Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

PubMed

Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

2018-06-12

This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P < 0.05). There was no significant difference in conspicuity, signal-to-noise ratio, or contrast-to-noise ratio of the smallest metastases (P > 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

Origin-of-transfer sequences facilitate mobilisation of non-conjugative antimicrobial-resistance plasmids in Staphylococcus aureus

PubMed Central

O'Brien, Frances G.; Yui Eto, Karina; Murphy, Riley J. T.; Fairhurst, Heather M.; Coombs, Geoffrey W.; Grubb, Warren B.; Ramsay, Joshua P.

2015-01-01

Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase proteins required for mobilisation. The pWBG749 family of S. aureus conjugative plasmids can facilitate the horizontal transfer of diverse antimicrobial-resistance plasmids that lack Mob genes. Here we reveal that these mobilisable plasmids carry copies of the pWBG749 origin-of-transfer (oriT) sequence and that these oriT sequences facilitate mobilisation by pWBG749. Sequences resembling the pWBG749 oriT were identified on half of all sequenced S. aureus plasmids, including the most prevalent large antimicrobial-resistance/virulence-gene plasmids, pIB485, pMW2 and pUSA300HOUMR. oriT sequences formed five subfamilies with distinct inverted-repeat-2 (IR2) sequences. pWBG749-family plasmids encoding each IR2 were identified and pWBG749 mobilisation was found to be specific for plasmids carrying matching IR2 sequences. Specificity of mobilisation was conferred by a putative ribbon-helix-helix-protein gene smpO. Several plasmids carried 2–3 oriT variants and pWBG749-mediated recombination occurred between distinct oriT sites during mobilisation. These observations suggest this relaxase-in trans mechanism of mobilisation by pWBG749-family plasmids is a common mechanism of plasmid dissemination in S. aureus. PMID:26243776

Synthesis of monoclinic IrTe 2 under high pressure and its physical properties

DOE PAGES

Li, X.; Yan, J. -Q.; Singh, D. J.; ...

2015-10-12

In a pressure-temperature (P-T) diagram for synthesizing IrTe 2 compounds, the well-studied trigonal (H) phase with the CdI 2-type structure is stable at low pressures. The superconducting cubic (C) phase can be synthesized under higher temperatures and pressures. A rhombohedral phase with the crystal structure similar to the C phase can be made at ambient pressure; but the phase contains a high concentration of Ir deficiency. Here, we report that a rarely studied monoclinic (M) phase can be stabilized in narrow ranges of pressure and temperature in this P-T diagram. Moreover, the peculiar crystal structure of the M-IrTe 2 eliminatesmore » the tendency to form Ir-Ir dimers found in the H phase. The M phase has been fully characterized by structural determination and measurements of electrical resistivity, thermoelectric power, DC magnetization, and specific heat. These physical properties have been compared with those in the H and C phases of Ir 1-xTe 2. Finally, we present magnetic and transport properties and specific heat of the M-IrTe 2 can be fully justified by calculations with the density-functional theory.« less

[Contrastive analysis of artifacts produced by metal dental crowns in 3.0 T magnetic resonance imaging with six sequences].

PubMed

Lan, Gao; Yunmin, Lian; Pu, Wang; Haili, Huai

2016-06-01

This study aimed to observe and evaluate six 3.0 T sequences of metallic artifacts produced by metal dental crowns. Dental crowns fabricated with four different materials (Co-Gr, Ni-Gr, Ti alloy and pure Ti) were evaluated. A mature crossbreed dog was used as the experimental animal, and crowns were fabricated for its upper right second premolar. Each crown was examined through head MRI (3.0 T) with six sequences, namely, T₁ weighted-imaging of spin echo (T₁W/SE), T₂ weighted-imaging of inversion recovery (T₂W/IR), T₂ star gradient echo (T₂*/GRE), T2 weighted-imaging of fast spin echo (T₂W/FSE), T₁ weighted-imaging of fluid attenuate inversion recovery (T₂W/FLAIR), and T₂ weighted-imaging of propeller (T₂W/PROP). The largest area and layers of artifacts were assessed and compared. The artifact in the T₂*/GRE sequence was significantly wider than those in the other sequences (P < 0.01), whose artifact extent was not significantly different (P > 0.05). T₂*/GRE exhibit the strongest influence on the artifact, whereas the five other sequences contribute equally to artifact generation.

Fast volumetric imaging of bound and pore water in cortical bone using three-dimensional ultrashort-TE (UTE) and inversion recovery UTE sequences.

PubMed

Chen, Jun; Carl, Michael; Ma, Yajun; Shao, Hongda; Lu, Xing; Chen, Bimin; Chang, Eric Y; Wu, Zhihong; Du, Jiang

2016-10-01

We report the three-dimensional ultrashort-TE (3D UTE) and adiabatic inversion recovery UTE (IR-UTE) sequences employing a radial trajectory with conical view ordering for bi-component T2 * analysis of bound water (T2 *(BW) ) and pore water (T2 *(PW) ) in cortical bone. An interleaved dual-echo 3D UTE acquisition scheme was developed for fast bi-component analysis of bound and pore water in cortical bone. A 3D IR-UTE acquisition scheme employing multiple spokes per IR was developed for bound water imaging. Two-dimensional UTE (2D UTE) and IR-UTE sequences were employed for comparison. The sequences were applied to bovine bone samples (n = 6) and volunteers (n = 6) using a 3-T scanner. Bi-component fitting of 3D UTE images of bovine samples showed a mean T2 *(BW) of 0.26 ± 0.04 ms and T2 *(PW) of 4.16 ± 0.35 ms, with fractions of 21.5 ± 3.6% and 78.5 ± 3.6%, respectively. The 3D IR-UTE signal showed a single-component decay with a mean T2 *(BW) of 0.29 ± 0.05 ms, suggesting selective imaging of bound water. Similar results were achieved with the 2D UTE and IR-UTE sequences. Bi-component fitting of 3D UTE images of the tibial midshafts of healthy volunteers showed a mean T2 *(BW) of 0.32 ± 0.08 ms and T2 *(PW) of 5.78 ± 1.24 ms, with fractions of 34.2 ± 7.4% and 65.8 ± 7.4%, respectively. Single-component fitting of 3D IR-UTE images showed a mean T2 *(BW) of 0.35 ± 0.09 ms. The 3D UTE and 3D IR-UTE techniques allow fast volumetric mapping of bound and pore water in cortical bone. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

PubMed Central

Li, Shihong; Chang, Eric Y.; Bae, Won C.; Chung, Christine B.; Hua, Yanqing; Zhou, Yi; Du, Jiang

2014-01-01

Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal models were utilized to calculate the T2*s and/or relative fractions of short and long T2*s. Results: For all bone samples UTE T2* signal decay showed bicomponent behavior. A higher short T2* fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2* fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2* fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2* components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2*s and relative fractions can be assessed using UTE bicomponent analysis

Optimization of Brain T2 Mapping Using Standard CPMG Sequence In A Clinical Scanner

NASA Astrophysics Data System (ADS)

Hnilicová, P.; Bittšanský, M.; Dobrota, D.

2014-04-01

In magnetic resonance imaging, transverse relaxation time (T2) mapping is a useful quantitative tool enabling enhanced diagnostics of many brain pathologies. The aim of our study was to test the influence of different sequence parameters on calculated T2 values, including multi-slice measurements, slice position, interslice gap, echo spacing, and pulse duration. Measurements were performed using standard multi-slice multi-echo CPMG imaging sequence on a 1.5 Tesla routine whole body MR scanner. We used multiple phantoms with different agarose concentrations (0 % to 4 %) and verified the results on a healthy volunteer. It appeared that neither the pulse duration, the size of interslice gap nor the slice shift had any impact on the T2. The measurement accuracy was increased with shorter echo spacing. Standard multi-slice multi-echo CPMG protocol with the shortest echo spacing, also the smallest available interslice gap (100 % of slice thickness) and shorter pulse duration was found to be optimal and reliable for calculating T2 maps in the human brain.

Magnetic characteristics of polymorphic single crystal compounds DyIr2Si2

NASA Astrophysics Data System (ADS)

Uchima, Kiyoharu; Shigeoka, Toru; Uwatoko, Yoshiya

2018-05-01

We have confirmed that the tetragonal ternary compound DyIr2Si2 shows polymorphism; the ThCr2Si2-type structure as a low temperature phase (I-phase) and the CaBe2Ge2-type one as a high temperature phase (P-phase) exist. A comparative study on magnetic characteristics of the morphs was performed on the I- and P-phase single crystals in order to elucidate how magnetic properties are influenced by crystallographic symmetry. The magnetic behavior changes drastically depending on the structure. The DyIr2Si2(I) shows an antiferromagnetic ordering below TN = 30 K, additional magnetic transitions of T1 = 17 K and T2 = 10 K, and a strong uniaxial magnetic anisotropy with the easy [001] direction. The [001] magnetization shows four metamagnetic transitions at low temperatures. On the other hand, the DyIr2Si2(P) has comparatively low ordering temperature of TN1 = 9.4 K and an additional transition temperature of TN2 = 3.0 K, and exhibits an easy-plane magnetic anisotropy with the easy [110] direction. Two metamagnetic transitions appear in the basal plane magnetization processes. In both the morphs, the χ-T behavior suggests the existence of component-separated magnetic transitions. The ab-component of magnetic moments orders at the higher transition temperature TN1 for the P-phase compound, which is contrast to the I-phase behavior; the c-component orders firstly at TN. The crystalline electric field (CEF) analysis was made, and the difference in magnetic behaviors between both the morphs is explained by the CEF effects.

Resequencing IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children

USDA-ARS?s Scientific Manuscript database

Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5' and 3' flanking regions of IRS2 (approx. 14.5 kb), were bidirectionally sequenced for single nucleotide...

Hyperhoneycomb Iridate β -Li2IrO3 as a Platform for Kitaev Magnetism

NASA Astrophysics Data System (ADS)

Takayama, T.; Kato, A.; Dinnebier, R.; Nuss, J.; Kono, H.; Veiga, L. S. I.; Fabbris, G.; Haskel, D.; Takagi, H.

2015-02-01

A complex iridium oxide β -Li2IrO3 crystallizes in a hyperhoneycomb structure, a three-dimensional analogue of honeycomb lattice, and is found to be a spin-orbital Mott insulator with Jeff=1 /2 moment. Ir ions are connected to the three neighboring Ir ions via Ir -O2-Ir bonding planes, which very likely gives rise to bond-dependent ferromagnetic interactions between the Jeff=1 /2 moments, an essential ingredient of Kitaev model with a spin liquid ground state. Dominant ferromagnetic interaction between Jeff=1 /2 moments is indeed confirmed by the temperature dependence of magnetic susceptibility χ (T ) which shows a positive Curie-Weiss temperature θCW˜+40 K . A magnetic ordering with a very small entropy change, likely associated with a noncollinear arrangement of Jeff=1 /2 moments, is observed at Tc=38 K . With the application of magnetic field to the ordered state, a large moment of more than 0.35 μB/Ir is induced above 3 T, a substantially polarized Jeff=1 /2 state. We argue that the close proximity to ferromagnetism and the presence of large fluctuations evidence that the ground state of hyperhoneycomb β -Li2IrO3 is located in close proximity of a Kitaev spin liquid.

MRI T2 Mapping of the Knee Articular Cartilage Using Different Acquisition Sequences and Calculation Methods at 1.5 Tesla.

PubMed

Mars, Mokhtar; Bouaziz, Mouna; Tbini, Zeineb; Ladeb, Fethi; Gharbi, Souha

2018-06-12

This study aims to determine how Magnetic Resonance Imaging (MRI) acquisition techniques and calculation methods affect T2 values of knee cartilage at 1.5 Tesla and to identify sequences that can be used for high-resolution T2 mapping in short scanning times. This study was performed on phantom and twenty-nine patients who underwent MRI of the knee joint at 1.5 Tesla. The protocol includes T2 mapping sequences based on Single Echo Spin Echo (SESE), Multi-Echo Spin Echo (MESE), Fast Spin Echo (FSE) and Turbo Gradient Spin Echo (TGSE). The T2 relaxation times were quantified and evaluated using three calculation methods (MapIt, Syngo Offline and monoexponential fit). Signal to Noise Ratios (SNR) were measured in all sequences. All statistical analyses were performed using the t-test. The average T2 values in phantom were 41.7 ± 13.8 ms for SESE, 43.2 ± 14.4 ms for MESE, 42.4 ± 14.1 ms for FSE and 44 ± 14.5 ms for TGSE. In the patient study, the mean differences were 6.5 ± 8.2 ms, 7.8 ± 7.6 ms and 8.4 ± 14.2 ms for MESE, FSE and TGSE compared to SESE respectively; these statistical results were not significantly different (p > 0.05). The comparison between the three calculation methods showed no significant difference (p > 0.05). t-Test showed no significant difference between SNR values for all sequences. T2 values depend not only on the sequence type but also on the calculation method. None of the sequences revealed significant differences compared to the SESE reference sequence. TGSE with its short scanning time can be used for high-resolution T2 mapping. ©2018The Author(s). Published by S. Karger AG, Basel.

Coexisting charge and magnetic orders in the dimer-chain iridate Ba 5AlIr 2O 11

DOE PAGES

Terzic, J.; Wang, J. C.; Ye, Feng; ...

2015-06-29

In this paper, we have synthesized and studied single-crystal Ba 5AlIr 2O 11 that features dimer chains of two inequivalent octahedra occupied by tetravalent Ir 4+(5d 5) and pentavalent Ir 5+(5d 4) ions, respectively. Ba 5AlIr 2O 11 is a Mott insulator that undergoes a subtle structural phase transition near T S=210K and a magnetic transition at T M=4.5K; the latter transition is surprisingly resistant to applied magnetic fields μ oH≤12T but more sensitive to modest applied pressure (dT M/dp ≈ +0.61K/GPa). All results indicate that the phase transition at T S signals an enhanced charge order that induces electricalmore » dipoles and strong dielectric response near T S. It is clear that the strong covalency and spin-orbit interaction (SOI) suppress double exchange in Ir dimers and stabilize a novel magnetic state that is neither S=3/2 nor J=1/2, but rather lies in an “intermediate” regime between these two states. Finally, the novel behavior of Ba 5AlIr 2O 11 therefore provides unique insights into the physics of SOI along with strong covalency in competition with double-exchange interactions of comparable strength.« less

Three-dimensional T1 and T2* mapping of human lung parenchyma using interleaved saturation recovery with dual echo ultrashort echo time imaging (ITSR-DUTE).

PubMed

Gai, Neville D; Malayeri, Ashkan A; Bluemke, David A

2017-04-01

To develop and assess a new technique for three-dimensional (3D) full lung T1 and T2* mapping using a single free breathing scan during a clinically feasible time. A 3D stack of dual-echo ultrashort echo time (UTE) radial acquisition interleaved with and without a WET (water suppression enhanced through T1 effects) saturation pulse was used to map T1 and T2* simultaneously in a single scan. Correction for modulation due to multiple views per segment was derived. Bloch simulations were performed to study saturation pulse excitation profile on lung tissue. Optimization of the saturation delay time (for T1 mapping) and echo time (for T2* mapping) was performed. Monte Carlo simulation was done to predict accuracy and precision of the sequence with signal-to-noise ratio of in vivo images used in the simulation. A phantom study was carried out using the 3D interleaved saturation recovery with dual echo ultrashort echo time imaging (ITSR-DUTE) sequence and reference standard inversion recovery spin echo sequence (IR-SE) to compare accuracy of the sequence. Nine healthy volunteers were imaged and mean (SD) of T1 and T2* in lung parenchyma at 3T were estimated through manually assisted segmentation. 3D lung coverage with a resolution of 2.5 × 2.5 × 6 mm 3 was performed and nominal scan time was recorded for the scans. Repeatability was assessed in three of the volunteers. Regional differences in T1/T2* values were also assessed. The phantom study showed accuracy of T1 values to be within 2.3% of values obtained from IR-SE. Mean T1 value in lung parenchyma was 1002 ± 82 ms while T2* was 0.85 ± 0.1 ms. Scan time was ∼10 min for volunteer scans. Mean coefficient of variation (CV) across slices was 0.057 and 0.09, respectively. Regional variation along the gravitational direction and between right and left lung were not significant (P = 0.25 and P = 0.06, respectively) for T1. T2* showed significant variation (P = 0.03) along the

Bulk electronic structure of non-centrosymmetric Eu T Ge3 (T =Co , Ni, Rh, Ir) studied by hard x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Utsumi, Yuki; Kasinathan, Deepa; Swatek, Przemysław; Bednarchuk, Oleksandr; Kaczorowski, Dariusz; Ablett, James M.; Rueff, Jean-Pascal

2018-03-01

Non-centrosymmetric Eu T Ge3 (T = Co, Ni, Rh, and Ir) possesses magnetic Eu2 + ions, and antiferromagnetic ordering appears at low temperatures. Transition-metal substitution leads to changes in the unit-cell volume and in the magnetic ordering. However, the magnetic ordering temperature does not scale with the volume change, and the Eu valence is expected to remain divalent. Here we study the bulk electronic structure of non-centrosymmetric Eu T Ge3 (T = Co, Ni, Rh, and Ir) by hard x-ray photoelectron spectroscopy. The Eu 3 d core-level spectrum confirms the robust Eu2 + valence state against the transition-metal substitution with a small contribution from Eu3 +. The estimated Eu mean valence is around 2.1 in these compounds, as confirmed by multiplet calculations. In contrast, the Ge 2 p spectrum shifts to higher binding energy upon changing the transition metal from 3 d to 4 d to 5 d elements, hinting at a change in the Ge-T bonding strength. The valence bands of the different compounds are found to be well reproduced by ab initio band structure calculations.

Mid-IR Spectra Herbig Ae/Be Stars

NASA Technical Reports Server (NTRS)

Wooden, Diane; Witteborn, Fred C. (Technical Monitor)

1997-01-01

Herbig Ae/Be stars are intermediate mass pre-main sequence stars, the higher mass analogues to the T Tauri stars. Because of their higher mass, they are expected form more rapidly than the T Tauri stars. Whether the Herbig Ae/Be stars accrete only from collapsing infalling envelopes or whether accrete through geometrically flattened viscous accretion disks is of current debate. When the Herbig Ae/Be stars reach the main sequence they form a class called Vega-like stars which are known from their IR excesses to have debris disks, such as the famous beta Pictoris. The evolutionary scenario between the pre-main sequence Herbig Ae/Be stars and the main sequence Vega-like stars is not yet revealed and it bears on the possibility of the presence of Habitable Zone planets around the A stars. Photometric studies of Herbig Ae/Be stars have revealed that most are variable in the optical, and a subset of stars show non-periodic drops of about 2 magnitudes. These drops in visible light are accompanied by changes in their colors: at first the starlight becomes reddened, and then it becomes bluer, the polarization goes from less than 0.1 % to roughly 1% during these minima. The theory postulated by V. Grinnin is that large cometary bodies on highly eccentric orbits occult the star on their way to being sublimed, for systems that are viewed edge-on. This theory is one of several controversial theories about the nature of Herbig Ae/Be stars. A 5 year mid-IR spectrophotometric monitoring campaign was begun by Wooden and Butner in 1992 to look for correlations between the variations in visible photometry and mid-IR dust emission features. Generally the approximately 20 stars that have been observed by the NASA Ames HIFOGS spectrometer have been steady at 10 microns. There are a handful, however, that have shown variable mid-IR spectra, with 2 showing variations in both the continuum and features anti-correlated with visual photometry, and 3 showing variations in the emission

Magnetism and anisotropy of Ir5+ based double perovskites Sr2CoIrO6andSr2FeIrO6

NASA Astrophysics Data System (ADS)

Terzic, Jasminka; Yuan, S. J.; Song, W. H.; Aswartham, S.; Cao, G.

2015-03-01

We report on structural, thermodynamic and transport study of single-crystal double perovskites Sr2CoIrO6andSr2FeIrO6.TheisostructuralSr2CoIrO6andSr2FeIrO6 feature a cubic crystal structure with pentavalent Ir5+(5d4) which are anticipated to have J =0 singlet ground states in the strong spin-orbit coupling limit. Here we observe magnetic coupling between 5d and 3d (Co, Fe) elements, which result in antiferromagnetic order at high temperatures in both double perovskites. Of the two, Sr2CoIrO6 displays antiferromagnetic metallic behavior with a pronounced magnetic anisotropy; in sharp contrast, the isostructural Sr2FeIrO6 exhibits an antiferroamagnetic, insulating ground state without discernible magnetic anisotropy. The data will be discussed and presented with comparisons drawn with similar systems. This work was supported by NSF via Grant DMR 1265162.

Adding a dimension to the infrared spectra of interfaces: 2D SFG spectroscopy via mid-IR pulse shaping

NASA Astrophysics Data System (ADS)

Zanni, Martin

2012-02-01

Sum-frequency generation spectroscopy provides an infrared spectrum of interfaces and thus has widespread use in the materials and chemical sciences. In this presentation, I will present our recent work in developing a 2D pulse sequence to generate 2D SFG spectra of interfaces, in analogy to 2D infrared spectra used to measure bulk species. To develop this spectroscopy, we have utilized many of the tricks-of-the-trade developed in the 2D IR and 2D Vis communities in the last decade, including mid-IR pulse shaping. With mid-IR pulse shaping, the 2D pulse sequence is manipulated by computer programming in the desired frequency resolution, rotating frame, and signal pathway. We believe that 2D SFG will become an important tool in the interfacial sciences in an analogous way that 2D IR is now being used in many disciplines.

Liver acquisition with acceleration volume acquisition gadolinium-enhanced magnetic resonance combined with T2 sequences in the diagnosis of local recurrence of rectal cancer.

PubMed

Cao, Wuteng; Li, Fangqian; Gong, Jiaying; Liu, Dechao; Deng, Yanhong; Kang, Liang; Zhou, Zhiyang

2016-11-22

To investigate the efficacy of liver acquisition with acceleration volume acquisition (LAVA) gadolinium-enhanced magnetic resonance (MR) sequences and to assess its added accuracy in diagnosing local recurrence (LR) of rectal cancer with conventional T2-weighted fast spin echo (FSE) sequences. Pelvic MRI, including T2-weighted FSE sequences, gadolinium-enhanced sequences of LAVA and T1-weighted FSE with fat suppression, was performed on 225 patients with postoperative rectal cancer. Two readers evaluated the presence of LR according to "T2" (T2 sequences only), "T2 + LAVA-Gad" (LAVA and T2 imaging), and "T2 + T1-fs-Gad" (T1 fat suppression-enhanced sequence with T2 images). To evaluate diagnostic efficiency, imaging quality with LAVA and T1-fs-Gad by subjective scores and the signal intensity (SI) ratio. In the result, the SI ratio of LAVA was significantly higher than that of T1-fs-Gad (p = 0.0001). The diagnostic efficiency of "T2 + LAVA-Gad" was better than that of "T2 + T1-fs-Gad" (p = 0.0016 for Reader 1, p = 0.0001 for Reader 2) and T2 imaging only (p = 0.0001 for Reader 1; p = 0.0001 for Reader 2). Therefore, LAVA gadolinium-enhanced MR increases the accuracy of diagnosis of LR from rectal cancer and could replace conventional T1 gadolinium-enhanced sequences in the postoperative pelvic follow-up of rectal cancer.

Photophysical dynamics of the efficient emission and photosensitization of [Ir(pqi)2(NN)]+ complexes.

PubMed

Zanoni, Kassio P S; Ito, Akitaka; Grüner, Malte; Murakami Iha, Neyde Y; de Camargo, Andrea S S

2018-01-23

The photophysical dynamics of three complexes in the highly-emissive [Ir(pqi) 2 (NN)] + series were investigated aiming at unique photophysical features and applications in light-emitting and singlet oxygen sensitizing research fields. Rational elucidation and Franck-Condon analyses of the observed emission spectra in nitrile solutions at 298 and 77 K reveal the true emissive nature of the lowest-lying triplet excited state (T 1 ), consisting of a hybrid 3 MLCT/LC Ir(pqi)→pqi state. Emissive deactivations from T 1 occur mainly by very intense, yellow-orange phosphorescence with high quantum yields and radiative rates. The emission nature experimentally verified is corroborated by theoretical calculations (TD-DFT), with T 1 arising from a mixing of several transitions induced by the spin-orbit coupling, majorly ascribed to 3 MLCT/LC Ir(pqi)→pqi and increasing contributions of 3 MLCT/LLCT Ir(pqi)→NN . The microsecond-lived emission of T 1 is rapidly quenched by molecular oxygen, with an efficient generation of singlet oxygen. Our findings show that the photophysics of [Ir(pqi) 2 (NN)][PF 6 ] complexes is suitable for many applications, from the active layer of electroluminescent devices to photosensitizers for photodynamic therapy and theranostics.

The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

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

Li, Shihong; Department of Radiology, Hua Dong Hospital, Fudan University, Shanghai 200040; Yancheng Medical College, Jiangsu

Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal modelsmore » were utilized to calculate the T2{sup *}s and/or relative fractions of short and long T2{sup *}s. Results: For all bone samples UTE T2{sup *} signal decay showed bicomponent behavior. A higher short T2{sup *} fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2{sup *} fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2{sup *} fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2{sup *} components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2{sup *}s and relative

k - dependent Jeff=1/2 band splitting and the electron-hole asymmetry in SrIrO3

NASA Astrophysics Data System (ADS)

Singh, Vijeta; Pulikkotil, J. J.

2017-02-01

The Ir ion in Srn+1 IrnO 3 n + 1 series of compounds is octahedrally coordinated. However, unlike Sr2IrO4 (n=1) and Sr3Ir2O7 (n=2) which are insulating due to spin-orbit induced Jeff splitting of the t2g bands, SrIrO3 (n= ∞) is conducting. To explore whether such a splitting is relevant in SrIrO3, and if so to what extent, we investigate the electronic structure of orthorhombic SrIrO3 using density functional theory. Calculations reveal that the crystal field split Ir t2 g bands in SrIrO3 are indeed split into Jeff=3/2 and and Jeff=1/2 states. However, the splitting is found to be strongly k - dependent with its magnitude determined by the Ir - O orbital hybridization. Besides, we find that the spin-orbit induced pseudo-gap, into which the Fermi energy is positioned, is composed of both light electron-like and heavy hole-like bands. These features in the band structure of SrIrO3 suggest that variations in the carrier concentration control the electronic transport properties in SrIrO3, which is consistent with the experiments.

Three-dimensional quantitative T1 and T2 mapping of the carotid artery: Sequence design and in vivo feasibility.

PubMed

Coolen, Bram F; Poot, Dirk H J; Liem, Madieke I; Smits, Loek P; Gao, Shan; Kotek, Gyula; Klein, Stefan; Nederveen, Aart J

2016-03-01

A novel three-dimensional (3D) T1 and T2 mapping protocol for the carotid artery is presented. A 3D black-blood imaging sequence was adapted allowing carotid T1 and T2 mapping using multiple flip angles and echo time (TE) preparation times. B1 mapping was performed to correct for spatially varying deviations from the nominal flip angle. The protocol was optimized using simulations and phantom experiments. In vivo scans were performed on six healthy volunteers in two sessions, and in a patient with advanced atherosclerosis. Compensation for patient motion was achieved by 3D registration of the inter/intrasession scans. Subsequently, T1 and T2 maps were obtained by maximum likelihood estimation. Simulations and phantom experiments showed that the bias in T1 and T2 estimation was < 10% within the range of physiological values. In vivo T1 and T2 values for carotid vessel wall were 844 ± 96 and 39 ± 5 ms, with good repeatability across scans. Patient data revealed altered T1 and T2 values in regions of atherosclerotic plaque. The 3D T1 and T2 mapping of the carotid artery is feasible using variable flip angle and variable TE preparation acquisitions. We foresee application of this technique for plaque characterization and monitoring plaque progression in atherosclerotic patients. © 2015 Wiley Periodicals, Inc.

Enhanced Activity and Durability of Nanosized Pt-SnO2/IrO2/CNTs Catalyst for Methanol Electrooxidation.

PubMed

Wang, Hongjuan; Wang, Xiaohui; Zheng, Jiadao; Peng, Feng; Yu, Hao

2015-05-01

Pt-SnO2/IrO2/CNTs anode catalyst for direct methanol fuel cell was designed and prepared with IrO2/CNTs as support for the subsequent immobilization of Pt and SnO2 at the same time. The structure of the catalysts and their catalytic performance in methanol electrooxidation were investigated and the roles of IrO2 and SnO2 in methanol electrooxidation were discussed as well. Results show that Pt-SnO2/IrO2/CNTs catalyst exhibits the best activity and durability for methanol electrooxidation when compared with Pt/CNTs, Pt/IrO2/CNTs and Pt-SnO2/CNTs. According to the results of electrochemical tests and physicochemical characterizations, the enhancements of Pt-SnO2/IrO2/CNTs were attributed to the special properties of IrO2 and SnO2, in which IrO2 mainly increases the methanol oxidation activity and SnO2 mainly improves the CO oxidation ability and durability. Therefore, Pt-SnO2/IrO2/CNTs exhibits excellent performance for methanol oxidation with higher electrocatalytic activity (I(f) of 1054 A g(Pt(-1)) and powerful anti-poisoning ability (the onset potential for CO oxidation of 0.3 V) and outstanding durability (the sustained time t in CP of 617 s), revealing a suitable anode catalyst for DMFCs.

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2 T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

DOE PAGES

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; ...

2016-09-08

Desulfurivibrio alkaliphilus strain AHT2 T is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2 T is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. Here, D. alkaliphilus AHT2 T is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2 T was sequenced by themore » DOE Joint Genome Institute as part of the Community Science Program.« less

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2 T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

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

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex

Desulfurivibrio alkaliphilus strain AHT2 T is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2 T is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. Here, D. alkaliphilus AHT2 T is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2 T was sequenced by themore » DOE Joint Genome Institute as part of the Community Science Program.« less

Nėščiųjų ir jaunų negimdžiusių moterų krūtų tūrio, kūno dydžio ir pasyviosios masės lyginamasis tyrimas

PubMed Central

Drąsutis, Jonas; Barkus, Arūnas; Kairienė, Elena; Drąsutienė, Gražina; Norvilaitė, Kristina; Tutkuvienė, Janina

2016-01-01

Tikslas. Palyginti nėščiųjų ir jaunų negimdžiusių moterų kūno ir krūtų dydžio rodiklius. Medžiaga ir metodika. 2008–2009 m. (I tyrimas) ištirti 82 jaunų negimdžiusių devyniolikos metų amžiaus merginų krūtų ir kūno dydžio rodikliai, jie palyginti su 2013–2015 m. (II tyrimas) Vilniuje tirtų nėščiųjų (pirmuoju nėštumo trečdaliu) tais pačiais kūno stambumo ir krūtų parametrais – ūgiu, svoriu, įvairių kūno dalių apimtimis, odos klostėmis, pasyviąja kūno mase ir krūtų tūriu. Kūno dydžio rodikliams palyginti visos tiriamosios buvo skirstomos į grupes pagal krūtų dydį ir kūno stambumą (procentiliniu metodu). Nėščiosios suskirstytos į gimdančias pirmą kartą ir pakartotinai. Abiejuose tyrimuose naudota standartinė antropometrinė metodika. Krūties tūris apskaičiuotas pagal R. Kramerio ir G. Dexlerio (1981) formulę. Pasyviosios kūno masės (riebalinio audinio) kiekis procentais – pagal odos ir poodžio riebalines klostes naudojant W. E. Sirio (1961), J. H. Wilmorės ir A. R. Behnkės (1970) formules. Rezultatai, nustatyti visų parametrų aprašomosios statistikos, įvairovės ir pasiskirstymo rodikliais, apdoroti naudojant SPSS 22.0 programą. Skirtumai tarp tiriamųjų grupių vertinti pagal Stjudento t kriterijų. Pasirinktas patikimumo lygmuo p < 0,05. Rezultatai. Statistiškai reikšmingai didesni nei jaunų negimdžiusių nėščiųjų grupės moterų rodikliai buvo šie: krūtinės, juosmens, klubų apimties, krūties tūrio ir juosmens klubų indeksas. Nėščių moterų riebalinis audinys kaupėsi daugiau viršutinėje kūno dalyje, nors santykinė ir absoliuti pasyvioji kūno masė tarp grupių skyrėsi nereikšmingai. Lyginant pirmą kartą ir pakartotinai gimdančių su jaunų negimdžiusių moterų rodmenimis paaiškėjo, kad pakartotinai gimdančios moterys turėjo didesnį riebalinio audinio kiekį, o pirmąkart ir jaunų negimdžiusių merginų rodikliai reikšmingai nesiskyrė. Ma

SWI or T2*: which MRI sequence to use in the detection of cerebral microbleeds? The Karolinska Imaging Dementia Study.

PubMed

Shams, S; Martola, J; Cavallin, L; Granberg, T; Shams, M; Aspelin, P; Wahlund, L O; Kristoffersen-Wiberg, M

2015-06-01

Cerebral microbleeds are thought to have potentially important clinical implications in dementia and stroke. However, the use of both T2* and SWI MR imaging sequences for microbleed detection has complicated the cross-comparison of study results. We aimed to determine the impact of microbleed sequences on microbleed detection and associated clinical parameters. Patients from our memory clinic (n = 246; 53% female; mean age, 62) prospectively underwent 3T MR imaging, with conventional thick-section T2*, thick-section SWI, and conventional thin-section SWI. Microbleeds were assessed separately on thick-section SWI, thin-section SWI, and T2* by 3 raters, with varying neuroradiologic experience. Clinical and radiologic parameters from the dementia investigation were analyzed in association with the number of microbleeds in negative binomial regression analyses. Prevalence and number of microbleeds were higher on thick-/thin-section SWI (20/21%) compared with T2*(17%). There was no difference in microbleed prevalence/number between thick- and thin-section SWI. Interrater agreement was excellent for all raters and sequences. Univariate comparisons of clinical parameters between patients with and without microbleeds yielded no difference across sequences. In the regression analysis, only minor differences in clinical associations with the number of microbleeds were noted across sequences. Due to the increased detection of microbleeds, we recommend SWI as the sequence of choice in microbleed detection. Microbleeds and their association with clinical parameters are robust to the effects of varying MR imaging sequences, suggesting that comparison of results across studies is possible, despite differing microbleed sequences. © 2015 by American Journal of Neuroradiology.

Congenital heart disease in adults: Quantitative and qualitative evaluation of IR FLASH and IR SSFP MRA techniques using a blood pool contrast agent in the steady state and comparison to first pass MRA.

