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Sample records for chemical shift imaging

  1. Applications of Chemical Shift Imaging to Marine Sciences

    Directory of Open Access Journals (Sweden)

    Haakil Lee

    2010-08-01

    Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.

  2. Chemical shift selective magnetic resonance imaging of the optic nerve in patients with acute optic neuritis

    DEFF Research Database (Denmark)

    Larsson, H B; Thomsen, C; Frederiksen, J;

    1988-01-01

    Optic neuritis is often the first manifestation of multiple sclerosis (MS). Sixteen patients with acute optic neuritis and one patient with benign intracranial hypertension (BIH) were investigated by magnetic resonance imaging, using a chemical shift selective double spin echo sequence. In 3...... were only shown in 3/16 (19%) of the patients with optic neuritis. Nevertheless, the presented chemical shift selective double spin echo sequence may be of great value for detection of retrobulbar lesions....

  3. Crime Scene Investigation: Clinical Application of Chemical Shift Imaging as a Problem Solving Tool

    Science.gov (United States)

    2016-02-26

    MDW/SGVU SUBJECT: Professional Presentation Approva l 26 FEB 2016 1. Your paper, entitled Crime Scene Investigation: Clinical Aoolication of...or technical information as a publication/presentation, a new 59 MDW Form 3039 must be submitted for review and approval.] Crime Scene Investiga...tion: Clinical Application of Chemical Shift Imaging as a Problem Solving Tool 1. TITLE OF MATERIAL TO BE PUBLISHED OR PRESENTED Crime Scene

  4. Chemical shift selective magnetic resonance imaging of the optic nerve in patients with acute optic neuritis

    Energy Technology Data Exchange (ETDEWEB)

    Larsson, H.B.W.; Thomsen, C.; Frederiksen, J.; Henriksen, O.; Olesen, J.

    Optic neuritis is often the first manifestion of multiple sclerosis (MS). Sixteen patients with acute optic neuritis and one patient with benign intracranial hypertension (BIH) were investigated by magnetic resonance imaging, using a chemical shift selective double spin echo sequence. In 3 of the 16 patients, abnormalities were seen. In one patient with bilateral symptoms, signal hyperintensity and swelling of the right side of the chiasm were found. In another patient the optic nerve was found diffusely enlarged with only a marginally increased signal in the second echo. In the third patient an area of signal hyperintensity and swelling was seen in the left optic nerve. In the patient with BIH the subarachnoid space which surrounds the optic nerves was enlarged. Even using this refined pulse sequence, avoiding the major artefact in imaging the optic nerve, the chemical shift artefact, lesions were only shown in 3/16 (19%) of the patients with optic neuritis. Nevertheless, the presented chemical shift selective double spin echo sequence may be of great value for detection of retrobulbar lesions.

  5. Two-Dimensional Proton Chemical-Shift Imaging of Human Muscle Metabolites

    Science.gov (United States)

    Hu, Jiani; Willcott, M. Robert; Moore, Gregory J.

    1997-06-01

    Large lipid signals and strong susceptibility gradients introduced by muscle-bone interfaces represent major technical challenges forin vivoproton MRS of human muscle. Here, the demonstration of two-dimensional proton chemical-shift imaging of human muscle metabolites is presented. This technique utilizes a chemical-shift-selective method for water and lipid suppression and automatic shimming for optimal homogeneity of the magnetic field. The 2D1H CSI technique described facilitates the acquisition of high-spatial-resolution spectra, and allows one to acquire data from multiple muscle groups in a single experiment. A preliminary investigation utilizing this technique in healthy adult males (n= 4) revealed a highly significant difference in the ratio of the creatine to trimethylamine resonance between the fast and slow twitch muscle groups examined. The technique is robust, can be implemented on a commercial scanner with relative ease, and should prove to be a useful tool for both clinical and basic investigators.

  6. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

    DEFF Research Database (Denmark)

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A;

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations...

  7. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

  8. Chemical shift imaging and localised magnetic resonance spectroscopy in full-term asphyxiated neonates

    Energy Technology Data Exchange (ETDEWEB)

    Brissaud, Olivier [Children' s Hospital, Paediatric Intensive Care Unit, Bordeaux (France); Chateil, Jean-Francois; Bordessoules, Martine; Brun, Muriel [Children' s Hospital, Radiology Unit, Bordeaux (France)

    2005-10-01

    Diagnosis of brain lesions after birth anoxia-ischemia is essential for appropriate management. Clinical evaluation is not sufficient. MRI has been proven to provide useful information. To compare abnormalities observed with MRI, including diffusion-weighted imaging (DWI), localised magnetic resonance spectroscopy (MRS) and chemical shift imaging (CSI) and correlate these findings with the clinical outcome. Fourteen full-term neonates with birth asphyxia were studied. MRI, MRS and CSI were performed within the first 4 days of life. Lesions observed with DWI were correlated with outcome, but the apparent diffusion coefficient (ADC) did improve diagnostic confidence. The mean value of Lac/Cr for the neonates with a favourable outcome was statically lower than for those who died (0.22 vs 1.04; P = 0.01). The same results were observed for the Lac/NAA ratio (0.21 vs 1.23; P = 0.01). Data obtained with localised MRS and CSI were correlated for the ratio N-acetyl-aspartate/choline, but not for the other metabolites. No correlation was found between the ADC values and the metabolite ratios. Combination of these techniques could be helpful in our understanding of the physiopathological events occurring in neonates with asphyxia. (orig.)

  9. Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.

    Science.gov (United States)

    Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise.

  10. Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

    Energy Technology Data Exchange (ETDEWEB)

    Min, Ji Hye [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Young Kon, E-mail: jmyr@dreamwiz.com [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Lim, Sanghyeok [Department of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2015-06-15

    Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain.

  11. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  12. Chemical shift imaging at 3 Tesla: effect of echo time on assessing bone marrow abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Del Grande, F. [The Johns Hopkins Medical Institutions, The Russell H. Morgan Department of Radiology and Radiological Science, Baltimore, MD (United States); Ospedale Regionale di Lugano, Servizio di Radiologia, Lugano, TI (Switzerland); Subhawong, Ty [University of Miami Miller School of Medicine, Department of Radiology, Miami, FL (United States); Flammang, A. [Siemens Medical Solutions USA, Inc., Malvern, PA (United States); Fayad, L.M. [The Johns Hopkins Medical Institutions, The Russell H. Morgan Department of Radiology and Radiological Science, Baltimore, MD (United States)

    2014-08-15

    Our purpose is to test the effect of varied in-phase (IP) and opposed-phase (OP) sequence order on characterizing marrow signal changes at 3T. The study was HIPAA compliant and IRB approved. Informed consent was waived. At 3T, IP and OP sequences were acquired in three patients with biopsy-proven osteosarcomas, using two methods: approach 1 (OP acquisition before IP acquisition) and approach 2 (OP after IP). Signal intensity (SI) measurements in 12 locations of biopsy-proven osteosarcoma and in six locations with normal bone marrow were performed independently by two experienced musculoskeletal radiologists. The signal intensity ratio (SIR) was measured within the marrow where there was T1 signal lower than skeletal muscle. A SIR < 20 % on the OP compared with IP imaging was considered positive for marrow replacement, while SIR > = 20 % was considered negative. Interobserver agreement was measured by the Lin concordance correlation coefficient (CCC). In 75 % (18/24) of locations within the biopsy-proven tumors, the SIR was >20 % (SI drop more than 20 % in OP compared to IP) using approach 2 and in 100 % (24/24) of the locations the SIR was <20 % (SI drop less than 20 % in OP compared to IP) using approach 1, indicating a high percentage of false-negative results by approach 2, and no false-negative results with approach 1. There was good agreement between observer measurement (CCC = 0.96). At 3T, the OP sequence should be acquired prior to the IP sequence, because susceptibility artifacts on a later-acquired OP sequence may lead to an erroneous interpretation of marrow signal abnormalities. (orig.)

  13. Diffusion tensor Imaging and chemical shift imaging assessment of heterogeneity in low grade glioma under temozolomide chemotherapy

    NARCIS (Netherlands)

    Sijens, P. E.; Heesters, Martinus; Enting, Roeline; van der Graaf, W. T. A.; Potze, J. H.; Irwan, Roy; Meiners, L. C.; Oudkerk, M.

    2007-01-01

    Diffusion tensor imaging and multiple voxel magnetic resonance spectroscopy were performed in the MRI follow-up of a patient with a glioma treated with temozolomide chemotherapy. Tumor shrinkage was paralleled by reductions in choline level and by increases in apparent diffusion coefficient indicati

  14. Evaluation of a rabbit model for osteomyelitis by high field, high resolution imaging using the chemical-shift-specific-slice-selection technique.

    Science.gov (United States)

    Volk, A; Crémieux, A C; Belmatoug, N; Vallois, J M; Pocidalo, J J; Carbon, C

    1994-01-01

    The rabbit model of osteomyelitis introduced by C.W. Norden, based on injection of an infecting solution (Staphylococcus aureus, sodium morrhuate) into the tibia, was studied at 4.7 Tesla with a time-efficient chemical shift selective imaging technique, Chemical Shift Specific Slice Selection (C4S). The evolution of the disease over several weeks was followed on water-selective, fat-selective, and sum images obtained simultaneously with this imaging sequence. Experiments were performed either on different groups of rabbits at different times after infection with subsequent sacrifice of the animal and microbiological analysis of the infected tibia or on the same group of animals imaged several times after infection. Associated analysis of the water and fat selective images revealed marrow modifications very early (Day 5 after inoculation) demonstrating the high sensitivity of the employed imaging technique. Later on, bone modifications were best identified on the sum images. Additional experiments performed on animals injected with a noninfecting solution containing only sodium morrhuate showed however that the sclerosing agent alone can yield images similar to those produced by infection at early stages after inoculation. Therefore, the Norden model would not be suitable for monitoring quantitatively outcome of therapy by magnetic resonance imaging. It is however well adapted for the evaluation and optimization of MRI techniques or protocols intended to detect early changes of bone marrow produced by septic or aseptic infarct.

  15. Diffusion tensor imaging and chemical shift imaging assessment of heterogeneity in low grade glioma under temozolomide chemotherapy.

    Science.gov (United States)

    Sijens, P E; Heesters, M A A M; Enting, R H; van der Graaf, W T A; Potze, J H; Irwan, R; Meiners, L C; Oudkerk, M

    2007-12-01

    Diffusion tensor imaging and multiple voxel magnetic resonance spectroscopy were performed in the MRI follow-up of a patient with a glioma treated with temozolomide chemotherapy. Tumor shrinkage was paralleled by reductions in choline level and by increases in apparent diffusion coefficient indicating decreased cellularity. Within the tumor, choline level and apparent diffusion coefficient showed a significant inverse correlation (P < 0.01). Fractional anisotropy distribution in the tumor correlated positively with N-acetyl aspartate level (P < 0.001), indicating that these parameters reflect (remaining) axonal structure. Tumor lactate level, also found to decrease under therapy, did not correlate with any other parameter.

  16. Chemical shift magnetic resonance imaging in differentiation of benign from malignant vertebral collapse in a rural tertiary care hospital in North India

    Science.gov (United States)

    Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep

    2016-01-01

    Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity.

  17. Free magnesium levels in normal human brain and brain tumors: sup 31 P chemical-shift imaging measurements at 1. 5 T

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. (Fox Chase Cancer Center, Philadelphia, PA (United States))

    1991-08-01

    The authors have studied a series of normal subjects and patients with brain tumors, by using {sup 31}P three-dimensional chemical shift imaging to obtain localized {sup 31}P spectra of the brain. A significant proportion of brain cytosolic ATP in normal brain is not complexed to Mg{sup 2+}, as indicated by the chemical shift {delta} of the {beta}-P resonance of ATP. The ATP {beta}P resonance position in brain thus is sensitive to changes in intracellular free Mg{sup 2+} concentration and in the proportion of ATP complexed with Mg because this shift lies on the rising portion of the {delta} vs. Mg{sup 2+} titration curve for ATP. They have measured the ATP {beta}-P shift and compared intracellular free Mg{sup 2+} concentration and fractions of free ATP for normal individuals and a limited series of patients with brain tumors. In four of the five spectra obtained from brain tissue containing a substantial proportion of tumor, intracellular free Mg{sup 2+} was increased, and the fraction of free ATP was decreased, compared with normal brain.

  18. Empirical isotropic chemical shift surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Czinki, Eszter; Csaszar, Attila G. [Eoetvoes University, Laboratory of Molecular Spectroscopy, Institute of Chemistry (Hungary)], E-mail: csaszar@chem.elte.hu

    2007-08-15

    A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles {phi} and {psi} characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS({phi},{psi}) surfaces obtained for the model peptides For-(l-Ala){sub n}-NH{sub 2}, with n = 1, 3, and 5, resulted in so-called empirical ICS({phi},{psi}) surfaces for all major nuclei of the 20 naturally occurring {alpha}-amino acids. Out of the many empirical surfaces determined, it is the 13C{sup {alpha}} ICS({phi},{psi}) surface which seems to be most promising for identifying major secondary structure types, {alpha}-helix, {beta}-strand, left-handed helix ({alpha}{sub D}), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring {alpha}-amino acids. Two-dimensional empirical 13C{sup {alpha}}-{sup 1}H{sup {alpha}} ICS({phi},{psi}) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins.

  19. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    Science.gov (United States)

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

  20. Liver steatosis (LS) evaluated through chemical-shift magnetic resonance imaging liver enzymes in morbid obesity; effect of weight loss obtained with intragastric balloon gastric banding.

    Science.gov (United States)

    Folini, Laura; Veronelli, Annamaria; Benetti, Alberto; Pozzato, Carlo; Cappelletti, Marco; Masci, Enzo; Micheletto, Giancarlo; Pontiroli, Antonio E

    2014-01-01

    The aim of this study was to evaluate in morbid obesity clinical and metabolic effects related to weight loss on liver steatosis (LS), measured through chemical-shift magnetic resonance imaging (MRI) and liver enzymes. Forty obese subjects (8 M/32 W; BMI 42.8 ± 7.12 kg/m(2), mean ± SD) were evaluated for LS through ultrasound (US-LS), chemical-shift MRI (MRI-LS), liver enzymes [aspartate aminotransferase (AST), alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), alkaline phosphatase (ALP)], anthropometric parameters [weight, BMI, waist circumference (WC)], lipids, insulin, insulin resistance (HOMA-IR), glycated hemoglobin (HbA1c), oral glucose tolerance test, and body composition [fat mass (FM) and fat-free mass (FFM) at bio-impedance analysis (BIA)]. Anthropometric measures, MRI-LS, BIA, and biochemical parameters were reevaluated 6 months later in 18 subjects undergoing restrictive bariatric approach, i.e., intragastric balloon (BIB, n = 13) or gastric banding (LAGB, n = 5), and in 13 subjects receiving hypocaloric diet. At baseline, US-LS correlates only with MRI-LS, and the latter correlates with ALT, AST, and GGT. After 6 months, subjects undergoing BIB or LAGB had significant changes of BMI, weight, WC, ALT, AST, GGT, ALP, HbA1c, insulin, HOMA-IR, FM, FFM, and MRI-LS. Diet-treated obese subjects had no significant change of any parameter under study; change of BMI, fat mass, and fat-free mass was significantly greater in LAGB/BIB subjects than in diet-treated subjects. Change of MRI-LS showed a significant correlation with changes in weight, BMI, WC, GGT, ALP, and basal MRI-LS. Significant weight loss after BIB or LAGB is associated with decrease in chemical-shift MRI-LS and with reduction in liver enzymes; chemical-shift MRI and liver enzymes allow monitoring of LS in follow-up studies.

  1. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  2. Linear Response Equilibrium versus echo-planar encoding for fast high-spatial resolution 3D chemical shift imaging

    Science.gov (United States)

    Fischer, Rudolf Fritz; Baltes, Christof; Weiss, Kilian; Pazhenkottil, Aju; Rudin, Markus; Boesiger, Peter; Kozerke, Sebastian

    2011-07-01

    In this work Linear Response Equilibrium (LRE) and Echo-planar spectroscopic imaging (EPSI) are compared in terms of sensitivity per unit time and power deposition. In addition an extended dual repetition time scheme to generate broad stopbands for improved inherent water suppression in LRE is presented. The feasibility of LRE and EPSI for assessing cholesterol esters in human carotid plaques with high spatial resolution of 1.95 × 1.15 × 1.15 mm 3 on a clinical 3T MR system is demonstrated. In simulations and phantom experiments it is shown that LRE has comparable but lower sensitivity per unit time relative to EPSI despite stronger signal generated. This relates to the lower sampling efficiency in LRE relative to EPSI as a result of limited gradient performance on clinical MR systems. At the same time, power deposition of LRE is significantly reduced compared to EPSI making it an interesting niche application for in vivo high field spectroscopic imaging of metabolites within a limited bandwidth.

  3. Chemical shift prediction for denatured proteins

    Energy Technology Data Exchange (ETDEWEB)

    Prestegard, James H., E-mail: jpresteg@ccrc.uga.edu; Sahu, Sarata C.; Nkari, Wendy K.; Morris, Laura C.; Live, David; Gruta, Christian

    2013-02-15

    While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in {sup 1}H-{sup 15}N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report {sup 1}H and {sup 15}N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.

  4. Double-echo gradient chemical shift MR imaging fails to differentiate minimal fat renal angiomyolipomas from other homogeneous solid renal tumors

    Energy Technology Data Exchange (ETDEWEB)

    Ferré, R., E-mail: kn638@yahoo.fr [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Cornelis, F. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Verkarre, V. [Department of Pathology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Eiss, D.; Correas, J.M. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Grenier, N. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Hélénon, O. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France)

    2015-03-15

    Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to

  5. Accessible surface area from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-07-15

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

  6. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    Science.gov (United States)

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging.

  7. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    . Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...

  8. Utility of chemical-shift MR imaging in detecting small amounts of fat in extrahepatic abdominal tumors; Utilidad de la tecnica de desplazamiento quimico den RM para la deteccion de pequenas cantidades de grasa en tumores abdominales extrahepaticos

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J.; Falco, J.; Puig, J.; Donoso, L. [Unidad de Diagnostico por Imagen de Alta Tecnologia (UDIAT). Sabadell (Spain)

    1999-07-01

    To determine the utility of the chemical shift technique in magnetic resonance imaging (MRI) to confirm small amounts of fat in extrahepatic intraabdominal tumours. 7 extrahepatic abdominal tumours that are suspected to have fat as seen in the axial computed tomography (TC) are analysed retrospectively. In order to confirm the fat content, the chemical displacement technique with gradient echo sequences (GE) in phase (P) and in opposite phase (OP) was used with MRI 1 T equipment. The tumours corresponded to renal angiomyolipoma (AML) (n=4), intraperitoneal liposarcoma (n=1), retroperitoneal liposarcoma (n=1) and intraabdominal extramedular hematopoiesis (n=1). To confirm the existence of fat in the tumours, we used a quantitative percentage variation parameter of the intensity of the signals (VIS) between the images in P and OP, according to the formula: IS{sub (}p)-IS({sub o}p)x100/IS{sub (}op), where IS is the intensity of the signal. The chemical shift technique showed fat in the seven tumours. Upon visual inspection, all the tumoral areas that were suspected to have fat showed a notable difference in the signal intensity, being hypointense in OP and hyperintense in P. In these areas the average VIS percentage was 170% while in the rest of the tumour the average VIS percentage was 3%. The chemical shift technique with RG sequences can be easily used in MRI equipment and allows us to confirm if a specific abdominal tumour has fat, even if there is only a small quantity. (Author) 13 refs.

  9. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term...... content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain......Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...

  10. Is the Lamb shift chemically significant?

    Science.gov (United States)

    Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

    2001-01-01

    The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

  11. Improved chemical shift prediction by Rosetta conformational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Tian Ye [Sanford Burnham Medical Research Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford Burnham Medical Research Institute (United States)

    2012-11-15

    Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.

  12. Calculations of proton chemical shifts in olefins and aromatics

    CERN Document Server

    Escrihuela, M C

    2000-01-01

    induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...

  13. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  14. Counterion influence on chemical shifts in strychnine salts

    Energy Technology Data Exchange (ETDEWEB)

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.

  15. A new paramagnetically shifted imaging probe for MRI

    Science.gov (United States)

    Senanayake, P. Kanthi; Rogers, Nicola J.; Finney, Katie‐Louise N.A.; Harvey, Peter; Funk, Alexander M.; Wilson, J. Ian; O'Hogain, Dara; Maxwell, Ross; Parker, David

    2016-01-01

    Purpose To develop and characterize a new paramagnetic contrast agent for molecular imaging by MRI. Methods A contrast agent was developed for direct MRI detection through the paramagnetically shifted proton magnetic resonances of two chemically equivalent tert‐butyl reporter groups within a dysprosium(III) complex. The complex was characterized in phantoms and imaged in physiologically intact mice at 7 Tesla (T) using three‐dimensional (3D) gradient echo and spectroscopic imaging (MRSI) sequences to measure spatial distribution and signal frequency. Results The reporter protons reside ∼6.5 Å from the paramagnetic center, resulting in fast T 1 relaxation (T 1 = 8 ms) and a large paramagnetic frequency shift exceeding 60 ppm. Fast relaxation allowed short scan repetition times with high excitation flip angle, resulting in high sensitivity. The large dipolar shift allowed direct frequency selective excitation and acquisition of the dysprosium(III) complex, independent of the tissue water signal. The biokinetics of the complex were followed in vivo with a temporal resolution of 62 s following a single, low‐dose intravenous injection. The lower concentration limit for detection was ∼23 μM. Through MRSI, the temperature dependence of the paramagnetic shift (0.28 ppm.K−1) was exploited to examine tissue temperature variation. Conclusions These data demonstrate a new MRI agent with the potential for physiological monitoring by MRI. Magn Reson Med 77:1307–1317, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:26922918

  16. Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

    Energy Technology Data Exchange (ETDEWEB)

    Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

    2016-04-15

    To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

  17. Tobacco and chemicals (image)

    Science.gov (United States)

    Some of the chemicals associated with tobacco smoke include ammonia, carbon dioxide, carbon monoxide, propane, methane, acetone, hydrogen cyanide and various carcinogens. Other chemicals that are associated with chewing ...

  18. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  19. Magnetic shift of the chemical freezeout and electric charge fluctuations

    CERN Document Server

    Fukushima, Kenji

    2016-01-01

    We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.

  20. Protein secondary structure prediction using NMR chemical shift data.

    Science.gov (United States)

    Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

    2010-10-01

    Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

  1. Estimation of optical chemical shift in nuclear spin optical rotation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Fang [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Yao, Guo-hua [Key Laboratory of Ion Beam Bio-engineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031 (China); He, Tian-jing [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Chen, Dong-ming, E-mail: dmchen@ustc.edu.cn [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Liu, Fan-chen, E-mail: fcliu@ustc.edu.cn [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2014-05-19

    Highlights: • Analytical theory of nuclear spin optical rotation (NSOR) is further developed. • Derive formula of NSOR ratio R between different nuclei in a same molecule. • Calculated results of R agree with the experiments. • Analyze influence factors on R and chemical distinction by NSOR. - Abstract: A recently proposed optical chemical shift in nuclear spin optical rotation (NSOR) is studied by theoretical comparison of NSOR magnitude between chemically non-equivalent or different element nuclei in the same molecule. Theoretical expressions of the ratio R between their NSOR magnitudes are derived by using a known semi-empirical formula of NSOR. Taking methanol, tri-ethyl-phosphite and 2-methyl-benzothiazole as examples, the ratios R are calculated and the results approximately agree with the experiments. Based on those, the important influence factors on R and chemical distinction by NSOR are discussed.

  2. Shift visual cryptography scheme of two secret images

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A new visual cryptography scheme of two secret images, which is named the shift visual cryptography of two secret images, is given. The compound function family of a general construction model is also introduced. The uniqueness and validity of this model are proved, and the minimum rows and columns for realizing the scheme are obtained. Compared with visual cryptography of one secret image, the shift visual cryptography scheme can share two secret images with the same size of pixels expansion without losing the contrast. It has randomness and various forms, and furthermore, we can also visually recover two secret images even if the two shares are different in form and color.

  3. Histological image segmentation using fast mean shift clustering method

    OpenAIRE

    Wu, Geming; Zhao, Xinyan; Luo, Shuqian; Shi, Hongli

    2015-01-01

    Background Colour image segmentation is fundamental and critical for quantitative histological image analysis. The complexity of the microstructure and the approach to make histological images results in variable staining and illumination variations. And ultra-high resolution of histological images makes it is hard for image segmentation methods to achieve high-quality segmentation results and low computation cost at the same time. Methods Mean Shift clustering approach is employed for histol...

  4. Comparison of brown and white adipose tissue fat fractions in ob, seipin, and Fsp27 gene knockout mice by chemical shift-selective imaging and (1)H-MR spectroscopy.

    Science.gov (United States)

    Peng, Xin-Gui; Ju, Shenghong; Fang, Fang; Wang, Yu; Fang, Ke; Cui, Xin; Liu, George; Li, Peng; Mao, Hui; Teng, Gao-Jun

    2013-01-15

    Brown adipose tissue (BAT) plays a key role in thermogenesis to protect the body from cold and obesity. White adipose tissue (WAT) stores excess energy in the form of triglycerides. To better understand the genetic effect on regulation of WAT and BAT, we investigated the fat fraction (FF) in two types of adipose tissues in ob/ob, human BSCL2/seipin gene knockout (SKO), Fsp27 gene knockout (Fsp27(-/-)), and wild-type (WT) mice in vivo using chemical shift selective imaging and (1)H-MR spectroscopy. We reported that the visceral fat volume in WAT was significantly larger in ob/ob mice, but visceral fat volumes were lower in SKO and Fsp27(-/-) mice compared with WT mice. BAT FF was significantly higher in ob/ob mice than the WT group and similar to that of WAT. In contrast, WAT FFs in SKO and Fsp27(-/-) mice were lower and similar to that of BAT. The adipocyte size of WAT in ob/ob mice and the BAT adipocyte size in ob/ob, SKO, and Fsp27 mice were significantly larger compared with WT mice. However, the WAT adipocyte size was significantly smaller in SKO mice than in WT mice. Positive correlations were observed between the adipocyte size and FFs of WAT and BAT. These results suggested that smaller adipocyte size correlates with lower FFs of WAT and BAT. In addition, the differences in FFs in WAT and BAT measured by MR methods in different mouse models were related to the different regulation effects of ob, seipin, or Fsp27 gene on developing WAT and BAT.

  5. Radar Subsurface Imaging by Phase Shift Migration Algorithm

    OpenAIRE

    Zhang, Hui; Benedix, Wolf-Stefan; Plettemeier, Dirk; Ciarletti, Valérie

    2013-01-01

    In this paper the phase shift migration based Syn- thetic Aperture Radar (SAR) is described and applied on radar imaging for dual polarized ground penetrating radar system (GPR). Conventional techniques for SAR imaging focusing use the matched filter concept and convolve the measurement data with a filter impulse response (convolution kernel) which is modified by the range. In fact, conventional techniques for SAR imaging technique can be considered as ray-tracing based SAR imaging technique....

  6. Mean shift based log-Gabor wavelet image coding

    Institute of Scientific and Technical Information of China (English)

    LI Ji-liang; FANG Xiang-zhong; HOU Jun

    2007-01-01

    In this paper, we propose a sparse overcomplete image approximation method based on the ideas of overcomplete log-Gabor wavelet, mean shift and energy concentration. The proposed approximation method selects the necessary wavelet coefficients with a mean shift based algorithm, and concentrates energy on the selected coefficients. It can sparsely approximate the original image, and converges faster than the existing local competition based method. Then, we propose a new compression scheme based on the above approximation method. The scheme has compression performance similar to JPEG 2000. The images decoded with the proposed compression scheme appear more pleasant to the human eyes than those with JPEG 2000.

  7. MRI of intraosseous fistulous systems and sequesters in chronic osteomyelitis with standard spin echo sequences, highly selective chemical-shift imaging, diffusion weighted imaging, and magnetization-transfer; MRT-Darstellung intraossaerer Sequester und Fistelsysteme bei chronischer Osteomyelitis durch Standardsequenzen, hochselektive Chemical-Shift-Bildgebung, Diffusionsgewichtung und Magnetisierungstransfer

    Energy Technology Data Exchange (ETDEWEB)

    Bitzer, M.; Hartmann, J.; Geist-Barth, B.; Stern, W.; Seemann, M.; Pereira, P.; Claussen, C.D. [Abteilung fuer Radiologische Diagnostik, Klinikum der Eberhart-Karls-Universitaet Tuebingen (Germany); Schick, F. [Sektion fuer Experimentelle Radiologie, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany); Krackhardt, T. [Berufsgenossenschaftliche Klinik, Tuebingen (Germany); Morgalla, M. [Chirurgische Klinik, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany)

    2002-11-01

    Purpose: To study and test the impact of modern MRI techniques in diagnostic imaging in the evaluation of intra-osseous fistulous systems and sequesters. Materials and Methods: In a prospective study, nine patients with chronic osteomyelitis of the legs were examined by MRI. Patients with clinical signs of osteomyelitis requiring surgery were included in the study. T1-weighted spin echo (SE) sequences, proton density (PD) and T2-weighted fast spin echo (FSE) sequences, water- and fat-selective FSE sequences, and diffusion weighted (DW) PSIF sequences were used preoperatively. Furthermore, magnetizing transfer (MT) with gradient echo (GRE) sequences was evaluated. Results: Water selective sequences revealed the highest sensitivity for the detection of fistulas (100%), providing the best delineation of the extent of the entire fistulous systems. Fat-selective sequences (sensitivity 55.6%) and T1-weighted sequences (sensitivity 77.8%) displayed fistulas as hypointense bands, which, however, cannot be well differentiated from cortical bone in the transcortical areas. PD and T2-weighted images were found to have a poor sensitivity (55.6% and 66.7%) for fistulas in any location. The sensitivity of water-selective sequences to demonstrate intraosseous sequesters was 100%. The sensitivity was low for the other sequences. In 4 of 5 patients with surgically proven infection, DW and MT revealed an abnormal spatial distribution, with high diffusion in the central parts of the fistulas and high MT effect peripherally surrounding a weak MT effect centrally. (orig.) [German] Zielsetzung: Die vorliegende Arbeit soll die Moeglichkeiten des Einsatzes spezieller Sequenztechniken der MRT bei der Diagnostik von intraossaeren Fisteln und Sequestern pruefen und beschreiben. Material und Methode: In einer prospektiven Studie wurden 9 Patienten mit chronischen Osteomyelitiden der unteren Extremitaeten kernspintomographisch untersucht. Die MRT-Befunde wurden qualitativ anhand der Operations

  8. Visual Attention Shift based on Image Segmentation Using Neurodynamic System

    Directory of Open Access Journals (Sweden)

    Lijuan Duan

    2011-01-01

    Full Text Available A method of predicting visual attention shift is proposed based on image segmentation using neurodynamic system in this paper. The input image is mapped to a neural oscillator network. Each oscillator corresponding to a pixel is modeled by means of simplified Wilson-Cowan equations, and is coupled with its 8-nearest neighbors. Then the image is segmented by classifying the oscillation curves of the excitatory groups of all the oscillators. The classifier is constructed based on features of frequency, offset, phase and amplitude of the curves. The visual attention shift between the regions on the image is predicted according to the saliency strength of each region. Referring to the mechanism of winner-take-all competition, the saliency of a region is the aggregation of the dissimilarities between this region and all the other ones. Experimental results on images show the effectiveness of our method.

  9. Correction of geometrically distorted underwater images using shift map analysis.

    Science.gov (United States)

    Halder, Kalyan Kumar; Paul, Manoranjan; Tahtali, Murat; Anavatti, Sreenatha G; Murshed, Manzur

    2017-04-01

    In underwater imaging, water waves cause severe geometric distortions and blurring of the acquired short-exposure images. Corrections for these distortions have been tackled reasonably well by previous efforts but still need improvement in the estimation of pixel shift maps to increase restoration accuracy. This paper presents a new algorithm that efficiently estimates the shift maps from geometrically distorted video sequences and uses those maps to restore the sequences. A nonrigid image registration method is employed to estimate the shift maps of the distorted frames against a reference frame. The sharpest frame of the sequence, determined using a sharpness metric, is chosen as the reference frame. A k-means clustering technique is employed to discard too-blurry frames that could result in inaccuracy in the shift maps' estimation. The estimated pixel shift maps are processed to generate the accurate shift map that is used to dewarp the input frames into their nondistorted forms. The proposed method is applied on several synthetic and real-world video sequences, and the obtained results exhibit significant improvements over the state-of-the-art methods.

  10. Transformation of Image Positions, Rotations, and Sizes into Shift Parameters

    DEFF Research Database (Denmark)

    Skov Jensen, A.; Lindvold, L.; Rasmussen, E.

    1987-01-01

    An optical image processing system is described that converts orientation and size to shift properties and simultaneously preserves the positional information as a shift. The system is described analytically and experimentally. The transformed image can be processed further with a classical...... correlator working with a rotational and size-invariant. multiplexed match filter. An optical robot vision system designed on this concept would be able to look at several objects simultaneously and determine their shape, size, orientation, and position with two measurements on the input scene at different...

  11. Categorization and Searching of Color Images Using Mean Shift Algorithm

    Directory of Open Access Journals (Sweden)

    Prakash PANDEY

    2009-07-01

    Full Text Available Now a day’s Image Searching is still a challenging problem in content based image retrieval (CBIR system. Most CBIR system operates on all images without pre-sorting the images. The image search result contains many unrelated image. The aim of this research is to propose a new object based indexing system Based on extracting salient region representative from the image, categorizing the image into different types and search images that are similar to given query images.In our approach, the color features are extracted using the mean shift algorithm, a robust clustering technique, Dominant objects are obtained by performing region grouping of segmented thumbnails. The category for an image is generated automatically by analyzing the image for the presence of a dominant object. The images in the database are clustered based on region feature similarity using Euclidian distance. Placing an image into a category can help the user to navigate retrieval results more effectively. Extensive experimental results illustrate excellent performance.

  12. An Improved Image Segmentation Based on Mean Shift Algorithm

    Institute of Scientific and Technical Information of China (English)

    CHENHanfeng; QIFeihu

    2003-01-01

    Gray image segmentation is to segment an image into some homogeneous regions and only one gray level is defined for each region as the result. These grayl evels are called major gray levels. Mean shift algorithm(MSA) has shown its efficiency in image segmentation. An improved gray image segmentation method based on MSAis proposed in this paper since usual image segmentation methods based on MSA often fail in segmenting imageswith weak edges. Corrupted block and its J-value are defined firstly in the proposed method. Then, J-matrix gotten from corrupted blocks are proposed to measure whether weak edges appear in the image. According to the J-matrix, major gray levels gotten with usual segmen-tation methods based on MSA are augmented and corre-sponding allocation windows are modified to detect weak edges. Experimental results demonstrate the effectiveness of the proposed method in gray image segmentation.

  13. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Gabriel B.; Andersen, Amity; Washton, Nancy M.; Chatterjee, Sayandev; Levitskaia, Tatiana G.

    2016-09-06

    Technetium (Tc) displays a rich chemistry due to the wide range of oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and 99Tc NMR spec-troscopy is widely used to probe chemical environments of Tc in odd oxidation states. However interpretation of the 99Tc NMR data is hindered by the lack of reference compounds. DFT computations can help fill this gap, but to date few com-putational studies have focused on 99Tc NMR of compounds and complexes. This work systematically evaluates the inclu-sion small percentages of Hartree-Fock exchange correlation and relativistic effects in DFT computations to support in-terpretation of the 99Tc NMR spectra. Hybrid functionals are found to perform better than their pure GGA counterparts, and non-relativistic calculations have been found to generally show a lower mean absolute deviation from experiment. Overall non-relativistic PBE0 and B3PW91 calculations are found to most accurately predict 99Tc NMR chemical shifts.

  14. High Resolution Image Reconstruction from Projection of Low Resolution Images DIffering in Subpixel Shifts

    Science.gov (United States)

    Mareboyana, Manohar; Le Moigne-Stewart, Jacqueline; Bennett, Jerome

    2016-01-01

    In this paper, we demonstrate a simple algorithm that projects low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithm is very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. used in projection yield comparable results. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML), and Maximum a posterior (MAP) algorithms. The algorithm is robust and is not overly sensitive to the registration inaccuracies.

  15. High resolution image reconstruction from projection of low resolution images differing in subpixel shifts

    Science.gov (United States)

    Mareboyana, Manohar; Le Moigne, Jacqueline; Bennett, Jerome

    2016-05-01

    In this paper, we demonstrate simple algorithms that project low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithms are very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. are used in projection. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML) algorithms. The algorithms are robust and are not overly sensitive to the registration inaccuracies.

  16. Relationship between chemical shift value and accessible surface area for all amino acid atoms

    Directory of Open Access Journals (Sweden)

    Rieping Wolfgang

    2009-04-01

    Full Text Available Abstract Background Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes. Results We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html. Conclusion Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.

  17. Coating induced phase shift and impact on Euclid imaging performance

    Science.gov (United States)

    Gaspar Venancio, Luis M.; Carminati, Lionel; Lorenzo Alvarez, Jose; Amiaux, Jérôme; Bonino, Luciana; Salvignol, Jean-Christophe; Vavrek, Roland; Laureijs, René; Short, Alex; Boenke, Tobias; Strada, Paulo

    2016-07-01

    The challenging constraints imposed on the Euclid telescope imaging performances have driven the design, manufacturing and characterisation of the multi-layers coatings of the dichroic. Indeed it was found that the coatings layers thickness inhomogeneity will introduce a wavelength dependent phase-shift resulting in degradation of the image quality of the telescope. Such changes must be characterized and/or simulated since they could be non-negligible contributors to the scientific performance accuracy. Several papers on this topic can be found in literature, however the results can not be applied directly to Euclid's dichroic coatings. In particular an applicable model of the phase-shift variation with the wavelength could not be found and was developed. The results achieved with the mathematical model are compared to experimental results of tests performed on a development prototype of the Euclid's dichroic.

  18. Imaging the Mott Insulator Shells using Atomic Clock Shifts

    OpenAIRE

    Campbell, Gretchen K.; Mun, Jongchul; Boyd, Micah; Medley, Patrick; Leanhardt, Aaron E.; Marcassa, Luis; Pritchard, David E.; Ketterle, Wolfgang

    2006-01-01

    Microwave spectroscopy was used to probe the superfluid-Mott Insulator transition of a Bose-Einstein condensate in a 3D optical lattice. Using density dependent transition frequency shifts we were able to spectroscopically distinguish sites with different occupation numbers, and to directly image sites with occupation number n=1 to n=5 revealing the shell structure of the Mott Insulator phase. We use this spectroscopy to determine the onsite interaction and lifetime for individual shells.

  19. Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.

    2013-01-01

    Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega......Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found...

  20. A probabilistic model for secondary structure prediction from protein chemical shifts.

    Science.gov (United States)

    Mechelke, Martin; Habeck, Michael

    2013-06-01

    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

  1. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  2. Shifting the Starspot Paradigm through Imaging Magnetic Structures and Evolution

    Science.gov (United States)

    Roettenbacher, Rachael M.

    2016-08-01

    Magnetism is present in stars across all masses and evolutionary states. For cool stars with a convective outer envelope, stellar magnetic fields are generated through complex interactions between the convective layer and radiative core due to rotation. Magnetism in cool stars fuels stellar activity, in particular as starspots. Using starspots as a proxy, this work concentrates on imaging stellar magnetism. With state-of-the-art observations and imaging techniques, I investigate shifting the spot paradigm of localized starspots blemishing an otherwise bright surface (analogous to the solar photosphere) to a surface hosting a widespread network of magnetically-suppressed convection. This network is capable of affecting measurements of fundamental stellar parameters, such as radius and temperature, leading to inaccurate mass and age estimates. To accomplish this shift, I use precision Kepler data and a light-curve inversion algorithm for studies of stellar differential rotation and starspot evolution. Additionally, with long-baseline interferometric data collected with the Michigan Infrared Combiner (MIRC) at Georgia State University's Center for High Angular Resolution Astronomy (CHARA) Array, I target the bright, spotted, giant primary stars of close binary (RS CVn) systems. For these stars, I combine interferometric detections with radial velocity data to measure orbital and stellar parameters, which are used in concert with long-term photometric light curves to observe ellipsoidal variations, measure gravity darkening, and isolate the starspot signatures. In direct imaging using the interferometric data, I observe a spotted RS CVn star through an entire rotation period to detect canonical starspots, a polar starspot, and globally-suppressed convection. The regions of magnetically-suppressed convection cover a large fraction of the surface, potentially impacting estimates of stellar parameters. The combination of these efforts provides a start to a new era of

  3. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  4. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

  5. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    Science.gov (United States)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  6. Chemical shift assignments of two oleanane triterpenes from Euonymus hederaceus

    Institute of Scientific and Technical Information of China (English)

    HU He-jiao; WANG Kui-wu; WU Bin; SUN Cui-rong; PAN Yuan-jiang

    2005-01-01

    1H-NMR and 13C-NMR assignments of 12-oleanene-3,11-dione (compound 1) were completely described for the first time through conventional 1D NMR and 2D shift-correlated NMR experiments using 1H-1HCOSY, HMQC, HMBC techniques.Based on its NMR data, the assignments of 28-hydroxyolean-12-ene-3,11-dione (compound 2) were partially revised.

  7. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  8. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  9. Phase classification by mean shift clustering of multispectral materials images.

    Science.gov (United States)

    Martins, Diego Schmaedech; Josa, Victor M Galván; Castellano, Gustavo; da Costa, José A T Borges

    2013-10-01

    A mean-shift clustering (MSC) algorithm is introduced as a valuable alternative to perform materials phase classification from multispectral images. As opposed to other multivariate statistical techniques, such as factor analysis or principal component analysis (PCA), clustering techniques directly assign a class label to each pixel, so that their outputs are phase segmented images, i.e., there is no need for an additional segmentation algorithm. On the other hand, as compared to other clustering procedures and classification methods, such as segmentation by thresholding of multiple spectral components, MSC has the advantages of not requiring previous knowledge of the number of data clusters and not assuming any shape for these clusters, i.e., neither the number nor the composition of the phases must be previously known. This makes MSC a particularly useful tool for exploratory research, assisting phase identification of unknown samples. Visualization and interpretation of the results are also simplified, since the information content of the output image does not depend on the particular choice of the content of the color channels.We applied MSC to the analysis of two sets of X-ray maps acquired in scanning electron microscopes equipped with energy-dispersive detection systems. Our results indicate that MSC is capable of detecting additional phases, not clearly identified through PCA or multiple thresholding, with a very low empirical reject rate.

  10. PPM-One: a static protein structure based chemical shift predictor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  11. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

    2015-09-15

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

  12. Intraoperative image updating for brain shift following dural opening.

    Science.gov (United States)

    Fan, Xiaoyao; Roberts, David W; Schaewe, Timothy J; Ji, Songbai; Holton, Leslie H; Simon, David A; Paulsen, Keith D

    2016-09-09

    OBJECTIVE Preoperative magnetic resonance images (pMR) are typically coregistered to provide intraoperative navigation, the accuracy of which can be significantly compromised by brain deformation. In this study, the authors generated updated MR images (uMR) in the operating room (OR) to compensate for brain shift due to dural opening, and evaluated the accuracy and computational efficiency of the process. METHODS In 20 open cranial neurosurgical cases, a pair of intraoperative stereovision (iSV) images was acquired after dural opening to reconstruct a 3D profile of the exposed cortical surface. The iSV surface was registered with pMR to detect cortical displacements that were assimilated by a biomechanical model to estimate whole-brain nonrigid deformation and produce uMR in the OR. The uMR views were displayed on a commercial navigation system and compared side by side with the corresponding coregistered pMR. A tracked stylus was used to acquire coordinate locations of features on the cortical surface that served as independent positions for calculating target registration errors (TREs) for the coregistered uMR and pMR image volumes. RESULTS The uMR views were visually more accurate and well aligned with the iSV surface in terms of both geometry and texture compared with pMR where misalignment was evident. The average misfit between model estimates and measured displacements was 1.80 ± 0.35 mm, compared with the average initial misfit of 7.10 ± 2.78 mm between iSV and pMR, and the average TRE was 1.60 ± 0.43 mm across the 20 patients in the uMR image volume, compared with 7.31 ± 2.82 mm on average in the pMR cases. The iSV also proved to be accurate with an average error of 1.20 ± 0.37 mm. The overall computational time required to generate the uMR views was 7-8 minutes. CONCLUSIONS This study compensated for brain deformation caused by intraoperative dural opening using computational model-based assimilation of iSV cortical surface displacements. The u

  13. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  14. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

    2008-07-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  15. Magnetic couplings in the chemical shift of paramagnetic NMR.

    Science.gov (United States)

    Vaara, Juha; Rouf, Syed Awais; Mareš, Jiří

    2015-10-13

    We apply the Kurland-McGarvey (J. Magn. Reson. 1970, 2, 286) theory for the NMR shielding of paramagnetic molecules, particularly its special case limited to the ground-state multiplet characterized by zero-field splitting (ZFS) interaction of the form S·D·S. The correct formulation for this problem was recently presented by Soncini and Van den Heuvel (J. Chem. Phys. 2013, 138, 054113). With the effective electron spin quantum number S, the theory involves 2S+1 states, of which all but one are low-lying excited states, between which magnetic couplings take place by Zeeman and hyperfine interactions. We investigate these couplings as a function of temperature, focusing on both the high- and low-temperature behaviors. As has been seen in work by others, the full treatment of magnetic couplings is crucial for a realistic description of the temperature behavior of NMR shielding up to normal measurement temperatures. At high temperatures, depending on the magnitude of ZFS, the effect of magnetic couplings diminishes, and the Zeeman and hyperfine interactions become effectively averaged in the thermally occupied states of the multiplet. At still higher temperatures, the ZFS may be omitted altogether, and the shielding properties may be evaluated using a doublet-like formula, with all the 2S+1 states becoming effectively degenerate at the limit of vanishing magnetic field. We demonstrate these features using first-principles calculations of Ni(II), Co(II), Cr(II), and Cr(III) complexes, which have ZFS of different sizes and signs. A non-monotonic inverse temperature dependence of the hyperfine shift is predicted for axially symmetric integer-spin systems with a positive D parameter of ZFS. This is due to the magnetic coupling terms that are proportional to kT at low temperatures, canceling the Curie-type 1/kT prefactor of the hyperfine shielding in this case.

  16. Effect of shifting cultivation on soil physical and chemical properties in Bandarban hill district, Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah

    2013-01-01

    This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.

  17. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  18. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  19. Spatially resolved chemical reaction monitoring using magnetic resonance imaging.

    Science.gov (United States)

    Feindel, Kirk W

    2016-06-01

    Over the previous three decades, the use of MRI for studying dynamic physical and chemical processes of materials systems has grown significantly. This mini-review provides a brief introduction to relevant principles of MRI, including methods of spatial localization, factors contributing to image contrast, and chemical shift imaging. A few historical examples of (1) H MRI for reaction monitoring will be presented, followed by a review of recent research including (1) H MRI studies of gelation and biofilms, (1) H, (7) Li, and (11) B MRI studies of electrochemical systems, in vivo glucose metabolism monitored with (19) F MRI, and in situ temperature monitoring with (27) Al MRI. Copyright © 2015 John Wiley & Sons, Ltd.

