010-09-01

auctions, and protocols and etiquettes . Command and control assignments are provided by the regulatory agency by reviewing specific licensing...devices and amateur licensees do not have specific frequency assignments. The Protocols and Etiquettes methods allow these devices to operate within a...with Collision Avoidance (CSMA/CA) a protocol . Etiquettes are rules that are followed without explicit interaction between devices. Simple etiquettes

Review of Livermore-Led Neutron Capture Studies Using DANCE

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

Parker, W; Sheets, S; Agvaanluvsan, U

2007-05-11

We have made neutron capture cross-section measurements using the white neutron source at the Los Alamos Science Center, the DANCE detector array (Detector for Advanced Neutron Capture Experiments) and targets important for basic science and stockpile stewardship. In this paper, we review results from (n,{gamma}) reactions on {sup 94,95}Mo, {sup 152,154,157,160,nat}Gd, {sup 151,153}Eu and {sup 242m}Am for neutron energies from < 1eV up to {approx} 20 keV. We measured details of the {gamma}-ray cascade following neutron capture, for comparison with results of statistical model simulations. We determined the neutron energy dependent (n,{gamma}) cross section and gained information about statistical decaymore » properties, including the nuclear level density and the photon strength function. Because of the high granularity of the detector array, it is possible to look at gamma cascades with a specified number of transitions (a specific multiplicity). We simulated {gamma}-ray cascades using a combination of the DICEBOX/GEANT computer codes. In the case of the deformed nuclei, we found evidence of a scissors-mode resonance. For the Eu, we also determined the (n,{gamma}) cross sections. For the {sup 94,95}Mo, we focused on the spin and parity assignments of the resonances and the determination of the photon strength functions for the compound nuclei {sup 95,96}Mo. Future plans include measurements on actinide targets; our immediate interest is in {sup 242m}Am.« less

48 CFR 1511.011-74 - Work assignments.

Code of Federal Regulations, 2010 CFR

2010-10-01

... insert the contract clause at 1552.211-74, Work Assignments, in cost-reimbursement type term form... conflict of interest certificates (e.g., Site Specific contracts, the Contract Laboratory Program (CLP...

Optically detected magnetic resonance studies on pi-conjugated polymers and novel carbon allotropes

NASA Astrophysics Data System (ADS)

Partee, Jonathan Farel

1997-12-01

The photophysics of poly(p-phenylene)-type ladder polymers (m-LPPP) and 2,5-dibutoxy poly(p-phenylene ethynylene) (DBO-PPE) films and solutions were studied by X-band photoluminescence detected magnetic resonance (PLDMR). Frequency resolved PLDMR measurements on LPPP, DBO-PPE, poly(3-hexylthiophene) (P3HT), poly(p-phenylene-vinylene) (PPV), and Csb{70} are also reported and discussed. All the polymer samples exhibit three distinct features when excited at wavelengths lambda≥ 458nm: (i) A narrow PL-enhancing spin-1/2 polaron resonance, (ii) broad full- and (iii) half-field spin-1 triplet exciton powder patterns due to the Deltamsbs = 1 and Deltamsbs = 2 transitions among the triplet sublevels, respectively. The full-width at half maximum (FWHM) of the spin-1/2 resonance in LPPP decreased from film to solution. However, the FWHM of that resonance in PPE was identical at all concentrations. This spin-1/2 resonance is assigned to the magnetic resonance enhancement of the recombination of both interchain and intrachain-intersegment polaron pairs which quench singlet exciton recombination. In solid m-LPPP samples, the aggregate PL gives rise to a proportionally higher magnetic resonance effect than other parts of the PL spectrum. In DBO-PPE and m-LPPP solutions, the triplet resonance decreased with decreasing concentration. This suggests that the triplet state is an intrinsic long-lived (˜30mus) trapped state localized on a phenylene ring and stabilized by coupling to a unit of an adjacent chain. Frequency resolved measurements of the lifetime of the species affected by the resonance conditions for all the polymers are described and discussed. The lifetimes appeared to include: (i) fast (9mus ≤ tausb1 ≤ 40mus) and (ii) slow (575mus\\ ≤ tausb2≤ 1868mus) components. The lifetimes increased with increasing concentration of the polymers in toluene solutions. These results can be interpreted to provide support for the interchain/intersegment polaron model or a distribution of lifetimes model.

Development of Novel Piezoelectric Biosensor Using PZT Ceramic Resonator for Detection of Cancer Markers.

PubMed

Su, Li; Fong, Chi-Chun; Cheung, Pik-Yuan; Yang, Mengsu

2017-01-01

A novel biosensor based on piezoelectric ceramic resonator was developed for direct detection of cancer markers in the study. For the first time, a commercially available PZT ceramic resonator with high resonance frequency was utilized as transducer for a piezoelectric biosensor. A dual ceramic resonators scheme was designed wherein two ceramic resonators were connected in parallel: one resonator was used as the sensing unit and the other as the control unit. This arrangement minimizes environmental influences including temperature fluctuation, while achieving the required frequency stability for biosensing applications. The detection of the cancer markers Prostate Specific Antigen (PSA) and α-Fetoprotein (AFP) was carried out through frequency change measurement. The device showed high sensitivity (0.25 ng/ml) and fast detection (within 30 min) with small samples (1 μl), which is compatible with the requirements of clinical measurements. The results also showed that the ceramic resonator-based piezoelectric biosensor platform could be utilized with different chemical interfaces, and had the potential to be further developed into biosensor arrays with different specificities for simultaneous detection of multiple analytes.

Photoexcitation and photoionization of the argon atom and the hydrogen bromide molecule

NASA Astrophysics Data System (ADS)

Feng, Ximao

2005-11-01

Interaction between synchrotron radiation with inner-shell electrons is a fundamental method to study the structure and dynamics of atoms and molecules. This thesis, under the guidance of Dr. Nora Berrah, concentrates on the study of the interaction between soft x-ray photons with Ar atoms and HBr molecules with time-of-flight (TOF) electron spectrometers and two-dimensional photoelectron spectroscopy (2DPES). Both of the experiments were performed on the Atomic, Molecular and Optical Physics undulator beamline at the Advanced Light Source at Lawrence Berkeley National Laboratory. The argon study focused on photoelectron recapture when the 2p electrons are ionized just above the thresholds of the two 2p-13/2,1/2 components. From our 2DPES maps, we obtained an experimental recapture curve at the 2p-11/2 threshold as a function of photon energy. The curve is derived by extracting all the reemission photoelectrons from a specific recaptured intermediate excited state and subtracting the contributions from the 2p -1nl resonances and the recapture at the 2p-13/2 threshold. The experimentally obtained curve is in good agreement with both our semi-classical calculation result and the calculation performed with quantum-mechanics by Tulkki et al. [Phys. Rev. A 41, 181 (1990)]. The HBr molecule study aimed mainly at measuring the atomic decay channel from the 3d-15/2,3/2s* resonances. At these resonances, the repulsive characteristics of the antibonding orbital cause the molecules to dissociate, resulting in both atomic Auger decay and molecular Auger decay. We separate the two resonances and find that the peak positions are at 70.89 and 71.92 eV, respectively. Some atomic lines are assigned based on their kinetic energy positions. We find that the profiles of the atomic Auger lines on the photon energy scale are not symmetric. The atomic line pair, produced from one of the two resonances and decaying to the same final Br+ state, have approximately the same angular distribution parameters, beta. The intrinsic anisotropy parameters, alpha2, of the atomic lines, derived from the beta values, are determined and are found to be similar to those of the equivalent Auger lines in krypton. The alignment parameters A 20 for the two resonances 3d-15/2,3/2s* are found to be -0.64(5) (2D5/2) and -0.60(5) (2D3/2), respectively, which are in good agreement with the theoretical value of -0.74 predicted for the 2D 5/2 resonance [Kabanchnik et al., J. Phys. B 31, 4791 (1998)].

The nature of the CO{sub 2}{sup −} radical anion in water

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

Janik, Ireneusz; Tripathi, G. N. R.

2016-04-21

The reductive conversion of CO{sub 2} into industrial products (e.g., oxalic acid, formic acid, methanol) can occur via aqueous CO{sub 2}{sup −} as a transient intermediate. While the formation, structure, and reaction pathways of this radical anion have been modelled for decades using various spectroscopic and theoretical approaches, we present here, for the first time, a vibrational spectroscopic investigation in liquid water, using pulse radiolysis time-resolved resonance Raman spectroscopy for its preparation and observation. Excitation of the radical in resonance with its 235 nm absorption displays a transient Raman band at 1298 cm{sup −1}, attributed to the symmetric CO stretch,more » which is at ∼45 cm{sup −1} higher frequency than in inert matrices. Isotopic substitution at C ({sup 13}CO{sub 2}{sup −}) shifts the frequency downwards by 22 cm{sup −1}, which confirms its origin and the assignment. A Raman band of moderate intensity compared to the stronger 1298 cm{sup −1} band also appears at 742 cm{sup −1} and is assignable to the OCO bending mode. A reasonable resonance enhancement of this mode is possible only in a bent CO{sub 2}{sup −}(C{sub 2v}/C{sub s}) geometry. These resonance Raman features suggest a strong solute-solvent interaction, the water molecules acting as constituents of the radical structure, rather than exerting a minor solvent perturbation. However, there is no evidence of the non-equivalence (C{sub s}) of the two CO bonds. A surprising resonance Raman feature is the lack of overtones of the symmetric CO stretch, which we interpret due to the detachment of the electron from the CO{sub 2}{sup −} moiety towards the solvation shell. Electron detachment occurs at the energies of 0.28 ± 0.03 eV or higher with respect to the zero point energy of the ground electronic state. The issue of acid-base equilibrium of the radical, which has been in contention for decades, as reflected in a wide variation in the reported pK{sub a} (−0.2 to 3.9), has been resolved. A value of 3.4 ± 0.2 measured in this work is consistent with the vibrational properties, bond structure, and charge distribution in aqueous CO{sub 2}{sup −}.« less

Calculation of the energy loss for an electron passing near giant fullerenes

NASA Astrophysics Data System (ADS)

Henrard, L.; Lambin, Ph

1996-11-01

We present a theoretical analysis of the electron energy-loss spectra of isolated giant fullerenes. We use a macroscopic dielectric description of spherical onion-like fullerenes and a discrete dipole approximation (DDA) framework for tubular fullerenes. In the DDA model, an anisotropic dynamical polarizability is assigned to each carbon site. We stress the fundamental importance of the hollow character of giant fullerenes in the electron energy-loss resonances.

Cross-polarization/magic-angle sample-spinning /sup 13/C NMR spectroscopic study of chlorophyll a in the solid state

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

Brown, C.E.; Spencer, R.B.; Burger, V.T.

1984-01-01

Solid-state cross-polarization/magic-angle sample-spinning /sup 13/C NMR spectra have been recorded on chlorophyll a-water aggregates, methyl pyrochlorophyllide a, and methyl pyropheophorbide a. Spectra have also been collected under a decoupling regime in which resonances of certain hydrogen-bearing carbon atoms are suppressed. These observations are used to assign the solid-state spectra. 18 references, 2 figures, 1 table.

13C nuclear magnetic resonance data of lanosterol derivatives—Profiling the steric topology of the steroid skeleton via substituent effects on its 13C NMR

NASA Astrophysics Data System (ADS)

Dias, Jerry Ray; Gao, Hongwu

2009-12-01

The 13C NMR spectra of over 24 tetracyclic triterpenoid derivatives have been structurally analyzed. The 13C NMR chemical shifts allow one to probe the steric topology of the rigid steroid skeleton and inductive effects of its substituents. Use of deuterium labeling in chemical shift assignment and B-ring aromatic terpenoids are also featured.

Solving the mystery of the internal structure of casein micelles.

PubMed

Ingham, B; Erlangga, G D; Smialowska, A; Kirby, N M; Wang, C; Matia-Merino, L; Haverkamp, R G; Carr, A J

2015-04-14

The interpretation of milk X-ray and neutron scattering data in relation to the internal structure of the casein micelle is an ongoing debate. We performed resonant X-ray scattering measurements on liquid milk and conclusively identified key scattering features, namely those corresponding to the size of and the distance between colloidal calcium phosphate particles. An X-ray scattering feature commonly assigned to the particle size is instead due to protein inhomogeneities.

Far-infrared laser magnetic resonance of vibrationally excited CD2

NASA Technical Reports Server (NTRS)

Evenson, K. M.; Sears, T. J.; Mckellar, A. R. W.

1984-01-01

The detection of 13 rotational transitions in the first excited bending state (010) of CD2 using the technique of far-infrared laser magnetic resonance spectroscopy is reported. Molecular parameters for this state are determined from these new data together with existing infrared observations of the v(2) band. Additional information on the ground vibrational state (000) is also provided by the observation of a new rotational transition, and this is combined with existing data to provide a refined set of molecular parameters for the CD2 ground state. One spectrum has been observed that is assigned as a rotational transition within the first excited symmetric stretching state (100) of CD2. These data will be of use in refining the structure and the potential function of the methylene radical.

Proton threshold states in the Na22(p,γ)Mg23 reaction and astrophysical implications

NASA Astrophysics Data System (ADS)

Comisel, H.; Hategan, C.; Graw, G.; Wolter, H. H.

2007-04-01

Proton threshold states in Mg23 are important for the astrophysically relevant proton capture reaction Na22(p,γ)Mg23. In the indirect determination of the resonance strength of the lowest states, which were not accessible by direct methods, some of the spin-parity-assignments remained experimentally uncertain. We have investigated these states with shell model, Coulomb displacement, and Thomas-Ehrman shift calculations. From the comparison of calculated and observed properties, we relate the lowest relevant resonance state at Ex=7643 keV to an excited 3/2+ state in accordance with a recent experimental determination by Jenkins From this we deduce significantly improved values for the Na22(p,γ)Mg23 reaction rate at stellar temperatures below T9=0.1 K.

Ontological Problem-Solving Framework for Assigning Sensor Systems and Algorithms to High-Level Missions

PubMed Central

Qualls, Joseph; Russomanno, David J.

2011-01-01

The lack of knowledge models to represent sensor systems, algorithms, and missions makes opportunistically discovering a synthesis of systems and algorithms that can satisfy high-level mission specifications impractical. A novel ontological problem-solving framework has been designed that leverages knowledge models describing sensors, algorithms, and high-level missions to facilitate automated inference of assigning systems to subtasks that may satisfy a given mission specification. To demonstrate the efficacy of the ontological problem-solving architecture, a family of persistence surveillance sensor systems and algorithms has been instantiated in a prototype environment to demonstrate the assignment of systems to subtasks of high-level missions. PMID:22164081

Position statement. The right to accept or reject an assignment. American Nurses Association.

PubMed

1996-01-01

The American Nurses Association (ANA) believes that nurses should reject assignment that puts patients or themselves in serious, immediate jeopardy. ANA supports the nurses obligation to reject an assignment in these situations even where there is not a specific legal protection for rejecting such an assignment. The professional obligations to the nurse to safeguard clients are grounded in the ethical norms of the profession, the Standards of Clinical Nursing Practice and state nurse practice acts.

Backbone ¹H, ¹³C, ¹⁵N NMR assignments of yeast OMP synthase in unliganded form and in complex with orotidine 5'-monophosphate.

PubMed

Hansen, Michael Riis; Harris, Richard; Barr, Eric W; Cheng, Hong; Girvin, Mark E; Grubmeyer, Charles

2014-04-01

The type I phosphoribosyltransferase OMP synthase (EC 2.4.2.10) is involved in de novo synthesis of pyrimidine nucleotides forming the UMP precursor orotidine 5'-monophosphate (OMP). The homodimeric enzyme has a Rossman α/β core topped by a base-enclosing "hood" domain and a flexible domain-swapped catalytic loop. High-resolution X-ray structures of the homologous Salmonella typhimurium and yeast enzymes show that a general compacting of the core as well as movement of the hood and a major disorder-to-order transition of the loop occur upon binding of ligands MgPRPP and orotate. Here we present backbone NMR assignments for the unliganded yeast enzyme (49 kDa) and its complex with product OMP. We were able to assign 212-213 of the 225 non-proline backbone (15)N and amide proton resonances. Significant difference in chemical shifts of the amide cross peaks occur in regions of the structure that undergo movement upon ligand occupancy in the S. typhimurium enzyme.

Assignment of selected hyperfine proton NMR resonances in the met forms of Glycera dibranchiata monomer hemoglobins and comparisons with sperm whale metmyoglobin

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

Constantinidis, I.; Satterlee, J.D.; Pandey, R.K.

1988-04-19

This work indicates a high degree of purity for our preparations of all three of the primary Glycera dibranchiata monomer hemoglobins and details assignments of the heme methyl and vinyl protons in the hyperfine shift region of the ferric (aquo.) protein forms. The assignments were carried out by reconstituting the apoproteins of each component with selectively deuteriated hemes. The results indicate that even though the individual component preparations consist of essentially a single protein, the proton NMR spectra indicate spectroscopic heterogeneity. Evidence is presented for identification and classification of major and minor protein forms that are present in solutions ofmore » each component. Finally, in contrast to previous results, a detailed analysis of the proton hyperfine shift patterns of the major and minor forms of each component, in comparison to the major and minor forms of metmyoglobin, leads to the conclusions that the corresponding forms of the proteins from each species have strikingly similar heme-globin contacts and display nearly identical heme electronic structures and coordination numbers.« less

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

Driscoll, P.C.; Clore, G.M.; Beress, L.

The sequential resonance assignment of the {sup 1}H NMR spectrum of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata is presented. This is carried out with two-dimensional NMR techniques to identify through-bond and through-space (< 5{angstrom}) connectivities. Added spectral complexity arises from the fact that the sample is an approximately 1:1 mixture of two BDS-I isoproteins, (Leu-18)-BDS-I and (Phe-18)-BDS-I. Complete assignments, however, are obtained, largely due to the increased resolution and sensitivity afforded at 600 MHz. In addition, the stereospecific assignment of a large number of {beta}-methylene protons is achieved from an analysis of the patternmore » of {sup 3}J{sub {alpha}{beta}} coupling constants and the relative magnitudes of intraresidue NOEs involving the NH, C{sup {alpha}}H, and C{sup {beta}}H protons. Regular secondary structure elements are deduced from a qualitative interpretation of the nuclear Overhauser enhancement, {sup 3}J{sub HN{alpha}} coupling constant, and amide NH exchange data. A triple-stranded antiparallel {beta}-sheet is found to be related to that found in partially homologous sea anemone polypeptide toxins.« less

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

Avetissian, H. K.; Avchyan, B. R.; Mkrtchian, G. F.

The multiphoton resonant excitation of three-level atoms by the two laser fields of different frequencies is investigated. The time evolution of the system and analytical solutions expressing Rabi oscillations of the probability amplitudes at the two-color multiphoton resonant excitation are found using a nonperturbative resonant approach. The specific examples for experimental implementation of two-color multiphoton resonant excitation of hydrogen atoms are considered.

The Impact of Computer-Based Assignments on Student Motivation to Complete Homework Assignments for Sixth-Grade Students

ERIC Educational Resources Information Center

Cyr, Mary Ann

2013-01-01

The purpose of this qualitative study was to examine the engagement of 11 middle school-aged students from a southeast Michigan public school, who were given laptop computers with twenty-four-hour-a-day Internet access in order to complete homework assignments. Specifically, this study examined the perceptions of sixth-grade students regarding the…

Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0)).

PubMed

Hu, Kaifeng; Westler, William M; Markley, John L

2011-02-16

Quantitative one-dimensional (1D) (1)H NMR spectroscopy is a useful tool for determining metabolite concentrations because of the direct proportionality of signal intensity to the quantity of analyte. However, severe signal overlap in 1D (1)H NMR spectra of complex metabolite mixtures hinders accurate quantification. Extension of 1D (1)H to 2D (1)H-(13)C HSQC leads to the dispersion of peaks along the (13)C dimension and greatly alleviates peak overlapping. Although peaks are better resolved in 2D (1)H-(13)C HSQC than in 1D (1)H NMR spectra, the simple proportionality of cross peaks to the quantity of individual metabolites is lost by resonance-specific signal attenuation during the coherence transfer periods. As a result, peaks for individual metabolites usually are quantified by reference to calibration data collected from samples of known concentration. We show here that data from a series of HSQC spectra acquired with incremented repetition times (the time between the end of the first (1)H excitation pulse to the beginning of data acquisition) can be extrapolated back to zero time to yield a time-zero 2D (1)H-(13)C HSQC spectrum (HSQC(0)) in which signal intensities are proportional to concentrations of individual metabolites. Relative concentrations determined from cross peak intensities can be converted to absolute concentrations by reference to an internal standard of known concentration. Clustering of the HSQC(0) cross peaks by their normalized intensities identifies those corresponding to metabolites present at a given concentration, and this information can assist in assigning these peaks to specific compounds. The concentration measurement for an individual metabolite can be improved by averaging the intensities of multiple, nonoverlapping cross peaks assigned to that metabolite.