PubMed

Febbo, Jennifer A; Galizia, Mauricio S; Murphy, Ian G; Popescu, Andrada; Bi, Xiaoming; Turin, Alexander; Collins, Jeremy; Markl, Michael; Edelman, Robert R; Carr, James C

2015-10-01

To evaluate magnetic resonance angiography sequences during the contrast steady-state (SS-MRA) using inversion recovery (IR) with fast low-angle shot (IR-FLASH) or steady-state free precession (IR-SSFP) read-outs, following the injection of a blood-pool contrast agent, and compare them to first-pass MR angiography (FP-MRA) in adults with congenital heart disease (CHD). Twenty-three adult patients with CHD who underwent both SS-MRA and FP-MRA using a 1.5-T scanner were retrospectively identified. Signal-to-noise and contrast-to-noise ratios were obtained at eight locations within the aorta and pulmonary vessels.. Image quality and the presence of artifacts were subjectively assessed by two radiologists. The presence of pathology was noted and given a confidence score. There was no difference in vessel dimensions among the sequences. IR-SSFP showed better image quality and fewer artifacts than IR-FLASH and FP-MRA. Confidence scores were significantly higher for SS-MRA compared to FP-MRA. Seven cases (30.4%) had findings detected at SS-MRA that were not detected at FP-MRA, and 2 cases (8.7%) had findings detected by IR-SSFP only. SS-MRA of the thoracic vasculature using a blood pool contrast agent offers superior image quality and reveals more abnormalities compared to standard FP-MRA in adults with CHD, and it is best achieved with an IR-SSFP sequence. These sequences could lead to increased detection rates of abnormalities and provide a simpler protocol image acquisition. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Is HOMA-IR a potential screening test for non-alcoholic fatty liver disease in adults with type 2 diabetes?

PubMed

Gutierrez-Buey, Gala; Núñez-Córdoba, Jorge M; Llavero-Valero, María; Gargallo, Javier; Salvador, Javier; Escalada, Javier

2017-06-01

Non-alcoholic fatty liver disease (NAFLD) is the commonest hepatic disease in many parts of the World, with particularly high prevalence in patients with type 2 diabetes (T2DM). However, a good screening test for NAFLD in T2DM has not been established. Insulin resistance (IR) has been associated with NAFLD, and homeostatic model assessment of insulin resistance (HOMA-IR), a good proxy for IR, may represent an affordable predictive test which could be easily applied in routine clinical practice. We aimed to evaluate the diagnostic accuracy of HOMA-IR for NAFLD in T2DM and sought to estimate an optimal cut-off value for discriminating NAFLD from non-NAFLD cases. We conducted a retrospective analysis of 56 well-controlled patients with T2DM (HbAc1<7%, on oral anti-diabetic and/or glucagon-like peptide-1 agonist treatment), who had at least one glucose and insulin level determined, and at least one hepatic imaging test (ultrasonography or computed tomography scanning). The prevalence of NAFLD was 73.2% (95% CI: 59.7-84.2) in our population. An association between HOMA-IR and NAFLD was found (OR 1.5; 95% CI: 1.03-2.1; p=0.033), independently of transaminases, fat percentage, BMI and triglyceride levels. The AUROC curve of HOMA-IR for identifying NAFLD was 80.7% (95% CI: 68.9-92.5). A value of HOMA-IR of 4.5 was estimated to be an optimal threshold for discriminating NAFLD from non-NAFLD cases. HOMA-IR is independently associated with the presence of NAFLD in adults with T2DM, and might potentially be applied in clinical practice as a screen for this condition. Copyright © 2017 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Validity and limitations of the superexchange model for the magnetic properties of Sr2IrO4 and Ba2IrO4 mediated by the strong spin-orbit coupling

NASA Astrophysics Data System (ADS)

Solovyev, I. V.; Mazurenko, V. V.; Katanin, A. A.

2015-12-01

Layered perovskites Sr2IrO4 and Ba2IrO4 are regarded as the key materials for understanding the properties of magnetic relativistic insulators, mediated by the strong spin-orbit (SO) coupling. One of the most fundamental issues is to which extent these properties can be described by the superexchange (SE) model, formulated in the limit of the large Coulomb repulsion for some appropriately selected pseudospin states, and whether these materials themselves can be classified as Mott insulators. In this work, we address these issues by deriving the relevant models and extracting parameters of these models from the electronic-structure calculations with the SO coupling, based on the density functional theory. First, we construct the effective Hubbard-type model for the magnetically active t2 g bands, by recasting the problem in the language of localized Wannier orbitals. Then, we map the obtained electron model onto the pseudospin model by applying the theory of SE interactions, which is based on the second-order perturbation theory with respect to the transfer integrals. We discuss the microscopic origin of anisotropic SE interactions, inherent to the compass Heisenberg model, and the appearance of the antisymmetric Dzyaloshinskii-Moriya term, associated with the additional rotation of the IrO6 octahedra in Sr2IrO4 . In order to solve the pseudospin Hamiltonian problem and evaluate the Néel temperature (TN), we employ the nonlinear sigma model. We have found that, while for Sr2IrO4 our value of TN agrees with the experimental data, for Ba2IrO4 it is overestimated by a factor of 2. We argue that this discrepancy is related to limitations of the SE model: while for more localized t2 g states in Sr2IrO4 it works reasonably well, the higher-order terms in the perturbation theory expansion play a more important role in the more "itinerant" Ba2IrO4 , giving rise to the new type of isotropic and anisotropic exchange interactions, which are not captured by the SE model. This

7T MRI-Histologic Correlation Study of Low Specific Absorption Rate T2-Weighted GRASE Sequences in the Detection of White Matter Involvement in Multiple Sclerosis.

PubMed

Bagnato, Francesca; Hametner, Simon; Pennell, David; Dortch, Richard; Dula, Adrienne N; Pawate, Siddharama; Smith, Seth A; Lassmann, Hans; Gore, John C; Welch, Edward B

2015-01-01

The high value of the specific absorption rate (SAR) of radio-frequency (RF) energy arising from the series of RF refocusing pulses in T2-weighted (T2-w) turbo spin echo (TSE) MRI hampers its clinical application at 7.0 Tesla (7T). T2-w gradient and spin echo (GRASE) uses the speed from gradient refocusing in combination with the chemical-shift/static magnetic field (B0) inhomogeneity insensitivity from spin-echo refocusing to acquire T2-w images with a limited number of refocusing RF pulses, thus reducing SAR. To investigate whether low SAR T2-w GRASE could replace T2-w TSE in detecting white matter (WM) disease in MS patients imaged at 7T. The .7 mm3 isotropic T2-w TSE and T2-w GRASE images with variable echo times (TEs) and echo planar imaging (EPI) factors were obtained on a 7T scanner from postmortem samples of MS brains. These samples were derived from brains of 3 female MS patients. WM lesions (WM-Ls) and normal-appearing WM (NAWM) signal intensity, WM-Ls/NAWM contrast-to-noise ratio (CNR) and MRI/myelin staining sections comparisons were obtained. GRASE sequences with EPI factor/TE = 3/50 and 3/75 ms were comparable to the SE technique for measures of CNR in WM-Ls and NAWM and for detection of WM-Ls. In all sequences, however, identification of areas with remyelination, Wallerian degeneration, and gray matter demyelination, as depicted by myelin staining, was not possible. T2-w GRASE images may replace T2-w TSE for clinical use. However, even at 7T, both sequences fail in detecting and characterizing MS disease beyond visible WM-Ls. Copyright © 2015 by the American Society of Neuroimaging.

Distribution of Vesicular Glutamate Transporter 2 (VGluT2) in the Primary Visual Cortex of the Macaque and Human

PubMed Central

Garcia-Marin, Virginia; Ahmed, Tunazzina H.; Afzal, Yasmeen C.; Hawken, Michael J.

2014-01-01

The majority of thalamic terminals in V1 arise from lateral geniculate nucleus (LGN) afferents. Thalamic afferent terminals are preferentially labeled by an isoform of the vesicular glutamate transporter, VGluT2. The goal of our study was to determine the distribution of VGluT2-ir puncta in macaque and human visual cortex. First, we investigated the distribution of VGluT2-ir puncta in all layers of macaque monkey primary visual cortex (V1), and found a very close correspondence between the known distribution of LGN afferents from previous studies and the distribution of VGluT2-immunoreactive (-ir) puncta. There was also a close correspondence between cytochrome oxidase density and VGluT2-ir puncta distribution. After validating the correspondence in macaque, we made a comparative study in human V1. In many aspects, the distribution of VGluT2-ir puncta in human was qualitatively similar to that of the macaque: high densities in layer 4C, patches of VGluT2-ir puncta in the supragranular layer (2/3), lower but clear distribution in layers 1 and 6, and very few puncta in layers 5 and 4B. However, there were also important differences between macaques and humans. In layer 4A of human, there was a sparse distribution of VGluT2-ir puncta, whereas in macaque, there was a dense distribution with the characteristic honeycomb organization. The results suggest important changes in the pattern of cortical VGluT2 immunostaining that may be related to evolutionary differences in the cortical organization of LGN afferents between Old World monkeys and humans. PMID:22684983

Sex-specific interactions between the IRS1 polymorphism and intakes of carbohydrates and fat on incident type 2 diabetes.

PubMed

Ericson, Ulrika; Rukh, Gull; Stojkovic, Ivana; Sonestedt, Emily; Gullberg, Bo; Wirfält, Elisabet; Wallström, Peter; Orho-Melander, Marju

2013-01-01

The minor T allele of rs2943641 near the gene encoding for insulin receptor substrate 1 (IRS1) has been associated with decreased risk of type 2 diabetes (T2D) and adiposity in genome-wide association studies. Dietary intake can influence the regulation of IRS1, and studies have indicated sex-specific associations between IRS1 and adiposity. The objective was to examine the interaction between IRS1 rs2943641 and macronutrient intakes on incident T2D and percentage body fat in the Malmö Diet and Cancer cohort. The study included 15,227 women and 9614 men aged 45-74 y without prevalent diabetes. Dietary data were collected with a modified diet history method. During 12 y of follow-up, 1567 incident T2D cases were identified. The T allele was associated with lower incidence of T2D (P-trend = 0.003) and, in men, with higher percentage body fat (P-trend = 0.00002). We observed 3-way interactions between sex, rs2943641, and carbohydrate intake (P = 0.01) as well as between sex, rs2943641, and fat intake (P = 0.01) on incident T2D. Among women, the T allele was associated with decreased risk only in the lower tertiles of carbohydrate intake (P-trend = 0.01, P-interaction = 0.01). In contrast, among men, the T allele was associated with decreased risk in the lowest tertile of fat intake (P-trend = 0.01, P-interaction = 0.02). No interaction was observed between macronutrient intakes and rs2943641 on percentage body fat. Our results indicate that IRS1 rs2943641 interacts with carbohydrate and fat intakes on incident T2D in a sex-specific fashion. A protective association between the rs2943641 T allele and T2D was restricted to women with low carbohydrate intake and to men with low fat intake.

Magnetic resonance enteroclysis in patients with Crohn's disease: fat saturated T2-weighted sequences for evaluation of inflammatory activity.

PubMed

Grieser, Christian; Denecke, Timm; Steffen, Ingo G; Werner, Scarlett; Kröncke, Thomas; Guckelberger, Olaf; Pape, Ulrich-Frank; Meier, Johannes; Thiel, Regina; Kivelitz, Dietmar; Sturm, Andreas; Hamm, Bernd; Röttgen, Rainer

2012-04-01

To evaluate fat saturated (fs) T2-weighted (w) fast relaxation fast spin echo (FRFSE)-sequences compared to the standard protocol with contrast agent for the evaluation of inflammatory activity in patients with Crohn's Disease (CD). Fourty-eight patients (male, 17; female, 33; mean age, 37 years) with suspicion of inflammatory activity in proven CD who underwent MR enteroclysis (MRE) at 1.5T (GE Healthcare) were retrospectively included. Two blinded radiologists analyzed MRE images for presence and extent of CD lesions and degree of local inflammation for fsT2-w FRFSE and contrast enhanced T1-w images (T2-activity; T1-activity; score, 1-4) in consensus. Furthermore, mural signal intensity (SI) ratios (T2-ratio; T1-ratio) were recorded. Patient based MRE findings were correlated with endoscopic (45 patients), surgical (6 patients), histopathological, and clinical data (CDAI) as a surrogate reference standard. In total, 24 of 48 eligible patients presented with acute inflammatory activity with 123 affected bowel segments. ROC analysis of the total inflammatory score presented an AUC of 0.93 (p<0.001) for T2-activity (T1-activity, AUC 0.63; p=0.019). ROC analysis revealed an AUC of 0.76 (p<0.001) for the T2-ratio (T1-ratio, AUC 0.51; p=0.93). General linear regression model revealed T2-activity (p=0.001) and age (p=0.024) as predictive factors of acute bowel inflammation. T2-w FRFSE-sequences can depict CD lesions and help to assess the inflammation activity, even with improved accuracy as compared to contrast-enhanced T1-w sequences. Copyright © 2011 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

Reaction mechanism for oxygen evolution on RuO 2, IrO 2, and RuO 2@IrO 2 core-shell nanocatalysts

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

Ma, Zhong; Zhang, Yu; Liu, Shizhong

Iridium dioxide, IrO 2, is second to the most active RuO 2 catalyst for the oxygen evolution reaction (OER) in acid, and is used in proton exchange membrane water electrolyzers due to its high durability. In order to improve the activity of IrO 2-based catalysts, we prepared RuO 2@IrO 2 core-shell nanocatalysts using carbon-supported Ru as the template. At 1.48 V, the OER specific activity of RuO 2@IrO 2 is threefold that of IrO 2. While the activity volcano plots over wide range of materials have been reported, zooming into the top region to clarify the rate limiting steps ofmore » most active catalysts is important for further activity enhancement. Here, we verified theory-proposed sequential water dissociation pathway in which the O—O bond forms on a single metal site, not via coupling of two adsorbed intermediates, by fitting measured polarization curves using a kinetic equation with the free energies of adsorption and activation as the parameters. Consistent with theoretical calculations, we show that the OER activities of IrO 2 and RuO 2@IrO 2 are limited by the formation of O adsorbed phase, while the OOH formation on the adsorbed O limits the reaction rate on RuO 2.« less

Reaction mechanism for oxygen evolution on RuO 2, IrO 2, and RuO 2@IrO 2 core-shell nanocatalysts

DOE PAGES

Ma, Zhong; Zhang, Yu; Liu, Shizhong; ...

2017-10-28

Iridium dioxide, IrO 2, is second to the most active RuO 2 catalyst for the oxygen evolution reaction (OER) in acid, and is used in proton exchange membrane water electrolyzers due to its high durability. In order to improve the activity of IrO 2-based catalysts, we prepared RuO 2@IrO 2 core-shell nanocatalysts using carbon-supported Ru as the template. At 1.48 V, the OER specific activity of RuO 2@IrO 2 is threefold that of IrO 2. While the activity volcano plots over wide range of materials have been reported, zooming into the top region to clarify the rate limiting steps ofmore » most active catalysts is important for further activity enhancement. Here, we verified theory-proposed sequential water dissociation pathway in which the O—O bond forms on a single metal site, not via coupling of two adsorbed intermediates, by fitting measured polarization curves using a kinetic equation with the free energies of adsorption and activation as the parameters. Consistent with theoretical calculations, we show that the OER activities of IrO 2 and RuO 2@IrO 2 are limited by the formation of O adsorbed phase, while the OOH formation on the adsorbed O limits the reaction rate on RuO 2.« less

High temperature Ir segregation in Ir-B ceramics: Effect of oxygen presence on stability of IrB 2 and other Ir-B phases

DOE PAGES

Xie, Zhilin; Terracciano, Anthony C.; Cullen, David A.; ...

2015-05-13

The formation of IrB 2, IrB 1.35, IrB 1.1 and IrB monoboride phases in the Ir–B ceramic nanopowder was confirmed during mechanochemical reaction between metallic Ir and elemental B powders. The Ir–B phases were analysed after 90 h of high energy ball milling and after annealing of the powder for 72 h at 1050°C in vacuo. The iridium monoboride (IrB) orthorhombic phase was synthesised experimentally for the first time and identified by powder X-ray diffraction. Additionally, the ReB 2 type IrB 2 hexagonal phase was also produced for the first time and identified by high resolution transmission electron microscope. Irmore » segregation along disordered domains of the boron lattice was found to occur during high temperature annealing. Furthermore, these nanodomains may have useful catalytic properties.« less

Magnetic properties of Sr 3 NiIrO 6 and Sr 3 CoIrO 6 : Magnetic hysteresis with coercive fields of up to 55 T

DOE PAGES

Singleton, John; Kim, Jae Wook; Topping, Craig V.; ...

2016-12-08

Here, we report extraordinarily large magnetic hysteresis loops in the iridates Sr 3NiIrO 5 and Sr 3CoIrO 6. We find coercive magnetic fields of up to 55 T with switched magnetic moments ≈1μ B per formula unit in Sr 3NiIrO 6 and coercive fields of up to 52 T with switched moments ≈3μ B per formula unit in Sr 3CoIrO 6. We propose that the magnetic hysteresis involves the field-induced evolution of quasi-one-dimensional chains in a frustrated triangular configuration. In conclusion, the striking magnetic behavior is likely to be linked to the unusual spin-orbit-entangled local state of the Ir 4+more » ion and its potential for anisotropic exchange interactions.« less

Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2 T

DOE PAGES

Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

2015-10-26

Thioalkalivibrio thiocyanoxidans strain ARh 2 T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na +. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. In conclusion, this organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

PubMed

Khan, Javed Mohammed; Cheruku, Harish Reddy; Tong, Joo Chuan; Ranganathan, Shoba

2011-04-15

Sequence-structure-function information is critical in understanding the mechanism of pMHC and TR/pMHC binding and recognition. A database for sequence-structure-function information on pMHC and TR/pMHC interactions, MHC-Peptide Interaction Database-TR version 2 (MPID-T2), is now available augmented with the latest PDB and IMGT/3Dstructure-DB data, advanced features and new parameters for the analysis of pMHC and TR/pMHC structures. http://biolinfo.org/mpid-t2. shoba.ranganathan@mq.edu.au Supplementary data are available at Bioinformatics online.

Sodium inversion recovery MRI of the knee joint in vivo at 7T

NASA Astrophysics Data System (ADS)

Madelin, Guillaume; Lee, Jae-Seung; Inati, Souheil; Jerschow, Alexej; Regatte, Ravinder R.

2010-11-01

The loss of proteoglycans (PG) in the articular cartilage is an early signature of osteoarthritis (OA). The ensuing changes in the fixed charge density in the cartilage can be directly linked to sodium concentration via charge balance. Sodium ions in the knee joint appear in two pools: in the synovial fluids or joint effusion where the ions are in free motion and bound within the cartilage tissue where the Na+ ions have a restricted motion. The ions in these two compartments have therefore different T1 and T2 relaxation times. The purpose of this study is to demonstrate the feasibility of a fluid-suppressed 3D ultrashort TE radial sodium sequence by implementing an inversion recovery (IR) preparation of the magnetization at 7T. This method could allow a more accurate and more sensitive quantification of loss of PG in patients with OA. It is shown that adiabatic pulses offer significantly improved performance in terms of robustness to B1 and B0 inhomogeneities when compared to the hard pulse sequence. Power deposition considerations further pose a limit to the RF inversion power, and we demonstrate in simulations and experiments how a practical compromise can be struck between clean suppression of fluid signals and power deposition levels. Two IR sequences with different types of inversion pulses (a rectangular pulse and an adiabatic pulse) were tested on a liquid phantom, ex vivo on a human knee cadaver and then in vivo on five healthy volunteers, with a (Nyquist) resolution of ∼3.6 mm and a signal-to-noise ratio of ∼30 in cartilage without IR and ∼20 with IR. Due to specific absorption rate limitations, the total acquisition time was ∼17 min for the 3D radial sequence without inversion or with the rectangular IR, and 24:30 min for the adiabatic IR sequence. It is shown that the adiabatic IR sequence generates a more uniform fluid suppression over the whole sample than the rectangular IR sequence.

Evaluation of the Subscapularis Tendon Tears on 3T Magnetic Resonance Arthrography: Comparison of Diagnostic Performance of T1-Weighted Spectral Presaturation with Inversion-Recovery and T2-Weighted Turbo Spin-Echo Sequences.

PubMed

Lee, Hoseok; Ahn, Joong Mo; Kang, Yusuhn; Oh, Joo Han; Lee, Eugene; Lee, Joon Woo; Kang, Heung Sik

2018-01-01

To compare the T1-weighted spectral presaturation with inversion-recovery sequences (T1 SPIR) with T2-weighted turbo spin-echo sequences (T2 TSE) on 3T magnetic resonance arthrography (MRA) in the evaluation of the subscapularis (SSC) tendon tear with arthroscopic findings as the reference standard. This retrospective study included 120 consecutive patients who had undergone MRA within 3 months between April and December 2015. Two musculoskeletal radiologists blinded to the arthroscopic results evaluated T1 SPIR and T2 TSE images in separate sessions for the integrity of the SSC tendon, examining normal/articular-surface partial-thickness tear (PTTa)/full-thickness tear (FTT). Diagnostic performance of T1 SPIR and T2 TSE was calculated with arthroscopic results as the reference standard, and sensitivity, specificity, and accuracy were compared using the McNemar test. Interobserver agreement was measured with kappa (κ) statistics. There were 74 SSC tendon tears (36 PTTa and 38 FTT) confirmed by arthroscopy. Significant differences were found in the sensitivity and accuracy between T1 SPIR and T2 TSE using the McNemar test, with respective rates of 95.9-94.6% vs. 71.6-75.7% and 90.8-91.7% vs. 79.2-83.3% for detecting tear; 55.3% vs. 31.6-34.2% and 85.8% vs. 78.3-79.2%, respectively, for FTT; and 91.7-97.2% vs. 58.3-61.1% and 89% vs. 78-79.3%, respectively, for PTTa. Interobserver agreement for T1 SPIR was almost perfect for T1 SPIR (κ = 0.839) and substantial for T2 TSE (κ = 0.769). T1-weighted spectral presaturation with inversion-recovery sequences is more sensitive and accurate compared to T2 TSE in detecting SSC tendon tear on 3T MRA.

Saturation-inversion-recovery: A method for T1 measurement

NASA Astrophysics Data System (ADS)

Wang, Hongzhi; Zhao, Ming; Ackerman, Jerome L.; Song, Yiqiao

2017-01-01

Spin-lattice relaxation (T1) has always been measured by inversion-recovery (IR), saturation-recovery (SR), or related methods. These existing methods share a common behavior in that the function describing T1 sensitivity is the exponential, e.g., exp(- τ /T1), where τ is the recovery time. In this paper, we describe a saturation-inversion-recovery (SIR) sequence for T1 measurement with considerably sharper T1-dependence than those of the IR and SR sequences, and demonstrate it experimentally. The SIR method could be useful in improving the contrast between regions of differing T1 in T1-weighted MRI.

Spin orientations of the spin-half Ir 4+ ions in Sr 3NiIrO 6, Sr 2IrO 4 and Na 2IrO 3: Density functional, perturbation theory and Madelung potential analyses

DOE PAGES

Gordon, Elijah E.; Xiang, Hongjun; Koehler, Jurgen; ...

2016-03-01

The spins of the low-spin Ir 4+ (S = 1/2, d 5) ions at the octahedral sites of the oxides Sr 3NiIrO 6, Sr 2IrO 4 and Na 2IrO 3 exhibit preferred orientations with respect to their IrO6 octahedra. We evaluated the magnetic anisotropies of these S = 1/2 ions on the basis of DFT calculations including spin-orbit coupling (SOC), and probed their origin by performing perturbation theory analyses with SOC as perturbation within the LS coupling scheme. The observed spin orientations of Sr 3NiIrO 6 and Sr 2IrO 4 are correctly predicted by DFT calculations, and are accounted formore » by the perturbation theory analysis. As for the spin orientation of Na 2IrO 3, both experimental studies and DFT calculations have not been unequivocal. Our analysis reveals that the Ir 4+ spin orientation of Na 2IrO 3 should have nonzero components along the c- and a-axes directions. The spin orientations determined by DFT calculations are sensitive to the accuracy of the crystal structures employed, which is explained by perturbation theory analyses when interactions between adjacent Ir 4+ ions are taken into consideration. There are indications implying that the 5d electrons of Na 2IrO 3 are less strongly localized compared with those of Sr 3NiIrO 6 and Sr 2IrO 4. This implication was confirmed by showing that the Madelung potentials of the Ir 4+ ions are less negative in Na 2IrO 3 than in Sr 3NiIrO 6, Sr 2IrO 4. Most transition-metal S = 1/2 ions do have magnetic anisotropies because the SOC induces interactions among their crystal-field split d-states, and the associated mixing of the states modifies only the orbital parts of the states. This finding cannot be mimicked by a spin Hamiltonian because this model Hamiltonian lacks the orbital degree of freedom, thereby leading to the spin-half syndrome. As a result, the spin-orbital entanglement for the 5d spin-half ions Ir 4+ is not as strong as has been assumed lately.« less

Spin orientations of the spin-half Ir4+ ions in Sr3NiIrO6, Sr2IrO4, and Na2IrO3: Density functional, perturbation theory, and Madelung potential analyses

NASA Astrophysics Data System (ADS)

Gordon, Elijah E.; Xiang, Hongjun; Köhler, Jürgen; Whangbo, Myung-Hwan

2016-03-01

The spins of the low-spin Ir4+ (S = 1/2, d5) ions at the octahedral sites of the oxides Sr3NiIrO6, Sr2IrO4, and Na2IrO3 exhibit preferred orientations with respect to their IrO6 octahedra. We evaluated the magnetic anisotropies of these S = 1/2 ions on the basis of density functional theory (DFT) calculations including spin-orbit coupling (SOC), and probed their origin by performing perturbation theory analyses with SOC as perturbation within the LS coupling scheme. The observed spin orientations of Sr3NiIrO6 and Sr2IrO4 are correctly predicted by DFT calculations, and are accounted for by the perturbation theory analysis. As for the spin orientation of Na2IrO3, both experimental studies and DFT calculations have not been unequivocal. Our analysis reveals that the Ir4+ spin orientation of Na2IrO3 should have nonzero components along the c- and a-axis directions. The spin orientations determined by DFT calculations are sensitive to the accuracy of the crystal structures employed, which is explained by perturbation theory analyses when interactions between adjacent Ir4+ ions are taken into consideration. There are indications implying that the 5d electrons of Na2IrO3 are less strongly localized compared with those of Sr3NiIrO6 and Sr2IrO4. This implication was confirmed by showing that the Madelung potentials of the Ir4+ ions are less negative in Na2IrO3 than in Sr3NiIrO6 and Sr2IrO4. Most transition-metal S = 1/2 ions do have magnetic anisotropies because the SOC induces interactions among their crystal-field split d-states, and the associated mixing of the states modifies only the orbital parts of the states. This finding cannot be mimicked by a spin Hamiltonian because this model Hamiltonian lacks the orbital degree of freedom, thereby leading to the spin-half syndrome. The spin-orbital entanglement for the 5d spin-half ions Ir4+ is not as strong as has been assumed.

Morin transition temperature in (0001)-oriented α-Fe{sub 2}O{sub 3} thin film and effect of Ir doping

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

Shimomura, Naoki, E-mail: shimomura@ecei.tohoku.ac.jp; Pati, Satya Prakash; Sato, Yuji

2015-05-07

The structural properties and Morin transition in c-plane-oriented α-Fe{sub 2}O{sub 3} and Ir-doped α-Fe{sub 2}O{sub 3} thin films have been investigated. The enhancement of the Morin transition temperature (T{sub M}) in α-Fe{sub 2}O{sub 3} film by Ir doping has been demonstrated. The T{sub M} in the c-plane-oriented α-Fe{sub 2}O{sub 3} thin film was determined from the temperature-dependent in-plane magnetization and change of coercivity (H{sub c}); this T{sub M} value was found close to that of bulk α-Fe{sub 2}O{sub 3}. The spin directions of non-doped and Ir-doped α-Fe{sub 2}O{sub 3} at room temperature were also estimated from conversion electron Mössbauer spectroscopymore » measurements. We confirmed that Ir doping dramatically enhances the T{sub M} of α-Fe{sub 2}O{sub 3} thin film.« less

The Disposition of Pt, Pd, Ir, Os, and Ru in Marine Sediments and the K/T Boundary

NASA Technical Reports Server (NTRS)

Lee, Cin-Ty; Wasserburg, Gerald; Kyte, Frank

2003-01-01

The marine record of platinum group elements (PGEs) and Os isotopic compositions provides information on different inputs of PGEs into the oceans. Some studies based on a smaller subset of the PGEs suggest that the PGEs may suffer post-depositional mobility during diagenesis. In some K/T boundary clays, Kyte and others showed that the relative abundances of Pt, Pd, Ir, and Os can differ significantly from chondritic, which is the signature expected from fallout of the meteorite impact. In some K/T boundary sections, elevated Ir concentrations are observed as far as 1 meter from the cm-thick boundary clay containing the meteoritic ejecta. The purpose of this study was to characterize Pt, Pd, Ir, Os, and Ru abundances in zones including the K/T boundary. We determined PGE abundances of boundary clays at two hemipelagic sites (Stevns Klint, Denmark and Caravaca, Spain) in which previous studies by Kyte and others showed that the Ir anomaly is confined to within a few cm. We also analyzed two pelagic Pacific sites: a boundary clay from the north Pacific (Hole 465A) characterized by a 0.5 m thick Ir anomaly and a transect across the K/T boundary from the south Pacific (Hole 596) where the Ir anomaly spans 2 m. The Stevns Klint, Caravaca, and north Pacific sites are characterized by abundant marls and limestones in the section, whereas the south Pacific site is dominated by clays. Samples were spiked with isotopic tracers, mixed with a flux, S and Ni, and equilibrated by fusion. PGEs were extracted from the Ni and analyzed on a Finnigan Element ICP-MS. We find that the narrow Caravaca and Stevns Klint boundary clays have relative PGE abundance patterns indistinguishable from chondritic values. The two Pacific sites were found to have nearly identical PGE patterns but have ratios at the peak, which differ from chondritic values as found earlier by Evans et al. The Pacific sites were found to have nearly identical PGE patterns but are extremely depleted in OS (Os/Ir = 0

Interleukins 2, 4, 7, and 15 stimulate tyrosine phosphorylation of insulin receptor substrates 1 and 2 in T cells. Potential role of JAK kinases.

PubMed

Johnston, J A; Wang, L M; Hanson, E P; Sun, X J; White, M F; Oakes, S A; Pierce, J H; O'Shea, J J

1995-12-01

The signaling molecules insulin receptor substrate (IRS)-1 and the newly described IRS-2 (4PS) molecule are major insulin and interleukin 4 (IL-4)-dependent phosphoproteins. We report here that IL-2, IL-7, and IL-15, as well as IL-4, rapidly stimulate the tyrosine phosphorylation of IRS-1 and IRS-2 in human peripheral blood T cells, NK cells, and in lymphoid cell lines. In addition, we show that the Janus kinases, JAK1 and JAK3, associate with IRS-1 and IRS-2 in T cells. Coexpression studies demonstrate that these kinases can tyrosine-phosphorylate IRS-2, suggesting a possible mechanism by which cytokine receptors may induce the tyrosine phosphorylation of IRS-1 and IRS-2. We further demonstrate that the p85 subunit of phosphoinositol 3-kinase associates with IRS-1 in response to IL-2 and IL-4 in T cells. Therefore, these data indicate that IRS-1 and IRS-2 may have important roles in T lymphocyte activation not only in response to IL-4, but also in response to IL-2, IL-7, and IL-15.

Quantitative T1 and T2* carotid atherosclerotic plaque imaging using a three-dimensional multi-echo phase-sensitive inversion recovery sequence: a feasibility study.

PubMed

Fujiwara, Yasuhiro; Maruyama, Hirotoshi; Toyomaru, Kanako; Nishizaka, Yuri; Fukamatsu, Masahiro

2018-06-01

Magnetic resonance imaging (MRI) is widely used to detect carotid atherosclerotic plaques. Although it is important to evaluate vulnerable carotid plaques containing lipids and intra-plaque hemorrhages (IPHs) using T 1 -weighted images, the image contrast changes depending on the imaging settings. Moreover, to distinguish between a thrombus and a hemorrhage, it is useful to evaluate the iron content of the plaque using both T 1 -weighted and T 2 *-weighted images. Therefore, a quantitative evaluation of carotid atherosclerotic plaques using T 1 and T 2 * values may be necessary for the accurate evaluation of plaque components. The purpose of this study was to determine whether the multi-echo phase-sensitive inversion recovery (mPSIR) sequence can improve T 1 contrast while simultaneously providing accurate T 1 and T 2 * values of an IPH. T 1 and T 2 * values measured using mPSIR were compared to values from conventional methods in phantom and in vivo studies. In the phantom study, the T 1 and T 2 * values estimated using mPSIR were linearly correlated with those of conventional methods. In the in vivo study, mPSIR demonstrated higher T 1 contrast between the IPH phantom and sternocleidomastoid muscle than the conventional method. Moreover, the T 1 and T 2 * values of the blood vessel wall and sternocleidomastoid muscle estimated using mPSIR were correlated with values measured by conventional methods and with values reported previously. The mPSIR sequence improved T 1 contrast while simultaneously providing accurate T 1 and T 2 * values of the neck region. Although further study is required to evaluate the clinical utility, mPSIR may improve carotid atherosclerotic plaque detection and provide detailed information about plaque components.

Ultrafast 2D IR microscopy

PubMed Central

Baiz, Carlos R.; Schach, Denise; Tokmakoff, Andrei

2014-01-01

We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear “one beam” geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments. PMID:25089490

Irs2 and Irs4 synergize in non-LepRb neurons to control energy balance and glucose homeostasis.

PubMed

Sadagurski, Marianna; Dong, X Charlie; Myers, Martin G; White, Morris F

2014-02-01

Insulin receptor substrates (Irs1, 2, 3 and Irs4) mediate the actions of insulin/IGF1 signaling. They have similar structure, but distinctly regulate development, growth, and metabolic homeostasis. Irs2 contributes to central metabolic sensing, partially by acting in leptin receptor (LepRb)-expressing neurons. Although Irs4 is largely restricted to the hypothalamus, its contribution to metabolic regulation is unclear because Irs4-null mice barely distinguishable from controls. We postulated that Irs2 and Irs4 synergize and complement each other in the brain. To examine this possibility, we investigated the metabolism of whole body Irs4(-/y) mice that lacked Irs2 in the CNS (bIrs2(-/-)·Irs4(-/y)) or only in LepRb-neurons (Lepr (∆Irs2) ·Irs4 (-/y) ). bIrs2(-/-)·Irs4(-/y) mice developed severe obesity and decreased energy expenditure, along with hyperglycemia and insulin resistance. Unexpectedly, the body weight and fed blood glucose levels of Lepr (∆Irs2) ·Irs4 (-/y) mice were not different from Lepr (∆Irs2) mice, suggesting that the functions of Irs2 and Irs4 converge upon neurons that are distinct from those expressing LepRb.