  20. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Marin, Antoine; Malliavin, Therese E. [Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Theorique, CNRS UPR 9080 (France)], E-mail: therese.malliavin@ibpc.fr; Nicolas, Pierre; Delsuc, Marc-Andre [INRA - Domaine de Vilvert, Unite Mathematique Informatique et Genome (France)

    2004-09-15

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C{sub {beta}} and H{sub {beta}}, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H{sub {beta}}, C{sub {beta}}, C{sub {alpha}} and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.

  1. Subpixel shift with Fourier transform to achieve efficient and high-quality image interpolation

    Science.gov (United States)

    Chen, Qin-Sheng; Weinhous, Martin S.

    1999-05-01

    A new approach to image interpolation is proposed. Different from the conventional scheme, the interpolation of a digital image is achieved with a sub-unity coordinate shift technique. In the approach, the original image is first shifted by sub-unity distances matching the locations where the image values need to be restored. The original and the shifted images are then interspersed together, yielding an interpolated image. High quality sub-unity image shift which is crucial to the approach is accomplished by implementing the shift theorem of Fourier transformation. It is well known that under the Nyquist sampling criterion, the most accurate image interpolation can be achieved with the interpolating function (sinc function). A major drawback is its computation efficiency. The present approach can achieve an interpolation quality as good as that with the sinc function since the sub-unity shift in Fourier domain is equivalent to shifting the sinc function in spatial domain, while the efficiency, thanks to the fast Fourier transform, is very much improved. In comparison to the conventional interpolation techniques such as linear or cubic B-spline interpolation, the interpolation accuracy is significantly enhanced. In order to compensate for the under-sampling effects in the interpolation of 3D medical images owing to a larger inter-slice distance, proper window functions were recommended. The application of the approach to 2- and 3-D CT and MRI images produced satisfactory interpolation results.

  2. 磁共振梯度双回波化学位移成像定量诊断脂肪肝的临床应用%Clinical application of MR dual-echo chemical shift gradient-echo imaging in quantitative diagnosis of fatty liver

    Institute of Scientific and Technical Information of China (English)

    徐东风; 施蒋巍; 沈莉; 戴鸿志; 赵雪文; 刘利; 沈一易; 刘柯柯; 李曼

    2011-01-01

    目的 探讨磁共振梯度双回波化学位移成像定量诊断脂肪肝的临床应用.方法 20例弥漫性脂肪肝病例,同期行CT及磁共振梯度双回波化学位移成像,分别对肝VI段及IV段(Couinaud法)选取同一部位感兴趣区进行测量.正反相位信号强度差/正相位信号强度(SIP-SOP)/SIP及正反相位信号强度差SIP-SOP与肝/脾CT值比值(L/S)进行Spearman相关性分析及建立直线回归方程.根据L/S评价脂肪肝程度的标准,计算(SIP-SOP)/SIP、SIP-SOP评价脂肪肝程度的标准.结果 (SIP-SOP)/SIP、SIP-SOP与L/S的相关系数分别是r=-0.908及r=-0.844(P(SIP-SOP)/SIP≥0.159、中度0.444>(SIP-SOP)/SIP≥0.329,重度为(SIP-SOP)/SIP≥0.444.SIP-SOP诊断脂肪肝的标准为轻度:193.0>SIP-SOP≥3.2,中度:319.6>SIP-SOP≥193.0,重度:SIP-SOP≥319.6.结论 磁共振梯度双回波化学位移技术与CT定量诊断脂肪肝具有较好的相关性,可成为临床定量诊断脂肪肝的一种简单、有效方法.%Objective To evaluate the clinical application of MR dual-echo chemical shift gradient-echo imaging in quantitative diagnosis of fatty liver. Methods 20 patients with diffused fatty liver underwent CT and MR dual-echo chemical shift gradient-echo imaging simutaneously. The liver segments (Couinaud) VI and IV were selected separately at region of interest (ROI) in the same site to study the relationship between(Sip -Sop )/Sip ,Sip - Sop and L/S (Sip :signal intensity of in-phase, Sop :signal intensity of out-phase, L/S: CT attenuation ratio of liver to spleen) using Spearman correlation coefficient and linear regression equation. The diagnostic criteria of fatty liver using(Sip-Sop)/Sip and Sip - Sop were calculated refer to the criteria of L/S. Results (Sip - Sop)/Sip and Sip - Sop had significant relationship with L/S(r= -0. 908 and r= -0. 844 ,P(S,P - Sop )/S,P>0. 159,moderate level :0. 444>(S,P - Sop ) /S,P>0. 329 and severe level; (S,P-Sop )/SipS?0. 444 ,and the diagnostic

  3. Deuterium isotope effects on 13C chemical shifts of negatively charged NH.N systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Pietrzak, Mariusz; Grech, Eugeniusz

    2013-01-01

    Deuterium isotope effects on 13C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH+ as counter ion. These compounds represent both “static......” and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on 13C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative...

  4. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  5. Ontogenetic shift in response to prey-derived chemical cues in prairie rattlesnakes Crotalus viridis viridis

    Institute of Scientific and Technical Information of China (English)

    Anthony J.SAVIOLA; David CHISZAR; Stephen P.MACKESSY

    2012-01-01

    Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake.Crotalus viridis viridis (prairie rattlesnake) takes different prey at different life stages,and neonates typically prey on ectotherms,while adults feed almost entirely on small endotherms.We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed,and that this response shifts from one prey type to another as individuals age.To examine if an ontogenetic shift in response to chemical cues occurred,we recorded the rate of tongue flicking for 25 neonate,20 subadult,and 20 adult (average SVL=280.9,552,789.5 mm,respectively) wild-caught C.v.viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard,Sceloporus undulatus,and house gecko,Hemidactylusfrenatus),two endotherms (deer mouse,Peromyscus maniculatus and lab mouse,Mus musculus),and water controls were used.Neonates tongue flicked significantly more to chemical cues of their common prey,S.undulatus,than to all other chemical cues; however,the response to this lizard's chemical cues decreased in adult rattlesnakes.Subadults tongue flicked with a higher rate of tongue flicking to both S.undulatus and P.maniculatus than to all other treatments,and adults tongue flicked significantly more to P.maniculatus than to all other chemical cues.In addition,all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M.musculus and H.frenatus).This shift in chemosensory response correlated with the previously described ontogenetic shifts in C.v.viridis diet.Because many vipers show a similar ontogenetic shift in diet and venom composition,we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid snakes.

  6. Energy gap in tunneling spectroscopy: effect of the chemical potential shift

    Science.gov (United States)

    Fedotov, N. I.; Zaitsev-Zotov, S. V.

    2016-12-01

    We study the effect of a shift of the chemical potential level on the tunneling conductance spectra. In the systems with gapped energy spectra, significant chemical-potential dependent distortions of the differential tunneling conductance curves, dI/dV, arise in the gap region. An expression is derived for the correction of the dI/dV, which in a number of cases was found to be large. The sign of the correction depends on the chemical potential level position with respect to the gap. The correction of the dI/dV associated with the chemical potential shift has a nearly linear dependence on the tip-sample separation z and vanishes at z → 0.

  7. Reversible watermarking based on invariant image classification and dynamical error histogram shifting.

    Science.gov (United States)

    Pan, W; Coatrieux, G; Cuppens, N; Cuppens, F; Roux, Ch

    2011-01-01

    In this article, we present a novel reversible watermarking scheme. Its originality stands in identifying parts of the image that can be watermarked additively with the most adapted lossless modulation between: Pixel Histogram Shifting (PHS) or Dynamical Error Histogram Shifting (DEHS). This classification process makes use of a reference image derived from the image itself, a prediction of it, which has the property to be invariant to the watermark addition. In that way, watermark embedded and reader remain synchronized through this image of reference. DEHS is also an original contribution of this work. It shifts predict-errors between the image and its reference image taking care of the local specificities of the image, thus dynamically. Conducted experiments, on different medical image test sets issued from different modalities and some natural images, show that our method can insert more data with lower distortion than the most recent and efficient methods of the literature.

  8. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

  9. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  10. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” ...

  11. Can the current density map topology be extracted from the nucleus independent chemical shifts?

    NARCIS (Netherlands)

    Van Damme, Sofie; Acke, Guillaume; Havenith, Remco W. A.; Bultinck, Patrick

    2016-01-01

    Aromatic compounds are characterised by the presence of a ring current when in a magnetic field. As a consequence, current density maps are used to assess (the degree of) aromaticity of a compound. However, often a more discrete set of so-called Nucleus Independent Chemical Shift (NICS) values is us

  12. Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

    Science.gov (United States)

    Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

    2014-01-01

    A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…

  13. The statistical shift of the chemical potential causing anomalous conductivity in hydrogenated microcrystalline silicon

    NARCIS (Netherlands)

    Lof, R.W.; Schropp, R.E.I.

    2010-01-01

    The behavior of the electrical conductivity in hydrogenated microcrystalline silicon (μ c-Si:H) that is frequently observed is explained by considering the statistical shift in the chemical potential as a function of the crystalline fraction (Xc), the dangling bond density (N db), and the doping den

  14. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  15. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso).

  16. Acquiring multi-viewpoint image of 3D object for integral imaging using synthetic aperture phase-shifting digital holography

    Science.gov (United States)

    Jeong, Min-Ok; Kim, Nam; Park, Jae-Hyeung; Jeon, Seok-Hee; Gil, Sang-Keun

    2009-02-01

    We propose a method generating elemental images for the auto-stereoscopic three-dimensional display technique, integral imaging, using phase-shifting digital holography. Phase shifting digital holography is a way recording the digital hologram by changing phase of the reference beam and extracting the complex field of the object beam. Since all 3D information is captured by the phase-shifting digital holography, the elemental images for any specifications of the lens array can be generated from single phase-shifting digital holography. We expanded the viewing angle of the generated elemental image by using the synthetic aperture phase-shifting digital hologram. The principle of the proposed method is verified experimentally.

  17. Magnetic Shift of the Chemical Freeze-out and Electric Charge Fluctuations

    Science.gov (United States)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

    We discuss the effect of a strong magnetic field on the chemical freeze-out points in ultrarelativistic heavy-ion collisions. As a result of inverse magnetic catalysis or magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freeze-out. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced, especially at high baryon density. The charge conservation partially cancels the enhancement, but our calculation shows that the electric charge fluctuation could serve as a magnetometer. We find that the fluctuation exhibits a crossover behavior rapidly increased for e B ≳(0.4 GeV )2, while the charge chemical potential has smoother behavior with an increasing magnetic field.

  18. Novel Frame Shift and Integral Technique for Enhancing Low-Light-Level Moving Images

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A novel frame shift and integral technique for the enhancement of low light level moving image sequence is introduced. According to the technique, motion parameters of target are measured by algorithm based on difference processing. To obtain spatial relativity, images are shifted according to the motion parameters. As a result, the processing of integral and average can be applied to images that have been shifted. The technique of frame shift and integral that includes the algorithm of motion parameter determination is discussed, experiments with low light level moving image sequences are also described. The experiment results show the effectiveness and the robustness of the parameter determination algorithm, and the improvement in the signal-to-noise ratio (SNR) of low light level moving images.

  19. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  20. Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

    DEFF Research Database (Denmark)

    Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

    2006-01-01

    the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2......) to anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11...

  1. Mean shift texture surface detection based on WT and COM feature image selection

    Institute of Scientific and Technical Information of China (English)

    HAN Yan-fang; SHI Peng-fei

    2006-01-01

    Mean shift is a widely used clustering algorithm in image segmentation. However, the segmenting results are not so good as expected when dealing with the texture surface due to the influence of the textures. Therefore, an approach based on wavelet transform (WT), co-occurrence matrix (COM) and mean shift is proposed in this paper. First, WT and COM are employed to extract the optimal resolution approximation of the original image as feature image. Then, mean shift is successfully used to obtain better detection results. Finally, experiments are done to show this approach is effective.

  2. Nanoscale chemical imaging by photoinduced force microscopy

    Science.gov (United States)

    Nowak, Derek; Morrison, William; Wickramasinghe, H. Kumar; Jahng, Junghoon; Potma, Eric; Wan, Lei; Ruiz, Ricardo; Albrecht, Thomas R.; Schmidt, Kristin; Frommer, Jane; Sanders, Daniel P.; Park, Sung

    2016-01-01

    Correlating spatial chemical information with the morphology of closely packed nanostructures remains a challenge for the scientific community. For example, supramolecular self-assembly, which provides a powerful and low-cost way to create nanoscale patterns and engineered nanostructures, is not easily interrogated in real space via existing nondestructive techniques based on optics or electrons. A novel scanning probe technique called infrared photoinduced force microscopy (IR PiFM) directly measures the photoinduced polarizability of the sample in the near field by detecting the time-integrated force between the tip and the sample. By imaging at multiple IR wavelengths corresponding to absorption peaks of different chemical species, PiFM has demonstrated the ability to spatially map nm-scale patterns of the individual chemical components of two different types of self-assembled block copolymer films. With chemical-specific nanometer-scale imaging, PiFM provides a powerful new analytical method for deepening our understanding of nanomaterials. PMID:27051870

  3. An Image Encryption Scheme Based on Bit Circular Shift and Bi-directional Diffusion

    Directory of Open Access Journals (Sweden)

    Ruisong Ye

    2013-12-01

    Full Text Available A novel image encryption scheme based on chaotic system is proposed. The proposed encryption scheme utilizes one tent map to generate a pseudo-random sequence and then shift the bits of the expanding 0-1 image circularly so as to shuffle the image gray values. To make the encryption scheme resist differential attack efficiently, generalized Arnold maps and Bernoulli shift maps are applied to produce two pseudo-random gray value sequences and then diffuse the gray values bi-directionally. The bit circular shift process and diffusion processes greatly confuse the statistical nature between plain-images and cipher-images. Security analyses including key sensitivity analysis, key space analysis, statistical analysis, differential attack analysis and information entropy analysis are performed. All the experimental results demonstrate that the proposed image encryption scheme possesses large key space to frustrate brute-force attack efficiently and can resist statistical attack, differential attack, etc.

  4. Shifting the image of an object in electromagnetic fields by multilayered transformation media

    CERN Document Server

    Li, Wei; Wang, Wei; Sun, Zhigang; Fu, Zhengyi

    2009-01-01

    We propose an "image shifter" to hide an object and shift its image for a distance. By putting the object eccentrically into a magnifying device, it is visually shifted for a distance from its original place regardless of the direction of wave incident and observation but with lager size. A minifying shell is added outside the object to counteract the magnification effect and thus we can shift an object's image without any changing. The shifting distance can be adjusted by the scaling factor of the magnifying device. This image shifter provides a new way to conceal an object: hiding the object itself and simultaneously releasing a false target far away from it to confuse the detector.

  5. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  6. PACSY, a relational database management system for protein structure and chemical shift analysis.

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  7. Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

    Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  8. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

  9. Application of shift-and-add algorithms for imaging objects within biological media

    Science.gov (United States)

    Aizert, Avishai; Moshe, Tomer; Abookasis, David

    2017-01-01

    The Shift-and-Add (SAA) technique is a simple mathematical operation developed to reconstruct, at high spatial resolution, atmospherically degraded solar images obtained from stellar speckle interferometry systems. This method shifts and assembles individual degraded short-exposure images into a single average image with significantly improved contrast and detail. Since the inhomogeneous refractive indices of biological tissue causes light scattering similar to that induced by optical turbulence in the atmospheric layers, we assume that SAA methods can be successfully implemented to reconstruct the image of an object within a scattering biological medium. To test this hypothesis, five SAA algorithms were evaluated for reconstructing images acquired from multiple viewpoints. After successfully retrieving the hidden object's shape, quantitative image quality metrics were derived, enabling comparison of imaging error across a spectrum of layer thicknesses, demonstrating the relative efficacy of each SAA algorithm for biological imaging.

  10. Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift

    Indian Academy of Sciences (India)

    M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj

    2005-01-01

    Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.

  11. Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

    Energy Technology Data Exchange (ETDEWEB)

    Perazzolo, Chiara; Wist, Julien [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland); Loth, Karine; Poggi, Luisa [Ecole Normale Superieure, Departement de chimie, associe au CNRS (France); Homans, Steve [University of Leeds, School of Biochemistry and Microbiology (United Kingdom); Bodenhausen, Geoffrey [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland)], E-mail: Geoffrey.Bodenhausen@ens.fr

    2005-12-15

    Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{l_brace}C'N{r_brace} and DQC{l_brace}C'N{r_brace}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

  12. Substituent effects in the 13C NMR chemical shifts of alpha-mono-substituted acetonitriles.

    Science.gov (United States)

    Reis, Adriana K C A; Rittner, Roberto

    2007-03-01

    13C chemical shifts empirical calculations, through a very simple additivity relationship, for the alpha-methylene carbon of some alpha-mono-substituted acetonitriles, Y-CH(2)-CN (Y=H, F, Cl, Br, I, OMe, OEt, SMe, SEt, NMe(2), NEt(2), Me and Et), lead to similar, or even better, results in comparison to the reported values obtained through Quantum Mechanics methods. The observed deviations, for some substituents, are very similar for both approaches. This divergence between experimental and calculated, either empirically or theoretically, values are smaller than for the corresponding acetones, amides, acetic acids and methyl esters, which had been named non-additivity effects (or intramolecular interaction chemical shifts, ICS) and attributed to some orbital interactions. Here, these orbital interactions do not seem to be the main reason for the non-additivity effects in the empirical calculations, which must be due solely to the magnetic anisotropy of the heavy atom present in the substituent. These deviations, which were also observed in the theoretical calculations, were attributed in that case to the non-inclusion of relativistic effects and spin-orbit coupling in the Hamiltonian. Some divergence is also observed for the cyano carbon chemical shifts, probably due to the same reasons.

  13. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    OpenAIRE

    2015-01-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ([superscript 13]C–[superscript 13]C, [superscript 15]N–[superscript 13]C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 [superscript 13]C chemical shifts and >3 million chemical...

  14. Multifocus Image Fusion in Q-Shift DTCWT Domain Using Various Fusion Rules

    Directory of Open Access Journals (Sweden)

    Yingzhong Tian

    2016-01-01

    Full Text Available Multifocus image fusion is a process that integrates partially focused image sequence into a fused image which is focused everywhere, with multiple methods proposed in the past decades. The Dual Tree Complex Wavelet Transform (DTCWT is one of the most precise ones eliminating two main defects caused by the Discrete Wavelet Transform (DWT. Q-shift DTCWT was proposed afterwards to simplify the construction of filters in DTCWT, producing better fusion effects. A different image fusion strategy based on Q-shift DTCWT is presented in this work. According to the strategy, firstly, each image is decomposed into low and high frequency coefficients, which are, respectively, fused by using different rules, and then various fusion rules are innovatively combined in Q-shift DTCWT, such as the Neighborhood Variant Maximum Selectivity (NVMS and the Sum Modified Laplacian (SML. Finally, the fused coefficients could be well extracted from the source images and reconstructed to produce one fully focused image. This strategy is verified visually and quantitatively with several existing fusion methods based on a plenty of experiments and yields good results both on standard images and on microscopic images. Hence, we can draw the conclusion that the rule of NVMS is better than others after Q-shift DTCWT.

  15. The remote sensing image segmentation mean shift algorithm parallel processing based on MapReduce

    Science.gov (United States)

    Chen, Xi; Zhou, Liqing

    2015-12-01

    With the development of satellite remote sensing technology and the remote sensing image data, traditional remote sensing image segmentation technology cannot meet the massive remote sensing image processing and storage requirements. This article put cloud computing and parallel computing technology in remote sensing image segmentation process, and build a cheap and efficient computer cluster system that uses parallel processing to achieve MeanShift algorithm of remote sensing image segmentation based on the MapReduce model, not only to ensure the quality of remote sensing image segmentation, improved split speed, and better meet the real-time requirements. The remote sensing image segmentation MeanShift algorithm parallel processing algorithm based on MapReduce shows certain significance and a realization of value.

  16. Numerical estimation of the total phase shift in complex spectral OCT in vivo imaging

    Science.gov (United States)

    Cyganek, Marta; Wojtkowski, Maciej; Targowski, Piotr; Kowalczyk, Andrzej

    2004-07-01

    Complex Spectral Optical Tomography (CSOCT) in comparison to ordinary SOCT produces images free of parasitic mirror terms which results in double extension of the measurement range. This technique, however, requires the exact knowledge about the values of the introduced phase shifts in consecutive measurements. Involuntary object movements, which shift the phase from one measurement to another are always present in in vivo experiments. This introduces residual ghosts in cross-sectional images. Here we present a new method of data analysis, which allows determining the real phase shifts introduced during the measurement, and which helps to reduce the ghost effect. Two-dimensional cross-sectional in vivo images of human eye and skin obtained with the aid of this improved complex spectral OCT technique are shown. The method is free of polychromatic phase error originating from the wavelength dependence of the phase shift introduced by the reference mirror translation.

  17. Temperature dependence of contact and dipolar NMR chemical shifts in paramagnetic molecules.

    Science.gov (United States)

    Martin, Bob; Autschbach, Jochen

    2015-02-07

    Using a recently proposed equation for NMR nuclear magnetic shielding for molecules with unpaired electrons [A. Soncini and W. Van den Heuvel, J. Chem. Phys. 138, 021103 (2013)], equations for the temperature (T) dependent isotropic shielding for multiplets with an effective spin S equal to 1/2, 1, 3/2, 2, and 5/2 in terms of electron paramagnetic resonance spin Hamiltonian parameters are derived and then expanded in powers of 1/T. One simplifying assumption used is that a matrix derived from the zero-field splitting (ZFS) tensor and the Zeeman coupling matrix (g-tensor) share the same principal axis system. The influence of the rhombic ZFS parameter E is only investigated for S = 1. Expressions for paramagnetic contact shielding (from the isotropic part of the hyperfine coupling matrix) and pseudo-contact or dipolar shielding (from the anisotropic part of the hyperfine coupling matrix) are considered separately. The leading order is always 1/T. A temperature dependence of the contact shielding as 1/T and of the dipolar shielding as 1/T(2), which is sometimes assumed in the assignment of paramagnetic chemical shifts, is shown to arise only if S ≥ 1 and zero-field splitting is appreciable, and only if the Zeeman coupling matrix is nearly isotropic (Δg = 0). In such situations, an assignment of contact versus dipolar shifts may be possible based only on linear and quadratic fits of measured variable-temperature chemical shifts versus 1/T. Numerical data are provided for nickelocene (S = 1). Even under the assumption of Δg = 0, a different leading order of contact and dipolar shifts in powers of 1/T is not obtained for S = 3/2. When Δg is not very small, dipolar and contact shifts both depend in leading order in 1/T in all cases, with sizable contributions in order 1/T(n) with n = 2 and higher.

  18. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  19. 化学位移 MRI 测量2型糖尿病患者胰腺脂肪含量的临床研究%Study of pancreatic steatosis in patients with type 2 diabetes by chemical shift magnetic resonance imaging

    Institute of Scientific and Technical Information of China (English)

    柴军; 刘朋; 洪旭; 尹洁; 于恒池; 苏天昊; 张洁; 史凯宁; 靳二虎

    2015-01-01

    Objective To investigate the fat content and distribution of the pancreas,and to explore its relation with hepatic fat content by chemical shift MRI in patients with newly - diagnosed type 2 diabetes. Methods 70 patients with newly - diagnosed type 2 diabetes were recrui-ted in this study. Fat content in the pancreatic head,body,tail and the liver was respectively measured with the technique of double - echo chemi-cal shift gradient - echo magnetic resonance imaging. The fat fraction in the pancreatic head,body and tail was compared. Its relation with hepatic fat fraction was analyzed. Results The fat fraction in the pancreatic head,body and tail was 5. 59% ± 4. 70% ,4. 80% ± 3. 75% and 4. 88% ± 3. 86% ,respectively,and there was no statistical difference among them( F = 1. 761,P ﹥ 0. 05). The mean value of fat fraction in the pancreas and the liver was 5. 15% ± 3. 75% and 9. 88% ± 3. 19% ,respectively. They were not correlated each other( r = 0. 053,P ﹥ 0. 05). Conclu-sion Fat content in the head,body and tail of the pancreas was basically even. And the pancreatic and hepatic fat content was not correlated in patients with newly - diagnosed type 2 diabetes.%目的:采用化学位移 MRI 研究初诊2型糖尿病患者的胰腺脂肪含量及分布特点,并探讨胰腺与肝脏脂肪含量的相关性。方法征集初诊的2型糖尿病患者70例,采用化学位移双回波 MRI 技术分别测量胰腺头部、体部、尾部及肝脏的脂肪含量,比较胰腺头部、体部、尾部的脂肪含量差异,分析胰腺脂肪含量与肝脏脂肪含量的相关性。结果本组患者胰腺头部、体部、尾部的脂肪分数分别为5.59%±4.70%、4.80%±3.75%、4.88%±3.86%,三个区域的脂肪含量没有统计学差异( F =1.761,P ﹥0.05)。胰腺的平均脂肪分数为5.15%±3.75%,肝脏为9.88%±3.19%,胰腺的脂肪含量与肝脏的脂肪含量没有相关性( r =0.053,P ﹥0.05

  20. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2016-02-15

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

  1. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.

    Science.gov (United States)

    Fritzsching, Keith J; Hong, Mei; Schmidt-Rohr, Klaus

    2016-02-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided

  2. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    Science.gov (United States)

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  3. Shortcut in DIC error assessment induced by image interpolation used for subpixel shifting

    Science.gov (United States)

    Bornert, Michel; Doumalin, Pascal; Dupré, Jean-Christophe; Poilane, Christophe; Robert, Laurent; Toussaint, Evelyne; Wattrisse, Bertrand

    2017-04-01

    In order to characterize errors of Digital Image Correlation (DIC) algorithms, sets of virtual images are often generated from a reference image by in-plane sub-pixel translations. This leads to the determination of the well-known S-shaped bias error curves and their corresponding random error curves. As images are usually shifted by using interpolation schemes similar to those used in DIC algorithms, the question of the possible bias in the quantification of measurement uncertainties of DIC softwares is raised and constitutes the main problematic of this paper. In this collaborative work, synthetic numerically shifted images are built from two methods: one based on interpolations of the reference image and the other based on the transformation of an analytic texture function. Images are analyzed using an in-house subset-based DIC software and results are compared and discussed. The effect of image noise is also highlighted. The main result is that the a priori choices to numerically shift the reference image modify DIC results and may lead to wrong conclusions in terms of DIC error assessment.

  4. Using ultrasound CBE imaging without echo shift compensation for temperature estimation.

    Science.gov (United States)

    Tsui, Po-Hsiang; Chien, Yu-Ting; Liu, Hao-Li; Shu, Yu-Chen; Chen, Wen-Shiang

    2012-09-01

    Clinical trials have demonstrated that hyperthermia improves cancer treatments. Previous studies developed ultrasound temperature imaging methods, based on the changes in backscattered energy (CBE), to monitor temperature variations during hyperthermia. Echo shift, induced by increasing temperature, contaminates the CBE image, and its tracking and compensation should normally ensure that estimations of CBE at each pixel are correct. To obtain a simplified algorithm that would allow real-time computation of CBE images, this study evaluated the usefulness of CBE imaging without echo shift compensation in detecting distributions in temperature. Experiments on phantoms, using different scatterer concentrations, and porcine livers were conducted to acquire raw backscattered data at temperatures ranging from 37°C to 45°C. Tissue samples of pork tenderloin were ablated in vitro by microwave irradiation to evaluate the feasibility of using the CBE image without compensation to monitor tissue ablation. CBE image construction was based on a ratio map obtained from the envelope image divided by the reference envelope image at 37°C. The experimental results demonstrated that the CBE image obtained without echo shift compensation has the ability to estimate temperature variations induced during uniform heating or tissue ablation. The magnitude of the CBE as a function of temperature obtained without compensation is stronger than that with compensation, implying that the CBE image without compensation has a better sensitivity to detect temperature. These findings suggest that echo shift tracking and compensation may be unnecessary in practice, thus simplifying the algorithm required to implement real-time CBE imaging.

  5. Complete (1)H and (13)C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program casper.

    Science.gov (United States)

    Roslund, Mattias U; Säwén, Elin; Landström, Jens; Rönnols, Jerk; Jonsson, K Hanna M; Lundborg, Magnus; Svensson, Mona V; Widmalm, Göran

    2011-08-16

    The computer program casper uses (1)H and (13)C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the (1)H and (13)C, as well as (31)P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 (1)H and (13)C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D (1)H,(13)C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t(1) incremented (1)H,(13)C-HSQC experiment and a 1D (1)H,(1)H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3Hz apart. The (1)H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental (1)H and (13)C NMR chemical shifts.

  6. Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...

  7. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents

    Directory of Open Access Journals (Sweden)

    Benjamin Görling

    2016-09-01

    Full Text Available Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored.

  8. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

    Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored. PMID:27598217

  9. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

    Science.gov (United States)

    Grodzka, P.; Facemire, B.

    1977-01-01

    Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

  10. HI Imaging the Low Red-shift Cosmic Web

    CERN Document Server

    Braun, R

    2004-01-01

    Only in recent years has the realization emerged that galaxies do not dominate the universal baryon budget but are merely the brightest pearls of an underlying Cosmic Web. Although the gas in these inter-galactic filaments is moderately to highly ionized, QSO absorption lines have shown that the surface area increases dramatically in going down to lower HI column densities. The first image of the Cosmic Web in HI emission has just been made of the Local Group filament connecting M31 and M33. The corresponding HI distribution function is in very good agreement with that of the QSO absorption lines, confirming the 30-fold increase in surface area expected between 10^19 cm^-2 and 10^17 cm^-2. The critical observational challenge is crossing the "HI desert", the range of log(N_HI) from about 19.5 down to 18, over which photo-ionization by the intergalactic radiation field produces an exponential decline in the neutral fraction from essentially unity down to a few percent. Nature is kinder again to the HI observer...

  11. Imaging the Low Red-shift Cosmic Web

    CERN Document Server

    Braun, R; Braun, Robert; Thilker, David

    2005-01-01

    The first image of a Cosmic Web, Lyman Limit System has just been made in HI emission within the Local Group filament connecting M31 and M33. The corresponding HI distribution function is in very good agreement with that of the QSO absorption lines, confirming the 30-fold increase in surface area expected between 10^19 cm^-2 and 10^17 cm^-2. The critical observational challenge is crossing the ``HI desert'', the range of log(N_HI) from about 19.5 down to 18, over which photo-ionization by the intergalactic radiation field produces an exponential decline in the neutral fraction from essentially unity down to a few percent. Nature is kinder again to the HI observer below log(N_HI) = 18, where the neutral fraction decreases only very slowly with log(N_HI). Average spectra of the M31/M33 filament suggest a kinetic temperature of 2x10^5 K for the parent ion population, consistent with significant shock-heating. The brightest knot within the filament, with only a 2x10^4 K apparent temperature, is suggestive of loca...

  12. Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.

    Science.gov (United States)

    Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F

    2016-10-01

    Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.

  13. A proposed increase in retinal field-of-view may lead to spatial shifts in images

    CERN Document Server

    Doshi, Rupak

    2010-01-01

    Visual information determines majority of our spatial behavior. The eye projects a 2-D image of the world on the retina. We demonstrate that when a monocular-like imaging system operates entirely with optically dense fluids, an increase in field-of-view (FOV) is observed compared to an experimental condition, where the ocular medium is optically neutral. Resulting spatial shifts in the retinal image towards the fovea complement the photoreceptor distribution pattern, incidentally revealing a new role for ocular fluids in the image space. Possible effects on the perceived egocentric object location are discussed.

  14. X-ray Bragg magnifier microscope as a linear shift invariant imaging system: image formation and phase retrieval.

    Science.gov (United States)

    Vagovič, P; Svéda, L; Cecilia, A; Hamann, E; Pelliccia, D; Gimenez, E N; Korytár, D; Pavlov, K M; Zápražný, Z; Zuber, M; Koenig, T; Olbinado, M; Yashiro, W; Momose, A; Fiederle, M; Baumbach, T

    2014-09-01

    We present the theoretical description of the image formation with the in-line germanium Bragg Magnifier Microscope (BMM) and the first successful phase retrieval of X-ray holograms recorded with this imaging system. The conditions under which the BMM acts as a linear shift invariant system are theoretically explained and supported by the experiment. Such an approach simplifies the mathematical treatment of the image formation and reconstruction as complicated propagation of the wavefront onto inclined planes can be avoided. Quantitative phase retrieval is demonstrated using a test sample and a proof of concept phase imaging of a spider leg is also presented.

  15. Non-iterative coherent diffractive imaging using a phase-shifting reference frame

    Energy Technology Data Exchange (ETDEWEB)

    Enders, B; Giewekemeyer, K; Salditt, T [Institut fuer Roentgenphysik, Universitaet Goettingen, Friedrich-Hund-Platz 1, 37077 Goettingen (Germany); Kurz, T [III. Physikalisches Institut, Universitaet Goettingen, Friedrich-Hund-Platz 1, 37077 Goettingen (Germany); Podorov, S [School of Physics, Monash University, Victoria 3800 (Australia)], E-mail: tsaldit@gwdg.de

    2009-04-15

    Lensless imaging is a high potential and currently intensely targeted research goal, in view of those fields of applications for which aberration-free high-resolution lenses are not available, for example for x-ray imaging. A recently proposed (direct inversion) variant of lensless imaging combines the advantages of two classical routes toward lensless imaging, the high-resolution characteristics of iterative object reconstruction, and the direct and deterministic nature of holographic reconstruction. Here, we use a simple standard optical setup using visible wavelength, a lithographic test object and a phase-shifting reference object to demonstrate the approach. Importantly, we show that a phase-shifting reference object, instead of the absorption mask proposed earlier, is sufficient for object reconstruction. This is relevant in view of the much easier implementation in future x-ray applications.

  16. Optical image hiding based on dual-channel simultaneous phase-shifting interferometry and compressive sensing

    Science.gov (United States)

    Li, Jiaosheng; Zhong, Liyun; Zhang, Qinnan; Zhou, Yunfei; Xiong, Jiaxiang; Tian, Jindong; Lu, Xiaoxu

    2017-01-01

    We propose an optical image hiding method based on dual-channel simultaneous phase-shifting interferometry (DCSPSI) and compressive sensing (CS) in all-optical domain. In the DCSPSI architecture, a secret image is firstly embedded in the host image without destroying the original host's form, and a pair of interferograms with the phase shifts of π/2 is simultaneously generated by the polarization components and captured by two CCDs. Then, the holograms are further compressed sampling to the less data by CS. The proposed strategy will provide a useful solution for the real-time optical image security transmission and largely reducing data volume of interferogram. The experimental result demonstrates the validity and feasibility of the proposed method.

  17. Rapid and robust medical image elastic registration using mean shift algorithm

    Institute of Scientific and Technical Information of China (English)

    Xuan Yang; Jihong Pei

    2008-01-01

    In landmark-based image registration, estimating the landmark correspondence plays an important role. In this letter, a novel landmark correspondence estimation technique using mean shift algorithm is proposed. Image corner points are detected as landmarks and mean shift iterations are adopted to find the most probable corresponding point positions in two images. Mutual information between intensity of two local regions is computed to eliminate mis-matching points. Multi-level estimation (MLE) technique is proposed to improve the stability of corresponding estimation. Experiments show that the precision in location of correspondence landmarks is exact. The proposed technique is shown to be feasible and rapid in the experiments of various mono-modal medical images.

  18. Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model%化学位移成像及MR波谱分析在体外水脂模型中对脂肪定量的研究

    Institute of Scientific and Technical Information of China (English)

    彭新桂; 居胜红; 方芳; 滕皋军

    2010-01-01

    Objective To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10% . The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test The correlation between the two methods was also analyzed. The concentration of saturated fatty acids ( FS), unsaturated fatty acids (FU) and the polyunsaturation degree (PUD) were calculated by using MRS. Results The fat concentration was (48.0 ±1.0)%, (57.0 ±0.5)%, (67.3±0.6)%, (77.3 ±0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3 ±0.6)%, (16.3 ±0.7)%, (27.7 ±0.6)%, (36.0 ±1.0)%, (43.5±0. 6)% and (56. 5 ±1. 0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P < 0.05 ), and had high linear correlation with the real concentration in phantoms ( CSI: r = 0. 998, MRS: r = 0.996, P < 0.01 ) . There was also a linear correlation between two methods (r = 0. 992, P < 0. 01 ) but no statistically significant difference ( pairedsamples t test, t = -0. 125 ,P = 0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15and 0. 85, the PUD was 0. 0325, respectively, and highly consistent with these in phantoms. Conclusion Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR.%目的 评价化学位移成像(chemical shift imaging,CSI)和MRS两种方法在脂肪研究中的作用,为进一步活体实验提供定量标准.方法 在7.0 T MR成像仪上运用CSI和MRS方法对体外水脂模型进行水脂定量分析.体外水脂模型的脂肪含量从0~100%平均分成11个组,各组间浓度相差10%,分别应用水、脂肪选择性CSI和1H-MRS对体外水脂模型进行图像和波谱数据采集,对2种方法所得

  19. Ultrasonic array imaging of multilayer structures using full matrix capture and extended phase shift migration

    Science.gov (United States)

    Wu, Haiteng; Chen, Jian; Yang, Keji; Hu, Xuxiao

    2016-04-01

    Multilayer structures have been widely used in industrial fields, and non-destructive evaluation of these structures is of great importance to assure their quality and performance. Recently, ultrasonic array imaging using full matrix capture, e.g. the total focusing method (TFM), has been shown to increase sensitivity to small defects and improve imaging resolution in homogeneous media. However, it cannot be applied to multilayer structures directly, due to the sound velocity variation in different layers and because refraction occurs at layer interfaces, which gives rise to difficulties in determining the propagation path and time. To overcome these problems, an extended phase shift migration (EPSM) is proposed for the full matrix imaging of multilayer structures in this paper. Based on the theory of phase shift migration for monostatic pulse-echo imaging, full matrix imaging using EPSM is derived by extrapolating the wavefields in both transmission and reception, and extended to the multilayer case. The performance of the proposed algorithm is evaluated by full matrix imaging of a two-layer structure with side-drilled holes conducted both in the simulation and the experiment. The results verify that the proposed algorithm is capable of full matrix imaging of a layered structure with a high resolution and signal-to-noise ratio. For comparison, full matrix imaging using the TFM with root-mean-squared velocity is also performed, and the results demonstrate that the proposed algorithm is superior to the TFM in improving both the image quality and resolution.

  20. Semi-automatic breast ultrasound image segmentation based on mean shift and graph cuts.

    Science.gov (United States)

    Zhou, Zhuhuang; Wu, Weiwei; Wu, Shuicai; Tsui, Po-Hsiang; Lin, Chung-Chih; Zhang, Ling; Wang, Tianfu

    2014-10-01

    Computerized tumor segmentation on breast ultrasound (BUS) images remains a challenging task. In this paper, we proposed a new method for semi-automatic tumor segmentation on BUS images using Gaussian filtering, histogram equalization, mean shift, and graph cuts. The only interaction required was to select two diagonal points to determine a region of interest (ROI) on an input image. The ROI image was shrunken by a factor of 2 using bicubic interpolation to reduce computation time. The shrunken image was smoothed by a Gaussian filter and then contrast-enhanced by histogram equalization. Next, the enhanced image was filtered by pyramid mean shift to improve homogeneity. The object and background seeds for graph cuts were automatically generated on the filtered image. Using these seeds, the filtered image was then segmented by graph cuts into a binary image containing the object and background. Finally, the binary image was expanded by a factor of 2 using bicubic interpolation, and the expanded image was processed by morphological opening and closing to refine the tumor contour. The method was implemented with OpenCV 2.4.3 and Visual Studio 2010 and tested for 38 BUS images with benign tumors and 31 BUS images with malignant tumors from different ultrasound scanners. Experimental results showed that our method had a true positive rate (TP) of 91.7%, a false positive (FP) rate of 11.9%, and a similarity (SI) rate of 85.6%. The mean run time on Intel Core 2.66 GHz CPU and 4 GB RAM was 0.49 ± 0.36 s. The experimental results indicate that the proposed method may be useful in BUS image segmentation.

  1. 125Te NMR chemical-shift trends in PbTe–GeTe and PbTe–SnTe alloys

    Energy Technology Data Exchange (ETDEWEB)

    Njegic, Bosiljka [Ames Laboratory; Levin, Evgenii M. [Ames Laboratory; Schmidt-Rohr, Klaus [Ames Laboratory

    2013-10-08

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in 125Te NMR chemical shift due to bonding to dopant or “solute” atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the 125Te NMR chemical shifts in PbTe-based alloys, Pb1-xGexTe and Pb1-xSnxTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS 125Te NMR spectra. A simple linear trend in chemical shifts with the number of Pb neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the 125Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.

  2. 125Te NMR chemical-shift trends in PbTe-GeTe and PbTe-SnTe alloys.

    Science.gov (United States)

    Njegic, B; Levin, E M; Schmidt-Rohr, K

    2013-01-01

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in (125)Te NMR chemical shift due to bonding to dopant or "solute" atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the (125)Te NMR chemical shifts in PbTe-based alloys, Pb1-xGexTe and Pb1-xSnxTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS (125)Te NMR spectra. A simple linear trend in chemical shifts with the number of Pb neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the (125)Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.

  3. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Science.gov (United States)

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  4. Ultrasonic imaging of seismic physical models using a phase-shifted fiber Bragg grating.

    Science.gov (United States)

    Guo, Jingjing; Xue, Shigui; Zhao, Qun; Yang, Changxi

    2014-08-11

    We report what is to our knowledge the first ultrasonic imaging of seismic physical models by using a phase-shifted fiber Bragg grating (PS-FBG). Seismic models, which consist of multiple layer structures, were immersed in water. Piezoelectric (PZT) transducer was used to generate ultrasonic waves and a PS-FBG as a receiver. Two-dimensional (2D) ultrasonic images were reconstructed by scanning the PS-FBG with a high-precision position scanning device. In order to suppress the low-frequency drift of the Bragg wavelength during scanning, a tight wavelength tracking method was employed to lock the laser to the PS-FBG resonance in its reflection bandgap. The ultrasonic images captured by the PS-FBG have been compared with the images obtained by the geophysical imaging system, Sinopec, demonstrating the feasibility of our PS-FBG based imaging system in seismic modeling studies.

  5. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    Science.gov (United States)

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  6. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  7. Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with 1H detection

    Science.gov (United States)

    Bellstedt, Peter; Ihle, Yvonne; Wiedemann, Christoph; Kirschstein, Anika; Herbst, Christian; Görlach, Matthias; Ramachandran, Ramadurai

    2014-03-01

    RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential 1H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential 1H data acquisition procedure in the study of RNA is also demonstrated here.

  8. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...

  9. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    CERN Document Server

    Sweany, M; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, M

    2011-01-01

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 $\\pm$ 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 $\\pm$ 0.03 for Carbostyril-124, and 1.20 $\\pm$ 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modele...

  10. Double-image encryption based on joint transform correlation and phase-shifting interferometry

    Institute of Scientific and Technical Information of China (English)

    Lina Shen; Jun Li; Hongsen Chang

    2007-01-01

    An image encryption method combining the joint transform correlator (JTC) architecture with phaseshifting interferometry to realize double random-phase encoding is proposed. The encrypted field and the decrypting key are registered as holograms by phase-shifting interferometry. This method can encrypt two images simultaneously to improve the encryption efficiency of the methods based on JTC architecture, and eliminate the system alignment constraint of the methods based on Mach-Zehnder interferometer (MZI)architecture. Its feasibility and validity are verified by computer simulations. Moreover, image encryption and decryption can be achieved at high speed optically or digitally. The encrypted data are suitable for Internet transmission.

  11. Multispectral image segmentation using parallel mean shift algorithm and CUDA technology

    Science.gov (United States)

    Zghidi, Hafedh; Walczak, Maksym; Świtoński, Adam

    2016-06-01

    We present a parallel mean shift algorithm running on CUDA and its possible application in segmentation of multispectral images. The aim of this paper is to present a method of analyzing highly noised multispectral images of various objects, so that important features are enhanced and easier to identify. The algorithm finds applications in analysis of multispectral images of eyes so that certain features visible only in specific wavelengths are made clearly visible despite high level of noise, for which processing time is very long.

  12. Aberrations in shift-invariant linear optical imaging systems using partially coherent fields

    CERN Document Server

    Beltran, Mario A; Paganin, David M

    2014-01-01

    Here the role and influence of aberrations in optical imaging systems employing partially coherent complex scalar fields is studied. Imaging systems require aberrations to yield contrast in the output image. For linear shift-invariant optical systems, we develop an expression for the output cross-spectral density under the space-frequency formulation of statistically stationary partially coherentfields. We also develop expressions for the output cross{spectral density and associated spectral density for weak-phase, weak-phase-amplitude, and single-material objects in one transverse spatial dimension.

  13. Ultrasound Image Segmentation based on the Mean-Shift and Graph Cuts Theory

    Directory of Open Access Journals (Sweden)

    Ting Yun

    2013-03-01

    Full Text Available This study addressed the issue of vascular ultrasound image segmentation and proposed a novel ultrasonic vascular location and detection method. We contributed in several aspects: Firstly using mean-shift segmentation algorithm to obtain the initial segmentation results of vascular images; Secondly new data item and smooth item of the graph cut energy function was constructed based on the MRF mode, then we put forward swap and α expansion ideas to optimize segmentation results, consequently accurately located the vessel wall and lumen in vascular images. Finally comparison with experts manually tagging results and Appling edge correlation coefficients and variance to verify the validity of our algorithm, experimental results show that our algorithm can efficiently combines the advantages of mean-shift and graph-cut algorithm and achieve better segmentation results.

  14. Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR

    Science.gov (United States)

    Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten; Vosegaard, Thomas; Nielsen, Niels Chr.; Nielsen, Anders B.

    2016-09-01

    We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization (RESPIRATIONCP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the RESPIRATIONCP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous 15N → 13CO and 15N → 13Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.

  15. 50 years anniversary of the discovery of the core level chemical shifts. The early years of photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mårtensson, Nils [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden); Sokolowski, Evelyn [Tvär-Ramsdal 1, 611 99 Tystberga (Sweden); Svensson, Svante, E-mail: Svante.Svensson@fysik.uu.se [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden)

    2014-03-01

    Highlights: • 50 years since the discovery of t the core level chemical shift. • The pioneering years of ESCA. • A critical review of the first core electron chemical shift results. - Abstract: The pioneering years of photoelectron spectroscopy in Uppsala are discussed, especially the work leading to the discovery of the core level chemical shifts. At a very early stage of the project, the pioneering group observed what they described as evidence for chemical shifts in the core level binding energies. However, it can now be seen that the initial observations to a large extent was due to charging of the samples. It is interesting to note that the decisive experiment was realized, not as a result of a systematic study, but was obtained with a large element of serendipity. Only when a chemical binding energy shift was observed between two S2p electron lines in the same molecule, the results were accepted internationally, and the fascinating expansion of modern core level photoelectron spectroscopy could start.