The Diagnostic Performance of Multiparametric Magnetic Resonance Imaging to Detect Significant Prostate Cancer.

PubMed

Thompson, J E; van Leeuwen, P J; Moses, D; Shnier, R; Brenner, P; Delprado, W; Pulbrook, M; Böhm, M; Haynes, A M; Hayen, A; Stricker, P D

2016-05-01

We assess the accuracy of multiparametric magnetic resonance imaging for significant prostate cancer detection before diagnostic biopsy in men with an abnormal prostate specific antigen/digital rectal examination. A total of 388 men underwent multiparametric magnetic resonance imaging, including T2-weighted, diffusion weighted and dynamic contrast enhanced imaging before biopsy. Two radiologists used PI-RADS to allocate a score of 1 to 5 for suspicion of significant prostate cancer (Gleason 7 with more than 5% grade 4). PI-RADS 3 to 5 was considered positive. Transperineal template guided mapping biopsy of 18 regions (median 30 cores) was performed with additional manually directed cores from magnetic resonance imaging positive regions. The anatomical location, size and grade of individual cancer areas in the biopsy regions (18) as the primary outcome and in prostatectomy specimens (117) as the secondary outcome were correlated to the magnetic resonance imaging positive regions. Of the 388 men who were enrolled in the study 344 were analyzed. Multiparametric magnetic resonance imaging was positive in 77.0% of patients, 62.5% had prostate cancer and 41.6% had significant prostate cancer. The detection of significant prostate cancer by multiparametric magnetic resonance imaging had a sensitivity of 96%, specificity of 36%, negative predictive value of 92% and positive predictive value of 52%. Adding PI-RADS to the multivariate model, including prostate specific antigen, digital rectal examination, prostate volume and age, improved the AUC from 0.776 to 0.879 (p <0.001). Anatomical concordance analysis showed a low mismatch between the magnetic resonance imaging positive regions and biopsy positive regions (4 [2.9%]), and the significant prostate cancer area in the radical prostatectomy specimen (3 [3.3%]). In men with an abnormal prostate specific antigen/digital rectal examination, multiparametric magnetic resonance imaging detected significant prostate cancer with an excellent negative predictive value and moderate positive predictive value. The use of multiparametric magnetic resonance imaging to diagnose significant prostate cancer may result in a substantial number of unnecessary biopsies while missing a minimum of significant prostate cancers. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Cascaded thermoacoustic devices

DOEpatents

Swift, Gregory W.; Backhaus, Scott N.; Gardner, David L.

2003-12-09

A thermoacoustic device is formed with a resonator system defining at least one region of high specific acoustic impedance in an acoustic wave within the resonator system. A plurality of thermoacoustic units are cascaded together within the region of high specific acoustic impedance, where at least one of the thermoacoustic units is a regenerator unit.

Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.

PubMed

Massiah, M A; Starich, M R; Paschall, C; Summers, M F; Christensen, A M; Sundquist, W I

1994-11-25

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance (1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H alpha protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively. A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 A2 or less and individual distance violations under 0.06 A was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (+/- 0.08) A. The folded HIV-1 matrix protein structure is composed of five alpha-helices, a short 3(10) helical stretch, and a three-strand mixed beta-sheet. Helices I to III and the 3(10) helix pack about a central helix (IV) to form a compact globular domain that is capped by the beta-sheet. The C-terminal helix (helix V) projects away from the beta-sheet to expose carboxyl-terminal residues essential for early steps in the HIV-1 infectious cycle. Basic residues implicated in membrane binding and nuclear localization functions cluster about an extruded cationic loop that connects beta-strands 1 and 2. The structure suggests that both membrane binding and nuclear localization may be mediated by complex tertiary structures rather than simple linear determinants.

Real-Time Detection of Staphylococcus Aureus Using Whispering Gallery Mode Optical Microdisks

PubMed Central

Ghali, Hala; Chibli, Hicham; Nadeau, Jay L.; Bianucci, Pablo; Peter, Yves-Alain

2016-01-01

Whispering Gallery Mode (WGM) microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q) factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 104 is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme. PMID:27153099

41 CFR 302-9.170 - Under what specific conditions may my agency authorize transportation of a POV to my post of duty...

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions may my agency authorize transportation of a POV to my post of duty subsequent to the time of my assignment to that post? 302-9.170 Section 302-9.170 Public Contracts and Property Management Federal Travel... Subsequent to the Time of Assignment § 302-9.170 Under what specific conditions may my agency authorize...

41 CFR 302-9.170 - Under what specific conditions may my agency authorize transportation of a POV to my post of duty...

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions may my agency authorize transportation of a POV to my post of duty subsequent to the time of my assignment to that post? 302-9.170 Section 302-9.170 Public Contracts and Property Management Federal Travel... Subsequent to the Time of Assignment § 302-9.170 Under what specific conditions may my agency authorize...

41 CFR 302-9.170 - Under what specific conditions may my agency authorize transportation of a POV to my post of duty...

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions may my agency authorize transportation of a POV to my post of duty subsequent to the time of my assignment to that post? 302-9.170 Section 302-9.170 Public Contracts and Property Management Federal Travel... the Time of Assignment § 302-9.170 Under what specific conditions may my agency authorize...

41 CFR 302-9.170 - Under what specific conditions may my agency authorize transportation of a POV to my post of duty...

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions may my agency authorize transportation of a POV to my post of duty subsequent to the time of my assignment to that post? 302-9.170 Section 302-9.170 Public Contracts and Property Management Federal Travel... the Time of Assignment § 302-9.170 Under what specific conditions may my agency authorize...

41 CFR 302-9.170 - Under what specific conditions may my agency authorize transportation of a POV to my post of duty...

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions may my agency authorize transportation of a POV to my post of duty subsequent to the time of my assignment to that post? 302-9.170 Section 302-9.170 Public Contracts and Property Management Federal Travel... Subsequent to the Time of Assignment § 302-9.170 Under what specific conditions may my agency authorize...

Time-resolved infrared and resonance Raman studies of benzil. Vibrational analysis and structures of the excited states

NASA Astrophysics Data System (ADS)

Mizuno, Misao; Iwata, Koichi; Takahashi, Hiroaki

2003-12-01

Structures of the S 1 and T 1 states of benzil are examined based on the experimental results from nanosecond time-resolved infrared spectroscopy and picosecond time-resolved Raman spectroscopy. Nanosecond time-resolved infrared spectra of the T 1 state of benzil as well as its three isotopically substituted analogues were measured in carbon tetrachloride. The observed infrared bands of T 1 benzil were assigned based on the frequency shifts on isotopic ( 18O, and deuteration) substitutions. The infrared band at 1312 cm -1 is assigned to the CO anti-symmetric stretch vibration. An infrared band that has large contribution from the central C-C stretch is not observed. Picosecond time-resolved resonance Raman spectra of the S 1 state of benzil were also measured. It has been reported that after the photoexcitation, the benzil molecule shows an ultrafast conformational change in the S 1 state. The observed resonance Raman bands are attributable to the vibrations of the relaxed form of the S 1 state. By comparing the Raman and infrared spectra of the S 0, S 1, and T 1 states of benzil, the structures of benzil in the excited states are discussed. Upon going from the S 0 state to the S 1 or T 1 state, the bond order of the CO bond decreases while that of the central C-C bond increases. Although several ground-state bands appear in both the infrared and Raman spectra, there is no band observed simultaneously in the infrared and Raman spectra of the T 1 state, except for bands attributable to the phenyl ring vibrations. We conclude that T 1 benzil has the inversion center that arises from the trans-planar structure. The spectral pattern of the resonance Raman scattering of the relaxed S 1 state is very similar to that of the T 1 state. This implies that the molecular structure of the relaxed S 1 state is similar to that of the T 1 state. The structure of the relaxed form of the S 1 state is also considered to be trans-planar.

Combined Diffusion Tensor and Magnetic Resonance Spectroscopic Imaging Methodology for Automated Regional Brain Analysis: Application in a Normal Pediatric Population.

PubMed

Ghosh, Nirmalya; Holshouser, Barbara; Oyoyo, Udo; Barnes, Stanley; Tong, Karen; Ashwal, Stephen

2017-01-01

During human brain development, anatomic regions mature at different rates. Quantitative anatomy-specific analysis of longitudinal diffusion tensor imaging (DTI) and magnetic resonance spectroscopic imaging (MRSI) data may improve our ability to quantify and categorize these maturational changes. Computational tools designed to quickly fuse and analyze imaging information from multiple, technically different datasets would facilitate research on changes during normal brain maturation and for comparison to disease states. In the current study, we developed a complete battery of computational tools to execute such data analyses that include data preprocessing, tract-based statistical analysis from DTI data, automated brain anatomy parsing from T1-weighted MR images, assignment of metabolite information from MRSI data, and co-alignment of these multimodality data streams for reporting of region-specific indices. We present statistical analyses of regional DTI and MRSI data in a cohort of normal pediatric subjects (n = 72; age range: 5-18 years; mean 12.7 ± 3.3 years) to establish normative data and evaluate maturational trends. Several regions showed significant maturational changes for several DTI parameters and MRSI ratios, but the percent change over the age range tended to be small. In the subcortical region (combined basal ganglia [BG], thalami [TH], and corpus callosum [CC]), the largest combined percent change was a 10% increase in fractional anisotropy (FA) primarily due to increases in the BG (12.7%) and TH (9%). The largest significant percent increase in N-acetylaspartate (NAA)/creatine (Cr) ratio was seen in the brain stem (BS) (18.8%) followed by the subcortical regions in the BG (11.9%), CC (8.9%), and TH (6.0%). We found consistent, significant (p < 0.01), but weakly positive correlations (r = 0.228-0.329) between NAA/Cr ratios and mean FA in the BS, BG, and CC regions. Age- and region-specific normative MR diffusion and spectroscopic metabolite ranges show brain maturation changes and are requisite for detecting abnormalities in an injured or diseased population. © 2017 S. Karger AG, Basel.

Nanogram per milliliter-level immunologic detection of alpha-fetoprotein with integrated rotating-resonance microcantilevers for early-stage diagnosis of heptocellular carcinoma.

PubMed

Liu, Yongjing; Li, Xinxin; Zhang, Zhixiang; Zuo, Guomin; Cheng, Zhenxing; Yu, Haitao

2009-02-01

Nanogram per milliliter-level ultra-low concentration detection of alpha-fetoprotein (AFP), which is an important marker for heptocellular carcinoma, is in favor of early-stage prognosis and disease diagnosis. On-the-spot rapid detection of such antigens as AFP highly requires innovative micro/nano techniques. To meet this requirement, an advanced resonant microcantilever is developed and used for screening the tumor marker at nanogram per milliliter level. The sensing principle of the resonant microcantilever is measuring frequency-shift versus specific-adsorbed mass. With both electromagnetic resonance-exciting and piezoresistive readout elements on-chip integrated, the microcantilever sensor is operated in a rotating resonance mode to improve sensitivity and resolution to specific mass adsorption. Prior to detection of AFP with previously immobilized anti-AFP antibody, the antigen-antibody specific-binding is confirmed with an enzyme linked immunosorbent assay experiment. By implementing the specific reaction in liquid and reading out the sensor signal in lab air environment, the micromechanical sensor has achieved the sensitive scale between 2 and 20 ng/ml. To effectively depress cross-talk signal and improve resolution, the insensitive regions of the cantilever surface are pre-modified with 2-[methoxy (polyethyleneoxy) propyl] trimethoxysilane for nonspecific bio-adsorption minimization. Finally, a better AFP detecting limit than 2 ng/mL is experimentally achieved. The label-free resonant microcantilever sensor is promising in low-cost or even disposable early-stage prognosis and diagnosis of tumors.

The Nature of the Dielectric Response of Methanol Revealed by the Terahertz Kerr Effect.

PubMed

Kampfrath, Tobias; Campen, R Kramer; Wolf, Martin; Sajadi, Mohsen

2018-03-15

The dielectric response of liquids in the terahertz (THz) and sub-THz frequency range arises from low-energy collective molecular motions, which are often strongly influenced by intermolecular interactions. To shed light on the microscopic origin of the THz dielectric response of the simplest alcohol, methanol, we resonantly excite this liquid with an intense THz electric-field pulse and monitor the relaxation of the induced optical birefringence. We find a unipolar THz-Kerr-effect signal which, in contrast to aprotic polar liquids, shows a weak coupling between the THz electric field and the permanent molecular dipole moment of the liquid. We assign this weak coupling to the restricted translational rather than rotational nature of the excited mode. Our approach opens a new avenue to the assignment of the dielectric spectrum of liquids to a microscopic origin.

The (HMI9293) acquisition of a 200 MHz nuclear magnetic resonance spectrometer

NASA Astrophysics Data System (ADS)

Hageman, James H.

1994-09-01

With the funds awarded from DOD-AFOSR and matching funds from New Mexico State a new Varian Gemini 200 MHz nmr was purchased and installed in the spring of 1994. This instrument is capable of 1H and 130 nmr, is very sensitive, and can also do Hetcor experiments to facilitate proton assignments. It is very easy to use and has proven thus far to be extremely reliable. The change in the research output in the department has been significant. Whereas previously students had to sometimes wait days to run routine nmr spectra because our high field instrument was otherwise occupied with longer experiments, now they can run spectra immediately (or with minimal wait). This speeds up structure assignments, and gives students instant gratification when experiments succeed and rapid feedback when they are not successful.

NMR analysis of the iron ligand ethylenediaminedi(o-hydroxyphenyl)acetic acid (EDDHA) employed in fertilizers.

PubMed

Cremonini, M A; Alvarez-Fernández, A; Lucena, J J; Rombolà, A; Marangoni, B; Placucci, G

2001-08-01

The exceptional efficiency of the iron chelate of ethylenediaminedi(o-hydroxyphenyl)acetic acid (o,o-EDDHA) in correcting iron chlorosis in plants and the medical applications of various metallic chelates of this compound have long been recognized. As commercial preparations of o,o-EDDHA usually contain impurities, a method for their detection is proposed. By using one- and two-dimensional nuclear magnetic resonance two impurities were identified. The structure of one of these compounds was assigned to an isomer of EDDHA containing at least one p-hydroxyphenyl moiety. The structure of the other impurity was tentatively assigned to a byproduct of the EDDHA synthesis: 2,6-di[CH(COOH)NHCH(2)CH(2)NHCH(COOH)Ar]phenol (Ar = hydroxyphenyl). Both compounds were also detected in the EDDHA extracted from a commercial iron fertilizer.

A Raman and UV-Vis study of catecholamines oxidized with Mn(III)

NASA Astrophysics Data System (ADS)

Barreto, W. J.; Ponzoni, S.; Sassi, P.

1998-12-01

A UV-Vis and Raman spectroscopy study of three aminochromes generated through Mn 3+ oxidation of the dopamine, L-dopa and adrenaline molecules at physiological pH was performed. The UV-Vis spectra of the catecholamines oxidized using Mn 3+ in buffer solution at pH 7.2 show a band at ca. 300 nm, formed by two transitions at 280 nm and 300 nm assigned to an La and Lb transition respectively, and other at ca. 470 nm assigned to an n- π* transition localized in the carbonyl group. This assignment is suggested by the UV-Vis and Raman spectra of ortho-aminoquinone generated by MnO 2 oxidation of a dopamine aqueous acidic solution. The resonance Raman spectra of the three chromes at buffer pH 7.2 show a very similar feature and the most intense bands are observed in the spectral range 1100-1800 cm -1. The band around 1680 cm -1 for the three compounds is assigned to a ν(CO) stretching vibration, 1630 cm -1 to the ν(CC) ring mode, two bands at 1423, 1439 cm -1; 1427, 1438 cm -1 and 1456, 1475 cm -1 are assigned to a ν(CN +) vibration, for aminochrome, dopachrome and adrenochrome, respectively. The excitation profiles for the most intense bands for aminochrome and adrenochrome were obtained. The band assigned to the ν(CN +) present a red shift with respect to the visible band peak, however the band in adrenochrome at 1475 cm -1 shows a profile similar to ν(CO) and ν(CC) modes that reflects the methyl group effect on mixing this mode more effectively with the ν(CC) ring mode.

Out-of-unison resonance in weakly nonlinear coupled oscillators

PubMed Central

Hill, T. L.; Cammarano, A.; Neild, S. A.; Wagg, D. J.

2015-01-01

Resonance is an important phenomenon in vibrating systems and, in systems of nonlinear coupled oscillators, resonant interactions can occur between constituent parts of the system. In this paper, out-of-unison resonance is defined as a solution in which components of the response are 90° out-of-phase, in contrast to the in-unison responses that are normally considered. A well-known physical example of this is whirling, which can occur in a taut cable. Here, we use a normal form technique to obtain time-independent functions known as backbone curves. Considering a model of a cable, this approach is used to identify out-of-unison resonance and it is demonstrated that this corresponds to whirling. We then show how out-of-unison resonance can occur in other two degree-of-freedom nonlinear oscillators. Specifically, an in-line oscillator consisting of two masses connected by nonlinear springs—a type of system where out-of-unison resonance has not previously been identified—is shown to have specific parameter regions where out-of-unison resonance can occur. Finally, we demonstrate how the backbone curve analysis can be used to predict the responses of forced systems. PMID:25568619

Fano resonances in bilayer graphene superlattices.

PubMed

Briones-Torres, J A; Rodríguez-Vargas, I

2017-12-01

In this work, we address the ubiquitous phenomenon of Fano resonances in bilayer graphene. We consider that this phenomenon is as exotic as other phenomena in graphene because it can arise without an external extended states source or elaborate nano designs. However, there are not theoretical and/or experimental studies that report the impact of Fano resonances on the transport properties. Here, we carry out a systematic assessment of the contribution of the Fano resonances on the transport properties of bilayer graphene superlattices. Specifically, we find that by changing the number of periods, adjusting the barriers height as well as modifying the barriers and wells width it is possible to identify the contribution of Fano resonances on the conductance. Particularly, the coupling of Fano resonances with the intrinsic minibands of the superlattice gives rise to specific and identifiable changes in the conductance. Moreover, by reducing the angular range for the computation of the transport properties it is possible to obtain conductance curves with line-shapes quite similar to the Fano profile and the coupling profile between Fano resonance and miniband states. In fact, these conductance features could serve as unequivocal characteristic of the existence of Fano resonances in bilayer graphene.

Alkane Soluble Transition Metal Complexes.

DTIC Science & Technology

1983-10-01

period April 7th 1963 to October 6th 1903 as well an the final report covering the complete period April 15th 1979 to October 6th 1993. The research ...reported In this document has beensmade possible through the support and sponsorship of the US Government through Its Ruropean Research Office. This report...the single triple at 1 0.6 (dowfhleld froma Sill., assigned to the phosphorus resonance Provided further evidence of purity. met),le end a~hy grups

A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution.

PubMed Central

Feigon, J; Wang, A H; van der Marel, G A; Van Boom, J H; Rich, A

1984-01-01

The deoxyribose hexanucleoside pentaphosphate (m5dC-dG)3 has been studied by 500 MHz 1H NMR in D2O (0.1 M NaCl) and in D2O/deuterated methanol mixtures. Two conformations, in slow equilibrium on the NMR time scale, were detected in methanolic solution. Two-dimensional nuclear Overhauser effect (NOE) experiments were used to assign the base and many of the sugar resonances as well as to determine structural features for both conformations. The results were consistent with the an equilibrium in solution between B-DNA and Z-DNA. The majority of the molecules have a B-DNA structure in low-salt D2O and a Z-DNA structure at high methanol concentrations. A cross-strand NOE between methyl groups on adjacent cytosines is observed for Z-DNA but not B-DNA. The B-DNA conformation predominates at low methanol concentrations and is stabilized by increasing temperature, while the Z-DNA conformation predominates at high methanol concentrations and low temperatures. 31P NMR spectra gave results consistent with those obtained by 1H NMR. Comparison of the 31P spectra with those obtained on poly(dG-m5dC) allow assignment of the lower field resonances to GpC in the Z conformation. PMID:6694910

Characterization of metabolic profile of intact non-tumor and tumor breast cells by high-resolution magic angle spinning nuclear magnetic resonance spectroscopy.