Effect of L1{sub 2} ordering in antiferromagnetic Ir-Mn epitaxial layer on exchange bias of FePd films

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

Chang, Y. C.; Duh, J. G., E-mail: pmami.hsiao@gmail.com, E-mail: lin.yg@nsrrc.org.tw, E-mail: jgd@mx.nthu.edu.tw; Hsiao, S. N., E-mail: pmami.hsiao@gmail.com, E-mail: lin.yg@nsrrc.org.tw, E-mail: jgd@mx.nthu.edu.tw

2015-05-07

Two series of samples of single-layer IrMn and IrMn/FePd bilayer films, deposited on a single-crystal MgO substrate at different IrMn deposition temperatures (T{sub s} = 300–700 °C), were investigated using magnetron sputtering. L1{sub 2} ordering was revealed for the 30 nm-thick IrMn epitaxial (001) films with T{sub s} ≥ 400 °C, determined by synchrotron radiation x-ray diffractometry (XRD). XRD results also provide evidence of the epitaxial growth of the IrMn films on MgO substrate. Increasing T{sub s} from 400 to 700 °C monotonically increases the ordering parameter of L1{sub 2} phases from 0.17 to 0.81. An in-plane exchange bias field (H{sub eb}) of 22 Oe is obtained in amore » 10 nm-thick FePd film that is deposited on the disordered IrMn films. As the L1{sub 2} ordering of the IrMn layers increases, the H{sub eb} gradually decreases to 0 Oe, meaning that the exchange bias behavior vanishes. The increased surface roughness, revealed by atomic force microscopy, of the epitaxial IrMn layers with increasing T{sub s} cannot be the main cause of the decrease in H{sub eb} due to the compensated surface spins regardless of the disordered and ordered (001) IrMn layers. The change of antiferromagnetic structure from the A1 to the L1{sub 2} phase was correlated with the evolution of H{sub eb}.« less

Ternary lithium stannides Li xT 3Sn 7-x ( T=Rh, Ir)

NASA Astrophysics Data System (ADS)

Sreeraj, Puravankara; Kurowski, Daniel; Hoffmann, Rolf-Dieter; Wu, Zhiyun; Pöttgen, Rainer

2005-11-01

The ternary stannides Li xRh 3Sn 7-x ( x=0.45, 0.64, 0.80) and Li xIr 3Sn 7-x ( x=0.62 and 0.66) were synthesized from the elements in sealed tantalum tubes in a water-cooled sample chamber of an induction furnace. The samples were characterized by X-ray diffraction on powders and single crystals. The stannides adopt the cubic Ir 3Ge 7-type structure (space group Im3¯m, Z=4). In this structure type the tin atoms occupy the Wyckoff positions 12 d and 16 f and form two interpenetrating frameworks consisting of cubes and square antiprisms. The rhodium and iridium atoms center the square antiprisms and are arranged in pairs. With increasing lithium substitution the lattice parameter of Ir 3Sn 7 (936.7) decreases via 932.2 pm ( x=0.62) to 931.2 pm ( x=0.66), while the Ir-Ir distance remains almost the same (290 pm). A similar trend is observed for the rhodium compounds. The lithium atoms substitute Sn on both framework sites. However, the 16 f site shows a substantially larger preference for Li occupation. This is in contrast to the isotypic magnesium based compounds.

The effects of a 2 week modified high intensity interval training program on the homeostatic model of insulin resistance (HOMA-IR) in adults with type 2 diabetes.

PubMed

Shaban, N; Kenno, K A; Milne, K J

2014-04-01

High intensity interval training (HIIT) induces similar metabolic adaptations to traditional steady state aerobic exercise training. Until recently, most HIIT studies have examined maximum efforts in healthy populations. The current study aimed to examine the effects of a 2 week modified HIIT program on the homeostatic model of insulin resistance (HOMA-IR) in individuals with type 2 diabetes (T2D). It was hypothesized that HIIT would improve HOMA-IR. Nine individuals with T2D (age=40.2±9.7 y; BMI=33.9±5.3; fasting plasma glucose [FPG]=8.7±2.9 mmol/L; HbA1C=7.3±1.2%; [mean±SD]) performed 6 individualized training sessions of HIIT (4x30 seconds at 100% of estimated maximum workload followed by 4 minutes of active rest) over 2 weeks. HOMA-IR was calculated from FPG and serum insulin and compared against a prior 2 week baseline period. Blood glucose was reduced immediately after each HIIT session (P<0.05). Anthropometrics, FPG, serum insulin, and HOMA-IR were unchanged after training. However, 6 of the 9 individuals exhibited reduced HOMA-IR values after the training period and there was a significant negative correlation between HOMA-IR value prior to training and change in HOMA-IR after HIIT. These observations tend to support the positive health benefits of HITT for individuals with T2D reported in recently published data using a modified HIIT protocol. However, they suggest that the magnitude of the disease should be assessed when examining the effects of exercise interventions in individuals with T2D.

Fast T1 and T2 mapping methods: the zoomed U-FLARE sequence compared with EPI and snapshot-FLASH for abdominal imaging at 11.7 Tesla.

PubMed

Pastor, Géraldine; Jiménez-González, María; Plaza-García, Sandra; Beraza, Marta; Reese, Torsten

2017-06-01

A newly adapted zoomed ultrafast low-angle RARE (U-FLARE) sequence is described for abdominal imaging applications at 11.7 Tesla and compared with the standard echo-plannar imaging (EPI) and snapshot fast low angle shot (FLASH) methods. Ultrafast EPI and snapshot-FLASH protocols were evaluated to determine relaxation times in phantoms and in the mouse kidney in vivo. Owing to their apparent shortcomings, imaging artefacts, signal-to-noise ratio (SNR), and variability in the determination of relaxation times, these methods are compared with the newly implemented zoomed U-FLARE sequence. Snapshot-FLASH has a lower SNR when compared with the zoomed U-FLARE sequence and EPI. The variability in the measurement of relaxation times is higher in the Look-Locker sequences than in inversion recovery experiments. Respectively, the average T1 and T2 values at 11.7 Tesla are as follows: kidney cortex, 1810 and 29 ms; kidney medulla, 2100 and 25 ms; subcutaneous tumour, 2365 and 28 ms. This study demonstrates that the zoomed U-FLARE sequence yields single-shot single-slice images with good anatomical resolution and high SNR at 11.7 Tesla. Thus, it offers a viable alternative to standard protocols for mapping very fast parameters, such as T1 and T2, or dynamic processes in vivo at high field.

Metastable Superconductivity in Two-Dimensional IrTe2 Crystals.

PubMed

Yoshida, Masaro; Kudo, Kazutaka; Nohara, Minoru; Iwasa, Yoshihiro

2018-05-09

Two-dimensional (2D) materials exhibit unusual physical and chemical properties that are attributed to the thinning-induced modification of their electronic band structure. Recently, reduced thickness was found to dramatically impact not only the static electronic structure, but also the dynamic ordering kinetics. The ordering kinetics of first-order phase transitions becomes significantly slowed with decreasing thickness, and metastable supercooled states can be realized by thinning alone. We therefore focus on layered iridium ditelluride (IrTe 2 ), a charge-ordering system that is transformed into a superconductor by suppressing its first-order transition. Here, we discovered a persistent superconducting zero-resistance state in mechanically exfoliated IrTe 2 thin flakes. The maximum superconducting critical temperature ( T c ) was identical to that which is chemically optimized, and the emergent superconductivity was revealed to have a metastable nature. The discovered robust metastable superconductivity suggests that 2D material is a new platform to induce, control, and functionalize metastable electronic states that are inaccessible in bulk crystals.

Oxidation of CO by NO on planar and faceted Ir(210)

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

Chen, Wenhua; Bartynski, Robert A.; Kaghazchi, Payam

2012-06-11

Oxidation of CO by pre-adsorbed NO has been studied on planar Ir(210) and nanofaceted Ir(210) with average facet sizes of 5 nm and 14 nm by temperature programmed desorption (TPD). Both surfaces favor oxidation of CO to CO 2, which is accompanied by simultaneous reduction of NO with high selectivity to N 2. At low NO pre-coverage, the temperature (T i) for the onset of CO 2 desorption as well as CO 2 desorption peak temperature (T p) decreases with increasing CO exposure, and NO dissociation is affected by co-adsorbed CO. At high NO pre-coverage, T i and T pmore » are independent of CO exposure, and co-adsorbed CO has no influence on dissociation of NO. Moreover, at low NO pre-coverage, planar Ir(210) is more active than faceted Ir(210) for oxidation of CO to CO 2: T i and T p are much lower on planar Ir(210) than that on faceted Ir(210). In addition, faceted Ir(210) with an average facet size of 5 nm is more active for oxidation of CO to CO 2 than faceted Ir(210) with an average facet size of 14 nm, i.e., oxidation of CO by pre-adsorbed NO on faceted Ir(210) exhibits size effects on the nanometer scale. In comparison, at low O pre-coverage planar Ir(210) is more active than faceted Ir(210) for oxidation of CO to CO 2 but no evidence has been found for size effects in oxidation of CO by pre-adsorbed oxygen on faceted Ir(210) for average facet sizes of 5 nm and 14 nm. The TPD data indicate the same reaction pathway for CO 2 formation from CO + NO and CO + O reactions on planar Ir(210). Lastly, the adsorption sites of CO, NO, O, CO + O, and CO + NO on Ir are characterized by density functional theory.« less

Tuning the giant magnetoelastic transition in Ba3BiIr2O9 and Ba3BiRu2O9

NASA Astrophysics Data System (ADS)

Huang, Zixin; Avdeev, Maxim; Kennedy, Brendan J.; Knight, Kevin S.; Zhou, Qingdi; Ling, Chris D.

2014-07-01

We have experimentally investigated the effects of pressure on the magnetoelastic transitions associated with the opening of spin-gaps in Ba3BiIr2O9 and Ba3BiRu2O9. For both compounds, reducing the unit cell volume by either external physical and internal chemical pressure was found to reduce the temperature T* of the transition and, to a lesser extent, the magnitude of the associated negative thermal volume expansion. The results yield the latent heat associated with the transitions, -3.34(3) × 102 J mol-1 for Ba3BiIr2O9 and -7.1(5) × 102 J mol-1 for Ba3BiRu2O9. The transition in Ba3BiRu2O9 is significantly more robust than in Ba3BiIr2O9, requiring an order of magnitude higher pressures to achieve the same reduction in T*. The differing responses of the two compounds points to differences between the 4d and 5d metals and hence to the importance of spin-orbit coupling, which is expected to be much stronger in the Ir compound.

[Variation of insulin receptor substrate-2 gene 3'-untranslated region in patients with type 2 diabetes mellitus].

PubMed

Zeng, Wei-Min; Chen, Shu-Hua; Xie, Ping; Liu, Mei-Lian; Song, Hui-Ping

2003-08-01

Insulin receptor substrate-2(IRS-2) belongs to a family of cytoplasmic adaptor proteins, which link insulin, insulin-like growth factor-1(IGF-1), and cytokine receptor tyrosine kinases to signaling pathways regulating metabolism, growth, differentiation, reproduction, and homestasis. Deficiency of IRS-2 in mice causes type 2 diabetes mellitus (T2DM), suggesting that abnormal structure and dysfunction of the IRS-2 gene may contribute to the pathogenesis of T2DM. Variations in the open reading frame (ORF) and promoter region of IRS-2 gene in patients with T2DM have been reported over the past few years. These genetic variations are from ethnically different patients, confounding any analysis of the contribution of IRS-2 gene variations to the development of T2DM. The 3'-untranslated region(3'-UTR) of IRS-2 gene variation may be contribute to the T2DM. So far, the relationship between 3'-UTR of IRS-2 gene variations and T2DM have not been investigated. Based on the 3'-UTR of eukaryotic gene plays an important role in the eukaryotic gene regulation, we investigated abnormalities of IRS-2 gene 3'-UTR and their relation with T2DM in the Chinese population. Genomic DNA was extracted from leukocyte of 128 patients with T2DM and 125 control subjects in Hunan, China. A segment of IRS-2 gene 3'-UTR was scanned by polymerase chain reaction (PCR)-denaturing high-performance liquid chromatography (DHPLC). All PCR products with abnormal DHPLC pattern were submitted to DNA sequence analysis. A T-->C mutation at 4064 bp of IRS-2 gene 3'-UTR was found in 18 patients with T2DM, while it was only found in 5 control subjects. The incidence of the mutation in patients with T2DM were much higher than that in contol subjects (14.1% vs 4.0%, x2 = 7.748, P = 0.005). These results indicate that the T4064-->C in IRS-2 gene 3'-UTR may be related to Chinese patients with T2DM.

Non-peptidergic small diameter primary afferents expressing VGluT2 project to lamina I of mouse spinal dorsal horn

PubMed Central

2011-01-01

Background Unmyelinated primary afferent nociceptors are commonly classified into two main functional types: those expressing neuropeptides, and non-peptidergic fibers that bind the lectin IB4. However, many small diameter primary afferent neurons neither contain any known neuropeptides nor bind IB4. Most express high levels of vesicular glutamate transporter 2 (VGluT2) and are assumed to be glutamatergic nociceptors but their terminations within the spinal cord are unknown. We used in vitro anterograde axonal tracing with Neurobiotin to identify the central projections of these putative glutamatergic nociceptors. We also quantitatively characterised the spatial arrangement of these terminals with respect to those that expressed the neuropeptide, calcitonin gene-related peptide (CGRP). Results Neurobiotin-labeled VGluT2-immunoreactive (IR) terminals were restricted to lamina I, with a medial-to-lateral distribution similar to CGRP-IR terminals. Most VGluT2-IR terminals in lateral lamina I were not labeled by Neurobiotin implying that they arose mainly from central neurons. 38 ± 4% of Neurobiotin-labeled VGluT2-IR terminals contained CGRP-IR. Conversely, only 17 ± 4% of Neurobiotin-labeled CGRP-IR terminals expressed detectable VGluT2-IR. Neurobiotin-labeled VGluT2-IR or CGRP-IR terminals often aggregated into small clusters or microdomains partially surrounding intrinsic lamina I neurons. Conclusions The central terminals of primary afferents which express high levels of VGluT2-IR but not CGRP-IR terminate mainly in lamina I. The spatial arrangement of VGluT2-IR and CGRP-IR terminals suggest that lamina I neurons receive convergent inputs from presumptive nociceptors that are primarily glutamatergic or peptidergic. This reveals a previously unrecognized level of organization in lamina I consistent with the presence of multiple nociceptive processing pathways. PMID:22152428

Magnetic structure of the antiferromagnetic Kondo lattice compounds CeRhAl 4Si 2 and CeIrAl 4Si 2

DOE PAGES

Ghimire, N. J.; Calder, S.; Janoschek, M.; ...

2015-06-01

In this article, we have investigated the magnetic ground state of the antiferromagnetic Kondo-lattice compounds CeMAl 4Si 2(M = Rh, Ir) using neutron powder diffraction. Although both of these compounds show two magnetic transitions T N1 and T N2 in the bulk properties measurements, evidence for magnetic long-range order was only found below the lower transition T N2. Analysis of the diffraction profiles reveals a commensurate antiferromagnetic structure with a propagation vector k = (0, 0, 1/2). The magnetic moment in the ordered state of CeRhAl 4Si 2 and CeIrAl 4Si 2 were determined to be 1.14(2) and 1.41(3) μB/Ce,more » respectively, and are parallel to the crystallographic c-axis in agreement with magnetic susceptibility measurements.« less

2D and 3D T2-weighted MR sequences for the assessment of neurovascular bundle changes after nerve-sparing radical retropubic prostatectomy with erectile function correlation.

PubMed

Panebianco, Valeria; Sciarra, Alessandro; Osimani, Marcello; Lisi, Danilo; Ciccariello, Mauro; Salciccia, Stefano; Gentile, Vincenzo; Di Silverio, Franco; Passariello, Roberto

2009-01-01

The aim of this study was to assess the capability of a 3D isotropic MRI T2-weighted sequence (3D T2 ISO) in the depiction of changes of neurovascular bundles (NVBs) after bilateral nerve-sparing radical retropubic prostatectomy (RRP). Furthermore, our aim was also to introduce a new MRI classification score of the NVB alteration patterns using the International Index Erectile Function Five-Item (IIEF-5) score as standard of reference. Fifty-three consecutive patients were postoperatively submitted to two MR examinations, including both 2D TSE T2-weighted (2D T2) and 3D T2 ISO sequences. Image findings were scored using a relative five-point classification and correlated with the postoperative IIEF-5 score. Radiologists attributed 13.2% of patients to class 0, 11.3% to class I, 34% to class II, 24.5% to class III, and 16.9% to class IV. With 3D T2 ISO images, the same radiologists determined 43.3% class 0, 32% class I, 11.4% class II, 7.5% class III, and 5.7% class IV. In all cases, the correlation and regression analysis between the 3D T2 ISO and IIEF-5 score resulted in higher coefficients values. The 3D sequence correlated most closely with patients' grading of erectile function.

Tuning the giant magnetoelastic transition in Ba3BiIr2O9 and Ba3BiRu2O9.

PubMed

Huang, Zixin; Avdeev, Maxim; Kennedy, Brendan J; Knight, Kevin S; Zhou, Qingdi; Ling, Chris D

2014-07-09

We have experimentally investigated the effects of pressure on the magnetoelastic transitions associated with the opening of spin-gaps in Ba3BiIr2O9 and Ba3BiRu2O9. For both compounds, reducing the unit cell volume by either external physical and internal chemical pressure was found to reduce the temperature T(*) of the transition and, to a lesser extent, the magnitude of the associated negative thermal volume expansion. The results yield the latent heat associated with the transitions, -3.34(3) × 10(2) J mol(-1) for Ba3BiIr2O9 and -7.1(5) × 10(2) J mol(-1) for Ba3BiRu2O9. The transition in Ba3BiRu2O9 is significantly more robust than in Ba3BiIr2O9, requiring an order of magnitude higher pressures to achieve the same reduction in T(*). The differing responses of the two compounds points to differences between the 4d and 5d metals and hence to the importance of spin-orbit coupling, which is expected to be much stronger in the Ir compound.

MRI of the lumbar spine: comparison of 3D isotropic turbo spin-echo SPACE sequence versus conventional 2D sequences at 3.0 T.

PubMed

Lee, Sungwon; Jee, Won-Hee; Jung, Joon-Yong; Lee, So-Yeon; Ryu, Kyeung-Sik; Ha, Kee-Yong

2015-02-01

Three-dimensional (3D) fast spin-echo sequence with variable flip-angle refocusing pulse allows retrospective alignments of magnetic resonance imaging (MRI) in any desired plane. To compare isotropic 3D T2-weighted (T2W) turbo spin-echo sequence (TSE-SPACE) with standard two-dimensional (2D) T2W TSE imaging for evaluating lumbar spine pathology at 3.0 T MRI. Forty-two patients who had spine surgery for disk herniation and had 3.0 T spine MRI were included in this study. In addition to standard 2D T2W TSE imaging, sagittal 3D T2W TSE-SPACE was obtained to produce multiplanar (MPR) images. Each set of MR images from 3D T2W TSE and 2D TSE-SPACE were independently scored for the degree of lumbar neural foraminal stenosis, central spinal stenosis, and nerve compression by two reviewers. These scores were compared with operative findings and the sensitivities were evaluated by McNemar test. Inter-observer agreements and the correlation with symptoms laterality were assessed with kappa statistics. The 3D T2W TSE and 2D TSE-SPACE had similar sensitivity in detecting foraminal stenosis (78.9% versus 78.9% in 32 foramen levels), spinal stenosis (100% versus 100% in 42 spinal levels), and nerve compression (92.9% versus 81.8% in 59 spinal nerves). The inter-observer agreements (κ = 0.849 vs. 0.451 for foraminal stenosis, κ = 0.809 vs. 0.503 for spinal stenosis, and κ = 0.681 vs. 0.429 for nerve compression) and symptoms correlation (κ = 0.449 vs. κ = 0.242) were better in 3D TSE-SPACE compared to 2D TSE. 3D TSE-SPACE with oblique coronal MPR images demonstrated better inter-observer agreements compared to 3D TSE-SPACE without oblique coronal MPR images (κ = 0.930 vs. κ = 0.681). Isotropic 3D T2W TSE-SPACE at 3.0 T was comparable to 2D T2W TSE for detecting foraminal stenosis, central spinal stenosis, and nerve compression with better inter-observer agreements and symptom correlation. © The Foundation Acta Radiologica 2014 Reprints and

tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.

PubMed

Abe, Takashi; Inokuchi, Hachiro; Yamada, Yuko; Muto, Akira; Iwasaki, Yuki; Ikemura, Toshimichi

2014-01-01

The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

VizieR Online Data Catalog: FIR data of IR-bright dust-obscured galaxies (DOGs) (Toba+, 2017)

NASA Astrophysics Data System (ADS)

Toba, Y.; Nagao, T.; Wang, W.-H.; Matsuhara, H.; Akiyama, M.; Goto, T.; Koyama, Y.; Ohyama, Y.; Yamamura, I.

2017-11-01

We investigate the star-forming activity of a sample of infrared (IR)-bright dust-obscured galaxies (DOGs) that show an extreme red color in the optical and IR regime, (i-[22])AB>7.0. Combining an IR-bright DOG sample with the flux at 22μm>3.8mJy discovered by Toba & Nagao (2016ApJ...820...46T) with the IRAS faint source catalog version 2 and AKARI far-IR (FIR) all-sky survey bright source catalog version 2, we selected 109 DOGs with FIR data. For a subsample of seven IR-bright DOGs with spectroscopic redshifts (0.07IR luminosity, star formation rate (SFR), and stellar mass based on the spectral energy distribution fitting. We found that (1) the WISE 22μm luminosity at the observed frame is a good indicator of IR luminosity for IR-bright DOGs and (2) the contribution of the active galactic nucleus to IR luminosity increases with IR luminosity. By comparing the stellar mass and SFR relation for our DOG sample and the literature, we found that most of the IR-bright DOGs lie significantly above the main sequence of star-forming galaxies at similar redshift, indicating that the majority of IRAS- or AKARI-detected IR-bright DOGs are starburst galaxies. (1 data file).

A Q-switched Ho:YAG laser assisted nanosecond time-resolved T-jump transient mid-IR absorbance spectroscopy with high sensitivity

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

Li, Deyong; Li, Yunliang; Li, Hao

2015-05-15

Knowledge of dynamical structure of protein is an important clue to understand its biological function in vivo. Temperature-jump (T-jump) time-resolved transient mid-IR absorbance spectroscopy is a powerful tool in elucidating the protein dynamical structures and the folding/unfolding kinetics of proteins in solution. A home-built setup of T-jump time-resolved transient mid-IR absorbance spectroscopy with high sensitivity is developed, which is composed of a Q-switched Cr, Tm, Ho:YAG laser with an output wavelength at 2.09 μm as the T-jump heating source, and a continuous working CO laser tunable from 1580 to 1980 cm{sup −1} as the IR probe. The results demonstrate thatmore » this system has a sensitivity of 1 × 10{sup −4} ΔOD for a single wavelength detection, and 2 × 10{sup −4} ΔOD for spectral detection in amide I′ region, as well as a temporal resolution of 20 ns. Moreover, the data quality coming from the CO laser is comparable to the one using the commercial quantum cascade laser.« less

Inhibition of PTP1B Restores IRS1-Mediated Hepatic Insulin Signaling in IRS2-Deficient Mice

PubMed Central

González-Rodríguez, Águeda; Gutierrez, Jose A. Mas; Sanz-González, Silvia; Ros, Manuel; Burks, Deborah J.; Valverde, Ángela M.

2010-01-01

OBJECTIVE Mice with complete deletion of insulin receptor substrate 2 (IRS2) develop hyperglycemia, impaired hepatic insulin signaling, and elevated gluconeogenesis, whereas mice deficient for protein tyrosine phosphatase (PTP)1B display an opposing hepatic phenotype characterized by increased sensitivity to insulin. To define the relationship between these two signaling pathways in the regulation of liver metabolism, we used genetic and pharmacological approaches to study the effects of inhibiting PTP1B on hepatic insulin signaling and expression of gluconeogenic enzymes in IRS2−/− mice. RESEARCH DESIGN AND METHODS We analyzed glucose homeostasis and insulin signaling in liver and isolated hepatocytes from IRS2−/− and IRS2−/−/PTP1B−/− mice. Additionally, hepatic insulin signaling was assessed in control and IRS2−/− mice treated with resveratrol, an antioxidant present in red wine. RESULTS In livers of hyperglycemic IRS2−/− mice, the expression levels of PTP1B and its association with the insulin receptor (IR) were increased. The absence of PTP1B in the double-mutant mice restored hepatic IRS1-mediated phosphatidylinositol (PI) 3-kinase/Akt/Foxo1 signaling. Moreover, resveratrol treatment of hyperglycemic IRS2−/− mice decreased hepatic PTP1B mRNA and inhibited PTP1B activity, thereby restoring IRS1-mediated PI 3-kinase/Akt/Foxo1 signaling and peripheral insulin sensitivity. CONCLUSIONS By regulating the phosphorylation state of IR, PTB1B determines sensitivity to insulin in liver and exerts a unique role in the interplay between IRS1 and IRS2 in the modulation of hepatic insulin action. PMID:20028942

IRS-1 activates phosphatidylinositol 3'-kinase by associating with src homology 2 domains of p85.

PubMed Central

Myers, M G; Backer, J M; Sun, X J; Shoelson, S; Hu, P; Schlessinger, J; Yoakim, M; Schaffhausen, B; White, M F

1992-01-01

IRS-1 is an insulin receptor substrate that undergoes tyrosine phosphorylation and associates with the phosphatidylinositol (PtdIns) 3'-kinase immediately after insulin stimulation. Recombinant IRS-1 protein was tyrosine phosphorylated by the insulin receptor in vitro and associated with the PtdIns 3'-kinase from lysates of quiescent 3T3 fibroblasts. Bacterial fusion proteins containing the src homology 2 domains (SH2 domains) of the 85-kDa subunit (p85) of the PtdIns 3'-kinase bound quantitatively to tyrosine phosphorylated, but not unphosphorylated, IRS-1, and this association was blocked by phosphotyrosine-containing synthetic peptides. Moreover, the phosphorylated peptides and the SH2 domains each inhibited binding of PtdIns 3'-kinase to IRS-1. Phosphorylated IRS-1 activated PtdIns 3'-kinase in anti-p85 immunoprecipitates in vitro, and this activation was blocked by SH2 domain fusion proteins. These data suggest that the interaction between PtdIns 3'-kinase and IRS-1 is mediated by tyrosine phosphorylated motifs on IRS-1 and the SH2 domains of p85, and IRS-1 activates PtdIns 3'-kinase by binding to the SH2 domains of p85. Thus, IRS-1 likely serves to transmit the insulin signal by binding and regulating intracellular enzymes containing SH2 domains. Images PMID:1332046

Anisotropic antiferromagnetic order in the spin-orbit coupled trigonal-lattice Ca2Sr2IrO6

NASA Astrophysics Data System (ADS)

Sheng, Jieming; Ye, Feng; Hoffmann, Christina; Cooper, Valentino R.; Okamoto, Satoshi; Terzic, Jasminka; Zheng, Hao; Zhao, Hengdi; Cao, G.

2018-06-01

We used single-crystal x-ray and neutron diffraction to investigate the crystal and magnetic structures of trigonal lattice iridate Ca2Sr2IrO6 . The crystal structure is determined to be R 3 ¯ with two distinct Ir sites. The system exhibits long-range antiferromagnetic order below TN=13.1 K. The magnetic wave vector is identified as (0,0.5,1) with ferromagnetic coupling along the a axis and antiferromagnetic correlation along the b axis. Spins align dominantly within the basal plane along the [1,2,0] direction and tilt 34∘ toward the c axis. The ordered moment is 0.66(3) μB/Ir, larger than other iridates where iridium ions form corner- or edge-sharing IrO6 octahedral networks. The tilting angle is reduced to ≈19∘ when a magnetic field of 4.9 T is applied along the c axis. Density functional theory calculations confirm that the experimentally determined magnetic configuration is the most probable ground state with an insulating gap ˜0.5 eV.

SH2-B promotes insulin receptor substrate 1 (IRS1)- and IRS2-mediated activation of the phosphatidylinositol 3-kinase pathway in response to leptin.

PubMed

Duan, Chaojun; Li, Minghua; Rui, Liangyou

2004-10-15

Leptin regulates energy homeostasis primarily by binding and activating its long form receptor (LRb). Deficiency of either leptin or LRb causes morbid obesity. Leptin stimulates LRb-associated JAK2, thus initiating multiple pathways including the Stat3 and phosphatidylinositol (PI) 3-kinase pathways that mediate leptin biological actions. Here we report that SH2-B, a JAK2-interacting protein, promotes activation of the PI 3-kinase pathway by recruiting insulin receptor substrate 1 (IRS1) and IRS2 in response to leptin. SH2-B directly bound, via its PH and SH2 domain, to both IRS1 and IRS2 both in vitro and in intact cells and mediated formation of a JAK2/SH2-B/IRS1 or IRS2 tertiary complex. Consequently, SH2-B dramatically enhanced leptin-stimulated tyrosine phosphorylation of IRS1 and IRS2 in HEK293 cells stably expressing LRb, thus promoting association of IRS1 and IRS2 with the p85 regulatory subunit of PI 3-kinase and phosphorylation and activation of Akt. SH2-B mutants with lower affinity for IRS1 and IRS2 exhibited reduced ability to promote association of JAK2 with IRS1, tyrosine phosphorylation of IRS1, and association of IRS1 with p85 in response to leptin. Moreover, deletion of the SH2-B gene impaired leptin-stimulated tyrosine phosphorylation of endogenous IRS1 in mouse embryonic fibroblasts (MEF), which was reversed by reintroduction of SH2-B. Similarly, SH2-B promoted growth hormone-stimulated tyrosine phosphorylation of IRS1 in both HEK293 and MEF cells. Our data suggest that SH2-B is a novel mediator of the PI 3-kinase pathway in response to leptin or other hormones and cytokines that activate JAK2.

Isotropic and anisotropic regimes of the field-dependent spin dynamics in Sr 2 IrO 4 : Raman scattering studies

DOE PAGES

Gim, Y.; Sethi, A.; Zhao, Q.; ...

2016-01-11

A major focus of experimental interest in Sr 2IrO 4 has been to clarify how the magnetic excitations of this strongly spin-orbit coupled system differ from the predictions of an isotropic 2D spin-1/2 Heisenberg model and to explore the extent to which strong spin-orbit coupling affects the magnetic properties of iridates. Here, we present a high-resolution inelastic light (Raman) scattering study of the low energy magnetic excitation spectrum of Sr 2IrO 4 and doped Eu-doped Sr 2IrO 4 as functions of both temperature and applied magnetic field. We show that the high-field (H > 1.5 T) in-plane spin dynamics ofmore » Sr 2IrO 4 are isotropic and governed by the interplay between the applied field and the small in-plane ferromagnetic spin components induced by the Dzyaloshinskii-Moriya interaction. However, the spin dynamics of Sr 2IrO 4 at lower fields (H < 1.5 T) exhibit important effects associated with interlayer coupling and in-plane anisotropy, including a spin-flop transition at Hc in Sr 2IrO 4 that occurs either discontinuously or via a continuous rotation of the spins, depending upon the in-plane orientation of the applied field. Furthermore, these results show that in-plane anisotropy and interlayer coupling effects play important roles in the low-field magnetic and dynamical properties of Sr 2IrO 4.« less

Epitaxial growth of iridate pyrochlore Nd 2Ir 2O 7 films

DOE PAGES

Gallagher, J. C.; Esser, B. D.; Morrow, R.; ...

2016-02-29

Epitaxial films of the pyrochlore Nd 2Ir 2O 7 have been grown on (111)-oriented yttria-stabilized zirconia (YSZ) substrates by off-axis sputtering followed by post-growth annealing. X-ray diffraction (XRD) results demonstrate phase-pure epitaxial growth of the pyrochlore films on YSZ. Scanning transmission electron microscopy (STEM) investigation of an Nd 2Ir 2O 7 film with a short post-annealing provides insight into the mechanism for crystallization of Nd 2Ir 2O 7 during the post-annealing process. STEM images reveal clear pyrochlore ordering of Nd and Ir in the films. As a result, the epitaxial relationship between the YSZ and Nd 2Ir 2O 7 ismore » observed clearly while some interfacial regions show a thin region with polycrystalline Ir nanocrystals.« less

Tanshinone I alleviates insulin resistance in type 2 diabetes mellitus rats through IRS-1 pathway.

PubMed

Wei, Ying; Gao, Jiaqi; Qin, Lingling; Xu, Yunling; Wang, Dongchao; Shi, Haoxia; Xu, Tunhai; Liu, Tonghua

2017-09-01

Tanshinone I from tanshen has been used in traditional Chinese medicine for treating cardiovascular diseases and inflammatory diseases. Given the link between inflammation and Type 2 diabetes mellitus (T2DM), we suspect that tanshinone I may have a beneficial effect on T2DM. This study was to investigate the potential effects of tanshinone I on T2DM and its underlying mechanism. T2DM was thus induced in Sprague-Dawley (SD) rats using streptozotocin (STZ) and high-fat diet. It was observed that T2DM rats had higher levels of total cholesterol (TC), nonesterified fatty acids (NEFAs), total triglyceride (TG) and total low density lipoprotein cholesterol (LDL-C) compared with normal, healthy SD rats. Treatment with tanshinone I decreased these levels and lowered blood glucose level in T2DM rats. In addition, enzyme-linked immunosorbent assay (ELISA) analysis showed that T2DM rats had elevated levels of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). Furthermore, Western blot analysis revealed that T2DM rats had enhanced nuclear translocation of NF-κB as well as elevated phosphorylation of Ser307 in IRS-1(insulin receptor substrate 1). Treatment by tanshinone I lowered the levels of IL-6 and TNF-α, decreased nuclear translocation of NF-κB as well as phosphorylation of Ser307 in IRS-1. These results demonstrated that tanshinone I could alleviate T2DM syndrome in rats. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Long T2 suppression in native lung 3-D imaging using k-space reordered inversion recovery dual-echo ultrashort echo time MRI.

PubMed

Gai, Neville D; Malayeri, Ashkan A; Bluemke, David A

2017-08-01

Long T2 species can interfere with visualization of short T2 tissue imaging. For example, visualization of lung parenchyma can be hindered by breathing artifacts primarily from fat in the chest wall. The purpose of this work was to design and evaluate a scheme for long T2 species suppression in lung parenchyma imaging using 3-D inversion recovery double-echo ultrashort echo time imaging with a k-space reordering scheme for artifact suppression. A hyperbolic secant (HS) pulse was evaluated for different tissues (T1/T2). Bloch simulations were performed with the inversion pulse followed by segmented UTE acquisition. Point spread function (PSF) was simulated for a standard interleaved acquisition order and a modulo 2 forward-reverse acquisition order. Phantom and in vivo images (eight volunteers) were acquired with both acquisition orders. Contrast to noise ratio (CNR) was evaluated in in vivo images prior to and after introduction of the long T2 suppression scheme. The PSF as well as phantom and in vivo images demonstrated reduction in artifacts arising from k-space modulation after using the reordering scheme. CNR measured between lung and fat and lung and muscle increased from -114 and -148.5 to +12.5 and 2.8 after use of the IR-DUTE sequence. Paired t test between the CNRs obtained from UTE and IR-DUTE showed significant positive change (p < 0.001 for lung-fat CNR and p = 0.03 for lung-muscle CNR). Full 3-D lung parenchyma imaging with improved positive contrast between lung and other long T2 tissue types can be achieved robustly in a clinically feasible time using IR-DUTE with image subtraction when segmented radial acquisition with k-space reordering is employed.