  16. [Application possibilities of chemical imaging in pharmaceutical technology].

    Science.gov (United States)

    Vajna, Balázs; Nagy, Zsombor; Patyi, Gergo; Zsigmond, Zsolt; Antal, István; Marosi, György

    2009-01-01

    Chemical imaging is a novel analytical method that simultaneously delivers spatial, chemical, structural, and functional information on the dosage forms. Both infrared and Raman spectroscopic imaging may serve as useful nondestructive analytical techniques in the pharmaceutical product development and quality control. Most important application possibilities are reviewed and some studies demonstrate the advantages of the structure exploration. Raman imaging is suitable to understand and control the quality attributes of different dosage forms.

  17. Nanohybrids Near-Field Optical Microscopy: From Image Shift to Biosensor Application

    Directory of Open Access Journals (Sweden)

    Nayla El-Kork

    2016-01-01

    Full Text Available Near-Field Optical Microscopy is a valuable tool for the optical and topographic study of objects at a nanometric scale. Nanoparticles constitute important candidates for such type of investigations, as they bear an important weight for medical, biomedical, and biosensing applications. One, however, has to be careful as artifacts can be easily reproduced. In this study, we examined hybrid nanoparticles (or nanohybrids in the near-field, while in solution and attached to gold nanoplots. We found out that they can be used for wavelength modulable near-field biosensors within conditions of artifact free imaging. In detail, we refer to the use of topographic/optical image shift and the imaging of Local Surface Plasmon hot spots to validate the genuineness of the obtained images. In summary, this study demonstrates a new way of using simple easily achievable comparative methods to prove the authenticity of near-field images and presents nanohybrid biosensors as an application.

  18. Quantitative analysis of chemical shift imaging in the differentiation of renal angiomyolipoma with minimal fat from clear cell renal cell carcinoma%化学位移成像定量分析鉴别乏脂肪肾血管平滑肌脂肪瘤与肾透明细胞癌

    Institute of Scientific and Technical Information of China (English)

    孙 军; 邢 伟; 陈 杰; 陈铜兵; 曹赟杰; 邢士军; 沈 楠

    2013-01-01

    Objective To evaluate the value of quantitative analysis of chemical shift imaging(CSI) in differential diagnosis of renal angiomyolipoma (RAML) with minimal fat from renal clear cell carcinoma (RCCC) at 3. 0 T MR. Methods The CSI images of 17 cases with pathologically proved RAML with minimal fat (Group 1) and 32 cases with pathologically confirmed RCCC (Group 2) were analyzed retrospectively. Signal intensity of tumor, spleen, and erector spinac were measured on in-phase and out-phase images, respectively. Three parameters, including signal intensity index(SII), tumor to spleen ratio(TSR) and tumor to muscle ratio (TMR) were calculated. These parameters were compared between two groups by Student's it-test respectively. The ROC curves were performed to evaluate the sensitivity and specificity of these parameters in differentiation between two groups respectively. Results There were significant differences in SII, TSR and TMR between two groups respectively (t= 12. 577, -5. 297, -05. 402, P = 0. 000). The area under curve(AUC) of ROC for SII was 0. 987, and the sensitivity and specificity were 94. 1 % and 93. 7% respectively when the optimal threshold was 18. 23%. The AUC for TSR was 0. 885, and the sensitivity and specificity were 88. 2% and 81. 2% respectively when the optimal threshold was - 12. 58%. The AUC for TMR was 0. 879, and the sensitivity and specificity were 82.4% and 78. 1% respectively when the optimal threshold was- 11. 62%. Conclusion The quantitative analysis of CSI plays an important role in differential diagnosis of RAML with minimal fat from RCCC.%目的 评价3.0T磁共振化学位移成像(CSI)定量分析在乏脂肪肾血管平滑肌脂肪瘤(RAML)与肾透明细胞癌(RCCC)鉴别诊断中的价值.方法 回顾性分析经病理证实的17例乏脂肪RAML与32例RCCC的CSI图像,测量同、反相位图像上肿瘤及参照组织脾脏、竖脊肌的信号强度,计算肿瘤信号强度指数(SII)、肿瘤脾脏信号比(TSR

  19. Chemical shift tensor determination using magnetically oriented microcrystal array (MOMA): 13C solid-state CP NMR without MAS

    Science.gov (United States)

    Kusumi, R.; Kimura, F.; Song, G.; Kimura, T.

    2012-10-01

    Chemical shift tensors for the carboxyl and methyl carbons of L-alanine crystals were determined using a magnetically oriented microcrystal array (MOMA) prepared from a microcrystalline powder sample of L-alanine. A MOMA is a single-crystal-like composite in which microcrystals are aligned three-dimensionally in a matrix resin. The single-crystal rotation method was applied to the MOMA to determine the principal values and axes of the chemical shift tensors. The result showed good agreement with the literature data for the single crystal of L-alanine. This demonstrates that the present technique is a powerful tool for determining the chemical shift tensor of a crystal from a microcrystal powder sample.

  20. Chemical shift assignments of zinc finger domain of methionine aminopeptidase 1 (MetAP1) from Homo sapiens.

    Science.gov (United States)

    Rachineni, Kavitha; Arya, Tarun; Singarapu, Kiran Kumar; Addlagatta, Anthony; Bharatam, Jagadeesh

    2015-10-01

    Methionine aminopeptidase Type I (MetAP1) cleaves the initiator methionine from about 70 % of all newly synthesized proteins in almost every living cell. Human MetAP1 is a two domain protein with a zinc finger on the N-terminus and a catalytic domain on the C-terminus. Here, we report the chemical shift assignments of the amino terminal zinc binding domain (ZBD) (1-83 residues) of the human MetAP1 derived by using advanced NMR spectroscopic methods. We were able to assign the chemical shifts of ZBD of MetAP1 nearly complete, which reveal two helical fragments involving residues P44-L49 (α1) and Q59-K82 (α2). The protein structure unfolds upon complex formation with the addition of 2 M excess EDTA, indicated by the appearance of amide resonances in the random coil chemical shift region of (15)NHSQC spectrum.

  1. Origin of the conformational modulation of the 13C NMR chemical shift of methoxy groups in aromatic natural compounds.

    Science.gov (United States)

    Toušek, Jaromír; Straka, Michal; Sklenář, Vladimír; Marek, Radek

    2013-01-24

    The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.

  2. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.

  3. Computational chemical imaging for cardiovascular pathology: chemical microscopic imaging accurately determines cardiac transplant rejection.

    Directory of Open Access Journals (Sweden)

    Saumya Tiwari

    Full Text Available Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients' biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures.

  4. Superresolution imaging method using phase-shifting digital lensless Fourier holography.

    Science.gov (United States)

    Granero, Luis; Micó, Vicente; Zalevsky, Zeev; García, Javier

    2009-08-17

    A method which is useful for obtaining superresolved imaging in a digital lensless Fourier holographic configuration is presented. By placing a diffraction grating between the input object and the CCD recording device, additional high-order spatial-frequency content of the object spectrum is directed towards the CCD. Unlike other similar methods, the recovery of the different band pass images is performed by inserting a reference beam in on-axis mode and using phase-shifting method. This strategy provides advantages concerning the usage of the whole frequency plane as imaging plane. Thus, the method is no longer limited by the zero order term and the twin image. Finally, the whole process results in a synthetic aperture generation that expands up the system cutoff frequency and yields a superresolution effect. Experimental results validate our concepts for a resolution improvement factor of 3.

  5. Frequency-shift low-pass filtering and least mean square adaptive filtering for ultrasound imaging

    Science.gov (United States)

    Wang, Shanshan; Li, Chunyu; Ding, Mingyue; Yuchi, Ming

    2016-04-01

    Ultrasound image quality enhancement is a problem of considerable interest in medical imaging modality and an ongoing challenge to date. This paper investigates a method based on frequency-shift low-pass filtering (FSLF) and least mean square adaptive filtering (LMSAF) for ultrasound image quality enhancement. FSLF is used for processing the ultrasound signal in the frequency domain, while LMSAPF in the time domain. Firstly, FSLF shifts the center frequency of the focused signal to zero. Then the real and imaginary part of the complex data are filtered respectively by finite impulse response (FIR) low-pass filter. Thus the information around the center frequency are retained while the undesired ones, especially background noises are filtered. Secondly, LMSAF multiplies the signals with an automatically adjusted weight vector to further eliminate the noises and artifacts. Through the combination of the two filters, the ultrasound image is expected to have less noises and artifacts and higher resolution, and contrast. The proposed method was verified with the RF data of the CIRS phantom 055A captured by SonixTouch DAQ system. Experimental results show that the background noises and artifacts can be efficiently restrained, the wire object has a higher resolution and the contrast ratio (CR) can be enhanced for about 12dB to 15dB at different image depth comparing to delay-and-sum (DAS).

  6. Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated "Safe Sites"?

    Science.gov (United States)

    2011-07-26

    Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated ‘‘Safe Sites’’? Hortance Manda*, Luana M. Arce... aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant...overall impact. Methods: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU) were evaluated

  7. SUBSTITUENT CHEMICAL SHIFT (SCS) AND THE SEQUENCE STRUCTURE OF ETHYLENE-VINYL ALCOHOL COPOLYMERS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zinan; TIAN Wenjing; WU Shengrong; DAI Yingkun; FENG Zhiliu; SHEN Lianfang; YUAN Hanzhen

    1992-01-01

    Three ethylene-vinyl alcohol copolymers were studied by means of the substituent chemical shift(SCS) method. The SCS parameters of hydroxy (-OH)in two different solvents were obtained: in deuterium oxide/phenol (20/80 W/W ) the parameters are S1 = 42.77 ± 0.08ppm, S2 = 7.15 ±0.06 ppm,S3(s )=-4.08±0.02ppm, S3(t)=-3.09±0.20ppm,S4=0.48±0.03ppm, S5 =0.26±0.05ppm. In o-dichlorobenzen-d4 S1(s)=44.79±0.61ppm, S2=7.40±0.00ppm, S3 (s)=-4.51±0.17ppm, S3 (t)= -3.13± 0.00 ppm, S4 =0 . 63±0.04ppm, S5=0.36±0.00ppm. Simultaneously the 13CNMR spectra of EVA copolymers were assigned by using the SCS parameters obtained.

  8. Effects of side-chain orientation on the {sup 13}C chemical shifts of antiparallel {beta}-sheet model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Villegas, Myriam E.; Vila, Jorge A. [Facultad de Ciencias Fisico Matematicas y Naturales, Instituto de Matematica Aplicada San Luis, Universidad Nacional de San Luis, CONICET (Argentina); Scheraga, Harold A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)], E-mail: has5@cornell.edu

    2007-02-15

    The dependence of the {sup 13}C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel {beta}-sheet model peptide represented by the amino acid sequence Ac-(Ala){sub 3}-X-(Ala){sub 12}-NH{sub 2} where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel {beta}-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the {sup 13}C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel {beta}-sheet, there is (i) good agreement between computed and observed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts as a function of {chi}{sup 1} for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed {sup 13}C{sup {alpha}} chemical shifts on {chi}{sup {xi}} (with {xi} {>=} 2) compared to {chi}{sup 1} for eleven out of seventeen residues. Our results suggest that predicted {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, based only on backbone ({phi},{psi}) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into

  9. Twin-image reduction method for in-line digital holography using periphery and random reference phase-shifting techniques

    Science.gov (United States)

    Oshima, Teppei; Matsudo, Yusuke; Kakue, Takashi; Arai, Daisuke; Shimobaba, Tomoyoshi; Ito, Tomoyoshi

    2015-09-01

    Digital holography has the twin image problem that unwanted lights (conjugate and direct lights) overlap in the object light in the reconstruction process. As a method for extracting only the object light, phase-shifting digital holography is widely used; however, this method is not applicable for the observation of moving objects, because this method requires the recording of plural holograms. In this study, we propose a twin-image reduction method by combining the "periphery" method with the "random phase-shifting" method. The proposed method succeeded in improving the reconstruction quality, compared to other one-shot recording methods ("parallel phase-shifting digital holography" and "random phase-shifting").

  10. Analysis of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Osvaldo A.; Villegas, Myriam E.; Vila, Jorge A. [Universidad Nacional de San Luis, Instituto de Matematica Aplicada San Luis (Argentina); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

    2010-03-15

    Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed {sup 13}C{sup {alpha}} chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed {sup 13}C{sup {alpha}} chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced -SH {sup 13}C{sup {beta}}, but not for the {sup 13}C{sup {alpha}}, chemical shifts, in good agreement with the observation of 375 {sup 13}C{sup {alpha}} and 337 {sup 13}C{sup {beta}} resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of cysteines in cystines.

  11. Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

    Science.gov (United States)

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

    Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

  12. Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

    DEFF Research Database (Denmark)

    Schripsema, Jan; Danigno, Denise

    1996-01-01

    In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported anthra...

  13. The local order of supercooled water in solution with LiCl studied by NMR proton chemical shift

    Science.gov (United States)

    Corsaro, C.; Mallamace, D.; Vasi, S.; Cicero, N.; Dugo, G.; Mallamace, F.

    2016-05-01

    We study by means of Nuclear Magnetic Resonance (NMR) spectroscopy the local order of water molecules in solution with lithium chloride at eutectic concentration. In particular, by measuring the proton chemical shift as a function of the temperature in the interval 203{ K}Widom line for water supporting the liquid-liquid transition hypothesis.

  14. Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  15. Super-resolution chemical imaging with dynamic placement of plasmonic hotspots

    Science.gov (United States)

    Olson, Aeli P.; Ertsgaard, Christopher T.; McKoskey, Rachel M.; Rich, Isabel S.; Lindquist, Nathan C.

    2015-08-01

    We demonstrate dynamic placement of plasmonic "hotspots" for super-resolution chemical imaging via Surface Enhanced Raman Spectroscopy (SERS). A silver nanohole array surface was coated with biological samples and illuminated with a laser. Due to the large plasmonic field enhancements, blinking behavior of the SERS hotspots was observed and processed using a Stochastic Optical Reconstruction Microscopy (STORM) algorithm enabling localization to within 10 nm. However, illumination of the sample with a single static laser beam (i.e., a slightly defocused Gaussian beam) only produced SERS hotspots in fixed locations on the surface, leaving noticeable gaps in any final image. But, by using a spatial light modulator (SLM), the illumination profile of the beam could be altered, shifting any hotspots across the nanohole array surface in sub-wavelength steps. Therefore, by properly structuring an illuminating light field with the SLM, we show the possibility of positioning plasmonic hotspots over a metallic nanohole surface on-the-fly. Using this and our SERS-STORM imaging technique, we show potential for high-resolution chemical imaging without the noticeable gaps that were present with static laser illumination. Interestingly, even illuminating the surface with randomly shifting SLM phase profiles was sufficient to completely fill in a wide field of view for super-resolution SERS imaging of a single strand of 100-nm thick collagen protein fibrils. Images were then compared to those obtained with a scanning electron microscope (SEM). Additionally, we explored alternative methods of phase shifting other than holographic illumination through the SLM to create localization of hotspots necessary for SERS-STORM imaging.

  16. Dislocation tomography made easy: a reconstruction from ADF STEM images obtained using automated image shift correction

    Energy Technology Data Exchange (ETDEWEB)

    Sharp, J H; Barnard, J S; Midgley, P A [Department of Materials Science, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ (United Kingdom); Kaneko, K; Higashida, K [Department of Materials Science and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan)], E-mail: jhd28@cam.ac.uk

    2008-08-15

    After previous work producing a successful 3D tomographic reconstruction of dislocations in GaN from conventional weak-beam dark-field (WBDF) images, we have reconstructed a cascade of dislocations in deformed and annealed silicon to a comparable standard using the more experimentally straightforward technique of STEM annular dark-field imaging (STEM ADF). In this mode, image contrast was much more consistent over the specimen tilt range than in conventional weak-beam dark-field imaging. Automatic acquisition software could thus restore the correct dislocation array to the field of view at each tilt angle, though manual focusing was still required. Reconstruction was carried out by sequential iterative reconstruction technique using FEI's Inspect3D software. Dislocations were distributed non-uniformly along cascades, with sparse areas between denser clumps in which individual dislocations of in-plane image width 24 nm could be distinguished in images and reconstruction. Denser areas showed more complicated stacking-fault contrast, hampering tomographic reconstruction. The general three-dimensional form of the denser areas was reproduced well, showing the dislocation array to be planar and not parallel to the foil surfaces.

  17. Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

    Science.gov (United States)

    Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming

    2016-01-01

    The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

  18. Forensic analysis of bicomponent fibers using infrared chemical imaging.

    Science.gov (United States)

    Flynn, Katherine; O'Leary, Robyn; Roux, Claude; Reedy, Brian J

    2006-05-01

    The application of infrared chemical imaging to the analysis of bicomponent fibers was evaluated. Eleven nominally bicomponent fibers were examined either side-on or in cross-section. In six of the 11 samples, infrared chemical imaging was able to spatially resolve two spectroscopically distinct regions when the fibers were examined side-on. As well as yielding characteristic infrared spectra of each component, the technique also provided images that clearly illustrated the side-by-side configuration of these components in the fiber. In one case it was possible to prepare and image a cross-section of the fiber, but in general the preparation of fiber cross-sections proved very difficult. In five of the 11 samples, the infrared spectra could be used to identify the overall chemical composition of the fibers, according to a published classification scheme, but the fiber components could not be spatially resolved. Difficulties that are inherent to conventional "single-point" infrared spectroscopy, such as interference fringing and sloping baselines, particularly when analyzing acrylic type fibers, were also encountered in the infrared chemical image analysis of bicomponent fibers. A number of infrared sampling techniques were investigated to overcome these problems, and recommendations for the best sampling technique are given. Chemical imaging results were compared with those obtained using conventional fiber microscopy techniques.

  19. Phase-shift effect of amplitude spread function on spectrum and image formation in coherent Raman scattering microspectroscopy.

    Science.gov (United States)

    Fukutake, Naoki

    2016-03-01

    Coherent Raman scattering microspectroscopy, which includes coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microspectroscopy, permits label-free hyperspectral imaging. We report the theoretical study of the phase-shift effect of the impulse response function on the spectral and image-forming properties of coherent Raman scattering microspectroscopy. We show that the spectrum and image are influenced by not only the NA of objective for excitation (NA(ex)) but also that for signal collection (NA(col)), in association with the phase-shift effect. We discuss that, under the condition NA(ex)≠NA(col), both the spectrum and the image become deformed by the phase-shift effect, which can be applied to the direct measurement of the imaginary part of the nonlinear susceptibility in CARS spectroscopy. We point out that, even in SRS microscopy, the nonresonant background can contribute to the image formation and cause the artifact in the image.

  20. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  1. Improving x-ray image resolution using subpixel shifts of the detector

    Science.gov (United States)

    Bruandet, Jean-Pierre; Dinten, Jean-Marc

    1999-05-01

    The resolution of digitized images is linked to the detector array pixel size. Aliasing effects result from a non- adequation between the detector sampling and the signal bandwidths. The aim of this study is to develop a super- resolution algorithm for X-ray images. Our technique uses controlled horizontal and vertical subpixel shifts. Generalized sampling theorem of Papoulis, based on a multichannel approach, is the theoretical justification for the recovery of a high resolution image thanks to a set of low resolution ones. A higher resolution image is recovered by a minimization of a quadratic criterion. An iterative relaxation method is used to compute the minimum. To regularize, a priori data about the signal are introduced in order to fight against noise effects. Because of the opposite effects of regularization and super-resolution an adapted regularization that preserves discontinuities has to be used. Results obtained show that our algorithm recovers high frequency components on X-ray images without noise amplification. An analysis of real acquisitions in terms of modulation transfer function (MTF) shows that we obtain, thanks to this method, a 'virtual' detector better than a low resolution one, and equivalent to a real high resolution one.

  2. Generation of Red-Shifted Cameleons for Imaging Ca2+ Dynamics of the Endoplasmic Reticulum

    Directory of Open Access Journals (Sweden)

    Markus Waldeck-Weiermair

    2015-06-01

    Full Text Available Cameleons are sophisticated genetically encoded fluorescent probes that allow quantifying cellular Ca2+ signals. The probes are based on Förster resonance energy transfer (FRET between terminally located fluorescent proteins (FPs, which move together upon binding of Ca2+ to the central calmodulin myosin light chain kinase M13 domain. Most of the available cameleons consist of cyan and yellow FPs (CFP and YFP as the FRET pair. However, red-shifted versions with green and orange or red FPs (GFP, OFP, RFP have some advantages such as less phototoxicity and minimal spectral overlay with autofluorescence of cells and fura-2, a prominent chemical Ca2+ indicator. While GFP/OFP- or GFP/RFP-based cameleons have been successfully used to study cytosolic and mitochondrial Ca2+ signals, red-shifted cameleons to visualize Ca2+ dynamics of the endoplasmic reticulum (ER have not been developed so far. In this study, we generated and tested several ER targeted red-shifted cameleons. Our results show that GFP/OFP-based cameleons due to miss-targeting and their high Ca2+ binding affinity are inappropriate to record ER Ca2+ signals. However, ER targeted GFP/RFP-based probes were suitable to sense ER Ca2+ in a reliable manner. With this study we increased the palette of cameleons for visualizing Ca2+ dynamics within the main intracellular Ca2+ store.

  3. Automated midline shift and intracranial pressure estimation based on brain CT images.

    Science.gov (United States)

    Chen, Wenan; Belle, Ashwin; Cockrell, Charles; Ward, Kevin R; Najarian, Kayvan

    2013-04-13

    In this paper we present an automated system based mainly on the computed tomography (CT) images consisting of two main components: the midline shift estimation and intracranial pressure (ICP) pre-screening system. To estimate the midline shift, first an estimation of the ideal midline is performed based on the symmetry of the skull and anatomical features in the brain CT scan. Then, segmentation of the ventricles from the CT scan is performed and used as a guide for the identification of the actual midline through shape matching. These processes mimic the measuring process by physicians and have shown promising results in the evaluation. In the second component, more features are extracted related to ICP, such as the texture information, blood amount from CT scans and other recorded features, such as age, injury severity score to estimate the ICP are also incorporated. Machine learning techniques including feature selection and classification, such as Support Vector Machines (SVMs), are employed to build the prediction model using RapidMiner. The evaluation of the prediction shows potential usefulness of the model. The estimated ideal midline shift and predicted ICP levels may be used as a fast pre-screening step for physicians to make decisions, so as to recommend for or against invasive ICP monitoring.

  4. Application of thermal wave imaging and phase shifting method for defect detection in Stainless steel

    Science.gov (United States)

    Shrestha, Ranjit; Park, Jeonghak; Kim, Wontae

    2016-05-01

    This paper presents an experimental arrangement for detection of artificial subsurface defects in a stainless steel sample by means of thermal wave imaging with lock-in thermography and consequently, the impact of excitation frequency on defect detectability. The experimental analysis was performed at several excitation frequencies to observe the sample beginning from 0.18 Hz all the way down to 0.01 Hz. The phase contrast between the defective and sound regions illustrates the qualitative and quantitative investigation of defects. The two, three, four and five-step phase shifting methods are investigated to obtain the information on defects. A contrast to noise ratio analysis was applied to each phase shifting method allowing the choice of the most appropriate one. Phase contrast with four-step phase shifting at an optimum frequency of 0.01 Hz provides excellent results. The inquiry with the effect of defect size and depth on phase contrast shows that phase contrast decreases with increase in defect depth and increases with the increase in defect size.

  5. Visualizing Chemistry: The Progess and Promise of Advanced Chemical Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Committee on Revealing Chemistry Through Advanced Chemical Imaging

    2006-09-01

    The field of chemical imaging can provide detailed structural, functional, and applicable information about chemistry and chemical engineering phenomena that have enormous impacts on medicine, materials, and technology. In recognizing the potential for more research development in the field of chemical imaging, the National Academies was asked by the National Science Foundation, Department of Energy, U.S. Army, and National Cancer Institute to complete a study that would review the current state of molecular imaging technology, point to promising future developments and their applications, and suggest a research and educational agenda to enable breakthrough improvements in the ability to image molecular processes simultaneously in multiple physical dimensions as well as time. The study resulted in a consensus report that provides guidance for a focused research and development program in chemical imaging and identifies research needs and possible applications of imaging technologies that can provide the breakthrough knowledge in chemistry, materials science, biology, and engineering for which we should strive. Public release of this report is expected in early October.

  6. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: a validation study.

    Science.gov (United States)

    Safari, Mohammad Reza; Rowe, Philip; Buis, Arjan

    2013-01-01

    The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/-2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

  7. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: A validation study

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Safari, PhD

    2013-02-01

    Full Text Available The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting. Casting can be quantified with magnetic resonance imaging (MRI technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS and 9 plastic sample vials (film containers to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98% (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm. The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/–2.18 mm based on voxel (three-dimensional pixel dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

  8. Cuticular hydrocarbon divergence in the jewel wasp Nasonia : evolutionary shifts in chemical communication channels?

    NARCIS (Netherlands)

    Buellesbach, J.; Gadau, J.; Beukeboom, L. W.; Echinger, F.; Raychoudhury, R.; Werren, J. H.; Schmitt, T.

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this s

  9. A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

    Science.gov (United States)

    Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

    2014-01-01

    A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

  10. Reversible Data Hiding Using Two Marked Images Based on Adaptive Coefficient-Shifting Algorithm

    Directory of Open Access Journals (Sweden)

    Ching-Yu Yang

    2012-01-01

    Full Text Available This paper proposes a novel form of reversible data hiding using two marked images by employing the adaptive coefficient-shifting (ACS algorithm. The proposed ACS algorithm consists of three parts: the minimum-preserved scheme, the minimum-preserved with squeezing scheme, and the base-value embedding scheme. More specifically, each input block of a host image can be encoded to two stego-blocks according to three predetermined rules by the above three schemes. Simulations validate that the proposed method not only completely recovers the host medium but also losslessly extracts the hidden message. The proposed method can handle various kinds of images without any occurrence of overflow/underflow. Moreover, the payload and peak signal-to-noise ratio (PSNR performance of the proposed method is superior to that of the conventional invertible data hiding schemes. Furthermore, the number of shadows required by the proposed method is less than that required by the approaches which are based upon secret image sharing with reversible steganography.

  11. Improvement of band segmentation in Epo images via column shift transformation with cost functions.

    Science.gov (United States)

    Stolc, S; Bajla, I

    2006-04-01

    In recent years, the development of methodology and laboratory techniques for doping control (DC) of recombinant erythropoietin (rEpo) has become one of the most important topics pursued by doping control laboratories accredited by World Anti-Doping Agency (WADA). The software system GASepo has been developed within the international WADA project as a support for Epo doping control. Although a great number of functions for automatic image processing have been involved in this software, for Epo images with considerably distorted bands additional effort is required from the user to interactively correct the results of improper band segmentation. In this paper a problem of geometrically distorted bands is addressed from the viewpoint of how to transform the lanes in distorted Epo images in order to reach better band segmentation. A method of band straightening via column shift transformation has been proposed that is formulated as an optimization procedure with cost functions. The method involves several novel approaches: two-stage optimization procedure, four cost functions and selection of relevant columns. The developed band straightening algorithm (BSA) has been tested on real Epo images with distorted bands. Based on the evaluation scheme involving the GASepo software itself a recommendation is made for implementation of the method with the cost function based on correlation matrix. Estimates of computational complexity of the individual steps of BSA are also given.

  12. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

    Science.gov (United States)

    Giessner-Prettre, C; Ribas Prado, F; Pullman, B; Kan, L; Kast, J R; Ts'o, P O

    1981-01-01

    A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.

  13. Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections.

    Science.gov (United States)

    Fedorov, Sergey V; Rusakov, Yury Yu; Krivdin, Leonid B

    2014-11-01

    The main factors affecting the accuracy and computational cost of the calculation of (31)P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of (31)P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS-2 or larger, and those of Pople, 6-311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta-zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of (31)P NMR chemical shifts within the 1-2-ppm error. Relativistic corrections to (31)P NMR absolute shielding constants are of major importance reaching about 20-30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1-2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO-DFT-KT2/pcS-3//pcS-2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of (31)P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm.

  14. Red-Shifted Aequorin Variants Incorporating Non-Canonical Amino Acids: Applications in In Vivo Imaging.

    Directory of Open Access Journals (Sweden)

    Kristen M Grinstead

    Full Text Available The increased importance of in vivo diagnostics has posed new demands for imaging technologies. In that regard, there is a need for imaging molecules capable of expanding the applications of current state-of-the-art imaging in vivo diagnostics. To that end, there is a desire for new reporter molecules capable of providing strong signals, are non-toxic, and can be tailored to diagnose or monitor the progression of a number of diseases. Aequorin is a non-toxic photoprotein that can be used as a sensitive marker for bioluminescence in vivo imaging. The sensitivity of aequorin is due to the fact that bioluminescence is a rare phenomenon in nature and, therefore, it does not suffer from autofluorescence, which contributes to background emission. Emission of bioluminescence in the blue-region of the spectrum by aequorin only occurs when calcium, and its luciferin coelenterazine, are bound to the protein and trigger a biochemical reaction that results in light generation. It is this reaction that endows aequorin with unique characteristics, making it ideally suited for a number of applications in bioanalysis and imaging. Herein we report the site-specific incorporation of non-canonical or non-natural amino acids and several coelenterazine analogues, resulting in a catalog of 72 cysteine-free, aequorin variants which expand the potential applications of these photoproteins by providing several red-shifted mutants better suited to use in vivo. In vivo studies in mouse models using the transparent tissue of the eye confirmed the activity of the aequorin variants incorporating L-4-iodophehylalanine and L-4-methoxyphenylalanine after injection into the eye and topical addition of coelenterazine. The signal also remained localized within the eye. This is the first time that aequorin variants incorporating non-canonical amino acids have shown to be active in vivo and useful as reporters in bioluminescence imaging.

  15. QCLs and the future of IR chemical imaging (Conference Presentation)

    Science.gov (United States)

    Rowlette, Jeremy A.; Fotheringham, Edeline; Weida, Miles J.; Chapman, William B.; Larson, Paul; Day, Tiim

    2016-09-01

    High-fidelity, broadly-tunable quantum cascade lasers (QCLs) are replacing thermal light sources in next-generation infrared chemical imaging and microscopy instrumentation. Their superior spectral brightness, beam quality, and reliability are enabling new applications in biomedical, pharmaceutical, and industrial markets which demand substantially better noise performance, higher throughput, and ease-of-use. In this talk we will discuss the state-of-the-art in QCL source technology and describe our systems approach to leveraging QCL sources in the next-generation of infrared chemical imaging microscopes.

  16. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; A K Yadav; S N Jha; D Bhattacharyya

    2013-11-01

    Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Mn and Cr cations in the above compounds.

  17. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis.

    Directory of Open Access Journals (Sweden)

    Elliott J Stollar

    Full Text Available There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences.

  18. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    Directory of Open Access Journals (Sweden)

    Ricardo Infante-Castillo

    2012-01-01

    Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

  19. Chemically Specific Cellular Imaging of Biofilm Formation

    Energy Technology Data Exchange (ETDEWEB)

    Herberg, J L; Schaldach, C; Horn, J; Gjersing, E; Maxwell, R

    2006-02-09

    complicated organism, we needed to first turn our attention to a well understood organism. Pseudomonas aeruginosa (PA) is a well-studied organism and will be used to compare our results with others. Then, we will turn our attention to TD. It is expected that the research performed will provide key data to validate biochemical studies of TD and result in high profile publications in leading journals. For this project, our ultimate goal was to combine both Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Resonance (NMR) experimental analysis with computer simulations to provide unique 3D molecular structural, dynamics, and functional information on the order of microns for this DOE mission relevant microorganism, T. denitrificans. For FY05, our goals were to: (1) Determine proper media for optimal growth of PA; growth rate measurements in that media and characterization of metabolite signatures during growth via {sup 1}H and {sup 13}C NMR, (2) Determine and build mineral, metal, and implant material surfaces to support growth of PA, (3) Implementing new MRI sequences to image biofilms more efficiently and increase resolution with new hardware design, (4) Develop further diffusion and flow MRI measurements of biofilms and biofilm formation with different MRI pulse sequences and different hardware design, and (5) Develop a zero dimension model of the rate of growth and the metabolite profiles of PA. Our major accomplishments are discussed in the following text. However, the bulk of this work is described in the attached manuscript entitled, ''NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa''. This paper will be submitted to the Journal of Bacteriology in coming weeks. In addition, this one-year effort has lead to our incorporation into the Enhanced Surveillance Campaign during FY05 for some proof-of-principle MRI measurements on polymers. We are currently using similar methods to evaluate these polymers. In addition

  20. Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.

    Science.gov (United States)

    Kornhaber, Gregory J; Snyder, David; Moseley, Hunter N B; Montelione, Gaetano T

    2006-04-01

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped 13Cbeta chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding 13Calpha chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 13Calpha/13Cbeta shift pairs from 79 proteins with known three-dimensional structures, including 86 13Calpha and 13Cbeta shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statistical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn

  1. Chemically Specific Cellular Imaging of Biofilm Formation

    Energy Technology Data Exchange (ETDEWEB)

    Herberg, J L; Schaldach, C; Horn, J; Gjersing, E; Maxwell, R

    2006-02-09

    complicated organism, we needed to first turn our attention to a well understood organism. Pseudomonas aeruginosa (PA) is a well-studied organism and will be used to compare our results with others. Then, we will turn our attention to TD. It is expected that the research performed will provide key data to validate biochemical studies of TD and result in high profile publications in leading journals. For this project, our ultimate goal was to combine both Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Resonance (NMR) experimental analysis with computer simulations to provide unique 3D molecular structural, dynamics, and functional information on the order of microns for this DOE mission relevant microorganism, T. denitrificans. For FY05, our goals were to: (1) Determine proper media for optimal growth of PA; growth rate measurements in that media and characterization of metabolite signatures during growth via {sup 1}H and {sup 13}C NMR, (2) Determine and build mineral, metal, and implant material surfaces to support growth of PA, (3) Implementing new MRI sequences to image biofilms more efficiently and increase resolution with new hardware design, (4) Develop further diffusion and flow MRI measurements of biofilms and biofilm formation with different MRI pulse sequences and different hardware design, and (5) Develop a zero dimension model of the rate of growth and the metabolite profiles of PA. Our major accomplishments are discussed in the following text. However, the bulk of this work is described in the attached manuscript entitled, ''NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa''. This paper will be submitted to the Journal of Bacteriology in coming weeks. In addition, this one-year effort has lead to our incorporation into the Enhanced Surveillance Campaign during FY05 for some proof-of-principle MRI measurements on polymers. We are currently using similar methods to evaluate these polymers. In addition

  2. Structural Expression of Chemical Environment and C-13 NMR Chemical Shift for Carbons in Alcohols%脂肪醇分子碳环境结构表征与碳谱化学位移

    Institute of Scientific and Technical Information of China (English)

    刘树深; 徐红

    2000-01-01

    A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various equivalent carbon in alcohols and four 4-parameter linear relationship between chemical shift and AEDV are created by using multiple linear regression.

  3. Pharmaceutical applications of vibrational chemical imaging and chemometrics: a review.

    Science.gov (United States)

    Gendrin, C; Roggo, Y; Collet, C

    2008-11-04

    The emergence of chemical imaging (CI) has gifted spectroscopy an additional dimension. Chemical imaging systems complement chemical identification by acquiring spatially located spectra that enable visualization of chemical compound distributions. Such techniques are highly relevant to pharmaceutics in that the distribution of excipients and active pharmaceutical ingredient informs not only a product's behavior during manufacture but also its physical attributes (dissolution properties, stability, etc.). The rapid image acquisition made possible by the emergence of focal plane array detectors, combined with publication of the Food and Drug Administration guidelines for process analytical technology in 2001, has heightened interest in the pharmaceutical applications of CI, notably as a tool for enhancing drug quality and understanding process. Papers on the pharmaceutical applications of CI have been appearing in steadily increasing numbers since 2000. The aim of the present paper is to give an overview of infrared, near-infrared and Raman imaging in pharmaceutics. Sections 2 and 3 deal with the theory, device set-ups, mode of acquisition and processing techniques used to extract information of interest. Section 4 addresses the pharmaceutical applications.

  4. An atomic electronegative distance vector and carbon-13 nuclear magnetic resonance chemical shifts of alcohols and alkanes

    Institute of Scientific and Technical Information of China (English)

    LIU, Shu-Shea; XIA, Zhi-Ning; CAI, Shao-Xi; LIU, Yan

    2000-01-01

    A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various chemically equivalent carbon atoms in alcohols and alkanes.Combining AEDV and γ parameter, four five-parameter Iinear relationship equations of chemical shift for four types of carbon atoms are created by using multiple linear regression.Correlation coefficients are R = 0.9887, 0.9972, 0.9978 and 0.9968 and roots of mean square error are RMS = 0.906, 0.821, 1.091and 1.091of four types of carbons, i.e., type1,2, 3, and 4 for primary, secondary, tertiary, and quaternary carbons, respectively. The stability and prediction capacity for external samples of four models have been tested by cross- validation.

  5. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Science.gov (United States)

    Chappell, P Dreux; Whitney, Leeann P; Haddock, Traci L; Menden-Deuer, Susanne; Roy, Eric G; Wells, Mark L; Jenkins, Bethany D

    2013-01-01

    Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  6. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

    Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  7. Observed and calculated 1H and 13C chemical shifts induced by the in situ oxidation of model sulfides to sulfoxides and sulfones.

    Science.gov (United States)

    Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos

    2010-09-01

    A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).

  8. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems.

    Science.gov (United States)

    Isley, William C; Zarra, Salvatore; Carlson, Rebecca K; Bilbeisi, Rana A; Ronson, Tanya K; Nitschke, Jonathan R; Gagliardi, Laura; Cramer, Christopher J

    2014-06-14

    The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation.

  9. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  10. Chemical imaging and solid state analysis at compact surfaces using UV imaging

    DEFF Research Database (Denmark)

    Wu, Jian X.; Rehder, Sönke; van den Berg, Frans;

    2014-01-01

    Fast non-destructive multi-wavelength UV imaging together with multivariate image analysis was utilized to visualize distribution of chemical components and their solid state form at compact surfaces. Amorphous and crystalline solid forms of the antidiabetic compound glibenclamide...... and excipients in a non-invasive way, as well as mapping the glibenclamide solid state form. An exploratory data analysis supported the critical evaluation of the mapping results and the selection of model parameters for the chemical mapping. The present study demonstrated that the multi-wavelength UV imaging...

  11. A calibration concept for passive MW imaging using beam steering by frequency shift and aperture synthesis

    Science.gov (United States)

    Schreiber, Eric; Peichl, Markus; Jirousek, Matthias

    2013-10-01

    Passive microwave (MW) remote sensing is used in Earth observation missions for example to estimate the salinity of oceans or the soil moisture of landscapes. In these cases the absolute brightness temperature numbers are important for sufficient accuracy of the estimated geo-physical parameters. Consequently a suitable system calibration network is required. At DLR a radiometric demonstrator for fully-electronic MW imaging was set up at Ka-band, which is based on a combination of beam steering by frequency shift using a broadband slotted-waveguide antenna for one scanning direction, and the application of aperture synthesis for the other direction. Aperture synthesis is well known from radio astronomy, but it is still a new imaging principle for Earth observation or security applications. Hence as well new calibration techniques have to be developed for this kind of scanning mechanism. In this paper a novel approach for a noise-source based calibration method taking into account the antenna losses will be introduced. When using aperture synthesis techniques to determine the absolute brightness temperature values, it is very important, among other things, to know the exact phase transfer function of the system in order to achieve the desired radiometric resolution. Consequently our approach enables phase calibration as well. The paper outlines a proof of concept for this calibration method using a two-element interferometer called VESAS (Voll Elektronischer Scanner mit AperturSynthese) as a demonstrator. The functionality of the demonstrator and the proof of concept of the imaging principle mentioned before are written in detail in [1].

  12. Halodemetallation of (Z)-1-[2-(Triarylstannyl)vinyl]-cyclooctanol and Correlation of Proton Chemical Shift with Electronegativity

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Introduction Organotin compounds have attracted attention as an optimal model for antitumour agents due to the function of the interesting intramolecular O→Sn coordination[1,2]. Our recent concern has been focused on the preparation of (Z)-1-[2-(triarylstannyl)vinyl]-cyclooctanol[3]. In order to find more appropriate compounds used as anticancer agents and explore the effect of the coordinate O→Sn interaction to the antitumor activity, the new compounds were halodemetallated and characterized. During the course of the process, some linear correlations between proton chemical shifts and the sum of the electronegativities of the tin substituents of halogens were found for the first time.

  13. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    OpenAIRE

    Ricardo Infante-Castillo; Samuel P. Hernández-Rivera

    2012-01-01

    This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO) charge and 15N NMR chemical shifts of the nitro groups (15NNitro) as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation re...

  14. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    Science.gov (United States)

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.

  15. 3.0T1H-MRS联合梯度回波化学位移技术定量分析评估脂肪肝治疗效果%Quantification of liver fat content by 1H-MR spectroscopy combined with chemical shift gradient-echo MR imaging at 3.0T for therapeutic evaluation of fatty liver—a preliminary study

    Institute of Scientific and Technical Information of China (English)

    张羲娥; 黄子星; 袁放; 宋彬; 刘曦娇; 张威

    2012-01-01

    Objective:To investigate the feasibility of proton magnetic resonance spectroscopy OH-MRS) and chemical shift gradient-echo imaging to quantitatively analyze liver fat content for therapeutic evaluation of fatty liver at 3. OT MR system. Methods:26 patients diagnosed as fatty liver were examined with proton MRS and magnetic resonance chemical shift based fat suppression sequences(Dixon and triple-echo Dixon)at 3. OT MR system before and 3,6 months after treatment respectively to calculate the fat index(FI)of Dixon, the water peak (Pwater), fat peak (Pliptd) and water peak area (Awater),fat peak area (Aliptd) were for MRS to calculate relative lipid content KRLCDand relative lipid content 2(RLC2). Fatty liver index(FLI)was referred to the standard which was calculated from triglycerides (TG),gamma-glutamyl-trans-ferase CGGT) ,waist circumference and body mass index(BMI). Results:Significant positive correlation (r>0,P0,P<0. 05)was demonstrated in MRI measured valuesCFI, RLCl,RLC2)and FLI. Significant difference between groups was demonstrated in FI, RLC1,RLC2 and FLI. Significance in statistics was demonstrated in time* type in the Polynomial test for the comparison of time change trend which point out the significant difference of FI-,RLC1,RLC2 between pre-treatment and pos-treatment. Reliability analysis showed that FI in both pre-treatment and pos-treatment groups and RLC1 ,RLC2 in pre-treatment group got significant repeatability while ICC ≥0. 75. Conclusion:' H-MRS combined with chemical shift gradient-echo techniques can quantitatively measure liver fat content. They can be reliably used for dynamic monitoring the therapeutic effects for fatty liver. Dixon technique is more stable, while 1H-MRS is more accurate. Both 1H-MRS and Dixon technique have good clinical application in dynamically monitoring the progression of fatty liver and evaluating the therapeutic effects of various treatments.%目的:探讨在3.0T MRI上联合运用氢质子波谱成像(1H-MRS

  16. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  17. A Novel Image Alignment Algorithm Based on Rotation-Discriminating Ring-Shifted Projection for Automatic Optical Inspection

    Directory of Open Access Journals (Sweden)

    Chin-Sheng Chen

    2016-05-01

    Full Text Available This paper proposes a novel image alignment algorithm based on rotation-discriminating ring-shifted projection for automatic optical inspection. This new algorithm not only identifies the location of the template image within an inspection image but also provides precise rotation information during the template-matching process by using a novel rotation estimation scheme, the so-called ring-shifted technique. We use a two stage framework with an image pyramid searching technique for realizing the proposed image alignment algorithm; in the first stage, the similarity based on hybrid projection transformation with the image pyramid searching technique is employed for quick selection and location of the candidates in the inspection image. In the second stage, the rotation angle of the object is estimated by a novel ring-shifted technique. The estimation is performed only for the most likely candidate which is the one having the highest similarity in the first stage. The experimental results show that the proposed method provides accurate estimation for template matching with arbitrary rotations and is applicable in various environmental conditions.

  18. Effect of pH, urea, peptide length, and neighboring amino acids on alanine alpha-proton random coil chemical shifts.

    Science.gov (United States)

    Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L

    2007-01-01

    Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding.

  19. NMR chemical shift as analytical derivative of the Helmholtz free energy.

    Science.gov (United States)

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case, the paramagnetic part of the shielding tensor is expressed in terms of the g and A tensors of the electron paramagnetic resonance spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C(60), with Ln = Ce(3+), Nd(3+), Sm(3+), Dy(3+), Er(3+), and Yb(3+), where the ground state can be a strongly spin-orbit coupled icosahedral sextet for which the paramagnetic shift cannot be described by previous theories.

  20. Modeling the chemical shift of lanthanide 4f electron binding energies

    NARCIS (Netherlands)

    Dorenbos, P.

    2012-01-01

    Lanthanides in compounds can adopt the tetravalent [Xe]4fn−1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4f n+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environ

  1. ATTENUATION OF DIFFRACTED MULTIPLES WITH AN APEX-SHIFTED TANGENT-SQUARED RADON TRANSFORM IN IMAGE SPACE

    Directory of Open Access Journals (Sweden)

    Alvarez Gabriel

    2006-12-01

    Full Text Available In this paper, we propose a method to attenuate diffracted multiples with an apex-shifted tangent-squared Radon transform in angle domain common image gathers (ADCIG . Usually, where diffracted multiples are a problem, the wave field propagation is complex and the moveout of primaries and multiples in data space is irregular. The method handles the complexity of the wave field propagation by wave-equation migration provided that migration velocities are reasonably accurate. As a result, the moveout of the multiples is well behaved in the ADCIGs. For 2D data, the apex-shifted tangent-squared Radon transform maps the 2D space image into a 3D space-cube model whose dimensions are depth, curvature and apex-shift distance.
    Well-corrected primaries map to or near the zero curvature plane and specularly-reflected multiples map to or near the zero apex-shift plane. Diffracted multiples map elsewhere in the cube according to their curvature and apex-shift distance. Thus, specularly reflected as well as diffracted multiples can be attenuated simultaneously. This approach is illustrated with a segment of a 2D seismic line over a large salt body in the Gulf of Mexico. It is shown that ignoring the apex shift compromises the attenuation of the diffracted multiples, whereas the approach proposed attenuates both the specularly-reflected and the diffracted multiples without compromising the primaries.

  2. Evaluation of the effects of sagging shifts on isocenter accuracy and image quality of cone-beam CT from kV on-board imagers.