PubMed

Maria, Roberta M; Altei, Wanessa F; Andricopulo, Adriano D; Becceneri, Amanda B; Cominetti, Márcia R; Venâncio, Tiago; Colnago, Luiz A

2015-11-01

(1)H high-resolution magic angle spinning nuclear magnetic resonance ((1)H HR-MAS NMR) spectroscopy was used to analyze the metabolic profile of an intact non-tumor breast cell line (MCF-10A) and intact breast tumor cell lines (MCF-7 and MDA-MB-231). In the spectra of MCF-10A cells, six metabolites were assigned, with glucose and ethanol in higher concentrations. Fifteen metabolites were assigned in MCF-7 and MDA-MB-231 (1)H HR-MAS NMR spectra. They did not show glucose and ethanol, and the major component in both tumor cells was phosphocholine (higher in MDA-MB-231 than in MCF-7), which can be considered as a tumor biomarker of breast cancer malignant transformation. These tumor cells also show acetone signal that was higher in MDA-MB-231 cells than in MCF-7 cells. The high acetone level may be an indication of high demand for energy in MDA-MB-231 to maintain cell proliferation. The higher acetone and phosphocholine levels in MDA-MB-231 cells indicate the higher malignance of the cell line. Therefore, HR-MAS is a rapid reproducible method to study the metabolic profile of intact breast cells, with minimal sample preparation and contamination, which are critical in the analyses of slow-growth cells. Copyright © 2015 Elsevier Inc. All rights reserved.

High-resolution solid-state 13C NMR spectroscopy of the paramagnetic metal-organic frameworks, STAM-1 and HKUST-1.

PubMed

Dawson, Daniel M; Jamieson, Lauren E; Mohideen, M Infas H; McKinlay, Alistair C; Smellie, Iain A; Cadou, Romain; Keddie, Neil S; Morris, Russell E; Ashbrook, Sharon E

2013-01-21

Solid-state (13)C magic-angle spinning (MAS) NMR spectroscopy is used to investigate the structure of the Cu(II)-based metal-organic frameworks (MOFs), HKUST-1 and STAM-1, and the structural changes occurring within these MOFs upon activation (dehydration). NMR spectroscopy is an attractive technique for the investigation of these materials, owing to its high sensitivity to local structure, without any requirement for longer-range order. However, interactions between nuclei and unpaired electrons in paramagnetic systems (e.g., Cu(II)-based MOFs) pose a considerable challenge, not only for spectral acquisition, but also in the assignment and interpretation of the spectral resonances. Here, we exploit the rapid T(1) relaxation of these materials to obtain (13)C NMR spectra using a spin-echo pulse sequence at natural abundance levels, and employ frequency-stepped acquisition to ensure uniform excitation of resonances over a wide frequency range. We then utilise selective (13)C isotopic labelling of the organic linker molecules to enable an unambiguous assignment of NMR spectra of both MOFs for the first time. We show that the monomethylated linker can be recovered from STAM-1 intact, demonstrating not only the interesting use of this MOF as a protecting group, but also the ability (for both STAM-1 and HKUST-1) to recover isotopically-enriched linkers, thereby reducing significantly the overall cost of the approach.

Development of a see-through hollow cathode discharge lamp for (Li/Ne) optogalvanic studies

NASA Astrophysics Data System (ADS)

Saini, V. K.; Kumar, P.; Sarangpani, K. K.; Dixit, S. K.; Nakhe, S. V.

2017-09-01

Development of a demountable and see-through hollow cathode (HC) discharge lamp suitable for optogalvanic (OG) spectroscopy is described. The design of the HC lamp is simple, compact, and inexpensive. Lithium, investigated rarely by the OG method, is selected for cathode material as its isotopes are important for nuclear industry. The HC lamp is characterized electrically and optically for discharge oscillations free OG effect. Strong OG signals of lithium as well as neon (as buffer gas) are produced precisely upon copper vapor laser pumped tunable dye laser irradiation. The HC lamp is capable of generating a clean OG resonance spectrum in the available dye laser wavelength scanning range (627.5-676 nm) obtained with 4-(Dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran dye. About 28 resonant OG lines are explicitly observed. Majority of them have been identified using j-l coupling scheme and assigned to the well-known neon transitions. One line that corresponds to wavelength near about 670.80 nm is assigned to lithium and resolved for its fine (2S1/2 → 2P1/2, 3/2) transitions. These OG transitions allow 0.33 cm-1 accuracy and can be used to supplement the OG transition data available from other sources to calibrate the wavelength of a scanning dye laser with precision at atomic levels.

Development of a see-through hollow cathode discharge lamp for (Li/Ne) optogalvanic studies.

PubMed

Saini, V K; Kumar, P; Sarangpani, K K; Dixit, S K; Nakhe, S V

2017-09-01

Development of a demountable and see-through hollow cathode (HC) discharge lamp suitable for optogalvanic (OG) spectroscopy is described. The design of the HC lamp is simple, compact, and inexpensive. Lithium, investigated rarely by the OG method, is selected for cathode material as its isotopes are important for nuclear industry. The HC lamp is characterized electrically and optically for discharge oscillations free OG effect. Strong OG signals of lithium as well as neon (as buffer gas) are produced precisely upon copper vapor laser pumped tunable dye laser irradiation. The HC lamp is capable of generating a clean OG resonance spectrum in the available dye laser wavelength scanning range (627.5-676 nm) obtained with 4-(Dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran dye. About 28 resonant OG lines are explicitly observed. Majority of them have been identified using j-l coupling scheme and assigned to the well-known neon transitions. One line that corresponds to wavelength near about 670.80 nm is assigned to lithium and resolved for its fine ( 2 S 1/2 → 2 P 1/2, 3/2 ) transitions. These OG transitions allow 0.33 cm -1 accuracy and can be used to supplement the OG transition data available from other sources to calibrate the wavelength of a scanning dye laser with precision at atomic levels.

Testing resonating vector strength: Auditory system, electric fish, and noise

NASA Astrophysics Data System (ADS)

Leo van Hemmen, J.; Longtin, André; Vollmayr, Andreas N.

2011-12-01

Quite often a response to some input with a specific frequency ν○ can be described through a sequence of discrete events. Here, we study the synchrony vector, whose length stands for the vector strength, and in doing so focus on neuronal response in terms of spike times. The latter are supposed to be given by experiment. Instead of singling out the stimulus frequency ν○ we study the synchrony vector as a function of the real frequency variable ν. Its length turns out to be a resonating vector strength in that it shows clear maxima in the neighborhood of ν○ and multiples thereof, hence, allowing an easy way of determining response frequencies. We study this "resonating" vector strength for two concrete but rather different cases, viz., a specific midbrain neuron in the auditory system of cat and a primary detector neuron belonging to the electric sense of the wave-type electric fish Apteronotus leptorhynchus. We show that the resonating vector strength always performs a clear resonance correlated with the phase locking that it quantifies. We analyze the influence of noise and demonstrate how well the resonance associated with maximal vector strength indicates the dominant stimulus frequency. Furthermore, we exhibit how one can obtain a specific phase associated with, for instance, a delay in auditory analysis.

Hydrogen Bond Network between Amino Acid Radical Intermediates on the Proton-Coupled Electron Transfer Pathway of E. coli α2 Ribonucleotide Reductase

PubMed Central

2015-01-01

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all organisms. In all Class Ia RNRs, initiation of nucleotide diphosphate (NDP) reduction requires a reversible oxidation over 35 Å by a tyrosyl radical (Y122•, Escherichia coli) in subunit β of a cysteine (C439) in the active site of subunit α. This radical transfer (RT) occurs by a specific pathway involving redox active tyrosines (Y122 ⇆ Y356 in β to Y731 ⇆ Y730 ⇆ C439 in α); each oxidation necessitates loss of a proton coupled to loss of an electron (PCET). To study these steps, 3-aminotyrosine was site-specifically incorporated in place of Y356-β, Y731- and Y730-α, and each protein was incubated with the appropriate second subunit β(α), CDP and effector ATP to trap an amino tyrosyl radical (NH2Y•) in the active α2β2 complex. High-frequency (263 GHz) pulse electron paramagnetic resonance (EPR) of the NH2Y•s reported the gx values with unprecedented resolution and revealed strong electrostatic effects caused by the protein environment. 2H electron–nuclear double resonance (ENDOR) spectroscopy accompanied by quantum chemical calculations provided spectroscopic evidence for hydrogen bond interactions at the radical sites, i.e., two exchangeable H bonds to NH2Y730•, one to NH2Y731• and none to NH2Y356•. Similar experiments with double mutants α-NH2Y730/C439A and α-NH2Y731/Y730F allowed assignment of the H bonding partner(s) to a pathway residue(s) providing direct evidence for colinear PCET within α. The implications of these observations for the PCET process within α and at the interface are discussed. PMID:25516424

Comparisons of node-based and element-based approaches of assigning bone material properties onto subject-specific finite element models.

PubMed

Chen, G; Wu, F Y; Liu, Z C; Yang, K; Cui, F

2015-08-01

Subject-specific finite element (FE) models can be generated from computed tomography (CT) datasets of a bone. A key step is assigning material properties automatically onto finite element models, which remains a great challenge. This paper proposes a node-based assignment approach and also compares it with the element-based approach in the literature. Both approaches were implemented using ABAQUS. The assignment procedure is divided into two steps: generating the data file of the image intensity of a bone in a MATLAB program and reading the data file into ABAQUS via user subroutines. The node-based approach assigns the material properties to each node of the finite element mesh, while the element-based approach assigns the material properties directly to each integration point of an element. Both approaches are independent from the type of elements. A number of FE meshes are tested and both give accurate solutions; comparatively the node-based approach involves less programming effort. The node-based approach is also independent from the type of analyses; it has been tested on the nonlinear analysis of a Sawbone femur. The node-based approach substantially improves the level of automation of the assignment procedure of bone material properties. It is the simplest and most powerful approach that is applicable to many types of analyses and elements. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Determination of Multiple φ-Torsion Angles in Proteins by Selective and Extensive 13C Labeling and Two-Dimensional Solid-State NMR

NASA Astrophysics Data System (ADS)

Hong, Mei

1999-08-01

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive 13C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective 13C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-13C]glucose preferentially labels the ends of the side chains, while [2-13C]glycerol labels the Cα of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles φ simultaneously, using an isotropic-anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively 13C labeled protein were performed using 15N-13C 2D correlation spectroscopy. From the time dependence of the 15N-13C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective 13C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.

Conformation-Specific IR and UV Spectroscopy of the Amino Acid Glutamine: Amide-Stacking and Hydrogen Bonding in AN Important Residue in Neurodegenerative Diseases

NASA Astrophysics Data System (ADS)

Walsh, Patrick S.; Dean, Jacob C.; Zwier, Timothy S.

2014-06-01

Glutamine plays an important role in several neurodegenerative diseases including Huntington's disease (HD) and Alzheimer's disease (AD). An intriguing aspect of the structure of glutamine is its incorporation of an amide group in its side chain, thereby opening up the possibility of forming amide-amide H-bonds between the peptide backbone and side chain. In this study the conformational preferences of two capped gluatamines Z(carboxybenzyl)-Glutamine-X (X=OH, NHMe) are studied under jet-cooled conditions in the gas phase in order to unlock the intrinsic structural motifs that are favored by this flexible sidechain. Conformational assignments are made by comparing the hydride stretch ( 3100-3700 cm-1) and amide I and II ( 1400-1800 cm-1) resonant ion-dip infrared spectra with predictions from harmonic frequency calculations. Assigned structures will be compared to previously published results on both natural and unnatural residues. Particular emphasis will be placed on the comparison between glutamine and unconstrained γ-peptides due to the similar three-carbon spacing between backbone and side chain in glutamine to the backbone spacing in γ-peptides. The ability of the glutamine side-chain to form amide stacked conformations will be a main focus, along with the prevalence of extended backbone type structures. W. H. James, III, C W. Müller, E. G. Buchanan, M. G. D. Nix, L. Guo, L. Roskop, M. S. Gordon, L. V. Slipchenko, S. H. Gellman, and T. S. Zwier, J. Am. Chem. Soc., 2009, 131(40), 14243-14245.

Identification of threshold prostate specific antigen levels to optimize the detection of clinically significant prostate cancer by magnetic resonance imaging/ultrasound fusion guided biopsy.

PubMed

Shakir, Nabeel A; George, Arvin K; Siddiqui, M Minhaj; Rothwax, Jason T; Rais-Bahrami, Soroush; Stamatakis, Lambros; Su, Daniel; Okoro, Chinonyerem; Raskolnikov, Dima; Walton-Diaz, Annerleim; Simon, Richard; Turkbey, Baris; Choyke, Peter L; Merino, Maria J; Wood, Bradford J; Pinto, Peter A

2014-12-01

Prostate specific antigen sensitivity increases with lower threshold values but with a corresponding decrease in specificity. Magnetic resonance imaging/ultrasound targeted biopsy detects prostate cancer more efficiently and of higher grade than standard 12-core transrectal ultrasound biopsy but the optimal population for its use is not well defined. We evaluated the performance of magnetic resonance imaging/ultrasound targeted biopsy vs 12-core biopsy across a prostate specific antigen continuum. We reviewed the records of all patients enrolled in a prospective trial who underwent 12-core transrectal ultrasound and magnetic resonance imaging/ultrasound targeted biopsies from August 2007 through February 2014. Patients were stratified by each of 4 prostate specific antigen cutoffs. The greatest Gleason score using either biopsy method was compared in and across groups as well as across the population prostate specific antigen range. Clinically significant prostate cancer was defined as Gleason 7 (4 + 3) or greater. Univariate and multivariate analyses were performed. A total of 1,003 targeted and 12-core transrectal ultrasound biopsies were performed, of which 564 diagnosed prostate cancer for a 56.2% detection rate. Targeted biopsy led to significantly more upgrading to clinically significant disease compared to 12-core biopsy. This trend increased more with increasing prostate specific antigen, specifically in patients with prostate specific antigen 4 to 10 and greater than 10 ng/ml. Prostate specific antigen 5.2 ng/ml or greater captured 90% of upgrading by targeted biopsy, corresponding to 64% of patients who underwent multiparametric magnetic resonance imaging and subsequent fusion biopsy. Conversely a greater proportion of clinically insignificant disease was detected by 12-core vs targeted biopsy overall. These differences persisted when controlling for potential confounders on multivariate analysis. Prostate cancer upgrading with targeted biopsy increases with an increasing prostate specific antigen cutoff. Above a prostate specific antigen threshold of 5.2 ng/ml most upgrading to clinically significant disease was achieved by targeted biopsy. In our population this corresponded to potentially sparing biopsy in 36% of patients who underwent multiparametric magnetic resonance imaging. Below this value 12-core biopsy detected more clinically insignificant cancer. Thus, the diagnostic usefulness of targeted biopsy is optimized in patients with prostate specific antigen 5.2 ng/ml or greater. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR

PubMed Central

Hammann, Christian; Norman, David G.; Lilley, David M. J.

2001-01-01

We have used 19F NMR to analyze the metal ion-induced folding of the hammerhead ribozyme by selective incorporation of 5fluorouridine. We have studied the chemical shift and linewidths of 19F resonances of 5-fluorouridine at the 4 and 7 positions in the ribozyme core as a function of added Mg2+. The data fit well to a simple two-state model whereby the formation of domain 1 is induced by the noncooperative binding of Mg2+ with an association constant in the range of 100 to 500 M−1, depending on the concentration of monovalent ions present. The results are in excellent agreement with data reporting on changes in the global shape of the ribozyme. However, the NMR experiments exploit reporters located in the center of the RNA sections undergoing the folding transitions, thereby allowing the assignment of specific nucleotides to the separate stages. The results define the folding pathway at high resolution and provide a time scale for the first transition in the millisecond range. PMID:11331743

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

PubMed

Oktaviani, Nur Alia; Risør, Michael W; Lee, Young-Ho; Megens, Rik P; de Jong, Djurre H; Otten, Renee; Scheek, Ruud M; Enghild, Jan J; Nielsen, Niels Chr; Ikegami, Takahisa; Mulder, Frans A A

2015-06-01

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

Temporal Lobe and “Default” Hemodynamic Brain Modes Discriminate Between Schizophrenia and Bipolar Disorder

PubMed Central

Calhoun, Vince D.; Maciejewski, Paul K.; Pearlson, Godfrey D.; Kiehl, Kent A.

2009-01-01

Schizophrenia and bipolar disorder are currently diagnosed on the basis of psychiatric symptoms and longitudinal course. The determination of a reliable, biologically-based diagnostic indicator of these diseases (a biomarker) could provide the groundwork for developing more rigorous tools for differential diagnosis and treatment assignment. Recently, methods have been used to identify distinct sets of brain regions or “spatial modes” exhibiting temporally coherent brain activity. Using functional magnetic resonance imaging (fMRI) data and a multivariate analysis method, independent component analysis, we combined the temporal lobe and the default modes to discriminate subjects with bipolar disorder, chronic schizophrenia, and healthy controls. Temporal lobe and default mode networks were reliably identified in all participants. Classification results on an independent set of individuals revealed an average sensitivity and specificity of 90 and 95%, respectively. The use of coherent brain networks such as the temporal lobe and default mode networks may provide a more reliable measure of disease state than task-correlated fMRI activity. A combination of two such hemodynamic brain networks shows promise as a biomarker for schizophrenia and bipolar disorder. PMID:17894392

Temporal lobe and "default" hemodynamic brain modes discriminate between schizophrenia and bipolar disorder.

PubMed

Calhoun, Vince D; Maciejewski, Paul K; Pearlson, Godfrey D; Kiehl, Kent A

2008-11-01

Schizophrenia and bipolar disorder are currently diagnosed on the basis of psychiatric symptoms and longitudinal course. The determination of a reliable, biologically-based diagnostic indicator of these diseases (a biomarker) could provide the groundwork for developing more rigorous tools for differential diagnosis and treatment assignment. Recently, methods have been used to identify distinct sets of brain regions or "spatial modes" exhibiting temporally coherent brain activity. Using functional magnetic resonance imaging (fMRI) data and a multivariate analysis method, independent component analysis, we combined the temporal lobe and the default modes to discriminate subjects with bipolar disorder, chronic schizophrenia, and healthy controls. Temporal lobe and default mode networks were reliably identified in all participants. Classification results on an independent set of individuals revealed an average sensitivity and specificity of 90 and 95%, respectively. The use of coherent brain networks such as the temporal lobe and default mode networks may provide a more reliable measure of disease state than task-correlated fMRI activity. A combination of two such hemodynamic brain networks shows promise as a biomarker for schizophrenia and bipolar disorder.

Selective Injection of Magnetization by Slow Chemical Exchange in NMR

NASA Astrophysics Data System (ADS)

Boulat, Benoit; Epstein, David M.; Rance, Mark

1999-06-01

In a system in slow dynamic equilibrium two NMR methods are shown to be suitable for injecting magnetization from one resonance to another by means of slow chemical exchange. The combined outputs of the methods may be employed to measure the value of the off-rate constant κoff in the complex. The methods are implemented experimentally using the complex of molecules composed of the enzyme Esherichia coli dihydrofolate reductase (DHFR) and the ligand folate. In an equilibrium solution with DHFR, folate is known to undergo chemical exchange between a free state and a bound state. The modified synchronous nutation method is applied to a spin of the folate molecule in the free and bound states; magnetization transfer occurs between the two sites due to the underlying exchange process. As a preliminary step for the application of the synchronous nutation method, a new one-dimensional 1H NMR technique is proposed which facilitates the assignment of the resonance of a spin in the bound state, provided the resonance of its exchange partner in the free state is known. This experiment is also used to obtain quantitative estimates of the transverse relaxation rate constant of the bound resonance. The numerical procedure necessary to analyze the experimental results of the synchronous nutation experiment is presented.