HOMA1-IR and HOMA2-IR indexes in identifying insulin resistance and metabolic syndrome: Brazilian Metabolic Syndrome Study (BRAMS).

PubMed

Geloneze, Bruno; Vasques, Ana Carolina Junqueira; Stabe, Christiane França Camargo; Pareja, José Carlos; Rosado, Lina Enriqueta Frandsen Paez de Lima; Queiroz, Elaine Cristina de; Tambascia, Marcos Antonio

2009-03-01

To investigate cut-off values for HOMA1-IR and HOMA2-IR to identify insulin resistance (IR) and metabolic syndrome (MS), and to assess the association of the indexes with components of the MS. Nondiabetic subjects from the Brazilian Metabolic Syndrome Study were studied (n = 1,203, 18 to 78 years). The cut-off values for IR were determined from the 90th percentile in the healthy group (n = 297) and, for MS, a ROC curve was generated for the total sample. In the healthy group, HOMA-IR indexes were associated with central obesity, triglycerides and total cholesterol (p < 0.001). The cut-off values for IR were: HOMA1-IR > 2.7 and HOMA2-IR > 1.8; and, for MS were: HOMA1-IR > 2.3 (sensitivity: 76.8%; specificity: 66.7%) and HOMA2-IR > 1.4 (sensitivity: 79.2%; specificity: 61.2%). The cut-off values identified for HOMA1-IR and HOMA2-IR indexes have a clinical and epidemiological application for identifying IR and MS in Westernized admixtured multi-ethnic populations.

Upconversion of the mid-IR pulses to the near-IR in LiGaS2

NASA Astrophysics Data System (ADS)

Kato, Kiyoshi; Umemura, Nobuhiro; Okamoto, Takuya; Petrov, Valentin

2018-02-01

This paper reports on the phase-matching properties of LiGaS2 for upconverting a Nd:YAG laser-pumped KTP and AgGaS2 optical parametric oscillator (OPO) at mid-IR to the near-IR by mixing with its pump source together with the new Sellmeier equations that provide a good reproduction of the present experimental results as well as the published data points of second-harmonic generation (SHG) and sum-frequency generation (SFG) of a CO2 laser, a Ti:Al2O3 laser-pumped optical parametric amplifier (OPA), and a Nd:YAG laser-pumped OPO in the mid-IR. This index formula gives the important information that group velocity mismatch (GVM) (Δsp = 1/υs - 1/υp) of LiGaS2 in the 4 - 11 μm range is 12 27 fs/mm lower than that of the widely used LiInS2, which makes it ideal for the upconversion of the mid-IR femtosecond pulses having large spectral bandwidths to the near-IR.

Spin orientations of the spin-half Ir{sup 4+} ions in Sr{sub 3}NiIrO{sub 6}, Sr{sub 2}IrO{sub 4}, and Na{sub 2}IrO{sub 3}: Density functional, perturbation theory, and Madelung potential analyses

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

Gordon, Elijah E.; Whangbo, Myung-Hwan, E-mail: mike-whangbo@ncsu.edu; Xiang, Hongjun

2016-03-21

The spins of the low-spin Ir{sup 4+} (S = 1/2, d{sup 5}) ions at the octahedral sites of the oxides Sr{sub 3}NiIrO{sub 6}, Sr{sub 2}IrO{sub 4}, and Na{sub 2}IrO{sub 3} exhibit preferred orientations with respect to their IrO{sub 6} octahedra. We evaluated the magnetic anisotropies of these S = 1/2 ions on the basis of density functional theory (DFT) calculations including spin-orbit coupling (SOC), and probed their origin by performing perturbation theory analyses with SOC as perturbation within the LS coupling scheme. The observed spin orientations of Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4} are correctly predicted by DFT calculations,more » and are accounted for by the perturbation theory analysis. As for the spin orientation of Na{sub 2}IrO{sub 3}, both experimental studies and DFT calculations have not been unequivocal. Our analysis reveals that the Ir{sup 4+} spin orientation of Na{sub 2}IrO{sub 3} should have nonzero components along the c- and a-axis directions. The spin orientations determined by DFT calculations are sensitive to the accuracy of the crystal structures employed, which is explained by perturbation theory analyses when interactions between adjacent Ir{sup 4+} ions are taken into consideration. There are indications implying that the 5d electrons of Na{sub 2}IrO{sub 3} are less strongly localized compared with those of Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4}. This implication was confirmed by showing that the Madelung potentials of the Ir{sup 4+} ions are less negative in Na{sub 2}IrO{sub 3} than in Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4}. Most transition-metal S = 1/2 ions do have magnetic anisotropies because the SOC induces interactions among their crystal-field split d-states, and the associated mixing of the states modifies only the orbital parts of the states. This finding cannot be mimicked by a spin Hamiltonian because this model Hamiltonian lacks the orbital degree of freedom, thereby leading to the spin

Study of (n,2n) reaction on 191,193Ir isotopes and isomeric cross section ratios

NASA Astrophysics Data System (ADS)

Vlastou, R.; Kalamara, A.; Kokkoris, M.; Patronis, N.; Serris, M.; Georgoulakis, M.; Hassapoglou, S.; Kobothanasis, K.; Axiotis, M.; Lagoyannis, A.

2017-09-01

The cross section of 191Ir(n,2n)190Irg+m1 and 191Ir(n,2n)190Irm2 reactions has been measured at 17.1 and 20.9 MeV neutron energies at the 5.5 MV tandem T11/25 Accelerator Laboratory of NCSR "Demokritos", using the activation method. The neutron beams were produced by means of the 3H(d,n)4He reaction at a flux of the order of 2 × 105 n/cm2s. The neutron flux has been deduced implementing the 27Al(n,α) reaction, while the flux variation of the neutron beam was monitored by using a BF3 detector. The 193Ir(n,2n)192Ir reaction cross section has also been determined, taking into account the contribution from the contaminant 191Ir(n,γ)192Ir reaction. The correction method is based on the existing data in ENDF for the contaminant reaction, convoluted with the neutron spectra which have been extensively studied by means of simulations using the NeusDesc and MCNP codes. Statistical model calculations using the code EMPIRE 3.2.2 and taking into account pre-equilibrium emission, have been performed on the data measured in this work as well as on data reported in literature.

Can T1 w/T2 w ratio be used as a myelin-specific measure in subcortical structures? Comparisons between FSE-based T1 w/T2 w ratios, GRASE-based T1 w/T2 w ratios and multi-echo GRASE-based myelin water fractions.

PubMed

Uddin, Md Nasir; Figley, Teresa D; Marrie, Ruth Ann; Figley, Chase R

2018-03-01

Given the growing popularity of T 1 -weighted/T 2 -weighted (T 1 w/T 2 w) ratio measurements, the objective of the current study was to evaluate the concordance between T 1 w/T 2 w ratios obtained using conventional fast spin echo (FSE) versus combined gradient and spin echo (GRASE) sequences for T 2 w image acquisition, and to compare the resulting T 1 w/T 2 w ratios with histologically validated myelin water fraction (MWF) measurements in several subcortical brain structures. In order to compare these measurements across a relatively wide range of myelin concentrations, whole-brain T 1 w magnetization prepared rapid acquisition gradient echo (MPRAGE), T 2 w FSE and three-dimensional multi-echo GRASE data were acquired from 10 participants with multiple sclerosis at 3 T. Then, after high-dimensional, non-linear warping, region of interest (ROI) analyses were performed to compare T 1 w/T 2 w ratios and MWF estimates (across participants and brain regions) in 11 bilateral white matter (WM) and four bilateral subcortical grey matter (SGM) structures extracted from the JHU_MNI_SS 'Eve' atlas. Although the GRASE sequence systematically underestimated T 1 w/T 2 w values compared to the FSE sequence (revealed by Bland-Altman and mountain plots), linear regressions across participants and ROIs revealed consistently high correlations between the two methods (r 2 = 0.62 for all ROIs, r 2 = 0.62 for WM structures and r 2 = 0.73 for SGM structures). However, correlations between either FSE-based or GRASE-based T 1 w/T 2 w ratios and MWFs were extremely low in WM structures (FSE-based, r 2 = 0.000020; GRASE-based, r 2 = 0.0014), low across all ROIs (FSE-based, r 2 = 0.053; GRASE-based, r 2 = 0.029) and moderate in SGM structures (FSE-based, r 2 = 0.20; GRASE-based, r 2 = 0.17). Overall, our findings indicated a high degree of correlation (but not equivalence) between FSE-based and GRASE-based T 1 w/T 2 w ratios, and low correlations between T 1 w/T 2 w ratios and MWFs. This

Volatility-dependent 2D IR correlation analysis of traditional Chinese medicine ‘Red Flower Oil’ preparation from different manufacturers

NASA Astrophysics Data System (ADS)

Wu, Yan-Wen; Sun, Su-Qin; Zhou, Qun; Tao, Jia-Xun; Noda, Isao

2008-06-01

As a traditional Chinese medicine (TCM), 'Red Flower Oil' preparation is widely used as a household remedy in China and Southeast Asia. Usually, the preparation is a mixture of several plant essential oils with different volatile features, such as wintergreen oil, turpentine oil and clove oil. The proportions of these plant essential oils in 'Red Flower Oil' vary from different manufacturers. Thus, it is important to develop a simple and rapid evaluation method for quality assurance of the preparations. Fourier transform infrared (FT-IR) was applied and two-dimensional correlation infrared spectroscopy (2D IR) based on the volatile characteristic of samples was used to enhance the resolution of FT-IR spectra. 2D IR technique could, not only easily provide the composition and their volatile sequences in 'Red flower Oil' preparations, but also rapidly discriminate the subtle differences in products from different manufacturers. Therefore, FT-IR combined with volatility-dependent 2D IR correlation analysis provides a very fast and effective method for the quality control of essential oil mixtures in TCM.

Complete genome sequence of Hippea maritima type strain (MH2T)

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

Huntemann, Marcel; Lu, Megan; Nolan, Matt

2011-01-01

Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- nus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genesmore » consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Bulk electronic structure of non-centrosymmetric EuTGe 3 (T=Co, Ni, Rh, Ir) studied by hard x-ray photoelectron spectroscopy

DOE PAGES

Utsumi, Yuki; Kasinathan, Deepa; Swatek, Przemys?aw; ...

2018-03-15

Non-centrosymmetric EuTGe 3 ( T = Co, Ni, Rh, and Ir) possesses magnetic Eu 2+ ions, and antiferromagnetic ordering appears at low temperatures. Transition-metal substitution leads to changes in the unit-cell volume and in the magnetic ordering. However, the magnetic ordering temperature does not scale with the volume change, and the Eu valence is expected to remain divalent. Here we study the bulk electronic structure of non-centrosymmetric Eu T Ge 3 ( T = Co, Ni, Rh, and Ir) by hard x-ray photoelectron spectroscopy. The Eu 3d core-level spectrum confirms the robust Eu 2+ valence state against the transition-metal substitutionmore » with a small contribution from Eu 3+ . The estimated Eu mean valence is around 2.1 in these compounds, as confirmed by multiplet calculations. In contrast, the Ge 2p spectrum shifts to higher binding energy upon cha nging the transition metal from 3d to 4d to 5d elements, hinting at a change in the Ge- T bonding strength. The valence bands of the different compounds are found to be well reproduced by ab initio band structure calculations.« less

Bulk electronic structure of non-centrosymmetric EuTGe 3 (T=Co, Ni, Rh, Ir) studied by hard x-ray photoelectron spectroscopy

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

Utsumi, Yuki; Kasinathan, Deepa; Swatek, Przemys?aw

Non-centrosymmetric EuTGe 3 ( T = Co, Ni, Rh, and Ir) possesses magnetic Eu 2+ ions, and antiferromagnetic ordering appears at low temperatures. Transition-metal substitution leads to changes in the unit-cell volume and in the magnetic ordering. However, the magnetic ordering temperature does not scale with the volume change, and the Eu valence is expected to remain divalent. Here we study the bulk electronic structure of non-centrosymmetric Eu T Ge 3 ( T = Co, Ni, Rh, and Ir) by hard x-ray photoelectron spectroscopy. The Eu 3d core-level spectrum confirms the robust Eu 2+ valence state against the transition-metal substitutionmore » with a small contribution from Eu 3+ . The estimated Eu mean valence is around 2.1 in these compounds, as confirmed by multiplet calculations. In contrast, the Ge 2p spectrum shifts to higher binding energy upon cha nging the transition metal from 3d to 4d to 5d elements, hinting at a change in the Ge- T bonding strength. The valence bands of the different compounds are found to be well reproduced by ab initio band structure calculations.« less

Local structural aspects of metal-metal transition in IrTe2 from x-ray PDF

NASA Astrophysics Data System (ADS)

Yu, Runze; Abeykoon, Milinda; Zhou, Haidong; Yin, Weiguo; Bozin, Emil S.

Evolution of local atomic structure across the metal-metal transition in IrTe2 is explored by pair distribution function (PDF) analysis of x-ray total scattering data over 80 K <T <300 K range. Local and average structures are found to be in accord at all temperatures conforming to P-1 and P-3m1 symmetry at low and high temperature, respectively. We find no evidence of short-range Ir-dimers surviving into the high-T regime, in stark contrast to the earlier EXAFS study proposing Ir-dimer order-disorder mechanism. Phase fraction obtained from explicit 2-phase structural modeling displays hysteretic behavior across the transition, in agreement with electronic transport measurements, indicative of a strong tie between the lattice and electronic configurations. Bond valence methodology applied to structural parameters further indicates significant bond charge disproportionation in association with the transition. Work at Brookhaven National Laboratory was supported by US DOE, Office of Science, Office of Basic Energy Sciences (DOE-BES) under Contract No. DE-SC0012704.

Simian T Lymphotropic Virus 1 Infection of Papio anubis: tax Sequence Heterogeneity and T Cell Recognition.

PubMed

Termini, James M; Magnani, Diogo M; Maxwell, Helen S; Lauer, William; Castro, Iris; Pecotte, Jerilyn; Barber, Glen N; Watkins, David I; Desrosiers, Ronald C

2017-10-15

Baboons naturally infected with simian T lymphotropic virus (STLV) are a potentially useful model system for the study of vaccination against human T lymphotropic virus (HTLV). Here we expanded the number of available full-length baboon STLV-1 sequences from one to three and related the T cell responses that recognize the immunodominant Tax protein to the tax sequences present in two individual baboons. Continuously growing T cell lines were established from two baboons, animals 12141 and 12752. Next-generation sequencing (NGS) of complete STLV genome sequences from these T cell lines revealed them to be closely related but distinct from each other and from the baboon STLV-1 sequence in the NCBI sequence database. Overlapping peptides corresponding to each unique Tax sequence and to the reference baboon Tax sequence were used to analyze recognition by T cells from each baboon using intracellular cytokine staining (ICS). Individual baboons expressed more gamma interferon and tumor necrosis factor alpha in response to Tax peptides corresponding to their own STLV-1 sequence than in response to Tax peptides corresponding to the reference baboon STLV-1 sequence. Thus, our analyses revealed distinct but closely related STLV-1 genome sequences in two baboons, extremely low heterogeneity of STLV sequences within each baboon, no evidence for superinfection within each baboon, and a ready ability of T cells in each baboon to recognize circulating Tax sequences. While amino acid substitutions that result in escape from CD8 + T cell recognition were not observed, premature stop codons were observed in 7% and 56% of tax sequences from peripheral blood mononuclear cells from animals 12141 and 12752, respectively. IMPORTANCE It has been estimated that approximately 100,000 people suffer serious morbidity and 10,000 people die each year from the consequences associated with human T lymphotropic virus (HTLV) infection. There are no antiviral drugs and no preventive vaccine. A

Up-regulation of K{sub ir}2.1 by ER stress facilitates cell death of brain capillary endothelial cells

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

Kito, Hiroaki; Yamazaki, Daiju; Department of Biological Chemistry, Kyoto University, Graduate School of Pharmaceutical Sciences, Kyoto

Highlights: {yields} We found that application of endoplasmic reticulum (ER) stress with tunicamycin to brain capillary endothelial cells (BCECs) induced cell death. {yields} The ER stress facilitated the expression of inward rectifier K{sup +} channel (K{sub ir}2.1) and induced sustained membrane hyperpolarization. {yields} The membrane hyperpolarization induced sustained Ca{sup 2+} entry through voltage-independent nonspecific cation channels and consequently facilitated cell death. {yields} The K{sub ir}2.1 up-regulation by ER stress is, at least in part, responsible for cell death of BCECs under pathological conditions. -- Abstract: Brain capillary endothelial cells (BCECs) form blood brain barrier (BBB) to maintain brain homeostasis. Cellmore » turnover of BCECs by the balance of cell proliferation and cell death is critical for maintaining the integrity of BBB. Here we found that stimuli with tunicamycin, endoplasmic reticulum (ER) stress inducer, up-regulated inward rectifier K{sup +} channel (K{sub ir}2.1) and facilitated cell death in t-BBEC117, a cell line derived from bovine BCECs. The activation of K{sub ir} channels contributed to the establishment of deeply negative resting membrane potential in t-BBEC117. The deep resting membrane potential increased the resting intracellular Ca{sup 2+} concentration due to Ca{sup 2+} influx through non-selective cation channels and thereby partly but significantly regulated cell death in t-BBEC117. The present results suggest that the up-regulation of K{sub ir}2.1 is, at least in part, responsible for cell death/cell turnover of BCECs induced by a variety of cellular stresses, particularly ER stress, under pathological conditions.« less

Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences.

PubMed

Altahawi, Faysal F; Blount, Kevin J; Morley, Nicholas P; Raithel, Esther; Omar, Imran M

2017-01-01

To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 × 0.5 × 3 mm 3 ; ∼10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 × 0.5 × 0.5 mm 3 ; ∼7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 × 0.5 × 0.5 mm 3 ; ∼5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci.

Rapid discrimination of Panax notogeinseng of different grades by FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Ma, Fang; Chen, Jian-bo; Wu, Xian-xue; Zhou, Qun; Sun, Su-qin

2016-11-01

The herbal material of Notoginseng (the root of Panax notoginseng) is sold by "Tou" (the number of Notoginseng in every 500 g) to distinguish the grade. Normally the better quality, the few number of the "Tou" and the size of Notoginseng is bigger. In this study, three grades of Notoginseng harvested from Yunnan province were discriminated and identified by Fourier transform infrared spectroscopy (FT-IR) and two-dimensional correlation infrared spectroscopy (2DCOS-IR)). The correlation coefficient of IR spectra between the three grades of Notoginseng and starch are greater than 0.95 in the range of 1300-800 cm-1, means the main compositions of Notoginseng are starch polysaccharide. Also, when the size of Notoginseng is bigger, it may contain more polysaccharide. There is no difference in range of 815-1000 cm-1 of the 2DCOS-IR synchronous spectra of the three grades means polysaccharides possess good thermal stability. In the range of 1200-1300 cm-1 shows the inverse ration between the thermal sensitivity of C-O and the number of "Tou". Combination with the 2DCOS-IR asynchronous spectra, the response speed of amino acid (1640 cm-1) on the thermal perturbation is the fastest, followed by nitrate (1384 cm-1); the response speed of polysaccharides (1079 cm-1) is the slowest. The result proved that the 2DCOS-IR could discriminate different grades of Notoginseng.

Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children.

PubMed

Butte, Nancy F; Voruganti, V Saroja; Cole, Shelley A; Haack, Karin; Comuzzie, Anthony G; Muzny, Donna M; Wheeler, David A; Chang, Kyle; Hawes, Alicia; Gibbs, Richard A

2011-09-22

Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5' and 3' flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3'-UTR, and 2 in the 5'-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001-0.009) were associated with obesity-related traits (P = 0.01-0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77-0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children.

Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children

PubMed Central

Voruganti, V. Saroja; Cole, Shelley A.; Haack, Karin; Comuzzie, Anthony G.; Muzny, Donna M.; Wheeler, David A.; Chang, Kyle; Hawes, Alicia; Gibbs, Richard A.

2011-01-01

Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5′ and 3′ flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3′-UTR, and 2 in the 5′-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001–0.009) were associated with obesity-related traits (P = 0.01–0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77–0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children. PMID:21771880

[Imaging characteristics of PROPELLER T2-weighted imaging].

PubMed

Goto, Masami; Aoki, Shigeki; Hayashi, Naoto; Mori, Harushi; Watanabe, Yasushi; Ino, Kenji; Satake, Yoshirou; Nishida, Katuji; Sato, Haruo; Iida, Kyouhito; Mima, Kazuo; Ohtomo, Kuni

2004-11-01

As the PROPELLER sequence is a combination of the radial scan and fast-spin-echo (FSE) sequence, it can be considered an FSE sequence with a motion correlation. However, there are some differences between PROPELLER and FSE owing to differences in k-space trajectory. We clarified the imaging characteristics of PROPELLER T2-weighted imaging (T2WI) for different parameters in comparison with usual FSE T2WI. When the same parameters were used, PROPELLER T2WI showed a higher signal-to-noise ratio (SNR) and lower spatial resolution than usual FSE. Effective echo time (TE) changed with different echo train lengths (ETL) or different bandwidths on PROPELLER, and imaging contrast changed accordingly to be more effective.

[Parametrial infiltration of cervix carcinoma: diagnostic value of contrast-enhanced fat-suppressed T1-weighted SE sequences at 1.5 tesla].

PubMed

Scheidler, J; Heuck, A; Wencke, K; Kimmig, R; Müller-Lisse, U; Reiser, M

1997-04-01

To determine whether contrast-enhanced and fat-suppressed sequences contribute to the MR imaging diagnosis of parametrial invasion. 21 patients with carcinoma of the cervix were prospectively examined with a phased-array coil and a 1.5T MR-scanner using the following sequences: transverse T2-weighted turbo spin echo (T2-TSE), T1-weighted spin echo (T1-SE) and fat suppressed T1-weighted SE sequences before and after Gd-DTPA. The sequences were evaluated separately for the presence of parametrial invasion. Image quality and diagnostic confidence were classified on a scale of 0-10 (nondiagnostic-excellent). Findings were compared to the results of the pathohistological examination. Sensitivity, specificity and diagnostic accuracy were highest for T2-TSE sequences (100%, 79% and 86%, respectively). Contrast-enhanced T1-SE sequences with fat-suppression (71%, 79%, and 76%) showed no improvement compared to T2-TSE. Unenhanced fat-suppressed T1-SE (100%, 30%, and 56%) and unenhanced T1-SE (100%, 7%, and 38%) as well as contrast-enhanced T1-SE (86%, 20%, and 47%) were significantly worse than T2-TSE. With similar image quality (p < 0.05) diagnostic confidence was higher on T2-TSE than on any of the other sequences (p < 0.001). Considering the cost-effectiveness of the examination, for the MR diagnosis of parametrial invasion the use of fat-suppressed contrast-enhanced sequences can be abandoned in favour of T2-weighted TSE sequences.

Diagnostic Quality of 3D T2-SPACE Compared with T2-FSE in the Evaluation of Cervical Spine MRI Anatomy.

PubMed

Chokshi, F H; Sadigh, G; Carpenter, W; Allen, J W

2017-04-01

Spinal anatomy has been variably investigated using 3D MRI. We aimed to compare the diagnostic quality of T2 sampling perfection with application-optimized contrasts by using flip angle evolution (SPACE) with T2-FSE sequences for visualization of cervical spine anatomy. We predicted that T2-SPACE will be equivalent or superior to T2-FSE for visibility of anatomic structures. Adult patients undergoing cervical spine MR imaging with both T2-SPACE and T2-FSE sequences for radiculopathy or myelopathy between September 2014 and February 2015 were included. Two blinded subspecialty-trained radiologists independently assessed the visibility of 12 anatomic structures by using a 5-point scale and assessed CSF pulsation artifact by using a 4-point scale. Sagittal images and 6 axial levels from C2-T1 on T2-FSE were reviewed; 2 weeks later and after randomization, T2-SPACE was evaluated. Diagnostic quality for each structure and CSF pulsation artifact visibility on both sequences were compared by using a paired t test. Interobserver agreement was calculated (κ). Forty-five patients were included (mean age, 57 years; 40% male). The average visibility scores for intervertebral disc signal, neural foramina, ligamentum flavum, ventral rootlets, and dorsal rootlets were higher for T2-SPACE compared with T2-FSE for both reviewers ( P < .001). Average scores for remaining structures were either not statistically different or the superiority of one sequence was discordant between reviewers. T2-SPACE showed less degree of CSF flow artifact ( P < .001). Interobserver variability ranged between -0.02-0.20 for T2-SPACE and -0.02-0.30 for T2-FSE (slight to fair agreement). T2-SPACE may be equivalent or superior to T2-FSE for the evaluation of cervical spine anatomic structures, and T2-SPACE shows a lower degree of CSF pulsation artifact. © 2017 by American Journal of Neuroradiology.

Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia

PubMed Central

Kiel, Mark J.; Velusamy, Thirunavukkarasu; Rolland, Delphine; Sahasrabuddhe, Anagh A.; Chung, Fuzon; Bailey, Nathanael G.; Schrader, Alexandra; Li, Bo; Li, Jun Z.; Ozel, Ayse B.; Betz, Bryan L.; Miranda, Roberto N.; Medeiros, L. Jeffrey; Zhao, Lili; Herling, Marco

2014-01-01

The comprehensive genetic alterations underlying the pathogenesis of T-cell prolymphocytic leukemia (T-PLL) are unknown. To address this, we performed whole-genome sequencing (WGS), whole-exome sequencing (WES), high-resolution copy-number analysis, and Sanger resequencing of a large cohort of T-PLL. WGS and WES identified novel mutations in recurrently altered genes not previously implicated in T-PLL including EZH2, FBXW10, and CHEK2. Strikingly, WGS and/or WES showed largely mutually exclusive mutations affecting IL2RG, JAK1, JAK3, or STAT5B in 38 of 50 T-PLL genomes (76.0%). Notably, gain-of-function IL2RG mutations are novel and have not been reported in any form of cancer. Further, high-frequency mutations in STAT5B have not been previously reported in T-PLL. Functionally, IL2RG-JAK1-JAK3-STAT5B mutations led to signal transducer and activator of transcription 5 (STAT5) hyperactivation, transformed Ba/F3 cells resulting in cytokine-independent growth, and/or enhanced colony formation in Jurkat T cells. Importantly, primary T-PLL cells exhibited constitutive activation of STAT5, and targeted pharmacologic inhibition of STAT5 with pimozide induced apoptosis in primary T-PLL cells. These results for the first time provide a portrait of the mutational landscape of T-PLL and implicate deregulation of DNA repair and epigenetic modulators as well as high-frequency mutational activation of the IL2RG-JAK1-JAK3-STAT5B axis in the pathogenesis of T-PLL. These findings offer opportunities for novel targeted therapies in this aggressive leukemia. PMID:24825865

Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia.

PubMed

Kiel, Mark J; Velusamy, Thirunavukkarasu; Rolland, Delphine; Sahasrabuddhe, Anagh A; Chung, Fuzon; Bailey, Nathanael G; Schrader, Alexandra; Li, Bo; Li, Jun Z; Ozel, Ayse B; Betz, Bryan L; Miranda, Roberto N; Medeiros, L Jeffrey; Zhao, Lili; Herling, Marco; Lim, Megan S; Elenitoba-Johnson, Kojo S J

2014-08-28

The comprehensive genetic alterations underlying the pathogenesis of T-cell prolymphocytic leukemia (T-PLL) are unknown. To address this, we performed whole-genome sequencing (WGS), whole-exome sequencing (WES), high-resolution copy-number analysis, and Sanger resequencing of a large cohort of T-PLL. WGS and WES identified novel mutations in recurrently altered genes not previously implicated in T-PLL including EZH2, FBXW10, and CHEK2. Strikingly, WGS and/or WES showed largely mutually exclusive mutations affecting IL2RG, JAK1, JAK3, or STAT5B in 38 of 50 T-PLL genomes (76.0%). Notably, gain-of-function IL2RG mutations are novel and have not been reported in any form of cancer. Further, high-frequency mutations in STAT5B have not been previously reported in T-PLL. Functionally, IL2RG-JAK1-JAK3-STAT5B mutations led to signal transducer and activator of transcription 5 (STAT5) hyperactivation, transformed Ba/F3 cells resulting in cytokine-independent growth, and/or enhanced colony formation in Jurkat T cells. Importantly, primary T-PLL cells exhibited constitutive activation of STAT5, and targeted pharmacologic inhibition of STAT5 with pimozide induced apoptosis in primary T-PLL cells. These results for the first time provide a portrait of the mutational landscape of T-PLL and implicate deregulation of DNA repair and epigenetic modulators as well as high-frequency mutational activation of the IL2RG-JAK1-JAK3-STAT5B axis in the pathogenesis of T-PLL. These findings offer opportunities for novel targeted therapies in this aggressive leukemia. © 2014 by The American Society of Hematology.

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action.

PubMed

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob; Kahn, C Ronald; Emanuelli, Brice

2018-07-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1 -/- and IRS-2 -/- mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1. These regulated sites included previously reported substrates of the insulin/IGF-1 signalling pathway, as well as novel substrates including Nuclear Factor I X and Semaphorin-4B. In silico prediction suggests the protein kinase B (PKB), protein kinase C (PKC), and cyclin-dependent kinase (CDK) as the main mediators of these phosphorylation events. Importantly, we found preferential phosphorylation patterns depending on the presence of either IRS-1 or IRS-2, which was associated with specific sets of kinases involved in signal transduction downstream of these substrates such as PDHK1, MAPK3, and PKD1 for IRS-1, and PIN1 and PKC beta for IRS-2. Overall, by generating a comprehensive phosphoproteomic profile from brown preadipocyte cells in response to IGF-1 stimulation, we reveal both common and distinct insulin/IGF-1 signalling events mediated by specific IRS proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Interface adjustment and exchange coupling in the IrMn/NiFe system

NASA Astrophysics Data System (ADS)

Spizzo, F.; Tamisari, M.; Chinni, F.; Bonfiglioli, E.; Del Bianco, L.

2017-01-01

The exchange bias effect was investigated, in the 5-300 K temperature range, in samples of IrMn [100 Å]/NiFe [50 Å] (set A) and in samples with inverted layer-stacking sequence (set B), produced at room temperature by DC magnetron sputtering in a static magnetic field of 400 Oe. The samples of each set differ for the nominal thickness (tCu) of a Cu spacer, grown at the interface between the antiferromagnetic and ferromagnetic layers, which was varied between 0 and 2 Å. It has been found out that the Cu insertion reduces the values of the exchange field and of the coercivity and can also affect their thermal evolution, depending on the stack configuration. Indeed, the latter also determines a peculiar variation of the exchange bias properties with time, shown and discussed with reference to the samples without Cu of the two sets. The results have been explained considering that, in this system, the exchange coupling mechanism is ruled by the glassy magnetic behavior of the IrMn spins located at the interface with the NiFe layer. Varying the stack configuration and tCu results in a modulation of the structural and magnetic features of the interface, which ultimately affects the spins dynamics of the glassy IrMn interfacial component.

Ferromagnetism and Crystalline Electric Field Effects in Cubic UX2Zn20 (X=Co, Rh, Ir)

NASA Astrophysics Data System (ADS)

Bauer, E. D.; Ronning, F.; Silhanek, A.; Harrison, N.; Thompson, J. D.; Sarrao, J. L.; Movshovich, R.; Hundley, M. F.; Jaime, M.; Daniel, E.; Booth, C. H.

2006-03-01

The properties of a new class of cubic UX2Zn20 (X=Co, Rh, Ir) heavy fermion compounds have been investigated by means of magnetic susceptibility, specific heat, electrical resistivity, and x-ray absorption spectroscopy. Both UCo2Zn20 and URh2Zn20 show peaks in C(T) and χ(T) at ˜5-10 K suggesting the presence of crystalline electric field (CEF) effects in these materials, i.e., a localized 5f^2 configuration of uranium. In addition, measurements in high magnetic fields up to 40 T are consistent with a CEF model of a nonmagnetic ground state and a magnetic first excited state separated by ˜ 20 K. In contrast, UIr2Zn20 exhibits a first-order ferromagnetic transition at Tc=2.75 K with a saturation moment μsat=0.5 μB in the ferromagnetic state. All compounds in this series are heavy fermion materials with enhanced electronic specific heat coefficients γ˜ 150-300 mJ/molK^2. The physical properties of UX2Zn20 (X=Co, Rh, Ir) will be discussed.

Complete genome sequence of Desulfarculus baarsii type strain (2st14T)

PubMed Central

Sun, Hui; Spring, Stefan; Lapidus, Alla; Davenport, Karen; Del Rio, Tijana Glavina; Tice, Hope; Nolan, Matt; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Pagani, Ionna; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Han, Cliff; Rohde, Manfred; Brambilla, Evelyne; Göker, Markus; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Land, Miriam

2010-01-01

Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO2. The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14T was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304732

Evolution of the vertebrate insulin receptor substrate (Irs) gene family.

PubMed

Al-Salam, Ahmad; Irwin, David M

2017-06-23

Insulin receptor substrate (Irs) proteins are essential for insulin signaling as they allow downstream effectors to dock with, and be activated by, the insulin receptor. A family of four Irs proteins have been identified in mice, however the gene for one of these, IRS3, has been pseudogenized in humans. While it is known that the Irs gene family originated in vertebrates, it is not known when it originated and which members are most closely related to each other. A better understanding of the evolution of Irs genes and proteins should provide insight into the regulation of metabolism by insulin. Multiple genes for Irs proteins were identified in a wide variety of vertebrate species. Phylogenetic and genomic neighborhood analyses indicate that this gene family originated very early in vertebrae evolution. Most Irs genes were duplicated and retained in fish after the fish-specific genome duplication. Irs genes have been lost of various lineages, including Irs3 in primates and birds and Irs1 in most fish. Irs3 and Irs4 experienced an episode of more rapid protein sequence evolution on the ancestral mammalian lineage. Comparisons of the conservation of the proteins sequences among Irs paralogs show that domains involved in binding to the plasma membrane and insulin receptors are most strongly conserved, while divergence has occurred in sequences involved in interacting with downstream effector proteins. The Irs gene family originated very early in vertebrate evolution, likely through genome duplications, and in parallel with duplications of other components of the insulin signaling pathway, including insulin and the insulin receptor. While the N-terminal sequences of these proteins are conserved among the paralogs, changes in the C-terminal sequences likely allowed changes in biological function.