    Science.gov (United States)

    Ali, Imad; Ahmad, Salahuddin

    2009-07-17

    To investigate the effects of sagging shifts of three on-board kV imaging systems (OBI) on the isocenter positioning accuracy and image quality of cone-beam CT (CBCT). A cubical phantom having a metal marker in the center that can be aligned with the radiation isocenter was used to measure sagging shifts and their variation with gantry angle on three Varian linacs with kV on-board imaging systems. A marker-tracking algorithm was applied to detect the shadow of the metal marker and localize its center in the two-dimensional cone-beam radiographic projections. This tracking algorithm is based on finding the position of maximum cross-correlation between a region-of-interest from a template image (including the metal marker) and the projections containing the shadow of the metal marker. Sagging shifts were corrected by mapping the center of the metal marker to a reference position for all projections acquired over a full gantry rotation (0-360 degrees). The sag-corrected radiographic projections were then used to reconstruct CBCT using Feldkamp back-projection. A standard quality assurance phantom was used to evaluate the image quality of CBCT before and after sagging correction. Sagging affects both the positioning accuracy of the OBI isocenter and the CBCT image quality. For example, on one linac, the position of the marker on the cone-beam radiographic projections depends on the angular view and has maximal shifts of about 2 mm along the imager x-direction (patient's cross-plane). Sagging produces systematic shifts of the OBI isocenter as large as 1 mm posterior and 1 mm left in patient coordinates relative to the radiation isocenter. Further, it causes spatial distortion and blurring in CBCT image reconstructed from radiographic projections that are not corrected for OBI sagging. CBCT numbers vary by about 1% in full-fan scans and up to 3.5% in half-fan scans because of sagging. In order to achieve better localization accuracy in image-guided radiation therapy

  3. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

    Science.gov (United States)

    Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H

    2015-11-17

    Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.

  4. Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

    2010-01-01

    Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

  5. Theory of NMR chemical shift in an electronic state with arbitrary degeneracy

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory of nuclear magnetic resonance (NMR) shielding tensors for electronic states with arbitrary degeneracy. The shieldings are here expressed in terms of generalized Zeeman ($g^{(k)}$) and hyperfine ($A^{(k)}$) tensors, of all ranks $k$ allowed by the size of degeneracy. Contrary to recent proposals [T. O. Pennanen and J. Vaara, Phys. Rev. Lett. 100, 133002 (2008)], our theory is valid in the strong spin-orbit coupling limit. Ab initio calculations for the 4-fold degenerate $\\Gamma_8$ ground state of lanthanide-doped fluorite crystals CaF$_2$:Ln (Ln = Pr$^{2+}$, Nd$^{3+}$, Sm$^{3+}$, and Dy$^{3+}$) show that previously neglected contributions can account for more than 50% of the paramagnetic shift.

  6. Quantitative analysis of deuterium using the isotopic effect on quaternary {sup 13}C NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Darwish, Tamim A., E-mail: tamim.darwish@ansto.gov.au [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); Yepuri, Nageshwar Rao; Holden, Peter J. [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); James, Michael [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia)

    2016-07-13

    Quantitative analysis of specifically deuterated compounds can be achieved by a number of conventional methods, such as mass spectroscopy, or by quantifying the residual {sup 1}H NMR signals compared to signals from internal standards. However, site specific quantification using these methods becomes challenging when dealing with non-specifically or randomly deuterated compounds that are produced by metal catalyzed hydrothermal reactions in D{sub 2}O, one of the most convenient deuteration methods. In this study, deuterium-induced NMR isotope shifts of quaternary {sup 13}C resonances neighboring deuterated sites have been utilized to quantify the degree of isotope labeling of molecular sites in non-specifically deuterated molecules. By probing {sup 13}C NMR signals while decoupling both proton and deuterium nuclei, it is possible to resolve {sup 13}C resonances of the different isotopologues based on the isotopic shifts and the degree of deuteration of the carbon atoms. We demonstrate that in different isotopologues, the same quaternary carbon, neighboring partially deuterated carbon atoms, are affected to an equal extent by relaxation. Decoupling both nuclei ({sup 1}H, {sup 2}H) resolves closely separated quaternary {sup 13}C signals of the different isotopologues, and allows their accurate integration and quantification under short relaxation delays (D1 = 1 s) and hence fast accumulative spectral acquisition. We have performed a number of approaches to quantify the deuterium content at different specific sites to demonstrate a convenient and generic analysis method for use in randomly deuterated molecules, or in cases of specifically deuterated molecules where back-exchange processes may take place during work up. - Graphical abstract: The relative intensities of quaternary {sup 13}C {"1H,"2H} resonances are equal despite the different relaxation delays, allowing the relative abundance of the different deuterated isotopologues to be calculated using NMR fast

  7. Hybrid Constraints of Pure and Mixed Pixels for Soft-Then-Hard Super-Resolution Mapping with Multiple Shifted Images

    NARCIS (Netherlands)

    Chen, Yuehong; Ge, Yong; Heuvelink, G.B.M.; Hu, Jianlong; Jiang, Yu

    2015-01-01

    Multiple shifted images (MSIs) have been widely applied to many super-resolution mapping (SRM) approaches to improve the accuracy of fine-scale land-cover maps. Most SRM methods with MSIs involve two processes: subpixel sharpening and class allocation. Complementary information from the MSIs has

  8. Photoacoustic Detection of Terahertz Radiation for Chemical Sensing and Imaging Applications

    Science.gov (United States)

    2013-03-01

    PHOTOACOUSTIC ... PHOTOACOUSTIC DETECTION OF TERAHERTZ RADIATION FOR CHEMICAL SENSING AND IMAGING THESIS Presented to the Faculty...AFIT-ENG-13-M-08 PHOTOACOUSTIC DETECTION OF TERAHERTZ RADIATION FOR CHEMICAL SENSING AND IMAGING Stjepan Blazevic, B. E. E

  9. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo D. [Yale Univ., New Haven, CT (United States). Dept. of Mechanical Engineering and Materials Science; Altman, Eric I. [Yale Univ., New Haven, CT (United States). Dept. of Chemical and Environmental Engineering

    2014-12-10

    The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3DAFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

  10. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo [Yale University

    2014-12-10

    The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3D-AFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

  11. NMR chemical shift as analytical derivative of the Helmholtz free energy

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case the paramagnetic part of the shielding tensor is expressed in terms of the $g$ and $A$ tensors of the EPR spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$, Nd$^{3+}$, Sm$^{3+...

  12. Infrared Chemical Nano-Imaging: Accessing Structure, Coupling, and Dynamics on Molecular Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Muller, Eric A.; Pollard, Benjamin; Raschke, Markus Bernd

    2015-04-02

    This Perspective highlights recent advances in infrared vibrational chemical nano-imaging. In its implementations of scattering scanning near-field optical microscopy (s-SNOM) and photothermal-induced resonance (PTIR), IR nanospectroscopy provides few-nanometer spatial resolution for the investigation of polymer, biomaterial, and related soft-matter surfaces and nanostructures. Broad-band IR s-SNOM with coherent laser and synchrotron sources allows for chemical recognition with small-ensemble sensitivity and the potential for sensitivity reaching the single-molecule limit. Probing selected vibrational marker resonances, it gives access to nanoscale chemical imaging of composition, domain morphologies, order/disorder, molecular orientation, or crystallographic phases. Local intra- and intermolecular coupling can be measured through frequency shifts of a vibrational marker in heterogeneous environments and associated inhomogeneities in vibrational dephasing. In combination with ultrafast spectroscopy, the vibrational coherent evolution of homogeneous sub-ensembles coupled to their environment can be observed. Outstanding challenges are discussed in terms of extensions to coherent and multidimensional spectroscopies, implementation in liquid and in situ environments, general sample limitations, and engineering s-SNOM scanning probes to better control the nano-localized optical excitation and to increase sensitivity.

  13. High-throughput Raman chemical imaging for evaluating food safety and quality

    Science.gov (United States)

    Qin, Jianwei; Chao, Kuanglin; Kim, Moon S.

    2014-05-01

    A line-scan hyperspectral system was developed to enable Raman chemical imaging for large sample areas. A custom-designed 785 nm line-laser based on a scanning mirror serves as an excitation source. A 45° dichroic beamsplitter reflects the laser light to form a 24 cm x 1 mm excitation line normally incident on the sample surface. Raman signals along the laser line are collected by a detection module consisting of a dispersive imaging spectrograph and a CCD camera. A hypercube is accumulated line by line as a motorized table moves the samples transversely through the laser line. The system covers a Raman shift range of -648.7-2889.0 cm-1 and a 23 cm wide area. An example application, for authenticating milk powder, was presented to demonstrate the system performance. In four minutes, the system acquired a 512x110x1024 hypercube (56,320 spectra) from four 47-mm-diameter Petri dishes containing four powder samples. Chemical images were created for detecting two adulterants (melamine and dicyandiamide) that had been mixed into the milk powder.

  14. In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Bohn, Paul W. [Univ. of Notre Dame, IN (United States); Shrout, J. D. [Univ. of Notre Dame, IN (United States); Sweedler, J. V. [Univ. of Illinois, Urbana-Champaign, IL (United States); Farrand, S. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2016-01-25

    This document constitutes the final technical report for DE-SC0006642, In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities, a project carried out collaboratively by investigators at Notre Dame and UIUC. The work carried out under DOE support in this project produced advances in two areas: development of new highly sophisticated correlated imaging approaches and the application of these new tools to the growth and differentiation of microbial communities under a variety of environmental conditions. A significant effort involved the creation of technical enhancements and sampling approaches to allow us to advance heterocorrelated mass spectrometry imaging (MSI) and correlated Raman microscopy (CRM) from bacterial cultures and biofilms. We then exploited these measurement advances in heterocorrelated MS/CRM imaging to determine relationship of signaling molecules and excreted signaling molecules produced by P. aeruginosa to conditions relevant to the rhizosphere. In particular, we: (1) developed a laboratory testbed mimic for the rhizosphere to enable microbial growth on slides under controlled conditions; (2) integrated specific measurements of (a) rhamnolipids, (b) quinolone/quinolones, and (c) phenazines specific to P. aeruginosa; and (3) utilized the imaging tools to probe how messenger secretion, quorum sensing and swarming behavior are correlated with behavior.

  15. PSK Shift Timing Information Detection Using Image Processing and a Matched Filter

    Science.gov (United States)

    2009-09-01

    PERR ). The probability of correct detection is defined as the probability of deciding there is a phase shift in the signal and its estimated location...detecting a phase shift when there is no actual phase shift. PACC and PERR are defined below in Equation(6.1): (0 | 0) (1 |1) and (1 | 0) (0 |1),ACC...agreed(:,1),agreedf(:,1),slen,wlen_u); % Calculates accuracy and error statistics for current run. disp(’ %H %Pfa %M %Pdet %Pacc % Perr

  16. Acoustic imaging for diagnostics of chemically reacting systems

    Science.gov (United States)

    Ramohalli, K.; Seshan, P.

    1983-01-01

    The concept of local diagnostics, in chemically reacting systems, with acoustic imaging is developed. The elements of acoustic imaging through ellipsoidal mirrors are theoretically discussed. In a general plan of the experimental program, the first system is chosen in these studies to be a simple open jet, non premixed turbulent flame. Methane is the fuel and enriched air is the oxidizer. This simple chemically reacting flow system is established at a Reynolds number (based on cold viscosity) of 50,000. A 1.5 m diameter high resolution acoustic mirror with an f-number of 0.75 is used to map the acoustic source zone along the axis of the flame. The results are presented as acoustic power spectra at various distances from the nozzle exit. It is seen that most of the reaction intensity is localized in a zone within 8 diameters from the exit. The bulk reactions (possibly around the periphery of the larger eddies) are evenly distributed along the length of the flame. Possibilities are seen for locally diagnosing single zones in a multiple cluster of reaction zones that occur frequently in practice. A brief outline is given of the future of this work which will be to apply this technique to chemically reacting flows not limited to combustion.

  17. Phase-shifting of correlation fringes created by image processing as an alternative to improve digital shearography

    Science.gov (United States)

    Braga, Roberto A.; González-Peña, Rolando J.; Marcon, Marlon; Magalhães, Ricardo R.; Paiva-Almeida, Thiago; Santos, Igor V. A.; Martins, Moisés

    2016-12-01

    The adoption of digital speckle pattern shearing interferometry, or speckle shearography, is well known in many areas when one needs to measure micro-displacements in-plane and out of the plane in biological and non-biological objects; it is based on the Michelson's Interferometer with the use of a piezoelectric transducer (PZT) in order to provide the phase-shift of the fringes and then to improve the quality of the final image. The creation of the shifting images using a PZT, despite its widespread use, has some drawbacks or limitations, such as the cost of the apparatus, the difficulties in applying the same displacement in the mirror repeated times, and when the phase-shift cannot be used in dynamic object measurement. The aim of this work was to create digitally phase-shift images avoiding the mechanical adjustments of the PZT, testing them with the digital shearography method. The methodology was tested using a well-known object, a cantilever beam of aluminium under deformation. The results documented the ability to create the deformation map and curves with reliability and sensitivity, reducing the cost, and improving the robustness and also the accessibility of digital speckle pattern shearing interferometry.

  18. Nonlinear chemical imaging microscopy: near-field third harmonic generation imaging of human red blood cells.

    Science.gov (United States)

    Schaller, R D; Johnson, J C; Saykally, R J

    2000-11-01

    Third harmonic generation (THG) imaging using a near-field scanning optical microscope (NSOM) is demonstrated for the first time. A femtosecond, tunable near-infrared laser was used to generate both nonresonant and resonantly enhanced third harmonic radiation in human red blood cells. We show that resonantly enhanced THG is a chemically specific bulk probe in NSOM imaging by tuning the excitation source onto and off of resonance with the Soret transition of oxyhemoglobin. Additionally, we provide evidence that tightly focused, nonresonant, far-field THG imaging experiments do not produce contrast that is truly surface specific.

  19. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Science.gov (United States)

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  20. Tabletop imaging of structural evolutions in chemical reactions

    CERN Document Server

    Ibrahim, Heide; Beaulieu, Samuel; Schmidt, Bruno E; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Sanderson, Joseph; Schuurman, Michael S; Légaré, François

    2014-01-01

    The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using VUV light from a Free Electron Laser [Phys. Rev. Lett. 105, 263002 (2010)]. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond-breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and definitively quantitative ab initio trajectory simulations.

  1. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning

    Science.gov (United States)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  2. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...... side missing structural elements in the models can be suggested. A number of proposed structures for humic and fulvic acids are discussed based on the above analysis....... shifts of all substructures from the proposed models. A full reconstruction makes sure that all carbons are accounted for and enables on the negative side to discuss structural elements identified from recorded spectra of humic substances that cannot be observed in the simulated spectrum. On the positive...

  3. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning.

    Science.gov (United States)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  4. Portable Sequentially Shifted Excitation Raman spectroscopy as an innovative tool for in situ chemical interrogation of painted surfaces.

    Science.gov (United States)

    Conti, Claudia; Botteon, Alessandra; Bertasa, Moira; Colombo, Chiara; Realini, Marco; Sali, Diego

    2016-08-07

    We present the first validation and application of portable Sequentially Shifted Excitation (SSE) Raman spectroscopy for the survey of painted layers in art. The method enables the acquisition of shifted Raman spectra and the recovery of the spectral data through the application of a suitable reconstruction algorithm. The technique has a great potentiality in art where commonly a strong fluorescence obscures the Raman signal of the target, especially when conventional portable Raman spectrometers are used for in situ analyses. Firstly, the analytical capability of portable SSE Raman spectroscopy is critically discussed using reference materials and laboratory specimens, comparing its results with other conventional high performance laboratory instruments (benchtop FT-Raman and dispersive Raman spectrometers with an external fiber optic probe); secondly, it is applied directly in situ to study the complex polychromy of Italian prestigious terracotta sculptures of the 16(th) century. Portable SSE Raman spectroscopy represents a new investigation modality in art, expanding the portfolio of non-invasive, chemically specific analytical tools.

  5. Microscopic structures of ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate in water probed by the relative chemical shift

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.

  6. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Science.gov (United States)

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts.

  7. Red, green, and blue gray-value shift-based approach to whole-field imaging for tissue diagnostics

    Science.gov (United States)

    Valiyambath Krishnan, Mohankumar; Vadakke Matham, Murukeshan; Krishnan, Sathiyamoorthy; Parasuraman, Padmanabhan; Joseph, James; Bhakoo, Kishore

    2012-07-01

    Identification of abnormal pathology in situ remains one of the challenges of medicine. The interpretation of tissue conditions relies mainly on optical assessment, which can be difficult due to inadequate visual differences or poor color delineation. We propose a methodology to identify regions of abnormal tissue in a targeted area based on red, green, blue (RGB) shift analysis employing a simple CCD color camera and light-emitting diode illumination in a whole-field-imaging scheme. The concept involves analysis of RGB components in an image with respect to a reference set of RGB values under different illumination wavelengths. The magnitude of the gray value shift is estimated by calculating the Euclidean distance between their normalized RGB coordinates. The shift values obtained using these concepts are thereafter used to construct pseudo-colored images with high contrast, enabling easy identification of abnormal areas in the tissue. Images processed from experiments conducted with excised Wistar rat colon sample (lightly doped with Alexafluor 488) and with simulated tumor (cancer cell pellet placed on colon) showed clear localization of tumor region. This proposed approach and methodology is expected to find potential applications for the in vivo diagnosis of disease.

  8. Zero discharge tanning: a shift from chemical to biocatalytic leather processing.

    Science.gov (United States)

    Thanikaivelan, Palanisamy; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni; Ramasami, Thirumalachari

    2002-10-01

    Beam house processes (Beam house processes generally mean liming-reliming processes, which employ beam.) contribute more than 60% of the total pollution from leather processing. The use of lime and sodium sulfide is of environmental concern (1, 2). Recently, the authors have developed an enzyme-based dehairing assisted with a very low amount of sodium sulfide, which completely avoids the use of lime. However, the dehaired pelt requires opening up of fiber bundles for further processing, where lime is employed to achieve this through osmotic swelling. Huge amounts of lime sludge and total solids are the main drawbacks of lime. An alternative bioprocess, based on alpha-amylase for fiber opening, has been attempted after enzymatic unhairing. This totally eliminates the use of lime in leather processing. This method enables subsequent processes and operations in leather making feasible without a deliming process. A control experiment was run in parallel using conventional liming-reliming processes. It has been found that the extent of opening up of fiber bundles using alpha-amylase is comparable to that of the control. This has been substantiated through scanning electron microscopic, stratigraphic chrome distribution analysis, and softness measurements. Performance of the leathers is shown to be on a par with leathers produced by the conventional process through physical and hand evaluation. Importantly, softness of the leathers is numerically proven to be comparable with that of control. The process also demonstrates reduction in chemical oxygen demand load by 45% and total solids load by 20% compared to the conventional process. The total dry sludge from the beam house processes is brought down from 152 to 8 kg for processing 1 ton of raw hides.

  9. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    Science.gov (United States)

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

  10. High-Frequency (1)H NMR Chemical Shifts of Sn(II) and Pb(II) Hydrides Induced by Relativistic Effects: Quest for Pb(II) Hydrides.

    Science.gov (United States)

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

    The role of relativistic effects on (1)H NMR chemical shifts of Sn(II) and Pb(II) hydrides is investigated by using fully relativistic DFT calculations. The stability of possible Pb(II) hydride isomers is studied together with their (1)H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These (1)H signals are dictated by sizable relativistic contributions due to spin-orbit coupling at the heavy atom and can be as large as 80 ppm for a hydrogen atom bound to Pb(II). Such high-frequency (1)H NMR chemical shifts of Pb(II) hydride resonances cannot be detected in the (1)H NMR spectra with standard experimental setup. Extended (1)H NMR spectral ranges are thus suggested for studies of Pb(II) compounds. Modulation of spin-orbit relativistic contribution to (1)H NMR chemical shift is found to be important also in the experimentally known Sn(II) hydrides. Because the (1)H NMR chemical shifts were found to be rather sensitive to the changes in the coordination sphere of the central metal in both Sn(II) and Pb(II) hydrides, their application for structural investigation is suggested.

  11. Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

    Science.gov (United States)

    Liu, Zizhong; Goddard, John D

    2009-12-17

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

  12. Electromagnetic organ tracking allows for real-time compensation of tissue shift in image-guided laparoscopic rectal surgery

    DEFF Research Database (Denmark)

    Wagner, Martin; Gondan, Matthias; Zöllner, Christian

    2016-01-01

    and intraoperative electromagnetic tracking(EMT) of the rectum. Methods. Three models were compared and evaluated for the compensation of tissue. deformation. For Model A no compensation was performed. Model B moved the corresponding points rigidly to the motion of the EMT sensor. Model C used five nested linear....... In laparoscopic rectal surgery the combination of electromagnetic organ tracking and preoperative imaging is a promising approach to compensate for intraoperative tissue shift in real-time....

  13. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    Science.gov (United States)

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique.

  14. Magnetic Doppler imaging of the chemically peculiar star HD 125248

    Science.gov (United States)

    Rusomarov, N.; Kochukhov, O.; Ryabchikova, T.; Ilyin, I.

    2016-04-01

    Context. Intermediate-mass, chemically peculiar stars with strong magnetic fields provide an excellent opportunity to study the topology of their surface magnetic fields and the interplay between magnetic geometries and abundance inhomogeneities in the atmospheres of these stars. Aims: We reconstruct detailed maps of the surface magnetic field and abundance distributions for the magnetic Ap star HD 125248. Methods: We performed the analysis based on phase-resolved, four Stokes parameter spectropolarimetric observations obtained with the HARPSpol instrument. These data were interpreted with the help of magnetic Doppler imaging techniques and model atmospheres taking the effects of strong magnetic fields and nonsolar chemical composition into account. Results: We improved the atmospheric parameters of the star, Teff = 9850 ± 250 K and log g = 4.05 ± 0.10. We performed detailed abundance analysis, which confirmed that HD 125248 has abundances typical of other Ap stars, and discovered significant vertical stratification effects for the Fe ii and Cr ii ions. We computed LSD Stokes profiles using several line masks corresponding to Fe-peak and rare earth elements, and studied their behavior with rotational phase. Combining previous longitudinal field measurements with our own observations, we improved the rotational period of the star Prot = 9.29558 ± 0.00006 d. Magnetic Doppler imaging of HD 125248 showed that its magnetic field is mostly poloidal and quasi-dipolar with two large spots of different polarity and field strength. The chemical maps of Fe, Cr, Ce, Nd, Gd, and Ti show abundance contrasts of 0.9-3.5 dex. Among these elements, the Fe abundance map does not show high-contrast features. Cr is overabundant around the negative magnetic pole and has 3.5 dex abundance range. The rare earth elements and Ti are overabundant near the positive magnetic pole. Conclusions: The magnetic field of HD 125248 has strong deviations from the classical oblique dipole field

  15. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

    Science.gov (United States)

    Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

    2013-06-11

    An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

  16. Reproducibility of Intra- and Inter-scanner Measurements of Liver Fat Using Complex Confounder-corrected Chemical Shift Encoded MRI at 3.0 Tesla

    Science.gov (United States)

    Wu, Bing; Han, Wei; Li, Zhenhong; Zhao, Yonghua; Ge, Mingmei; Guo, Xueqing; Wu, Xinhuai

    2016-01-01

    The purpose of this study was to prospectively evaluate the reproducibility of the proton density fat-fraction (PDFF) of the liver using the IDEAL algorithm, a quantitative confounder-corrected chemical-shift-encoded MRI method. Data were obtained from 15 volunteers on four different days. The first and the third examinations were conducted on scanner one with one-week intervals, while the second and the fourth tests were performed on scanner two with same time interval. For each test, two MR scans were performed, one before and one after a meal. Regions-of-interest measurements were manually calculated to estimate the PDFF in the right and left lobes on the PDFF images. Reproducibility was measured using the intra-class correlation coefficient (ICC). The ICCs of the PDFF in the right and left lobes were 0.935 and 0.878, respectively. The intra-scanner ICCs of the right lobe before and after a meal or at a one-week interval were 0.924 and 0.953, respectively. The inter-scanner ICCs of PDFF the next day and at a one-week interval were 0.920 and 0.864, respectively. The PDFF of liver derived from IDEAL demonstrated high intra- and inter-scanner measurement reproducibility. The PDFF of the right lobe before a meal was more reproducible than after-meal measurements. PMID:26763303

  17. Magnetic Doppler imaging of the chemically peculiar star HD 125248

    CERN Document Server

    Rusomarov, N; Ryabchikova, T; Ilyin, I

    2016-01-01

    Intermediate-mass, chemically peculiar stars with strong magnetic fields give us an excellent opportunity to study the topology of their surface magnetic fields and the interplay between magnetic geometries and abundance inhomogeneities in their atmospheres. We reconstruct detailed maps of the surface magnetic field and abundance distributions for the magnetic Ap star HD 125248. We performed the analysis based on phase-resolved, four Stokes parameter spectropolarimetric observations obtained with the HARPSpol instrument. These data were interpreted with the magnetic Doppler imaging technique. We improved the atmospheric parameters of the star, T_eff = 9850K +/- 250K and logg = 4.05 +/- 0.10. We performed detailed abundance analysis and discovered vertical stratification effects for the FeII and CrII ions. We computed LSD Stokes profiles and studied their behavior with rotational phase. We improved the rotational period of the star P_rot = 9.29558(6)d. Magnetic Doppler imaging of HD 125248 showed that its magn...

  18. Shifting Phases for Patchy Particles - Effect of mutagenesis and chemical modification on the phase diagram of human gamma D crystallin

    Science.gov (United States)

    McManus, Jennifer J.; James, Susan; McNamara, Ruth; Quinn, Michelle

    2014-03-01

    Single mutations in human gamma D crystallin (HGD), a protein found in the eye lens are associated with several childhood cataracts. Phase diagrams for several of these protein mutants have been measured and reveal that phase boundaries are shifted compared with the native protein, leading to condensation of protein in a physiologically relevant regime. Using HGD as a model protein, we have constructed phase diagrams for double mutants of the protein, incorporating two single amino acid substitutions for which phase diagrams are already known. In doing so, the characteristics of each of the single mutations are maintained but both are now present in the same protein particle. While these proteins are not of interest physiologically, this strategy allows the controlled synthesis of nano-scale patchy particles in which features associated with a known phase behavior can be included. It can also provide a strategy for the controlled crystallisation of proteins. Phase boundaries also change after the chemical modification of the protein, through the covalent attachment of fluorescent labels, for example, and this will also be discussed. The authors acknowledge Science Foundation Ireland Stokes Lectureship and Grant 11/RFP.1/PHY/3165. The authors also acknowledge the Irish Research Council and the John and Pat Hume Scholarship.

  19. Molecular structure and vibrational and chemical shift assignments of 3'-chloro-4-dimethylamino azobenzene by DFT calculations.

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-1) for solid state. The (1)H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  20. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    Science.gov (United States)

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

    The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

  1. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    Science.gov (United States)

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  2. Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

    Science.gov (United States)

    Jose, K V Jovan; Raghavachari, Krishnan

    2017-03-14

    We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0.01 ppm for (1)H chemical shifts and 0.07 ppm for (13)C chemical shifts. In addition, the performance of MIM-NMR has been assessed on two large peptides: the helical portion of ubiquitin ( 1UBQ ) containing 12 residues where the X-ray structure is known, and E6-binding protein of papilloma virus ( 1RIJ ) containing 23 residues where the structure has been derived from solution-phase NMR analysis. The solvation environment is incorporated in these MIM-NMR calculations, either through an explicit, implicit, or a combination of both solvation models. Using an explicit treatment of the solvent molecules within the first solvation sphere (3 Å) and an implicit solvation model for the rest of the interactions, the (1)H and (13)C chemical shifts of ubiquitin show excellent agreement with experiment (mean absolute deviation of 0.31 ppm for (1)H and 1.72 ppm for (13)C), while the larger E6-binding protein yields a mean absolute deviation of 0.34 ppm for (1)H chemical shifts. The proposed MIM-NMR method is computationally cost-effective and provides a substantial speedup relative to conventional full calculations, the largest density functional NMR calculation included in this work involving more than 600 atoms and over 10,000 basis functions. The MIM

  3. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)

    1998-07-15

    We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

  4. Multilinear relations between {sup 13} C NMR chemical shifts of aliphatic halides; Relacoes lineares multiplas entre deslocamentos quimicos em RMN {sup 13} C de haletos alifaticos

    Energy Technology Data Exchange (ETDEWEB)

    Doyama, Julio Toshimi [UNESP, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Quimica e Bioquimica; Tornero, Maria Teresinha Trovarelli [UNESP, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Bioestatistica; Yoshida, Massayoshi [UNESP, Araraquara, SP (Brazil). Inst. de Quimica. Dept. de Quimica Organica

    1999-07-01

    The {sup 13} C NMR chemical shifts of the {alpha}, {beta}, {gamma} and {delta} carbons of 17 sets of aliphatic halides (F, Cl, Br and I), including mono, bi and tricyclic compounds, can be reproduced by a linear equation composed with two constants and two variables: {delta}{sub RX} = A{sup *} {delta}{sub R-X2}, where A and B are constants derived from multilinear regression of {sup 13} C chemical shifts observed; {delta}{sub R-X}, the chemical shifts of aliphatic halide (R-X); and {delta}{sub R-X1}, {delta}{sub R-X2} the chemical shifts of other halides. It was observed a better correlation for aliphatic bromides (R-X) by using data of aliphatic fluorides (R-X 1) and aliphatic iodides (R-X 2), resulting R{sup 2} of 0.9989 and average absolute deviation (AVG) of 0.39 ppm. For the chlorides (R-X), the better correlation was observed by using data of bromides (R-X 1) was observed better correlation with data of bromides (R-X 1) and iodides (R-X 2), R{sup 2} of 0.997 and AVG of 1.10 ppm. For the iodides (R-X) was observed better correlation with data of fluorides (R-X 1) and bromides (R-X 2), R{sup 2} of 0.9972 and AVG of 0.60 ppm. (author)

  5. Chemical Imaging of the Cell Membrane by NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P K; Kraft, M L; Frisz, J F; Carpenter, K J; Hutcheon, I D

    2010-02-23

    The existence of lipid microdomains and their role in cell membrane organization are currently topics of great interest and controversy. The cell membrane is composed of a lipid bilayer with embedded proteins that can flow along the two-dimensional surface defined by the membrane. Microdomains, known as lipid rafts, are believed to play a central role in organizing this fluid system, enabling the cell membrane to carry out essential cellular processes, including protein recruitment and signal transduction. Lipid rafts are also implicated in cell invasion by pathogens, as in the case of the HIV. Therefore, understanding the role of lipid rafts in cell membrane organization not only has broad scientific implications, but also has practical implications for medical therapies. One of the major limitations on lipid organization research has been the inability to directly analyze lipid composition without introducing artifacts and at the relevant length-scales of tens to hundreds of nanometers. Fluorescence microscopy is widely used due to its sensitivity and specificity to the labeled species, but only the labeled components can be observed, fluorophores can alter the behavior of the lipids they label, and the length scales relevant to imaging cell membrane domains are between that probed by fluorescence resonance energy transfer (FRET) imaging (<10 nm) and the diffraction limit of light. Topographical features can be imaged on this length scale by atomic force microscopy (AFM), but the chemical composition of the observed structures cannot be determined. Immuno-labeling can be used to study the distribution of membrane proteins at high resolution, but not lipid composition. We are using imaging mass spectrometry by secondary ion mass spectrometry (SIMS) in concert with other high resolution imaging methods to overcome these limitations. The experimental approach of this project is to combine molecule-specific stable isotope labeling with high-resolution SIMS using a

  6. Three-dimensional surface imaging by multi-frequency phase shift profilometry with angle and pattern modeling for system calibration

    Science.gov (United States)

    Wang, Zhenzhou

    2016-08-01

    In this paper, we present a 3D surface imaging system based on the well-known phase shift profilometry. To yield the analytical solutions, four shifted phases and three high carrier frequencies are used to compute the phase map and reduce the noises that are caused by the inherent optical aberrations and external influences, e.g. different illumination light sources, uneven intensity distribution and automatic image processing algorithms. To reduce the system noise, we propose to model the pattern of the calibration grid in a virtual space. To obtain the modeled pattern, we use a plane to intercept the rays that are modeled by the proposed angle modeling method. In the world coordinate system, the angle and the pattern are computed based on the calibration data. A registration method is used to transform the modeled pattern in the virtual space to the ideal pattern in the world coordinate system by computing the least squared errors between the true points in the modeled pattern and the measured points in the practical pattern. The modeled (true) points are used for re-calibration of the 3D imaging system. Experimental results showed that the measurement accuracy increases considerably and the MSE is reduced from 0.95 mm to 0.65 mm (32% average error decrease) after replacing the measured points with the true points for calibration.

  7. Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; C Nayak; P Venu Babu; S N Jha; D Bhattacharyya

    2014-05-01

    Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2–3 eV were observed for U L3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds.

  8. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  9. Framework for a low-cost intra-operative image-guided neuronavigator including brain shift compensation

    CERN Document Server

    Bucki, Marek; Payan, Yohan

    2007-01-01

    In this paper we present a methodology to address the problem of brain tissue deformation referred to as 'brain-shift'. This deformation occurs throughout a neurosurgery intervention and strongly alters the accuracy of the neuronavigation systems used to date in clinical routine which rely solely on pre-operative patient imaging to locate the surgical target, such as a tumour or a functional area. After a general description of the framework of our intra-operative image-guided system, we describe a procedure to generate patient specific finite element meshes of the brain and propose a biomechanical model which can take into account tissue deformations and surgical procedures that modify the brain structure, like tumour or tissue resection.

  10. Relativistic four-component DFT calculations of 1H NMR chemical shifts in transition-metal hydride complexes: unusual high-field shifts beyond the Buckingham-Stephens model.

    Science.gov (United States)

    Hrobárik, Peter; Hrobáriková, Veronika; Meier, Florian; Repiský, Michal; Komorovský, Stanislav; Kaupp, Martin

    2011-06-09

    State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

  11. Catapulting Shifts in Images, Understandings, and Actions for Family Members through Research-Based Drama

    Science.gov (United States)

    Dupuis, Sherry L.; Gillies, Jennifer; Mitchell, Gail J.; Jonas-Simpson, Christine; Whyte, Colleen; Carson, Jennifer

    2011-01-01

    This article examined how images, understandings, and actions change for family members of persons with dementia after the introduction of a research-based drama called I'm Still Here. Guided by interpretivist phenomenology, a set of seven pre- and post-performance focus groups were conducted with family members (n = 48) in four cities. Findings…

  12. Shift of the pyramidal tract during resection of the intraaxial brain tumors estimated by intraoperative diffusion-weighted imaging.

    Science.gov (United States)

    Ozawa, Norihiko; Muragaki, Yoshihiro; Nakamura, Ryoichi; Hori, Tomokatsu; Iseki, Hiroshi

    2009-02-01

    The present study evaluated the shift of the pyramidal tract during resection of 17 proximal intraaxial brain tumors. In each case intraoperative diffusion-weighted (iDW) magnetic resonance imaging with a motion-probing gradient applied in the anteroposterior direction was performed using a scanner with a 0.3 T vertical magnetic field. The position of the white matter bundles containing the pyramidal tract was estimated on the coronal images before and after resection of the neoplasm, and both quantitative and directional evaluation of its displacement was done. In all cases iDW imaging provided visualization of the structure of interest. The magnitude of the pyramidal tract displacement due to removal of the neoplasm varied from 0.5 to 8.7 mm (mean 4.4 +/- 2.5 mm) on the lesion side and from 0 to 3.6 mm (mean 1.3 +/- 1.1 mm) on the normal side (p iDW imaging with updated neuronavigation.

  13. Translation of infrared chemical imaging for cardiovascular evaluation

    Science.gov (United States)

    Tiwari, Saumya; Raman, Jai; Reddy, Vijaya; Dawson, Miranda; Bhargava, Rohit

    2016-03-01

    Infrared (IR) spectroscopic imaging has been applied to study histology of cardiovascular tissue, primarily using Fourier transform IR (FTIR) Imaging. Here we describe results for histologic imaging of cardiac biopsies using a fast, discrete frequency IR (DFIR) imaging system. Histologic classification of tissue is understood in terms of the constituent frequencies and speeded up by careful optimization of the data acquired. Results are compared to FTIR imaging in terms of the signal to noise ratio and information content.

  14. Proton-detected 3D (15)N/(1)H/(1)H isotropic/anisotropic/isotropic chemical shift correlation solid-state NMR at 70kHz MAS.

    Science.gov (United States)

    Pandey, Manoj Kumar; Yarava, Jayasubba Reddy; Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2016-01-01

    Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL).

  15. Solvent-induced chemical shifts of methoxyl nuclear resonance signals in chalcones by benzene and trifluoroacetic acid

    Science.gov (United States)

    Khurana, Shashi K.; Krishnamoorthy, V.; Parmar, Virinder S.

    The 1H NMR spectra of eight different methoxylated chalcones have separately been recorded, (1) in deuterated chloroform; (2) in a mixture (1:1) of deuterated chloroform and benzene; and (3) in a mixture of deuterated chloroform, benzene and trifluoroacetic acid (2:2:1) and the benzene induced and TFA induced shift values have been assigned to different methoxyl groups. These shift values can serve as a guide in determining the structures of natural or new chalcones. The steric, electronic and conformational factors are discussed to explain the shift values.

  16. Precision Measurement of the Quadrupole Coupling and Chemical Shift Tensors of the Deuterons in α-Calcium Formate

    Science.gov (United States)

    Schmitt, Heike; Zimmermann, H.; Körner, O.; Stumber, M.; Meinel, C.; Haeberlen, U.

    2001-07-01

    Using calcium formate, α-Ca(DCOO)2, as a test sample, we explore how precisely deuteron quadrupole coupling (QC) and chemical shift (CS) tensors Q and σ can currently be measured. The error limits, ±0.09 kHz for the components of Q and ±0.06 ppm for those of σ, are at least three times lower than in any comparable previous experiment. The concept of a new receiver is described. A signal/noise ratio of 100 is realized in single-shot FT spectra. The measurement strategies and a detailed error analysis are presented. The precision of the measurement of Q is limited by the uncertainty of the rotation angles of the sample and that of σ by the uncertainty of the phase correction parameters needed in FT spectroscopy. With a 4-sigma confidence, it is demonstrated for the first time that the unique QC tensor direction of a deuteron attached to a carbon deviates from the bond direction; the deviation found is (1.2±0.3°). Evidence is provided for intermolecular QC contributions. In terms of Q, their size is roughly 4 kHz. The deuteron QC tensors in α-Ca(DCOO)2 (two independent deuteron sites) are remarkable in three respects. For deuterons attached to sp2 carbons, first, the asymmetry factors η and, second, the quadrupole coupling constants CQ, are unusually small, η1=0.018, η2=0.011, and CQ1=(151.27±0.06) kHz, CQ2=(154.09±0.06) kHz. Third, the principal direction associated with the largest negative QC tensor component lies in and not, as usual, perpendicular to the molecular plane. A rationalization is provided for these observations. The CS tensors obtained are in quantitative agreement with the results of an earlier, less precise, line-narrowing multiple-pulse study of α-Ca(HCOO)2. The assignment proposed in that work is confirmed. Finally we argue that a further 10-fold increase of the measurement precision of deuteron QC tensors, and a 2-fold increase of that of CS tensors, should be possible. We indicate the measures that need to be taken.

  17. Detection of chemical vapor with high sensitivity by using the symmetrical metal-cladding waveguide-enhanced Goos-Hänchen shift.

    Science.gov (United States)

    Nie, Yiyou; Li, Yuanhua; Wu, Zhijing; Wang, Xianping; Yuan, Wen; Sang, Minghuang

    2014-04-21

    We present a novel and simple optical structure, i.e., the symmetrical metal-cladding waveguide, in which a polymer layer is added into the guiding layer, for sensitive detection of chemical vapor by using the enhanced Goos-Hänchen (GH) shift (nearly a millimeter scale). Owing to the high sensitivity of the excited ultrahigh-order modes, the vapor-induced effect (swelling effect and refractive index change) in the polymer layer will lead to a dramatic variation of the GH shift. The detected GH shift signal is irrelevant to the power fluctuation of the incident light. The detection limit of 9.5 ppm for toluene and 28.5 ppm for benzene has been achieved.

  18. Chemical shifts of K-X-ray absorption edges on copper in different compounds by X-ray absorption spectroscopy (XAS) with Synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, D., E-mail: djoseph@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S.; Jha, S.N.; Bhattacharyya, D. [Applied Spectroscopy Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH{sub 3}CO{sub 2}){sub 2}, Cu(CO{sub 3}){sub 2}, and CuSO{sub 4} where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of {approx}4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

  19. Chemical shifts of K-X-ray absorption edges on copper in different compounds by X-ray absorption spectroscopy (XAS) with Synchrotron radiation

    Science.gov (United States)

    Joseph, D.; Basu, S.; Jha, S. N.; Bhattacharyya, D.

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH3CO2)2, Cu(CO3)2, and CuSO4 where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of ˜4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

  20. Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

    2012-12-15

    We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

  1. EVALUATION OF CHROMATICITY COORDINATES SHIFT FOR IMAGE DISPLAYED ON LIQUID CRYSTAL PANELS WITH VARIOUS PROPERTIES ON COLOR REPRODUCTION

    Directory of Open Access Journals (Sweden)

    I. O. Zharinov

    2016-03-01

    Full Text Available Subject of Research.We consider the problem of evaluation of chromaticity coordinates shift for image displayed on liquid crystal panels with various properties on color reproduction. A mathematical model represents the color reproduction characteristics. The spread of the color characteristics of the screens has a statistical nature. Differences of color reproduction for screens are perceived by the observer in the form of different colors and shades that are displayed on the same type of commercially available screens. Color differences are characterized by numerical measure of the difference of colors and can be mathematically compensated. The solution of accounting problem of the statistical nature of the color characteristics spread for the screens has a particular relevance to aviation instrumentation. Method. Evaluation of chromaticity coordinates shift of the image is based on the application of the Grassmann laws of color mixing.Basic data for quantitative calculation of shift are the profiles of two different liquid crystal panels defined by matrixes of scales for components of primary colors (red, green, blue. The calculation is based on solving the system of equations and calculating the color difference in the XY-plane. In general, the calculation can be performed in other color spaces: UV, Lab. The statistical nature of the spread of the color characteristics for the screens is accounted for in the proposed mathematical model based on the interval setting of coordinate values of the color gamut triangle vertices on the set of commercially available samples. Main Results. Carried outresearches result in the mathematical expressions allowing to recalculate values of chromaticity coordinates of the image displayed on various samples of liquid crystal screens. It is shown that the spread of the color characteristics of the screens follows bivariate normal distribution law with the accuracy sufficient for practice. The results of

  2. Evidence of chemical-potential shift with hole doping in Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8+. delta

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Z.; Dessau, D.S.; Wells, B.O. (Stanford Electronics Laboratory, Stanford University, Stanford, California 94305 (United States)); Olson, C.G. (Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States)); Mitzi, D.B.; Lombado, L. (Department of Applied Physics, Stanford University, Stanford, California 94305 (United States)); List, R.S.; Arko, A.J. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States))

    1991-12-01

    We have performed photoemission studies on high-quality Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} samples with various {delta}. Our results show a clear chemical-potential shift (0.15--0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime.

  3. Progress in spin dynamics solid-state nuclear magnetic resonance with the application of Floquet-Magnus expansion to chemical shift anisotropy.

    Science.gov (United States)

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence.

  4. Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging

    Directory of Open Access Journals (Sweden)

    Trong-Kha Truong

    2015-01-01

    Full Text Available In most diffusion tensor imaging (DTI studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR. However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact. Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2*-weighting (i.e., Type 3 artifact. These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

  5. Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging.

    Science.gov (United States)

    Truong, Trong-Kha; Song, Allen W; Chen, Nan-Kuei

    2015-01-01

    In most diffusion tensor imaging (DTI) studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI) sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR). However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact). Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact) associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2(∗) -weighting (i.e., Type 3 artifact). These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

  6. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  7. Homonuclear chemical shift correlation in rotating solids via RN{sup {nu}}{sub n} symmetry-based adiabatic RF pulse schemes

    Energy Technology Data Exchange (ETDEWEB)

    Riedel, Kerstin; Leppert, Joerg; Haefner, Sabine; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai [Institut fuer Molekulare Biotechnologie, Abteilung Molekulare Biophysik/NMR-Spektroskopie (Germany)], E-mail: raman@imb-jena.de

    2004-12-15

    The efficacy of RN{sup {nu}}{sub n} symmetry-based adiabatic Zero-Quantum (ZQ) dipolar recoupling schemes for obtaining chemical shift correlation data at moderate magic angle spinning frequencies has been evaluated. RN{sub n}{sup {nu}} sequences generally employ basic inversion elements that correspond to a net 180 deg. rotation about the rotating frame x-axis. It is shown here via numerical simulations and experimental measurements that it is also possible to achieve efficient ZQ dipolar recoupling via RN{sub n}{sup {nu}} schemes employing adiabatic pulses. Such an approach was successfully used for obtaining {sup 1}3C chemical shift correlation spectra of a uniformly labelled sample of (CUG){sub 9}7- a triplet repeat expansion RNA that has been implicated in the neuromuscular disease myotonic dystrophy. An analysis of the {sup 1}3C sugar carbon chemical shifts suggests, in agreement with our recent {sup 1}5N MAS-NMR studies, that this RNA adopts an A-helical conformation.

  8. Doppler shift of the quiet region measured by meridional scans with the EUV Imaging Spectrometer onboard Hinode

    CERN Document Server

    Kitagawa, N; Yokoyama, T

    2015-01-01

    Spatially averaged (> 50'') EUV spectral lines in the transition region of solar quiet regions are known to be redshifted. Because the mechanism underlying this phenomenon is unclear, we require additional physical information on the lower corona for limiting the theoretical models. To acquire this information, we measured the Doppler shifts over a wide coronal temperature range (log T[K]=5.7--6.3) using the spectroscopic data taken by the Hinode EUV Imaging Spectrometer. By analyzing the data over the center-to-limb variations covering the meridian from the south to the north pole, we successfully measured the velocity to an accuracy of 3 km/s. Below log T[K] = 6.0, the Doppler shifts of the emission lines were almost zero with an error of 1--3 km/s; above this temperature, they were blueshifted with a gradually increasing magnitude, reaching - 6.3 +/- 2.1 km/s at log T[K]=6.25.

  9. Identification of Zinc-ligated Cysteine Residues Based on {sup 13}C{alpha} and {sup 13}C{beta} Chemical Shift Data

    Energy Technology Data Exchange (ETDEWEB)

    Kornhaber, Gregory J.; Snyder, David; Moseley, Hunter N. B.; Montelione, Gaetano T. [Rutgers University, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry (United States)], E-mail: guy@cabm.rutgers.edu

    2006-04-15

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped {sup 13}C{beta} chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding {sup 13}C{alpha} chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 {sup 13}C{alpha}/{sup 13}C{beta} shift pairs from 79 proteins with known three-dimensional structures, including 86 {sup 13}C{alpha} and{sup 13}C{beta} shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statisical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into

  10. X-ray photon-in/photon-out methods for chemical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Marcus, Matthew A.