The breakout of the Hot CNO cycle via ^18Ne resonant states

NASA Astrophysics Data System (ADS)

Almaraz-Calderon, S.; Tan, W.; Aprahamian, A.; Bucher, B.; Gorres, J.; Roberts, A.; Villano, A.; Wiescher, M.; Brune, C.; Heinen, Z.; Massey, T.; Ozkan, N.; Guray, R. T.; Mach, H.

2010-11-01

The energy generation rate in the HCNO cycle is limited by the β decay of the waiting point nuclei ^14O and ^15O. However, when the temperatures and densities are high enough (e.g. Novae and X-ray Bursts) it is possible to bypass them by p/α captures resulting in a thermonuclear runaway towards the rp-process. One of the two paths for breakouts from the HCNO cycle is the reaction chain ^14O(α,p)^17F(p,γ)^18Ne(α,p), which proceeds through resonant states on ^18Ne, making their reactions rates very sensitive on the partial and total widths, excitation energies and spins of such resonances. We studied the resonant states in ^18Ne via ^16O(^3He,n) reaction. The neutrons were measured with an array of liquid scintillators using Time-of-Flight and pulse-shape discrimination techniques. The charged particles were detected in coincidence with neutrons by an array of silicon detectors, allowing us to measure α, p, p' and 2p decay branching ratios. Tentative spin assignments were made in comparison with zero range DWBA calculations. This new information will be included in reaction network calculations to evaluate its impact on the nuclear energy generation that occurs in these stellar explosive environments.

A meson-baryon molecular interpretation for some Ωc excited states

NASA Astrophysics Data System (ADS)

Montaña, Glòria; Feijoo, Albert; Ramos, Àngels

2018-04-01

We explore the possibility that some of the five narrow Ωc resonances recently observed at LHCb could correspond to pentaquark states, structured as meson-baryon bound states or molecules. The interaction of the low-lying pseudoscalar mesons with the ground-state baryons in the charm +1 , strangeness -2 and isospin 0 sector is built from t-channel vector meson exchange, using effective Lagrangians. The resulting s-wave coupled-channel unitarized amplitudes show the presence of two structures with similar masses and widths to those of the observed Ωc(3050)0 and Ωc(3090)0. The identification of these resonances with the meson-baryon bound states found in this work would also imply assigning the values 1/2- for their spin-parity. An experimental determination of the spin-parity of the Ωc(3090)0 would contribute to a better understanding of its structure, as the quark-based models predict its spin-parity to be either 3/2- or 5/2-. Predictions for the analogue bottom Ωb- resonances are also given.

Relative Intensity of a Cross-Over Resonance to Lamb Dips Observed in Stark Spectroscopy of Methane

NASA Astrophysics Data System (ADS)

Okuda, Shoko; Sasada, Hiroyuki

2017-06-01

Last ISMS, we reported on Stark effects of the νb{3} band of methane observed with a sub-Doppler resolution spectrometer. We determined the rotation-induced permanent dipole moment (PEDM) in the vibrational ground state and the vibration-, rotation-, and Coriolis-type-interaction-induced PEDMs in the v_{3}=1 state. Figure illustrates Stark modulation spectrum of the Q(6)E with the external electric field of 31.0 kV/cm and the selection rule of Δ M=±1, where M is the magnetic quantum number. The Δ M=1 and -1 components of the Lamb dips labeled by A and B are resolved, and the central component C is identified with the cross-over resonance. The Lamb dips are assigned to the magnetic quantum numbers of the lower and upper states, (M'',M') according to the Clebsch-Gordan coefficients. We found that the relative intensity of the cross-over resonance to the associated Lamb dips depends on the P, Q, and R branches. We ascribe the dependence to the collisional relaxation processes.

{gamma}-ray spectroscopy study of states in {sup 27}Si relevant for the {sup 26}Al{sup m}(p,{gamma}){sup 27}Si reaction in novae and supernovae

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

Lotay, G.; Woods, P. J.; Seweryniak, D.

2009-11-15

The heavy-ion, fusion-evaporation reaction {sup 12}C({sup 16}O,n) was used to identify {gamma}-decay transitions from excited states in {sup 27}Si above the proton threshold. The precise level energy measurements, J{sup {pi}} assignments, and lifetime measurements of astrophysically important {sup 26}Al{sup m}+p resonances have allowed an evaluation of the {sup 26}Al{sup m}(p,{gamma}){sup 27}Si reaction rate. An l{sub p}=0 resonance has been newly identified at a center-of-mass energy in the {sup 26}Al{sup m}+p system of 146.3(3) keV and is expected to dominate the rate for low stellar temperatures. In addition, an l{sub p}=1 resonance has been identified at 378.3(30) keV and is likelymore » to dominate the rate at high astrophysical temperatures, such as those found in oxygen-neon novae and core-collapse supernovae.« less

Nature of isomerism of solid isothiourea salts, inhibitors of nitric oxide synthases, as studied by 1H-14N nuclear quadrupole double resonance, X-ray, and density functional theory/quantum theory of atoms in molecules.

PubMed

Latosińska, J N; Latosińska, M; Seliger, J; Žagar, V; Maurin, J K; Kazimierczuk, Z

2012-02-09

Isothioureas, inhibitors of nitric oxide synthases, have been studied experimentally in solid state by nuclear quadrupole double resonance (NQDR) and X-ray methods and theoretically by the quantum theory of atoms in molecules/density functional theory. Resonance frequencies on (14)N have been detected and assigned to particular nitrogen sites in each molecule. The crystal packings of (S)-3,4-dichlorobenzyl-N-methylisothiouronium chloride with the disordered chlorine positions in benzene ring and (S)-butyloisothiouronium bromide have been resolved in X-ray diffraction studies. (14)N NQDR spectra have been found good indicators of isomer type and strength of intra- or intermolecular N-H···X (X = Cl, Br) interactions. From among all salts studied, only for (S)-2,3,4,5,6-pentabromobenzylisothiouronium chloride are both nitrogen sites equivalent, which has been explained by the slow exchange. This unique structural feature can be a key factor in the high biological activity of (S)-2,3,4,5,6-pentabromobenzylisothiouronium salts.

Search for Θ+(1540) Pentaquark in High-Statistics Measurement of γp→K¯0K+n at CLAS

NASA Astrophysics Data System (ADS)

Battaglieri, M.; Vita, R. De; Kubarovsky, V.; Guo, L.; Mutchler, G. S.; Stoler, P.; Weygand, D. P.; Ambrozewicz, P.; Anghinolfi, M.; Asryan, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Batourine, V.; Bedlinskiy, I.; Bellis, M.; Benmouna, N.; Berman, B. L.; Biselli, A. S.; Bouchigny, S.; Boiarinov, S.; Bradford, R.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Butuceanu, C.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Chen, S.; Clinton, E.; Cole, P. L.; Coltharp, P.; Crabb, D.; Crannell, H.; Cummings, J. P.; Dale, D.; de Sanctis, E.; Degtyarenko, P. V.; Deur, A.; Dharmawardane, K. V.; Djalali, C.; Dodge, G. E.; Donnelly, J.; Doughty, D.; Dugger, M.; Dzyubak, O. P.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Funsten, H.; Gabrielyan, M. Y.; Gan, L.; Garçon, M.; Gasparian, A.; Gavalian, G.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Glamazdin, O.; Goett, J.; Goetz, J. T.; Golovach, E.; Gonenc, A.; Gordon, C. I. O.; Gothe, R. W.; Griffioen, K. A.; Guidal, M.; Guler, N.; Gyurjyan, V.; Hadjidakis, C.; Hakobyan, R. S.; Hardie, J.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Joo, K.; Juengst, H. G.; Kellie, J. D.; Khandaker, M.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Kossov, M.; Kramer, L. H.; Kuhn, J.; Kuhn, S. E.; Kuleshov, S. V.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Lee, T.; Li, Ji; Livingston, K.; McKinnon, B.; Mecking, B. A.; Melone, J. J.; Mestayer, M. D.; Meyer, C. A.; Mibe, T.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mochalov, V.; Mokeev, V.; Morand, L.; Morrow, S. A.; Nadel-Turonski, P.; Nakagawa, I.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; Osipenko, M.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Paterson, C.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Ronchetti, F.; Rosner, G.; Rossi, P.; Sabatié, F.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Strakovsky, I. I.; Strauch, S.; Taiuti, M.; Tedeschi, D. J.; Teymurazyan, A.; Thoma, U.; Tkabladze, A.; Tkachenko, S.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Weinstein, L. B.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Zana, L.; Zhang, J.; Zhao, B.

2006-02-01

The exclusive reaction γp→ Kmacr 0K+n was studied in the photon energy range between 1.6 and 3.8 GeV searching for evidence of the exotic baryon Θ+(1540)→nK+. The decay to nK+ requires the assignment of strangeness S=+1 to any observed resonance. Data were collected with the CLAS detector at the Thomas Jefferson National Accelerator Facility corresponding to an integrated luminosity of 70pb-1. No evidence for the Θ+ pentaquark was found. Upper limits were set on the production cross section as function of center-of-mass angle and nK+ mass. The 95% C.L. upper limit on the total cross section for a narrow resonance at 1540 MeV was found to be 0.8 nb.

Context-Aware Reviewer Assignment for Trust Enhanced Peer Review

PubMed Central

Li, Lei; Wang, Yan; Liu, Guanfeng; Wang, Meng; Wu, Xindong

2015-01-01

Reviewer assignment is critical to peer review systems, such as peer-reviewed research conferences or peer-reviewed funding applications, and its effectiveness is a deep concern of all academics. However, there are some problems in existing peer review systems during reviewer assignment. For example, some of the reviewers are much more stringent than others, leading to an unfair final decision, i.e., some submissions (i.e., papers or applications) with better quality are rejected. In this paper, we propose a context-aware reviewer assignment for trust enhanced peer review. More specifically, in our approach, we first consider the research area specific expertise of reviewers, and the institution relevance and co-authorship between reviewers and authors, so that reviewers with the right expertise are assigned to the corresponding submissions without potential conflict of interest. In addition, we propose a novel cross-assignment paradigm, and reviewers are cross-assigned in order to avoid assigning a group of stringent reviewers or a group of lenient reviewers to the same submission. More importantly, on top of them, we propose an academic CONtext-aware expertise relevanCe oriEnted Reviewer cross-assignmenT approach (CONCERT), which aims to effectively estimate the “true” ratings of submissions based on the ratings from all reviewers, even though no prior knowledge exists about the distribution of stringent reviewers and lenient reviewers. The experiments illustrate that compared with existing approaches, our proposed CONCERT approach can less likely assign more than one stringent reviewers or lenient reviewers to a submission simultaneously and significantly reduce the influence of ratings from stringent reviewers and lenient reviewers, leading to trust enhanced peer review and selection, no matter what kind of distributions of stringent reviewers and lenient reviewers are. PMID:26090849

Noise suppression for micromechanical resonator via intrinsic dynamic feedback

NASA Astrophysics Data System (ADS)

Ian, Hou; Gong, Zhi-Rui; Sun, Chang-Pu

2008-09-01

We study a dynamic mechanism to passively suppress the thermal noise of a micromechanical resonator through an intrinsic self-feedback that is genuinely non-Markovian. We use two coupled resonators, one as the target resonator and the other as an ancillary resonator, to illustrate the mechanism and its noise reduction effect. The intrinsic feedback is realized through the dynamics of coupling between the two resonators: the motions of the target resonator and the ancillary resonator mutually inthence each other in a cyclic fashion. Specifically, the states that the target resonator has attained earlier will affect the state it attains later due to the presence of the ancillary resonator. We show that the feedback mechanism will bring forth the effect of noise suppression in the spectrum of displacement, but not in the spectrum of momentum.

A comparison of physicians and medical assistants in interpreting verbal autopsy interviews for allocating cause of neonatal death in Matlab, Bangladesh: can medical assistants be considered an alternative to physicians?

PubMed Central

2010-01-01

Objective This study assessed the agreement between medical physicians in their interpretation of verbal autopsy (VA) interview data for identifying causes of neonatal deaths in rural Bangladesh. Methods The study was carried out in Matlab, a rural sub-district in eastern Bangladesh. Trained persons conducted the VA interview with the mother or another family member at the home of the deceased. Three physicians and a medical assistant independently reviewed the VA interviews to assign causes of death using the International Classification of Diseases - Tenth Revision (ICD-10) codes. A physician assigned cause was decided when at least two physicians agreed on a cause of death. Cause-specific mortality fraction (CSMF), kappa (k) statistic, sensitivity, specificity, and positive predictive values were applied to compare agreement between the reviewers. Results Of the 365 neonatal deaths reviewed, agreement on a direct cause of death was reached by at least two physicians in 339 (93%) of cases. Physician and medical assistant reviews of causes of death demonstrated the following levels of diagnostic agreement for the main causes of deaths: for birth asphyxia the sensitivity was 84%, specificity 93%, and kappa 0.77. For prematurity/low birth weight, the sensitivity, specificity, and kappa statistics were, respectively, 53%, 96%, and 0.55, for sepsis/meningitis they were 48%, 98%, and 0.53, and for pneumonia they were 75%, 94%, and 0.51. Conclusion This study revealed a moderate to strong agreement between physician- assigned and medical assistant- assigned major causes of neonatal death. A well-trained medical assistant could be considered an alternative for assigning major causes of neonatal deaths in rural Bangladesh and in similar settings where physicians are scarce and their time costs more. A validation study with medically confirmed diagnosis will improve the performance of VA for assigning cause of neonatal death. PMID:20712906

Assigning value to energy storage systems at multiple points in an electrical grid

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

Balducci, Patrick J.; Alam, M. Jan E.; Hardy, Trevor D.

This article presents a taxonomy for assigning benefits to the services provided by energy storage systems (ESSs), defines approaches for monetizing the value associated with these services, assigns values to major ESS applications by region based on a review of an extensive set of literature, and summarizes and evaluates the capabilities of several tools currently used to estimate value for specific ESS deployments.

Assigning value to energy storage systems at multiple points in an electrical grid

DOE PAGES

Balducci, Patrick J.; Alam, M. Jan E.; Hardy, Trevor D.; ...

2018-01-01

This article presents a taxonomy for assigning benefits to the services provided by energy storage systems (ESSs), defines approaches for monetizing the value associated with these services, assigns values to major ESS applications by region based on a review of an extensive set of literature, and summarizes and evaluates the capabilities of several tools currently used to estimate value for specific ESS deployments.

46 CFR 174.300 - Specific applicability.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PERTAINING TO SPECIFIC VESSEL TYPES Hopper Dredges With Working Freeboard Assignments § 174.300 Specific applicability. This subpart applies to each self-propelled hopper dredge for which a working freeboard...

46 CFR 174.300 - Specific applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PERTAINING TO SPECIFIC VESSEL TYPES Hopper Dredges With Working Freeboard Assignments § 174.300 Specific applicability. This subpart applies to each self-propelled hopper dredge for which a working freeboard...

The Concept of Oxidation States in Metal Complexes

ERIC Educational Resources Information Center

Steinborn, Dirk

2004-01-01

The concepts of oxidation numbers when applied means electrons that are shared between atoms in molecules are assigned to a specific atom. Oxidation numbers are assigned from the Lewis structure of a molecule, with knowledge of the electronegativities of elements.

2 CFR 200.203 - Notices of funding opportunities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Federal awarding agency must announce specific funding opportunities by providing the following... the announcement: (1) Federal Awarding Agency Name; (2) Funding Opportunity Title; (3) Announcement...). If the Federal awarding agency has assigned or will assign a number to the funding opportunity...

Geometrical optics model of Mie resonances

PubMed

Roll; Schweiger

2000-07-01

The geometrical optics model of Mie resonances is presented. The ray path geometry is given and the resonance condition is discussed with special emphasis on the phase shift that the rays undergo at the surface of the dielectric sphere. On the basis of this model, approximate expressions for the positions of first-order resonances are given. Formulas for the cavity mode spacing are rederived in a simple manner. It is shown that the resonance linewidth can be calculated regarding the cavity losses. Formulas for the mode density of Mie resonances are given that account for the different width of resonances and thus may be adapted to specific experimental situations.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

PubMed

Summers, Samantha R; Sprenger, K G; Pfaendtner, Jim; Marchant, Jan; Summers, Michael F; Kaar, Joel L

2017-12-07

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1 H- 15 N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1 H- 15 N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

Fluid density and concentration measurement using noninvasive in situ ultrasonic resonance interferometry

DOEpatents

Pope, Noah G.; Veirs, Douglas K.; Claytor, Thomas N.

1994-01-01

The specific gravity or solute concentration of a process fluid solution located in a selected structure is determined by obtaining a resonance response spectrum of the fluid/structure over a range of frequencies that are outside the response of the structure itself. A fast fourier transform (FFT) of the resonance response spectrum is performed to form a set of FFT values. A peak value for the FFT values is determined, e.g., by curve fitting, to output a process parameter that is functionally related to the specific gravity and solute concentration of the process fluid solution. Calibration curves are required to correlate the peak FFT value over the range of expected specific gravities and solute concentrations in the selected structure.

Fluid density and concentration measurement using noninvasive in situ ultrasonic resonance interferometry

DOEpatents

Pope, N.G.; Veirs, D.K.; Claytor, T.N.

1994-10-25

The specific gravity or solute concentration of a process fluid solution located in a selected structure is determined by obtaining a resonance response spectrum of the fluid/structure over a range of frequencies that are outside the response of the structure itself. A fast Fourier transform (FFT) of the resonance response spectrum is performed to form a set of FFT values. A peak value for the FFT values is determined, e.g., by curve fitting, to output a process parameter that is functionally related to the specific gravity and solute concentration of the process fluid solution. Calibration curves are required to correlate the peak FFT value over the range of expected specific gravities and solute concentrations in the selected structure. 7 figs.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts

PubMed Central

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2018-01-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments. PMID:29375930

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

PubMed

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2017-11-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments.

Electron Paramagnetic Resonance Spectroscopy of Vanadium (IV) Complexes and Related Species.

DTIC Science & Technology

1980-07-27

Extensive near infrared (4000-650cm " ) investigations on VOCl 2 complexes have been made by many workers [21,39,43-49]. However the far infrared ...to facilitate the assignment of cation and ligand bacds. 4.2.1.2 Near Infrared Spectroscopy There are three principal reasons for measuriiio the... near infrared spectra of the co!;,plexes: (a) To establish the purity of the complex (b) To establish the bondi ng mode of the 1 i ( nd (c) To establish

IR and NMR spectral studies of 4-bromo-1-naphthyl chalcones-assessment of substituent effects

NASA Astrophysics Data System (ADS)

Thirunarayanan, G.; Gopalakrishnan, M.; Vanangamudi, G.

2007-07-01

Infrared νCO (cm -1) of s-cis and s-trans frequencies and nuclear magnetic resonance chemical shifts δ1H (ppm) of H-α and H-β, δ13C (ppm) of C-α and C-β data were assigned from their respective spectra of a series of various substituted styryl 4-bromo-1-naphthyl chalcones. These values are correlated with various Hammett substituent constants. From the results of statistical analysis, the effect of substituents can be explained.

Tissue specific resonance frequencies of water and metabolites within the human brain

NASA Astrophysics Data System (ADS)

Chadzynski, Grzegorz L.; Bender, Benjamin; Groeger, Adriane; Erb, Michael; Klose, Uwe

2011-09-01

Chemical shift imaging (CSI) without water suppression was used to examine tissue-specific resonance frequencies of water and metabolites within the human brain. The aim was to verify if there are any regional differences in those frequencies and to determine the influence of chemical shift displacement in slice-selection direction. Unsuppressed spectra were acquired at 3 T from nine subjects. Resonance frequencies of water and after water signal removal of total choline, total creatine and NAA were estimated. Furthermore, frequency distances between the water and those resonances were calculated. Results were corrected for chemical shift displacement. Frequency distances between water and metabolites were consistent and greater for GM than for WM. The highest value of WM to GM difference (14 ppb) was observed for water to NAA frequency distance. This study demonstrates that there are tissue-specific differences between frequency distances of water and metabolites. Moreover, the influence of chemical shift displacement in slice-selection direction is showed to be negligible.