Preferential accumulation of amyloid-beta in presynaptic glutamatergic terminals (VGluT1 and VGluT2) in Alzheimer’s disease cortex

PubMed Central

Sokolow, Sophie; Luu, Sanh H.; Nandy, Karabi; Miller, Carol A.; Vinters, Harry V.; Poon, Wayne W.; Gylys, Karen H.

2011-01-01

Amyloid-beta (Aβ) is thought to play a central role in synaptic dysfunction (e.g. neurotransmitter release) and synapse loss. Glutamatergic dysfunction is involved in the pathology of Alzheimer’s disease (AD) and perhaps plays a central role in age-related cognitive impairment. Yet, it is largely unknown whether Aβ accumulates in excitatory boutons. To assess the possibility that glutamatergic terminals are lost in AD patients, control and AD synaptosomes were immunolabeled for the most abundant vesicular glutamate transporters (VGluT1 and VGluT2) and quantified by flow cytometry and immunoblot methods. In post-mortem parietal cortex from aged control subjects, glutamatergic boutons are fairly abundant as approximately 40% were immunoreactive for VGluT1 (37%) and VGluT2 (39%). However, the levels of these specific markers of glutamatergic synapses were not significantly different among control and AD cases. To test the hypothesis that Aβ is associated with excitatory terminals, AD synaptosomes were double-labeled for Aβ and for VGluT1 and VGluT2, and analyzed by flow cytometry and confocal microscopy. Our study demonstrated that Aβ immunoreactivity (IR) was present in glutamatergic terminals of AD patients. Quantification of Aβ and VGluT1 in a large population of glutamatergic nerve terminals was performed by flow cytometry, showing that 42% of VGluT1 synaptosomes were immunoreactive for Aβ compared to 9% of VGluT1 synaptosomes lacking Aβ-IR. Percentage of VGluT2 synaptosomes immunoreactive for Aβ (21%) was significantly higher than VGluT2 synaptosomes lacking Aβ-IR (9%). Moreover, Aβ preferentially affects VGluT1 (42% positive) compared to VGluT2 terminals (21%). These data represent the first evidence of high levels of Aβ in excitatory boutons in AD cortex and support the hypothesis that Aβ may play a role in modulating glutamate transmission in AD terminals. PMID:21914482

Child dermoid cyst mimicking a craniopharyngioma: the benefit of MRI T2-weighted diffusion sequence.

PubMed

Amelot, Aymeric; Borha, Alin; Calmon, Raphael; Barbet, Patrick; Puget, Stephanie

2018-02-01

Brain dermoid cysts are very rare lesions. Although benign, these cysts may be associated with devastating complications due to mass effect or meningitis. The discovery of completely asymptomatic dermoid cysts in the pediatric population is exceedingly rare. Despite the advances in imaging modalities, it sometimes remains difficult to exclude the differential diagnosis of craniopharyngioma. We describe a 12-year-old boy addressed for suspicion of craniopharyngioma diagnosed by decreased visual acuity, bitemporal hemianopia and a CT scan showing a large hypodense suprasellar lesion with intralesional calcifications. Despite the unusual localization and size of this lesion, the absence of dermal sinus commonly found, and before visualizing a hyperintense mass on MRI-diffusion, the diagnosis of craniopharyngioma was ruled out in favor of a dermoid cyst. Radical excision was performed. In the suprasellar area, craniopharyngioma and dermoid cyst may have very similar radiological aspects: low density masses on CT scan and a hyperintense signal on T1-weighted MRI sequences with a variable signal on T2-weighted sequences. Hitherto, only two cases in literature have described suprasellar dermoid cyst. Their initial diagnosis was facilitated by the presence of a dermal sinus.

Sequence conservation predicts T cell reactivity against ragweed allergens.

PubMed

Pham, J; Oseroff, C; Hinz, D; Sidney, J; Paul, S; Greenbaum, J; Vita, R; Phillips, E; Mallal, S; Peters, B; Sette, A

2016-09-01

Ragweed is a major cause of seasonal allergy, affecting millions of people worldwide. Several allergens have been defined based on IgE reactivity, but their relative immunogenicity in terms of T cell responses has not been studied. We comprehensively characterized T cell responses from atopic, ragweed-allergic subjects to Amb a 1, Amb a 3, Amb a 4, Amb a 5, Amb a 6, Amb a 8, Amb a 9, Amb a 10, Amb a 11, and Amb p 5 and examined their correlation with serological reactivity and sequence conservation in other allergens. Peripheral blood mononuclear cells (PBMCs) from donors positive for IgE towards ragweed extracts after in vitro expansion for secretion of IL-5 (a representative Th2 cytokine) and IFN-γ (Th1) in response to a panel of overlapping peptides spanning the above-listed allergens were assessed. Three previously identified dominant T cell epitopes (Amb a 1 176-191, 200-215, and 344-359) were confirmed, and three novel dominant epitopes (Amb a 1 280-295, 304-319, and 320-335) were identified. Amb a 1, the dominant IgE allergen, was also the dominant T cell allergen, but dominance patterns for T cell and IgE responses for the other ragweed allergens did not correlate. Dominance for T cell responses correlated with conservation of ragweed epitopes with sequences of other well-known allergens. These results provide the first assessment of the hierarchy of T cell reactivity in ragweed allergens, which is distinct from that observed for IgE reactivity and influenced by T cell epitope sequence conservation. The results suggest that ragweed allergens associated with lesser IgE reactivity and significant T cell reactivity may be targeted for T cell immunotherapy, and further support the development of immunotherapies against epitopes conserved across species to generate broad reactivity against many common allergens. © 2016 John Wiley & Sons Ltd.

Fast T2*-weighted MRI of the prostate at 3 Tesla.

PubMed

Hardman, Rulon L; El-Merhi, Fadi; Jung, Adam J; Ware, Steve; Thompson, Ian M; Friel, Harry T; Peng, Qi

2011-04-01

To describe a rapid T2*-weighted (T2*W), three-dimensional (3D) echo planar imaging (EPI) sequence and its application in mapping local magnetic susceptibility variations in 3 Tesla (T) prostate MRI. To compare the sensitivity of T2*W EPI with routinely used T1-weighted turbo-spin echo sequence (T1W TSE) in detecting hemorrhage and the implications on sequences sensitive to field inhomogeneities such as MR spectroscopy (MRS). B(0) susceptibility weighted mapping was performed using a 3D EPI sequence featuring a 2D spatial excitation pulse with gradients of spiral k-space trajectory. A series of 11 subjects were imaged using 3T MRI and combination endorectal (ER) and six-channel phased array cardiac coils. T1W TSE and T2*W EPI sequences were analyzed quantitatively for hemorrhage contrast. Point resolved spectroscopy (PRESS MRS) was performed and data quality was analyzed. Two types of susceptibility variation were identified: hemorrhagic and nonhemorrhagic T2*W-positive areas. Post-biopsy hemorrhage lesions showed on average five times greater contrast on the T2*W images than T1W TSE images. Six nonhemorrhage regions of severe susceptibility artifact were apparent on the T2*W images that were not seen on standard T1W or T2W images. All nonhemorrhagic susceptibility artifact regions demonstrated compromised spectral quality on 3D MRS. The fast T2*W EPI sequence identifies hemorrhagic and nonhemorrhagic areas of susceptibility variation that may be helpful in prostate MRI planning at 3.0T. Copyright © 2011 Wiley-Liss, Inc.

[The use of the T2-weighted turbo-spin-echo sequence in studying the neurocranium. A comparison with the conventional T2-weighted spin-echo sequence].

PubMed

Siewert, C; Hosten, N; Felix, R

1994-07-01

T2-weighted spin-echo imaging is the standard screening procedure in MR imaging of the neurocranium. We evaluated fast spin-echo T2-weighted imaging (TT2) of the neurocranium in comparison to conventional spin-echo T2-weighted imaging (T2). Signal-to-noise and contrast-to-noise ratio of normal brain tissues (basal ganglia, grey and white matter, CSF fluid) and different pathologies were calculated. Signal-to-noise ratio and contrast-to-noise ratio were significantly higher in TT2 than in T2 (with the exception of gray-to-white matter contrast). Tissues with increased content of water protons (mobile protons) showed the highest contrast to surrounding tissues. The increased signal intensity of fat must be given due attention in fatty lesions. Because the contrast-to-noise ratio between white matter and basal ganglia is less in TT2, Parkinson patients have to be examined by conventional T2. If these limitations are taken into account, fast spin-echo T2-weighted imaging is well appropriate for MR imaging of the neurocranium, resulting in heavy T2-weighting achieved in a short acquisition time.

Macro-fingerprint analysis-through-separation of licorice based on FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Wang, Yang; Wang, Ping; Xu, Changhua; Yang, Yan; Li, Jin; Chen, Tao; Li, Zheng; Cui, Weili; Zhou, Qun; Sun, Suqin; Li, Huifen

2014-07-01

In this paper, a step-by-step analysis-through-separation method under the navigation of multi-step IR macro-fingerprint (FT-IR integrated with second derivative IR (SD-IR) and 2DCOS-IR) was developed for comprehensively characterizing the hierarchical chemical fingerprints of licorice from entirety to single active components. Subsequently, the chemical profile variation rules of three parts (flavonoids, saponins and saccharides) in the separation process were holistically revealed and the number of matching peaks and correlation coefficients with standards of pure compounds was increasing along the extracting directions. The findings were supported by UPLC results and a verification experiment of aqueous separation process. It has been demonstrated that the developed multi-step IR macro-fingerprint analysis-through-separation approach could be a rapid, effective and integrated method not only for objectively providing comprehensive chemical characterization of licorice and all its separated parts, but also for rapidly revealing the global enrichment trend of the active components in licorice separation process.

Evaluation of T2-weighted versus short-tau inversion recovery sagittal sequences in the identification and localization of canine intervertebral disc extrusion with low-field magnetic resonance imaging.

PubMed

Housley, Daniel; Caine, Abby; Cherubini, Giunio; Taeymans, Olivier

2017-07-01

Sagittal T2-weighted sequences (T2-SAG) are the foundation of spinal protocols when screening for the presence of intervertebral disc extrusion. We often utilize sagittal short-tau inversion recovery sequences (STIR-SAG) as an adjunctive screening series, and experience suggests that this combined approach provides superior detection rates. We hypothesized that STIR-SAG would provide higher sensitivity than T2-SAG in the identification and localization of intervertebral disc extrusion. We further hypothesized that the parallel evaluation of paired T2-SAG and STIR-SAG series would provide a higher sensitivity than could be achieved with either independent sagittal series when viewed in isolation. This retrospective diagnostic accuracy study blindly reviewed T2-SAG and STIR-SAG sequences from dogs (n = 110) with surgically confirmed intervertebral disc extrusion. A consensus between two radiologists found no significant difference in sensitivity between T2-SAG and STIR-SAG during the identification of intervertebral disc extrusion (T2-SAG: 92.7%, STIR-SAG: 94.5%, P = 0.752). Nevertheless, STIR-SAG accurately identified intervertebral disc extrusion in 66.7% of cases where the evaluation of T2-SAG in isolation had provided a false negative diagnosis. Additionally, one radiologist found that the parallel evaluation of paired T2-SAG and STIR-SAG series provided a significantly higher sensitivity than T2-SAG in isolation, during the identification of intervertebral disc extrusion (T2-SAG: 78.2%, paired T2-SAG, and STIR-SAG: 90.9%, P = 0.017). A similar nonsignificant trend was observed when the consensus of both radiologists was taken into consideration (T2-SAG: 92.7%, paired T2-SAG, and STIR-SAG = 97.3%, P = 0.392). We therefore conclude that STIR-SAG is capable of identifying intervertebral disc extrusion that is inconspicuous in T2-SAG, and that STIR-SAG should be considered a useful adjunctive sequence during preliminary sagittal screening for intervertebral disc

Evaluation of the articular cartilage of the knee joint: value of adding a T2 mapping sequence to a routine MR imaging protocol.

PubMed

Kijowski, Richard; Blankenbaker, Donna G; Munoz Del Rio, Alejandro; Baer, Geoffrey S; Graf, Ben K

2013-05-01

To determine whether the addition of a T2 mapping sequence to a routine magnetic resonance (MR) imaging protocol could improve diagnostic performance in the detection of surgically confirmed cartilage lesions within the knee joint at 3.0 T. This prospective study was approved by the institutional review board, and the requirement to obtain informed consent was waived. The study group consisted of 150 patients (76 male and 74 female patients with an average age of 41.2 and 41.5 years, respectively) who underwent MR imaging and arthroscopy of the knee joint. MR imaging was performed at 3.0 T by using a routine protocol with the addition of a sagittal T2 mapping sequence. Images from all MR examinations were reviewed in consensus by two radiologists before surgery to determine the presence or absence of cartilage lesions on each articular surface, first by using the routine MR protocol alone and then by using the routine MR protocol with T2 maps. Each articular surface was then evaluated at arthroscopy. Generalized estimating equation models were used to compare the sensitivity and specificity of the routine MR imaging protocol with and without T2 maps in the detection of surgically confirmed cartilage lesions. The sensitivity and specificity in the detection of 351 cartilage lesions were 74.6% and 97.8%, respectively, for the routine MR protocol alone and 88.9% and 93.1% for the routine MR protocol with T2 maps. Differences in sensitivity and specificity were statistically significant (P < .001). The addition of T2 maps to the routine MR imaging protocol significantly improved the sensitivity in the detection of 24 areas of cartilage softening (from 4.2% to 62%, P < .001), 41 areas of cartilage fibrillation (from 20% to 66%, P < .001), and 96 superficial partial-thickness cartilage defects (from 71% to 88%, P = .004). The addition of a T2 mapping sequence to a routine MR protocol at 3.0 T improved sensitivity in the detection of cartilage lesions within the knee

Preferential accumulation of amyloid-beta in presynaptic glutamatergic terminals (VGluT1 and VGluT2) in Alzheimer's disease cortex.

PubMed

Sokolow, Sophie; Luu, Sanh H; Nandy, Karabi; Miller, Carol A; Vinters, Harry V; Poon, Wayne W; Gylys, Karen H

2012-01-01

Amyloid-beta (Aβ) is thought to play a central role in synaptic dysfunction (e.g. neurotransmitter release) and synapse loss. Glutamatergic dysfunction is involved in the pathology of Alzheimer's disease (AD) and perhaps plays a central role in age-related cognitive impairment. Yet, it is largely unknown whether Aβ accumulates in excitatory boutons. To assess the possibility that glutamatergic terminals are lost in AD patients, control and AD synaptosomes were immunolabeled for the most abundant vesicular glutamate transporters (VGluT1 and VGluT2) and quantified by flow cytometry and immunoblot methods. In post-mortem parietal cortex from aged control subjects, glutamatergic boutons are fairly abundant as approximately 40% were immunoreactive for VGluT1 (37%) and VGluT2 (39%). However, the levels of these specific markers of glutamatergic synapses were not significantly different among control and AD cases. To test the hypothesis that Aβ is associated with excitatory terminals, AD synaptosomes were double-labeled for Aβ and for VGluT1 and VGluT2, and analyzed by flow cytometry and confocal microscopy. Our study demonstrated that Aβ immunoreactivity (IR) was present in glutamatergic terminals of AD patients. Quantification of Aβ and VGluT1 in a large population of glutamatergic nerve terminals was performed by flow cytometry, showing that 42% of VGluT1 synaptosomes were immunoreactive for Aβ compared to 9% of VGluT1 synaptosomes lacking Aβ-IR. Percentage of VGluT2 synaptosomes immunoreactive for Aβ (21%) was significantly higher than VGluT2 synaptosomes lacking Aβ-IR (9%). Moreover, Aβ preferentially affects VGluT1 (42% positive) compared to VGluT2 terminals (21%). These data represent the first evidence of high levels of Aβ in excitatory boutons in AD cortex and support the hypothesis that Aβ may play a role in modulating glutamate transmission in AD terminals. Copyright © 2011 Elsevier Inc. All rights reserved.

Detection of aneurysmal subarachnoid hemorrhage 3 months after initial bleeding: evaluation of T2* and FLAIR MR sequences at 3 T in comparison with initial non-enhanced CT as a gold standard.

PubMed

Mulé, Sébastien; Soize, Sébastien; Benaissa, Azzedine; Portefaix, Christophe; Pierot, Laurent

2016-08-01

To investigate the ability of T2* and fluid-attenuated inversion recovery (FLAIR) MR sequences to detect hemosiderin deposition 3 months after aneurysmal subarachnoid hemorrhage (SAH) in comparison with early non-enhanced CT (NECT) as a gold standard. From September 2008 through May 2013, patients with aneurysmal SAH were included if a NECT less than 24 h after the onset of symptoms showed a SAH, and MRI, including T2* and FLAIR sequences, was performed 3 months later. All aneurysms were treated endovascularly. NECT and MR sequences were blindly analyzed for the presence of SAH (NECT) or hemosiderin deposition (MRI). When positive, details of the spatial distribution of SAH or hemosiderin deposits were noted. Sensitivities were calculated for each patient. Sensitivities, specificities, and positive predictive values (PPVs) were calculated for each location. Forty-nine patients (mean age 52.9 years) were included. Bleeding-related patterns were identified in 43 patients (87.8%) on T2* and 10 patients (20.4%) on FLAIR. T2* was highly predictive of the location of the initial hemorrhage, especially in the Sylvian cisterns (PPVs 95% and 100%) and the anterior interhemispheric fissure (PPV 90%). The T2* sequence can detect and localize a previous SAH a few months after aneurysmal bleeding. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Energetic electrons, hard x-ray emission and MHD activity studies in the IR-T1 tokamak.

PubMed

Agah, K Mikaili; Ghoranneviss, M; Elahi, A Salar

2015-01-01

Determinations of plasma parameters as well as the Magnetohydrodynamics (MHD) activity, energetic electrons energy and energy confinement time are essential for future fusion reactors experiments and optimized operation. Also some of the plasma information can be deduced from these parameters, such as plasma equilibrium, stability, and MHD instabilities. In this contribution we investigated the relation between energetic electrons, hard x-ray emission and MHD activity in the IR-T1 Tokamak. For this purpose we used the magnetic diagnostics and a hard x-ray spectroscopy in IR-T1 tokamak. A hard x-ray emission is produced by collision of the runaway electrons with the plasma particles or limiters. The mean energy was calculated from the slope of the energy spectrum of hard x-ray photons.

Effect of Zn-site substitution with Ga on non-Fermi liquid behavior in PrIr2Zn20

NASA Astrophysics Data System (ADS)

Yamada, R. J.; Onimaru, T.; Uenishi, K.; Yamane, Y.; Wakiya, K.; Matsumoto, K. T.; Umeo, K.; Takabatake, T.

2018-05-01

PrIr2Zn20 exhibits an antiferroquadrupolar (AFQ) order at TQ = 0.11 K, above which temperature the electrical resistivity ρ(T) shows an upward curvature and the magnetic specific heat divided by temperature Cm/T follows - lnT dependence. The non-Fermi Liquid (NFL) behaviors have suggested formation of a quadrupole Kondo lattice. In the present work, we have studied the effect of Ga substitution for Zn on the NFL behavior by the measurements of the specific heat C, the magnetic susceptibility χ, and ρ of PrIr2Zn20-xGax (0 ≤ x ≤ 0.25). With increasing x, the characteristic temperature T0 defined as the temperature where the magnetic entropy Sm reaches (3/4)Rln2 is increased by a factor of 3.5. Similarly, another characteristic temperature TR below which ρ(T) starts decreasing with the upward curvature increases with x by a factor of 1.2. The increments of both T0 and TR may be attributed to the possible split of the Γ3 doublet by symmetry lowering of the Pr sites. Otherwise, the quadrupole Kondo lattice would be stabilized by the enhanced c-f hybridization due to the increment of the 4p electronic density and/or the chemical pressure effect.

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2.

PubMed

Su, Chun; Xiang, Zhaoju; Liu, Yibo; Zhao, Xinqing; Sun, Yan; Li, Zhi; Li, Lijun; Chang, Fan; Chen, Tianjun; Wen, Xinrong; Zhou, Yidan; Zhao, Furong

2016-11-03

Gram-negative bacteria of the genus Serratia are potential producers of many useful secondary metabolites, such as prodigiosin and serrawettins, which have potential applications in environmental bioremediation or in the pharmaceutical industry. Several Serratia strains produce prodigiosin and serrawettin W1 as the main bioactive compounds, and the biosynthetic pathways are co-regulated by quorum sensing (QS). In contrast, the Serratia strain, which can simultaneously produce prodigiosin and serrawettin W2, has not been reported. This study focused on analyzing the genomic sequence of Serratia sp. strain YD25 T isolated from rhizosphere soil under continuously planted burley tobacco collected from Yongding, Fujian province, China, which is unique in producing both prodigiosin and serrawettin W2. A hybrid polyketide synthases (PKS)-non-ribosomal peptide synthetases (NRPS) gene cluster putatively involved in biosynthesis of antimicrobial serrawettin W2 was identified in the genome of YD25 T , and its biosynthesis pathway was proposed. We found potent antimicrobial activity of serrawettin W2 purified from YD25 T against various pathogenic bacteria and fungi as well as antitumor activity against Hela cells. Subsequently, comparative genomic analyses were performed among a total of 133 Serratia species. The prodigiosin biosynthesis gene cluster in YD25 T belongs to the type I pig cluster, which is the main form of pig-encoding genes existing in most of the pigmented Serratia species. In addition, a complete autoinducer-2 (AI-2) system (including luxS, lsrBACDEF, lsrGK, and lsrR) as a conserved bacterial operator is found in the genome of Serratia sp. strain YD25 T . Phylogenetic analysis based on concatenated Lsr and LuxS proteins revealed that YD25 T formed an independent branch and was clearly distant from the strains that solely produce either prodigiosin or serrawettin W2. The Fe (III) ion reduction assay confirmed that strain YD25 T could produce an AI-2 signal

Electronic excitations in γ -Li2IrO3

NASA Astrophysics Data System (ADS)

Li, Ying; Winter, Stephen M.; Jeschke, Harald O.; Valentí, Roser

2017-01-01

We investigate the electronic properties of the three-dimensional stripyhoneycomb γ -Li2IrO3 via relativistic density functional theory calculations as well as exact diagonalization of finite clusters and explore the details of the optical conductivity. Our analysis of this quantity reveals the microscopic origin of the experimentally observed (i) optical transitions and (ii) anisotropic behavior along the various polarization directions. In particular, we find that the optical excitations are overall dominated by transitions between jeff=1 /2 and 3/2 states and the weight of transitions between jeff=1 /2 states at low frequencies can be correlated to deviations from a pure Kitaev description. We furthermore reanalyze within this approach the electronic excitations in the known two-dimensional honeycomb systems α -Li2IrO3 and Na2IrO3 and discuss the results in comparison to γ -Li2IrO3 .

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney

PubMed Central

Copeland, Alex; Gu, Wei; Yasawong, Montri; Lapidus, Alla; Lucas, Susan; Deshpande, Shweta; Pagani, Ioanna; Tapia, Roxanne; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Pan, Chongle; Brambilla, Evelyne-Marie; Rohde, Manfred; Tindall, Brian J.; Sikorski, Johannes; Göker, Markus; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Woyke, Tanja

2012-01-01

Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum “Thermus-Deinococcus” to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1T is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:22675595

Diagnosis of hepatic metastasis: comparison of respiration-triggered diffusion-weighted echo-planar MRI and five t2-weighted turbo spin-echo sequences.

PubMed

Bruegel, Melanie; Gaa, Jochen; Waldt, Simone; Woertler, Klaus; Holzapfel, Konstantin; Kiefer, Berthold; Rummeny, Ernst J

2008-11-01

The purpose of this study was to compare the value of respiration-triggered diffusion-weighted (DW) single-shot echo-planar MRI (EPI) and five variants of T2-weighted turbo spin-echo (TSE) sequences in the diagnosis of hepatic metastasis. Fifty-two patients with extrahepatic primary malignant tumors underwent 1.5-T MRI that included DW EPI and the following variants of T2-weighted TSE techniques: breath-hold fat-suppressed HASTE, breath-hold fat-supressed TSE, respiration-triggered fat-suppressed TSE, breath-hold STIR, and respiration-triggered STIR. Images were reviewed independently by two blinded observers who used a 5-point confidence scale to identify lesions. Results were correlated with surgical and histopathologic findings and follow-up imaging findings. The accuracy of each technique was measured with free-response receiver operating characteristic analysis. A total of 118 hepatic metastatic lesions (mean diameter, 12.8 mm; range, 3-84 mm) were evaluated. Accuracy values were higher (p < 0.001) with DW EPI (0.91-0.92) than with the T2-weighted TSE techniques (0.47-0.67). Imaging with the HASTE sequence (0.47-0.52) was less accurate (p < 0.05) than imaging with the breath-hold TSE, breath-hold STIR, respiration-triggered TSE, and respiration-triggered STIR sequences (0.59-0.67). Sensitivity was higher (p < 0.001) with DW EPI (0.88-0.91) than with T2-weighted TSE techniques (0.45-0.62). For small (< or = 10 mm) metastatic lesions only, the differences in sensitivity between DW EPI (0.85) and T2-weighted TSE techniques (0.26-0.44) were even more pronounced. DW EPI was more sensitive and more accurate than imaging with T2-weighted TSE techniques. Because of the black-blood effect on vessels and low susceptibility to motion artifacts, DW EPI was particularly useful for the detection of small (< or = 10 mm) metastatic lesions.

Rapid discrimination of cultivated Codonopsis lanceolata in different ages by FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Zhu, Yun; Xu, Chang-hua; Huang, Jian; Li, Guo-yu; Liu, Xin-Hu; Sun, Su-qin; Wang, Jin-hui

2014-07-01

Deodeok (Codonopsis lanceolata) root, a traditional Chinese herbal medicine, has been used to treat lung ailments, rheumatism, menstrual disturbance and bruises with a long history in China and some other Asian countries. In this study, four types of Deodeok with different growth years were discriminated and identified by a Tri-step infrared spectroscopy method (Fourier transform-infrared spectroscopy (conventional FT-IR) coupled with second derivative infrared spectroscopy (SD-IR) and two dimensional correlation infrared spectroscopy(2DCOS-IR) under thermal perturbation. Although only small differences were found in the FT-IR spectra of the samples, the positions and intensities of peaks around 1736, 1634, 1246, 1055, 1033, 818, 779 cm-1 could be considered as the key factors for discriminating them. The differences among them were amplified by their SD-IR spectra. The 2DCOS-IR spectra provided obvious dynamic chemical structure information of Deodeok samples, which present different particular auto peak clusters in the range of 875-1130 cm-1 and 1170-1630 cm-1, respectively. It was demonstrated that the content of triterpene were decreasing when C. lanceolata were growing older, but the relative content of saccharides initially increased and decreased significantly afterwards. It indicated a general trend that the content of polysaccharides accumulated with increasing years. Specifically, the content of polysaccharides accumulated in the root of 2-year-old plant was the lowest, 4-years-old was the highest, and then the content decreased gradually. Furthermore, according to the differences of locations and intensities of auto-peaks in 2D-IR spectra, the integral changes of components were revealed. This study offers a promising method inherent with cost-effective and time-saving to characterize and discriminate the complicated system like Deodeok.

In search of the elusive IrB{sub 2}: Can mechanochemistry help?

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

Xie, Zhilin; Blair, Richard G.; Department of Physics, University of Central Florida, Orlando, FL 32816

The previously unknown hexagonal ReB{sub 2}-type IrB{sub 2} diboride and orthorhombic IrB monoboride phases were produced by mechanochemical syntheses. High energy ball milling of elemental Ir and B powder for 30 h, followed by annealing of the powder at 1050 °C for 48 h, resulted in the formation of the desired phases. Both traditional laboratory and high resolution synchrotron X-ray diffraction (XRD) analyses were used for phase identification of the synthesized powder. In addition to XRD, scanning electron microscopy and transmission electron microscopy were employed to further characterize the microstructure of the phases produced. - Graphical abstract: ReB{sub 2}-type IrB{submore » 2} and a new IrB have been successfully synthesized for the first time using mechanochemical method. Crystal structures of IrB{sub 2} and IrB were studied by synchrotron X-ray diffraction. Microstructures of the new phases were characterized by SEM and TEM. - Highlights: • ReB{sub 2}-type IrB{sub 2} and a new IrB have been synthesized by mechanochemical method. • Crystal structures of IrB{sub 2} and IrB were studied by synchrotron XRD. • Microstructures of the new phases were characterized by SEM and TEM.« less

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed

Spielmann, A; Stutz, E

1983-10-25

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

Ultrahigh-field imaging of the biliary tract at 7 T: initial results of gadoxetic acid-enhanced magnetic resonance cholangiography.

PubMed

Fischer, Anja; Kraff, Oliver; Orzada, Stephan; Nensa, Felix; Schäfer, Lena C; Ladd, Mark E; Umutlu, Lale; Lauenstein, Thomas C

2014-05-01

The objectives of this study were to assess the feasibility of magnetic resonance cholangiography (MRC) using biliary-secreted gadoxetic acid at 7 T and to compare it with T2-weighted (w) MRC at 3 T. Ten healthy volunteers were examined on a 7-T whole-body magnetic resonance system. T2-weighted turbo-spin-echo sequence, T1-w volume-interpolated breath-hold examination (VIBE), and fast low-angle shot (FLASH) with inversion recovery (IR) were acquired in coronal orientation. For dynamic imaging, gadoxetic acid was administrated and data were collected for a period of 5 to 40 minutes after injection. The volunteers underwent subsequent T2-w respiratory-gated MRC at 3 T. For qualitative analysis, a 5-point scale was used. Contrast ratios (CRs) were calculated for quantitative assessment. Contrast-enhanced T1-w MRC at 7 T showed a homogeneous depiction of the intrahepatic and extrahepatic biliary tract with a maximum enhancement of 20 minutes after contrast. Volume-interpolated breath-hold examination and FLASH IR provided a good image quality for the intrahepatic (VIBE, 3.60; FLASH IR, 3.67) and extrahepatic bile ducts (VIBE, 3.50; FLASH IR, 3.72). The quantitative analysis revealed high CR values for FLASH IR (intrahepatic CR, 0.41; extrahepatic CR, 0.45) because of an effective suppression of hepatic tissue and vessels. The T2-w TSE at 7 T showed only a poor image quality without diagnostic potential (intrahepatic, 2.22; extrahepatic, 1.93). Seven-tesla VIBE and FLASH revealed superiority in the depiction of the intrahepatic bile ducts, whereas 3-T MRC was superior in the delineation of the extrahepatic biliary tract. Our results demonstrate the feasibility of contrast-enhanced imaging of the biliary ducts at 7 T.

Can a single-shot black-blood T2-weighted spin-echo echo-planar imaging sequence with sensitivity encoding replace the respiratory-triggered turbo spin-echo sequence for the liver? An optimization and feasibility study.