    2010-03-24

    Most interesting materials in nature are heterogeneous, so it is useful to have analytical techniques with spatial resolution sufficient to resolve these heterogeneities.This article presents the basics of X-ray photon-in/photon-out chemical imaging. This family of methods allows one to derive images reflectingthe chemical state of a given element in a complex sample, at micron or deep sub-micron scale. X-ray chemical imaging is relatively non-destructiveand element-selective, and requires minimal sample preparation. The article presents the basic concepts and some considerations of data takingand data analysis, along with some examples.

  11. Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Wookyung [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of); Lee, Woonghee; Lee, Weontae [Yonsei University, Department of Biochemistry, Structural Biochemistry and Molecular Biophysics Laboratory (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry, Biochemistry and Bio-NMR Laboratory (Korea, Republic of); Chang, Iksoo, E-mail: iksoochang@pusan.ac.kr [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of)

    2011-12-15

    Unravelling the complex correlation between chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the

  12. Metal Artifact Reduction and Segmentation of Dental Computerized Tomography Images Using Least Square Support Vector Machine and Mean Shift Algorithm.

    Science.gov (United States)

    Mortaheb, Parinaz; Rezaeian, Mehdi

    2016-01-01

    Segmentation and three-dimensional (3D) visualization of teeth in dental computerized tomography (CT) images are of dentists' requirements for both abnormalities diagnosis and the treatments such as dental implant and orthodontic planning. On the other hand, dental CT image segmentation is a difficult process because of the specific characteristics of the tooth's structure. This paper presents a method for automatic segmentation of dental CT images. We present a multi-step method, which starts with a preprocessing phase to reduce the metal artifact using the least square support vector machine. Integral intensity profile is then applied to detect each tooth's region candidates. Finally, the mean shift algorithm is used to partition the region of each tooth, and all these segmented slices are then applied for 3D visualization of teeth. Examining the performance of our proposed approach, a set of reliable assessment metrics is utilized. We applied the segmentation method on 14 cone-beam CT datasets. Functionality analysis of the proposed method demonstrated precise segmentation results on different sample slices. Accuracy analysis of the proposed method indicates that we can increase the sensitivity, specificity, precision, and accuracy of the segmentation results by 83.24%, 98.35%, 72.77%, and 97.62% and decrease the error rate by 2.34%. The experimental results show that the proposed approach performs well on different types of CT images and has better performance than all existing approaches. Moreover, segmentation results can be more accurate by using the proposed algorithm of metal artifact reduction in the preprocessing phase.

  13. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    Science.gov (United States)

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order.

  14. The 'Densitometric Image Analysis Software' and its application to determine stepwise equilibrium constants from electrophoretic mobility shift assays.

    Directory of Open Access Journals (Sweden)

    Liesbeth van Oeffelen

    Full Text Available Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad and the Intelligent or Advanced Quantifier (Bio Image do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the 'Densitometric Image Analysis Software' has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs. For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.

  15. Effects of irritant chemicals on Aedes aegypti resting behavior: is there a simple shift to untreated "safe sites"?

    Directory of Open Access Journals (Sweden)

    Hortance Manda

    2011-07-01

    Full Text Available BACKGROUND: Previous studies have identified the behavioral responses of Aedes aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant chemical actions will, however, require full knowledge of variables that influence vector resting behavior and how untreated "safe sites" contribute to overall impact. METHODS: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU were evaluated against two material types (cotton and polyester at various dark:light surface area coverage (SAC ratio and contrast configuration (horizontal and vertical under chemical-free and treated conditions. Chemicals evaluated were alphacypermethrin and DDT at varying concentrations. RESULTS: Under chemical-free conditions, dark material had significantly higher resting counts compared to light material at all SAC, and significantly increased when material was in horizontal configuration. Cotton elicited stronger response than polyester. Within the treatment assays, significantly higher resting counts were observed on chemical-treated dark material compared to untreated light fabric. However, compared to matched controls, significantly less resting observations were made on chemical-treated dark material overall. Most importantly, resting observations on untreated light material (or "safe sites" in the treatment assay did not significantly increase for many of the tests, even at 25% SAC. Knockdown rates were ≤5% for all assays. Significantly more observations of flying mosquitoes were made in test assays under chemical-treatment conditions as compared to controls. CONCLUSIONS/SIGNIFICANCE: When preferred Ae. aegypti resting sites are treated with chemicals, even at reduced treatment coverage area, mosquitoes do not simply move to safe sites (untreated areas following contact with the treated material. Instead, they become agitated

  16. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  17. Influence of volumes of prostate, rectum, and bladder on treatment planning CT on interfraction prostate shifts during ultrasound image-guided IMRT

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Nandanuri M. S.; Nori, Dattatreyudu; Sartin, William; Maiorano, Samuel; Modena, Jennifer; Mazur, Andrej; Osian, Adrian; Sood, Brijmohan; Ravi, Akkamma; Sampath, Seshadri; Lange, Christopher S. [Department of Radiation Oncology, New York Hospital Queens, Flushing, New York 11355 (United States); Department of Radiation Oncology, New York Hospital Queens, Flushing, New York 11355 and Department of Radiation Oncology, New York Presbyterian Hospital Weill-Cornell Medical Center, New York, New York 10021 (United States); Department of Radiation Oncology, New York Hospital Queens, Flushing, New York 11355 (United States); Department of Radiation Oncology, New York Hospital Queens, Flushing, New York 11355 and Department of Radiation Oncology, New York Presbyterian Hospital Weill-Cornell Medical Center, New York, New York 10021 (United States); Department of Radiation Oncology, New York Hospital Queens, Flushing, New York 11355 (United States); Department of Radiation Oncology, State University of New York, Brooklyn, New York 11203 (United States)

    2009-12-15

    Purpose: The purpose of this study was to analyze the relationship between prostate, bladder, and rectum volumes on treatment planning CT day and prostate shifts in the XYZ directions on treatment days. Methods: Prostate, seminal vesicles, bladder, and rectum were contoured on CT images obtained in supine position. Intensity modulated radiation therapy plans was prepared. Contours were exported to BAT-ultrasound imaging system. Patients were positioned on the couch using skin marks. An ultrasound probe was used to obtain ultrasound images of prostate, bladder, and rectum, which were aligned with CT images. Couch shifts in the XYZ directions as recommended by BAT system were made and recorded. 4698 couch shifts for 42 patients were analyzed to study the correlations between interfraction prostate shifts vs bladder, rectum, and prostate volumes on planning CT. Results: Mean and range of volumes (cc): Bladder: 179 (42-582), rectum: 108 (28-223), and prostate: 55 (21-154). Mean systematic prostate shifts were (cm, {+-}SD) right and left lateral: -0.047{+-}0.16 (-0.361-0.251), anterior and posterior: 0.14{+-}0.3 (-0.466-0.669), and superior and inferior: 0.19{+-}0.26 (-0.342-0.633). Bladder volume was not correlated with lateral, anterior/posterior, and superior/inferior prostate shifts (P>0.2). Rectal volume was correlated with anterior/posterior (P<0.001) but not with lateral and superior/inferior prostate shifts (P>0.2). The smaller the rectal volume or cross sectional area, the larger was the prostate shift anteriorly and vice versa (P<0.001). Prostate volume was correlated with superior/inferior (P<0.05) but not with lateral and anterior/posterior prostate shifts (P>0.2). The smaller the prostate volume, the larger was prostate shift superiorly and vice versa (P<0.05). Conclusions: Prostate and rectal volumes, but not bladder volumes, on treatment planning CT influenced prostate position on treatment fractions. Daily image-guided adoptive radiotherapy would be

  18. Radiochemistry, PET Imaging, and the Internet of Chemical Things.

    Science.gov (United States)

    Thompson, Stephen; Kilbourn, Michael R; Scott, Peter J H

    2016-08-24

    The Internet of Chemical Things (IoCT), a growing network of computers, mobile devices, online resources, software suites, laboratory equipment, synthesis apparatus, analytical devices, and a host of other machines, all interconnected to users, manufacturers, and others through the infrastructure of the Internet, is changing how we do chemistry. While in its infancy across many chemistry laboratories and departments, it became apparent when considering our own work synthesizing radiopharmaceuticals for positron emission tomography (PET) that a more mature incarnation of the IoCT already exists. How does the IoCT impact our lives today, and what does it hold for the smart (radio)chemical laboratories of the future?

  19. 平衡电负性与烷烃核磁共振碳谱位移%EQUILIBRIUM ELECTRONEGATIVITY AND 13C NMR CHEMICAL SHIFTS OF ALKANES

    Institute of Scientific and Technical Information of China (English)

    聂长明; 文松年

    2001-01-01

    In this paper, the atomic equilibrium electronegativity in a molecule has been defined and the model of 13C NMR chemical shifts of alkanes has been studied with the atomic equilibrium electronegativity and the structural information parameters NiH(i=0,α,β,γ) and NjC(j=α,β,γ). The results indicate that the 13C NMR chemical shifts of alkanes can be described as follows: CS=-1736.776+755.118AEE+5.2539N0H+1.8837NβH-0.2066NγH By the use of the formula the chemical shifts of 99 carbon atoms are predicated, and the standard error is only 0.9861ppm. The average absolute error is 0.78ppm, The calculated values conform very much to the observed values.%定义了烷烃分子中碳原子的平衡电负性(AEE),用平衡电负性和NiH(i=0,α,β,γ)和NjC(j=α,β,γ)结构信息参数研究了烷烃的13C NMR化学位移模型.结果表明,烷烃13C NMR化学位移(CS)可用下式来定量描述: CS=-1736.776+755.118AEE+5.2539N0H+1.8837NβH-0.2066NγH   用上式估算了99个碳原子的化学位移,标准差为0.9861ppm,平均绝对误差0.78ppm,预测值与实验值十分吻合.

  20. 1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

    Science.gov (United States)

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2013-03-01

    The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons.

  1. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof

    2013-01-01

    Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory and their 13C NMR isotropic nuclear shieldings were predicted using density functional theory (DFT). The model compounds contained 9H-, N-methyl and N-ethyl derivatives......). The decreasing electronegativity of the halogen substituent (F, Cl, Br and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions...

  2. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  3. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    Science.gov (United States)

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  4. 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide.

    Science.gov (United States)

    Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J

    2011-10-01

    SH2 domains are interaction modules uniquely dedicated to recognize phosphotyrosine sites, playing a central role in for instance the activation of tyrosine kinases or phosphatases. Here we report the (1)H, (15)N and (13)C backbone and side-chain chemical shift assignments of the SH2 domain of the human protein tyrosine kinase Fyn, both in its free state and bound to a high-affinity phosphotyrosine peptide corresponding to a specific sequence in the hamster middle-T antigen. The BMRB accession numbers are 17,368 and 17,369, respectively.

  5. Wafer-based aberration metrology for lithographic systems using overlay measurements on targets imaged from phase-shift gratings.

    Science.gov (United States)

    van Haver, Sven; Coene, Wim M J; D'havé, Koen; Geypen, Niels; van Adrichem, Paul; de Winter, Laurens; Janssen, Augustus J E M; Cheng, Shaunee

    2014-04-20

    In this paper, a new methodology is presented to derive the aberration state of a lithographic projection system from wafer metrology data. For this purpose, new types of phase-shift gratings (PSGs) are introduced, with special features that give rise to a simple linear relation between the PSG image displacement and the phase aberration function of the imaging system. By using the PSGs as the top grating in a diffraction-based overlay stack, their displacement can be measured as an overlay error using a standard wafer metrology tool. In this way, the overlay error can be used as a measurand based on which the phase aberration function in the exit pupil of the lithographic system can be reconstructed. In practice, the overlay error is measured for a set of different PSG targets, after which this information serves as input to a least-squares optimization problem that, upon solving, provides estimates for the Zernike coefficients describing the aberration state of the lithographic system. In addition to a detailed method description, this paper also deals with the additional complications that arise when the method is implemented experimentally and this leads to a number of model refinements and a required calibration step. Finally, the overall performance of the method is assessed through a number of experiments in which the aberration state of the lithographic system is intentionally detuned and subsequently estimated by the new method. These experiments show a remarkably good agreement, with an error smaller than 5  mλ, among the requested aberrations, the aberrations measured by the on-tool aberration sensor, and the results of the new wafer-based method.

  6. Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

    Science.gov (United States)

    Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A

    2016-01-01

    Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

  7. Excitation-resolved wide-field fluorescence imaging of indocyanine green visualizes the microenvironment properties in vivo via solvatochromic shift (Conference Presentation)

    Science.gov (United States)

    Cho, Jaedu; Kim, Chang-Seok; Gulsen, Gultekin

    2016-03-01

    Near-infrared fluorescence imaging (NIRF) is a powerful wide-field optical imaging tool that has a potential to visualize molecular-specific exogenous fluorescence agents, such as FDA approved Indocyanine Green (ICG), in thick tissue. Indeed, ICG is sensitive to biochemical environment such that it can be used to detect micro- or macroscopic environmental changes in tissue by solvatochromic shift that is defined by the dependence of absorption and emission spectra with the solvent polarity. For example, dimethyl sulfoxide (DMSO) is a very powerful drug carrier that can penetrate biological barriers such as the skin, the membranes, and the blood-brain-barrier. In presence of DMSO, ICG in tissue shows the excitation blue shift. However, NIRF imaging of microenvironment dependent changes of ICG has been challenging for the following reasons. First, the Stoke's shift of ICG is too small to separate the excitation and emission spectra easily. Second, the solvatochromic shift of ICG is too small to be detected by conventional NIRF techniques. Last but not least, the multiple scattering in tissue degrades not only the spatial information but also the spectral contents by the red-shift. We developed a wavelength-swept laser-based NIRF system that can resolve the excitation shift of ICG in tissue such that DMSO can be indirectly visualized. We plan to conduct an in-vivo lymph-node drug-delivery study in a mouse model to show feasibility of the indirect imaging of the drug-carrier with the wavelength-swept-laser based NIRF system.

  8. Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

    Energy Technology Data Exchange (ETDEWEB)

    Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)

    2012-07-15

    The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 {+-} 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. (orig.)

  9. Ultrasound imaging of oxidative stress in vivo with chemically-generated gas microbubbles.

    Science.gov (United States)

    Perng, John Kangchun; Lee, Seungjun; Kundu, Kousik; Caskey, Charles F; Knight, Sarah F; Satir, Sarp; Ferrara, Katherine W; Taylor, W Robert; Degertekin, F Levent; Sorescu, Daniel; Murthy, Niren

    2012-09-01

    Ultrasound contrast agents (UCAs) have tremendous potential for in vivo molecular imaging because of their high sensitivity. However, the diagnostic potential of UCAs has been difficult to exploit because current UCAs are based on pre-formed microbubbles, which can only detect cell surface receptors. Here, we demonstrate that chemical reactions that generate gas forming molecules can be used to perform molecular imaging by ultrasound in vivo. This new approach was demonstrated by imaging reactive oxygen species in vivo with allylhydrazine, a liquid compound that is converted into nitrogen and propylene gas after reacting with radical oxidants. We demonstrate that allylhydrazine encapsulated within liposomes can detect a 10 micromolar concentration of radical oxidants by ultrasound, and can image oxidative stress in mice, induced by lipopolysaccharide, using a clinical ultrasound system. We anticipate numerous applications of chemically-generated microbubbles for molecular imaging by ultrasound, given ultrasound's ability to detect small increments above the gas saturation limit, its spatial resolution and widespread clinical use.

  10. Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

    2015-07-15

    A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.

  11. Free variable selection QSPR study to predict (19)F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods.

    Science.gov (United States)

    Goudarzi, Nasser

    2016-04-05

    In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the (19)F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the (19)F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.

  12. Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

    Science.gov (United States)

    Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

    2010-03-17

    Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

  13. Optical Red shift in ZnO Nanoflowers Fabricated on Non-Seeded Substrates by Soft Wet Chemical Route

    Science.gov (United States)

    Murali, K. V.; Preetha, K. C.; Ragina, A. J.; Deepa, K.; Remadevi, T. L.

    2011-10-01

    Zinc oxide (ZnO) nanoflowers were fabricated on non-seeded glass substrates by successive ionic layer adsorption and reaction (SILAR) method using different complex agents. Influence of complex agents ammonia, lithium hydroxide and hexamine on the optical properties of the as-synthesized and the samples annealed at 400 °C was studied. Optical red shift was observed in ZnO samples and was analyzed with respect to the complex agents. All samples possessed a steep absorption edge in the wavelength range 375-425 nm. ZnO nanostructures except that synthesized using hexamine have low and steady absorbance and show higher transmittance (70-85%) in the entire visible region. SEM, XRD and EDAX studies confirmed the high surface-to-volume ratio, good optical quality, excellent crystalline nature and purity of the formed and annealed ZnO nanostructures.

  14. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  15. Phase-shifting digital holography in image reconstruction%基于数字移相全息的图像重构

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A phase-shifting digital holography scheme developed to investigate internal defects in artworks is described. Phase-shifting is utilized to obtain a clear reconstructed object wave from a rough surface texture. A reverse-transform algorithm is employed to reconstruct the object wave on its original position of unknown distance or the imaging position from the object wave information on the holographic plane. To get the clearest reconstruction the exact registration of the unknown distance is determined by applying the intensity sum as the auto-focusing function. The spatial resolution of the reconstruction image is also investigated for a variety of affecting factors. Laboratory results of reconstruction images under deformation are presented.

  16. In vivo single-shot (13)C spectroscopic imaging of hyperpolarized metabolites by spatiotemporal encoding

    DEFF Research Database (Denmark)

    Schmidt, Rita; Laustsen, Christoffer; Dumez, Jean-Nicolas;

    2014-01-01

    on spatiotemporal encoding (SPEN) principles, to derive chemical-shift images within a sub-second period. By contrast to EPSI, SPEN does not require oscillating acquisition gradients to deliver chemical-shift information: its signal encodes both spatial as well as chemical shift information, at no extra cost...

  17. Imaging the neural circuitry and chemical control of aggressive motivation

    Directory of Open Access Journals (Sweden)

    Blanchard D Caroline

    2008-11-01

    Full Text Available Abstract Background With the advent of functional magnetic resonance imaging (fMRI in awake animals it is possible to resolve patterns of neuronal activity across the entire brain with high spatial and temporal resolution. Synchronized changes in neuronal activity across multiple brain areas can be viewed as functional neuroanatomical circuits coordinating the thoughts, memories and emotions for particular behaviors. To this end, fMRI in conscious rats combined with 3D computational analysis was used to identifying the putative distributed neural circuit involved in aggressive motivation and how this circuit is affected by drugs that block aggressive behavior. Results To trigger aggressive motivation, male rats were presented with their female cage mate plus a novel male intruder in the bore of the magnet during image acquisition. As expected, brain areas previously identified as critical in the organization and expression of aggressive behavior were activated, e.g., lateral hypothalamus, medial basal amygdala. Unexpected was the intense activation of the forebrain cortex and anterior thalamic nuclei. Oral administration of a selective vasopressin V1a receptor antagonist SRX251 or the selective serotonin reuptake inhibitor fluoxetine, drugs that block aggressive behavior, both caused a general suppression of the distributed neural circuit involved in aggressive motivation. However, the effect of SRX251, but not fluoxetine, was specific to aggression as brain activation in response to a novel sexually receptive female was unaffected. Conclusion The putative neural circuit of aggressive motivation identified with fMRI includes neural substrates contributing to emotional expression (i.e. cortical and medial amygdala, BNST, lateral hypothalamus, emotional experience (i.e. hippocampus, forebrain cortex, anterior cingulate, retrosplenial cortex and the anterior thalamic nuclei that bridge the motor and cognitive components of aggressive responding

  18. Chemical imaging of Fischer-Tropsch catalysts under operating conditions

    Science.gov (United States)

    Price, Stephen W. T.; Martin, David J.; Parsons, Aaron D.; Sławiński, Wojciech A.; Vamvakeros, Antonios; Keylock, Stephen J.; Beale, Andrew M.; Mosselmans, J. Frederick W.

    2017-01-01

    Although we often understand empirically what constitutes an active catalyst, there is still much to be understood fundamentally about how catalytic performance is influenced by formulation. Catalysts are often designed to have a microstructure and nanostructure that can influence performance but that is rarely considered when correlating structure with function. Fischer-Tropsch synthesis (FTS) is a well-known and potentially sustainable technology for converting synthetic natural gas (“syngas”: CO + H2) into functional hydrocarbons, such as sulfur- and aromatic-free fuel and high-value wax products. FTS catalysts typically contain Co or Fe nanoparticles, which are often optimized in terms of size/composition for a particular catalytic performance. We use a novel, “multimodal” tomographic approach to studying active Co-based catalysts under operando conditions, revealing how a simple parameter, such as the order of addition of metal precursors and promoters, affects the spatial distribution of the elements as well as their physicochemical properties, that is, crystalline phase and crystallite size during catalyst activation and operation. We show in particular how the order of addition affects the crystallinity of the TiO2 anatase phase, which in turn leads to the formation of highly intergrown cubic close-packed/hexagonal close-packed Co nanoparticles that are very reactive, exhibiting high CO conversion. This work highlights the importance of operando microtomography to understand the evolution of chemical species and their spatial distribution before any concrete understanding of impact on catalytic performance can be realized. PMID:28345057

  19. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy; Korrelationen der chemischen Verschiebung an schnell rotierenden biologischen Festkoerpern mittels NMR-Spektroskopie

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Christian

    2010-04-27

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97

  20. Standoff chemical D and Id with extended LWIR hyperspectral imaging spectroradiometer

    Science.gov (United States)

    Prel, Florent; Moreau, Louis; Lavoie, Hugo; Bouffard, François; Thériault, Jean-Marc; Vallieres, Christian; Roy, Claude; Dubé, Denis

    2013-05-01

    Standoff detection and identification (D and Id) of unknown volatile chemicals such as chemical pollutants and consequences of industrial incidents has been increasingly desired for first responders and for environmental monitoring. On site gas detection sensors are commercially available and several of them can even detect more than one chemical species, however only few of them have the capabilities of detecting a wide variety of gases at long and safe distances. The ABB Hyperspectral Imaging Spectroradiometer (MR-i), configured for gas detection detects and identifies a wide variety of chemical species including toxic industrial chemicals (TICs) and surrogates several kilometers away from the sensor. This configuration is called iCATSI for improved Compact Atmospheric Sounding Interferometer. iCATSI is a standoff passive system. The modularity of the MR-i platform allows optimization of the detection configuration with a 256 x 256 Focal Plane Array imager or a line scanning imager both covering the long wave IR atmospheric window up to 14 μm. The uniqueness of its extended LWIR cut off enables to detect more chemicals as well as provide higher probability of detection than usual LWIR sensors.

  1. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

  2. Stereochemistry of Complex Marine Natural Products by Quantum Mechanical Calculations of NMR Chemical Shifts: Solvent and Conformational Effects on Okadaic Acid

    Directory of Open Access Journals (Sweden)

    Humberto J. Domínguez

    2014-01-01

    Full Text Available Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory calculations to predict the correct stereoisomer has been studied.

  3. Investigation of drug distribution in tablets using surface enhanced Raman chemical imaging.

    Science.gov (United States)

    Firkala, Tamás; Farkas, Attila; Vajna, Balázs; Farkas, István; Marosi, György

    2013-03-25

    This paper reports the first application of surface enhanced Raman chemical imaging on pharmaceutical tablets containing the active ingredient (API) in very low concentrations. Taking advantage of the extremely intensive Raman signals in the presence of silver colloids, image aquisition time was radically decreased. Moreover, the investigation of drug distribution below the detection limit of regular micro-Raman spectrometry was made feasible. The characteristics of different manufacturing technologies could be revealed at very low API concentrations by using chemometric methods for processing and evaluating the large number of varying spectra provided with this imaging method.

  4. ACM-based automatic liver segmentation from 3-D CT images by combining multiple atlases and improved mean-shift techniques.

    Science.gov (United States)

    Ji, Hongwei; He, Jiangping; Yang, Xin; Deklerck, Rudi; Cornelis, Jan

    2013-05-01

    In this paper, we present an autocontext model(ACM)-based automatic liver segmentation algorithm, which combines ACM, multiatlases, and mean-shift techniques to segment liver from 3-D CT images. Our algorithm is a learning-based method and can be divided into two stages. At the first stage, i.e., the training stage, ACM is performed to learn a sequence of classifiers in each atlas space (based on each atlas and other aligned atlases). With the use of multiple atlases, multiple sequences of ACM-based classifiers are obtained. At the second stage, i.e., the segmentation stage, the test image will be segmented in each atlas space by applying each sequence of ACM-based classifiers. The final segmentation result will be obtained by fusing segmentation results from all atlas spaces via a multiclassifier fusion technique. Specially, in order to speed up segmentation, given a test image, we first use an improved mean-shift algorithm to perform over-segmentation and then implement the region-based image labeling instead of the original inefficient pixel-based image labeling. The proposed method is evaluated on the datasets of MICCAI 2007 liver segmentation challenge. The experimental results show that the average volume overlap error and the average surface distance achieved by our method are 8.3% and 1.5 m, respectively, which are comparable to the results reported in the existing state-of-the-art work on liver segmentation.

  5. Chemical imaging of cotton fibers using an infrared microscope and a focal-plane array detector

    Science.gov (United States)

    In this presentation, the chemical imaging of cotton fibers with an infrared microscope and a Focal-Plane Array (FPA) detector will be discussed. Infrared spectroscopy can provide us with information on the structure and quality of cotton fibers. In addition, FPA detectors allow for simultaneous spe...

  6. Visualization and prediction of porosity in roller compacted ribbonswith near infrared chemical imaging (NIR-CI)

    DEFF Research Database (Denmark)

    Khorasani, Milad Rouhi; Amigo Rubio, Jose Manuel; Sonnergaard, Jørn

    2015-01-01

    The porosity of roller compacted ribbon is recognized as an important critical quality attribute which has a huge impact on the final product quality. The purpose of this study was to investigate the use of near-infrared chemical imaging (NIR-CI) for porosity estimation of ribbons produced...

  7. Investigation of Raman chemical imaging for detection of Lycopene changes in tomatoes during postharvest ripening

    Science.gov (United States)

    Lycopene is a major carotenoid in tomatoes and detecting changes in lycopene content can be used to monitor the ripening of tomatoes. Raman chemical imaging is a new technique that shows promise for mapping constituents of interest in complex food matrices. In this study, a benchtop point-scanning...

  8. Chemical-state imaging of Li using scanning Auger electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ishida, Nobuyuki, E-mail: ISHIDA.Nobuyuki@nims.go.jp [Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Fujita, Daisuke [Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Advanced Nanocharacterization Unit, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan)

    2013-02-15

    Highlights: •Scanning Auger electron microscopy is used to image chemical states of Li. •The combined use of AES and EELS signals for the elemental mapping is powerful. •Distribution corresponding to metallic and oxidized states of Li can be imaged. -- Abstract: The demand for measurement tools to detect Li with high spatial resolution and precise chemical sensitivity is increasing with the spread of lithium-ion batteries (LIBs) for use in a wide range of applications. In this work, scanning Auger electron microscopy (SAM) is used to image chemical states of a partially oxidized Li surface on the basis of the Auger electron spectroscopy (AES) and electron energy loss spectroscopy (EELS) data obtained during an oxidation process of a metal Li. We show that distribution of metallic and oxidized states of Li is clearly imaged by mapping the intensity of the corresponding AES and EELS peaks. Furthermore, a tiny difference in the extent of oxidation can be distinguished by comparing the elemental map of an AES peak with that of an EELS peak owing to the different behaviors of those signals to the chemical states of Li.

  9. Generation of chemical movies: FT-IR spectroscopic imaging of segmented flows.

    Science.gov (United States)

    Chan, K L Andrew; Niu, X; deMello, A J; Kazarian, S G

    2011-05-01

    We have previously demonstrated that FT-IR spectroscopic imaging can be used as a powerful, label-free detection method for studying laminar flows. However, to date, the speed of image acquisition has been too slow for the efficient detection of moving droplets within segmented flow systems. In this paper, we demonstrate the extraction of fast FT-IR images with acquisition times of 50 ms. This approach allows efficient interrogation of segmented flow systems where aqueous droplets move at a speed of 2.5 mm/s. Consecutive FT-IR images separated by 120 ms intervals allow the generation of chemical movies at eight frames per second. The technique has been applied to the study of microfluidic systems containing moving droplets of water in oil and droplets of protein solution in oil. The presented work demonstrates the feasibility of the use of FT-IR imaging to study dynamic systems with subsecond temporal resolution.

  10. Quantitative Chemically-Specific Coherent Diffractive Imaging of Buried Interfaces using a Tabletop EUV Nanoscope

    CERN Document Server

    Shanblatt, Elisabeth R; Gardner, Dennis F; Mancini, Giulia F; Karl, Robert M; Tanksalvala, Michael D; Bevis, Charles S; Vartanian, Victor H; Kapteyn, Henry C; Adams, Daniel E; Murnane, Margaret M

    2016-01-01

    Characterizing buried layers and interfaces is critical for a host of applications in nanoscience and nano-manufacturing. Here we demonstrate non-invasive, non-destructive imaging of buried interfaces using a tabletop, extreme ultraviolet (EUV), coherent diffractive imaging (CDI) nanoscope. Copper nanostructures inlaid in SiO2 are coated with 100 nm of aluminum, which is opaque to visible light and thick enough that neither optical microscopy nor atomic force microscopy can image the buried interfaces. Short wavelength (29 nm) high harmonic light can penetrate the aluminum layer, yielding high-contrast images of the buried structures. Moreover, differences in the absolute reflectivity of the interfaces before and after coating reveal the formation of interstitial diffusion and oxidation layers at the Al-Cu and Al-SiO2 boundaries. Finally, we show that EUV CDI provides a unique capability for quantitative, chemically-specific imaging of buried structures, and the material evolution that occurs at these buried ...

  11. From multispectral imaging of autofluorescence to chemical and sensory images of lipid oxidation in cod caviar paste.

    Science.gov (United States)

    Airado-Rodríguez, Diego; Høy, Martin; Skaret, Josefine; Wold, Jens Petter

    2014-05-01

    The potential of multispectral imaging of autofluorescence to map sensory flavour properties and fluorophore concentrations in cod caviar paste has been investigated. Cod caviar paste was used as a case product and it was stored over time, under different headspace gas composition and light exposure conditions, to obtain a relevant span in lipid oxidation and sensory properties. Samples were divided in two sets, calibration and test sets, with 16 and 7 samples, respectively. A third set of samples was prepared with induced gradients in lipid oxidation and sensory properties by light exposure of certain parts of the sample surface. Front-face fluorescence emission images were obtained for excitation wavelength 382 nm at 11 different channels ranging from 400 to 700 nm. The analysis of the obtained sets of images was divided in two parts: First, in an effort to compress and extract relevant information, multivariate curve resolution was applied on the calibration set and three spectral components and their relative concentrations in each sample were obtained. The obtained profiles were employed to estimate the concentrations of each component in the images of the heterogeneous samples, giving chemical images of the distribution of fluorescent oxidation products, protoporphyrin IX and photoprotoporphyrin. Second, regression models for sensory attributes related to lipid oxidation were constructed based on the spectra of homogeneous samples from the calibration set. These models were successfully validated with the test set. The models were then applied for pixel-wise estimation of sensory flavours in the heterogeneous images, giving rise to sensory images. As far as we know this is the first time that sensory images of odour and flavour are obtained based on multispectral imaging.

  12. Evaluation of C60 secondary ion mass spectrometry for the chemical analysis and imaging of fingerprints.

    Science.gov (United States)

    Sisco, Edward; Demoranville, Leonard T; Gillen, Greg

    2013-09-10

    The feasibility of using C60(+) cluster primary ion bombardment secondary ion mass spectrometry (C60(+) SIMS) for the analysis of the chemical composition of fingerprints is evaluated. It was found that C60(+) SIMS could be used to detect and image the spatial localization of a number of sebaceous and eccrine components in fingerprints. These analyses were also found to not be hindered by the use of common latent print powder development techniques. Finally, the ability to monitor the depth distribution of fingerprint constituents was found to be possible - a capability which has not been shown using other chemical imaging techniques. This paper illustrates a number of strengths and potential weaknesses of C60(+) SIMS as an additional or complimentary technique for the chemical analysis of fingerprints.

  13. Multicomponent chemical imaging of pharmaceutical solid dosage forms with broadband CARS microscopy.

    Science.gov (United States)

    Hartshorn, Christopher M; Lee, Young Jong; Camp, Charles H; Liu, Zhen; Heddleston, John; Canfield, Nicole; Rhodes, Timothy A; Hight Walker, Angela R; Marsac, Patrick J; Cicerone, Marcus T

    2013-09-03

    We compare a coherent Raman imaging modality, broadband coherent anti-Stokes Raman scattering (BCARS) microscopy, with spontaneous Raman microscopy for quantitative and qualitative assessment of multicomponent pharmaceuticals. Indomethacin was used as a model active pharmaceutical ingredient (API) and was analyzed in a tabulated solid dosage form, embedded within commonly used excipients. In comparison with wide-field spontaneous Raman chemical imaging, BCARS acquired images 10× faster, at higher spatiochemical resolution and with spectra of much higher SNR, eliminating the need for multivariate methods to identify chemical components. The significant increase in spatiochemical resolution allowed identification of an unanticipated API phase that was missed by the spontaneous wide-field method and bulk Raman spectroscopy. We confirmed the presence of the unanticipated API phase using confocal spontaneous Raman, which provided spatiochemical resolution similar to BCARS but at 100× slower acquisition times.

  14. Screening of adulterants in powdered foods and ingredients using line-scan Raman chemical imaging

    Science.gov (United States)

    Qin, Jianwei; Chao, Kuanglin; Kim, Moon S.

    2015-05-01

    A newly developed line-scan Raman imaging system using a 785 nm line laser was used to authenticate powdered foods and ingredients. The system was used to collect hyperspectral Raman images in a wavenumber range of 102-2865 cm-1 from three representative food powders mixed with selected adulterants with a concentration of 0.5%, including milk and melamine, flour and benzoyl peroxide, and starch and maleic anhydride. An acoustic mixer was used to create food adulterant mixtures. All the mixed samples were placed in sample holders with a surface area of 50 mm×50 mm. Spectral and image processing algorithms were developed based on single-band images at unique Raman peaks of the individual adulterants. Chemical images were created to show identification, spatial distribution, and morphological features of the adulterant particles mixed in the food powders. The potential of estimating mass concentrations of the adulterants using the percentages of the adulterant pixels in the chemical images was also demonstrated.

  15. Evaluating carotenoid changes in tomatoes during postharvest ripening using Raman chemical imaging

    Science.gov (United States)

    Qin, Jianwei; Chao, Kuanglin; Kim, Moon S.

    2011-06-01

    Lycopene is a major carotenoid in tomatoes and its content varies considerably during postharvest ripening. Hence evaluating lycopene changes can be used to monitor the ripening of tomatoes. Raman chemical imaging technique is promising for mapping constituents of interest in complex food matrices. In this study, a benchtop point-scanning Raman chemical imaging system was developed to evaluate lycopene content in tomatoes at different maturity stages. The system consists of a 785 nm laser, a fiber optic probe, a dispersive imaging spectrometer, a spectroscopic CCD camera, and a two-axis positioning table. Tomato samples at different ripeness stages (i.e., green, breaker, turning, pink, light red, and red) were selected and cut before imaging. Hyperspectral Raman images were acquired from cross sections of the fruits in the wavenumber range of 200 to 2500 cm-1 with a spatial resolution of 1 mm. The Raman spectrum of pure lycopene was measured as reference for spectral matching. A polynomial curve-fitting method was used to correct for the underlying fluorescence background in the Raman spectra of the tomatoes. A hyperspectral image classification method was developed based on spectral information divergence to identify lycopene in the tomatoes. Raman chemical images were created to visualize quantity and spatial distribution of the lycopene at different ripeness stages. The lycopene patterns revealed the mechanism of lycopene generation during the postharvest development of the tomatoes. The method and findings of this study form a basis for the future development of a Raman-based nondestructive approach for monitoring internal maturity of the tomatoes.

  16. Measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons with the 2D-SUPER technique and dipolar dephasing (DD-SUPER)

    Science.gov (United States)

    Liu, Wei; Wang, Wei D.; Wang, Wei; Bai, Shi; Dybowski, Cecil

    2010-09-01

    A modified 2D-SUPER technique is demonstrated to allow independent measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons. The insertion of a dipolar-dephasing period into the sequence causes loss of signal from protonated carbons. The spectrum obtained with this modification allows one to determine the principal values of the unprotonated carbons with high precision. Subsequent fitting of the usual 2D-SUPER spectrum, with the chemical-shift parameters of the unprotonated carbons fixed, gives the parameters of the overlapped resonances of the protonated carbons. As an example, we report the determination of the 13C chemical-shift parameters of the carbons of form II of piroxicam. The experimental results are compared with those obtained from calculations using the DFT/GIAO method. Potential applications of this method are discussed.

  17. Analysis of pharmaceutical pellets: An approach using near-infrared chemical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Sabin, Guilherme P.; Breitkreitz, Marcia C.; Souza, Andre M. de [Institute of Chemistry, University of Campinas, P.O. Box 6154, 13084-971 Campinas, SP (Brazil); Fonseca, Patricia da; Calefe, Lupercio; Moffa, Mario [Zelus Servicos para Industria Farmaceutica Ltda., Av. Professor Lineu Prestes n. 2242, Sao Paulo, SP (Brazil); Poppi, Ronei J., E-mail: ronei@iqm.unicamp.br [Institute of Chemistry, University of Campinas, P.O. Box 6154, 13084-971 Campinas, SP (Brazil)

    2011-11-07

    Highlights: {yields} Near-Infrared Chemical Imaging was used for pellets analysis. {yields} Distribution of the components throughout the coatings layers and core of the pellets was estimated. {yields} Classical Least Squares (CLS) was used for calculation of the concentration maps. - Abstract: Pharmaceutical pellets are spherical or nearly spherical multi-unit dosage forms designed to optimize pharmacokinetics and pharmacodynamics features of drug release. The distribution of the pharmaceutical ingredients in the layers and core is a very important parameter for appropriate drug release, especially for pellets manufactured by the process of layer gain. Physical aspects of the sample are normally evaluated by Scanning Electron Microscopy (SEM), but it is in many cases unsuitable to provide conclusive chemical information about the distribution of the pharmaceutical ingredients in both layers and core. On the other hand, methods based on spectroscopic imaging can be very promising for this purpose. In this work, a Near-Infrared Chemical Imaging (NIR-CI) method was developed and applied to the analysis of diclophenac sodium pellets. Since all the compounds present in the sample were known in advance, Classical Least Squares (CLS) was used for calculations. The results have shown that the method was capable of providing chemical information about the distribution of the active ingredient and excipients in the core and coating layers and therefore can be complementary to SEM for the pharmaceutical development of pellets.

  18. A Raman chemical imaging system for detection of contaminants in food

    Science.gov (United States)

    Chao, Kaunglin; Qin, Jianwei; Kim, Moon S.; Mo, Chang Yeon

    2011-06-01

    This study presented a preliminary investigation into the use of macro-scale Raman chemical imaging for the screening of dry milk powder for the presence of chemical contaminants. Melamine was mixed into dry milk at concentrations (w/w) of 0.2%, 0.5%, 1.0%, 2.0%, 5.0%, and 10.0% and images of the mixtures were analyzed by a spectral information divergence algorithm. Ammonium sulfate, dicyandiamide, and urea were each separately mixed into dry milk at concentrations of (w/w) of 0.5%, 1.0%, and 5.0%, and an algorithm based on self-modeling mixture analysis was applied to these sample images. The contaminants were successfully detected and the spatial distribution of the contaminants within the sample mixtures was visualized using these algorithms. Although further studies are necessary, macro-scale Raman chemical imaging shows promise for use in detecting contaminants in food ingredients and may also be useful for authentication of food ingredients.

  19. Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging

    Science.gov (United States)

    Bassan, Paul; Sachdeva, Ashwin; Shanks, Jonathan H.; Brown, Mick D.; Clarke, Noel W.; Gardner, Peter

    2014-03-01

    Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. FT-IR chemical imaging allows the spatial distribution of chemistry to be rapidly imaged at a high (diffraction-limited) spatial resolution where each pixel represents an area of 5.5 × 5.5 μm2 and contains a full infrared spectrum providing a chemical fingerprint which studies have shown contains the diagnostic potential to discriminate between different cell-types, and even the benign or malignant state of prostatic epithelial cells. We report a label-free (i.e. no chemical de-waxing, or staining) method of imaging large pieces of prostate tissue (typically 1 cm × 2 cm) in tens of minutes (at a rate of 0.704 × 0.704 mm2 every 14.5 s) yielding images containing millions of spectra. Due to refractive index matching between sample and surrounding paraffin, minimal signal processing is required to recover spectra with their natural profile as opposed to harsh baseline correction methods, paving the way for future quantitative analysis of biochemical signatures. The quality of the spectral information is demonstrated by building and testing an automated cell-type classifier based upon spectral features.

  20. The effects of librations on the 13C chemical shift and 2H electric field gradient tensors in β-calcium formate

    Science.gov (United States)

    Hallock, Kevin J.; Lee, Dong Kuk; Ramamoorthy, A.

    2000-12-01

    The magnitudes and orientations of the principal elements of the 13C chemical shift anisotropy (CSA) tensor in the molecular frame of the formate ion in β-calcium formate is determined using one-dimensional dipolar-shift spectroscopy. The magnitudes of the principal elements of the 13C CSA tensor are σ11C=104 ppm, σ22C=179 ppm, and σ33C=233 ppm. The least shielding element of the 13C CSA tensor, σ33C, is found to be collinear with the C-H bond. The temperature dependence of the 13C CSA and the 2H quadrupole coupling tensors in β-calcium formate are analyzed for a wide range of temperature (173-373 K). It was found that the span of the 13C CSA and the magnitude of the 2H quadrupole coupling interactions are averaged with the increasing temperature. The experimental results also show that the 2H quadrupole coupling tensor becomes more asymmetric with increasing temperature. A librational motion about the σ22C axis of the 13C CSA tensor is used to model the temperature dependence of the 13C CSA tensor. The temperature dependence of the mean-square amplitude of the librational motion is found to be =2.6×10-4(T) rad2 K-1. The same librational motion also accounts for the temperature-dependence of the 2H quadrupole coupling tensor after the relative orientation of the 13C CSA and 2H electric field gradient tensors are taken into account. Reconsideration of the results of a previous study found that the librational motion, not the vibrational motion, accounts for an asymmetry in the 1H-13C dipolar coupling tensor of α-calcium formate at room temperature.

  1. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    Science.gov (United States)

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-08

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

  2. High-resolution chemical imaging of gold nanoparticles using hard x-ray ptychography

    DEFF Research Database (Denmark)

    Hoppe, R.; Reinhardt, J.; Hofmann, G.

    2013-01-01

    We combine resonant scattering with (ptychographic) scanning coherent diffraction microscopy to determine the chemical state of gold nanoparticles with high spatial resolution. Ptychographic images of the sample are recorded for a series of energies around the gold L3 absorption edge. From...... these data, chemical information in the form of absorption and resonant scattering spectra is reconstructed at each location in the sample. For gold nanoparticles of about 100 nm diameter, a spatial resolution of about 20-30 nm is obtained. In the future, this microscopy approach will open the way...

  3. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...

  4. Hierarchy of Electronic Properties of Chemically Derived and Pristine Graphene Probed by Microwave Imaging

    KAUST Repository

    Kundhikanjana, Worasom

    2009-11-11

    Local electrical imaging using microwave impedance microscope is performed on graphene in different modalities, yielding a rich hierarchy of the local conductivity. The low-conductivity graphite oxide and its derivatives show significant electronic inhomogeneity. For the conductive chemical graphene, the residual defects lead to a systematic reduction of the microwave signals. In contrast, the signals on pristine graphene agree well with a lumped-element circuit model. The local impedance information can also be used to verify the electrical contact between overlapped graphene pieces. © 2009 American Chemical Society.

  5. Infrared chemical imaging: Spatial resolution evaluation and super-resolution concept

    Energy Technology Data Exchange (ETDEWEB)

    Offroy, Marc [Laboratoire de Spectrochimie Infrarouge et Raman, LASIR, CNRS UMR 8516, Bat. C5, Universite des Sciences et Technologies de Lille, 59655 Villeneuve d' Ascq Cedex (France); Roggo, Yves [F. Hoffmann-La Roche A.G., Basel (Switzerland); Milanfar, Peyman [Multi-Dimensional Signal Processing Laboratory, Electrical Engineering Department, Baskin School of Engineering, University of California, 1156 High Street, Mailcode SOE2, Santa Cruz, CA 95064 (United States); Duponchel, Ludovic, E-mail: ludovic.duponchel@univ-lille1.fr [Laboratoire de Spectrochimie Infrarouge et Raman, LASIR, CNRS UMR 8516, Bat. C5, Universite des Sciences et Technologies de Lille, 59655 Villeneuve d' Ascq Cedex (France)

    2010-08-03

    Chemical imaging systems help to solve many challenges in various scientific fields. Able to deliver rapid spatial and chemical information, modern infrared spectrometers using Focal Plane Array detectors (FPA) are of great interest. Considering conventional infrared spectrometers with a single element detector, we can consider that the diffraction-limited spatial resolution is more or less equal to the wavelength of the light (i.e. 2.5-25 {mu}m). Unfortunately, the spatial resolution of FPA spectroscopic setup is even lower due to the detector pixel size. This becomes a real constraint when micron-sized samples are analysed. New chemometrics methods are thus of great interest to overcome such resolution drawback, while keeping our far-field infrared imaging spectrometers. The aim of the present work is to evaluate the super-resolution concept in order to increase the spatial resolution of infrared imaging spectrometers using FPA detectors. The main idea of super-resolution is the fusion of several low-resolution images of the same sample to obtain a higher-resolution image. Applying the super-resolution concept on a relatively low number of FPA acquisitions, it was possible to observe a 30% decrease in spatial resolution.

  6. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: {sup 1}H and {sup 13}C chemical shift assignments; Constituintes quimicos de Ottonia corcovadensis Miq. da floresta Amazonica - atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Facundo, Valdir A. [Rondonia Univ., Porto Velho, RO (Brazil). Dept. de Quimica; Morais, Selene M. [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica e Fisica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Setor de Quimica de Produtos Naturais. Lab. de Ciencias Quimicas. Setor de Quimica de Produtos Naturais]. E-mail: braz@uenf.br

    2004-02-01

    In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete {sup 1}H and {sup 13}C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

  7. Two decades of chemical imaging of solutes in sediments and soils

    DEFF Research Database (Denmark)

    Santner, Jakob; Larsen, Morten; Kreuzeder, Andreas;

    2015-01-01

    sampling of solutes (diffusive equilibration in thin films, diffusive gradients in thin films) followed by planar luminescent sensors (planar optodes) have been used as analytical tools for studies on solute distribution and dynamics. These approaches have provided new conceptual and quantitative......-called sandwich sensors for multianalyte measurements. Here we review the capabilities and limitations of the chemical imaging methods that are currently at hand, using a number of case studies, and provide an outlook on potential future developments for two-dimensional solute imaging in soils and sediments....