Tissue specific resonance frequencies of water and metabolites within the human brain.

PubMed

Chadzynski, Grzegorz L; Bender, Benjamin; Groeger, Adriane; Erb, Michael; Klose, Uwe

2011-09-01

Chemical shift imaging (CSI) without water suppression was used to examine tissue-specific resonance frequencies of water and metabolites within the human brain. The aim was to verify if there are any regional differences in those frequencies and to determine the influence of chemical shift displacement in slice-selection direction. Unsuppressed spectra were acquired at 3T from nine subjects. Resonance frequencies of water and after water signal removal of total choline, total creatine and NAA were estimated. Furthermore, frequency distances between the water and those resonances were calculated. Results were corrected for chemical shift displacement. Frequency distances between water and metabolites were consistent and greater for GM than for WM. The highest value of WM to GM difference (14ppb) was observed for water to NAA frequency distance. This study demonstrates that there are tissue-specific differences between frequency distances of water and metabolites. Moreover, the influence of chemical shift displacement in slice-selection direction is showed to be negligible. Copyright © 2011 Elsevier Inc. All rights reserved.

Optimal assignment of workers to supporting services in a hospital

NASA Astrophysics Data System (ADS)

Sawik, Bartosz; Mikulik, Jerzy

2008-01-01

Supporting services play an important role in health care institutions such as hospitals. This paper presents an application of operations research model for optimal allocation of workers among supporting services in a public hospital. The services include logistics, inventory management, financial management, operations management, medical analysis, etc. The optimality criterion of the problem is to minimize operations costs of supporting services subject to some specific constraints. The constraints represent specific conditions for resource allocation in a hospital. The overall problem is formulated as an integer program in the literature known as the assignment problem, where the decision variables represent the assignment of people to various jobs. The results of some computational experiments modeled on a real data from a selected Polish hospital are reported.

Trial to assess the utility of genetic sequencing to improve patient outcomes

Cancer.gov

A pilot trial to assess whether assigning treatment based on specific gene mutations can provide benefit to patients with metastatic solid tumors is being launched this month by the NCI. The Molecular Profiling based Assignment of Cancer Therapeutics, or

47 CFR 87.37 - Developmental license.

Code of Federal Regulations, 2012 CFR

2012-10-01

... understanding. The showing must be signed by the applicant. (c) Assignable frequencies. Developmental stations may be authorized to use frequencies available for the service and class of station proposed. The number of frequencies assigned will depend upon the specific requirements of the developmental program...

48 CFR 1552.211-72 - Monthly progress report.

Code of Federal Regulations, 2010 CFR

2010-10-01

... a description of the work accomplished to support the cost. If the work is ordered using work... for each work assignment or delivery order. (b) Specific discussions shall include difficulties... actions awaiting Contracting Officer authorization, noted with the corresponding work assignment, such as...

Angle-resolved photoelectron spectroscopy of cyclopropane

NASA Astrophysics Data System (ADS)

Keller, P. R.; Taylor, J. W.; Carlson, Thomas A.; Whitley, T. A.; Grimm, F. A.

1985-10-01

The angular distribution parameter, β, determined for the valence orbitals (IP < 18 eV) of cyclopropane in the 10-30 eV photon energy range using dispersed polarized synchrotron radiation. The energy dependence of β for photoelectron energies between, 2 and 10 eV above threshold was found to be similar to those found previously for other σ orbitals. The effects of Jahn-Teller splitting on β for the 3e' orbital were found to be small but definitely present. The overall shape and magnitude of the β( hv) curve are, however, sufficiently for the different Jahn-Teller components that, for purposes of orbital assignments using β( hv) curves the shape and magnitude of the curves can be considered associated only with the initial state. Resonance photoionization features at a photon ener of ≈ 18 eV were observed in the 3e' and 3a' 1 orbitals and tentatively assigned to autoionization.

NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

PubMed

Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

2018-04-01

Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

NMR assignments of the N-terminal domain of Nephila clavipes spidroin 1

PubMed Central

Parnham, Stuart; Gaines, William A.; Duggan, Brendan M.; Marcotte, William R.

2011-01-01

The building blocks of spider dragline silk are two fibrous proteins secreted from the major ampullate gland named spidroins 1 and 2 (MaSp1, MaSp2). These proteins consist of a large central domain composed of approximately 100 tandem copies of a 35–40 amino acid repeat sequence. Non-repetitive N and C-terminal domains, of which the C-terminal domain has been implicated to transition from soluble and insoluble states during spinning, flank the repetitive core. The N-terminal domain until recently has been largely unknown due to difficulties in cloning and expression. Here, we report nearly complete assignment for all 1H, 13C, and 15N resonances in the 14 kDa N-terminal domain of major ampullate spidroin 1 (MaSp1-N) of the golden orb-web spider Nephila clavipes. PMID:21152998

Prevalence of the Wish to be of the Opposite Gender in Adolescents and Adults with Autism Spectrum Disorder.

PubMed

van der Miesen, Anna I R; Hurley, Hannah; Bal, Anneloes M; de Vries, Annelou L C

2018-05-07

Several studies have suggested an overrepresentation of (symptoms of) autism spectrum disorder (ASD) among individuals with gender dysphoria. Three studies have taken the inverse approach in children with ASD and showed increased parent report of the wish to be of the opposite gender in this group. This study compared the self-reported wish to be of the opposite gender (one item of the Youth Self-Report [YSR] and the Adult Self-Report [ASR]) of 573 adolescents (469 assigned boys and 104 assigned girls) and 807 adults (616 assigned males and 191 assigned females) with ASD to 1016 adolescents and 846 adults from the general population. Emotional and behavioral problems were measured by the DSM-oriented scales of the YSR and ASR. In addition, the Children's Social Behavior Questionnaire and the Adult Social Behavior Questionnaire were used to measure specific subdomains of the ASD spectrum to test whether specific subdomains of ASD were particularly involved. Significantly more adolescents (6.5%) and adults (11.4%) with ASD endorsed this item as compared to the general population (3-5%). In adolescents, assigned girls endorsed this item more than assigned boys. No significant gender differences were found in the adults with ASD. In addition, on all DSM-oriented scales of both the YSR and ASR, adolescents and adults with ASD who endorsed the gender item had significantly higher scores compared to those without. There were no significant associations between endorsement of the gender item and any specific subdomain of ASD, providing no evidence for a sole role of one of the ASD subdomains and endorsement of the wish to be the opposite gender.

Backbone and side-chain resonance assignments of (Ca2+)4-calmodulin bound to beta calcineurin A CaMBD peptide.

PubMed

Fowler, C Andrew; Núñez Hernandez, Maria F; O'Donnell, Susan E; Yu, Liping; Shea, Madeline A

2017-10-01

Calcineurin (CaN) is a heterodimeric and highly conserved serine/threonine phosphatase (PP2B) that plays a critical role in coupling calcium signals to physiological processes including embryonic cardiac development, NF-AT-regulated gene expression in immune responses, and apoptosis. The catalytic subunit (CaN A ) has three isoforms (α, β, and γ,) in humans and seven isoforms in Paramecium. In all eukaryotes, the EF-hand protein calmodulin (CaM) regulates CaN activity in a calcium-dependent manner. The N- and C-domains of CaM (CaM N and CaM C ) recognize a CaM-binding domain (CaMBD) within an intrinsically disordered region of CaN A that precedes the auto-inhibitory domain (AID) of CaN A . Here we present nearly complete 1 H, 13 C, and 15 N resonance assignments of (Ca 2+ ) 4 -CaM bound to a peptide containing the CaMBD sequence in the beta isoform of CaN A (βCaN A -CaMBDp). Its secondary structure elements predicted from the assigned chemical shifts were in good agreement with those observed in the high-resolution structures of (Ca 2+ ) 4 -CaM bound to CaMBDs of multiple enzymes. Based on the reported literature, the CaMBD of the α isoform of CaN A can bind to CaM in two opposing orientations which may influence the regulatory function of CaM. Because a high resolution structure of (Ca 2+ ) 4 -CaM bound to βCaN A -CaMBDp has not been reported, our studies serve as a starting point for determining the solution structure of this complex. This will demonstrate the preferred orientation of (Ca 2+ ) 4 -CaM on the CaMBD as well as the orientations of CaM N and CaM C relative to each other and to the AID of βCaN A .

Disability Evaluation System and Temporary Limited Duty Assignment Process: A Qualitative Review.

DTIC Science & Technology

1998-03-01

Statement addressing the requirement for monitoring, frequency of treat- ments/ therapy , and the associated operational assignment limitation; Informed...ACC does not exist in the EAIS, ARIS, or the EMF data bases. The system is able to track changes in duty station, but not ACC’s. If a member is on...specific geographic assignment. 4. Requires extensive or prolonged medical therapy . 5. Who through continued military service would probably result in

TH-CD-206-07: Determination of Patient-Specific Myocardial Mass at Risk Using Computed Tomography Angiography

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

Hubbard, L; Ziemer, B; Malkasian, S

Purpose: To evaluate the accuracy of a patient-specific coronary perfusion territory assignment algorithm that uses CT angiography (CTA) and a minimum-cost-path approach to assign coronary perfusion territories on a voxel-by-voxel basis for determination of myocardial mass at risk. Methods: Intravenous (IV) contrast (370 mg/mL iodine, 25 mL, 7 mL/s) was injected centrally into five swine (35–45 kg) and CTA was performed using a 320-slice CT scanner at 100 kVp and 200 mA. Additionally, a 4F catheter was advanced into the left anterior descending (LAD), left circumflex (LCX), and right coronary artery (RCA) and contrast (30 mg/mL iodine, 10 mL, 1.5more » mL/s) was directly injected into each coronary artery for isolation of reference coronary perfusion territories. Semiautomatic myocardial segmentation of the CTA data was then performed and the centerlines of the LAD, LCX, and RCA were digitally extracted through image processing. Individual coronary perfusion territories were then assigned using a minimum-cost-path approach, and were quantitatively compared to the reference coronary perfusion territories. Results: The results of the coronary perfusion territory assignment algorithm were in good agreement with the reference coronary perfusion territories. The average volumetric assignment error from mitral orifice to apex was 5.5 ± 1.1%, corresponding to 2.1 ± 0.7 grams of myocardial mass misassigned for each coronary perfusion territory. Conclusion: The results indicate that accurate coronary perfusion territory assignment is possible on a voxel-by-voxel basis using CTA data and an assignment algorithm based on a minimum-cost-path approach. Thus, the technique can potentially be used to accurately determine patient-specific myocardial mass at risk distal to a coronary stenosis, improving coronary lesion assessment and treatment. Conflict of Interest (only if applicable): Grant funding from Toshiba America Medical Systems.« less

Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

NASA Technical Reports Server (NTRS)

Zhang, Xiang (Inventor); Chen, Fanqing Frank (Inventor); Su, Kai-Hang (Inventor); Wei, Qi-Huo (Inventor); Ellman, Jonathan A. (Inventor); Sun, Cheng (Inventor)

2014-01-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

DOEpatents

Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

2014-04-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Assigning breed origin to alleles in crossbred animals.

PubMed

Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

2016-08-22

For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns breed origin to alleles of crossbred animals, even if their pedigree is not recorded.

Finite volume analysis of temperature effects induced by active MRI implants with cylindrical symmetry: 1. Properly working devices.

PubMed

Busch, Martin H J; Vollmann, Wolfgang; Schnorr, Jörg; Grönemeyer, Dietrich H W

2005-04-08

Active Magnetic Resonance Imaging implants are constructed as resonators tuned to the Larmor frequency of a magnetic resonance system with a specific field strength. The resonating circuit may be embedded into or added to the normal metallic implant structure. The resonators build inductively coupled wireless transmit and receive coils and can amplify the signal, normally decreased by eddy currents, inside metallic structures without affecting the rest of the spin ensemble. During magnetic resonance imaging the resonators generate heat, which is additional to the usual one described by the specific absorption rate. This induces temperature increases of the tissue around the circuit paths and inside the lumen of an active implant and may negatively influence patient safety. This investigation provides an overview of the supplementary power absorbed by active implants with a cylindrical geometry, corresponding to vessel implants such as stents, stent grafts or vena cava filters. The knowledge of the overall absorbed power is used in a finite volume analysis to estimate temperature maps around different implant structures inside homogeneous tissue under worst-case assumptions. The "worst-case scenario" assumes thermal heat conduction without blood perfusion inside the tissue around the implant and mostly without any cooling due to blood flow inside vessels. The additional power loss of a resonator is proportional to the volume and the quality factor, as well as the field strength of the MRI system and the specific absorption rate of the applied sequence. For properly working devices the finite volume analysis showed only tolerable heating during MRI investigations in most cases. Only resonators transforming a few hundred mW into heat may reach temperature increases over 5 K. This requires resonators with volumes of several ten cubic centimeters, short inductor circuit paths with only a few 10 cm and a quality factor above ten. Using MR sequences, for which the MRI system manufacturer declares the highest specific absorption rate of 4 W/kg, vascular implants with a realistic construction, size and quality factor do not show temperature increases over a critical value of 5 K. The results show dangerous heating for the assumed "worst-case scenario" only for constructions not acceptable for vascular implants. Realistic devices are safe with respect to temperature increases. However, this investigation discusses only properly working devices. Ruptures or partial ruptures of the wires carrying the electric current of the resonance circuits or other defects can set up a power source inside an extremely small volume. The temperature maps around such possible "hot spots" should be analyzed in an additional investigation.

Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping.

PubMed

Smelter, Andrey; Rouchka, Eric C; Moseley, Hunter N B

2017-08-01

Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values. However, peak grouping is further complicated by multiple sources of variance in peak position limiting the effectiveness of grouping methods that utilize uniform match tolerances. In addition, no method currently exists for deriving peak positional variances from single peak lists for grouping peaks into spin systems, i.e. spin system grouping within a single peak list. Therefore, we developed a complementary pair of peak list registration analysis and spin system grouping algorithms designed to overcome these limitations. We have implemented these algorithms into an approach that can identify multiple dimension-specific positional variances that exist in a single peak list and group peaks from a single peak list into spin systems. The resulting software tools generate a variety of useful statistics on both a single peak list and pairwise peak list alignment, especially for quality assessment of peak list datasets. We used a range of low and high quality experimental solution NMR and solid-state NMR peak lists to assess performance of our registration analysis and grouping algorithms. Analyses show that an algorithm using a single iteration and uniform match tolerances approach is only able to recover from 50 to 80% of the spin systems due to the presence of multiple sources of variance. Our algorithm recovers additional spin systems by reevaluating match tolerances in multiple iterations. To facilitate evaluation of the algorithms, we developed a peak list simulator within our nmrstarlib package that generates user-defined assigned peak lists from a given BMRB entry or database of entries. In addition, over 100,000 simulated peak lists with one or two sources of variance were generated to evaluate the performance and robustness of these new registration analysis and peak grouping algorithms.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Improving Motivation for Academics in Children with Autism

ERIC Educational Resources Information Center

Koegel, Lynn Kern; Singh, Anjileen K.; Koegel, Robert L.

2010-01-01

Many children with autism show very little interest in academic assignments and exhibit disruptive behavior when assignments are presented. Research indicates that incorporating specific motivational variables such as choice, interspersal of maintenance tasks, and natural reinforcers during intervention leads to improvements in core symptoms of…

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

Huang X. R.; Siddons D.; Macrander, A.T.

Realization of x-ray Fabry-Perot (FP) resonance in back-Bragg-reflection crystal cavities has been proposed and explored for many years, but to date no satisfactory performance has been achieved. Here we show that single-cavity crystal resonators intrinsically have limited finesse and efficiency. To break this limit, we demonstrate that monolithic multicavity resonators with equal-width cavities and specific plate thickness ratios can generate ultrahigh-resolution FP resonance with high efficiency, steep peak tails, and ultrahigh contrast simultaneously. The resonance mechanism is similar to that of sequentially cascaded single-cavity resonators. The ultranarrow-bandwidth FP resonance is anticipated to have various applications, including modern ultrahigh-resolution or precisionmore » x-ray monochromatization, spectroscopy, coherence purification, coherent diffraction, phase contrast imaging, etc.« less

Magnetic Resonance-Based Electrical Property Tomography (MR-EPT) for Prostate Cancer Grade Imaging

DTIC Science & Technology

2016-07-01

Award Number: W81XWH-13-1-0127 TITLE: Magnetic Resonance-Based Electrical Property Tomography (MR- EPT) for Prostate Cancer Grade Imaging...SUBTITLE 5a. CONTRACT NUMBER W81XWH-13-1-0127 Magnetic Resonance-Based Electrical Property Tomography (MR- EPT) for Prostate Cancer Grade Imaging...developing Magnetic Resonance – Electrical Property Tomography (MR-EPT) specifically for prostate imaging. MR-EPT is an imaging modality that may enable

Pump-probe photoelectron velocity-map imaging of autoionizing singly excited 4s{sup 1}4p{sup 6}np{sup 1}(n=7,8) and doubly excited 4s{sup 2}4p{sup 4}5s{sup 1}6p{sup 1} resonances in atomic krypton

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

Doughty, Benjamin; Haber, Louis H.; Leone, Stephen R.

2011-10-15

Pump-probe photoelectron velocity-map imaging, using 27-eV high-harmonic excitation and 786-nm ionization, is used to resolve overlapping autoionizing resonances in atomic krypton, obtaining two-photon photoelectron angular distributions (PADs) for singly and doubly excited states. Two features in the photoelectron spectrum are assigned to singly excited 4s{sup 1}4p{sup 6}np{sup 1} (n = 7,8) configurations and four features provide information about double excitation configurations. The anisotropy parameters for the singly excited 7p configuration are measured to be {beta}{sub 2} = 1.61 {+-} 0.06 and {beta}{sub 4} = 1.54 {+-} 0.16 while the 8p configuration gives {beta}{sub 2} = 1.23 {+-} 0.19 and {beta}{submore » 4} = 0.60 {+-} 0.15. These anisotropies most likely represent the sum of overlapping PADs from states of singlet and triplet spin multiplicities. Of the four bands corresponding to ionization of doubly excited states, two are assigned to 4s{sup 2}4p{sup 4}5s{sup 1}6p{sup 1} configurations that are probed to different J-split ion states. The two remaining doubly excited states are attributed to a previously observed, but unassigned, resonance in the vacuum-ultraviolet photoabsorption spectrum. The PADs from each of the double excitation states are also influenced by overlap from neighboring states that are not completely spectrally resolved. The anisotropies of the observed double excitation states are reported, anticipating future theoretical and experimental work to separate the overlapping PADs into the state resolved PADs. The results can be used to test theories of excited state ionization.« less

Examination of the role of the O14(α,p)F17 reaction rate in type-I x-ray bursts

NASA Astrophysics Data System (ADS)

Hu, J.; He, J. J.; Parikh, A.; Xu, S. W.; Yamaguchi, H.; Kahl, D.; Ma, P.; Su, J.; Wang, H. W.; Nakao, T.; Wakabayashi, Y.; Teranishi, T.; Hahn, K. I.; Moon, J. Y.; Jung, H. S.; Hashimoto, T.; Chen, A. A.; Irvine, D.; Lee, C. S.; Kubono, S.

2014-08-01

The O14(α,p)F17 reaction is one of the key reactions involved in the breakout from the hot-CNO cycle to the rp-process in type-I x-ray bursts (XRBs). The resonant properties in the compound nucleus Ne18 have been investigated through resonant elastic scattering of F17+p. The radioactive F17 beam was separated by the Center for Nuclear Study radioactive ion beam separator (CRIB) and bombarded a thick H2 gas target at 3.6 MeV/nucleon. The recoiling light particles were measured by three ΔE-E silicon telescopes at laboratory angles of θlab≈3∘,10∘, and 18∘. Five resonances at Ex=6.15, 6.28, 6.35, 6.85, and 7.05 MeV were observed in the excitation functions, and their spin-parities have been determined based on an R-matrix analysis. In particular, Jπ=1- was firmly assigned to the 6.15-MeV state which dominates the thermonuclear O14(α ,p)F17 rate below 2 GK. As well, a possible new excited state in Ne18 was observed at Ex=6.85±0.11 MeV with tentative J =0 assignment. This state could be the analog state of the 6.880 MeV (0-) level in the mirror nucleus O18, or a bandhead state (0+) of the six-particle four-hole (6p-4h) band. A new thermonuclear O14(α ,p)F17 rate has been determined, and the astrophysical impact of multiple recent rates has been examined using an XRB model. Contrary to previous expectations, we find only a modest impact on predicted nuclear energy generation rates from using reaction rates differing by up to several orders of magnitude.