PubMed

Hussain, Shahid M; De Becker, Jan; Hop, Wim C J; Dwarkasing, Soendersing; Wielopolski, Piotr A

2005-03-01

To optimize and assess the feasibility of a single-shot black-blood T2-weighted spin-echo echo-planar imaging (SSBB-EPI) sequence for MRI of the liver using sensitivity encoding (SENSE), and compare the results with those obtained with a T2-weighted turbo spin-echo (TSE) sequence. Six volunteers and 16 patients were scanned at 1.5T (Philips Intera). In the volunteer study, we optimized the SSBB-EPI sequence by interactively changing the parameters (i.e., the resolution, echo time (TE), diffusion weighting with low b-values, and polarity of the phase-encoding gradient) with regard to distortion, suppression of the blood signal, and sensitivity to motion. The influence of each change was assessed. The optimized SSBB-EPI sequence was applied in patients (N = 16). A number of items, including the overall image quality (on a scale of 1-5), were used for graded evaluation. In addition, the signal-to-noise ratio (SNR) of the liver was calculated. Statistical analysis was carried out with the use of Wilcoxon's signed rank test for comparison of the SSBB-EPI and TSE sequences, with P = 0.05 considered the limit for significance. The SSBB-EPI sequence was improved by the following steps: 1) less frequency points than phase-encoding steps, 2) a b-factor of 20, and 3) a reversed polarity of the phase-encoding gradient. In patients, the mean overall image quality score for the optimized SSBB-EPI (3.5 (range: 1-4)) and TSE (3.6 (range: 3-4)), and the SNR of the liver on SSBB-EPI (mean +/- SD = 7.6 +/- 4.0) and TSE (8.9 +/- 4.6) were not significantly different (P > .05). Optimized SSBB-EPI with SENSE proved to be feasible in patients, and the overall image quality and SNR of the liver were comparable to those achieved with the standard respiratory-triggered T2-weighted TSE sequence. (c) 2005 Wiley-Liss, Inc.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

PubMed

Flannick, Jason; Fuchsberger, Christian; Mahajan, Anubha; Teslovich, Tanya M; Agarwala, Vineeta; Gaulton, Kyle J; Caulkins, Lizz; Koesterer, Ryan; Ma, Clement; Moutsianas, Loukas; McCarthy, Davis J; Rivas, Manuel A; Perry, John R B; Sim, Xueling; Blackwell, Thomas W; Robertson, Neil R; Rayner, N William; Cingolani, Pablo; Locke, Adam E; Tajes, Juan Fernandez; Highland, Heather M; Dupuis, Josee; Chines, Peter S; Lindgren, Cecilia M; Hartl, Christopher; Jackson, Anne U; Chen, Han; Huyghe, Jeroen R; van de Bunt, Martijn; Pearson, Richard D; Kumar, Ashish; Müller-Nurasyid, Martina; Grarup, Niels; Stringham, Heather M; Gamazon, Eric R; Lee, Jaehoon; Chen, Yuhui; Scott, Robert A; Below, Jennifer E; Chen, Peng; Huang, Jinyan; Go, Min Jin; Stitzel, Michael L; Pasko, Dorota; Parker, Stephen C J; Varga, Tibor V; Green, Todd; Beer, Nicola L; Day-Williams, Aaron G; Ferreira, Teresa; Fingerlin, Tasha; Horikoshi, Momoko; Hu, Cheng; Huh, Iksoo; Ikram, Mohammad Kamran; Kim, Bong-Jo; Kim, Yongkang; Kim, Young Jin; Kwon, Min-Seok; Lee, Juyoung; Lee, Selyeong; Lin, Keng-Han; Maxwell, Taylor J; Nagai, Yoshihiko; Wang, Xu; Welch, Ryan P; Yoon, Joon; Zhang, Weihua; Barzilai, Nir; Voight, Benjamin F; Han, Bok-Ghee; Jenkinson, Christopher P; Kuulasmaa, Teemu; Kuusisto, Johanna; Manning, Alisa; Ng, Maggie C Y; Palmer, Nicholette D; Balkau, Beverley; Stančáková, Alena; Abboud, Hanna E; Boeing, Heiner; Giedraitis, Vilmantas; Prabhakaran, Dorairaj; Gottesman, Omri; Scott, James; Carey, Jason; Kwan, Phoenix; Grant, George; Smith, Joshua D; Neale, Benjamin M; Purcell, Shaun; Butterworth, Adam S; Howson, Joanna M M; Lee, Heung Man; Lu, Yingchang; Kwak, Soo-Heon; Zhao, Wei; Danesh, John; Lam, Vincent K L; Park, Kyong Soo; Saleheen, Danish; So, Wing Yee; Tam, Claudia H T; Afzal, Uzma; Aguilar, David; Arya, Rector; Aung, Tin; Chan, Edmund; Navarro, Carmen; Cheng, Ching-Yu; Palli, Domenico; Correa, Adolfo; Curran, Joanne E; Rybin, Dennis; Farook, Vidya S; Fowler, Sharon P; Freedman, Barry I; Griswold, Michael; Hale, Daniel Esten; Hicks, Pamela J; Khor, Chiea-Chuen; Kumar, Satish; Lehne, Benjamin; Thuillier, Dorothée; Lim, Wei Yen; Liu, Jianjun; Loh, Marie; Musani, Solomon K; Puppala, Sobha; Scott, William R; Yengo, Loïc; Tan, Sian-Tsung; Taylor, Herman A; Thameem, Farook; Wilson, Gregory; Wong, Tien Yin; Njølstad, Pål Rasmus; Levy, Jonathan C; Mangino, Massimo; Bonnycastle, Lori L; Schwarzmayr, Thomas; Fadista, João; Surdulescu, Gabriela L; Herder, Christian; Groves, Christopher J; Wieland, Thomas; Bork-Jensen, Jette; Brandslund, Ivan; Christensen, Cramer; Koistinen, Heikki A; Doney, Alex S F; Kinnunen, Leena; Esko, Tõnu; Farmer, Andrew J; Hakaste, Liisa; Hodgkiss, Dylan; Kravic, Jasmina; Lyssenko, Valeri; Hollensted, Mette; Jørgensen, Marit E; Jørgensen, Torben; Ladenvall, Claes; Justesen, Johanne Marie; Käräjämäki, Annemari; Kriebel, Jennifer; Rathmann, Wolfgang; Lannfelt, Lars; Lauritzen, Torsten; Narisu, Narisu; Linneberg, Allan; Melander, Olle; Milani, Lili; Neville, Matt; Orho-Melander, Marju; Qi, Lu; Qi, Qibin; Roden, Michael; Rolandsson, Olov; Swift, Amy; Rosengren, Anders H; Stirrups, Kathleen; Wood, Andrew R; Mihailov, Evelin; Blancher, Christine; Carneiro, Mauricio O; Maguire, Jared; Poplin, Ryan; Shakir, Khalid; Fennell, Timothy; DePristo, Mark; de Angelis, Martin Hrabé; Deloukas, Panos; Gjesing, Anette P; Jun, Goo; Nilsson, Peter; Murphy, Jacquelyn; Onofrio, Robert; Thorand, Barbara; Hansen, Torben; Meisinger, Christa; Hu, Frank B; Isomaa, Bo; Karpe, Fredrik; Liang, Liming; Peters, Annette; Huth, Cornelia; O'Rahilly, Stephen P; Palmer, Colin N A; Pedersen, Oluf; Rauramaa, Rainer; Tuomilehto, Jaakko; Salomaa, Veikko; Watanabe, Richard M; Syvänen, Ann-Christine; Bergman, Richard N; Bharadwaj, Dwaipayan; Bottinger, Erwin P; Cho, Yoon Shin; Chandak, Giriraj R; Chan, Juliana Cn; Chia, Kee Seng; Daly, Mark J; Ebrahim, Shah B; Langenberg, Claudia; Elliott, Paul; Jablonski, Kathleen A; Lehman, Donna M; Jia, Weiping; Ma, Ronald C W; Pollin, Toni I; Sandhu, Manjinder; Tandon, Nikhil; Froguel, Philippe; Barroso, Inês; Teo, Yik Ying; Zeggini, Eleftheria; Loos, Ruth J F; Small, Kerrin S; Ried, Janina S; DeFronzo, Ralph A; Grallert, Harald; Glaser, Benjamin; Metspalu, Andres; Wareham, Nicholas J; Walker, Mark; Banks, Eric; Gieger, Christian; Ingelsson, Erik; Im, Hae Kyung; Illig, Thomas; Franks, Paul W; Buck, Gemma; Trakalo, Joseph; Buck, David; Prokopenko, Inga; Mägi, Reedik; Lind, Lars; Farjoun, Yossi; Owen, Katharine R; Gloyn, Anna L; Strauch, Konstantin; Tuomi, Tiinamaija; Kooner, Jaspal Singh; Lee, Jong-Young; Park, Taesung; Donnelly, Peter; Morris, Andrew D; Hattersley, Andrew T; Bowden, Donald W; Collins, Francis S; Atzmon, Gil; Chambers, John C; Spector, Timothy D; Laakso, Markku; Strom, Tim M; Bell, Graeme I; Blangero, John; Duggirala, Ravindranath; Tai, E Shyong; McVean, Gilean; Hanis, Craig L; Wilson, James G; Seielstad, Mark; Frayling, Timothy M; Meigs, James B; Cox, Nancy J; Sladek, Rob; Lander, Eric S; Gabriel, Stacey; Mohlke, Karen L; Meitinger, Thomas; Groop, Leif; Abecasis, Goncalo; Scott, Laura J; Morris, Andrew P; Kang, Hyun Min; Altshuler, David; Burtt, Noël P; Florez, Jose C; Boehnke, Michael; McCarthy, Mark I

2017-12-19

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

PubMed Central

Jason, Flannick; Fuchsberger, Christian; Mahajan, Anubha; Teslovich, Tanya M.; Agarwala, Vineeta; Gaulton, Kyle J.; Caulkins, Lizz; Koesterer, Ryan; Ma, Clement; Moutsianas, Loukas; McCarthy, Davis J.; Rivas, Manuel A.; Perry, John R. B.; Sim, Xueling; Blackwell, Thomas W.; Robertson, Neil R.; Rayner, N William; Cingolani, Pablo; Locke, Adam E.; Tajes, Juan Fernandez; Highland, Heather M.; Dupuis, Josee; Chines, Peter S.; Lindgren, Cecilia M.; Hartl, Christopher; Jackson, Anne U.; Chen, Han; Huyghe, Jeroen R.; van de Bunt, Martijn; Pearson, Richard D.; Kumar, Ashish; Müller-Nurasyid, Martina; Grarup, Niels; Stringham, Heather M.; Gamazon, Eric R.; Lee, Jaehoon; Chen, Yuhui; Scott, Robert A.; Below, Jennifer E.; Chen, Peng; Huang, Jinyan; Go, Min Jin; Stitzel, Michael L.; Pasko, Dorota; Parker, Stephen C. J.; Varga, Tibor V.; Green, Todd; Beer, Nicola L.; Day-Williams, Aaron G.; Ferreira, Teresa; Fingerlin, Tasha; Horikoshi, Momoko; Hu, Cheng; Huh, Iksoo; Ikram, Mohammad Kamran; Kim, Bong-Jo; Kim, Yongkang; Kim, Young Jin; Kwon, Min-Seok; Lee, Juyoung; Lee, Selyeong; Lin, Keng-Han; Maxwell, Taylor J.; Nagai, Yoshihiko; Wang, Xu; Welch, Ryan P.; Yoon, Joon; Zhang, Weihua; Barzilai, Nir; Voight, Benjamin F.; Han, Bok-Ghee; Jenkinson, Christopher P.; Kuulasmaa, Teemu; Kuusisto, Johanna; Manning, Alisa; Ng, Maggie C. Y.; Palmer, Nicholette D.; Balkau, Beverley; Stančáková, Alena; Abboud, Hanna E.; Boeing, Heiner; Giedraitis, Vilmantas; Prabhakaran, Dorairaj; Gottesman, Omri; Scott, James; Carey, Jason; Kwan, Phoenix; Grant, George; Smith, Joshua D.; Neale, Benjamin M.; Purcell, Shaun; Butterworth, Adam S.; Howson, Joanna M. M.; Lee, Heung Man; Lu, Yingchang; Kwak, Soo-Heon; Zhao, Wei; Danesh, John; Lam, Vincent K. L.; Park, Kyong Soo; Saleheen, Danish; So, Wing Yee; Tam, Claudia H. T.; Afzal, Uzma; Aguilar, David; Arya, Rector; Aung, Tin; Chan, Edmund; Navarro, Carmen; Cheng, Ching-Yu; Palli, Domenico; Correa, Adolfo; Curran, Joanne E.; Rybin, Dennis; Farook, Vidya S.; Fowler, Sharon P.; Freedman, Barry I.; Griswold, Michael; Hale, Daniel Esten; Hicks, Pamela J.; Khor, Chiea-Chuen; Kumar, Satish; Lehne, Benjamin; Thuillier, Dorothée; Lim, Wei Yen; Liu, Jianjun; Loh, Marie; Musani, Solomon K.; Puppala, Sobha; Scott, William R.; Yengo, Loïc; Tan, Sian-Tsung; Taylor, Herman A.; Thameem, Farook; Wilson, Gregory; Wong, Tien Yin; Njølstad, Pål Rasmus; Levy, Jonathan C.; Mangino, Massimo; Bonnycastle, Lori L.; Schwarzmayr, Thomas; Fadista, João; Surdulescu, Gabriela L.; Herder, Christian; Groves, Christopher J.; Wieland, Thomas; Bork-Jensen, Jette; Brandslund, Ivan; Christensen, Cramer; Koistinen, Heikki A.; Doney, Alex S. F.; Kinnunen, Leena; Esko, Tõnu; Farmer, Andrew J.; Hakaste, Liisa; Hodgkiss, Dylan; Kravic, Jasmina; Lyssenko, Valeri; Hollensted, Mette; Jørgensen, Marit E.; Jørgensen, Torben; Ladenvall, Claes; Justesen, Johanne Marie; Käräjämäki, Annemari; Kriebel, Jennifer; Rathmann, Wolfgang; Lannfelt, Lars; Lauritzen, Torsten; Narisu, Narisu; Linneberg, Allan; Melander, Olle; Milani, Lili; Neville, Matt; Orho-Melander, Marju; Qi, Lu; Qi, Qibin; Roden, Michael; Rolandsson, Olov; Swift, Amy; Rosengren, Anders H.; Stirrups, Kathleen; Wood, Andrew R.; Mihailov, Evelin; Blancher, Christine; Carneiro, Mauricio O.; Maguire, Jared; Poplin, Ryan; Shakir, Khalid; Fennell, Timothy; DePristo, Mark; de Angelis, Martin Hrabé; Deloukas, Panos; Gjesing, Anette P.; Jun, Goo; Nilsson, Peter; Murphy, Jacquelyn; Onofrio, Robert; Thorand, Barbara; Hansen, Torben; Meisinger, Christa; Hu, Frank B.; Isomaa, Bo; Karpe, Fredrik; Liang, Liming; Peters, Annette; Huth, Cornelia; O'Rahilly, Stephen P; Palmer, Colin N. A.; Pedersen, Oluf; Rauramaa, Rainer; Tuomilehto, Jaakko; Salomaa, Veikko; Watanabe, Richard M.; Syvänen, Ann-Christine; Bergman, Richard N.; Bharadwaj, Dwaipayan; Bottinger, Erwin P.; Cho, Yoon Shin; Chandak, Giriraj R.; Chan, Juliana CN; Chia, Kee Seng; Daly, Mark J.; Ebrahim, Shah B.; Langenberg, Claudia; Elliott, Paul; Jablonski, Kathleen A.; Lehman, Donna M.; Jia, Weiping; Ma, Ronald C. W.; Pollin, Toni I.; Sandhu, Manjinder; Tandon, Nikhil; Froguel, Philippe; Barroso, Inês; Teo, Yik Ying; Zeggini, Eleftheria; Loos, Ruth J. F.; Small, Kerrin S.; Ried, Janina S.; DeFronzo, Ralph A.; Grallert, Harald; Glaser, Benjamin; Metspalu, Andres; Wareham, Nicholas J.; Walker, Mark; Banks, Eric; Gieger, Christian; Ingelsson, Erik; Im, Hae Kyung; Illig, Thomas; Franks, Paul W.; Buck, Gemma; Trakalo, Joseph; Buck, David; Prokopenko, Inga; Mägi, Reedik; Lind, Lars; Farjoun, Yossi; Owen, Katharine R.; Gloyn, Anna L.; Strauch, Konstantin; Tuomi, Tiinamaija; Kooner, Jaspal Singh; Lee, Jong-Young; Park, Taesung; Donnelly, Peter; Morris, Andrew D.; Hattersley, Andrew T.; Bowden, Donald W.; Collins, Francis S.; Atzmon, Gil; Chambers, John C.; Spector, Timothy D.; Laakso, Markku; Strom, Tim M.; Bell, Graeme I.; Blangero, John; Duggirala, Ravindranath; Tai, E. Shyong; McVean, Gilean; Hanis, Craig L.; Wilson, James G.; Seielstad, Mark; Frayling, Timothy M.; Meigs, James B.; Cox, Nancy J.; Sladek, Rob; Lander, Eric S.; Gabriel, Stacey; Mohlke, Karen L.; Meitinger, Thomas; Groop, Leif; Abecasis, Goncalo; Scott, Laura J.; Morris, Andrew P.; Kang, Hyun Min; Altshuler, David; Burtt, Noël P.; Florez, Jose C.; Boehnke, Michael; McCarthy, Mark I.

2017-01-01

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1–5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D. PMID:29257133

The impact of cerebellar transcranial direct current stimulation (tDCS) on learning fine-motor sequences

PubMed Central

Wu, Allan D.; Samra, Jasmine K.

2017-01-01

The cerebellum has been shown to be important for skill learning, including the learning of motor sequences. We investigated whether cerebellar transcranial direct current stimulation (tDCS) would enhance learning of fine motor sequences. Because the ability to generalize or transfer to novel task variations or circumstances is a crucial goal of real world training, we also examined the effect of tDCS on performance of novel sequences after training. In Study 1, participants received either anodal, cathodal or sham stimulation while simultaneously practising three eight-element key press sequences in a non-repeating, interleaved order. Immediately after sequence practice with concurrent tDCS, a transfer session was given in which participants practised three interleaved novel sequences. No stimulation was given during transfer. An inhibitory effect of cathodal tDCS was found during practice, such that the rate of learning was slowed in comparison to the anodal and sham groups. In Study 2, participants received anodal or sham stimulation and a 24 h delay was added between the practice and transfer sessions to reduce mental fatigue. Although this consolidation period benefitted subsequent transfer for both tDCS groups, anodal tDCS enhanced transfer performance. Together, these studies demonstrate polarity-specific effects on fine motor sequence learning and generalization. This article is part of the themed issue ‘New frontiers for statistical learning in the cognitive sciences’. PMID:27872369

The impact of cerebellar transcranial direct current stimulation (tDCS) on learning fine-motor sequences.

PubMed

Shimizu, Renee E; Wu, Allan D; Samra, Jasmine K; Knowlton, Barbara J

2017-01-05

The cerebellum has been shown to be important for skill learning, including the learning of motor sequences. We investigated whether cerebellar transcranial direct current stimulation (tDCS) would enhance learning of fine motor sequences. Because the ability to generalize or transfer to novel task variations or circumstances is a crucial goal of real world training, we also examined the effect of tDCS on performance of novel sequences after training. In Study 1, participants received either anodal, cathodal or sham stimulation while simultaneously practising three eight-element key press sequences in a non-repeating, interleaved order. Immediately after sequence practice with concurrent tDCS, a transfer session was given in which participants practised three interleaved novel sequences. No stimulation was given during transfer. An inhibitory effect of cathodal tDCS was found during practice, such that the rate of learning was slowed in comparison to the anodal and sham groups. In Study 2, participants received anodal or sham stimulation and a 24 h delay was added between the practice and transfer sessions to reduce mental fatigue. Although this consolidation period benefitted subsequent transfer for both tDCS groups, anodal tDCS enhanced transfer performance. Together, these studies demonstrate polarity-specific effects on fine motor sequence learning and generalization.This article is part of the themed issue 'New frontiers for statistical learning in the cognitive sciences'. © 2016 The Author(s).

Motion corrected DWI with integrated T2-mapping for simultaneous estimation of ADC, T2-relaxation and perfusion in prostate cancer.

PubMed

Skorpil, M; Brynolfsson, P; Engström, M

2017-06-01

Multiparametric magnetic resonance imaging (MRI) and PI-RADS (Prostate Imaging - Reporting and Data System) has become the standard to determine a probability score for a lesion being a clinically significant prostate cancer. T2-weighted and diffusion-weighted imaging (DWI) are essential in PI-RADS, depending partly on visual assessment of signal intensity, while dynamic-contrast enhanced imaging is less important. To decrease inter-rater variability and further standardize image evaluation, complementary objective measures are in need. We here demonstrate a sequence enabling simultaneous quantification of apparent diffusion coefficient (ADC) and T2-relaxation, as well as calculation of the perfusion fraction f from low b-value intravoxel incoherent motion data. Expandable wait pulses were added to a FOCUS DW SE-EPI sequence, allowing the effective echo time to change at run time. To calculate both ADC and f, b-values 200s/mm 2 and 600s/mm 2 were chosen, and for T2-estimation 6 echo times between 64.9ms and 114.9ms were used. Three patients with prostate cancer were examined and all had significantly decreased ADC and T2-values, while f was significantly increased in 2 of 3 tumors. T2 maps obtained in phantom measurements and in a healthy volunteer were compared to T2 maps from a SE sequence with consecutive scans, showing good agreement. In addition, a motion correction procedure was implemented to reduce the effects of prostate motion, which improved T2-estimation. This sequence could potentially enable more objective tumor grading, and decrease the inter-rater variability in the PI-RADS classification. Copyright © 2017 Elsevier Inc. All rights reserved.

MR fingerprinting for rapid quantification of myocardial T1 , T2 , and proton spin density.

PubMed

Hamilton, Jesse I; Jiang, Yun; Chen, Yong; Ma, Dan; Lo, Wei-Ching; Griswold, Mark; Seiberlich, Nicole

2017-04-01

To introduce a two-dimensional MR fingerprinting (MRF) technique for quantification of T 1 , T 2 , and M 0 in myocardium. An electrocardiograph-triggered MRF method is introduced for mapping myocardial T 1 , T 2 , and M 0 during a single breath-hold in as short as four heartbeats. The pulse sequence uses variable flip angles, repetition times, inversion recovery times, and T 2 preparation dephasing times. A dictionary of possible signal evolutions is simulated for each scan that incorporates the subject's unique variations in heart rate. Aspects of the sequence design were explored in simulations, and the accuracy and precision of cardiac MRF were assessed in a phantom study. In vivo imaging was performed at 3 Tesla in 11 volunteers to generate native parametric maps. T 1 and T 2 measurements from the proposed cardiac MRF sequence correlated well with standard spin echo measurements in the phantom study (R 2  > 0.99). A Bland-Altman analysis revealed good agreement for myocardial T 1 measurements between MRF and MOLLI (bias 1 ms, 95% limits of agreement -72 to 72 ms) and T 2 measurements between MRF and T 2 -prepared balanced steady-state free precession (bias, -2.6 ms; 95% limits of agreement, -8.5 to 3.3 ms). MRF can provide quantitative single slice T 1 , T 2 , and M 0 maps in the heart within a single breath-hold. Magn Reson Med 77:1446-1458, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

A cross-sectional study on the associations of insulin resistance with sex hormone, abnormal lipid metabolism in T2DM and IGT patients

PubMed Central

Wang, Xiaoxia; Xian, Tongzhang; Jia, Xiaofan; Zhang, Lina; Liu, Li; Man, Fuli; Zhang, Xianbo; Zhang, Jie; Pan, Qi; Guo, Lixin

2017-01-01

Abstract Type 2 diabetes mellitus (T2DM) is a long-term metabolic disorder. It is characterized by hyperglycemia, insulin resistance (IR), and relative impairment in insulin secretion. IR plays a major role in the pathogenesis of T2DM. Many previous studies have investigated the relationship between estrogen, androgen, and obesity, but few focused on the relationship between sex hormones, abnormal lipid metabolism, and IR. The goal for the present study was to identify the association of IR with sex hormone, abnormal lipid metabolism in type 2 diabetes, and impaired glucose tolerance (IGT) patients. In total 13,400 participants were analyzed based on the results of the glucose tolerance test. Using a cross-sectional study, we showed the relationship between IR and the level of sex hormones among 3 different glucose tolerance states: normal control people, IGT, and T2DM patients. We also analyzed the relationship between IR and abnormal lipid metabolism. Significantly, luteinizing, progesterone, estradiol, prolactin, and follicle-stimulating hormone levels decreased in T2DM and IGT patients compared with those in normal control people. The association between IR and lipid metabolism disorders in T2DM and IGT patients was also observed. Our clinical findings may offer new insights into understanding the mechanism of metabolic disorders and in new therapeutic methods for the treatment of the prevalence of type 2 diabetes. PMID:28658166

Magnetic and crystal structures of the honeycomb lattice Na2IrO3 and single layer Sr2IrO4

NASA Astrophysics Data System (ADS)

Ye, Feng

2013-03-01

5 d based iridates have recently attracted great attention due to the large spin-orbit coupling (SOC). It is now recognized that the SOC that competes with other relevant energies, particularly the on-site Coulomb interaction U, and have driven novel electronic and magnetic phases. Combining single crystal neutron and x-ray diffractions, we have investigated the magnetic and crystal structures of the honeycomb lattice Na2IrO3. The system orders magnetically below 18.1 K with Ir4+ ions forming zigzag spin chains within the layered honeycomb network with ordered moment of 0.22 μB /Ir site. Such a configuration sharply contrasts the Neel or stripe states proposed in the Kitaev-Heisenberg model. The structure refinement reveals that the Ir atoms form nearly ideal 2D honeycomb lattice while the IrO6 octahedra experience a trigonal distortion that is critical to the ground state. The results of this study provide much-needed experimental insights into the magnetic and crystal structure crucial to the understanding of the exotic magnetic order and possible topological characteristics in the 5 d-electron based honeycomb lattice. Neutron diffraction experiments are also performed to investigate the magnetic and crystal structure of the single layer iridate Sr2IrO4, where new structural information and spin order are obtained that is not available from previous neutron powder diffraction measurement. This work was sponsored in part by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy.

Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy.

PubMed

Kramer, Patrick L; Nishida, Jun; Giammanco, Chiara H; Tamimi, Amr; Fayer, Michael D

2015-05-14

In nearly all applications of ultrafast multidimensional infrared spectroscopy, the spectral degrees of freedom (e.g., transition frequency) and the orientation of the transition dipole are assumed to be decoupled. We present experimental results which confirm that frequency fluctuations can be caused by rotational motion and observed under appropriate conditions. A theory of the frequency-frequency correlation function (FFCF) observable under various polarization conditions is introduced, and model calculations are found to reproduce the qualitative trends in FFCF rates. The FFCF determined with polarization-selective two-dimensional infrared (2D IR) spectroscopy is a direct reporter of the frequency-rotational coupling. For the solute methanol in a room temperature ionic liquid, the FFCF of the hydroxyl (O-D) stretch decays due to spectral diffusion with different rates depending on the polarization of the excitation pulses. The 2D IR vibrational echo pulse sequence consists of three excitation pulses that generate the vibrational echo, a fourth pulse. A faster FFCF decay is observed when the first two excitation pulses are polarized perpendicular to the third pulse and the echo, 〈XXY Y〉, than in the standard all parallel configuration, 〈XXXX〉, in which all four pulses have the same polarization. The 2D IR experiment with polarizations 〈XY XY〉 ("polarization grating" configuration) gives a FFCF that decays even more slowly than in the 〈XXXX〉 configuration. Polarization-selective 2D IR spectra of bulk water do not exhibit polarization-dependent FFCF decays; spectral diffusion is effectively decoupled from reorientation in the water system.

Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy

NASA Astrophysics Data System (ADS)

Kramer, Patrick L.; Nishida, Jun; Giammanco, Chiara H.; Tamimi, Amr; Fayer, Michael D.

2015-05-01

In nearly all applications of ultrafast multidimensional infrared spectroscopy, the spectral degrees of freedom (e.g., transition frequency) and the orientation of the transition dipole are assumed to be decoupled. We present experimental results which confirm that frequency fluctuations can be caused by rotational motion and observed under appropriate conditions. A theory of the frequency-frequency correlation function (FFCF) observable under various polarization conditions is introduced, and model calculations are found to reproduce the qualitative trends in FFCF rates. The FFCF determined with polarization-selective two-dimensional infrared (2D IR) spectroscopy is a direct reporter of the frequency-rotational coupling. For the solute methanol in a room temperature ionic liquid, the FFCF of the hydroxyl (O-D) stretch decays due to spectral diffusion with different rates depending on the polarization of the excitation pulses. The 2D IR vibrational echo pulse sequence consists of three excitation pulses that generate the vibrational echo, a fourth pulse. A faster FFCF decay is observed when the first two excitation pulses are polarized perpendicular to the third pulse and the echo, , than in the standard all parallel configuration, , in which all four pulses have the same polarization. The 2D IR experiment with polarizations ("polarization grating" configuration) gives a FFCF that decays even more slowly than in the configuration. Polarization-selective 2D IR spectra of bulk water do not exhibit polarization-dependent FFCF decays; spectral diffusion is effectively decoupled from reorientation in the water system.

Theory of a quantum spin liquid in the hydrogen-intercalated honeycomb iridate H3LiIr2O6

NASA Astrophysics Data System (ADS)

Slagle, Kevin; Choi, Wonjune; Chern, Li Ern; Kim, Yong Baek

2018-03-01

We propose a theoretical model for a gapless spin liquid phase that may have been observed in a recent experiment on H3LiIr2O6 . Despite the insulating and nonmagnetic nature of the material, the specific heat coefficient C /T ˜1 /√{T } in zero magnetic field and C /T ˜T /B3 /2 with finite magnetic field B have been observed. In addition, the NMR relaxation rate shows 1 /(T1T ) ˜(C/T ) 2 . Motivated by the fact that the interlayer/in-plane lattice parameters are reduced/elongated by the hydrogen intercalation of the parent compound Li2IrO3 , we consider four layers of the Kitaev honeycomb lattice model with additional interlayer exchange interactions. It is shown that the resulting spin liquid excitations reside mostly in the top and bottom layers of such a layered structure and possess a quartic dispersion. In an applied magnetic field, each quartic mode is split into four Majorana cones with the velocity v ˜B3 /4 . We suggest that the spin liquid phase in these "defect" layers, placed between different stacking patterns of the honeycomb layers, can explain the major phenomenology of the experiment, which can be taken as evidence that the Kitaev interaction plays the primary role in the formation of a quantum spin liquid in this material.

Direct Measurement of T Cell Receptor Affinity and Sequence from Naïve Anti-Viral T Cells

PubMed Central

Zhang, Shuqi; Parker, Patricia; Ma, Keyue; He, Chenfeng; Shi, Qian; Cui, Zhonghao; Williams, Chad; Wendel, Ben S.; Meriwether, Amanda; Salazar, Mary A.; Jiang, Ning

2016-01-01

T cells recognize and kill a myriad of pathogen-infected or cancer cells using a diverse set of T cell receptors (TCR). The affinity of TCR to cognate antigen is of high interest in adoptive T cell transfer immunotherapy and antigen-specific T cell repertoire immune profiling because it is widely known to correlate with downstream T cell responses. Here, we introduce the in situ TCR affinity and sequence test (iTAST) for simultaneous measurement of TCR affinity and sequence from single primary CD8+ T cells in human blood. We demonstrate that the repertoire of primary antigen-specific T cells from pathogen inexperienced individuals has a surprisingly broad affinity range of 1000-fold composed of diverse TCR sequences. Within this range, samples from older individuals contained a reduced frequency of high affinity T cells compared to young individuals, demonstrating an age-related effect of T cell attrition that could cause holes in the repertoire. iTAST should enable the rapid selection of high affinity TCRs ex vivo for adoptive immunotherapy and measurement of T cell response for immune monitoring applications. PMID:27252176

2D IR spectra of cyanide in water investigated by molecular dynamics simulations

USGS Publications Warehouse

Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

2013-01-01

Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

Comparison of post-contrast 3D-T1-MPRAGE, 3D-T1-SPACE and 3D-T2-FLAIR MR images in evaluation of meningeal abnormalities at 3-T MRI.

PubMed

Jeevanandham, Balaji; Kalyanpur, Tejas; Gupta, Prashant; Cherian, Mathew

2017-06-01

This study was to assess the usefulness of newer three-dimensional (3D)-T 1 sampling perfection with application optimized contrast using different flip-angle evolutions (SPACE) and 3D-T 2 fluid-attenuated inversion recovery (FLAIR) sequences in evaluation of meningeal abnormalities. 78 patients who presented with high suspicion of meningeal abnormalities were evaluated using post-contrast 3D-T 2 -FLAIR, 3D-T 1 magnetization-prepared rapid gradient-echo (MPRAGE) and 3D-T 1 -SPACE sequences. The images were evaluated independently by two radiologists for cortical gyral, sulcal space, basal cisterns and dural enhancement. The diagnoses were confirmed by further investigations including histopathology. Post-contrast 3D-T 1 -SPACE and 3D-T 2 -FLAIR images yielded significantly more information than MPRAGE images (p < 0.05 for both SPACE and FLAIR images) in detection of meningeal abnormalities. SPACE images best demonstrated abnormalities in dural and sulcal spaces, whereas FLAIR was useful for basal cisterns enhancement. Both SPACE and FLAIR performed equally well in detection of gyral enhancement. In all 10 patients, where both SPACE and T 2 -FLAIR images failed to demonstrate any abnormality, further analysis was also negative. The 3D-T 1 -SPACE sequence best demonstrated abnormalities in dural and sulcal spaces, whereas FLAIR was useful for abnormalities in basal cisterns. Both SPACE and FLAIR performed holds good for detection of gyral enhancement. Post-contrast SPACE and FLAIR sequences are superior to the MPRAGE sequence for evaluation of meningeal abnormalities and when used in combination have the maximum sensitivity for leptomeningeal abnormalities. The negative-predictive value is nearly 100%, where no leptomeningeal abnormality was detected on these sequences. Advances in knowledge: Post-contrast 3D-T 1 -SPACE and 3D-T 2 -FLAIR images are more useful than 3D-T 1 -MPRAGE images in evaluation of meningeal abnormalities.

193Ir Mössbauer spectroscopy of Pt-IrO 2 nanoparticle catalysts developed for detection and removal of carbon monoxide from air

NASA Astrophysics Data System (ADS)

Sawicki, J. A.; Marcinkowska, K.; Wagner, F. E.

2010-08-01

Mössbauer spectroscopy of 73.0 keV gamma-ray transition in 193Ir and supplementary analytical techniques were used to study the microstructure and chemical form of polymer-supported hydrophobic bimetallic Pt-Ir catalysts for detection and removal of CO from humid air at ambient conditions. The catalysts, typically with a composition of 9 wt.% Pt and 1 wt.% Ir, were prepared by incipient wetness impregnation of polystyrene-divinylbenzene (SDB) granules with ethanol solutions of hexachloroplatinic and hexachloroiridic acids. This procedure, followed by reduction in H 2 or CO at only 200 °C or 250 °C, resulted in formation of highly-dispersed Pt-Ir particles usually smaller than 20 nm and having high catalytic activity and selectivity. Mössbauer spectra of 73.0 keV gamma-ray transition in 193Ir were taken after consecutive steps of preparation and exposure of catalysts to better understand and further improve the fabrication processes. In the as-impregnated state, iridium was found mostly as Ir(III) in [IrCl 6] 3- ions, with only a small fraction of Ir(IV) in [IrCl 6] 2- ions. The iridium in bimetallic clusters formed by reduction in hydrogen showed a strong tendency towards oxidation on exposure to air at room temperature, while Pt remained mostly metallic. In the most active and stable catalysts, the Ir and Pt in metallic regions of the clusters did not tend to segregate, unlike in Pt-Ir/silica-supported catalysts studied by us earlier. Further, this study shows that the IrO 2-like regions in the clusters exhibit stronger deviations from local symmetry and stoichiometry of crystalline IrO 2 than observed previously in Pt-Ir/silica catalysts. Our study also indicates that in the examined Pt-IrO 2 nanoparticles iridium largely provides the dissociative O 2 adsorption sites, while the CO adsorption occurs primarily at metallic Pt sites.

VLT near- to mid-IR imaging and spectroscopy of the M 17 UC1 - IRS5 region

NASA Astrophysics Data System (ADS)

Chen, Zhiwei; Nürnberger, Dieter E. A.; Chini, Rolf; Jiang, Zhibo; Fang, Min

2015-06-01

Aims: We investigate the surroundings of the hypercompact H ii region M 17 UC1 to probe the physical properties of the associated young stellar objects and the environment of massive star formation. Methods: We use diffraction-limited near-IR (VLT/NACO) and mid-IR (VLT/VISIR) images to reveal the different morphologies at various wavelengths. Likewise, we investigate the stellar and nebular content of the region with VLT/SINFONI integral field spectroscopy with a resolution R ˜ 1500 at H + K bands. Results: Five of the seven point sources in this region show L-band excess emission. A geometric match is found between the H2 emission and near-IR polarized light in the vicinity of IRS5A, and between the diffuse mid-IR emission and near-IR polarization north of UC1. The H2 emission is typical for dense photodissociation regions (PDRs), which are initially far-ultraviolet pumped and repopulated by collisional de-excitation. The spectral types of IRS5A and B273A are B3-B7 V/III and G4-G5 III, respectively. The observed infrared luminosity LIR in the range 1-20 μm is derived for three objects; we obtain 2.0 × 103 L⊙ for IRS5A, 13 L⊙ for IRS5C, and 10 L⊙ for B273A. Conclusions: IRS5 might be a young quadruple system. Its primary star IRS5A is confirmed to be a high-mass protostellar object (˜9 M⊙, ˜1 × 105 yrs); it might have terminated accretion due to the feedback from stellar activities (radiation pressure, outflow) and the expanding H ii region of M 17. The object UC1 might also have terminated accretion because of the expanding hypercompact H ii region, which it ionizes. The disk clearing process of the low-mass young stellar objects in this region might be accelerated by the expanding H ii region. The outflows driven by UC1 are running south-north with its northeastern side suppressed by the expanding ionization front of M 17; the blue-shifted outflow lobe of IRS5A is seen in two types of tracers along the same line of sight in the form of H2 emission

Differential insulin receptor substrate-1 (IRS1)-related modulation of neuropeptide Y and proopiomelanocortin expression in nondiabetic and diabetic IRS2-/- mice.