  8. Biochemical imaging of cervical intervertebral discs with glycosaminoglycan chemical exchange saturation transfer magnetic resonance imaging: feasibility and initial results

    Energy Technology Data Exchange (ETDEWEB)

    Schleich, Christoph; Mueller-Lutz, Anja; Zimmermann, Lisa; Boos, Johannes; Wittsack, Hans-Joerg; Antoch, Gerald; Miese, Falk [Department of Diagnostic and Interventional Radiology, University Dusseldorf, Medical Faculty, Dusseldorf (Germany); Schmitt, Benjamin [Siemens Ltd. Australia, Healthcare Sector, Macquarie Park, NSW (Australia)

    2016-01-15

    To evaluate glycosaminoglycan chemical exchange saturation transfer (gagCEST) imaging at 3T in the assessment of the GAG content of cervical IVDs in healthy volunteers. Forty-two cervical intervertebral discs of seven healthy volunteers (four females, three males; mean age: 21.4 ± 1.4 years; range: 19-24 years) were examined at a 3T MRI scanner in this prospective study. The MRI protocol comprised standard morphological, sagittal T2 weighted (T2w) images to assess the magnetic resonance imaging (MRI) based grading system for cervical intervertebral disc degeneration (IVD) and biochemical imaging with gagCEST to calculate a region-of-interest analysis of nucleus pulposus (NP) and annulus fibrosus (AF). GagCEST of cervical IVDs was technically successful at 3T with significant higher gagCEST values in NP compared to AF (1.17 % ± 1.03 % vs. 0.79 % ± 1.75 %; p = 0.005). We found topological differences of gagCEST values of the cervical spine with significant higher gagCEST effects in lower IVDs (r = 1; p = 0). We could demonstrate a significant, negative correlation between gagCEST values and cervical disc degeneration of NP (r = -0.360; p = 0.019). Non-degenerated IVDs had significantly higher gagCEST effects compared to degenerated IVDs in NP (1.76 % ± 0.92 % vs. 0.52 % ± 1.17 %; p < 0.001). Biochemical imaging of cervical IVDs is feasible at 3T. GagCEST analysis demonstrated a topological GAG distribution of the cervical spine. The depletion of GAG in the NP with increasing level of morphological degeneration can be assessed using gagCEST imaging. (orig.)

  9. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  10. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Science.gov (United States)

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations.

  11. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  12. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., {sup 13}C-{sup 13}C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  13. Efficient gradient field generation providing a multi-dimensional arbitrary shifted field-free point for magnetic particle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kaethner, Christian, E-mail: kaethner@imt.uni-luebeck.de; Ahlborg, Mandy; Buzug, Thorsten M., E-mail: buzug@imt.uni-luebeck.de [Institute of Medical Engineering, Universität zu Lübeck, 23562 Lübeck (Germany); Knopp, Tobias [Thorlabs GmbH, 23562 Lübeck (Germany); Sattel, Timo F. [Philips Medical Systems DMC GmbH, 22335 Hamburg (Germany)

    2014-01-28

    Magnetic Particle Imaging (MPI) is a tomographic imaging modality capable to visualize tracers using magnetic fields. A high magnetic gradient strength is mandatory, to achieve a reasonable image quality. Therefore, a power optimization of the coil configuration is essential. In order to realize a multi-dimensional efficient gradient field generator, the following improvements compared to conventionally used Maxwell coil configurations are proposed: (i) curved rectangular coils, (ii) interleaved coils, and (iii) multi-layered coils. Combining these adaptions results in total power reduction of three orders of magnitude, which is an essential step for the feasibility of building full-body human MPI scanners.

  14. Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging

    Directory of Open Access Journals (Sweden)

    Davidson Michael W

    2008-03-01

    Full Text Available Abstract Background In the 15 years that have passed since the cloning of Aequorea victoria green fluorescent protein (avGFP, the expanding set of fluorescent protein (FP variants has become entrenched as an indispensable toolkit for cell biology research. One of the latest additions to the toolkit is monomeric teal FP (mTFP1, a bright and photostable FP derived from Clavularia cyan FP. To gain insight into the molecular basis for the blue-shifted fluorescence emission we undertook a mutagenesis-based study of residues in the immediate environment of the chromophore. We also employed site-directed and random mutagenesis in combination with library screening to create new hues of mTFP1-derived variants with wavelength-shifted excitation and emission spectra. Results Our results demonstrate that the protein-chromophore interactions responsible for blue-shifting the absorbance and emission maxima of mTFP1 operate independently of the chromophore structure. This conclusion is supported by the observation that the Tyr67Trp and Tyr67His mutants of mTFP1 retain a blue-shifted fluorescence emission relative to their avGFP counterparts (that is, Tyr66Trp and Tyr66His. Based on previous work with close homologs, His197 and His163 are likely to be the residues with the greatest contribution towards blue-shifting the fluorescence emission. Indeed we have identified the substitutions His163Met and Thr73Ala that abolish or disrupt the interactions of these residues with the chromophore. The mTFP1-Thr73Ala/His163Met double mutant has an emission peak that is 23 nm red-shifted from that of mTFP1 itself. Directed evolution of this double mutant resulted in the development of mWasabi, a new green fluorescing protein that offers certain advantages over enhanced avGFP (EGFP. To assess the usefulness of mTFP1 and mWasabi in live cell imaging applications, we constructed and imaged more than 20 different fusion proteins. Conclusion Based on the results of our

  15. Handheld hyperspectral imager for standoff detection of chemical and biological aerosols

    Science.gov (United States)

    Hinnrichs, Michele; Jensen, James O.; McAnally, Gerard

    2004-08-01

    Pacific Advanced Technology has developed a small hand held imaging spectrometer, Sherlock, for gas leak and aerosol detection and imaging. The system is based on a patented technique, (IMSS Image Multi-spectral Sensing), that uses diffractive optics and image processing algorithms to detect spectral information about objects in the scene of the camera. This cameras technology has been tested at Dugway Proving Ground and Dstl Porton Down facilities looking at Chemical and Biological agent simulants. In addition to Chemical and Biological detection, the camera has been used for environmental monitoring of green house gases and is currently undergoing extensive laboratory and field testing by the Gas Technology Institute, British Petroleum and Shell Oil for applications for gas leak detection and repair. In this paper we will present some of the results from the data collection at the TRE test at Dugway Proving Ground during the summer of 2002 and laboratory testing at the Dstl facility at Porton Down in the UK in the fall of 2002.

  16. Two decades of chemical imaging of solutes in sediments and soils

    DEFF Research Database (Denmark)

    Santner, Jakob; Larsen, Morten; Kreuzeder, Andreas;

    2015-01-01

    -called sandwich sensors for multianalyte measurements. Here we review the capabilities and limitations of the chemical imaging methods that are currently at hand, using a number of case studies, and provide an outlook on potential future developments for two-dimensional solute imaging in soils and sediments.......The increasing appreciation of the small-scale (sub-mm) heterogeneity of biogeochemical processes in sediments, wetlands and soils has led to the development of several methods for high-resolution two-dimensional imaging of solute distribution in porewaters. Over the past decades, localised...... sampling of solutes (diffusive equilibration in thin films, diffusive gradients in thin films) followed by planar luminescent sensors (planar optodes) have been used as analytical tools for studies on solute distribution and dynamics. These approaches have provided new conceptual and quantitative...

  17. Raman imaging to study structural and chemical features of the dentin enamel junction

    Science.gov (United States)

    Alebrahim, M. Anwar; Krafft, C.; Popp, J.

    2015-10-01

    The structure and chemical features of the human dentin enamel junction (DEJ) were characterized using Raman spectroscopic imaging. Slices were prepared from 10 German, and 10 Turkish teeth. Raman images were collected at 785 nm excitation and the average Raman spectra were calculated for analysis. Univariate and multivariate spectral analysis were applied for investigation. Raman images were obtained based on the intensity ratios of CH at 1450 cm-1 (matrix) to phosphate at 960 cm-1 (mineral), and carbonate to phosphate (1070/960) ratios. Different algorithms (HCA, K-means cluster and VCA) also used to study the DEJ. The obtained results showed that the width of DEJ is about 5 pm related to univariate method while it varies from 6 to 12 μm based on multivariate spectral technique. Both spectral analyses showed increasing in carbonate content inside the DEJ compared to the dentin, and the amide I (collagen) peak in dentin spectra is higher than DEJ spectra peak.

  18. Mapping lipid and collagen by multispectral photoacoustic imaging of chemical bond vibration

    Science.gov (United States)

    Wang, Pu; Wang, Ping; Wang, Han-Wei; Cheng, Ji-Xin

    2012-09-01

    Photoacoustic microscopy using vibrational overtone absorption as a contrast mechanism allows bond-selective imaging of deep tissues. Due to the spectral similarity of molecules in the region of overtone vibration, it is difficult to interrogate chemical components using photoacoustic signal at single excitation wavelength. Here we demonstrate that lipids and collagen, two critical markers for many kinds of diseases, can be distinguished by multispectral photoacoustic imaging of the first overtone of C-H bond. A phantom consisting of rat-tail tendon and fat was constructed to demonstrate this technique. Wavelengths between 1650 and 1850 nm were scanned to excite both the first overtone and combination bands of C-H bonds. B-scan multispectral photoacoustic images, in which each pixel contains a spectrum, were analyzed by a multivariate curve resolution-alternating least squares algorithm to recover the spatial distribution of collagen and lipids in the phantom.

  19. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...

  20. Development of Methods for Obtaining Position Image and Chemical Binding Information from Flow Experiments of Porous Media

    Energy Technology Data Exchange (ETDEWEB)

    Haugan, Are

    1998-12-01

    Existing oil reservoirs might be more fully exploited if the properties of the flow of oil and water in porous media were better known. In laboratory experiments it is important to collect as much information as possible to make a descriptive model of the system, including position imaging and chemical binding information. This thesis develops nuclear methods for obtaining position image and chemical binding information from flow experiments of porous media. A combined positron emission tomography and single photon emission computed tomography system to obtain position images, and a time-differential perturbed angular correlation system to obtain chemical binding information, have been built and thoroughly tested. 68 refs., 123 figs., 14 tabs.

  1. Bio-Mechanical Model of the Brain for a Per-Operative Image-Guided Neuronavigator Compensating for "Brain-Shift" Deformations

    CERN Document Server

    Bucki, Marek; Payan, Yohan

    2007-01-01

    In this paper we present a methodology to address the problem of brain tissue deformation referred to as 'brain-shift'. This deformation occurs throughout a neurosurgery intervention and strongly alters the accuracy of the neuronavigation systems used to date in clinical routine which rely solely on pre-operative patient imaging to locate the surgical target, such as a tumour or a functional area. After a general description of the framework of our intra-operative image-guided system, we describe a procedure to generate patient specific finite element meshes of the brain and propose a biomechanical model which can take into account tissue deformations and surgical procedures that modify the brain structure, like tumour or tissue resection.

  2. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;

    2015-01-01

    in a student dormitory and found that players did not shift their electricity use, because they were unwilling to change their schedules and found it easier to focus on reducing electricity use. Based on our findings, we discuss the implications for encouraging shifting, and also the challenges of integrating...

  3. Estimation of the stand ages of tropical secondary forests after shifting cultivation based on the combination of WorldView-2 and time-series Landsat images

    Science.gov (United States)

    Fujiki, Shogoro; Okada, Kei-ichi; Nishio, Shogo; Kitayama, Kanehiro

    2016-09-01

    We developed a new method to estimate stand ages of secondary vegetation in the Bornean montane zone, where local people conduct traditional shifting cultivation and protected areas are surrounded by patches of recovering secondary vegetation of various ages. Identifying stand ages at the landscape level is critical to improve conservation policies. We combined a high-resolution satellite image (WorldView-2) with time-series Landsat images. We extracted stand ages (the time elapsed since the most recent slash and burn) from a change-detection analysis with Landsat time-series images and superimposed the derived stand ages on the segments classified by object-based image analysis using WorldView-2. We regarded stand ages as a response variable, and object-based metrics as independent variables, to develop regression models that explain stand ages. Subsequently, we classified the vegetation of the target area into six age units and one rubber plantation unit (1-3 yr, 3-5 yr, 5-7 yr, 7-30 yr, 30-50 yr, >50 yr and 'rubber plantation') using regression models and linear discriminant analyses. Validation demonstrated an accuracy of 84.3%. Our approach is particularly effective in classifying highly dynamic pioneer vegetation younger than 7 years into 2-yr intervals, suggesting that rapid changes in vegetation canopies can be detected with high accuracy. The combination of a spectral time-series analysis and object-based metrics based on high-resolution imagery enabled the classification of dynamic vegetation under intensive shifting cultivation and yielded an informative land cover map based on stand ages.

  4. Image shifts resulting from the misorientation of two individuals in GdCa4O(BO3)3 crystal

    Institute of Scientific and Technical Information of China (English)

    XiaoboHu; JiyangWang; ShushengJiang; HongLiu; MingGuo; HuaidongJian

    2001-01-01

    Large GdCa4O(BO3)3 crystal has been grown by the Czochralski method.The quality of GdCa4(BO3)3 crystal was assessed by white-beam synchrotron radiation topography.It has been found that there is a sub-grain boundary in the GdCa4O(BO3)3 crystal.The boundary divides the large GdCa4O(BO3)3 crystal into two individuals.Due to the misorientation between the two individuals,the image shifts can be observed in the synchrotron topopraphs.Based on the misorientation determined by high resolution X-ray diffractometer,the image shifts were calculated for several reflections.The calculations are in agreement with the measurements from the topogrphs very Well.In addition,the formation mechanism of sub-grain boundary is discussed.2001 Elsevier science B.V.All rights reserved.

  5. Chemical exchange saturation transfer MR imaging of Parkinson's disease at 3 Tesla

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chunmei; Peng, Shuai; Wang, Rui; Chen, Min [Beijing Hospital, Department of Radiology, Beijing (China); Chen, Haibo; Su, Wen [Beijing Hospital, Department of Neurology, Beijing (China); Zhao, Xuna [Peking University, Center for MRI Research and Beijing City Key Lab for Medical Physics and Engineering, Beijing (China); Zhou, Jinyuan [Johns Hopkins University, Department of Radiology, Baltimore, MD (United States)

    2014-10-15

    To demonstrate the feasibility of using chemical exchange saturation transfer (CEST) imaging to detect Parkinson's disease (PD) in patients at 3 Tesla. Twenty-seven PD patients (17 men and 10 women; age range, 54-77 years) and 22 age-matched normal controls (13 men and 9 women; age range, 55-73 years) were examined on a 3-Tesla MRI system. Magnetization transfer spectra with 31 different frequency offsets (-6 to 6 ppm) were acquired at two transverse slices of the head, including the basal ganglia and midbrain. One-way analysis of variance tests was used to compare the differences in CEST imaging signals between PD patients and normal controls. Total CEST signal between the offsets of 0 and 4 ppm in the substantia nigra was significantly lower in PD patients than in normal controls (P = 0.006), which could be associated with the loss of dopaminergic neurons. Protein-based CEST imaging signals at the offset of 3.5 ppm in the globus pallidus, putamen and caudate were significantly increased in PD patients, compared to normal controls (P < 0.001, P = 0.003, P < 0.001, respectively). CEST imaging signals could potentially serve as imaging biomarkers to aid in the non-invasive molecular diagnosis of PD. (orig.)

  6. Comparative Investigation of Guided Fuzzy Clustering and Mean Shift Clustering for Edge Detection in Electrical Resistivity Tomography Images of Mineral Deposits

    Science.gov (United States)

    Ward, Wil; Wilkinson, Paul; Chambers, Jon; Bai, Li

    2014-05-01

    Geophysical surveying using electrical resistivity tomography (ERT) can be used as a rapid non-intrusive method to investigate mineral deposits [1]. One of the key challenges with this approach is to find a robust automated method to assess and characterise deposits on the basis of an ERT image. Recent research applying edge detection techniques has yielded a framework that can successfully locate geological interfaces in ERT images using a minimal assumption data clustering technique, the guided fuzzy clustering method (gfcm) [2]. Non-parametric clustering techniques are statistically grounded methods of image segmentation that do not require any assumptions about the distribution of data under investigation. This study is a comparison of two such methods to assess geological structure based on the resistivity images. In addition to gfcm, a method called mean-shift clustering [3] is investigated with comparisons directed at accuracy, computational expense, and degree of user interaction. Neither approach requires the number of clusters as input (a common parameter and often impractical), rather they are based on a similar theory that data can be clustered based on peaks in the probability density function (pdf) of the data. Each local maximum in these functions represents the modal value of a particular population corresponding to a cluster and as such the data are assigned based on their relationships to these model values. The two methods differ in that gfcm approximates the pdf using kernel density estimation and identifies population means, assigning cluster membership probabilities to each resistivity value in the model based on its distance from the distribution averages. Whereas, in mean-shift clustering, the density function is not calculated, but a gradient ascent method creates a vector that leads each datum towards high density distributions iteratively using weighted kernels to calculate locally dense regions. The only parameter needed in both methods

  7. The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: Implication for structure determination/refinement in paramagnetic metalloproteins

    Energy Technology Data Exchange (ETDEWEB)

    Xia Zhicheng; Nguyen, Bao D.; La Mar, Gerd N. [University of California, Department of Chemistry (United States)

    2000-06-15

    The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift, which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein.

  8. The shifting appearance/disappearance of holographic images and the dynamic ontology of perceptual and cognitive processes

    Science.gov (United States)

    Boissonnet, Philippe

    2013-02-01

    The French philosopher M Merleau-Ponty captured the dynamic of perception with his idea of the intertwining of perceiver and perceived. Light is what links them. In the case of holographic images, not only is spatial and colour perception the pure product of light, but this light information is always in the process of self-construction with our eyes, according to our movements and the point of view adopted. According to the aesthetic reception of a work of art, Holographic images vary greatly from those of cinema, photography and even every kind of digital 3D animation. This particular image's status truly makes perceptually apparent the "co-emergence" of light and our gaze. But holography never misleads us with respect to the precarious nature of our perceptions. We have no illusion as to the limits of our empirical understanding of the perceived reality. Holography, like our knowledge of the visible, thus brings to light the phenomenon of reality's "co-constitution" and contributes to a dynamic ontology of perceptual and cognitive processes. The cognitivist Francico Varela defines this as the paradigm of enaction,i which I will adapt and apply to the appearance/disappearance context of holographic images to bring out their affinities on a metaphorical level.

  9. Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations.

    Science.gov (United States)

    Lu, Ping; Yuan, Ren Liang; Ihlefeld, Jon F; Spoerke, Erik David; Pan, Wei; Zuo, Jian Min

    2016-04-13

    Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena.

  10. A Potential Magnetic Resonance Imaging Technique Based on Chemical Exchange Saturation Transfer for In Vivo γ-Aminobutyric Acid Imaging

    Science.gov (United States)

    Yan, Gen; Zhang, Tao; Dai, Zhuozhi; Yi, Meizhi; Jia, Yanlong; Nie, Tingting; Zhang, Handi; Xiao, Gang; Wu, Renhua

    2016-01-01

    Purpose We developed a novel magnetic resonance imaging (MRI) technique based on chemical exchange saturation transfer (CEST) for GABA imaging and investigated the concentration-dependent CEST effect ofGABA in a rat model of brain tumor with blood—brain barrier (BBB) disruption. Materials and Methods All MRI studies were performed using a 7.0-T Agilent MRI scanner. Z-spectra for GABA were acquired at 7.0 T, 37°C, and a pH of 7.0 using varying B1 amplitudes. CEST images of phantoms with different concentrations of GABA solutions (pH, 7.0) and other metabolites (glutamine, myoinositol, creatinine, and choline) were collected to investigate the concentration-dependent CEST effect of GABA and the potential contribution from other brain metabolites. CEST maps for GABA in rat brains with tumors were collected at baseline and 50 min, 1.5 h, and 2.0 h after the injection of GABA solution. Results The CEST effect of GABA was observed at approximately 2.75 parts per million(ppm) downfield from bulk water, and this effect increased with an increase in the B1 amplitude and remained steady after the B1 amplitude reached 6.0 μT (255 Hz). The CEST effect of GABA was proportional to the GABA concentration in vitro. CEST imaging of GABA in a rat brain with a tumor and compromised BBB showed a gradual increase in the CEST effect after GABA injection. Conclusion The findings of this study demonstrate the feasibility and potential of CEST MRI with the optimal B1 amplitude, which exhibits excellent spatial and temporal resolutions, to map changes in GABA. PMID:27711138

  11. Comparative performance studies between tunable filter and push-broom chemical imaging systems

    Science.gov (United States)

    Malinen, Jouko; Saari, Heikki; Kemeny, Gabor; Shi, Zhenqi; Anderson, Carl

    2010-04-01

    This paper reports instrument characterization measurements, which were recently arranged to provide comparative information on different hyperspectral chemical imaging systems. Three different instruments were studied covering both tunable filter and push-broom techniques: The first instrument MatrixNIRTM is based on a LCTF tunable filter and InGaAs camera and covers wavelengths from 1000 to 1700 nm. The second one SisuCHEMATM is based on push-broom technology and MCT camera operating from 1000 to 2500 nm. The third system is an instrument prototype from VTT Technical Research Centre of Finland exploiting high speed Fabry-Perot interferometer and MCT camera, currently calibrated from 1260 to 2500 nm. The characterization procedure was designed to study instrumental noise, signal-to-noise ratio, linearity and spectral as well as spatial resolution. Finally, a pharmaceutical tablet sample was measured with each instrument to demonstrate speed of measurement in a typical application. In spite of differences in wavelength ranges and camera technologies used, the results provide interesting information on relative instrumental advantages and disadvantages, which may be useful for selecting appropriate instrumentation for defined applications. Further, an additional aim of this study is to compare the high speed Fabry-Perot imaging technology under development against the established chemical imaging techniques available on the market today.

  12. Laser Microdissection and Atmospheric Pressure Chemical Ionization Mass Spectrometry Coupled for Multimodal Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Lorenz, Matthias [ORNL; Ovchinnikova, Olga S [ORNL; Kertesz, Vilmos [ORNL; Van Berkel, Gary J [ORNL

    2013-01-01

    This paper describes the coupling of ambient laser ablation surface sampling, accomplished using a laser capture microdissection system, with atmospheric pressure chemical ionization mass spectrometry for high spatial resolution multimodal imaging. A commercial laser capture microdissection system was placed in close proximity to a modified ion source of a mass spectrometer designed to allow for sampling of laser ablated material via a transfer tube directly into the ionization region. Rhodamine 6G dye of red sharpie ink in a laser etched pattern as well as cholesterol and phosphatidylcholine in a cerebellum mouse brain thin tissue section were identified and imaged from full scan mass spectra. A minimal spot diameter of 8 m was achieved using the 10X microscope cutting objective with a lateral oversampling pixel resolution of about 3.7 m. Distinguishing between features approximately 13 m apart in a cerebellum mouse brain thin tissue section was demonstrated in a multimodal fashion including co-registered optical and mass spectral chemical images.

  13. Mid-infrared (MIR) photonics: MIR passive and active fiberoptics chemical and biomedical, sensing and imaging

    Science.gov (United States)

    Seddon, Angela B.

    2016-10-01

    The case for new, portable, real-time mid-infrared (MIR) molecular sensing and imaging is discussed. We set a record in demonstrating extreme broad-band supercontinuum (SC) generated light 1.4-13.3 μm in a specially engineered, step-index MIR optical fiber of high numerical aperture. This was the first experimental demonstration truly to reveal the potential of MIR fibers to emit across the MIR molecular "fingerprint spectral region" and a key first step towards bright, portable, broadband MIR sources for chemical and biomedical, molecular sensing and imaging in real-time. Potential applications are in the healthcare, security, energy, environmental monitoring, chemical-processing, manufacturing and the agriculture sectors. MIR narrow-line fiber lasers are now required to pump the fiber MIR-SC for a compact all-fiber solution. Rare-earth-ion (RE-) doped MIR fiber lasers are not yet demonstrated >=4 μm wavelength. We have fabricated small-core RE-fiber with photoluminescence across 3.5-6 μm, and long excited-state lifetimes. MIR-RE-fiber lasers are also applicable as discrete MIR fiber sensors in their own right, for applications including: ship-to-ship free-space communications, aircraft counter-measures, coherent MIR imaging, MIR-optical coherent tomography, laser-cutting/ patterning of soft materials and new wavelengths for fiber laser medical surgery.

  14. In Situ Environmental TEM in Imaging Gas and Liquid Phase Chemical Reactions for Materials Research.

    Science.gov (United States)

    Wu, Jianbo; Shan, Hao; Chen, Wenlong; Gu, Xin; Tao, Peng; Song, Chengyi; Shang, Wen; Deng, Tao

    2016-11-01

    Gas and liquid phase chemical reactions cover a broad range of research areas in materials science and engineering, including the synthesis of nanomaterials and application of nanomaterials, for example, in the areas of sensing, energy storage and conversion, catalysis, and bio-related applications. Environmental transmission electron microscopy (ETEM) provides a unique opportunity for monitoring gas and liquid phase reactions because it enables the observation of those reactions at the ultra-high spatial resolution, which is not achievable through other techniques. Here, the fundamental science and technology developments of gas and liquid phase TEM that facilitate the mechanistic study of the gas and liquid phase chemical reactions are discussed. Combined with other characterization tools integrated in TEM, unprecedented material behaviors and reaction mechanisms are observed through the use of the in situ gas and liquid phase TEM. These observations and also the recent applications in this emerging area are described. The current challenges in the imaging process are also discussed, including the imaging speed, imaging resolution, and data management.

  15. Gel for simultaneous chemical imaging of anionic and cationic solutes using diffusive gradients in thin films.

    Science.gov (United States)

    Kreuzeder, Andreas; Santner, Jakob; Prohaska, Thomas; Wenzel, Walter W

    2013-12-17

    We report on a novel gel based on diffusive gradients in thin films (DGT) for the simultaneous measurement of cations and anions and its suitability for high resolution chemical imaging by using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). The new high resolution mixed binding gel (HR-MBG) is based on zirconium-hydroxide and suspended particulate reagent-iminodiacetate (SPR-IDA) as resin materials which are embedded in an ether-based urethane polymer hydrogel. The use of this polymer hydrogel material allows the production of ultrathin, highly stable and tear-proof resin gel layers with superior handling properties compared to existing ultrathin polyacrylamide gels. The gel was characterized regarding its uptake kinetics, the anion and cation capacities, and the effects of pH, ionic strength, and aging on the performance of the HR-MBG. Our results demonstrate the capability of this novel gel for concomitant sampling of anions and cations. The suitability of this new gel type for DGT chemical imaging at submm spatial resolution in soils using LA-ICPMS is shown. 2D images of P, As, Co, Cu, Mn, and Zn distributions around roots of Zea mays L. demonstrate the new opportunities offered by the HR-MBG for high-resolution mapping of solute dynamics in soil and sediment hotspots, such as the rhizosphere, by simultaneous observation of anionic and cationic solute species.

  16. Vapor Phase Alkyne Coating of Pharmaceutical Excipients: Discrimination Enhancement of Raman Chemical Imaging for Tablets.

    Science.gov (United States)

    Yamashita, Mayumi; Sasaki, Hiroaki; Moriyama, Kei

    2015-12-01

    Raman chemical imaging has become a powerful analytical tool to investigate the crystallographic characteristics of pharmaceutical ingredients in tablet. However, it is often difficult to discriminate some pharmaceutical excipients from each other by Raman spectrum because of broad and overlapping signals, limiting their detailed assessments. To overcome this difficulty, we developed a vapor phase coating method of excipients by an alkyne, which exhibits a distinctive Raman signal in the range of 2100-2300 cm(-1) . We found that the combination of two volatile reagents, propargyl bromide and triethylamine, formed a thin and nonvolatile coating on the excipient and observed the Raman signal of the alkyne at the surface. We prepared alkyne-coated cellulose by this method and formed a tablet. The Raman chemical imaging of the tablet cross-section using the alkyne peak area intensity of 2120 cm(-1) as the index showed a much clearer particle image of cellulose than using the peak area intensity of 1370 cm(-1) , which originated from the cellulose itself. Our method provides an innovative technique to analyze the solid-state characteristics of pharmaceutical excipients in tablets.

  17. Molecular Origin of Color Variation in Firefly (Beetle) Bioluminescence: A Chemical Basis for Biological Imaging.

    Science.gov (United States)

    Hirano, Takashi

    2016-01-01

    Firefly shows bioluminescence by "luciferin-luciferase" (L-L) reaction using luciferin, luciferase, ATP and O2. The chemical photon generation by an enzymatic reaction is widely utilized for analytical methods including biological imaging in the life science fields. To expand photondetecting analyses with firefly bioluminescence, it is important for users to understand the chemical basis of the L-L reaction. In particular, the emission color variation of the L-L reaction is one of the distinguishing characteristics for multicolor luciferase assay and in vivo imaging. From the viewpoint of fundamental chemistry, this review explains the recent progress in the studies on the molecular mechanism of emission color variation after showing the outline of the reaction mechanism of the whole L-L reaction. On the basis of the mechanism, the progresses in organic synthesis of luciferin analogs modulating their emission colors are also presented to support further developments of red/near infrared in vivo biological imaging utility of firefly bioluminescence.

  18. Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds

    NARCIS (Netherlands)

    de Vries, AH; Hozoi, L; Broer, R; Broer-Braam, H.B.

    2003-01-01

    The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the obse

  19. AFM-IR: Technology and Applications in Nanoscale Infrared Spectroscopy and Chemical Imaging.

    Science.gov (United States)

    Dazzi, Alexandre; Prater, Craig B

    2016-12-13

    Atomic force microscopy-based infrared spectroscopy (AFM-IR) is a rapidly emerging technique that provides chemical analysis and compositional mapping with spatial resolution far below conventional optical diffraction limits. AFM-IR works by using the tip of an AFM probe to locally detect thermal expansion in a sample resulting from absorption of infrared radiation. AFM-IR thus can provide the spatial resolution of AFM in combination with the chemical analysis and compositional imaging capabilities of infrared spectroscopy. This article briefly reviews the development and underlying technology of AFM-IR, including recent advances, and then surveys a wide range of applications and investigations using AFM-IR. AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage. In the Supporting Information , the authors provide a theoretical section that reviews the physics underlying the AFM-IR measurement and detection mechanisms.

  20. Aerolian erosion, transport, and deposition of volcaniclastic sands among the shifting sand dunes, Christmas Lake Valley, Oregon: TIMS image analysis

    Science.gov (United States)

    Edgett, Kenneth S.; Ramsey, Michael S.; Christensen, Philip R.

    1995-01-01

    Remote sensing is a tool that, in the context of aeolian studies, offers a synoptic view of a dune field, sand sea, or entire desert region. Blount et al. (1990) presented one of the first studies demonstrating the power of multispectral images for interpreting the dynamic history of an aeolian sand sea. Blount's work on the Gran Desierto of Mexico used a Landsat TM scene and a linear spectral mixing model to show where different sand populations occur and along what paths these sands may have traveled before becoming incorporated into dunes. Interpretation of sand transport paths and sources in the Gran Desierto led to an improved understanding of the origin and Holocene history of the dunes. With the anticipated advent of the EOS-A platform and ASTER thermal infrared capability in 1998, it will become possible to look at continental sand seas and map sand transport paths using 8-12 mu m bands that are well-suited to tracking silicate sediments. A logical extension of Blount's work is to attempt a similar study using thermal infrared images. One such study has already begun by looking at feldspar, quartz, magnetite, and clay distributions in the Kelso Dunes of southern California. This paper describes the geology and application of TIMS image analysis of a less-well known Holocene dune field in south central Oregon using TIMS data obtained in 1991.

  1. (1) H NMR Spectra. Part 28: Proton chemical shifts and couplings in three-membered rings. A ring current model for cyclopropane and a novel dihedral angle dependence for (3) J(HH) couplings involving the epoxy proton.

    Science.gov (United States)

    Abraham, Raymond J; Leonard, Paul; Tormena, Cláudio F

    2012-04-01

    The (1) H chemical shifts of selected three-membered ring compounds in CDCl(3) solvent were obtained. This allowed the determination of the substituent chemical shifts of the substituents in the three-membered rings and the long-range effect of these rings on the distant protons. The substituent chemical shifts of common substituents in the cyclopropane ring differ considerably from the same substituents in acyclic fragments and in cyclohexane and were modelled in terms of a three-bond (γ)-effect. For long-range protons (more than three bonds removed), the substituent effects of the cyclopropane ring were analysed in terms of the cyclopropane magnetic anisotropy and steric effect. The cyclopropane magnetic anisotropy (ring current) shift was modelled by (a) a single equivalent dipole perpendicular to and at the centre of the cyclopropane ring and (b) by three identical equivalent dipoles perpendicular to the ring placed at each carbon atom. Model (b) gave a more accurate description of the (1) H chemical shifts and was the selected model. After parameterization, the overall root mean square error for the dataset of 289 entries was 0.068 ppm. The anisotropic effects are significant for the cyclopropane protons (ca 1 ppm) but decrease rapidly with distance. The heterocyclic rings of oxirane, thiirane and aziridine do not possess a ring current. (3) J(HH) couplings of the epoxy ring proton with side-chain protons were obtained and shown to be dependent on both the H-C-C-H and H-C-C-O orientations. Both density functional theory calculations and a simple Karplus-type equation gave general agreement with the observed couplings (root mean square error 0.5 Hz over a 10-Hz range).

  2. Monitoring chemical degradation of thermally cycled glass-fibre composites using hyperspectral imaging

    Science.gov (United States)

    Papadakis, V. M.; Müller, B.; Hagenbeek, M.; Sinke, J.; Groves, R. M.

    2016-04-01

    Nowadays, the application of glass-fibre composites in light-weight structures is growing. Although mechanical characterizations of those structures are commonly performed in testing, chemical changes of materials under stresses have not yet been well documented. In the present work coupon tests and Hyperspectral Imaging (HSI) have been used to categorise possible chemical changes of glass-fibre reinforced polymers (GFRP) which are currently used in the aircraft industry. HSI is a hybrid technique that combines spectroscopy with imaging. It is able to detect chemical degradation of surfaces and has already been successfully applied in a wide range of fields including astronomy, remote sensing, cultural heritage and medical sciences. GFRP specimens were exposed to two different thermal loading conditions. One thermal loading condition was a continuous thermal exposure at 120°C for 24h, 48 h and 96h, i.e. ageing at a constant temperature. The other thermal loading condition was thermal cycling with three different numbers of cycles (4000, 8000, 12000) and two temperature ranges (0°C to 120°C and -25°C to 95°C). The effects of both conditions were measured using both HSI and interlaminar shear (ILSS) tests. No significant changes of the physical properties of the thermally cycled GFRP specimens were detected using interlaminar shear strength tests and optical microscopy. However, when using HIS, differences of the surface conditions were detected. The results showed that the different thermal loading conditions could be successfully clustered in different colours, using the HSI linear unmixing technique. Each different thermal loading condition showed a different chemical degradation level on its surface which was indicated using different colours.

  3. Hierarchy of Electronic Properties of Chemically Derived and Pristine Graphene Probed by Microwave Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kundhikanjana, W.

    2010-06-02

    Local electrical imaging using microwave impedance microscope is performed on graphene in different modalities, yielding a rich hierarchy of the local conductivity. The low-conductivity graphite oxide and its derivatives show significant electronic inhomogeneity. For the conductive chemical graphene, the residual defects lead to a systematic reduction of the microwave signals. In contrast, the signals on pristine graphene agree well with a lumped-element circuit model. The local impedance information can also be used to verify the electrical contact between overlapped graphene pieces.

  4. Microfluidic electrochemical device and process for chemical imaging and electrochemical analysis at the electrode-liquid interface in-situ

    Science.gov (United States)

    Yu, Xiao-Ying; Liu, Bingwen; Yang, Li; Zhu, Zihua; Marshall, Matthew J.

    2016-03-01

    A microfluidic electrochemical device and process are detailed that provide chemical imaging and electrochemical analysis under vacuum at the surface of the electrode-sample or electrode-liquid interface in-situ. The electrochemical device allows investigation of various surface layers including diffuse layers at selected depths populated with, e.g., adsorbed molecules in which chemical transformation in electrolyte solutions occurs.

  5. Near-infrared chemical imaging (NIR-CI) of 3D printed pharmaceuticals

    DEFF Research Database (Denmark)

    Khorasani, Milad; Edinger, Magnus; Raijada, Dhara

    2016-01-01

    Hot-melt extrusion and 3D printing are enabling manufacturing approaches for patient-centred medicinal products. Hot-melt extrusion is a flexible and continuously operating technique which is a crucial part of a typical processing cycle of printed medicines. In this work we use hot-melt extrusion...... for manufacturing of medicinal films containing indomethacin (IND) and polycaprolactone (PCL), extruded strands with nitrofurantoin monohydrate (NFMH) and poly (ethylene oxide) (PEO), and feedstocks for 3D printed dosage forms with nitrofurantoin anhydrate (NFAH), hydroxyapatite (HA) and poly (lactic acid) (PLA......). These feedstocks were printed into a prototype solid dosage form using a desktop 3D printer. These model formulations were characterized using near-infrared chemical imaging (NIR-CI) and, more specifically, the image analytical data were analysed using multivariate curve resolution-alternating least squares (MCR...

  6. Chemically modified STM tips for atomic-resolution imaging of ultrathin NaCI films

    Institute of Scientific and Technical Information of China (English)

    Zhe Li[1; Koen Schouteden[1; Violeta lancu[1; Ewald Janssens[1; Peter Lievens[1; Chris Van Haesendonck[1; Jorge I. Cerda[2

    2015-01-01

    Cl-functionalized scanning tunneling microscopy (STM) tips are fabricated by modifying a tungsten STM tip in situ on islands of ultrathin NaCI(100) films on Au(111) surfaces. The functionalized tips are used to achieve clear atomic- resolution imaging of NaCI(100) islands. In comparison with bare metal tips, the chemically modified tips yield drastically enhanced spatial resolution as well as contrast reversal in STM topographs, implying that Na atoms, rather than C1 atoms, are imaged as protrusions. STM simulations based on a Green's function formalism reveal that the experimentally observed contrast reversal in the STM topographs is due to the highly localized character of the Cl-pz states at the tip apex. An additional remarkable characteristic of the modified tips is that in dI/dV maps, a Na atom appears as a ring with a diameter that depends crucially on the tip-sample distance.

  7. Imaging in Vivo Extracellular pH with a Single Paramagnetic Chemical Exchange Saturation Transfer Magnetic Resonance Imaging Contrast Agent

    Directory of Open Access Journals (Sweden)

    Guanshu Liu

    2012-01-01

    Full Text Available The measurement of extracellular pH (pHe has potential utility for cancer diagnoses and for assessing the therapeutic effects of pH-dependent therapies. A single magnetic resonance imaging (MRI contrast agent that is detected through paramagnetic chemical exchange saturation transfer (PARACEST was designed to measure tumor pHe throughout the range of physiologic pH and with magnetic resonance saturation powers that are not harmful to a mouse model of cancer. The chemical characterization and modeling of the contrast agent Yb3+-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid, 10-o-aminoanilide (Yb-DO3A-oAA suggested that the aryl amine of the agent forms an intramolecular hydrogen bond with a proximal carboxylate ligand, which was essential for generating a practical chemical exchange saturation transfer (CEST effect from an amine. A ratio of CEST effects from the aryl amine and amide was linearly correlated with pH throughout the physiologic pH range. The pH calibration was used to produce a parametric pH map of a subcutaneous flank tumor on a mouse model of MCF-7 mammary carcinoma. Although refinements in the in vivo CEST MRI methodology may improve the accuracy of pHe measurements, this study demonstrated that the PARACEST contrast agent can be used to generate parametric pH maps of in vivo tumors with saturation power levels that are not harmful to a mouse model of cancer.

  8. Histopathological image analysis of chemical-induced hepatocellular hypertrophy in mice.

    Science.gov (United States)

    Asaoka, Yoshiji; Togashi, Yuko; Mutsuga, Mayu; Imura, Naoko; Miyoshi, Tomoya; Miyamoto, Yohei

    2016-04-01

    Chemical-induced hepatocellular hypertrophy is frequently observed in rodents, and is mostly caused by the induction of phase I and phase II drug metabolic enzymes and peroxisomal lipid metabolic enzymes. Liver weight is a sensitive and commonly used marker for detecting hepatocellular hypertrophy, but is also increased by a number of other factors. Histopathological observations subjectively detect changes such as hepatocellular hypertrophy based on the size of a hepatocyte. Therefore, quantitative microscopic observations are required to evaluate histopathological alterations objectively. In the present study, we developed a novel quantitative method for an image analysis of hepatocellular hypertrophy using liver sections stained with hematoxylin and eosin, and demonstrated its usefulness for evaluating hepatocellular hypertrophy induced by phenobarbital (a phase I and phase II enzyme inducer) and clofibrate (a peroxisomal enzyme inducer) in mice. The algorithm of this imaging analysis was designed to recognize an individual hepatocyte through a combination of pixel-based and object-based analyses. Hepatocellular nuclei and the surrounding non-hepatocellular cells were recognized by the pixel-based analysis, while the areas of the recognized hepatocellular nuclei were then expanded until they ran against their expanding neighboring hepatocytes and surrounding non-hepatocellular cells by the object-based analysis. The expanded area of each hepatocellular nucleus was regarded as the size of an individual hepatocyte. The results of this imaging analysis showed that changes in the sizes of hepatocytes corresponded with histopathological observations in phenobarbital and clofibrate-treated mice, and revealed a correlation between hepatocyte size and liver weight. In conclusion, our novel image analysis method is very useful for quantitative evaluations of chemical-induced hepatocellular hypertrophy.

  9. Handheld hyperspectral imager system for chemical/biological and environmental applications

    Science.gov (United States)

    Hinnrichs, Michele; Piatek, Bob

    2004-08-01

    A small, hand held, battery operated imaging infrared spectrometer, Sherlock, has been developed by Pacific Advanced Technology and was field tested in early 2003. The Sherlock spectral imaging camera has been designed for remote gas leak detection, however, the architecture of the camera is versatile enough that it can be applied to numerous other applications such as homeland security, chemical/biological agent detection, medical and pharmaceutical applications as well as standard research and development. This paper describes the Sherlock camera, theory of operations, shows current applications and touches on potential future applications for the camera. The Sherlock has an embedded Power PC and performs real-time-image processing function in an embedded FPGA. The camera has a built in LCD display as well as output to a standard monitor, or NTSC display. It has several I/O ports, ethernet, firewire, RS232 and thus can be easily controlled from a remote location. In addition, software upgrades can be performed over the ethernet eliminating the need to send the camera back to the factory for a retrofit. Using the USB port a mouse and key board can be connected and the camera can be used in a laboratory environment as a stand alone imaging spectrometer.

  10. Lactate Chemical Exchange Saturation Transfer (LATEST) Imaging in vivo A Biomarker for LDH Activity.

    Science.gov (United States)

    DeBrosse, Catherine; Nanga, Ravi Prakash Reddy; Bagga, Puneet; Nath, Kavindra; Haris, Mohammad; Marincola, Francesco; Schnall, Mitchell D; Hariharan, Hari; Reddy, Ravinder

    2016-01-22

    Non-invasive imaging of lactate is of enormous significance in cancer and metabolic disorders where glycolysis dominates. Here, for the first time, we describe a chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) method (LATEST), based on the exchange between lactate hydroxyl proton and bulk water protons to image lactate with high spatial resolution. We demonstrate the feasibility of imaging lactate with LATEST in lactate phantoms under physiological conditions, in a mouse model of lymphoma tumors, and in skeletal muscle of healthy human subjects pre- and post-exercise. The method is validated by measuring LATEST changes in lymphoma tumors pre- and post-infusion of pyruvate and correlating them with lactate determined from multiple quantum filtered proton magnetic resonance spectroscopy (SEL-MQC (1)H-MRS). Similarly, dynamic LATEST changes in exercising human skeletal muscle are correlated with lactate determined from SEL-MQC (1)H-MRS. The LATEST method does not involve injection of radioactive isotopes or labeled metabolites. It has over two orders of magnitude higher sensitivity compared to conventional (1)H-MRS. It is anticipated that this technique will have a wide range of applications including diagnosis and evaluation of therapeutic response of cancer, diabetes, cardiac, and musculoskeletal diseases. The advantages of LATEST over existing methods and its potential challenges are discussed.

  11. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  12. Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering

    Science.gov (United States)

    Hu, Fanghao; Lamprecht, Michael R.; Wei, Lu; Morrison, Barclay; Min, Wei

    2016-12-01

    Brain is an immensely complex system displaying dynamic and heterogeneous metabolic activities. Visualizing cellular metabolism of nucleic acids, proteins, and lipids in brain with chemical specificity has been a long-standing challenge. Recent development in metabolic labeling of small biomolecules allows the study of these metabolisms at the global level. However, these techniques generally require nonphysiological sample preparation for either destructive mass spectrometry imaging or secondary labeling with relatively bulky fluorescent labels. In this study, we have demonstrated bioorthogonal chemical imaging of DNA, RNA, protein and lipid metabolism in live rat brain hippocampal tissues by coupling stimulated Raman scattering microscopy with integrated deuterium and alkyne labeling. Heterogeneous metabolic incorporations for different molecular species and neurogenesis with newly-incorporated DNA were observed in the dentate gyrus of hippocampus at the single cell level. We further applied this platform to study metabolic responses to traumatic brain injury in hippocampal slice cultures, and observed marked upregulation of protein and lipid metabolism particularly in the hilus region of the hippocampus within days of mechanical injury. Thus, our method paves the way for the study of complex metabolic profiles in live brain tissue under both physiological and pathological conditions with single-cell resolution and minimal perturbation.

  13. Synthesis, NMR spectroscopic characterization and structure of a divinyldisilazane-(triphenylphosphine)platinum(0) complex: observation of isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt).

    Science.gov (United States)

    Wrackmeyer, Bernd; Klimkina, Elena V; Schmalz, Thomas; Milius, Wolfgang

    2013-05-01

    Tetramethyldivinyldisilazane-(triphenylphosphine)platinum(0) was prepared, characterized in solid state by X-ray crystallography and in solution by multinuclear magnetic resonance spectroscopy ((1)H, (13)C, (15)N, (29)Si, (31)P and (195)Pt NMR). Numerous signs of spin-spin coupling constants were determined by two-dimensional heteronuclear shift correlations (HETCOR) and two-dimensional (1)H/(1)H COSY experiments. Isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt) were measured from (195)Pt NMR spectra of the title compound as well as of other Pt(0), Pt(II) and Pt(IV) compounds for comparison. In contrast to other heavy nuclei such as (199)Hg or (207)Pb, the "normal" shifts of the heavy isotopomers to low frequencies are found, covering a range of >500 ppb.

  14. Determination of pKa values of tenoxicam from 1H NMR chemical shifts and of oxicams from electrophoretic mobilities (CZE) with the aid of programs SQUAD and HYPNMR.