From Goal-Oriented Requirements to Event-B Specifications

NASA Technical Reports Server (NTRS)

Aziz, Benjamin; Arenas, Alvaro E.; Bicarregui, Juan; Ponsard, Christophe; Massonet, Philippe

2009-01-01

In goal-oriented requirements engineering methodologies, goals are structured into refinement trees from high-level system-wide goals down to fine-grained requirements assigned to specific software/ hardware/human agents that can realise them. Functional goals assigned to software agents need to be operationalised into specification of services that the agent should provide to realise those requirements. In this paper, we propose an approach for operationalising requirements into specifications expressed in the Event-B formalism. Our approach has the benefit of aiding software designers by bridging the gap between declarative requirements and operational system specifications in a rigorous manner, enabling powerful correctness proofs and allowing further refinements down to the implementation level. Our solution is based on verifying that a consistent Event-B machine exhibits properties corresponding to requirements.

Serial Magnetic Resonance Imaging in Active Surveillance of Prostate Cancer: Incremental Value.

PubMed

Felker, Ely R; Wu, Jason; Natarajan, Shyam; Margolis, Daniel J; Raman, Steven S; Huang, Jiaoti; Dorey, Fred; Marks, Leonard S

2016-05-01

We assessed whether changes in serial multiparametric magnetic resonance imaging can help predict the pathological progression of prostate cancer in men on active surveillance. A retrospective cohort study was conducted of 49 consecutive men with Gleason 6 prostate cancer who underwent multiparametric magnetic resonance imaging at baseline and again more than 6 months later, each followed by a targeted prostate biopsy, between January 2011 and May 2015. We evaluated whether progression on multiparametric magnetic resonance imaging (an increase in index lesion suspicion score, increase in index lesion volume or decrease in index lesion apparent diffusion coefficient) could predict pathological progression (Gleason 3 + 4 or greater on subsequent biopsy, in systematic or targeted cores). Diagnostic performance of multiparametric magnetic resonance imaging was determined with and without clinical data using a binary logistic regression model. The mean interval between baseline and followup multiparametric magnetic resonance imaging was 28.3 months (range 11 to 43). Pathological progression occurred in 19 patients (39%). The sensitivity, specificity, positive predictive value and negative predictive value of multiparametric magnetic resonance imaging was 37%, 90%, 69% and 70%, respectively. Area under the receiver operating characteristic curve was 0.63. A logistic regression model using clinical information (maximum cancer core length greater than 3 mm on baseline biopsy or a prostate specific antigen density greater than 0.15 ng/ml(2) at followup biopsy) had an AUC of 0.87 for predicting pathological progression. The addition of serial multiparametric magnetic resonance imaging data significantly improved the AUC to 0.91 (p=0.044). Serial multiparametric magnetic resonance imaging adds incremental value to prostate specific antigen density and baseline cancer core length for predicting Gleason 6 upgrading in men on active surveillance. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

THERMUS—A thermal model package for ROOT

NASA Astrophysics Data System (ADS)

Wheaton, S.; Cleymans, J.; Hauer, M.

2009-01-01

THERMUS is a package of C++ classes and functions allowing statistical-thermal model analyses of particle production in relativistic heavy-ion collisions to be performed within the ROOT framework of analysis. Calculations are possible within three statistical ensembles; a grand-canonical treatment of the conserved charges B, S and Q, a fully canonical treatment of the conserved charges, and a mixed-canonical ensemble combining a canonical treatment of strangeness with a grand-canonical treatment of baryon number and electric charge. THERMUS allows for the assignment of decay chains and detector efficiencies specific to each particle yield, which enables sensible fitting of model parameters to experimental data. Program summaryProgram title: THERMUS, version 2.1 Catalogue identifier: AEBW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 17 152 No. of bytes in distributed program, including test data, etc.: 93 581 Distribution format: tar.gz Programming language: C++ Computer: PC, Pentium 4, 1 GB RAM (not hardware dependent) Operating system: Linux: FEDORA, RedHat, etc. Classification: 17.7 External routines: Numerical Recipes in C [1], ROOT [2] Nature of problem: Statistical-thermal model analyses of heavy-ion collision data require the calculation of both primordial particle densities and contributions from resonance decay. A set of thermal parameters (the number depending on the particular model imposed) and a set of thermalized particles, with their decays specified, is required as input to these models. The output is then a complete set of primordial thermal quantities for each particle, together with the contributions to the final particle yields from resonance decay. In many applications of statistical-thermal models it is required to fit experimental particle multiplicities or particle ratios. In such analyses, the input is a set of experimental yields and ratios, a set of particles comprising the assumed hadron resonance gas formed in the collision and the constraints to be placed on the system. The thermal model parameters consistent with the specified constraints leading to the best-fit to the experimental data are then output. Solution method: THERMUS is a package designed for incorporation into the ROOT [2] framework, used extensively by the heavy-ion community. As such, it utilizes a great deal of ROOT's functionality in its operation. ROOT features used in THERMUS include its containers, the wrapper TMinuit implementing the MINUIT fitting package, and the TMath class of mathematical functions and routines. Arguably the most useful feature is the utilization of CINT as the control language, which allows interactive access to the THERMUS objects. Three distinct statistical ensembles are included in THERMUS, while additional options to include quantum statistics, resonance width and excluded volume corrections are also available. THERMUS provides a default particle list including all mesons (up to the K4∗ (2045)) and baryons (up to the Ω) listed in the July 2002 Particle Physics Booklet [3]. For each typically unstable particle in this list, THERMUS includes a text-file listing its decays. With thermal parameters specified, THERMUS calculates primordial thermal densities either by performing numerical integrations or else, in the case of the Boltzmann approximation without resonance width in the grand-canonical ensemble, by evaluating Bessel functions. Particle decay chains are then used to evaluate experimental observables (i.e. particle yields following resonance decay). Additional detector efficiency factors allow fine-tuning of the model predictions to a specific detector arrangement. When parameters are required to be constrained, use is made of the 'Numerical Recipes in C' [1] function which applies the Broyden globally convergent secant method of solving nonlinear systems of equations. Since the NRC software is not freely-available, it has to be purchased by the user. THERMUS provides the means of imposing a large number of constraints on the chosen model (amongst others, THERMUS can fix the baryon-to-charge ratio of the system, the strangeness density of the system and the primordial energy per hadron). Fits to experimental data are accomplished in THERMUS by using the ROOT TMinuit class. In its default operation, the standard χ function is minimized, yielding the set of best-fit thermal parameters. THERMUS allows the assignment of separate decay chains to each experimental input. In this way, the model is able to match the specific feed-down corrections of a particular data set. Running time: Depending on the analysis required, run-times vary from seconds (for the evaluation of particle multiplicities given a set of parameters) to several minutes (for fits to experimental data subject to constraints). References:W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes in C: The Art of Scientific Computing, Cambridge University Press, Cambridge, 2002. R. Brun, F. Rademakers, Nucl. Inst. Meth. Phys. Res. A 389 (1997) 81. See also http://root.cern.ch/. K. Hagiwara et al., Phys. Rev. D 66 (2002) 010001.

Ability of preoperative 3.0-Tesla magnetic resonance imaging to predict the absence of side-specific extracapsular extension of prostate cancer.

PubMed

Hara, Tomohiko; Nakanishi, Hiroyuki; Nakagawa, Tohru; Komiyama, Motokiyo; Kawahara, Takashi; Manabe, Tomoko; Miyake, Mototaka; Arai, Eri; Kanai, Yae; Fujimoto, Hiroyuki

2013-10-01

Recent studies have shown an improvement in prostate cancer diagnosis with the use of 3.0-Tesla magnetic resonance imaging. We retrospectively assessed the ability of this imaging technique to predict side-specific extracapsular extension of prostate cancer. From October 2007 to August 2011, prostatectomy was carried out in 396 patients after preoperative 3.0-Tesla magnetic resonance imaging. Among these, 132 (primary sample) and 134 patients (validation sample) underwent 12-core prostate biopsy at the National Cancer Center Hospital of Tokyo, Japan, and at other institutions, respectively. In the primary dataset, univariate and multivariate analyses were carried out to predict side-specific extracapsular extension using variables determined preoperatively, including 3.0-Tesla magnetic resonance imaging findings (T2-weighted and diffusion-weighted imaging). A prediction model was then constructed and applied to the validation study sample. Multivariate analysis identified four significant independent predictors (P < 0.05), including a biopsy Gleason score of ≥8, positive 3.0-Tesla diffusion-weighted magnetic resonance imaging findings, ≥2 positive biopsy cores on each side and a maximum percentage of positive cores ≥31% on each side. The negative predictive value was 93.9% in the combination model with these four predictors, meanwhile the positive predictive value was 33.8%. Good reproducibility of these four significant predictors and the combination model was observed in the validation study sample. The side-specific extracapsular extension prediction by the biopsy Gleason score and factors associated with tumor location, including a positive 3.0-Tesla diffusion-weighted magnetic resonance imaging finding, have a high negative predictive value, but a low positive predictive value. © 2013 The Japanese Urological Association.

Point defects in crystalline zircon (zirconium silicate), ZrSiO4: electron paramagnetic resonance studies

NASA Astrophysics Data System (ADS)

Tennant, W. C.; Claridge, R. F. C.; Walsby, C. J.; Lees, N. S.

This article outlines the present state of knowledge of paramagnetic defects in crystalline zircon as obtained mainly, but not exclusively, from electron paramagnetic resonance (EPR) studies in crystalline zircon (zirconium silicate, ZrSiO4). The emphasis is on single-crystal studies where, in principle, unambiguous analysis is possible. Firstly, the crystallography of zircon is presented. Secondly, the relationships between available crystal-site symmetries and the symmetries of observed paramagnetic species in zircon, and how these observations lead to unambiguous assignments of point-group symmetries for particular paramagnetic species are detailed. Next, spin-Hamiltonian (SH) analysis is discussed with emphasis on the symmetry relationships that necessarily exist amongst the Laue classes of the crystal sites in zircon, the paramagnetic species occupying those sites and the SH itself. The final sections of the article then survey the results of EPR studies on zircon over the period 1960-2002.

The High-Resolution Infrared Spectrum of the ν 5Band of Deuterated Formic Acid (DCOOH)

NASA Astrophysics Data System (ADS)

Goh, K. L.; Ong, P. P.; Tan, T. L.; Wang, W. F.; Teo, H. H.

1998-07-01

The Fourier transform infrared spectrum of the ν5band of deuterated formic acid (DCOOH) has been measured with a resolution of 0.004 cm-1in the frequency range of 1090-1180 cm-1. Using a Watson'sA-reduced Hamiltonian in theIrrepresentation, a total of 1731 assigned unperturbed transitions have been analyzed to provide rovibrational constants for the upper state (v5= 1) with a standard deviation of 0.000363 cm-1. The band isAtype with an unperturbed band center at 1142.31075 ± 0.00002 cm-1. The band is expected to be perturbed by a nearby ν4band through a Fermi resonance term and possibly a Coriolis term. The resonance is particularly noticeable forKa= 10, and 11, at highJvalues. About 215 perturbed lines were identified but they were not included in the final fit.

(1 + 1) resonant enhanced multiphoton ionization via the A2Sigma(+) state of NO - Ionic rotational branching ratios and their intensity dependence

NASA Technical Reports Server (NTRS)

Rudolph, H.; Mckoy, V.; Dixit, S. N.; Huo, W. M.

1988-01-01

Rotational branching ratios resulting from the (1 + 1) resonant enhanced multiphoton ionization spectroscopy of NO via the 0-0 transition of the A-X band for the four possible branches that can be assigned as R(21.5) are explored using calculation performed in the frozen-core approximation at the Hartree-Fock level. The four different branches, of which three are distinctly different in the perturbative limit, have rather different branching ratios. The mixed R12 + Q22(21.5) branch, which is not intense and has the lowest transition energy, appears to give the best agreement with experimental branching ratio for parallel detection. The agreement is less satisfactory for perpendicular detection. Neither the effect of finite-acceptance angle of the photoelectron detector nor high intensities can explain the discrepancy.

Excitonic Transitions and Off-resonant Optical Limiting in CdS Quantum Dots Stabilized in a Synthetic Glue Matrix

PubMed Central

2007-01-01

Stable films containing CdS quantum dots of mean size 3.4 nm embedded in a solid host matrix are prepared using a room temperature chemical route of synthesis. CdS/synthetic glue nanocomposites are characterized using high resolution transmission electron microscopy, infrared spectroscopy, differential scanning calorimetry and thermogravimetric analysis. Significant blue shift from the bulk absorption edge is observed in optical absorption as well as photoacoustic spectra indicating strong quantum confinement. The exciton transitions are better resolved in photoacoustic spectroscopy compared to optical absorption spectroscopy. We assign the first four bands observed in photoacoustic spectroscopy to 1se–1sh, 1pe–1ph, 1de–1dhand 2pe–2phtransitions using a non interacting particle model. Nonlinear absorption studies are done using z-scan technique with nanosecond pulses in the off resonant regime. The origin of optical limiting is predominantly two photon absorption mechanism.

The boron abundance of Procyon

NASA Technical Reports Server (NTRS)

Lemke, Michael; Lambert, David L.; Edvardsson, Bengt

1993-01-01

The B I 2496.8 A resonance line and HST/GHRS echelle spectra are used with model atmospheres and synthetic spectra to derive the B abundance of the F dwarfs Procyon (Alpha Canis Minoris), Theta Ursae Majoris, and Iota Pegasi. The B abundance of Theta UMa and Iota Peg is similar to that derived by Boesgaard and Heacox (1978) from the B II resonance line in spectra of A- and B-type stars. These two dwarfs show normal abundances of Li, Be, and B. Procyon, which is highly depleted in Li and Be, is depleted in B by a factor of at least 3. Comparison of the spectra of Procyon and the halo dwarf HD 140283 shows that the B abundance assigned by Duncan et al. (1992) to three halo dwarfs is not greatly overestimated as a result of contamination of the B I line by an unidentified line.

CACA-TOCSY with alternate 13C–12C labeling: a 13Cα direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification

PubMed Central

Takeuchi, Koh; Frueh, Dominique P.; Sun, Zhen-Yu J.; Hiller, Sebastian

2010-01-01

We present a 13C direct detection CACA-TOCSY experiment for samples with alternate 13C–12C labeling. It provides inter-residue correlations between 13Cα resonances of residue i and adjacent Cαs at positions i − 1 and i + 1. Furthermore, longer mixing times yield correlations to Cα nuclei separated by more than one residue. The experiment also provides Cα-to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate 13C–12C labeling with [1,3-13C] glycerol or [2-13C] glycerol, which allows utilizing the small scalar 3JCC couplings that are masked by strong 1JCC couplings in uniformly 13C labeled samples. PMID:20383561

CACA-TOCSY with alternate 13C-12C labeling: a 13Calpha direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification.

PubMed

Takeuchi, Koh; Frueh, Dominique P; Sun, Zhen-Yu J; Hiller, Sebastian; Wagner, Gerhard

2010-05-01

We present a (13)C direct detection CACA-TOCSY experiment for samples with alternate (13)C-(12)C labeling. It provides inter-residue correlations between (13)C(alpha) resonances of residue i and adjacent C(alpha)s at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C(alpha) nuclei separated by more than one residue. The experiment also provides C(alpha)-to-sidechain correlations, some amino acid type identifications and estimates for psi dihedral angles. The power of the experiment derives from the alternate (13)C-(12)C labeling with [1,3-(13)C] glycerol or [2-(13)C] glycerol, which allows utilizing the small scalar (3)J(CC) couplings that are masked by strong (1)J(CC) couplings in uniformly (13)C labeled samples.

Photodissociation of the CH3Cl/+/ and N2O/+/ cations.

NASA Technical Reports Server (NTRS)

Dunbar, R. C.

1971-01-01

Use of the ion cyclotron resonance (icr) technique to observe the photodissociation of the cations CH3Cl(+) and N2O(+) in the gas phase. Ions were trapped in the icr cell for periods of the order of seconds, which permitted the photodissociation process to be observed with wavelength-selected light. A cyclotron resonance ejection technique was employed to show that CH3Cl(+) ions were being dissociated rather than the CH3ClH(+) ions which were also present. The photodissociation cross section for N2O(+) was found to be without strong wavelength dependence between 4000 and 6500 A. The cross section for CH3Cl(+) showed a large peak at 3150 A. Possible assignments of this peak are considered, and it is suggested that a photodissociation occurs through an ion excitation involving a change in occupation of the bonding or antibonding orbitals of the C-Cl bond.

Proton threshold states in the {sup 22}Na(p,{gamma}){sup 23}Mg reaction and astrophysical implications

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

Comisel, H.; Hategan, C.; Graw, G.

Proton threshold states in {sup 23}Mg are important for the astrophysically relevant proton capture reaction {sup 22}Na(p,{gamma}){sup 23}Mg. In the indirect determination of the resonance strength of the lowest states, which were not accessible by direct methods, some of the spin-parity-assignments remained experimentally uncertain. We have investigated these states with shell model, Coulomb displacement, and Thomas-Ehrman shift calculations. From the comparison of calculated and observed properties, we relate the lowest relevant resonance state at E{sub x}=7643 keV to an excited 3/2{sup +} state in accordance with a recent experimental determination by Jenkins et al. From this we deduce significantly improvedmore » values for the {sup 22}Na(p,{gamma}){sup 23}Mg reaction rate at stellar temperatures below T{sub 9}=0.1 K.« less

Time-Domain Nuclear Magnetic Resonance Investigation of Water Dynamics in Different Ginger Cultivars.

PubMed

Huang, Chongyang; Zhou, Qi; Gao, Shan; Bao, Qingjia; Chen, Fang; Liu, Chaoyang

2016-01-20

Different ginger cultivars may contain different nutritional and medicinal values. In this study, a time-domain nuclear magnetic resonance method was employed to study water dynamics in different ginger cultivars. Significant differences in transverse relaxation time T2 values assigned to the distribution of water in different parts of the plant were observed between Henan ginger and four other ginger cultivars. Ion concentration and metabolic analysis showed similar differences in Mn ion concentrations and organic solutes among the different ginger cultivars, respectively. On the basis of Pearson's correlation analysis, many organic solutes and 6-gingerol, the main active substance of ginger, exhibited significant correlations with water distribution as determined by NMR T2 relaxation, suggesting that the organic solute differences may impact water distribution. Our work demonstrates that low-field NMR relaxometry provides useful information about water dynamics in different ginger cultivars as affected by the presence of different organic solutes.

Information on co-morbidities collected by history is useful for assigning Otitis Media risk to children.

PubMed

Casselbrant, Margaretha L; Mandel, Ellen M; Doyle, William J

2016-06-01

Determine if a 2-Step multivariate analysis of historical symptom/sign data for comorbid diseases can abstract high-level constructs useful in assigning a child's "risk" for different Otitis Media expressions. Seventeen items related to the symptom/sign expression of hypothesized Otitis Media comorbidities were collected by history on 141 3-year-old children. Using established criteria, the children were assigned to 1 of 3 groups: Control (no significant past Otitis Media, n=45), Chronic Otitis Media with Effusion (n=45) and Recurrent Acute Otitis Media (n=51). Principal Component Analysis was used to identify factors representing the non-redundant shared information among related items and Discriminant Analysis operating on those factors was used to estimate the best predictor equation for pairwise group assignments. Six multivariate factors representing the assignable comorbidities of frequent colds, nasal allergy, gastroesophageal disease (specific and general), nasal congestion and asthma were identified and explained 81% of the variance in the 17 items. Discriminant Analysis showed that, for the Control-Chronic Otitis Media with Effusion comparison, a combination of 3 factors and, for the Control-Recurrent Acute Otitis Media comparison, a combination of 2 factors had assignment accuracies of 74% and 68%, respectively. For the contrast between the two disease expressions, a 2-factor combination had an assignment accuracy of 61%. These results show that this analytic methodology can abstract high-level constructs, comorbidities, from low-level data, symptom/sign scores, support a linkage between certain comorbidities and Otitis Media risk and suggest that specific comorbidity combinations contain information relevant to assigning the risk for different Otitis Media expressions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Approaches for grouping of pesticides into cumulative assessment groups for risk assessment of pesticide residues in food.