PubMed

Burgos-Ramos, Emma; González-Rodríguez, Agueda; Canelles, Sandra; Baquedano, Eva; Frago, Laura M; Revuelta-Cervantes, Jesús; Gómez-Ambrosi, Javier; Frühbeck, Gema; Chowen, Julie A; Argente, Jesús; Valverde, Angela M; Barrios, Vicente

2012-03-01

Insulin resistance and type 2 diabetes correlate with impaired leptin and insulin signaling. Insulin receptor substrate-2 deficient (IRS2(-/-)) mice are an accepted model for the exploration of alterations in these signaling pathways and their relationship with diabetes; however, disturbances in hypothalamic signaling and the effect on neuropeptides controlling food intake remain unclear. Our aim was to analyze how leptin and insulin signaling may differentially affect the expression of hypothalamic neuropeptides regulating food intake and hypothalamic inflammation in diabetic (D) and nondiabetic (ND) IRS2(-/-) mice. We analyzed the activation of leptin and insulin targets by Western blotting and their association by immunoprecipitation, as well as the mRNA levels of neuropeptide Y (NPY), proopiomelanocortin, and inflammatory markers by real-time PCR and colocalization of forkhead box protein O1 (FOXO1) and NPY by double immunohistochemistry in the hypothalamus. Serum leptin and insulin levels and hypothalamic Janus kinase 2 and signal transducer and activator of transcription factor 3 activation were increased in ND IRS2(-/-) mice. IRS1 levels and its association with Janus kinase 2 and p85 and protein kinase B activation were increased in ND IRS2(-/-). Increased FOXO1 positively correlated with NPY mRNA levels in D IRS2(-/-) mice, with FOXO1 showing mainly nuclear localization in D IRS2(-/-) and cytoplasmic in ND IRS2(-/-) mice. D IRS2(-/-) mice exhibited higher hypothalamic inflammation markers than ND IRS2(-/-) mice. In conclusion, differential activation of these pathways and changes in the expression of NPY and inflammation may exert a protective effect against hypothalamic deregulation of appetite, suggesting that manipulation of these targets could be of interest in the treatment of insulin resistance and type 2 diabetes.

CHARACTERIZATION AND NUCLEOTIDE SEQUENCE DETERMINATION OF A REPEAT ELEMENT ISOLATED FROM A 2,4,5,-T DEGRADING STRAIN OF PSEUDOMONAS CEPACIA

EPA Science Inventory

Pseudomonas cepacia strain AC1100, capable of growth on 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), was mutated to the 2,4,5-T− strain PT88 by a ColE1 :: Tn5 chromosomal insertion. Using cloned DNA from the region flanking the insertion, a 1477-bp sequence (designated RS1100) wa...

GRE T2∗-Weighted MRI: Principles and Clinical Applications

PubMed Central

Tang, Meng Yue; Chen, Tian Wu; Zhang, Xiao Ming; Huang, Xiao Hua

2014-01-01

The sequence of a multiecho gradient recalled echo (GRE) T2*-weighted imaging (T2*WI) is a relatively new magnetic resonance imaging (MRI) technique. In contrast to T2 relaxation, which acquires a spin echo signal, T2* relaxation acquires a gradient echo signal. The sequence of a GRE T2*WI requires high uniformity of the magnetic field. GRE T2*WI can detect the smallest changes in uniformity in the magnetic field and can improve the rate of small lesion detection. In addition, the T2* value can indirectly reflect changes in tissue biochemical components. Moreover, it can be used for the early diagnosis and quantitative diagnosis of some diseases. This paper reviews the principles and clinical applications as well as the advantages and disadvantages of GRE T2*WI. PMID:24987676

Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).

PubMed

Frank, Oliver; Pradella, Silke; Rohde, Manfred; Scheuner, Carmen; Klenk, Hans-Peter; Göker, Markus; Petersen, Jörn

2014-06-15

Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.

Insulin Resistance-Associated Interhemispheric Functional Connectivity Alterations in T2DM: A Resting-State fMRI Study

PubMed Central

Xia, Wenqing; Wang, Shaohua; Spaeth, Andrea M.; Rao, Hengyi; Wang, Pin; Yang, Yue; Huang, Rong; Cai, Rongrong; Sun, Haixia

2015-01-01

We aim to investigate whether decreased interhemispheric functional connectivity exists in patients with type 2 diabetes mellitus (T2DM) by using resting-state functional magnetic resonance imaging (rs-fMRI). In addition, we sought to determine whether interhemispheric functional connectivity deficits associated with cognition and insulin resistance (IR) among T2DM patients. We compared the interhemispheric resting state functional connectivity of 32 T2DM patients and 30 healthy controls using rs-fMRI. Partial correlation coefficients were used to detect the relationship between rs-fMRI information and cognitive or clinical data. Compared with healthy controls, T2DM patients showed bidirectional alteration of functional connectivity in several brain regions. Functional connectivity values in the middle temporal gyrus (MTG) and in the superior frontal gyrus were inversely correlated with Trail Making Test-B score of patients. Notably, insulin resistance (log homeostasis model assessment-IR) negatively correlated with functional connectivity in the MTG of patients. In conclusion, T2DM patients exhibit abnormal interhemispheric functional connectivity in several default mode network regions, particularly in the MTG, and such alteration is associated with IR. Alterations in interhemispheric functional connectivity might contribute to cognitive dysfunction in T2DM patients. PMID:26064945

Optimal Cut-Offs of Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) to Identify Dysglycemia and Type 2 Diabetes Mellitus: A 15-Year Prospective Study in Chinese.

PubMed

Lee, C H; Shih, A Z L; Woo, Y C; Fong, C H Y; Leung, O Y; Janus, E; Cheung, B M Y; Lam, K S L

The optimal reference range of homeostasis model assessment of insulin resistance (HOMA-IR) in normal Chinese population has not been clearly defined. Here we address this issue using the Hong Kong Cardiovascular Risk Factor Prevalence Study (CRISPS), a prospective population-based cohort study with long-term follow-up. In this study, normal glucose tolerance (NGT), impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and type 2 diabetes mellitus (T2DM) were defined according to the 1998 World Health Organization criteria. Dysglycemia referred to IFG, IGT or T2DM. This study comprised two parts. Part one was a cross-sectional study involving 2,649 Hong Kong Chinese subjects, aged 25-74 years, at baseline CRISPS-1 (1995-1996). The optimal HOMA-IR cut-offs for dysglycemia and T2DM were determined by the receiver-operating characteristic (ROC) curve. Part two was a prospective study involving 872 subjects who had persistent NGT at CRISPS-4 (2010-2012) after 15 years of follow-up. At baseline, the optimal HOMA-IR cut-offs to identify dysglyceia and T2DM were 1.37 (AUC = 0.735; 95% confidence interval [CI] = 0.713-0.758; Sensitivity [Se] = 65.6%, Specificity [Sp] = 71.3%] and 1.97 (AUC = 0.807; 95% CI = 0.777-0.886; Se = 65.5%, Sp = 82.9%) respectively. These cut-offs, derived from the cross-sectional study at baseline, corresponded closely to the 75th (1.44) and 90th (2.03) percentiles, respectively, of the HOMA-IR reference range derived from the prospective study of subjects with persistent NGT. HOMA-IR cut-offs, of 1.4 and 2.0, which discriminated dysglycemia and T2DM respectively from NGT in Southern Chinese, can be usefully employed as references in clinical research involving the assessment of insulin resistance.

Evaluation of MR imaging with T1 and T2* mapping for the determination of hepatic iron overload.

PubMed

Henninger, B; Kremser, C; Rauch, S; Eder, R; Zoller, H; Finkenstedt, A; Michaely, H J; Schocke, M

2012-11-01

To evaluate MRI using T1 and T2* mapping sequences in patients with suspected hepatic iron overload (HIO). Twenty-five consecutive patients with clinically suspected HIO were retrospectively studied. All underwent MRI and liver biopsy. For the quantification of liver T2* values we used a fat-saturated multi-echo gradient echo sequence with 12 echoes (TR = 200 ms, TE = 0.99 ms +  n × 1.41 ms, flip angle 20°). T1 values were obtained using a fast T1 mapping sequence based on an inversion recovery snapshot FLASH sequence. Parameter maps were analysed using regions of interest. ROC analysis calculated cut-off points at 10.07 ms and 15.47 ms for T2* in the determination of HIO with accuracy 88 %/88 %, sensitivity 84 %/89.5 % and specificity 100 %/83 %. MRI correctly classified 20 patients (80 %). All patients with HIO only had decreased T1 and T2* relaxation times. There was a significant difference in T1 between patients with HIO only and patients with HIO and steatohepatitis (P = 0.018). MRI-based T2* relaxation diagnoses HIO very accurately, even at low iron concentrations. Important additional information may be obtained by the combination of T1 and T2* mapping. It is a rapid, non-invasive, accurate and reproducible technique for validating the evidence of even low hepatic iron concentrations. • Hepatic iron overload causes fibrosis, cirrhosis and increases hepatocellular carcinoma risk. • MRI detects iron because of the field heterogeneity generated by haemosiderin. • T2* relaxation is very accurate in diagnosing hepatic iron overload. • Additional information may be obtained by T1 and T2* mapping.

Electronic signatures of dimerization in IrTe2

NASA Astrophysics Data System (ADS)

Dai, Jixia; Wu, Weida; Oh, Yoon Seok; Cheong, S.-W.; Yang, J. J.

2014-03-01

Recently, the mysterious phase transition around Tc ~ 260 K in IrTe2 has been intensively studied. A structural supermodulation with q =1/5 was identified below Tc. A variety of microscopic mechanisms have been proposed to account for this transition, including charge-density wave due to Fermi surface nesting, Te p-orbital driven structure instability, anionic depolymerization, ionic dimerization, and so on. However, there has not been an unified picture on the nature of this transition. To address this issue, we have performed low-temperature scanning tunneling microscopy and spectroscopy (STM/STS) experiments on IrTe2 and IrTe2-xSex. Our STM data clearly shows a strong bias dependence in both topography and local density of states (STS) maps. High resolution spectroscopic data further confirms the stripe-like electronic states modulation, which provides insight to the ionic dimerization revealed by X-ray diffraction.

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed Central

Spielmann, A; Stutz, E

1983-01-01

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2. PMID:6314279

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

PubMed

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

BH3-Only Molecule Bim Mediates β-Cell Death in IRS2 Deficiency

PubMed Central

Ren, Decheng; Sun, Juan; Mao, Liqun; Ye, Honggang

2014-01-01

Irs2-deficient mice develop type 2–like diabetes due to a reduction in β-cell mass and a failure of pancreatic islets to undergo compensatory hyperplasia in response to insulin resistance. In order to define the molecular mechanisms, we knocked down Irs2 gene expression in mouse MIN6 insulinoma cells. Insulin receptor substrate 2 (IRS2) suppression induced apoptotic cell death, which was associated with an increase in expression of the BH3-only molecule Bim. Knockdown (KD) of Bim reduced apoptotic β-cell death induced by IRS2 suppression. In Irs2-deficient mice, Bim ablation restored β-cell mass, decreased the number of TUNEL-positive cells, and restored normal glucose tolerance after glucose challenge. FoxO1 mediates Bim upregulation induced by IRS2 suppression, and FoxO1 KD partially inhibits β-cell death induced by IRS2 suppression. These results suggest that Bim plays an important role in mediating the increase in β-cell apoptosis and the reduction in β-cell mass that occurs in IRS2-deficient diabetes. PMID:24760140

Membrane localization of insulin receptor substrate-2 (IRS-2) is associated with decreased overall survival in breast cancer

PubMed Central

Clark, Jennifer L.; Dresser, Karen; Hsieh, Chung-Cheng; Sabel, Michael; Kleer, Celina G.; Khan, Ashraf

2011-01-01

Recent studies have identified a role for insulin receptor substrate-2 (IRS-2) in promoting motility and metastasis in breast cancer. However, no published studies to date have examined IRS-2 expression in human breast tumors. We examined IRS-2 expression by immunohistochemistry (IHC) in normal breast tissue, benign breast lesions, and malignant breast tumors from the institutional pathology archives and a tumor microarray from a separate institution. Three distinct IRS-2 staining patterns were noted: diffusely cytoplasmic, punctate cytoplasmic, and localized to the cell membrane. The individual and pooled datasets were analyzed for associations of IRS-2 staining pattern with core clinical parameters and clinical outcomes. Univariate analysis revealed a trend toward decreased overall survival (OS) with IRS-2 membrane staining, and this association became significant upon multivariate analysis (P = 0.01). In progesterone receptor negative (PR−) tumors, in particular, IRS-2 staining at the membrane correlated with significantly worse OS than other IRS-2 staining patterns (P < 0.001). When PR status and IRS-2 staining pattern were evaluated in combination, PR− tumors with IRS-2 at the membrane were associated with a significantly decreased OS when compared with all other combinations (P = 0.002). Evaluation of IRS-2 staining patterns could potentially be used to identify patients with PR− tumors who would most benefit from aggressive treatment. PMID:21258861

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.

PubMed

Fiston-Lavier, Anna-Sophie; Barrón, Maite G; Petrov, Dmitri A; González, Josefa

2015-02-27

Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Wushenziye Formula Improves Skeletal Muscle Insulin Resistance in Type 2 Diabetes Mellitus via PTP1B-IRS1-Akt-GLUT4 Signaling Pathway.

PubMed

Tian, Chunyu; Chang, Hong; La, Xiaojin; Li, Ji-An

2017-01-01

Background. Wushenziye formula (WSZYF) is an effective traditional Chinese medicine in the treatment of type 2 diabetes mellitus (T2DM). Aim. This study aimed to identify the effects and underlying mechanisms of WSZYF on improving skeletal muscle insulin resistance in T2DM. Methods. An animal model of T2DM was induced by Goto-Kakizaki diabetes prone rats fed with high fat and sugar for 4 weeks. Insulin resistance model was induced in skeletal muscle cell. Results. In vivo , WSZYF improved general conditions and decreased significantly fasting blood glucose, glycosylated serum protein, glycosylated hemoglobin, insulin concentration, and insulin resistance index of T2DM rats. In vitro , WSZYF enhanced glucose consumption in insulin resistance model of skeletal muscle cell. Furthermore, WSZYF affected the expressions of molecules in regulating T2DM, including increasing the expressions of p-IRS1, p-Akt, and GLUT4, reducing PTP1B expression. Conclusion . These findings displayed the potential of WSZYF as a new drug candidate in the treatment of T2DM and the antidiabetic mechanism of WSZYF is probably mediated through modulating the PTP1B-IRS1-Akt-GLUT4 signaling pathway.

Wushenziye Formula Improves Skeletal Muscle Insulin Resistance in Type 2 Diabetes Mellitus via PTP1B-IRS1-Akt-GLUT4 Signaling Pathway

PubMed Central

La, Xiaojin; Li, Ji-an

2017-01-01

Background. Wushenziye formula (WSZYF) is an effective traditional Chinese medicine in the treatment of type 2 diabetes mellitus (T2DM). Aim. This study aimed to identify the effects and underlying mechanisms of WSZYF on improving skeletal muscle insulin resistance in T2DM. Methods. An animal model of T2DM was induced by Goto-Kakizaki diabetes prone rats fed with high fat and sugar for 4 weeks. Insulin resistance model was induced in skeletal muscle cell. Results. In vivo, WSZYF improved general conditions and decreased significantly fasting blood glucose, glycosylated serum protein, glycosylated hemoglobin, insulin concentration, and insulin resistance index of T2DM rats. In vitro, WSZYF enhanced glucose consumption in insulin resistance model of skeletal muscle cell. Furthermore, WSZYF affected the expressions of molecules in regulating T2DM, including increasing the expressions of p-IRS1, p-Akt, and GLUT4, reducing PTP1B expression. Conclusion. These findings displayed the potential of WSZYF as a new drug candidate in the treatment of T2DM and the antidiabetic mechanism of WSZYF is probably mediated through modulating the PTP1B-IRS1-Akt-GLUT4 signaling pathway. PMID:29479370

Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

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

Stackebrandt, Erko; Zeytun, Ahmet; Lapidus, Alla L.

2013-01-01

Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for whichmore » complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

HST WFC3/IR Calibration Updates

NASA Astrophysics Data System (ADS)

Durbin, Meredith; Brammer, Gabriel; Long, Knox S.; Pirzkal, Norbert; Ryan, Russell E.; McCullough, Peter R.; Baggett, Sylvia M.; Gosmeyer, Catherine; Bourque, Matthew; HST WFC3 Team

2016-01-01

We report on several improvements to the characterization, monitoring, and calibration of the HST WFC3/IR detector. The detector performance has remained overall stable since its installation during HST Servicing Mission 4 in 2009. We present an updated persistence model that takes into account effects of exposure time and spatial variations in persistence across the detector, new grism wavelength solutions and master sky images, and a new SPARS sample sequence. We also discuss the stability of the IR gain, the time evolution and photometric properties of IR "snowballs," and the effect of IR "blobs" on point-source photometry.

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

PubMed

Rizzetto, Simone; Eltahla, Auda A; Lin, Peijie; Bull, Rowena; Lloyd, Andrew R; Ho, Joshua W K; Venturi, Vanessa; Luciani, Fabio

2017-10-06

Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% - 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.

{sup 45}Sc Solid State NMR studies of the silicides ScTSi (T=Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt)

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

Harmening, Thomas; Eckert, Hellmut, E-mail: eckerth@uni-muenster.de; Fehse, Constanze M.

The silicides ScTSi (T=Fe, Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt) were synthesized by arc-melting and characterized by X-ray powder diffraction. The structures of ScCoSi, ScRuSi, ScPdSi, and ScIrSi were refined from single crystal diffractometer data. These silicides crystallize with the TiNiSi type, space group Pnma. No systematic influences of the {sup 45}Sc isotropic magnetic shift and nuclear electric quadrupolar coupling parameters on various structural distortion parameters calculated from the crystal structure data can be detected. {sup 45}Sc MAS-NMR data suggest systematic trends in the local electronic structure probed by the scandium atoms: both the electric field gradients andmore » the isotropic magnetic shifts relative to a 0.2 M aqueous Sc(NO{sub 3}){sub 3} solution decrease with increasing valence electron concentration and within each T group the isotropic magnetic shift decreases monotonically with increasing atomic number. The {sup 45}Sc nuclear electric quadrupolar coupling constants are generally well reproduced by quantum mechanical electric field gradient calculations using the WIEN2k code. Highlights: Black-Right-Pointing-Pointer Arc-melting synthesis of silicides ScTSi. Black-Right-Pointing-Pointer Single crystal X-ray data of ScCoSi, ScRuSi, ScPdSi, and ScIrSi. Black-Right-Pointing-Pointer {sup 45}Sc solid state NMR of silicides ScTSi.« less

Insulin Receptor Substrate (IRS)-2 negatively regulates alternative macrophage activation and allergic lung inflammation

PubMed Central

Dasgupta, Preeta; Dorsey, Nicolas J.; Li, Jiaqi; Qi, Xiulan; Smith, Elizabeth P.; Yamaji-Kegan, Kazuyo; Keegan, Achsah D.

2017-01-01

Insulin Receptor Substrate (IRS)-2 is an adaptor protein that becomes tyrosine phosphorylated in response to IL-4 and IL-13 resulting in activation of the PI-3′ kinase/Akt pathway. While the contribution of IL-4 and IL-13 to allergic lung inflammation has been studied extensively, the functional significance of the IRS2 pathway is unclear. To examine the role of IRS2 in allergic disease, we evaluated responses in IRS2-deficient mice. Deficiency of IRS2 resulted in a substantial increase in expression of a subset of genes associated with alternatively activated macrophages (AAM) in response to IL-4 or IL-13 in vitro. Moreover, IRS2+/− and IRS2−/− mice developed enhanced pulmonary inflammation, accumulation of eosinophils and AAM, and airway and vascular remodeling upon allergen stimulation in comparison to IRS2+/+ mice; this enhanced response was in part macrophage intrinsic. Loss of IRS2 led to greater phosphorylation of Akt and ribosomal S6 protein in the basal state and upon IL-4 stimulation. Thus, we identify a critical negative regulatory loop downstream of IRS2, demonstrating a previously unrecognized role for IRS2 in suppressing allergic lung inflammation and remodeling. PMID:27330190

Simultaneous Quantitative MRI Mapping of T1, T2* and Magnetic Susceptibility with Multi-Echo MP2RAGE

PubMed Central

Kober, Tobias; Möller, Harald E.; Schäfer, Andreas

2017-01-01

The knowledge of relaxation times is essential for understanding the biophysical mechanisms underlying contrast in magnetic resonance imaging. Quantitative experiments, while offering major advantages in terms of reproducibility, may benefit from simultaneous acquisitions. In this work, we demonstrate the possibility of simultaneously recording relaxation-time and susceptibility maps with a prototype Multi-Echo (ME) Magnetization-Prepared 2 RApid Gradient Echoes (MP2RAGE) sequence. T1 maps can be obtained using the MP2RAGE sequence, which is relatively insensitive to inhomogeneities of the radio-frequency transmit field, B1+. As an extension, multiple gradient echoes can be acquired in each of the MP2RAGE readout blocks, which permits the calculation of T2* and susceptibility maps. We used computer simulations to explore the effects of the parameters on the precision and accuracy of the mapping. In vivo parameter maps up to 0.6 mm nominal resolution were acquired at 7 T in 19 healthy volunteers. Voxel-by-voxel correlations and the test-retest reproducibility were used to assess the reliability of the results. When using optimized paramenters, T1 maps obtained with ME-MP2RAGE and standard MP2RAGE showed excellent agreement for the whole range of values found in brain tissues. Simultaneously obtained T2* and susceptibility maps were of comparable quality as Fast Low-Angle SHot (FLASH) results. The acquisition times were more favorable for the ME-MP2RAGE (≈ 19 min) sequence as opposed to the sum of MP2RAGE (≈ 12 min) and FLASH (≈ 10 min) acquisitions. Without relevant sacrifice in accuracy, precision or flexibility, the multi-echo version may yield advantages in terms of reduced acquisition time and intrinsic co-registration, provided that an appropriate optimization of the acquisition parameters is performed. PMID:28081157

Using the dGEMRIC technique to evaluate cartilage health in the presence of surgical hardware at 3T: comparison of inversion recovery and saturation recovery approaches.

PubMed

d'Entremont, Agnes G; Kolind, Shannon H; Mädler, Burkhard; Wilson, David R; MacKay, Alexander L

2014-03-01

To evaluate the effect of metal artifact reduction techniques on dGEMRIC T(1) calculation with surgical hardware present. We examined the effect of stainless-steel and titanium hardware on dGEMRIC T(1) maps. We tested two strategies to reduce metal artifact in dGEMRIC: (1) saturation recovery (SR) instead of inversion recovery (IR) and (2) applying the metal artifact reduction sequence (MARS), in a gadolinium-doped agarose gel phantom and in vivo with titanium hardware. T(1) maps were obtained using custom curve-fitting software and phantom ROIs were defined to compare conditions (metal, MARS, IR, SR). A large area of artifact appeared in phantom IR images with metal when T(I) ≤ 700 ms. IR maps with metal had additional artifact both in vivo and in the phantom (shifted null points, increased mean T(1) (+151 % IR ROI(artifact)) and decreased mean inversion efficiency (f; 0.45 ROI(artifact), versus 2 for perfect inversion)) compared to the SR maps (ROI(artifact): +13 % T(1) SR, 0.95 versus 1 for perfect excitation), however, SR produced noisier T(1) maps than IR (phantom SNR: 118 SR, 212 IR). MARS subtly reduced the extent of artifact in the phantom (IR and SR). dGEMRIC measurement in the presence of surgical hardware at 3T is possible with appropriately applied strategies. Measurements may work best in the presence of titanium and are severely limited with stainless steel. For regions near hardware where IR produces large artifacts making dGEMRIC analysis impossible, SR-MARS may allow dGEMRIC measurements. The position and size of the IR artifact is variable, and must be assessed for each implant/imaging set-up.

4PS/insulin receptor substrate (IRS)-2 is the alternative substrate of the insulin receptor in IRS-1-deficient mice.

PubMed

Patti, M E; Sun, X J; Bruening, J C; Araki, E; Lipes, M A; White, M F; Kahn, C R

1995-10-20

Insulin receptor substrate-1 (IRS-1) is the major cytoplasmic substrate of the insulin and insulin-like growth factor (IGF)-1 receptors. Transgenic mice lacking IRS-1 are resistant to insulin and IGF-1, but exhibit significant residual insulin action which corresponds to the presence of an alternative high molecular weight substrate in liver and muscle. Recently, Sun et al. (Sun, X.-J., Wang, L.-M., Zhang, Y., Yenush, L. P., Myers, M. G., Jr., Glasheen, E., Lane, W.S., Pierce, J. H., and White, M. F. (1995) Nature 377, 173-177) purified and cloned 4PS, the major substrate of the IL-4 receptor-associated tyrosine kinase in myeloid cells, which has significant structural similarity to IRS-1. To determine if 4PS is the alternative substrate of the insulin receptor in IRS-1-deficient mice, we performed immunoprecipitation, immunoblotting, and phosphatidylinositol (PI) 3-kinase assays using specific antibodies to 4PS. Following insulin stimulation, 4PS is rapidly phosphorylated in liver and muscle, binds to the p85 subunit of PI 3-kinase, and activates the enzyme. Insulin stimulation also results in the association of 4PS with Grb 2 in both liver and muscle. In IRS-1-deficient mice, both the phosphorylation of 4PS and associated PI 3-kinase activity are enhanced, without an increase in protein expression. Immunodepletion of 4PS from liver and muscle homogenates removes most of the phosphotyrosine-associated PI 3-kinase activity in IRS-1-deficient mice. Thus, 4PS is the primary alternative substrate, i.e. IRS-2, which plays a major role in physiologic insulin signal transduction via both PI 3-kinase activation and Grb 2/Sos association. In IRS-1-deficient mice, 4PS/IRS-2 provides signal transduction to these two major pathways of insulin signaling.

Synthesis, structures, and phase transitions of barium bismuth iridium oxide perovskites Ba{sub 2}BiIrO{sub 6} and Ba{sub 3}BiIr{sub 2}O{sub 9}

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

Ling, Chris D., E-mail: c.ling@chem.usyd.edu.a; Bragg Institute, ANSTO, PMB 1, Menai 2234; Kennedy, Brendan J.

The Ba-Bi-Ir-O system is found to contain two distinct perovskite-type phases: a rock-salt ordered double perovskite Ba{sub 2}BiIrO{sub 6}; and a 6H-type hexagonal perovskite Ba{sub 3}BiIr{sub 2}O{sub 9}. Ba{sub 2}BiIrO{sub 6} undergoes a series of symmetry-lowering phase transitions on cooling Fm3-barm->R3-barc->12/m(C2/m)->I1-bar(P1-bar), all of which are second order except the rhombohedral->monoclinic one, which is first order. The monoclinic phase is only observed in a 2-phase rhombohedral+monoclinic regime. The transition and 2-phase region lie very close to 300 K, making the room-temperature X-ray diffraction patterns extremely complex and potentially explaining why Ba{sub 2}BiIrO{sub 6} had not previously been identified and reported. Amore » solid solution Ba{sub 2}Bi{sub 1+x}Ir{sub 1-x}O{sub 6}, analogous to Ba{sub 2}Bi{sub 1+x}Ru{sub 1-x}O{sub 6}, 0<=x<=2/3, was not observed. The 6H-type phase Ba{sub 3}BiIr{sub 2}O{sub 9} undergoes a clean second-order phase transition P6{sub 3}/mmc->C2/c at 750 K, unlike 6H-type Ba{sub 3}LaIr{sub 2}O{sub 9}, the P6{sub 3}/mmc structure of which is highly strained below {approx}750 K but fails to distort coherently to the monoclinic phase. - Graphical abstract: Structure of Ba{sub 3}BiIr{sub 2}O{sub 9} at 300 K. BiO{sub 6} octahedra are purple, IrO{sub 6} octahedra are gold, and Ba atoms are green. Thermal ellipsoids at 90% probability.« less

Comparison of Different Magnetic Resonance Cholangiography Techniques in Living Liver Donors Including Gd-EOB-DTPA Enhanced T1-Weighted Sequences

PubMed Central

Kinner, Sonja; Steinweg, Verena; Maderwald, Stefan; Radtke, Arnold; Sotiropoulos, Georgios; Forsting, Michael; Schroeder, Tobias

2014-01-01

Objectives Preoperative evaluation of potential living liver donors (PLLDs) includes the assessment of the biliary anatomy to avoid postoperative complications. Aim of this study was to compare T2-weighted (T2w) and Gd-EOB-DTPA enhanced T1-weighted (T1w) magnetic resonance cholangiography (MRC) techniques in the evaluation of PLLDs. Materials and Methods 30 PLLDs underwent MRC on a 1.5 T Magnetom Avanto (Siemens, Erlangen, Germany) using (A) 2D T2w HASTE (Half Fourier Acquisition Single Shot Turbo Spin Echo) fat saturated (fs) in axial plane, (B) 2D T2w HASTE fs thick slices in coronal plane, (C) free breathing 3D T2w TSE (turbo spin echo) RESTORE (high-resolution navigator corrected) plus (D) maximum intensity projections (MIPs), (E) T2w SPACE (sampling perfection with application optimized contrasts using different flip angle evolutions) plus (F) MIPs and (G) T2w TSE BLADE as well as Gd-EOB-DTPA T1w images without (G) and with (H) inversion recovery. Contrast enhanced CT cholangiography served as reference imaging modality. Two independent reviewers evaluated the biliary tract anatomy on a 5-point scale subjectively and objectively. Data sets were compared using a Mann-Whitney-U-test. Kappa values were also calculated. Results Source images and maximum intensity projections of 3D T2w TSE sequences (RESTORE and SPACE) proved to be best for subjective and objective evaluation directly followed by 2D HASTE sequences. Interobserver variabilities were good to excellent (k = 0.622–0.804). Conclusions 3D T2w sequences are essential for preoperative biliary tract evaluation in potential living liver donors. Furthermore, our results underline the value of different MRCP sequence types for the evaluation of the biliary anatomy in PLLDs including Gd-EOB-DTPA enhanced T1w MRC. PMID:25426932

Multipole Superconductivity in Nonsymmorphic Sr_{2}IrO_{4}.

PubMed

Sumita, Shuntaro; Nomoto, Takuya; Yanase, Youichi

2017-07-14

Discoveries of marked similarities to high-T_{c} cuprate superconductors point to the realization of superconductivity in the doped J_{eff}=1/2 Mott insulator Sr_{2}IrO_{4}. Contrary to the mother compound of cuprate superconductors, several stacking patterns of in-plane canted antiferromagnetic moments have been reported, which are distinguished by the ferromagnetic components as -++-, ++++, and -+-+. In this paper, we clarify unconventional features of the superconductivity coexisting with -++- and -+-+ structures. Combining the group theoretical analysis and numerical calculations for an effective J_{eff}=1/2 model, we show unusual superconducting gap structures in the -++- state protected by nonsymmorphic magnetic space group symmetry. Furthermore, our calculation shows that the Fulde-Ferrell-Larkin-Ovchinnikov superconductivity is inevitably stabilized in the -+-+ state since the odd-parity magnetic -+-+ order makes the band structure asymmetric by cooperating with spin-orbit coupling. These unusual superconducting properties are signatures of magnetic multipole order in nonsymmorphic crystal.

Rapid discrimination of three Uighur medicine of Eremurus by FT-IR combined with 2DCOS-IR

NASA Astrophysics Data System (ADS)

Zhu, Yun; Xu, Chang-hua; Huang, Jian; Li, Guo-yu; Zhou, Qun; Liu, Xin-Hu; Sun, Su-qin; Wang, Jin-hui

2014-07-01

As complicated mixture systems, traditional Chinese medicines (TCMs) are difficult to be identified and discriminated, especially for the drug samples originated from the same source. In this study, a tri-step infrared spectroscopy method, i.e., conventional infrared spectroscopy (FT-IR) combined with second derivatives spectra and two-dimensional correlation infrared spectroscopy (2DCOS-IR), was employed to study and identify three Uighur drugs of Eremurus in Xinjiang, i.e. Eremurus altaicus (Pall.) Stev (AET), E. inderiensis (M.Bieb.)Regel(CB), E. anisopterus (Kar.et Kir.) Regel(YC). It was founded that the conventional IR spectra of the three species Eremurus were very similar based on the peak positions and shapes, indicating that the three had similar chemical profiles. On the basis of the different IR spectra of reference compounds and microscopic identification, the roots of YC, CB and AET all have comparable amount of calcium oxalate. The second derivative spectra of Eremurus enhanced the spectral resolution and amplified the small differences, especially at about 1468 cm-1, 1454 cm-1, and 1164 cm-1, and subsequently provided some dissimilarity in their calcium oxalate content. AET has relatively higher content of calcium oxalate but the lower content of anthraquinones. Moreover, the 2D-IR spectra revealed tiny differences among the three species by providing dynamic structural information of their chemical components in a more direct and visual way. The differences embodied mainly on the intensity of the auto-peaks at 971 cm-1, 1008 cm-1, 1468 cm-1 and 1578 cm-1. As a result, it was demonstrated that the macroscopic IR fingerprint method could discriminate the three similar Uighur drugs, YC, CB and AET.

Draft Genome Sequence of Vibrio mimicus Strain CAIM 602T

PubMed Central

Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Yepiz-Plascencia, Gloria; Sifuentes-Romero, Itzel

2013-01-01

Vibrio mimicus is a Gram-negative bacterium associated with gastrointestinal diseases in humans around the world. We report the complete genome sequence of the Vibrio mimicus strain CAIM 602T (CDC1721-77, LMG 7896T, ATCC 33653T). PMID:23516211

T2-Weighted Liver MRI Using the MultiVane Technique at 3T: Comparison with Conventional T2-Weighted MRI

PubMed Central

Kang, Kyung A; Kim, EunJu; Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae; Jung, Sin-Ho; Baek, Sun-Young

2015-01-01

Objective To assess the value of applying MultiVane to liver T2-weighted imaging (T2WI) compared with conventional T2WIs with emphasis on detection of focal liver lesions. Materials and Methods Seventy-eight patients (43 men and 35 women) with 86 hepatic lesions and 20 pancreatico-biliary diseases underwent MRI including T2WIs acquired using breath-hold (BH), respiratory-triggered (RT), and MultiVane technique at 3T. Two reviewers evaluated each T2WI with respect to artefacts, organ sharpness, and conspicuity of intrahepatic vessels, hilar duct, and main lesion using five-point scales, and made pairwise comparisons between T2WI sequences for these categories. Diagnostic accuracy (Az) and sensitivity for hepatic lesion detection were evaluated using alternative free-response receiver operating characteristic analysis. Results MultiVane T2WI was significantly better than BH-T2WI or RT-T2WI for organ sharpness and conspicuity of intrahepatic vessels and main lesion in both separate reviews and pairwise comparisons (p < 0.001). With regard to motion artefacts, MultiVane T2WI or BH-T2WI was better than RT-T2WI (p < 0.001). Conspicuity of hilar duct was better with BH-T2WI than with MultiVane T2WI (p = 0.030) or RT-T2WI (p < 0.001). For detection of 86 hepatic lesions, sensitivity (mean, 97.7%) of MultiVane T2WI was significantly higher than that of BH-T2WI (mean, 89.5%) (p = 0.008) or RT-T2WI (mean, 84.9%) (p = 0.001). Conclusion Applying the MultiVane technique to T2WI of the liver is a promising approach to improving image quality that results in increased detection of focal liver lesions compared with conventional T2WI. PMID:26357498

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

Complete genome sequence of Thauera aminoaromatica strain MZ1T

PubMed Central

Jiang, Ke; Sanseverino, John; Chauhan, Archana; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Del Rio, Tijana Glavina; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Chang, Y.J.; Larimer, Frank; Land, Miriam; Hauser, Loren; Kyrpides, Nikos C.; Mikhailova, Natalia; Moser, Scott; Jegier, Patricia; Close, Dan; DeBruyn, Jennifer M.; Wang, Ying; Layton, Alice C.; Allen, Michael S.; Sayler, Gary S.