    Science.gov (United States)

    Rodríguez-Barrientos, Damaris; Rojas-Hernández, Alberto; Gutiérrez, Atilano; Moya-Hernández, Rosario; Gómez-Balderas, Rodolfo; Ramírez-Silva, María Teresa

    2009-12-15

    In this work it is explained, by the first time, the application of programs SQUAD and HYPNMR to refine equilibrium constant values through the fit of electrophoretic mobilities determined by capillary zone electrophoresis experiments, due to the mathematical isomorphism of UV-vis absorptivity coefficients, NMR chemical shifts and electrophoretic mobilities as a function of pH. Then, the pK(a) values of tenoxicam in H(2)O/DMSO 1:4 (v/v) have been obtained from (1)H NMR chemical shifts, as well as of oxicams in aqueous solution from electrophoretic mobilities determined by CZE, at 25 degrees C. These values are in very good agreement with those reported by spectrophotometric and potentiometric measurements.

  15. Chemical modifications and bioconjugate reactions of nanomaterials for sensing, imaging, drug delivery and therapy.

    Science.gov (United States)

    Biju, Vasudevanpillai

    2014-02-07

    As prepared nanomaterials of metals, semiconductors, polymers and carbon often need surface modifications such as ligand exchange, and chemical and bioconjugate reactions for various biosensor, bioanalytical, bioimaging, drug delivery and therapeutic applications. Such surface modifications help us to control the physico-chemical, toxicological and pharmacological properties of nanomaterials. Furthermore, introduction of various reactive functional groups on the surface of nanomaterials allows us to conjugate a spectrum of contrast agents, antibodies, peptides, ligands, drugs and genes, and construct multifunctional and hybrid nanomaterials for the targeted imaging and treatment of cancers. This tutorial review is intended to provide an introduction to newcomers about how chemical and bioconjugate reactions transform the surface of nanomaterials such as silica nanoparticles, gold nanoparticles, gold quantum clusters, semiconductor quantum dots, carbon nanotubes, fullerene and graphene, and accordingly formulate them for applications such as biosensing, bioimaging, drug and gene delivery, chemotherapy, photodynamic therapy and photothermal therapy. Nonetheless, controversial reports and our growing concerns about toxicity and pharmacokinetics of nanomaterials suggest the need for not only rigorous in vivo experiments in animal models but also novel nanomaterials for practical applications in the clinical settings. Further reading of original and review articles cited herein is necessary to buildup in-depth knowledge about the chemistry, bioconjugate chemistry and biological applications of individual nanomaterials.

  16. Direct imaging of mechanical and chemical gradients across the thickness of graded organosilicone microwave PECVD coatings.

    Science.gov (United States)

    Hall, Colin J; Murphy, Peter J; Griesser, Hans J

    2014-01-22

    The characterization of variations in the chemical composition and ensuing mechanical properties across the thickness of coatings with continuously varying compositions through their thickness (graded coatings) presents considerable challenges for current analytical techniques in materials science. We report here the direct imaging of nanomechanical and chemical gradients across cross-sections of an organosilicone coating fabricated via microwave plasma enhanced chemical vapor deposition (PECVD). Cross-sectional nanoindentation was used to determine the mechanical properties of uniform and graded organosilicone coatings. Both hardness and modulus across the coatings were directly measured. Additionally, "modulus mapping" on cross-sections was used to map the complex modulus. For the graded coating, it was found that variations in the complex modulus was predominantly due to varying storage modulus. It was observed that at the interface with the substrate there was a low storage modulus, which linearly increased to a relatively high storage modulus at the surface. It is proposed that the increase in stiffness, from the substrate interface to the outer surface, is due to the increasing content of a cross-linked O-Si-O network. This mechanical gradient has been linked to a change in the Si:O ratio via direct compositional mapping using ToF-SIMS. Direct mapping of the mechanical and compositional gradients across these protective coatings provides insight into the changes in properties with depth and supports optimization of the critical mechanical performance of PECVD graded coatings.

  17. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Brückner, Michael [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Becker, Katja [Justus Liebig University Giessen, Biochemistry and Molecular Biology, 35392 Giessen (Germany); Popp, Jürgen [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany); Frosch, Torsten, E-mail: torsten.frosch@uni-jena.de [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany)

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  18. Temporally shifted hemodynamic response model helps to extract acupuncture-induced functional magnetic resonance imaging blood oxygenation-level dependent activities

    Institute of Scientific and Technical Information of China (English)

    Tsung-Jung Ho; Jeng-Ren Duann; Chun-Ming Chen; Jeon-Hor Chen; Wu-Chung Shen; Tung-Wu Lu; Jan-Ray Liao; Zen-Pin Lin; Kuo-Ning Shaw; Jaung-Geng Lin

    2009-01-01

    Background The onsets of needling sensation introduced by acupuncture stimulus can vary widely from subject to subject.This should be explicitly accounted for by the model blood oxygenation-level dependent (BOLD) time course used in general linear model (GLM) analysis to obtain more consistent across-subject group results.However,in standard GLM analysis,the model BOLD time course obtained by convolving a canonical hemodynamic response function with an experimental paradigm time course is assumed identical across subjects.Although some added-on properties to the model BOLD time course,such as temporal and dispersion derivatives,may be used to account for different BOLD response onsets,they can only account for the BOLD onset deviations to the extent of less than one repetition time (TR).Methods In this study,we explicitly manipulated the onsets of model BOLD time course by shifting it with-2,-1,or 1 TR and used these temporally shifted BOLD model to analyze the functional magnetic resonance imaging (fMRI) data obtained from three acupuncture fMRI experiments with GLM analysis.One involved acupuncture stimulus on left ST42acupoint and the other two on left GB40 and left BL64 acupoints.Results The model BOLD time course with temporal shifts,in addition to temporal and dispersion derivatives,could result in better statistical power of the data analysis in terms of the average correlation coefficients between the used BOLD models and extracted BOLD responses from individual subject data and the T-values of the activation clusters in the grouped random effects.Conclusions The GLM analysis with ordinary BOLD model failed to catch the large variability of the onsets of the BOLD responses associated with the acupuncture needling sensation.Shifts in time with more than a TR on model BOLD time course might be required to better extract the acupuncture stimulus-induced BOLD activities from individual fMRI data.

  19. Miniature Variable Pressure Scanning Electron Microscope for In-Situ Imaging and Chemical Analysis

    Science.gov (United States)

    Gaskin, Jessica A.; Jerman, Gregory; Gregory, Don; Sampson, Allen R.

    2012-01-01

    NASA Marshall Space Flight Center (MSFC) is leading an effort to develop a Miniaturized Variable Pressure Scanning Electron Microscope (MVP-SEM) for in-situ imaging and chemical analysis of uncoated samples. This instrument development will be geared towards operation on Mars and builds on a previous MSFC design of a mini-SEM for the moon (funded through the NASA Planetary Instrument Definition and Development Program). Because Mars has a dramatically different environment than the moon, modifications to the MSFC lunar mini-SEM are necessary. Mainly, the higher atmospheric pressure calls for the use of an electron gun that can operate at High Vacuum, rather than Ultra-High Vacuum. The presence of a CO2-rich atmosphere also allows for the incorporation of a variable pressure system that enables the in-situ analysis of nonconductive geological specimens. Preliminary testing of Mars meteorites in a commercial Environmental SEM(Tradmark) (FEI) confirms the usefulness of lowcurrent/low-accelerating voltage imaging and highlights the advantages of using the Mars atmosphere for environmental imaging. The unique capabilities of the MVP-SEM make it an ideal tool for pursuing key scientific goals of NASA's Flagship Mission Max-C; to perform in-situ science and collect and cache samples in preparation for sample return from Mars.

  20. Power Shift

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ "We are entering a new era of world history: the end of Western domination and the arrival of the Asian century. The question is: will Washington wake up to this reality?" This is the central premise of Kishore Mahbubani's provocative new book The New Asian Hemisphere: The Irresistible Shift of Global Power to the East.

  1. A shift in Jupiter's equatorial haze distribution imaged with the Multi-Conjugate Adaptive Optics Demonstrator at the VLT

    CERN Document Server

    Wong, Michael H; Marchetti, Enrico; Amico, Paola; Tordo, Sebastien; Bouy, Herve; de Pater, Imke

    2008-01-01

    Jupiter was imaged during the Science Demonstration of the MCAO Demonstrator (MAD) at the European Southern Observatory's UT3 Very Large Telescope unit. Io and Europa were used as natural guide stars on either side of Jupiter, separated from each other by about 1.6 arcmin from 23:41 to 01:32 UT (2008 Aug 16/17). The corrected angular resolution was 0.090 arcsec across the entire field of view, as measured on background stars. The observations at 2.02, 2.14, and 2.16 micrometers were sensitive to portions of the Jovian spectrum with strong methane absorption. The data probe the upper troposphere, which is populated with a fine (~0.5 micrometer) haze. Two haze sources have been proposed: lofting of fine cloud particles into the stable upper troposphere, and condensation of hydrazine produced via ammonia photochemistry. The upper tropospheric haze is enhanced over Jupiter's equatorial region. Dramatic changes in the underlying cloud cover--part of the 2006/2007 "global upheaval"--may be associated with changes i...

  2. Frequency-modulated atomic force microscopy operation by imaging at the frequency shift minimum: The dip-df mode

    Science.gov (United States)

    Rode, Sebastian; Schreiber, Martin; Kühnle, Angelika; Rahe, Philipp

    2014-04-01

    In frequency modulated non-contact atomic force microscopy, the change of the cantilever frequency (Δf) is used as the input signal for the topography feedback loop. Around the Δf(z) minimum, however, stable feedback operation is challenging using a standard proportional-integral-derivative (PID) feedback design due to the change of sign in the slope. When operated under liquid conditions, it is furthermore difficult to address the attractive interaction regime due to its often moderate peakedness. Additionally, the Δf signal level changes severely with time in this environment due to drift of the cantilever frequency f0 and, thus, requires constant adjustment. Here, we present an approach overcoming these obstacles by using the derivative of Δf with respect to z as the input signal for the topography feedback loop. Rather than regulating the absolute value to a preset setpoint, the slope of the Δf with respect to z is regulated to zero. This new measurement mode not only makes the minimum of the Δf(z) curve directly accessible, but it also benefits from greatly increased operation stability due to its immunity against f0 drift. We present isosurfaces of the Δf minimum acquired on the calcite CaCO3(10overline{1}4) surface in liquid environment, demonstrating the capability of our method to image in the attractive tip-sample interaction regime.

  3. Frequency-modulated atomic force microscopy operation by imaging at the frequency shift minimum: The dip-df mode

    Energy Technology Data Exchange (ETDEWEB)

    Rode, Sebastian; Schreiber, Martin; Kühnle, Angelika; Rahe, Philipp, E-mail: rahe@uni-mainz.de [Institut für Physikalische Chemie, Fachbereich Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55099 Mainz (Germany)

    2014-04-15

    In frequency modulated non-contact atomic force microscopy, the change of the cantilever frequency (Δf) is used as the input signal for the topography feedback loop. Around the Δf(z) minimum, however, stable feedback operation is challenging using a standard proportional-integral-derivative (PID) feedback design due to the change of sign in the slope. When operated under liquid conditions, it is furthermore difficult to address the attractive interaction regime due to its often moderate peakedness. Additionally, the Δf signal level changes severely with time in this environment due to drift of the cantilever frequency f{sub 0} and, thus, requires constant adjustment. Here, we present an approach overcoming these obstacles by using the derivative of Δf with respect to z as the input signal for the topography feedback loop. Rather than regulating the absolute value to a preset setpoint, the slope of the Δf with respect to z is regulated to zero. This new measurement mode not only makes the minimum of the Δf(z) curve directly accessible, but it also benefits from greatly increased operation stability due to its immunity against f{sub 0} drift. We present isosurfaces of the Δf minimum acquired on the calcite CaCO{sub 3}(101{sup ¯}4) surface in liquid environment, demonstrating the capability of our method to image in the attractive tip-sample interaction regime.

  4. A clickable UTP analog for the posttranscriptional chemical labeling and imaging of RNA.

    Science.gov (United States)

    Sawant, Anupam A; Mukherjee, Progya P; Jangid, Rahul K; Galande, Sanjeev; Srivatsan, Seergazhi G

    2016-06-28

    The development of robust tools and practical RNA labeling strategies that would facilitate the biophysical analysis of RNA in both cell-free and cellular systems will have profound implications in the discovery of new RNA diagnostic tools and therapeutic strategies. In this context, we describe the development of a new alkyne-modified UTP analog, 5-(1,7-octadinyl)uridine triphosphate (ODUTP), which serves as an efficient substrate for the introduction of a clickable alkyne label into RNA transcripts by bacteriophage T7 RNA polymerase and mammalian cellular RNA polymerases. The ODU-labeled RNA is effectively used by reverse transcriptase to produce cDNA, a property which could be utilized in expanding the chemical space of a RNA library in the aptamer selection scheme. Further, the alkyne label on RNA provides a convenient tool for the posttranscriptional chemical functionalization with a variety of biophysical tags (fluorescent, affinity, amino acid and sugar) by using alkyne-azide cycloaddition reaction. Importantly, the ability of endogenous RNA polymerases to specifically incorporate ODUTP into cellular RNA transcripts enabled the visualization of newly transcribing RNA in cells by microscopy using click reactions. In addition to a clickable alkyne group, ODU contains a Raman scattering label (internal disubstituted alkyne), which exhibits characteristic Raman shifts that fall in the Raman-silent region of cells. Our results indicate that an ODU label could potentially facilitate two-channel visualization of RNA in cells by using click chemistry and Raman spectroscopy. Taken together, ODU represents a multipurpose ribonucleoside tool, which is expected to provide new avenues to study RNA in cell-free and cellular systems.

  5. Application of magnetic resonance imaging in transgenic and chemical mouse models of hepatocellular carcinoma

    Directory of Open Access Journals (Sweden)

    Liedtke Christian

    2010-04-01

    Full Text Available Abstract Background Hepatocellular carcinoma (HCC is one of the most common cancers worldwide. The molecular mechanisms underlying hepatocarcinogenesis are still poorly understood. Genetically modified mice are powerful tools to further investigate the mechanisms of HCC development. However, this approach is limited due to the lack of non-invasive detection methods in small rodents. The aim of this study was to establish a protocol for the non-invasive analysis of hepatocarcinogenesis in transgenic mice using a clinical 1.5 Tesla Magnetic Resonance Imaging scanner. Results As a model system we used hepatocyte-specific c-myc transgenic mice developing hepatocellular carcinoma at the age of 12-15 months. The scans of the murine livers included axial T2-weighted turbo-spin echo (TSE images, axial T1-weighted and contrast enhanced T1-weighted gradient echo (fast field echo, FFE and sagittal true Fast Imaging with Steady state Precession (true-FISP images. Application of contrast agent was performed via tail vein-catheter and confirmed by evaluation of the altered longitudinal relaxation T1 time before and after application. Through technical adaptation and optimization we could detect murine liver lesions with a minimum diameter of approximately 2 mm and provided histopathological evidence that these MR findings correspond to hepatocellular carcinoma. Tumor growth was repeatedly measured using sequential MRI with intervals of 5 weeks and subsequent volumetric analysis facilitating direct comparison of tumor progression between individual animals. We finally demonstrated that our protocol is also applicable in the widely- used chemical model of N-nitrosodiethylamine-induced hepatocarcinogenesis. Conclusion Our protocol allows the non-invasive, early detection of HCC and the subsequent continuous monitoring of liver tumorgenesis in transgenic mice thereby facilitating future investigations of transgenic tumor mouse models of the liver.

  6. Evaluation of chemical fluorescent dyes as a protein conjugation partner for live cell imaging.

    Directory of Open Access Journals (Sweden)

    Yoko Hayashi-Takanaka

    Full Text Available To optimize live cell fluorescence imaging, the choice of fluorescent substrate is a critical factor. Although genetically encoded fluorescent proteins have been used widely, chemical fluorescent dyes are still useful when conjugated to proteins or ligands. However, little information is available for the suitability of different fluorescent dyes for live imaging. We here systematically analyzed the property of a number of commercial fluorescent dyes when conjugated with antigen-binding (Fab fragments directed against specific histone modifications, in particular, phosphorylated H3S28 (H3S28ph and acetylated H3K9 (H3K9ac. These Fab fragments were conjugated with a fluorescent dye and loaded into living HeLa cells. H3S28ph-specific Fab fragments were expected to be enriched in condensed chromosomes, as H3S28 is phosphorylated during mitosis. However, the degree of Fab fragment enrichment on mitotic chromosomes varied depending on the conjugated dye. In general, green fluorescent dyes showed higher enrichment, compared to red and far-red fluorescent dyes, even when dye:protein conjugation ratios were similar. These differences are partly explained by an altered affinity of Fab fragment after dye-conjugation; some dyes have less effect on the affinity, while others can affect it more. Moreover, red and far-red fluorescent dyes tended to form aggregates in the cytoplasm. Similar results were observed when H3K9ac-specific Fab fragments were used, suggesting that the properties of each dye affect different Fab fragments similarly. According to our analysis, conjugation with green fluorescent dyes, like Alexa Fluor 488 and Dylight 488, has the least effect on Fab affinity and is the best for live cell imaging, although these dyes are less photostable than red fluorescent dyes. When multicolor imaging is required, we recommend the following dye combinations for optimal results: Alexa Fluor 488 (green, Cy3 (red, and Cy5 or CF640 (far-red.

  7. Nuclear overhauser enhancement mediated chemical exchange saturation transfer imaging at 7 Tesla in glioblastoma patients.

    Directory of Open Access Journals (Sweden)

    Daniel Paech

    Full Text Available BACKGROUND AND PURPOSE: Nuclear Overhauser Enhancement (NOE mediated chemical exchange saturation transfer (CEST is a novel magnetic resonance imaging (MRI technique on the basis of saturation transfer between exchanging protons of tissue proteins and bulk water. The purpose of this study was to evaluate and compare the information provided by three dimensional NOE mediated CEST at 7 Tesla (7T and standard MRI in glioblastoma patients. PATIENTS AND METHODS: Twelve patients with newly diagnosed histologically proven glioblastoma were enrolled in this prospective ethics committee-approved study. NOE mediated CEST contrast was acquired with a modified three-dimensional gradient-echo sequence and asymmetry analysis was conducted at 3.3 ppm (B1 = 0.7 µT to calculate the magnetization transfer ratio asymmetry (MTR(asym. Contrast enhanced T1 (CE-T1 and T2-weighted images were acquired at 3T and used for data co-registration and comparison. RESULTS: Mean NOE mediated CEST signal based on MTR(asym values over all patients was significantly increased (p<0.001 in CE-T1 tumor (-1.99 ± 1.22%, tumor necrosis (-1.36 ± 1.30% and peritumoral CEST hyperintensities (PTCH within T2 edema margins (-3.56 ± 1.24% compared to contralateral normal appearing white matter (-8.38 ± 1.19%. In CE-T1 tumor (p = 0.015 and tumor necrosis (p<0.001 mean MTR(asym values were significantly higher than in PTCH. Extent of the surrounding tumor hyperintensity was smaller in eight out of 12 patients on CEST than on T2-weighted images, while four displayed at equal size. In all patients, isolated high intensity regions (0.40 ± 2.21% displayed on CEST within the CE-T1 tumor that were not discernible on CE-T1 or T2-weighted images. CONCLUSION: NOE mediated CEST Imaging at 7 T provides additional information on the structure of peritumoral hyperintensities in glioblastoma and displays isolated high intensity regions within the CE-T1 tumor that cannot be acquired on CE-T1 or T2

  8. Dual Raman-Brillouin Microscope for Chemical and Mechanical Characterization and Imaging.

    Science.gov (United States)

    Traverso, Andrew J; Thompson, Jonathan V; Steelman, Zachary A; Meng, Zhaokai; Scully, Marlan O; Yakovlev, Vladislav V

    2015-08-01

    We present a unique confocal microscope capable of measuring the Raman and Brillouin spectra simultaneously from a single spatial location. Raman and Brillouin scattering offer complementary information about a material's chemical and mechanical structure, respectively, and concurrent monitoring of both of these spectra would set a new standard for material characterization. We achieve this by applying recent innovations in Brillouin spectroscopy that reduce the necessary acquisition times to durations comparable to conventional Raman spectroscopy while attaining a high level of spectral accuracy. To demonstrate the potential of the system, we map the Raman and Brillouin spectra of a molded poly(ethylene glycol) diacrylate (PEGDA) hydrogel sample in cyclohexane to create two-dimensional images with high contrast at microscale resolutions. This powerful tool has the potential for very diverse analytical applications in basic science, industry, and medicine.

  9. Application of Image Analysis Based on SEM and Chemical Mapping on PC Mortars under Sulfate Attack

    Institute of Scientific and Technical Information of China (English)

    YU Cheng; SUN Wei; Scrivener Karen

    2014-01-01

    The degradation mechanisms of cementitious materials exposed to sulfate solutions have been controversial, despite considerable research. In this paper, two methodologies of image analysis based on scanning electron microscope and chemical mapping are used to analyse Portland cement mortars exposed to sodium sulfate solution. The effects of sulfate concentration in solution and water to cement ratio of mortar, which are considered as the most sensitive factors to sulfate attack, are investigated respectively by comparing the macro expansion with microstructure analysis. It is found that the sulfate concentration in pore solution, expressed as sulfate content in C-S-H, plays a critical role on the supersaturation with respect to ettringite and so on the expansion force generated.

  10. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    Science.gov (United States)

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  11. 线性移位寄存器在图像加密中的应用%The Application in Image Encryption by Line Feedback Shift Register

    Institute of Scientific and Technical Information of China (English)

    荆锐; 朱平; 杨恒欢; 冯涛

    2011-01-01

    图像加密技术作为数字信息保护的一种有效手段,随着信息技术的发展,人们对其安全性的要求越来越高。讨论了关于线性移位寄存器(LFSR)在图像加密中的应用。本算法先采用LFSR算法产生伪混沌比特密钥流,将该密钥流作为随机值映射算法和加密算法的初始参数。随机值映射算法取其中较高位的密钥流,生成置乱序列用于图像像素的位置置乱。另一组密钥流作为加密序列可对图像的像素值进行加密。实验结果表明该方法运算速度快,通过随机值映射算法产生的伪随机置乱和加密序列具有很强的可操作性、保密性,而且截取伪混沌比特密钥流的位数也可作为密钥存在。%For digital information protection, image encryption is an effective technology. As the development of information technology, people also need more and more security on image encryption. This thesis discussed the application in image encryption by line feedback shift register. At first the system generated the initial pseudo-chaos bit key stream by LSFR. The key stream becomed the initial parameter of the random value mapped scrambling algorithm and chaos encryption algorithm. Mapping the image with the mapped stream which was generated by the random value mapped scrambling algorithm with the higher digital key stream, then encrypted the image with the encrypted stream which was generated by another key stream. The result shows this system runs lastly. The pseudo-random mapped stream and pseudo-encrypted stream that were generated by the random value scrambling algorithm both had a strong operational, confidentiality. Also the chosen pseudo-chaos bit key stream can become the keywords.

  12. Chemical sensing and imaging based on photon upconverting nano- and microcrystals: a review

    Science.gov (United States)

    Christ, Simon; Schäferling, Michael

    2015-09-01

    The demand for photostable luminescent reporters that absorb and emit light in the red to near-infrared (NIR) spectral region continues in biomedical research and bioanalysis. In recent years, classical organic fluorophores have increasingly been displaced by luminescent nanoparticles. These consist of either polymer or silica based beads that are loaded with luminescent dyes, conjugated polymers, or inorganic nanomaterials such as semiconductor nanocrystals (quantum dots), colloidal clusters of silver and gold, or carbon dots. Among the inorganic materials, photon upconversion nanocrystals exhibit a high potential for application to bioimaging or biomolecular assays. They offer an exceptionally high photostability, can be excited in the NIR, and their anti-Stokes emission enables luminescence detection free of background and perturbing scatter effects even in complex biological samples. These lanthanide doped inorganic crystals have multiple emission lines that can be tuned by the selection of the dopants. This review article is focused on the applications of functionalized photon upconversion nanoparticles (UCNPs) to chemical sensing. This is a comparatively new field of research activity and mainly directed at the sensing and imaging of ubiquitous chemical analytes in biological samples, particularly in living cells. For this purpose, the particles have to be functionalized with suitable indicator dyes or recognition elements, as they do not show an intrinsic or specific luminescence response to most of these analytes (e.g. pH, oxygen, metal ions). We describe the strategies for the design of such responsive nanocomposites utilizing either luminescence resonance energy transfer or emission-reabsorption (inner filter effect) mechanisms and also highlight examples for their use either immobilized in sensor layers or directly as nanoprobes for intracellular sensing and imaging.

  13. Chemical design of a radiolabeled gelatinase inhibitor peptide for the imaging of gelatinase activity in tumors

    Energy Technology Data Exchange (ETDEWEB)

    Hanaoka, Hirofumi [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan); Graduate School of Medicine, Gunma University, Maebashi 371-8511 (Japan); Mukai, Takahiro [Graduate School of Medicine, Kyoto University, Kyoto 606-8507 (Japan); Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582 (Japan); Habashita, Sayo [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan); Asano, Daigo [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan); Ogawa, Kazuma [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan); Kuroda, Yoshihiro [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan); Akizawa, Hiromichi [Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675 (Japan); Iida, Yasuhiko [Graduate School of Medicine, Gunma University, Maebashi 371-8511 (Japan); Endo, Keigo [Graduate School of Medicine, Gunma University, Maebashi 371-8511 (Japan); Saga, Tsuneo [Graduate School of Medicine, Kyoto University, Kyoto 606-8507 (Japan); Saji, Hideo [Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachi-cho, Kyoto 606-8501 (Japan)]. E-mail: hsaji@pharm.kyoto-u.ac.jp

    2007-07-15

    Since elevated levels of gelatinases [matrix metalloproteinase (MMP)-2 and MMP-9] are associated with a poor prognosis in cancer patients, these enzymes are potential targets for tumor imaging. In the present study, a cyclic decapeptide, cCTTHWGFTLC (CTT), was selected as a mother compound because of its selective inhibitory activity toward gelatinases. For imaging gelatinase activity in tumors, we designed a CTT-based radiopharmaceutical taking into consideration that (1) the HWGF motif of the peptide is important for the activity (2) hydrophilic radiolabeled peptides show low-level accumulation in the liver and (3) an increase in the negative charge of radiolabeled peptides is effective in reducing renal accumulation. Thus, a highly hydrophilic and negatively charged radiolabel, indiun-111-diethylenetriaminepentaacetic acid ({sup 111}In-DTPA), was attached to an N-terminal residue distant from the HWGF motif ({sup 111}In-DTPA-CTT). In MMP-2 inhibition assays, In-DTPA-CTT significantly inhibited the proteolytic activity in a concentration-dependent fashion. When injected into normal mice, {sup 111}In-DTPA-CTT showed low levels of radioactivity in the liver and kidney. A comparison of the pharmacokinetic characteristics of {sup 111}In-DTPA-CTT with those of other CTT derivatives having different physicochemical properties revealed that the increase in hydrophilicity and negative charge caused by the conjugation of {sup 111}In-DTPA reduced levels of radioactivity in the liver and kidney. In tumor-bearing mice, a significant correlation was observed between the accumulation in the tumor as well as tumor-to-blood ratio of {sup 111}In-DTPA-CTT and gelatinase activity. These findings support the validity of the chemical design of {sup 111}In-DTPA-CTT for reducing accumulation in nontarget tissues and maintaining the inhibitory activity of the mother compound. Furthermore, {sup 111}In-DTPA-CTT derivatives would be potential radiopharmaceuticals for the imaging of

  14. Fluid Shifts

    Science.gov (United States)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  15. Is an "ideal" service institution image the same for all referral sources? The case of chemical dependency treatment programs.

    Science.gov (United States)

    Johnson, K; LaTour, M S

    1993-01-01

    In a competitive market like chemical dependency treatment, segmenting the professional referral market according to an "ideal" service image may offer a service institution a strategic advantage. Results of this study suggest that while different professionals in a referral market may attach differential importance to the same service feature, a favorable or unfavorable "image" seems to encompass how well both the professional and the professionals' client are treated by the service institution.

  16. In-line phase shift tomosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Hammonds, Jeffrey C.; Price, Ronald R.; Pickens, David R.; Donnelly, Edwin F. [Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee 37232 (United States)

    2013-08-15

    Purpose: The purpose of this work is to (1) demonstrate laboratory measurements of phase shift images derived from in-line phase-contrast radiographs using the attenuation-partition based algorithm (APBA) of Yan et al.[Opt. Express 18(15), 16074–16089 (2010)], (2) verify that the APBA reconstructed images obey the linearity principle, and (3) reconstruct tomosynthesis phase shift images from a collection of angularly sampled planar phase shift images.Methods: An unmodified, commercially available cabinet x-ray system (Faxitron LX-60) was used in this experiment. This system contains a tungsten anode x-ray tube with a nominal focal spot size of 10 μm. The digital detector uses CsI/CMOS with a pixel size of 50 × 50 μm. The phantoms used consisted of one acrylic plate, two polystyrene plates, and a habanero pepper. Tomosynthesis images were reconstructed from 51 images acquired over a ±25° arc. All phase shift images were reconstructed using the APBA.Results: Image contrast derived from the planar phase shift image of an acrylic plate of uniform thickness exceeded the contrast of the traditional attenuation image by an approximate factor of two. Comparison of the planar phase shift images from a single, uniform thickness polystyrene plate with two polystyrene plates demonstrated an approximate linearity of the estimated phase shift with plate thickness (−1600 rad vs −2970 rad). Tomographic phase shift images of the habanero pepper exhibited acceptable spatial resolution and contrast comparable to the corresponding attenuation image.Conclusions: This work demonstrated the feasibility of laboratory-based phase shift tomosynthesis and suggests that phase shift imaging could potentially provide a new imaging biomarker. Further investigation will be needed to determine if phase shift contrast will be able to provide new tissue contrast information or improved clinical performance.

  17. 基于Mean Shift和随机游走的图像分割算法%Image Segmentation Algorithm Based on Mean Shift and Random Walk

    Institute of Scientific and Technical Information of China (English)

    穆克; 程伟; 褚俊霞

    2012-01-01

    An improved random walk algorithm was proposed herein.First,Mean Shift algorithm was adopted to preprocess the image,which was partitioned into a series of homogeneous areas,so that the homogeneous areas were taken as nodes to walk at random,with noise inhibited while reducing the number of nodes.Second,PMD was used to define the weight between regions.Thirdly,seeds were improved to have added the auxiliary seeds,and the auxiliary and signed seeds were used to walk random,with region merging realized.The final image segmentation was reached.Experimental results expatiates that the proposed method highlights the segmentation accuracy.%提出了一种改进的随机游走算法。首先,采用Mean Shift算法对图像进行预处理,将图像划分成一些同质区域,用同质区域作为节点进行随机游走,在降低节点数的同时也抑制了噪声对分割的影响;其次,利用马氏距离定义区域之间的权值;对种子点进行了改进,增加了辅助种子点,利用辅助种子点和用户标记的种子点进行随机游走,实现同质区域的合并,实现图像的最终分割。实验结果表明,该算法提高了图像分割的精度。

  18. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells.

    Science.gov (United States)

    Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes.

  19. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  20. Imaging Taurine in the Central Nervous System Using Chemically Specific X-ray Fluorescence Imaging at the Sulfur K-Edge

    Energy Technology Data Exchange (ETDEWEB)

    Hackett, Mark J.; Paterson, Phyllis G.; Pickering, Ingrid J.; George, Graham N. (Curtin U.); (Saskatchewan)

    2016-11-15

    A method to image taurine distributions within the central nervous system and other organs has long been sought. Since taurine is small and mobile, it cannot be chemically “tagged” and imaged using conventional immuno-histochemistry methods. Combining numerous indirect measurements, taurine is known to play critical roles in brain function during health and disease and is proposed to act as a neuro-osmolyte, neuro-modulator, and possibly a neuro-transmitter. Elucidation of taurine’s neurochemical roles and importance would be substantially enhanced by a direct method to visualize alterations, due to physiological and pathological events in the brain, in the local concentration of taurine at or near cellular spatial resolution in vivo or in situ in tissue sections. We thus have developed chemically specific X-ray fluorescence imaging (XFI) at the sulfur K-edge to image the sulfonate group in taurine in situ in ex vivo tissue sections. To our knowledge, this represents the first undistorted imaging of taurine distribution in brain at 20 μm resolution. We report quantitative technique validation by imaging taurine in the cerebellum and hippocampus regions of the rat brain. Further, we apply the technique to image taurine loss from the vulnerable CA1 (cornus ammonis 1) sector of the rat hippocampus following global brain ischemia. The location-specific loss of taurine from CA1 but not CA3 neurons following ischemia reveals osmotic stress may be a key factor in delayed neurodegeneration after a cerebral ischemic insult and highlights the significant potential of chemically specific XFI to study the role of taurine in brain disease.

  1. 3D Nanoscale Chemical Imaging of the Distribution of Aluminum Coordination Environments in Zeolites with Soft X-Ray Microscopy

    NARCIS (Netherlands)

    Aramburo, Luis R.; Liu, Yijin; Tyliszczak, Tolek; de Groot, Frank M. F.; Andrews, Joy C.; Weckhuysen, Bert M.

    2013-01-01

    Here, we present the first nanoscale chemical imaging study revealing the spatial distribution of the amount and coordination environment of aluminum in zeolite materials with 3D scanning transmission X-ray microscopy (STXM). For this purpose, we have focused on two showcase samples involving the in

  2. Chemical imaging of protein adsorption and crystallization on a wettability gradient surface.

    Science.gov (United States)

    Glassford, Stefanie; Chan, K L Andrew; Byrne, Bernadette; Kazarian, Sergei G

    2012-02-14

    The use of self-assembled monolayers is an established method to study the effect of surface properties on proteins and other biological materials. The generation of a monolayer with a gradient of chemical properties allows for the study of multiple surface properties simultaneously in a high throughput manner. Typically, in order to detect the presence of proteins or biological material on a surface, the use of additional dyes or tags is required. Here we present a novel method of studying the effect of gradient surface properties on protein adsorption and crystallization in situ through the use of ATR-FTIR spectroscopic imaging, which removes the need for additional labeling. We describe the successful application of this technique to the measurement of the growth of a gradient monolayer of octyltrichlorosilane across the surface of a silicon ATR element. ATR-FTIR imaging was also used to study the adsorption of lysozyme, as a model protein, onto the modified surface. The sensitivity of measurements obtained with a focal plane array (FPA) detector were improved though the use of pixel averaging which allowed small absorption bands to be detected with minimal effect on the spatial resolution along the gradient. Study of the effect of surface hydrophobicity on both adsorption of lysozyme to the element and lysozyme crystallization revealed that more lysozyme adsorbed to the hydrophobic side of the ATR element and more lysozyme crystals formed in the same region. These findings strongly suggest a correlation exists between surface protein adsorption and protein crystallization. This method could be applied to the study of other proteins and whole cells.

  3. Effect of the Temperature-Emissivity Contrast on the Chemical Signal for Gas Plume Detection Using Thermal Image Data

    Directory of Open Access Journals (Sweden)

    Candace Metoyer

    2008-10-01

    Full Text Available Detecting and identifying weak gaseous plumes using thermal imaging data is complicated by many factors. These include variability due to atmosphere, ground and plume temperature, and background clutter. This paper presents an analysis of one formulation of the physics-based radiance model, which describes at-sensor observed radiance. The background emissivity and plume/ground temperatures are isolated, and their effects on chemical signal are described. This analysis shows that the plume’s physical state, emission or absorption, is directly dependent on the background emissivity and plume/ground temperatures. It then describes what conditions on the background emissivity and plume/ground temperatures have inhibiting or amplifying effects on the chemical signal. These claims are illustrated by analyzing synthetic hyperspectral imaging data with the adaptive matched filter using two chemicals and three distinct background emissivities.

  4. Label-free chemical imaging of live Euglena gracilis by high-speed SRS spectral microscopy (Conference Presentation)

    Science.gov (United States)

    Wakisaka, Yoshifumi; Suzuki, Yuta; Tokunaga, Kyoya; Hirose, Misa; Domon, Ryota; Akaho, Rina; Kuroshima, Mai; Tsumura, Norimichi; Shimobaba, Tomoyoshi; Iwata, Osamu; Suzuki, Kengo; Nakashima, Ayaka; Goda, Keisuke; Ozeki, Yasuyuki

    2016-03-01

    Microbes, especially microalgae, have recently been of great interest for developing novel biofuels, drugs, and biomaterials. Imaging-based screening of live cells can provide high selectivity and is attractive for efficient bio-production from microalgae. Although conventional cellular screening techniques use cell labeling, labeling of microbes is still under development and can interfere with their cellular functions. Furthermore, since live microbes move and change their shapes rapidly, a high-speed imaging technique is required to suppress motion artifacts. Stimulated Raman scattering (SRS) microscopy allows for label-free and high-speed spectral imaging, which helps us visualize chemical components inside biological cells and tissues. Here we demonstrate high-speed SRS imaging, with temporal resolution of 0.14 seconds, of intracellular distributions of lipid, polysaccharide, and chlorophyll concentrations in rapidly moving Euglena gracilis, a unicellular phytoflagellate. Furthermore, we show that our method allows us to analyze the amount of chemical components inside each living cell. Our results indicate that SRS imaging may be applied to label-free screening of living microbes based on chemical information.

  5. Multispectral UV imaging for fast and non-destructive quality control of chemical and physical tablet attributes.

    Science.gov (United States)

    Klukkert, Marten; Wu, Jian X; Rantanen, Jukka; Carstensen, Jens M; Rades, Thomas; Leopold, Claudia S

    2016-07-30

    Monitoring of tablet quality attributes in direct vicinity of the production process requires analytical techniques that allow fast, non-destructive, and accurate tablet characterization. The overall objective of this study was to investigate the applicability of multispectral UV imaging as a reliable, rapid technique for estimation of the tablet API content and tablet hardness, as well as determination of tablet intactness and the tablet surface density profile. One of the aims was to establish an image analysis approach based on multivariate image analysis and pattern recognition to evaluate the potential of UV imaging for automatized quality control of tablets with respect to their intactness and surface density profile. Various tablets of different composition and different quality regarding their API content, radial tensile strength, intactness, and surface density profile were prepared using an eccentric as well as a rotary tablet press at compression pressures from 20MPa up to 410MPa. It was found, that UV imaging can provide both, relevant information on chemical and physical tablet attributes. The tablet API content and radial tensile strength could be estimated by UV imaging combined with partial least squares analysis. Furthermore, an image analysis routine was developed and successfully applied to the UV images that provided qualitative information on physical tablet surface properties such as intactness and surface density profiles, as well as quantitative information on variations in the surface density. In conclusion, this study demonstrates that UV imaging combined with image analysis is an effective and non-destructive method to determine chemical and physical quality attributes of tablets and is a promising approach for (near) real-time monitoring of the tablet compaction process and formulation optimization purposes.

  6. Nanoparticle probes and mid-infrared chemical imaging for DNA microarray detection.

    Science.gov (United States)

    Mossoba, Magdi M; Al-Khaldi, Sufian F; Schoen, Brianna; Yakes, Betsy Jean

    2010-11-01

    To date most mid-infrared spectroscopic studies have been limited, due to lack of sensitivity, to the structural characterization of a single oligonucleotide probe immobilized over the entire surface of a gold-coated slide or other infrared substrate. By contrast, widely used and commercially available glass slides and a microarray spotter that prints approximately 120-μm-diameter DNA spots were employed in the present work. To our knowledge, mid-infrared chemical imaging (IRCI) in the external reflection mode has been applied in the present study for the first time to the detection of nanostructure-based DNA microarrays spotted on glass slides. Alkyl amine-modified oligonucleotide probes were immobilized on glass slides that had been prefunctionalized with succinimidyl ester groups. This molecular fluorophore-free method entailed the binding of gold-nanoparticle-streptavidin conjugates to biotinylated DNA targets. Hybridization was visualized by the silver enhancement of gold nanoparticles. The adlayer of silver, selectively bound only to hybridized spots in a microarray, formed the external reflective infrared substrate that was necessary for the detection of DNA hybridization by IRCI in the present proof-of-concept study. IRCI made it possible to discriminate between diffuse and specular external reflection modes. The promising qualitative results are presented herein, and the implications for quantitative determination of DNA microarrays are discussed.

  7. Diagnostic accuracy of digital images for detection of artificial chemical proximal caries

    Energy Technology Data Exchange (ETDEWEB)

    Park, Geum Mee; Nah, Kyung Soo [Pusan National University College of Medicine, Busan (Korea, Republic of)

    2003-06-15

    To compare the diagnostic accuracy of proximal caries detection between Kodak Insight film and the Biomedisys CDX2000HQ digital (CCD) sensor. 156 proximal surfaces of extracted teeth, 78 of which had chemical artificial caries, were used in this study. Four observers interpreted the radiographs using a five-point confidence rating scale to record their diagnoses. The results were analyzed by receiver operating characteristic curves, ANOVA and Kappa values. Analysis using receiver operating characteristic curves revealed the areas under each curve which indicated a diagnostic accuracy of 0.951 in Insight and 0.952 in CDX2000HQ digital sensor. ANOVA revealed no significant differences between the two images with respect to caries detection. Kappa values indicated that the mean intra-observer agreement was 0.85 and inter-observer agreement 0.71 in conventional radiography. In digital radiography, the mean intra-observer agreement was 0.84 and inter-observer agreement 0.72. The results suggest that no significant difference exists between the two modalities for artificial caries detection and that CDX2000HQ was as good as Insight film for this purpose.

  8. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

    Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

  9. Near-infrared chemical imaging (NIR-CI) on roll compacted ribbons and tablets--multivariate mapping of physical and chemical properties.

    Science.gov (United States)

    Souihi, Nabil; Nilsson, David; Josefson, Mats; Trygg, Johan

    2015-04-10

    Near-infrared chemical imaging (NIR-CI) is an attractive technique within the pharmaceutical industry, where tools are continuously in demand to assess the quality of the intermediate and final products. The present paper demonstrates how NIR-CI in combination with multivariate methods was utilized to spatially map physical properties and content of roll compacted ribbons and tablets. Additionally, extracted textural parameters from tablet images were correlated to the design parameters of the roll compaction process as well as to the physical properties of the granules. The results established the use of NIR-CI as a complementary nondestructive tool to determine the ribbon density and map the density distribution across the width and along the length of the ribbons. For the tablets, the compaction pressure developed during compression increased with the lateral distance from the center. Therefore, NIR-CI can be an effective tool to provide information about the spatial distribution of the compaction pressures on the surface of the tablet. Moreover, low roll compaction roll force correlated to a heterogeneous type of texture in the API chemical image. Overall, texture analysis of the tablets enabled efficient investigation of the spatial variation and could be used to advance process understanding. Finally, orthogonal projections to latent structures (O2PLS) model facilitated the understanding of the interrelationships between textural features, design parameters and physical properties data by separately joint and unique variations.

  10. Micro-Spectroscopic Chemical Imaging of Individual Identified Marine Biogenic and Ambient Organic Ice Nuclei (Invited)

    Science.gov (United States)

    Knopf, D. A.; Alpert, P. A.; Wang, B.; OBrien, R. E.; Moffet, R. C.; Aller, J. Y.; Laskin, A.; Gilles, M.

    2013-12-01

    Atmospheric ice formation represents one of the least understood atmospheric processes with important implications for the hydrological cycle and climate. Current freezing descriptions assume that ice active sites on the particle surface initiate ice nucleation, however, the nature of these sites remains elusive. Here, we present a new experimental method that allows us to relate physical and chemical properties of individual particles with observed water uptake and ice nucleation ability using a combination of micro-spectroscopic and optical single particle analytical techniques. We apply this method to field-collected particles and particles generated via bursting of bubbles produced by glass frit aeration and plunging water impingement jets in a mesocosm containing artificial sea water and bacteria and/or phytoplankton. The most efficient ice nuclei (IN) within a particle population are identified and characterized. Single particle characterization is achieved by computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy. A vapor controlled cooling-stage coupled to an optical microscope is used to determine the onsets of water uptake, immersion freezing, and deposition ice nucleation of the individual particles as a function of temperature (T) as low as 200 K and relative humidity (RH) up to water saturation. In addition, we perform CCSEM/EDX to obtain on a single particle level the elemental composition of the entire particle population. Thus, we can determine if the IN are exceptional in nature or belong to a major particle type class with respect to composition and size. We find that ambient and sea spray particles are coated by organic material and can induce ice formation under tropospheric relevant conditions. Micro-spectroscopic single particle analysis of the investigated particle samples invokes a potential

  11. 4D Non-uniformly sampled HCBCACON and {sup 1}J(NC{sup {alpha}})-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Haba, Noam Y.; Chill, Jordan H. [Bar Ilan University, Department of Chemistry (Israel); Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2012-06-15

    A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit {sup 13}C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H{sup {alpha}}, and H{sup {beta}}) and carbon (C{sup {alpha}}, C{sup {beta}}) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H{sup {alpha}}, C{sup {alpha}}, C{sup {beta}}, C Prime , and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C{sup {alpha}} and C{sup {beta}} chemical shifts, inclusion of the H{sup {alpha}} and H{sup {beta}} provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

  12. Influence of Chemical Effect on the Kβ/Kα Intensity Ratios and Kβ Energy Shift of Co, Ni, Cu, and Zn Complexes

    Institute of Scientific and Technical Information of China (English)

    G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin

    2008-01-01

    Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.

  13. Topographical and Chemical Imaging of a Phase Separated Polymer Using a Combined Atomic Force Microscopy/Infrared Spectroscopy/Mass Spectrometry Platform.

    Science.gov (United States)

    Tai, Tamin; Karácsony, Orsolya; Bocharova, Vera; Van Berkel, Gary J; Kertesz, Vilmos

    2016-03-01

    In this paper, the use of a hybrid atomic force microscopy/infrared spectroscopy/mass spectrometry imaging platform was demonstrated for the acquisition and correlation of nanoscale sample surface topography and chemical images based on infrared spectroscopy and mass spectrometry. The infrared chemical imaging component of the system utilized photothermal expansion of the sample at the tip of the atomic force microscopy probe recorded at infrared wave numbers specific to the different surface constituents. The mass spectrometry-based chemical imaging component of the system utilized nanothermal analysis probes for thermolytic surface sampling followed by atmospheric pressure chemical ionization of the gas phase species produced with subsequent mass analysis. The basic instrumental setup, operation, and image correlation procedures are discussed, and the multimodal imaging capability and utility are demonstrated using a phase separated poly(2-vinylpyridine)/poly(methyl methacrylate) polymer thin film. The topography and both the infrared and mass spectral chemical images showed that the valley regions of the thin film surface were comprised primarily of poly(2-vinylpyridine) and hill or plateau regions were primarily poly(methyl methacrylate). The spatial resolution of the mass spectral chemical images was estimated to be 1.6 μm based on the ability to distinguish surface features in those images that were also observed in the topography and infrared images of the same surface.