PubMed

Colnot, Thomas; Dekant, Wolfgang

2017-02-01

The European Food Safety Authority (EFSA) is developing approaches to cumulative risk assessment of pesticides by assigning individual pesticides to cumulative assessment groups (CAGs). For assignment to CAGs, EFSA recommended to rely on adverse effects on the specific target system. Contractors to EFSA have proposed to allocate individual pesticides into CAGs relying on NOAELs for effects on target organs. This manuscript evaluates the assignments by applying EFSAs criteria to the CAGs "Toxicity to the nervous system" and "Toxicity to the thyroid hormone system (gland or hormones)". Assignment to the CAG "Toxicity to the nervous system" based, for example, on neurochemical effects like choline esterase inhibition is well supported, whereas assignment to the CAG "Toxicity to the thyroid hormone system (gland or hormones)" has been based in the examined case studies on non-reproducible effects seen in single studies or on observations that are not adverse. Therefore, a more detailed effects evaluation is required to assign a pesticide to a CAG for a target organ where many confounders regarding effects are present. Relative potency factors in cumulative risk assessment should be based on benchmark doses from studies in one species with identical study design and human relevance of effects on specific target organs should be analyzed to define minimal margins of exposure. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Hazard banding in compliance with the new Globally Harmonised System (GHS) for use in control banding tools.

PubMed

Arnone, Mario; Koppisch, Dorothea; Smola, Thomas; Gabriel, Stefan; Verbist, Koen; Visser, Remco

2015-10-01

Many control banding tools use hazard banding in risk assessments for the occupational handling of hazardous substances. The outcome of these assessments can be combined with advice for the required risk management measures (RMMs). The Globally Harmonised System of Classification and Labelling of Chemicals (GHS) has resulted in a change in the hazard communication elements, i.e. Hazard (H) statements instead of Risk-phrases. Hazard banding schemes that depend on the old form of safety information have to be adapted to the new rules. The purpose of this publication is to outline the rationales for the assignment of hazard bands to H statements under the GHS. Based on this, this publication proposes a hazard banding scheme that uses the information from the safety data sheets as the basis for assignment. The assignment of hazard bands tiered according to the severity of the underlying hazards supports the important principle of substitution. Additionally, the set of assignment rules permits an exposure-route-specific assignment of hazard bands, which is necessary for the proposed route-specific RMMs. Ideally, all control banding tools should apply the same assignment rules. This GHS-compliant hazard banding scheme can hopefully help to establish a unified hazard banding strategy in the various control banding tools. Copyright © 2015 Elsevier Inc. All rights reserved.

12 CFR 3.4 - Reservation of authority.

Code of Federal Regulations, 2010 CFR

2010-01-01

... risk weight for any asset or the credit equivalent amount or credit conversion factor for any off..., if no risk weight, credit equivalent amount, or credit conversion factor is specifically assigned, the OCC may assign any risk weight, credit equivalent amount, or credit conversion factor that the OCC...

Generalised Assignment Matrix Methodology in Linear Programming

ERIC Educational Resources Information Center

Jerome, Lawrence

2012-01-01

Discrete Mathematics instructors and students have long been struggling with various labelling and scanning algorithms for solving many important problems. This paper shows how to solve a wide variety of Discrete Mathematics and OR problems using assignment matrices and linear programming, specifically using Excel Solvers although the same…

40 CFR 799.9120 - TSCA acute dermal toxicity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... identification number. A system to randomly assign animals to test groups and control groups is required. (E... source of test animals. (2) Method of randomization in assigning animals to test and control groups. (3... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9120 - TSCA acute dermal toxicity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... identification number. A system to randomly assign animals to test groups and control groups is required. (E... source of test animals. (2) Method of randomization in assigning animals to test and control groups. (3... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9110 - TSCA acute oral toxicity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... number. A system to assign animals to test groups and control groups randomly is required. (E) Housing... randomization in assigning animals to test and control groups. (3) Rationale for selection of species, if other... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9110 - TSCA acute oral toxicity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... number. A system to assign animals to test groups and control groups randomly is required. (E) Housing... randomization in assigning animals to test and control groups. (3) Rationale for selection of species, if other... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9120 - TSCA acute dermal toxicity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... identification number. A system to randomly assign animals to test groups and control groups is required. (E... source of test animals. (2) Method of randomization in assigning animals to test and control groups. (3... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9110 - TSCA acute oral toxicity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... number. A system to assign animals to test groups and control groups randomly is required. (E) Housing... randomization in assigning animals to test and control groups. (3) Rationale for selection of species, if other... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9110 - TSCA acute oral toxicity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... number. A system to assign animals to test groups and control groups randomly is required. (E) Housing... randomization in assigning animals to test and control groups. (3) Rationale for selection of species, if other... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9120 - TSCA acute dermal toxicity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... identification number. A system to randomly assign animals to test groups and control groups is required. (E... source of test animals. (2) Method of randomization in assigning animals to test and control groups. (3... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9110 - TSCA acute oral toxicity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... number. A system to assign animals to test groups and control groups randomly is required. (E) Housing... randomization in assigning animals to test and control groups. (3) Rationale for selection of species, if other... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

40 CFR 799.9120 - TSCA acute dermal toxicity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... identification number. A system to randomly assign animals to test groups and control groups is required. (E... source of test animals. (2) Method of randomization in assigning animals to test and control groups. (3... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS...

Examining Teachers' Decisions on Test-Type Assignment for Statewide Assessments

ERIC Educational Resources Information Center

Cho, Hyun-jeong; Kingston, Neal

2015-01-01

Recent studies have raised concerns about the vagueness of alternate assessment eligibility guidelines, specifically, that students with mild disabilities (SWMD) have been inappropriately assigned to alternate assessment--alternate achievement standards (AA-AAS). In this study, special education teachers (N = 317) were surveyed about SWMD in…

Briefing Teams in World Affairs Class.

ERIC Educational Resources Information Center

Dunn, Joe P.

1992-01-01

In a college world affairs course, the teacher acted as foreign policy/national security advisor to the president and assigned students as staff members for different geographic regions. Students briefed him daily, first on current events, then on specific issues. Students enjoyed the challenging assignments, intensive questioning, and policy…

Image Guided Focal Therapy for Magnetic Resonance Imaging Visible Prostate Cancer: Defining a 3-Dimensional Treatment Margin Based on Magnetic Resonance Imaging Histology Co-Registration Analysis.

PubMed

Le Nobin, Julien; Rosenkrantz, Andrew B; Villers, Arnauld; Orczyk, Clément; Deng, Fang-Ming; Melamed, Jonathan; Mikheev, Artem; Rusinek, Henry; Taneja, Samir S

2015-08-01

We compared prostate tumor boundaries on magnetic resonance imaging and radical prostatectomy histological assessment using detailed software assisted co-registration to define an optimal treatment margin for achieving complete tumor destruction during image guided focal ablation. Included in study were 33 patients who underwent 3 Tesla magnetic resonance imaging before radical prostatectomy. A radiologist traced lesion borders on magnetic resonance imaging and assigned a suspicion score of 2 to 5. Three-dimensional reconstructions were created from high resolution digitalized slides of radical prostatectomy specimens and co-registered to imaging using advanced software. Tumors were compared between histology and imaging by the Hausdorff distance and stratified by the magnetic resonance imaging suspicion score, Gleason score and lesion diameter. Cylindrical volume estimates of treatment effects were used to define the optimal treatment margin. Three-dimensional software based registration with magnetic resonance imaging was done in 46 histologically confirmed cancers. Imaging underestimated tumor size with a maximal discrepancy between imaging and histological boundaries for a given tumor of an average ± SD of 1.99 ± 3.1 mm, representing 18.5% of the diameter on imaging. Boundary underestimation was larger for lesions with an imaging suspicion score 4 or greater (mean 3.49 ± 2.1 mm, p <0.001) and a Gleason score of 7 or greater (mean 2.48 ± 2.8 mm, p = 0.035). A simulated cylindrical treatment volume based on the imaging boundary missed an average 14.8% of tumor volume compared to that based on the histological boundary. A simulated treatment volume based on a 9 mm treatment margin achieved complete histological tumor destruction in 100% of patients. Magnetic resonance imaging underestimates histologically determined tumor boundaries, especially for lesions with a high imaging suspicion score and a high Gleason score. A 9 mm treatment margin around a lesion visible on magnetic resonance imaging would consistently ensure treatment of the entire histological tumor volume during focal ablative therapy. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Coherent Raman scattering with incoherent light for a multiply resonant mixture: Theory

NASA Astrophysics Data System (ADS)

Kirkwood, Jason C.; Ulness, Darin J.; Stimson, Michael J.; Albrecht, A. C.

1998-02-01

The theory for coherent Raman scattering (CRS) with broadband incoherent light is presented for a multiply resonant, multicomponent mixture of molecules that exhibits simultaneous multiple resonances with the frequencies of the driving fields. All possible pairwise hyperpolarizability contributions to the signal intensity are included in the theoretical treatment-(resonant-resonant, resonant-nonresonant, and nonresonant-nonresonant correlations between chromophores) and it is shown how the different types of correlations manifest themselves as differently behaved components of the signal intensity. The Raman resonances are modeled as Lorentzians in the frequency domain, as is the spectral density of the incoherent light. The analytic results for this multiply resonant mixture are presented and applied to a specific binary mixture. These analytic results will be used to recover frequencies and dephasing times in a series of experiments on multiply resonant mixtures.

Nuclear resonance fluorescence in U-238 using LaBr detectors for nuclear security

NASA Astrophysics Data System (ADS)

Hayakawa, Takehito; Negm, Hani; Ohgaki, Hideaki; Daito, Izuru; Kii, Toshiteru; Zen, Heishun; Omer, Mohamed; Shizuma, Toshiyuki; Hajima, Ryoichi

2014-09-01

Recently, a nondestructive measurement method of shielded fissional isotopes such as 235U or 239Pu has been proposed for the nuclear security. These isotopes are measured by using nuclear resonance fluorescence (NRF) with monochromatic energy gamma-ray beams generated by laser Compton-scattering (LCS). We have proposed that one measure scattered gamma-rays from NRF with LCS gamma-ray beams using the LaBr3(Ce) detectors. The LaBr3(Ce) crystals include internal radioisotopes of a meta-stable isotope 138La and alpha decay chains from some actinides as 227Ac. There is a broad pump at about 2 MeV. This pump is considered to be an overlap of alpha-rays from decay chains of some actinides but its detailed structure has not been established. Here we have measured NRF spectra of 238U using the LCS gamma-rays with energy of about 2.5 MeV at the HIgS facility of the Duke University. The background has been evaluated using a simulation code GEAT4. The 9 peaks, 8 NRF gamma-rays plus the Compton scattered gamma-ray of the incident beam, are finally assigned in an energy range of about 200 keV at about 2.5 MeV. The 8 integrated NRF cross-sections measured by LaBr3(Ce) have been consistent with results by an HPGe detector. The three levels are newly assigned using the HPGe detector. Two of them are also measured by LaBr3(Ce).

Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

PubMed Central

Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

1993-01-01

Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

Gene Expression During the Development of Bacteriophage φ29 III. Analysis of Viral-Specific Protein Synthesis with Suppressible Mutants

PubMed Central

McGuire, Jeffrey C.; Pène, Jacques J.; Barrow-Carraway, Joyce

1974-01-01

Fifty-four suppressible mutants of bacteriophage φ29 have been isolated with a variety of mutagens and assigned to eight complementation groups. Viral-specific protein synthesis in UV light-irradiated, nonsuppressing Bacillus subtilis 60084 was analyzed with exponential acrylamide gels. Four additional φ29 proteins which were undetected on ordinary acrylamide gels are reported in this paper. Five phage φ29 proteins have been unambiguously assigned to specific cistrons. Two cistrons had pleiotropic effects on viral protein synthesis. Mutants in cistrons I or II were unable to synthesize DNA in nonsuppressing bacteria. Mutants in cistron I were unable to attach viral chromosomes to the host cell membrane, and the protein responsible for this function has been identified. The other viral protein playing a role in phage φ29 DNA synthesis is also identified and assigned to cistron II. Mutants in cistron II can attach viral chromosomes to membrane, but cannot synthesize DNA in nonsuppressing bacteria. Images PMID:4362871

Magnetic resonance fingerprinting.

PubMed

Ma, Dan; Gulani, Vikas; Seiberlich, Nicole; Liu, Kecheng; Sunshine, Jeffrey L; Duerk, Jeffrey L; Griswold, Mark A

2013-03-14

Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.

The resonator handbook

NASA Technical Reports Server (NTRS)

Cook, Jerry D.; Zhou, Shiliang

1993-01-01

The purpose of this work is to extend resonator theory into the region in which the planar mirror is quite small. Results of the theoretical description are then extended to resonator design and experimental arrangements as discussed in further sections of this work. Finally, a discussion of dielectric measurements for small samples is included as a specific application of this work.

Changing resonator geometry to boost sound power decouples size and song frequency in a small insect.

PubMed

Mhatre, Natasha; Montealegre-Z, Fernando; Balakrishnan, Rohini; Robert, Daniel

2012-05-29

Despite their small size, some insects, such as crickets, can produce high amplitude mating songs by rubbing their wings together. By exploiting structural resonance for sound radiation, crickets broadcast species-specific songs at a sharply tuned frequency. Such songs enhance the range of signal transmission, contain information about the signaler's quality, and allow mate choice. The production of pure tones requires elaborate structural mechanisms that control and sustain resonance at the species-specific frequency. Tree crickets differ sharply from this scheme. Although they use a resonant system to produce sound, tree crickets can produce high amplitude songs at different frequencies, varying by as much as an octave. Based on an investigation of the driving mechanism and the resonant system, using laser Doppler vibrometry and finite element modeling, we show that it is the distinctive geometry of the crickets' forewings (the resonant system) that is responsible for their capacity to vary frequency. The long, enlarged wings enable the production of high amplitude songs; however, as a mechanical consequence of the high aspect ratio, the resonant structures have multiple resonant modes that are similar in frequency. The drive produced by the singing apparatus cannot, therefore, be locked to a single frequency, and different resonant modes can easily be engaged, allowing individual males to vary the carrier frequency of their songs. Such flexibility in sound production, decoupling body size and song frequency, has important implications for conventional views of mate choice, and offers inspiration for the design of miniature, multifrequency, resonant acoustic radiators.

Gadolinium-enhanced magnetic resonance angiography in renal artery stenosis: comparison with digital subtraction angiography.

PubMed

Law, Y M; Tay, K H; Gan, Y U; Cheah, F K; Tan, B S

2008-04-01

To evaluate the accuracy of gadolinium-enhanced magnetic resonance angiography in assessing renal artery stenosis compared to catheter digital subtraction angiography. Retrospective study. Singapore General Hospital. Records of patients who underwent magnetic resonance angiography as well as digital subtraction angiography for assessment of renal artery stenosis from January 2003 to December 2005 were reviewed. There were 27 patients (14 male, 13 female) with a mean age of 62 (range, 44-77) years. There were 10 patients with renal transplants; their native renal arteries were not evaluated. Each of the two experienced interventional and body magnetic resonance radiologists, who were blinded to the results, reviewed the digital subtraction angiography and magnetic resonance angiography images respectively. Digital subtraction angiography was used as the standard of reference. A total of 39 renal arteries from these 27 patients were evaluated. One of the arteries was previously stented and could not be assessed with magnetic resonance angiography due to severe artefacts. Of the remaining 38 renal arteries, two were graded as normal, seven as having mild stenosis (<50%), eight as having moderate stenosis (> or =50% but <75%), and 21 as having severe stenosis (> or =75%). Magnetic resonance angiography and digital subtraction angiography were concordant in 89% of the arteries; magnetic resonance angiography overestimated the degree of stenosis in 8% and underestimated it in 3% of them. In the evaluation of clinically significant renal artery stenosis (> or =50%) with magnetic resonance angiography, the overall sensitivity, specificity, positive predictive value, and negative predictive value were 97%, 67%, 90%, and 86% respectively. The sensitivity and specificity of magnetic resonance angiography in transplant renal artery stenosis was 100%. CONCLUSION. Our experience suggested that gadolinium-enhanced magnetic resonance angiography is a sensitive non-invasive modality useful in the assessment of clinically significant renal artery stenosis.

Multi circular-cavity surface coil for magnetic resonance imaging of monkey's brain at 4 Tesla

NASA Astrophysics Data System (ADS)

Osorio, A. I.; Solis-Najera, S. E.; Vázquez, F.; Wang, R. L.; Tomasi, D.; Rodriguez, A. O.

2014-11-01

Animal models in medical research has been used to study humans diseases for several decades. The use of different imaging techniques together with different animal models offers a great advantage due to the possibility to study some human pathologies without the necessity of chirurgical intervention. The employ of magnetic resonance imaging for the acquisition of anatomical and functional images is an excellent tool because its noninvasive nature. Dedicated coils to perform magnetic resonance imaging experiments are obligatory due to the improvement on the signal-to-noise ratio and reduced specific absorption ratio. A specifically designed surface coil for magnetic resonance imaging of monkey's brain is proposed based on the multi circular-slot coil. Numerical simulations of the magnetic and electric fields were also performed using the Finite Integration Method to solve Maxwell's equations for this particular coil design and, to study the behavior of various vector magnetic field configurations and specific absorption ratio. Monkey's brain images were then acquired with a research-dedicated magnetic resonance imaging system at 4T, to evaluate the anatomical images with conventional imaging sequences. This coil showed good quality images of a monkey's brain and full compatibility with standard pulse sequences implemented in research-dedicated imager.

Coding OSICS sports injury diagnoses in epidemiological studies: does the background of the coder matter?

PubMed

Finch, Caroline F; Orchard, John W; Twomey, Dara M; Saad Saleem, Muhammad; Ekegren, Christina L; Lloyd, David G; Elliott, Bruce C

2014-04-01

To compare Orchard Sports Injury Classification System (OSICS-10) sports medicine diagnoses assigned by a clinical and non-clinical coder. Assessment of intercoder agreement. Community Australian football. 1082 standardised injury surveillance records. Direct comparison of the four-character hierarchical OSICS-10 codes assigned by two independent coders (a sports physician and an epidemiologist). Adjudication by a third coder (biomechanist). The coders agreed on the first character 95% of the time and on the first two characters 86% of the time. They assigned the same four-digit OSICS-10 code for only 46% of the 1082 injuries. The majority of disagreements occurred for the third character; 85% were because one coder assigned a non-specific 'X' code. The sports physician code was deemed correct in 53% of cases and the epidemiologist in 44%. Reasons for disagreement included the physician not using all of the collected information and the epidemiologist lacking specific anatomical knowledge. Sports injury research requires accurate identification and classification of specific injuries and this study found an overall high level of agreement in coding according to OSICS-10. The fact that the majority of the disagreements occurred for the third OSICS character highlights the fact that increasing complexity and diagnostic specificity in injury coding can result in a loss of reliability and demands a high level of anatomical knowledge. Injury report form details need to reflect this level of complexity and data management teams need to include a broad range of expertise.

46 CFR 174.300 - Specific applicability.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 7 2014-10-01 2014-10-01 false Specific applicability. 174.300 Section 174.300 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SUBDIVISION AND STABILITY SPECIAL RULES PERTAINING TO SPECIFIC VESSEL TYPES Hopper Dredges With Working Freeboard Assignments § 174.300 Specific...

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2013 CFR

2013-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

Men and Women in Ships: Preconceptions of the Crews.

ERIC Educational Resources Information Center

Greebler, Carol S.; And Others

Preintegration attitudes and expectations of 1,936 men and 346 women assigned to six Navy ships were measured before the women reported aboard, through the administration of gender-specific versions of the "Navy in Transition" questionnaire. An additional 483 men assigned to a ship not scheduled for integration completed the…

Personal, Expository, Critical, and Creative: Using Writing in Mathematics Courses

ERIC Educational Resources Information Center

Braun, Benjamin

2014-01-01

This article provides a framework for creating and using writing assignments based on four types of writing: personal, expository, critical, and creative. This framework includes specific areas of student growth affected by these writing styles. Illustrative sample assignments are given throughout for each type of writing and various combinations…

The Communication Audit: A Framework for Teaching Management Communication.