  14. X-ray chemical imaging and the electronic structure of a single nanoplatelet Ni/graphene composite.

    Science.gov (United States)

    Zhou, Chunyu; Wang, Jian; Szpunar, Jerzy A

    2014-03-01

    Chemical imaging and quantitative analysis of a single graphene nanoplatelet grown with Ni nanoparticles (Ni/graphene) has been performed by scanning transmission X-ray microscopy (STXM). Local electronic and chemical structure of Ni/graphene has been investigated by spatially resolved C, O K-edges and Ni L-edge X-ray absorption near edge structure (XANES) spectroscopy, revealing the covalent anchoring of Ni(0) on graphene. This study facilitates the understanding of the structure modification of host materials for hydrogen storage and offers a better understanding of interaction between Ni particles and graphene.

  15. Mixing and transport during pharmaceutical twin-screw wet granulation: experimental analysis via chemical imaging.

    Science.gov (United States)

    Kumar, Ashish; Vercruysse, Jurgen; Toiviainen, Maunu; Panouillot, Pierre-Emmanuel; Juuti, Mikko; Vanhoorne, Valérie; Vervaet, Chris; Remon, Jean Paul; Gernaey, Krist V; De Beer, Thomas; Nopens, Ingmar

    2014-07-01

    Twin-screw granulation is a promising continuous alternative for traditional batch high shear wet granulation (HSWG). The extent of HSWG in a twin screw granulator (TSG) is greatly governed by the residence time of the granulation materials in the TSG and degree of mixing. In order to determine the residence time distribution (RTD) and mixing in TSG, mostly visual observation and particle tracking methods are used, which are either inaccurate and difficult for short RTD, or provide an RTD only for a finite number of preferential tracer paths. In this study, near infrared chemical imaging, which is more accurate and provides a complete RTD, was used. The impact of changes in material throughput (10-17 kg/h), screw speed (500-900 rpm), number of kneading discs (2-12) and stagger angle (30-90°) on the RTD and axial mixing of the material was characterised. The experimental RTD curves were used to calculate the mean residence time, mean centred variance and the Péclet number to determine the axial mixing and predominance of convective over dispersive transport. The results showed that screw speed is the most influential parameter in terms of RTD and axial mixing in the TSG and established a significant interaction between screw design parameters (number and stagger angle of kneading discs) and the process parameters (material throughput and number of kneading discs). The results of the study will allow the development and validation of a transport model capable of predicting the RTD and macro-mixing in the TSG. These can later be coupled with a population balance model in order to predict granulation yields in a TSG more accurately.

  16. Universal imaging: Dissociative ionization of polyatomic molecules, chemical dynamics beamline 9.0.2

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, M.; Chen, D.; Suits, A.G. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

    1997-04-01

    A third endstation was recently added to the Chemical Dynamics beamline, designed to exploit the high flux broadband undulator light for a range of studies of reactive scattering, photochemistry and photoionization processes using time-of-flight mass spectroscopy coupled with position-sensitive detection. Two molecular beam sources are fixed at right angles, with the undulator light, or laser beams, intersecting the molecular beams at 45{degrees}. To date, beamline experiments have included a study of dissociative photoionization of a variety of molecules including N{sub 2}O and SF{sub 6}. In this mode, a single molecular beam source is used, with the tunable undulator light inducing, in SF{sub 6} for example, the process SF{sub 6} {r_arrow} SF{sub 6}{sup +} + e{sup {minus}} {r_arrow} SF{sub 5}{sup +} + F + e{sup {minus}}. The SF{sub 5}{sup +} ions are accelerated up the flight tube, mass selected and detected as a function of position on a phosphor screen viewed by a CCD camera. The position directly reveals the recoil speed (or translational energy release) and angular distribution for the dissociative ionization process. Furthermore, this measurement is obtained for all recoil speeds and angles simultaneously. Such detailed angular information has not previously been obtained for dissociative ionization processes; typically ion time-of-flight profiles are deconvoluted to yield rough insight into the angular distributions. The recorded image is actually a 2-dimensional projection of the nascent 3-dimensional velocity distribution, but established tomographic techniques enable the authors to reconstruct the 3-D distribution.

  17. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    Science.gov (United States)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  18. Chemical Imaging and Dynamical Studies of Reactivity and Emergent Behavior in Complex Interfacial Systems. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Sibener, Steven J. [University of Chicago, IL (United States)

    2014-03-11

    This research program explored the efficacy of using molecular-level manipulation, imaging and scanning tunneling spectroscopy in conjunction with supersonic molecular beam gas-surface scattering to significantly enhance our understanding of chemical processes occurring on well-characterized interfaces. One program focus was on the spatially-resolved emergent behavior of complex reaction systems as a function of the local geometry and density of adsorbate-substrate systems under reaction conditions. Another focus was on elucidating the emergent electronic and related reactivity characteristics of intentionally constructed single and multicomponent atom- and nanoparticle-based materials. We also examined emergent chirality and self-organization in adsorbed molecular systems where collective interactions between adsorbates and the supporting interface lead to spatial symmetry breaking. In many of these studies we combined the advantages of scanning tunneling (STM) and atomic force (AFM) imaging, scanning tunneling local electronic spectroscopy (STS), and reactive supersonic molecular beams to elucidate precise details of interfacial reactivity that had not been observed by more traditional surface science methods. Using these methods, it was possible to examine, for example, the differential reactivity of molecules adsorbed at different bonding sites in conjunction with how reactivity is modified by the local configuration of nearby adsorbates. At the core of this effort was the goal of significantly extending our understanding of interfacial atomic-scale interactions to create, with intent, molecular assemblies and materials with advanced chemical and physical properties. This ambitious program addressed several key topics in DOE Grand Challenge Science, including emergent chemical and physical properties in condensed phase systems, novel uses of chemical imaging, and the development of advanced reactivity concepts in combustion and catalysis including carbon

  19. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Barrio, L.; Kubacka, A; Zhou, G; Estrella, M; Martinez-Arias, A; Hanson, J; Fernandez-Garcia, M; Rodriguez, J

    2010-01-01

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni-O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate-carbonate route is operative for the production of hydrogen.

  20. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, J.A.; Barrio, L.; Kubacka, A.; Zhou, G.; Estrella, M.; Mart& #305; nez-Arias, A.; Hanson, J.C.; Fernandez-Garc& #305; a, M.

    2010-07-29

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni?O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate?carbonate route is operative for the production of hydrogen.

  1. Segmentation algorithm of chemical molecular structure images%化学分子结构图分割算法

    Institute of Scientific and Technical Information of China (English)

    管燕; 李存华; 仲兆满; 孙兰兰

    2012-01-01

    为了将化学分子结构图中化学键与杂原子、基团分割开,提出了基于区域尺寸和弯曲度的化学分子结构图分割算法。首先,根据连通区域尺寸大小,将化学分子结构图分割成两部分:一部分是由化学键组成的所有大尺寸连通区域的组合,另一部分是杂原子、基团和单化学键等小尺寸区域的组合。然后,根据弯曲度将小尺寸组合图中的表示化学键的单线段和类线段“I”、“1”、“-”提取出。最后根据位置等信息将“I”、“1”、“-”和单线段进行区分,将单线段的化学键和大尺寸连通区组合,实现了化学键与杂原子、基团的分离。实验结果表明,该图像分割算法准确率高达98.3%,与人类视觉感知具有一致性。这为后续的化学分子结构图像信息的自动提取奠定了基础。%The segmentation algorithm of chemical molecular structure based on area size and bending degree was proposed to segment chemical bonds, heteroatoms and perssad. First, chemical molecular structure images were segmented into two parts according to connection area size. One was the combination of all big size connection areas containing chemical bonds, and the other was the combination of heteroatoms, perssad and single chemical bonds. Second, single lines were extracted based on bending degree, which represents small size combination images, and like-lines such as "I" ,"l" and " - ". Finally, "I" ,"l", " - " and single lines were distinguished, chemical bonds of single lines and big size connection areas were combined, and the segmentation of chemical bonds, heteroatoms and perssad was realized. The accuracy by the proposed algorithm reached to 98. 3%, and the segmentation effect was consistent with human visual perception. This is the foundation for automatically extracting chemical molecular structure images.

  2. Doppler imaging of chemical spots on magnetic Ap/Bp stars. Numerical tests and assessment of systematic errors

    CERN Document Server

    Kochukhov, O

    2016-01-01

    Doppler imaging (DI) is a powerful spectroscopic inversion technique that enables conversion of a line profile time series into a two-dimensional map of the stellar surface inhomogeneities. In this paper we investigate the accuracy of chemical abundance DI of Ap/Bp stars and assess the impact of several different systematic errors on the reconstructed spot maps. We simulate spectroscopic observational data for different spot distributions in the presence of a moderately strong dipolar magnetic field. We then reconstruct chemical maps using different sets of spectral lines and making different assumptions about line formation in the inversion calculations. Our numerical experiments demonstrate that a modern DI code successfully recovers the input chemical spot distributions comprised of multiple circular spots at different latitudes or an element overabundance belt at the magnetic equator. For the optimal reconstruction the average reconstruction errors do not exceed ~0.10 dex. The errors increase to about 0.1...

  3. Stealth technology of optical-electro imaging devices based on focal shift%基于离焦方式的光电成像设备激光隐身技术

    Institute of Scientific and Technical Information of China (English)

    张玉发; 孙晓泉; 雷鹏; 余大斌

    2015-01-01

    Electro-optical devices can easily be captured by active laser detection weapons according to the Cat-eye effect of optical windows. The focal shift method was proposed to decrease retroreflected wave power for Cat-eye target stealth when the image quality of these devices was under controlled. The principle of focal shift was analyzed and experimental validation was carried out respectively. Furthermore, digital image of focal shift device was evaluated based on gray gradient function, and the blurred images were restored. The results show that the divergent angle of reflected wave is enlarged and retroreflected wave power decreased when the focal shift distance increases. Meanwhile, high-frequency information of images captured by focal shift electro-optical devices decrease accordingly. However, the deteriorative range of image quality is acceptable. After restoration, the visual effects of the images are improved efficiently.%光电成像装备的猫眼效应使其易遭受激光主动侦察装备的探测,在光电装备成像质量变化允许的范围内,采用离焦的方式来减小猫眼目标的回波功率,可实现相应的隐身。在研究离焦对光电成像设备激光回波强度影响的基础上,利用实验的方法对猫眼目标隐身后的成像质量进行验证和评价,并对离焦后的图像进行清晰度增强。结果表明,通过离焦的方式可有效增大猫眼目标回波发散角,降低回波功率,并且离焦量越大,猫眼效应越弱。对离焦光电设备所采集的图像进行分析后发现,离焦量越大,图像高频分量越少,但是适当的离焦量所造成的成像质量下降在可接受范围内,并且通过采取相应的修复措施,光电成像设备的图像质量得到有效改善。

  4. Programmable Adaptive Spectral Imagers for Mission-Specific Application in Chemical/Biological Sensing

    Science.gov (United States)

    2006-01-01

    detection of chemical/biological agents. Extensive research into both passive remote chemical/biological sensors and active laser- based ( LIDAR ... photodetector (Fig. 1). Fig. 1. Adaptive spectrograph concept: light from a standoff spectral scene is dispersed, dynamically encoded with...the purpose. Data acquisition and processing software was developed for the control of the DMA, capturing data from the photodetectors , and for

  5. Iboga alkaloids from Peschiera affinis (Apocynaceae) - unequivocal {sup 1}H and {sup 13}C chemical shift assignments: antioxidant activity; Alcaloides iboga de Peschiera affinis (Apocynaceae) - atribuicao inequivoca dos deslocamentos quimicos dos atomos de hidrogenio e carbono: atividade antioxidante

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br

    2009-07-01

    Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)

  6. Time and Frequency Resolved Nanoscale Chemical Imaging of Dimercaptostilbene on Silver

    CERN Document Server

    El-Khoury, Patrick Z; Hess, Wayne P

    2014-01-01

    Non-resonant tip-enhanced Raman images of dimercaptostilbene on silver reveal that different vibrational resonances of the reporter are selectively enhanced at different sites on the metal substrate. Sequentially recorded images track molecular diffusion within the diffraction-limited laser spot which illuminates the substrate. In effect, the recorded time resolved (dt = 10 s) pixelated images (25 nm x 8 cm-1) broadcast molecule-local field interactions which take place on much finer scales.

  7. Hard X-ray photoelectron spectra (HXPES) of bulk non-conductor vitreous SiO{sub 2}: Minimum linewidths and surface chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Y.F., E-mail: Yongfeng.hu@lightsource.ca [Canadian Light Source, Saskatoon, SK (Canada); Xiao, Q.; Wang, D.; Cui, X. [Canadian Light Source, Saskatoon, SK (Canada); Nesbitt, H.W. [Department of Earth Sciences, University of Western Ontario, London, ONT (Canada); Bancroft, G.M. [Department of Chemistry, University of Western Ontario, London, ONT (Canada)

    2015-07-15

    Highlights: • Electronic structure of non-conducting glass studied by hard X-ray photoelectron spectroscopy. • A thin film of Cr was deposited on the vitreous SiO{sub 2} glass to overcome the sample charging. • Excellent O 1s and Si 1s linewidths were obtained, matching those reported using the laboratory based Kratos Axis Ultra spectrometer equipped with a magnetic compensation system. • The bulk and interface states of non-conducting samples are studied as a function of photon energy. - Abstract: Hard X-ray photoelectron spectra (2200 eV to 5000 eV photon energies) have been obtained for the first time on a bulk non-conductor, vitreous SiO{sub 2}, on a high resolution (E/ΔE of 10,000) synchrotron beamline at the Canadian Light Source (CLS). To minimize charging and differential charging, the SiO{sub 2} was coated with very thin layers (0.5 to 1.5 nm) of Cr metal. The O 1s linewidth obtained at 2500 eV photon energy was 1.26 eV—the minimum linewidth for SiO{sub 2}—and in good agreement with that obtained at 1486 eV on a Kratos Axis Ultra spectrometer equipped with a magnetic charge compensation system. The Si 1s linewidth of 1.5 eV, somewhat broader than that previously obtained at 1486 eV on the Si 2p{sub 3/2} line of 1.16 eV, is mainly due to the much larger inherent Si 1s linewidth (0.5 eV) compared to the inherent Si 2p linewidth (<0.1 eV). Both linewidths are dominated by the large final state vibrational broadening previously described. The Cr coating produces surface monolayers of interfacial Cr “suboxide” (Cr-subox), Cr metal, and a surface Cr oxide (Cr-surfox). Cr-subox (Si−O−Cr) gives rise to the weak near-surface Si 1s peak, while both oxides give rise to both the weak surface O 1s peak and the Cr 2p oxide peak. Both the O 1s and Si 1s surface peaks are shifted by ∼2 eV relative to the large bulk Si 1s and O 1s peaks. The weak Si 1s and O 1s surface peaks along with the Cr 2p oxide peak decrease in intensity greatly as the photon

  8. Chemical exchange saturation transfer MR imaging of articular cartilage glycosaminoglycans at 3 T: Accuracy of B0 Field Inhomogeneity corrections with gradient echo method.

    Science.gov (United States)

    Wei, Wenbo; Jia, Guang; Flanigan, David; Zhou, Jinyuan; Knopp, Michael V

    2014-01-01

    Glycosaminoglycan Chemical Exchange Saturation Transfer (gagCEST) is an important molecular MRI methodology developed to assess changes in cartilage GAG concentrations. The correction for B0 field inhomogeneity is technically crucial in gagCEST imaging. This study evaluates the accuracy of the B0 estimation determined by the dual gradient echo method and the effect on gagCEST measurements. The results were compared with those from the commonly used z-spectrum method. Eleven knee patients and three healthy volunteers were scanned. Dual gradient echo B0 maps with different ∆TE values (1, 2, 4, 8, and 10 ms) were acquired. The asymmetry of the magnetization transfer ratio at 1 ppm offset referred to the bulk water frequency, MTRasym(1 ppm), was used to quantify cartilage GAG levels. The B0 shifts for all knee patients using the z-spectrum and dual gradient echo methods are strongly correlated for all ∆TE values used (r = 0.997 to 0.786, corresponding to ∆TE = 10 to 1 ms). The corrected MTRasym(1 ppm) values using the z-spectrum method (1.34% ± 0.74%) highly agree only with those using the dual gradient echo methods with ∆TE = 10 ms (1.72% ± 0.80%; r = 0.924) and 8 ms (1.50% ± 0.82%; r = 0.712). The dual gradient echo method with longer ∆TE values (more than 8 ms) has an excellent correlation with the z-spectrum method for gagCEST imaging at 3T.

  9. Chemical Exchange Saturation Transfer MR Imaging Is Superior to Diffusion Tensor Imaging in the Diagnosis and Severity Evaluation of Parkinson's Disease: a Study on Substantia Nigra and Striatum

    Directory of Open Access Journals (Sweden)

    Chunmei eLi

    2015-10-01

    Full Text Available Parkinson’s disease (PD is a neurodegenerative disorder characterized by nigrostriatal cell loss. To date the diagnosis of PD is still based primarily on the clinical manifestations which may be typical and obvious only in advanced-stage PD. Thus, it is crucial to find a reliable marker for the diagnosis of PD. We conducted this study to assess the diagnostic efficiency of chemical-exchange-saturation-transfer (CEST imaging and diffusion-tensor imaging (DTI in PD at 3 Tesla by evaluating changes on substantia nigra and striatum. Twenty-three PD patients and twenty-three age-matched normal controls were recruited. All patients and controls were imaged on a 3 Tesla MR system, using an 8-channel head coil. CEST imaging was acquired in two transverse slices of the head, including substantia nigra and striatum. The magnetization-transfer-ratio asymmetry at 3.5 ppm, MTRasym(3.5ppm, and the total CEST signal intensity between 0 and 4 ppm were calculated. Multi-slice DTI was acquired for all the patients and normal controls. Quantitative analysis was performed on the substantia nigra, globus pallidus, putamen and caudate. The MTRasym(3.5ppm value, the total CEST signal intensity and fractional anisotropy (FA value of the substantia nigra were all significantly lower in PD patients than in normal controls (P = 0.003, P = 0.004 and P < 0.001, respectively. The MTRasym(3.5ppm values of the putamen and the caudate were significantly higher in PD patients than in normal controls (P = 0.010 and P = 0.009, respectively. There were no significant differences for the mean diffusivity (MD in these four regions between PD patients and normal controls. In conclusion, CEST MR imaging provided multiple CEST image contrasts in the substantia nigra and the striatum in PD and may be superior to DTI in the diagnosis of PD.

  10. In vivo imaging of C. elegans ASH neurons: cellular response and adaptation to chemical repellents

    OpenAIRE

    Hilliard, Massimo A.; Apicella, Alfonso J.; Kerr, Rex; Suzuki, Hiroshi; Bazzicalupo, Paolo; Schafer, William R

    2004-01-01

    ASH sensory neurons are required in Caenorhabditis elegans for a wide range of avoidance behaviors in response to chemical repellents, high osmotic solutions and nose touch. The ASH neurons are therefore hypothesized to be polymodal nociceptive neurons. To understand the nature of polymodal sensory response and adaptation at the cellular level, we expressed the calcium indicator protein cameleon in ASH and analyzed intracellular Ca2+ responses following stimulation with chemical repellents, o...

  11. 傅里叶望远镜中激光频移误差对成像质量影响的分析%Effect Analysis of Laser Frequency-Shift Error on Imaging Quality in Fourier Telescope

    Institute of Scientific and Technical Information of China (English)

    孔新新; 黄旻; 张文喜

    2012-01-01

    傅里叶望远镜成像技术,综合了激光主动成像技术、光学合成孔径技术和相位闭合技术是一种新的高分辨率成像探测技术.激光频移的效果是影响傅里叶望远镜成像质量的重要因素,特别是使用大功率、宽光束和宽调制带宽激光的系统.构建了不同的误差模型,推导了频移误差在系统中的传递函数,利用仿真实验分析其对系统成像的影响,得到了对应的误差影响分析.结果表明,频移精度和稳定度严重影响到系统的成像效果,部分情况下含有误差的反演图像与理论反演图像的施特雷尔值已降到0.2,因此合理的设计和选择声光频移器是改善系统成像的一个关键因素.%Fourier telescopy (FT) is a sort of high-resolution imaging technology, which integrates laser initiative imaging technology, optical synthetic aperture technology and phase close technology. The effect of frequency shifting of laser is one of the most important factors to influence imaging quality of the FT system, especially in the situation of high power, broad beam and large modulation bandwidth. Various frequency-shifting error models are proposed, the transfer function of error in system is built, the effect of which on imaging of the system is researched by simulation, error analysis results of the various models are obtained. According to the results, the image quality of the system is directly influenced by the frequency shift accuracy and stability, the value of Strehl between the inverted image with error and the theoretically inverted image is below 0. 2 in some of the models. As indicated, the reasonable design of acousto-optical frequency shifter and the driver circuit is an important way to improve the imaging of the system.

  12. Infrared hyperspectral tunable filter imaging spectrometer for remote leak detection, chemical speciation, and stack/vent analysis applications

    Science.gov (United States)

    Hinnrichs, Michele

    2002-02-01

    With support from the Department of Energy, the State of California and the Gas Technology Institute, Pacific Advanced Technology is developing a small field portable infrared imaging spectrometer (Sherlock) based on the advances in hyperspectral tunable filter technology, that will be applied to the detection of fugitive gas leaks. This imaging spectrometer uses the Image Multi-spectral Sensing (IMSS) diffractive optic tunable filter invented by Pacific Advanced Technology . The Sherlock has an embedded digital signal processor for real time detection of the gas leak while surrounded by severe background noise. The infrared sensor engine is a 256 x 320 midwave cooled focal plane array which spans the spectral range from 3 to 5 microns, ideal for most hydrocarbon leaks. The technology is by no means limited to this spectral region, and can just as easily work in the longwave infrared from 8 to 12 microns for chemical detection applications. This paper will present the design of the Sherlock camera as well as processed data collected at a gas processing plant and an instrumented kiln at LSU using the prototype camera. The processed data shows that the IMSS imaging spectrometer, using an all passive approach, has the sensitivity to detect methane gas leaks at short range with a flow rate as low as 0.01 scfm2. In addition, the IMSS imaging spectrometer can measure hot gas plumes at longer ranges. As will be shown in this paper the IMSS can detect and image warm species gas additives of methane and propane in the Kiln exhaust stack. The methane injected gas with a concentration of 72 ppm and the propane with a concentration of 49 ppm (as seen by the IMSS sensor) at a range of 60 meters. The atmospheric path was a stressing environment, being hot and humid, for any imaging infrared spectrometer.

  13. Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

    Science.gov (United States)

    Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

    2012-12-01

    Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

  14. Chemical imaging analysis of the brain with X-ray methods

    Science.gov (United States)

    Collingwood, Joanna F.; Adams, Freddy

    2017-04-01

    Cells employ various metal and metalloid ions to augment the structure and the function of proteins and to assist with vital biological processes. In the brain they mediate biochemical processes, and disrupted metabolism of metals may be a contributing factor in neurodegenerative disorders. In this tutorial review we will discuss the particular role of X-ray methods for elemental imaging analysis of accumulated metal species and metal-containing compounds in biological materials, in the context of post-mortem brain tissue. X-rays have the advantage that they have a short wavelength and can penetrate through a thick biological sample. Many of the X-ray microscopy techniques that provide the greatest sensitivity and specificity for trace metal concentrations in biological materials are emerging at synchrotron X-ray facilities. Here, the extremely high flux available across a wide range of soft and hard X-rays, combined with state-of-the-art focusing techniques and ultra-sensitive detectors, makes it viable to undertake direct imaging of a number of elements in brain tissue. The different methods for synchrotron imaging of metals in brain tissues at regional, cellular, and sub-cellular spatial resolution are discussed. Methods covered include X-ray fluorescence for elemental imaging, X-ray absorption spectrometry for speciation imaging, X-ray diffraction for structural imaging, phase contrast for enhanced contrast imaging and scanning transmission X-ray microscopy for spectromicroscopy. Two- and three-dimensional (confocal and tomographic) imaging methods are considered as well as the correlation of X-ray microscopy with other imaging tools.

  15. Spectral imaging of chemical compounds using multivariate optically enhanced filters integrated with InGaAs VGA cameras

    Science.gov (United States)

    Priore, Ryan J.; Jacksen, Niels

    2016-05-01

    Infrared hyperspectral imagers (HSI) have been fielded for the detection of hazardous chemical and biological compounds, tag detection (friend versus foe detection) and other defense critical sensing missions over the last two decades. Low Size/Weight/Power/Cost (SWaPc) methods of identification of chemical compounds spectroscopy has been a long term goal for hand held applications. We describe a new HSI concept for low cost / high performance InGaAs SWIR camera chemical identification for military, security, industrial and commercial end user applications. Multivariate Optical Elements (MOEs) are thin-film devices that encode a broadband, spectroscopic pattern allowing a simple broadband detector to generate a highly sensitive and specific detection for a target analyte. MOEs can be matched 1:1 to a discrete analyte or class prediction. Additionally, MOE filter sets are capable of sensing an orthogonal projection of the original sparse spectroscopic space enabling a small set of MOEs to discriminate a multitude of target analytes. This paper identifies algorithms and broadband optical filter designs that have been demonstrated to identify chemical compounds using high performance InGaAs VGA detectors. It shows how some of the initial models have been reduced to simple spectral designs and tested to produce positive identification of such chemicals. We also are developing pixilated MOE compressed detection sensors for the detection of a multitude of chemical targets in challenging backgrounds/environments for both commercial and defense/security applications. This MOE based, real-time HSI sensor will exhibit superior sensitivity and specificity as compared to currently fielded HSI systems.

  16. 融合均值漂移和加权谱聚类的彩色图像分割%Color image segmentation combining mean shift and weighted spectral clustering

    Institute of Scientific and Technical Information of China (English)

    桂阳; 苑云; 杜晶

    2012-01-01

    This paper proposed a novel algorithm for improving efficiency of color image segmentation. Firstly, it filtered noise and transformed input image from pixel-based to region-based model by using mean shift algorithm, and composed the input image after mean shift procedure by some disjoint regions. Then it treated the regions as nodes in image plane and applied a graph structure to represent them. Finally it applied the weighted spectral clustering algorithm which merged the information of area differences and spatial distances among the regions to perform final clustering, and abtained the result of image segmentation. Experimental results show that the proposed algorithm is effective on color image segmentation, and it also has the prop-erties of low computation cost, keeping boundary well and reducing noise interference.%为了提高彩色图像分割的效率,提出了一种彩色图像分割新方法.该方法首先利用均值漂移算法滤除噪声干扰并对图像进行初始分割,初始分割后的图像由一些互不相交的区域组成;然后将这些区域视为图的节点建立区域连接图;最后采用融入了区域之间面积差异信息与空间距离信息的加权谱聚类算法进行聚类,获得最终分割结果.实验结果表明,该方法可较好地对彩色图像进行分割,并能有效地降低噪声的影响,保持图像边缘,且运算速度较快.

  17. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    Science.gov (United States)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-01-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed. PMID:28194036

  18. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    Science.gov (United States)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-02-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

  19. Extraction of structural and chemical information from high angle annular dark-field image by an improved peaks finding method.

    Science.gov (United States)

    Yin, Wenhao; Huang, Rong; Qi, Ruijuan; Duan, Chungang

    2016-09-01

    With the development of spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM), high angle annular dark filed (HAADF) imaging technique has been widely applied in the microstructure characterization of various advanced materials with atomic resolution. However, current qualitative interpretation of the HAADF image is not enough to extract all the useful information. Here a modified peaks finding method was proposed to quantify the HAADF-STEM image to extract structural and chemical information. Firstly, an automatic segmentation technique including numerical filters and watershed algorithm was used to define the sub-areas for each atomic column. Then a 2D Gaussian fitting was carried out to determine the atomic column positions precisely, which provides the geometric information at the unit-cell scale. Furthermore, a self-adaptive integration based on the column position and the covariance of statistical Gaussian distribution were performed. The integrated intensities show very high sensitivity on the mean atomic number with improved signal-to-noise (S/N) ratio. Consequently, the polarization map and strain distributions were rebuilt from a HAADF-STEM image of the rhombohedral and tetragonal BiFeO3 interface and a MnO2 monolayer in LaAlO3 /SrMnO3 /SrTiO3 heterostructure was discerned from its neighbor TiO2 layers. Microsc. Res. Tech. 79:820-826, 2016. © 2016 Wiley Periodicals, Inc.

  20. Real time chemical imaging of a working catalytic membrane reactor during oxidative coupling of methane.

    Science.gov (United States)

    Vamvakeros, A; Jacques, S D M; Middelkoop, V; Di Michiel, M; Egan, C K; Ismagilov, I Z; Vaughan, G B M; Gallucci, F; van Sint Annaland, M; Shearing, P R; Cernik, R J; Beale, A M

    2015-08-18

    We report the results from an operando XRD-CT study of a working catalytic membrane reactor for the oxidative coupling of methane. These results reveal the importance of the evolving solid state chemistry during catalytic reaction, particularly the chemical interaction between the catalyst and the oxygen transport membrane.

  1. On the calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2007-01-01

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc

  2. SIMS ion microscopy as a novel, practical tool for subcellular chemical imaging in cancer research

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, S

    2003-01-15

    The development of cryogenic sample preparations, subcellular image quantification schemes, and correlative confocal laser scanning microscopy and ion microscopy have made dynamic SIMS a versatile tool in biology and medicine. For example, ion microscopy can provide much needed, novel information on calcium influx and intracellular calcium stores at organelle resolution in normal and transformed cells in order to better understand the altered calcium signaling in malignant cells. 3-D SIMS imaging of cells revealed dynamic gradients of calcium in cells undergoing mitosis and cytokinesis. Studies of subcellular localization of anticancer drugs is another area of research where ion microscopy can provide novel observations in many types of cancers. Ion microscopy is already an essential tool in boron neutron capture therapy (BNCT) of brain cancer as it can be used to quantitatively image the subcellular location of boron in cells and tissues. This information is critically needed for testing the efficacy of boronated agents and for calculations of radiation dosimetry.

  3. [Paradigm shifts in aortic pathology: clinical and therapeutic implications. Clinical imaging in chronic and acute aortic syndromes. The aorta as a cause of cardiac disease].

    Science.gov (United States)

    Nistri, Stefano; Roghi, Alberto; Mele, Donato; Biagini, Elena; Chiodi, Elisabetta; Colombo, Ettore; d'Amati, Giulia; Leone, Ornella; Angelini, Annalisa; Basso, Cristina; Pepe, Guglielmina; Rapezzi, Claudio; Thiene, Gaetano

    2014-06-01

    Multimodal imaging plays a pivotal role in the assessment of the thoracic aorta, both in chronic and acute settings. Moving from improved knowledge on the structure and function of the aortic wall, as well as on its pathophysiology and histopathology, appropriate utilization of each imaging modality results into a better definition of the patient's need and proper treatment strategy. This review is aimed at highlighting the most critical aspects in this field, providing cardiologists with some novel clues for the imaging approach to patients with thoracic aortic disease.

  4. Super-resolution and super-localization microscopy: A novel tool for imaging chemical and biological processes

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Bin [Iowa State Univ., Ames, IA (United States)

    2015-01-01

    Optical microscopy imaging of single molecules and single particles is an essential method for studying fundamental biological and chemical processes at the molecular and nanometer scale. The best spatial resolution (~ λ/2) achievable in traditional optical microscopy is governed by the diffraction of light. However, single molecule-based super-localization and super-resolution microscopy imaging techniques have emerged in the past decade. Individual molecules can be localized with nanometer scale accuracy and precision for studying of biological and chemical processes.This work uncovered the heterogeneous properties of the pore structures. In this dissertation, the coupling of molecular transport and catalytic reaction at the single molecule and single particle level in multilayer mesoporous nanocatalysts was elucidated. Most previous studies dealt with these two important phenomena separately. A fluorogenic oxidation reaction of non-fluorescent amplex red to highly fluorescent resorufin was tested. The diffusion behavior of single resorufin molecules in aligned nanopores was studied using total internal reflection fluorescence microscopy (TIRFM).

  5. Xinjiang Guanghui Shifts to Coal Chemical Business

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Xinjiang Guanghui Industry Co., Ltd.(Xinjiang Guanghui, SH: 600256) was established on April 10th, 1999. It is located in Urumqi Economic and Technological Development Zone,Xinjiang of western China. The company got listed in Shanghai Stock Exchange on May 26th, 2000.

  6. Coordinated Chemical and Isotopic Imaging of Bells (CM2) Meteorite Matrix

    Science.gov (United States)

    Clemett, S. J.; Messenger, S.; Naklamura-Messenger, K.; Thomas-Keprta, K. L.

    2014-01-01

    Meteoritic organic matter is a complex conglomeration of species formed in distinct environments and processes in circumstellar space, the interstellar medium, the Solar Nebula and asteroids. Consequently meteorites constitute a unique record of primordial organic chemical evolution. While bulk chemical analysis has provided a detailed description of the range and diversity of organic species present in carbonaceous chondrites, there is little information as to how these species are spatially distributed and their relationship to the host mineral matrix. The distribution of organic phases is nevertheless critical to understanding parent body processes. The CM and CI chondrites all display evidence of low temperature (meteorite using a newly developed two-step laser mass spectrometer (mu-L(sup 2)MS) capable of measuring a broad range of organic compounds.

  7. Conversion electron surface imaging

    CERN Document Server

    Irwin, G M; Wehner, A

    1999-01-01

    A method of imaging the Moessbauer absorption over the surface of a sample based on counting conversion electrons emitted from the surface following resonant absorption of gamma radiation is described. This Conversion Electron Surface Imaging (CESI) method is somewhat analogous to Magnetic Resonance Imaging (MRI), particularly chemical shift imaging, and similar tomographic reconstruction techniques are involved in extracting the image. The theory behind the technique and a prototype device is described, as well as the results of proof-of-principle experiments which demonstrate the function of the device. Eventually this same prototype device will be part of a system to determine the spatial variation of the Moessbauer spectrum over the surface of a sample. Applications include imaging of variations of surface properties of steels and other iron containing alloys, as well as other surfaces over which sup 5 sup 7 Fe has been deposited.

  8. Assessment of active pharmaceutical ingredient particle size in tablets by Raman chemical imaging validated using polystyrene microsphere size standards.

    Science.gov (United States)

    Kuriyama, Atsushi; Ozaki, Yukihiro

    2014-04-01

    Particle size is a critical parameter for controlling pharmaceutical quality. The aim of this study was to assess the size of the micrometer-scale active pharmaceutical ingredients (API) in tablets using Raman chemical imaging and to understand the effects of formulation on particle size. Model tablets containing National Institute of Standards and Technology traceable polystyrene microsphere size standards were developed to determine the binarization threshold value of Raman chemical images for API particle sizing in specific formulations and processes. Three sets of model tablets containing 5, 10, and 15 μm polystyrene microspheres, used to mimic API, were prepared using a commercial tablet formulation (Ebastel tablets, mean API particle size was about 5 μm). Raman mapping with a 50× objective (NA, 0.75) was applied to tablet cross-sections, and particle size of polystyrene microspheres was estimated from binary images using several binarization thresholds. Mean particle size for three sets of polystyrene microspheres showed good agreement between pre- and postformulation (the slope = 1.024, R = 1.000) at the specific threshold value ((mean + 0.5σ) of the polystyrene-specific peak intensity histogram), regardless of particle agglomeration, tablet surface roughness, and laser penetration depth. The binarization threshold value showed good applicability to Ebastel tablets, where the API-specific peak intensity histogram showed a pattern similar to that of polystyrene microspheres in model tablets. The model tablets enabled determination of an appropriate binarization threshold for assessing the mean particle size of micrometer-scale API in tablets by utilizing the unique physicochemical properties of polystyrene microspheres.

  9. Recycling-oriented characterization of plastic frames and printed circuit boards from mobile phones by electronic and chemical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Palmieri, Roberta; Bonifazi, Giuseppe; Serranti, Silvia, E-mail: silvia.serranti@uniroma1.it

    2014-11-15

    Highlights: • A recycling oriented characterization of end-of-life mobile phones was carried out. • Characterization was developed in a zero-waste-perspective, aiming to recover all the mobile phone materials. • Plastic frames and printed circuit boards were analyzed by electronic and chemical imaging. • Suitable milling/classification strategies were set up to define specialized-pre-concentrated-streams. • The proposed approach can improve the recovery of polymers, base/precious metals, rare earths and critical raw materials. - Abstract: This study characterizes the composition of plastic frames and printed circuit boards from end-of-life mobile phones. This knowledge may help define an optimal processing strategy for using these items as potential raw materials. Correct handling of such a waste is essential for its further “sustainable” recovery, especially to maximize the extraction of base, rare and precious metals, minimizing the environmental impact of the entire process chain. A combination of electronic and chemical imaging techniques was thus examined, applied and critically evaluated in order to optimize the processing, through the identification and the topological assessment of the materials of interest and their quantitative distribution. To reach this goal, end-of-life mobile phone derived wastes have been systematically characterized adopting both “traditional” (e.g. scanning electronic microscopy combined with microanalysis and Raman spectroscopy) and innovative (e.g. hyperspectral imaging in short wave infrared field) techniques, with reference to frames and printed circuit boards. Results showed as the combination of both the approaches (i.e. traditional and classical) could dramatically improve recycling strategies set up, as well as final products recovery.

  10. Non-invasive evaluation of culprit lesions by PET imaging: shifting the clinical paradigm away from resultant anatomy toward causative physiology.

    Science.gov (United States)

    Caobelli, Federico; Bengel, Frank M

    2014-12-01

    Although coronary angiography is the gold standard for assessing coronary artery disease (CAD), there is at best a weak correlation between degree of stenosis and the risk of developing cardiac events. Plaque rupture is the most common type of plaque complication, accounting for about 70% of fatal acute myocardial infarctions or sudden coronary deaths. Recently, the feasibility of (18)F-fluoride PET/CT in the evaluation of atherosclerotic lesions was assessed. Radionuclide techniques allow non-invasive biologic assessment of atherosclerotic plaques. This may help to further shift the clinical paradigm in coronary disease away from anatomy toward causative physiology and biology.

  11. Structurally Rigid 9-Amino-benzo[c]cinnoliniums Make Up a Class of Compact and Large Stokes-Shift Fluorescent Dyes for Cell-Based Imaging Applications.

    Science.gov (United States)

    Shen, Yanming; Shang, Zhihao; Yang, Yanhong; Zhu, Shaojia; Qian, Xuhong; Shi, Ping; Zheng, Jing; Yang, Youjun

    2015-06-05

    Classic fluorescent dyes, such as coumarin, naphthalimide, fluorescein, BODIPY, rhodamine, and cyanines, are cornerstones of various spectroscopic and microscopic methods, which hold a prominent position in biological studies. We recently found that 9-amino-benzo[c]cinnoliniums make up a novel group of fluorophores that can be used in biological studies. They are featured with a succinct conjugative push-pull backbone, a broad absorption band, and a large Stokes shift. They are potentially useful as a small-molecule alternative to R-phycoerythrin to pair with fluorescein in multiplexing applications.

  12. Magnitude of shift of tumor position as a function of moderated deep inspiration breath-hold: An analysis of pooled data of lung patients with active breath control in image-guided radiotherapy

    Directory of Open Access Journals (Sweden)

    Muralidhar K

    2008-01-01

    Full Text Available The purpose of this study was to evaluate the reproducibility and magnitude of shift of tumor position by using active breathing control and iView-GT for patients with lung cancer with moderate deep-inspiration breath-hold (mDIBH technique. Eight patients with 10 lung tumors were studied. CT scans were performed in the breath-holding phase. Moderate deep-inspiration breath-hold under spirometer-based monitoring system was used. Few important bony anatomic details were delineated by the radiation oncologist. To evaluate the interbreath-hold reproducibility of the tumor position, we compared the digital reconstruction radiographs (DRRs from planning system with the DRRs from the iView-GT in the machine room. We measured the shift in x, y, and z directions. The reproducibility was defined as the difference between the bony landmarks from the DRR of the planning system and those from the DRR of the iView-GT. The maximum shift of the tumor position was 3.2 mm, 3.0 mm, and 2.9 mm in the longitudinal, lateral, and vertical directions. In conclusion, the moderated deep-inspiration breath-hold method using a spirometer is feasible, with relatively good reproducibility of the tumor position for image-guided radiotherapy in lung cancers.

  13. Chemically Modified Bacteriophage as a Streamlined Approach to Noninvasive Breast Cancer Imaging

    Science.gov (United States)

    2013-12-01

    filamentous phage were used for western blotting experiments. Because M13KE lacks antibiotic resistance, it was grown from plaques rather than colonies. It...surface marker-specific phage identified from library screens into imaging agents that can target and differentiate breast cancer cell types. This is...accomplished by using efficient synthetic protocols to conjugate small molecules to phage coat proteins. In the current work, I have examined the use of

  14. Extracting knowledge from chemical imaging data using computational algorithms for digital cancer diagnosis.

    Science.gov (United States)

    Tiwari, Saumya; Bhargava, Rohit

    2015-06-01

    Fourier transform infrared (FTIR) spectroscopic imaging is an emerging microscopy modality for clinical histopathologic diagnoses as well as for biomedical research. Spectral data recorded in this modality are indicative of the underlying, spatially resolved biochemical composition but need computerized algorithms to digitally recognize and transform this information to a diagnostic tool to identify cancer or other physiologic conditions. Statistical pattern recognition forms the backbone of these recognition protocols and can be used for highly accurate results. Aided by biochemical correlations with normal and diseased states and the power of modern computer-aided pattern recognition, this approach is capable of combating many standing questions of traditional histology-based diagnosis models. For example, a simple diagnostic test can be developed to determine cell types in tissue. As a more advanced application, IR spectral data can be integrated with patient information to predict risk of cancer, providing a potential road to precision medicine and personalized care in cancer treatment. The IR imaging approach can be implemented to complement conventional diagnoses, as the samples remain unperturbed and are not destroyed. Despite high potential and utility of this approach, clinical implementation has not yet been achieved due to practical hurdles like speed of data acquisition and lack of optimized computational procedures for extracting clinically actionable information rapidly. The latter problem has been addressed by developing highly efficient ways to process IR imaging data but remains one that has considerable scope for progress. Here, we summarize the major issues and provide practical considerations in implementing a modified Bayesian classification protocol for digital molecular pathology. We hope to familiarize readers with analysis methods in IR imaging data and enable researchers to develop methods that can lead to the use of this promising

  15. "Mirror-image" manipulation of curdione stereoisomer scaffolds by chemical and biological approaches: development of a sesquiterpenoid library.

    Science.gov (United States)

    Qin, Bin; Li, Yuxin; Meng, Lingxin; Ouyang, Jingping; Jin, Danni; Wu, Lei; Zhang, Xin; Jia, Xian; You, Song

    2015-02-27

    The sesquiterpenoid curdione is one of the main bioactive components in the essential oil of Rhizoma Curcumae (Curcuma wenyujin, Curcuma phaeocaulis, and Curcuma kwangsiensis), which has been clinically used for the treatment of cancer in mainland China. Recently it was reported that natural curdione could be hydroxylated by Aspergillus niger and transferred to its corresponding curcumalactones under acidic conditions. Based on this study, the development of a sesquiterpenoid library through the "mirror-image" manipulation of bioactive (non)natural curdione scaffolds by chemical and biological approaches is presented herein. A. niger induced the hydroxylation of two pairs of curdione enantiomers, yielding the corresponding mirror-image hydroxylated curdiones. Simultaneously, the acid-mediated intramolecular "ene" rearrangements of these curdiones and hydroxylated curdione enantiomers yielded the corresponding mirror-image curcumalactones and hydroxylated curcumalactones. Among the 16 pairs of enantiomers obtained in this study, 23 compounds are new sesquiterpenoids. These curdione and curcumalactone derivatives are of particular interest, as they have the potential to be used as lead compounds and scaffolds in drug discovery.

  16. Images

    Data.gov (United States)

    National Aeronautics and Space Administration — Images for the website main pages and all configurations. The upload and access points for the other images are: Website Template RSW images BSCW Images HIRENASD...

  17. Nanoscale Chemical Imaging of an Individual Catalyst Particle with Soft X-ray Ptychography

    Science.gov (United States)

    2016-01-01

    Understanding Fe deposition in fluid catalytic cracking (FCC) catalysis is critical for the mitigation of catalyst degradation. Here we employ soft X-ray ptychography to determine at the nanoscale the distribution and chemical state of Fe in an aged FCC catalyst particle. We show that both particle swelling due to colloidal Fe deposition and Fe penetration into the matrix as a result of precracking of large organic molecules occur. The application of ptychography allowed us to provide direct visual evidence for these two distinct Fe-based deactivation mechanisms, which have so far been proposed only on the basis of indirect evidence. PMID:27076990

  18. Doppler imaging of chemical spots on magnetic Ap/Bp stars. Numerical tests and assessment of systematic errors

    Science.gov (United States)

    Kochukhov, O.

    2017-01-01

    Context. Doppler imaging (DI) is a powerful spectroscopic inversion technique that enables conversion of a line profile time series into a two-dimensional map of the stellar surface inhomogeneities. DI has been repeatedly applied to reconstruct chemical spot topologies of magnetic Ap/Bp stars with the goal of understanding variability of these objects and gaining an insight into the physical processes responsible for spot formation. Aims: In this paper we investigate the accuracy of chemical abundance DI and assess the impact of several different systematic errors on the reconstructed spot maps. Methods: We have simulated spectroscopic observational data for two different Fe spot distributions with a surface abundance contrast of 1.5 dex in the presence of a moderately strong dipolar magnetic field. We then reconstructed chemical maps using different sets of spectral lines and making different assumptions about line formation in the inversion calculations. Results: Our numerical experiments demonstrate that a modern DI code successfully recovers the input chemical spot distributions comprised of multiple circular spots at different latitudes or an element overabundance belt at the magnetic equator. For the optimal reconstruction based on half a dozen spectral intervals, the average reconstruction errors do not exceed 0.10 dex. The errors increase to about 0.15 dex when abundance distributions are recovered from a few and/or blended spectral lines. Ignoring a 2.5 kG dipolar magnetic field in chemical abundance DI leads to an average relative error of 0.2 dex and maximum errors of 0.3 dex. Similar errors are encountered if a DI inversion is carried out neglecting a non-uniform continuum brightness distribution and variation of the local atmospheric structure. None of the considered systematic effects lead to major spurious features in the recovered abundance maps. Conclusions: This series of numerical DI simulations proves that inversions based on one or two spectral

  19. Chemically-activatable alkyne-tagged probe for imaging microdomains in lipid bilayer membranes

    Science.gov (United States)

    Yamaguchi, Satoshi; Matsushita, Taku; Izuta, Shin; Katada, Sumika; Ura, Manami; Ikeda, Taro; Hayashi, Gosuke; Suzuki, Yuta; Kobayashi, Koya; Tokunaga, Kyoya; Ozeki, Yasuyuki; Okamoto, Akimitsu</