ERIC Educational Resources Information Center

Shelby, Annette N.; Reinsch, N. Lamar, Jr.

1996-01-01

Describes a communication audit project used in a graduate-level management communication course. Reviews literature concerning communication audits, explains why and how an audit project is used in the author's classes, and describes specific audit-related assignments. Concludes that, although a challenging assignment, the audit is worthwhile.…

5 CFR 930.207 - Details and assignments to other duties within the same agency.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) PROGRAMS FOR SPECIFIC POSITIONS AND EXAMINATIONS (MISCELLANEOUS) Administrative Law Judge Program § 930.207 Details and assignments to other duties within the same agency. (a) An agency may detail an administrative law judge from one administrative law judge...

5 CFR 930.207 - Details and assignments to other duties within the same agency.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) PROGRAMS FOR SPECIFIC POSITIONS AND EXAMINATIONS (MISCELLANEOUS) Administrative Law Judge Program § 930.207 Details and assignments to other duties within the same agency. (a) An agency may detail an administrative law judge from one administrative law judge...

5 CFR 930.207 - Details and assignments to other duties within the same agency.

Code of Federal Regulations, 2013 CFR

2013-01-01

... (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) PROGRAMS FOR SPECIFIC POSITIONS AND EXAMINATIONS (MISCELLANEOUS) Administrative Law Judge Program § 930.207 Details and assignments to other duties within the same agency. (a) An agency may detail an administrative law judge from one administrative law judge...

5 CFR 930.207 - Details and assignments to other duties within the same agency.

Code of Federal Regulations, 2012 CFR

2012-01-01

... (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) PROGRAMS FOR SPECIFIC POSITIONS AND EXAMINATIONS (MISCELLANEOUS) Administrative Law Judge Program § 930.207 Details and assignments to other duties within the same agency. (a) An agency may detail an administrative law judge from one administrative law judge...

5 CFR 930.207 - Details and assignments to other duties within the same agency.

Code of Federal Regulations, 2014 CFR

2014-01-01

... (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) PROGRAMS FOR SPECIFIC POSITIONS AND EXAMINATIONS (MISCELLANEOUS) Administrative Law Judge Program § 930.207 Details and assignments to other duties within the same agency. (a) An agency may detail an administrative law judge from one administrative law judge...

Teaching Historical Analysis through Creative Writing Assignments

ERIC Educational Resources Information Center

Peterson, Janine Larmon; Graham, Lea

2015-01-01

Incorporating creative writing exercises in history courses can heighten students' critical reading and analytical skills in an active learning model. We identify and define two types of possible assignments that use model texts as their locus: centripetal, which focuses on specific context and disciplinary terms, and centrifugal, which address…

Minority Images: A Project Guide.

ERIC Educational Resources Information Center

Murphy, Sharon; Estrada, Paula

The reading list and assignments in this study guide are designed to involve high school students in examining the media from a nonwhite perspective. The beginning assignments require students to assemble their own bibliography relating to minority groups in the media, to examine the lives and contributions of specific Chicano, black, and American…

Principals Make Assignments Matter

ERIC Educational Resources Information Center

Dougherty, Eleanor

2013-01-01

The inner-city high school in Washington, DC, that Guillaume Gendre joined as an assistant principal had a modest reputation for achievement but was nevertheless challenged to raise expectations for student work. In other schools, Gendre had used assignments--a specific kind of instructional task in which students are charged to think about an…

Land-Use-Planning Writing Assignment for an Environmental-Geology Course.

ERIC Educational Resources Information Center

Carson, Robert James; Sadd, James Lester

1991-01-01

Describes writing environmental impact statement concerning land use as assignment in geology courses. Students select area, propose land-use project, analyze available literature, choose specific site within map area for project, and write report addressing site access, water supply, liquid and solid waste disposal, mitigation of environmental…

Advances in the stability of high precision crystal resonators

NASA Technical Reports Server (NTRS)

Ballato, A.; Vig, J. R.

1979-01-01

Advances in technology directed toward minimizing the temporal changes in frequency of crystal resonators are described. Specific emphasis is placed on reducing their susceptibility to temperature, acceleration, and other environmental effects.

Magnetic resonance imaging of breast implants.

PubMed

Shah, Mala; Tanna, Neil; Margolies, Laurie

2014-12-01

Silicone breast implants have significantly evolved since their introduction half a century ago, yet implant rupture remains a common and expected complication, especially in patients with earlier-generation implants. Magnetic resonance imaging is the primary modality for assessing the integrity of silicone implants and has excellent sensitivity and specificity, and the Food and Drug Administration currently recommends periodic magnetic resonance imaging screening for silent silicone breast implant rupture. Familiarity with the types of silicone implants and potential complications is essential for the radiologist. Signs of intracapsular rupture include the noose, droplet, subcapsular line, and linguine signs. Signs of extracapsular rupture include herniation of silicone with a capsular defect and extruded silicone material. Specific sequences including water and silicone suppression are essential for distinguishing rupture from other pathologies and artifacts. Magnetic resonance imaging provides valuable information about the integrity of silicone implants and associated complications.

A rapid method to assess a broad inventory of organic species in marine sediments using ultra-high resolution mass spectrometry.

PubMed

Radović, Jagoš R; Silva, Renzo C; Snowdon, Ryan W; Brown, Melisa; Larter, Steve; Oldenburg, Thomas B P

2016-06-15

A broad range of organic species in marine sediments is routinely used as biogeochemical proxies of Earth history. These species are typically analyzed using different analytical methods, targeting very specific components and often including time-intensive sample preparation. There is, therefore, a need for a more comprehensive, rapid and high-throughput approach to simultaneously analyze a broad range of known sedimentary polar species and also have a surveillance capability able to identify candidate new species classes. Whole solvent extracts from recently deposited Gulf of Mexico marine sediments were obtained after a simple, one-step extraction. They were analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), using atmospheric pressure photoionization in positive ion mode (APPI-P), over a broad mass range (m/z 150-1500). From 3000 to over 5000 peaks per sample were assigned molecular formulae, and the majority of assignments (90%) showed an absolute error lower than 200 ppb. The detected species belong to the NO1-7 , N4 O2-8 , O1-9 , HC, N and OS compound classes, including known biomarker species such as pigments (e.g. tetrapyrrole macrocycles and carotenoids) and lipids (e.g. glycerol dialkyl glycerol tetraethers, GDGTs), but also compounds of still unknown detailed molecular structure, but with clear potential geochemical relevance. The reported method enables rapid (12 min FTICR-MS analysis time) and simultaneous detection of a broad range of multi-heteroatom, polar organic species in whole sediment extracts. This allows for higher sample throughput, a more comprehensive investigation of sedimentary geochemistry, and potentially the discovery of new components and derivation of novel, multi-species proxies. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Male-to-female gender dysphoria: Gender-specific differences in resting-state networks.

PubMed

Clemens, Benjamin; Junger, Jessica; Pauly, Katharina; Neulen, Josef; Neuschaefer-Rube, Christiane; Frölich, Dirk; Mingoia, Gianluca; Derntl, Birgit; Habel, Ute

2017-05-01

Recent research found gender-related differences in resting-state functional connectivity (rs-FC) measured by functional magnetic resonance imaging (fMRI). To the best of our knowledge, there are no studies examining the differences in rs-FC between men, women, and individuals who report a discrepancy between their anatomical sex and their gender identity, i.e. gender dysphoria (GD). To address this important issue, we present the first fMRI study systematically investigating the differences in typical resting-state networks (RSNs) and hormonal treatment effects in 26 male-to-female GD individuals (MtFs) compared with 19 men and 20 women. Differences between male and female control groups were found only in the auditory RSN, whereas differences between both control groups and MtFs were found in the auditory and fronto-parietal RSNs, including both primary sensory areas (e.g. calcarine gyrus) and higher order cognitive areas such as the middle and posterior cingulate and dorsomedial prefrontal cortex. Overall, differences in MtFs compared with men and women were more pronounced before cross-sex hormonal treatment. Interestingly, rs-FC between MtFs and women did not differ significantly after treatment. When comparing hormonally untreated and treated MtFs, we found differences in connectivity of the calcarine gyrus and thalamus in the context of the auditory network, as well as the inferior frontal gyrus in context of the fronto-parietal network. Our results provide first evidence that MtFs exhibit patterns of rs-FC which are different from both their assigned and their aspired gender, indicating an intermediate position between the two sexes. We suggest that the present study constitutes a starting point for future research designed to clarify whether the brains of individuals with GD are more similar to their assigned or their aspired gender.

Short-Term Effect of Two Semi-Occluded Vocal Tract Training Programs on the Vocal Quality of Future Occupational Voice Users: "Resonant Voice Training Using Nasal Consonants" Versus "Straw Phonation".

PubMed

Meerschman, Iris; Van Lierde, Kristiane; Peeters, Karen; Meersman, Eline; Claeys, Sofie; D'haeseleer, Evelien

2017-09-18

The purpose of this study was to determine the short-term effect of 2 semi-occluded vocal tract training programs, "resonant voice training using nasal consonants" versus "straw phonation," on the vocal quality of vocally healthy future occupational voice users. A multigroup pretest-posttest randomized control group design was used. Thirty healthy speech-language pathology students with a mean age of 19 years (range: 17-22 years) were randomly assigned into a resonant voice training group (practicing resonant exercises across 6 weeks, n = 10), a straw phonation group (practicing straw phonation across 6 weeks, n = 10), or a control group (receiving no voice training, n = 10). A voice assessment protocol consisting of both subjective (questionnaire, participant's self-report, auditory-perceptual evaluation) and objective (maximum performance task, aerodynamic assessment, voice range profile, acoustic analysis, acoustic voice quality index, dysphonia severity index) measurements and determinations was used to evaluate the participants' voice pre- and posttraining. Groups were compared over time using linear mixed models and generalized linear mixed models. Within-group effects of time were determined using post hoc pairwise comparisons. No significant time × group interactions were found for any of the outcome measures, indicating no differences in evolution over time among the 3 groups. Within-group effects of time showed a significant improvement in dysphonia severity index in the resonant voice training group, and a significant improvement in the intensity range in the straw phonation group. Results suggest that the semi-occluded vocal tract training programs using resonant voice training and straw phonation may have a positive impact on the vocal quality and vocal capacities of future occupational voice users. The resonant voice training caused an improved dysphonia severity index, and the straw phonation training caused an expansion of the intensity range in this population.

Photoionization of Cl+ from the 3s23p4 3P2,1,0 and the 3s23p4 1D2,1S0 states in the energy range 19-28 eV

NASA Astrophysics Data System (ADS)

McLaughlin, Brendan M.

2017-01-01

Absolute photoionization cross-sections for the Cl+ ion in its ground and the metastable states, 3s23p4 3P2,1,0 and 3s23p4 1D2,1S0, were measured recently at the Advanced Light Source at Lawrence Berkeley National Laboratory using the merged beams photon-ion technique at a photon energy resolution of 15 meV in the energy range 19-28 eV. These measurements are compared with large-scale Dirac-Coulomb R-matrix calculations in the same energy range. Photoionization of this sulphur-like chlorine ion is characterized by multiple Rydberg series of auto-ionizing resonances superimposed on a direct photoionization continuum. A wealth of resonance features observed in the experimental spectra is spectroscopically assigned, and their resonance parameters are tabulated and compared with the recent measurements. Metastable fractions in the parent ion beam are determined from this study. Theoretical resonance energies and quantum defects of the prominent Rydberg series 3s23p3nd, identified in the spectra as 3p → nd transitions, are compared with the available measurements made on this element. Weaker Rydberg series 3s23p3ns, identified as 3p → ns transitions and window resonances 3s3p4(4P)np features, due to 3s → np transitions, are also found in the spectra.

Lithofacies identification using multiple adaptive resonance theory neural networks and group decision expert system

USGS Publications Warehouse

Chang, H.-C.; Kopaska-Merkel, D. C.; Chen, H.-C.; Rocky, Durrans S.

2000-01-01

Lithofacies identification supplies qualitative information about rocks. Lithofacies represent rock textures and are important components of hydrocarbon reservoir description. Traditional techniques of lithofacies identification from core data are costly and different geologists may provide different interpretations. In this paper, we present a low-cost intelligent system consisting of three adaptive resonance theory neural networks and a rule-based expert system to consistently and objectively identify lithofacies from well-log data. The input data are altered into different forms representing different perspectives of observation of lithofacies. Each form of input is processed by a different adaptive resonance theory neural network. Among these three adaptive resonance theory neural networks, one neural network processes the raw continuous data, another processes categorial data, and the third processes fuzzy-set data. Outputs from these three networks are then combined by the expert system using fuzzy inference to determine to which facies the input data should be assigned. Rules are prioritized to emphasize the importance of firing order. This new approach combines the learning ability of neural networks, the adaptability of fuzzy logic, and the expertise of geologists to infer facies of the rocks. This approach is applied to the Appleton Field, an oil field located in Escambia County, Alabama. The hybrid intelligence system predicts lithofacies identity from log data with 87.6% accuracy. This prediction is more accurate than those of single adaptive resonance theory networks, 79.3%, 68.0% and 66.0%, using raw, fuzzy-set, and categorical data, respectively, and by an error-backpropagation neural network, 57.3%. (C) 2000 Published by Elsevier Science Ltd. All rights reserved.

A Near-Threshold Shape Resonance in the Valence-Shell Photoabsorption of Linear Alkynes

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

Jacovella, U.; Holland, D. M. P.; Boyé-Péronne, S.

2015-12-17

The room-temperature photoabsorption spectra of a number of linear alkynes with internal triple bonds (e.g., 2-butyne, 2-pentyne, and 2- and 3-hexyne) show similar resonances just above the lowest ionization threshold of the neutral molecules. These features result in a substantial enhancement of the photoabsorption cross sections relative to the cross sections of alkynes with terminal triple bonds (e.g., propyne, 1-butyne, 1-pentyne,...). Based on earlier work on 2-butyne [Xu et al., J. Chem. Phys. 2012, 136, 154303], these features are assigned to excitation from the neutral highest occupied molecular orbital (HOMO) to a shape resonance with g (l = 4) charactermore » and approximate pi symmetry. This generic behavior results from the similarity of the HOMOs in all internal alkynes, as well as the similarity of the corresponding g pi virtual orbital in the continuum. Theoretical calculations of the absorption spectrum above the ionization threshold for the 2- and 3-alkynes show the presence of a shape resonance when the coupling between the two degenerate or nearly degenerate pi channels is included, with a dominant contribution from l = 4. These calculations thus confirm the qualitative arguments for the importance of the l = 4 continuum near threshold for internal alkynes, which should also apply to other linear internal alkynes and alkynyl radicals. The 1-alkynes do not have such high partial waves present in the shape resonance. The lower l partial waves in these systems are consistent with the broader features observed in the corresponding spectra.« less

Drawing enhances cross-modal memory plasticity in the human brain: a case study in a totally blind adult

PubMed Central

Likova, Lora T.

2012-01-01

In a memory-guided drawing task under blindfolded conditions, we have recently used functional Magnetic Resonance Imaging (fMRI) to demonstrate that the primary visual cortex (V1) may operate as the visuo-spatial buffer, or “sketchpad,” for working memory. The results implied, however, a modality-independent or amodal form of its operation. In the present study, to validate the role of V1 in non-visual memory, we eliminated not only the visual input but all levels of visual processing by replicating the paradigm in a congenitally blind individual. Our novel Cognitive-Kinesthetic method was used to train this totally blind subject to draw complex images guided solely by tactile memory. Control tasks of tactile exploration and memorization of the image to be drawn, and memory-free scribbling were also included. FMRI was run before training and after training. Remarkably, V1 of this congenitally blind individual, which before training exhibited noisy, immature, and non-specific responses, after training produced full-fledged response time-courses specific to the tactile-memory drawing task. The results reveal the operation of a rapid training-based plasticity mechanism that recruits the resources of V1 in the process of learning to draw. The learning paradigm allowed us to investigate for the first time the evolution of plastic re-assignment in V1 in a congenitally blind subject. These findings are consistent with a non-visual memory involvement of V1, and specifically imply that the observed cortical reorganization can be empowered by the process of learning to draw. PMID:22593738

The spectrum of muscle histopathologic findings in 42 weak scleroderma patients

PubMed Central

Paik, Julie J.; Wigley, Fredrick M.; Lloyd, Thomas E.; Corse, Andrea M.; Casciola-Rosen, Livia; Shah, Ami A.; Boin, Francesco; Hummers, Laura K.; Mammen, Andrew L.

2015-01-01

Objective To determine if distinct muscle pathological features exist in scleroderma subjects with weakness. Methods This retrospective study included weak scleroderma subjects with muscle biopsies available for review. Biopsies were systematically assessed for individual pathologic features including inflammation, necrosis, fibrosis, and acute neurogenic atrophy. Based on the aggregate individual features, biopsies were assigned a histopathologic category of polymyositis, dermatomyositis, necrotizing myopathy, non-specific myositis, “acute denervation”, “fibrosis only”, or “other”. Clinical data analyzed included autoantibody profiles, scleroderma subtype and disease duration, Medsger muscle severity scores, creatine kinase (CK), electromyography (EMG), and muscle magnetic resonance imaging (MRI). Results 42 subjects (79% female and 64% diffuse scleroderma) were included in this study. Necrosis (67%), inflammation (48%), acute neurogenic atrophy (48%), and fibrosis (33%) were the most prevalent pathologic features. The presence of fibrosis was strongly associated with anti-PM-Scl antibodies. Histopathologic categories included non-specific myositis (36%), necrotizing myopathy (21%), dermatomyositis (7%), “acute denervation” (7%), “fibrosis only” (7%), and polymyositis (5%). Disease duration of scleroderma at the time of muscle biopsy was shorter in polymyositis than other histopathologic categories. Patients with anti-PM-Scl and Scl-70 antibodies also had a shorter disease duration than those with other auto-antibody profiles. Conclusion Non-specific myositis and necrotizing myopathy were the most common histopathologic categories in weak scleroderma subjects. Surprisingly, nearly half of the subjects studied had histological evidence of acute motor denervation (acute neurogenic atrophy); this has not been previously reported. Taken together, these observations suggest that a variety of pathologic mechanisms may underlie the development of myopathy in scleroderma. PMID:25989455

Drawing enhances cross-modal memory plasticity in the human brain: a case study in a totally blind adult.

PubMed

Likova, Lora T

2012-01-01

In a memory-guided drawing task under blindfolded conditions, we have recently used functional Magnetic Resonance Imaging (fMRI) to demonstrate that the primary visual cortex (V1) may operate as the visuo-spatial buffer, or "sketchpad," for working memory. The results implied, however, a modality-independent or amodal form of its operation. In the present study, to validate the role of V1 in non-visual memory, we eliminated not only the visual input but all levels of visual processing by replicating the paradigm in a congenitally blind individual. Our novel Cognitive-Kinesthetic method was used to train this totally blind subject to draw complex images guided solely by tactile memory. Control tasks of tactile exploration and memorization of the image to be drawn, and memory-free scribbling were also included. FMRI was run before training and after training. Remarkably, V1 of this congenitally blind individual, which before training exhibited noisy, immature, and non-specific responses, after training produced full-fledged response time-courses specific to the tactile-memory drawing task. The results reveal the operation of a rapid training-based plasticity mechanism that recruits the resources of V1 in the process of learning to draw. The learning paradigm allowed us to investigate for the first time the evolution of plastic re-assignment in V1 in a congenitally blind subject. These findings are consistent with a non-visual memory involvement of V1, and specifically imply that the observed cortical reorganization can be empowered by the process of learning to draw.

STS-107 Crew Surgeon

NASA Technical Reports Server (NTRS)

Johnston, Smith

2005-01-01

NASA Crew Surgeons (CS) provides medical support to crewmembers assigned to a space flight. Upon this mission assignment, CS s develop close working and personal relationships with crewmembers, their families and close friends. This discussion covers the role of the NASA CS from start of a mission assignment through its completion. Specific emphasis is placed on events associated with the Columbia accident to include; premission planning, initial family medical support, interface with the astronaut Casualty Assistance Control Officers (CACOs), AFIP relationship and on-going care for the families.