2012-01-01

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Sequencing Program CSP_776774. PMID:23407619

Standardized cell samples for midIR technology development

NASA Astrophysics Data System (ADS)

Kastl, Lena; Rommel, Christina E.; Kemper, Björn; Schnekenburger, Jürgen

2015-03-01

The application of midIR spectroscopy towards human cell and tissue samples is impaired by the need for technical solutions and lacking sample standards for technology development. We here present the standardization of stable test samples for the continuous development and testing of novel optical system components. We have selected cell lines representing the major cellular skin constituents keratinocytes and fibroblasts (NIH-3T3, HaCaT). In addition, two skin cancer cell types (A-375 and SK-MEL-28 cells) were analyzed. Cells were seeded on CaF2 substrates and measured dried and under aqueous medium as well as fixated and unfixated. Several independent cell preparations were analyzed with an FTIR spectrometer in the wave number range from 1000 - 4000 cm-1. The obtained data demonstrate that fixed and dehydrated cells on CaF2 can be stored in pure ethanol for several weeks without significant losses in quality of the spectral properties. The established protocol of cell seeding on CaF2 substrates, chemical fixation, dehydration, storage under ethanol and air-drying is suitable for the production of reliable midIR standards. The retrieved spectra demonstrate that fixed cells on CaF2 can be prepared reproducibly; with stable midIR spectral properties over several weeks and properties mimicking reliable unfixed cells. Moreover, the fixated samples on CaF2 show clear differences in the cell type specific spectra that can be identified by principle component analysis. In summary, the standardized cell culture samples on CaF2 substrates are suitable for the development of a midIR device and the optimization of the specific midIR spectra.

Decoupling of the antiferromagnetic and insulating states in Tb-doped Sr 2IrO 4

DOE PAGES

Wang, J. C.; Aswartham, S.; Ye, Feng; ...

2015-12-08

Sr 2IrO 4 is a spin-orbit coupled insulator with an antiferromagnetic (AFM) transition at T N = 240 K. We report results of a comprehensive study of single-crystal Sr 2Ir 1-xTb xO 4 (0≤x≤0.03). This study found that mere 3% (x=0.03) tetravalent Tb 4+(4f 7) substituting for Ir 4+ (rather than Sr 2+) completely suppresses the long-range collinear AFM transition but retains the insulating state, leading to a phase diagram featuring a decoupling of magnetic interactions and charge gap. The insulating state at x = 0.03 is characterized by an unusually large specific heat at low temperatures and an incommensuratemore » magnetic state having magnetic peaks at (0.95, 0, 0) and (0, 0.95, 0) in the neutron diffraction, suggesting a spiral or spin density wave order. It is apparent that Tb doping effectively changes the relative strength of the SOI and the tetragonal CEF and enhances the Hund’s rule coupling that competes with the SOI, and destabilizes the AFM state. However, the disappearance of the AFM accompanies no metallic state chiefly because an energy level mismatch for the Ir and Tb sites weakens charge carrier hopping and renders a persistent insulating state. Furthermore, this work highlights an unconventional correlation between the AFM and insulating states in which the magnetic transition plays no critical role in the formation of the charge gap in the iridate.« less

Experimental bandstructure of the 5 d transition metal oxide IrO2

NASA Astrophysics Data System (ADS)

Kawasaki, Jason; Nie, Yuefeng; Uchida, Masaki; Schlom, Darrell; Shen, Kyle

2015-03-01

In the 5 d iridium oxides the close energy scales of spin-orbit coupling and electron-electron correlations lead to emergent quantum phenomena. Much research has focused on the ternary iridium oxides, e.g. the Ruddlesden-Poppers An + 1BnO3 n + 1 , which exhibit behavior from metal to antiferromagnetic insulator ground states, share common features with the cuprates, and may host a number of topological phases. The binary rutile IrO2 is another important 5 d oxide, which has technological importance for spintronics due to its large spin Hall effect and also applications in catalysis. IrO2 is expected to share similar physics as its perovskite-based cousins; however, due to bond-length distortions of the IrO6 octahedra in the rutile structure, the extent of similarities remains an open question. Here we use angle-resolved photoemission spectroscopy to perform momentum-resolved measurements of the electronic structure of IrO2 . IrO2 thin films were grown by molecular beam epitaxy on TiO2 (110) substrates using an Ir e-beam source and distilled ozone. Films were subsequently transferred through ultrahigh vacuum to a connected ARPES system. Combined with first-principles calculations we explore the interplay of spin-orbit coupling and correlations in IrO2 .

Rutile IrO2/TiO2 superlattices: A hyperconnected analog to the Ruddelsden-Popper structure

NASA Astrophysics Data System (ADS)

Kawasaki, Jason K.; Baek, David; Paik, Hanjong; Nair, Hari P.; Kourkoutis, Lena F.; Schlom, Darrell G.; Shen, Kyle M.

2018-05-01

Dimensionality and connectivity among octahedra play important roles in determining the properties, electronic structure, and phase transitions of transition-metal oxides. Here we demonstrate the epitaxial growth of (110)-oriented alternating layers of IrO2 and TiO2, both of which have the rutile structure. These (IrO2)n/(TiO2)2 superlattices consist of IrO6 and TiO6 octahedra tiled in a hyperconnected, edge- and corner-sharing network. Despite the large lattice mismatch between constituent layers (Δ d∥=-2.1 % and Δ c =+6.6 % ), our reactive molecular-beam epitaxy-grown superlattices show high structural quality as determined by x-ray diffraction and sharp interfaces as observed by transmission electron microscopy. The large strain at the interface is accommodated by an ordered interfacial reconstruction. The superlattices show persistent metallicity down to n =3 atomic layers, and angle-resolved photoemission spectroscopy measurements reveal quantized sub-bands with signatures of IrO2-IrO2 interlayer coupling.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

PubMed

Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

2015-01-01

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Magnetic resonance imaging of focal cortical dysplasia: Comparison of 3D and 2D fluid attenuated inversion recovery sequences at 3T.

PubMed

Tschampa, Henriette J; Urbach, Horst; Malter, Michael; Surges, Rainer; Greschus, Susanne; Gieseke, Jürgen

2015-10-01

Focal cortical dysplasia (FCD) is a frequent finding in drug resistant epilepsy. The aim of our study was to evaluate an isotropic high-resolution 3-dimensional Fluid-attenuated inversion recovery sequence (3D FLAIR) at 3T in comparison to standard 2D FLAIR in the diagnosis of FCD. In a prospective study, 19 epilepsy patients with the MR diagnosis of FCD were examined with a sagittal 3D FLAIR sequence with modulated refocusing flip angle (slice thickness 1.10mm) and a 2D FLAIR in the coronal (thk. 3mm) and axial planes (thk. 2mm). Manually placed regions of interest were used for quantitative analysis. Qualitative image analysis was performed by two neuroradiologists in consensus. Contrast between gray and white matter (p ≤ 0.02), the lesion (p ≤ 0.031) or hyperintense extension to the ventricle (p ≤ 0.021) and white matter was significantly higher in 2D than in 3D FLAIR sequences. In the visual analysis there was no difference between 2D and 3D sequences. Conventional 2D FLAIR sequences yield a higher image contrast compared to the employed 3D FLAIR sequence in patients with FCDs. Potential advantages of 3D imaging using surface rendering or automated techniques for lesion detection have to be further elucidated. Copyright © 2015 Elsevier B.V. All rights reserved.

The Unique IR2 Protein of Equine Herpesvirus 1 Negatively Regulates Viral Gene Expression

PubMed Central

Kim, Seong K.; Ahn, Byung C.; Albrecht, Randy A.; O'Callaghan, Dennis J.

2006-01-01

The IR2 protein (IR2P) is a truncated form of the immediate-early protein (IEP) lacking the essential acidic transcriptional activation domain (TAD) and serine-rich tract and yet retaining binding domains for DNA and TFIIB and nuclear localization signal (NLS). Analysis of the IR2 promoter indicated that the IR2 promoter was upregulated by the EICP0P. The IR2P was first detected in the nucleus at 5 h postinfection in equine herpesvirus 1 (EHV-1)-infected HeLa and equine NBL6 cells. Transient-transfection assays revealed that (i) the IR2P by itself downregulated EHV-1 early promoters (EICP0, TK, EICP22, and EICP27) in a dose-dependent manner; (ii) the IR2P abrogated the IEP and the EICP27P (UL5) mediated transactivation of viral promoters in a dose-dependent manner; and (iii) the IR2P, like the IEP itself, also downregulated the IE promoter, indicating that the IEP TAD is not necessary to downregulate the IE promoter. In vitro interaction assays revealed that the IR2P interacts with TATA box-binding protein (TBP). The essential domain(s) of the IR2P that mediate negative regulation were mapped to amino acid residues 1 to 706, indicating that the DNA-binding domain and the NLS of the IR2P may be important for the downregulation. In transient-transfection and virus growth assays, the IR2P reduced EHV-1 production by 23-fold compared to virus titers achieved in cells transfected with the empty vector. Overall, these studies suggest that the IR2P downregulates viral gene expression by acting as a dominant-negative protein that blocks IEP-binding to viral promoters and/or squelching the limited supplies of TFIIB and TBP. PMID:16641295

The unique IR2 protein of equine herpesvirus 1 negatively regulates viral gene expression.

PubMed

Kim, Seong K; Ahn, Byung C; Albrecht, Randy A; O'Callaghan, Dennis J

2006-05-01

The IR2 protein (IR2P) is a truncated form of the immediate-early protein (IEP) lacking the essential acidic transcriptional activation domain (TAD) and serine-rich tract and yet retaining binding domains for DNA and TFIIB and nuclear localization signal (NLS). Analysis of the IR2 promoter indicated that the IR2 promoter was upregulated by the EICP0P. The IR2P was first detected in the nucleus at 5 h postinfection in equine herpesvirus 1 (EHV-1)-infected HeLa and equine NBL6 cells. Transient-transfection assays revealed that (i) the IR2P by itself downregulated EHV-1 early promoters (EICP0, TK, EICP22, and EICP27) in a dose-dependent manner; (ii) the IR2P abrogated the IEP and the EICP27P (UL5) mediated transactivation of viral promoters in a dose-dependent manner; and (iii) the IR2P, like the IEP itself, also downregulated the IE promoter, indicating that the IEP TAD is not necessary to downregulate the IE promoter. In vitro interaction assays revealed that the IR2P interacts with TATA box-binding protein (TBP). The essential domain(s) of the IR2P that mediate negative regulation were mapped to amino acid residues 1 to 706, indicating that the DNA-binding domain and the NLS of the IR2P may be important for the downregulation. In transient-transfection and virus growth assays, the IR2P reduced EHV-1 production by 23-fold compared to virus titers achieved in cells transfected with the empty vector. Overall, these studies suggest that the IR2P downregulates viral gene expression by acting as a dominant-negative protein that blocks IEP-binding to viral promoters and/or squelching the limited supplies of TFIIB and TBP.

Measurements of RF heating during 3.0-T MRI of a pig implanted with deep brain stimulator.

PubMed

Gorny, Krzysztof R; Presti, Michael F; Goerss, Stephan J; Hwang, Sun C; Jang, Dong-Pyo; Kim, Inyong; Min, Hoon-Ki; Shu, Yunhong; Favazza, Christopher P; Lee, Kendall H; Bernstein, Matt A

2013-06-01

To present preliminary, in vivo temperature measurements during MRI of a pig implanted with a deep brain stimulation (DBS) system. DBS system (Medtronic Inc., Minneapolis, MN) was implanted in the brain of an anesthetized pig. 3.0-T MRI was performed with a T/R head coil using the low-SAR GRE EPI and IR-prepped GRE sequences (SAR: 0.42 and 0.39 W/kg, respectively), and the high-SAR 4-echo RF spin echo (SAR: 2.9 W/kg). Fluoroptic thermometry was used to directly measure RF-related heating at the DBS electrodes, and at the implantable pulse generator (IPG). For reference the measurements were repeated in the same pig at 1.5 T and, at both field strengths, in a phantom. At 3.0T, the maximal temperature elevations at DBS electrodes were 0.46 °C and 2.3 °C, for the low- and high-SAR sequences, respectively. No heating was observed on the implanted IPG during any of the measurements. Measurements of in vivo heating differed from those obtained in the phantom. The 3.0-T MRI using GRE EPI and IR-prepped GRE sequences resulted in local temperature elevations at DBS electrodes of no more than 0.46 °C. Although no extrapolation should be made to human exams and much further study will be needed, these preliminary data are encouraging for the future use 3.0-T MRI in patients with DBS. Copyright © 2013 Elsevier Inc. All rights reserved.

Measurements of RF Heating during 3.0T MRI of a Pig Implanted with Deep Brain Stimulator

PubMed Central

Gorny, Krzysztof R; Presti, Michael F; Goerss, Stephan J; Hwang, Sun C; Jang, Dong-Pyo; Kim, Inyong; Shu, Yunhong; Favazza, Christopher P; Lee, Kendall H; Bernstein, Matt A

2012-01-01

Purpose To present preliminary, in vivo temperature measurements during MRI of a pig implanted with a deep brain stimulation (DBS) system. Materials and Methods DBS system (Medtronic Inc., Minneapolis, MN) was implanted in the brain of an anesthetized pig. 3.0T MRI was performed with a T/R head coil using the low-SAR GRE EPI and IR-prepped GRE sequences (SAR: 0.42 W/kg and 0.39 W/kg, respectively), and the high-SAR 4-echo RF spin echo (SAR: 2.9 W/kg). Fluoroptic thermometry was used to directly measure RF-related heating at the DBS electrodes, and at the implantable pulse generator (IPG). For reference the measurements were repeated in the same pig at 1.5T and, at both field strengths, in a phantom. Results At 3.0T, the maximal temperature elevations at DBS electrodes were 0.46 °C and 2.3 °C, for the low- and high-SAR sequences, respectively. No heating was observed on the implanted IPG during any of the measurements. Measurements of in-vivo heating differed from those obtained in the phantom. Conclusion The 3.0T MRI using GRE EPI and IR-prepped GRE sequences resulted in local temperature elevations at DBS electrodes of no more than 0.46°C. Although no extrapolation should be made to human exams and much further study will be needed, these preliminary data are encouraging for the future use 3.0T MRI in patients with DBS. PMID:23228310

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

PubMed Central

2012-01-01

Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas. PMID:23256920

Complete genome sequence of Lactobacillus heilongjiangensis DSM 28069(T): Insight into its probiotic potential.

PubMed

Zheng, Beiwen; Jiang, Xiawei; Cheng, Hong; Xu, Zemin; Li, Ang; Hu, Xinjun; Xiao, Yonghong

2015-12-20

Lactobacillus heilongjiangensis DSM 28069(T) is a potential probiotic isolated from traditional Chinese pickle. Here we report the complete genome sequence of this strain. The complete genome is 2,790,548bp with the GC content of 37.5% and devoid of plasmids. Sets of genes involved in the biosynthesis of riboflavin and folate were identified in the genome, which revealed its potential application in biotechnological industry. The genome sequence of L. heilongjiangensis DSM 28069(T) now provides the fundamental information for future studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid discrimination of extracts of Chinese propolis and poplar buds by FT-IR and 2D IR correlation spectroscopy

NASA Astrophysics Data System (ADS)

Wu, Yan-Wen; Sun, Su-Qin; Zhao, Jing; Li, Yi; Zhou, Qun

2008-07-01

The extract of Chinese propolis (ECP) has recently been adulterated with that of poplar buds (EPB), because most of ECP is derived from the poplar plant, and ECP and EPB have almost identical chemical compositions. It is very difficult to differentiate them by using the chromatographic methods such as high performance liquid chromatography (HPLC) and gas chromatography (GC). Therefore, how to effectively discriminate these two mixtures is a problem to be solved urgently. In this paper, a rapid method for discriminating ECP and EPB was established by the Fourier transform infrared (FT-IR) spectra combined with the two-dimensional infrared correlation (2D IR) analysis. Forty-three ECP and five EPB samples collected from different areas of China were analyzed by the FT-IR spectroscopy. All the ECP and EPB samples tested show similar IR spectral profiles. The significant differences between ECP and EPB appear in the region of 3000-2800 cm -1 of the spectra. Based on such differences, the two species were successfully classified with the soft independent modeling of class analogy (SIMCA) pattern recognition technique. Furthermore, these differences were well validated by a series of temperature-dependent dynamic FT-IR spectra and the corresponding 2D IR plots. The results indicate that the differences in these two natural products are caused by the amounts of long-chain alkyl compounds (including long-chain alkanes, long-chain alkyl esters and long chain alkyl alcohols) in them, rather than the flavonoid compounds, generally recognized as the bioactive substances of propolis. There are much more long-chain alkyl compounds in ECP than those in EPB, and the carbon atoms of the compounds in ECP remain in an order Z-shaped array, but those in EPB are disorder. It suggests that FT-IR and 2D IR spectroscopy can provide a valuable method for the rapid differentiation of similar natural products, ECP and EPB. The IR spectra could directly reflect the integrated chemical

Bacteroides fragilis mobilizable transposon Tn5520 requires a 71 base pair origin of transfer sequence and a single mobilization protein for relaxosome formation during conjugation.

PubMed

Vedantam, Gayatri; Knopf, Sarah; Hecht, David W

2006-01-01

Tn5520 is the smallest known bacterial mobilizable transposon and was isolated from an antibiotic resistant Bacteroides fragilis clinical isolate. When a conjugation apparatus is provided in trans, Tn5520 is mobilized (transferred) efficiently within, and from, both Bacteroides spp. and Escherichia coli. Only two genes are present on Tn5520; one encodes an integrase, and the other a multifunctional mobilization (Mob) protein BmpH. BmpH is essential for Tn5520 mobility. The focus of this study was to identify the Tn5520 origin of conjugative transfer (oriT) and to study BmpH-oriT binding. We delimited the functional Tn5520 oriT to a 71 bp sequence upstream of the bmpH gene. A plasmid vector harbouring this minimal 71 bp oriT was mobilized at the same frequency as that of intact Tn5520. The minimal oriT contains one 17 bp inverted repeat (IR) sequence. We constructed and tested multiple IR mutants and showed that the IR was essential in its entirety for mobilization. A nick site sequence (5'-GCTAC-3') was also identified within the minimal oriT; this sequence resembled nick sites found in plasmids of Gram positive origin. We further showed that mutation of a highly conserved GC dinucleotide in the nick site sequence completely abolished mobilization. We also purified BmpH and showed that it specifically bound a Tn5520 oriT fragment in electrophoretic mobility shift assays. We also identified non-nick site sequences within the minimal oriT that were essential for mobilization. We hypothesize that transposon-based single Mob protein systems may contribute to efficient gene dissemination from Bacteroides spp., because fewer DNA processing proteins are required for relaxosome formation.

Optimal Cut-Offs of Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) to Identify Dysglycemia and Type 2 Diabetes Mellitus: A 15-Year Prospective Study in Chinese

PubMed Central

Lee, C. H.; Shih, A. Z. L.; Woo, Y. C.; Fong, C. H. Y.; Leung, O. Y.; Janus, E.; Cheung, B. M. Y.; Lam, K. S. L.

2016-01-01

Background The optimal reference range of homeostasis model assessment of insulin resistance (HOMA-IR) in normal Chinese population has not been clearly defined. Here we address this issue using the Hong Kong Cardiovascular Risk Factor Prevalence Study (CRISPS), a prospective population-based cohort study with long-term follow-up. Material & Methods In this study, normal glucose tolerance (NGT), impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and type 2 diabetes mellitus (T2DM) were defined according to the 1998 World Health Organization criteria. Dysglycemia referred to IFG, IGT or T2DM. This study comprised two parts. Part one was a cross-sectional study involving 2,649 Hong Kong Chinese subjects, aged 25–74 years, at baseline CRISPS-1 (1995–1996). The optimal HOMA-IR cut-offs for dysglycemia and T2DM were determined by the receiver-operating characteristic (ROC) curve. Part two was a prospective study involving 872 subjects who had persistent NGT at CRISPS-4 (2010–2012) after 15 years of follow-up. Results At baseline, the optimal HOMA-IR cut-offs to identify dysglyceia and T2DM were 1.37 (AUC = 0.735; 95% confidence interval [CI] = 0.713–0.758; Sensitivity [Se] = 65.6%, Specificity [Sp] = 71.3%] and 1.97 (AUC = 0.807; 95% CI = 0.777–0.886; Se = 65.5%, Sp = 82.9%) respectively. These cut-offs, derived from the cross-sectional study at baseline, corresponded closely to the 75th (1.44) and 90th (2.03) percentiles, respectively, of the HOMA-IR reference range derived from the prospective study of subjects with persistent NGT. Conclusions HOMA-IR cut-offs, of 1.4 and 2.0, which discriminated dysglycemia and T2DM respectively from NGT in Southern Chinese, can be usefully employed as references in clinical research involving the assessment of insulin resistance. PMID:27658115

Wideband Arrhythmia-Insensitive-Rapid (AIR) Pulse Sequence for Cardiac T1 mapping without Image Artifacts induced by ICD

PubMed Central

Hong, KyungPyo; Jeong, Eun-Kee; Wall, T. Scott; Drakos, Stavros G.; Kim, Daniel

2015-01-01

Purpose To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). Methods We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz), in order to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and “wideband” AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5T. Results In 5 phantoms representing native myocardium and blood and post-contrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error >29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error <5%). Similarly, in 11 human subjects, compared with the control T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error >10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error <2.0%). Conclusion This study demonstrates the feasibility of a wideband pulse sequence for cardiac T1 mapping without significant image artifacts induced by ICD. PMID:25975192

Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

PubMed Central

Lepage, Étienne; Zampini, Éric; Boyle, Brian; Brisson, Normand

2013-01-01

Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity. PMID:23951038

The type 2 diabetes and insulin-resistance locus near IRS1 is a determinant of HDL cholesterol and triglycerides levels among diabetic subjects.

PubMed

Sharma, Rajani; Prudente, Sabrina; Andreozzi, Francesco; Powers, Christine; Mannino, Gaia; Bacci, Simonetta; Gervino, Ernest V; Hauser, Thomas H; Succurro, Elena; Mercuri, Luana; Goheen, Elizabeth H; Shah, Hetal; Trischitta, Vincenzo; Sesti, Giorgio; Doria, Alessandro

2011-05-01

SNP rs2943641 near the insulin receptor substrate 1 (IRS1) gene has been found to be associated with type 2 diabetes (T2D) and insulin-resistance in genome-wide association studies. We investigated whether this SNP is associated with cardiovascular risk factors and coronary artery disease (CAD) among diabetic individuals. SNP rs2943641 was typed in 2133 White T2D subjects and tested for association with BMI, serum HDL cholesterol and triglycerides, hypertension history, and CAD risk. HDL cholesterol decreased by 1mg/dl (p = 0.004) and serum triglycerides increased by 6 mg/dl (p = 0.016) for each copy of the insulin-resistance allele. Despite these effects, no association was found with increased CAD risk (OR = 1.00, 95% CI 0.88-1.13). The insulin-resistance and T2D locus near the IRS1 gene is a determinant of lower HDL cholesterol among T2D subjects. However, this effect is small and does not translate into a detectable increase in CAD risk in this population. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Elastic, magnetic and electronic properties of iridium phosphide Ir 2P

DOE PAGES

Wang, Pei; Wang, Yonggang; Wang, Liping; ...

2016-02-24

Cubic (space group: Fm3¯m) iridium phosphide, Ir 2P, has been synthesized at high pressure and high temperature. Angle-dispersive synchrotron X-ray diffraction measurements on Ir 2P powder using a diamond-anvil cell at room temperature and high pressures (up to 40.6 GPa) yielded a bulk modulus of B 0 = 306(6) GPa and its pressure derivative B 0'= 6.4(5). Such a high bulk modulus attributed to the short and strongly covalent Ir-P bonds as revealed by first – principles calculations and three-dimensionally distributed [IrP 4] tetrahedron network. Indentation testing on a well–sintered polycrystalline sample yielded the hardness of 11.8(4) GPa. Relatively lowmore » shear modulus of ~64 GPa from theoretical calculations suggests a complicated overall bonding in Ir 2P with metallic, ionic, and covalent characteristics. Additionally, a spin glass behavior is indicated by magnetic susceptibility measurements.« less

Coffee extract inhibits adipogenesis in 3T3-L1 preadipocyes by interrupting insulin signaling through the downregulation of IRS1

PubMed Central

Maki, Chihiro; Funakoshi-Tago, Megumi; Aoyagi, Ryohei; Ueda, Fumihito; Kimura, Masaki; Kobata, Kenji; Tago, Kenji; Tamura, Hiroomi

2017-01-01

Although epidemiological data have indicated that a strong negative association exists between coffee consumption and the prevalence of obesity-associated diseases, the molecular mechanisms by which coffee intake prevents obesity-associated diseases has not yet been elucidated. In this study, we found that coffee intake significantly suppressed high-fat diet (HFD)-induced metabolic alternations such as increases in body weight and the accumulation of adipose tissue, and up-regulation of glucose, free fatty acid, total cholesterol and insulin levels in the blood. We also found that coffee extract significantly inhibited adipogenesis in 3T3-L1 preadipocytes. In the early phase of adipogenesis, 3T3-L1 cells treated with coffee extract displayed the retardation of cell cycle entry into the G2/M phase called as mitotic clonal expansion (MCE). Coffee extract also inhibited the activation of CCAAT/enhancer-binding protein β (C/EBPβ) by preventing its phosphorylation by ERK. Furthermore, the coffee extract suppressed the adipogenesis-related events such as MCE and C/EBPβ activation through the down-regulation of insulin receptor substrate 1 (IRS1). The stability of the IRS1 protein was markedly decreased by the treatment with coffee extract due to proteasomal degradation. These results have revealed an anti-adipogenic function for coffee intake and identified IRS1 as a novel target for coffee extract in adipogenesis. PMID:28282409

Coffee extract inhibits adipogenesis in 3T3-L1 preadipocyes by interrupting insulin signaling through the downregulation of IRS1.

PubMed

Maki, Chihiro; Funakoshi-Tago, Megumi; Aoyagi, Ryohei; Ueda, Fumihito; Kimura, Masaki; Kobata, Kenji; Tago, Kenji; Tamura, Hiroomi

2017-01-01

Although epidemiological data have indicated that a strong negative association exists between coffee consumption and the prevalence of obesity-associated diseases, the molecular mechanisms by which coffee intake prevents obesity-associated diseases has not yet been elucidated. In this study, we found that coffee intake significantly suppressed high-fat diet (HFD)-induced metabolic alternations such as increases in body weight and the accumulation of adipose tissue, and up-regulation of glucose, free fatty acid, total cholesterol and insulin levels in the blood. We also found that coffee extract significantly inhibited adipogenesis in 3T3-L1 preadipocytes. In the early phase of adipogenesis, 3T3-L1 cells treated with coffee extract displayed the retardation of cell cycle entry into the G2/M phase called as mitotic clonal expansion (MCE). Coffee extract also inhibited the activation of CCAAT/enhancer-binding protein β (C/EBPβ) by preventing its phosphorylation by ERK. Furthermore, the coffee extract suppressed the adipogenesis-related events such as MCE and C/EBPβ activation through the down-regulation of insulin receptor substrate 1 (IRS1). The stability of the IRS1 protein was markedly decreased by the treatment with coffee extract due to proteasomal degradation. These results have revealed an anti-adipogenic function for coffee intake and identified IRS1 as a novel target for coffee extract in adipogenesis.

A novel IRS-1-associated protein, DGKζ regulates GLUT4 translocation in 3T3-L1 adipocytes

PubMed Central

Liu, TingYu; Yu, BuChin; Kakino, Mamoru; Fujimoto, Hitoshi; Ando, Yasutoshi; Hakuno, Fumihiko; Takahashi, Shin-Ichiro

2016-01-01

Insulin receptor substrates (IRSs) are major targets of insulin receptor tyrosine kinases. Here we identified diacylglycerol kinase zeta (DGKζ) as an IRS-1-associated protein, and examined roles of DGKζ in glucose transporter 4 (GLUT4) translocation to the plasma membrane. When DGKζ was knocked-down in 3T3-L1 adipocytes, insulin-induced GLUT4 translocation was inhibited without affecting other mediators of insulin-dependent signaling. Similarly, knockdown of phosphatidylinositol 4-phosphate 5-kinase 1α (PIP5K1α), which had been reported to interact with DGKζ, also inhibited insulin-induced GLUT4 translocation. Moreover, DGKζ interacted with IRS-1 without insulin stimulation, but insulin stimulation decreased this interaction. Over-expression of sDGKζ (short-form DGKζ), which competed out DGKζ from IRS-1, enhanced GLUT4 translocation without insulin stimulation. Taking these results together with the data showing that cellular PIP5K activity was correlated with GLUT4 translocation ability, we concluded that IRS-1-associated DGKζ prevents GLUT4 translocation in the absence of insulin and that the DGKζ dissociated from IRS-1 by insulin stimulation enhances GLUT4 translocation through PIP5K1α activity. PMID:27739494

Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study

USDA-ARS?s Scientific Manuscript database

Using PCR and IPCR techniques we obtained a 4498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine IRS4 gene and its proximal promoter. The 1269-amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesse...

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough

PubMed Central

Zhu, Yixin; Fang, Daiqiong; Shi, Ding; Li, Ang; Lv, Longxian; Yan, Ren; Yao, Jian; Hua, Dasong; Hu, Xinjun; Guo, Feifei; Wu, Wenrui; Guo, Jing; Chen, Yanfei; Jiang, Xiawei; Chen, Xiaoxiao

2015-01-01

We report a draft genome sequence of Lactobacillus panis DSM 6035T, isolated from sourdough. The genome of this strain is 2,082,789 bp long, with 47.9% G+C content. A total of 2,047 protein-coding genes were predicted. PMID:26205855

Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis.

PubMed

Spotin, Adel; Moslemzadeh, Hamid Reza; Mahami-Oskouei, Mahmoud; Ahmadpour, Ehsan; Niyyati, Maryam; Hejazi, Seyed Hossein; Memari, Fatemeh; Noori, Jafar

2017-09-01

To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F ST ) was from low to high values (0.02433-0.41892). The statistically F ST points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates. An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first

Diphosphine- and CO-Induced Fragmentation of Chloride-bridged Dinuclear Complex and Cp*Ir(mu-Cl)(3)Re(CO)(3) and Attempted Synthesis of Cp*Ir(mu-Cl)(3)Mn(CO)(3): Spectroscopic Data and X-ray Diffraction Structures of the Pentamethylcyclopentadienyl Compounds [Cp*IrCl{(Z)-Ph2PCH = CHPPh2}][Cl]center dot 2CHCl(3) and Cp*Ir(CO)Cl-2

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

Hammons, Casey; Wang, Xiaoping; Nesterov, Vladimir

2010-01-01

The confacial bioctahedral compound Cp*Ir(mu-Cl)(3)Re(CO)(3) (1) undergoes rapid fragmentation in the presence of the unsaturated diphosphine ligand (Z)-Ph2PCH = CHPPh2 to give the mononuclear compounds [Cp*IrCl {(Z)-Ph2PCH = CHPPh2}][Cl] (2) and fac-ClRe(CO)(3)[(Z)-Ph2PCH = CHPPh2] (3). 2 has been characterized by H-1 and P-31 NMR spectroscopy and X-ray diffraction analysis. 2 center dot 2CHCl(3) crystallizes in the monoclinic space group C2/c, a = 35.023 (8) angstrom, b = 10.189 (2) angstrom, c = 24.003 (6) angstrom, b = 103.340 (3), V = 8,335 (3) angstrom 3, Z = 8, and d(calc) = 1.647 Mg/m(3); R = 0.0383, R-w = 0.1135 formore » 8,178 reflections with I> 2 sigma(I). The Ir(III) center in 2 exhibits a six-coordinate geometry and displays a chelating diphosphine group. Compound 1 reacts with added CO with fragmentation to yield the known compounds Cp*Ir(CO)Cl-2 (4) and ClRe(CO)(5) (5) in near quantitative yield by IR spectroscopy. Using the protocol established by our groups for the synthesis of 1, we have explored the reaction of [Cp*IrCl2](2) with ClMn(CO)(5) as a potential route to Cp*Ir(mu-Cl)(3)Mn(CO)(3); unfortunately, 4 was the only product isolated from this reaction. The solid-state structure of 4 was determined by X-ray diffraction analysis. 4 crystallizes in the triclinic space group P-1, a = 7.4059 (4) angstrom, b = 7.8940 (4) angstrom, c = 11.8488 (7) angstrom, alpha = 80.020 (1), beta = 79.758 (1), gamma = 68.631 (1), V = 630.34 (6) angstrom(3), Z = 2, and d(calc) = 2.246 Mg/m(3); R = 0.0126, R-w = 0.0329 for 2,754 reflections with I> 2 sigma(I). The expected three-legged piano-stool geometry in 4 has been crystallographically confirmed.« less

High-throughput analysis of T-DNA location and structure using sequence capture

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

Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

High-throughput analysis of T-DNA location and structure using sequence capture

DOE PAGES

Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; ...

2015-10-07

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

Facile Dehydrogenation of Ethane on the IrO2(110) Surface.

PubMed

Bian, Yingxue; Kim, Minkyu; Li, Tao; Asthagiri, Aravind; Weaver, Jason F

2018-02-21

Realizing the efficient and selective conversion of ethane to ethylene is important for improving the utilization of hydrocarbon resources, yet remains a major challenge in catalysis. Herein, ethane dehydrogenation on the IrO 2 (110) surface is investigated using temperature-programmed reaction spectroscopy (TPRS) and density functional theory (DFT) calculations. The results show that ethane forms strongly bound σ-complexes on IrO 2 (110) and that a large fraction of the complexes undergo C-H bond cleavage during TPRS at temperatures below 200 K. Continued heating causes as much as 40% of the dissociated ethane to dehydrogenate and desorb as ethylene near 350 K, with the remainder oxidizing to CO x species. Both TPRS and DFT show that ethylene desorption is the rate-controlling step in the conversion of ethane to ethylene on IrO 2 (110) during TPRS. Partial hydrogenation of the IrO 2 (110) surface is found to enhance ethylene production from ethane while suppressing oxidation to CO x species. DFT predicts that hydrogenation of reactive oxygen atoms of the IrO 2 (110) surface effectively deactivates these sites as H atom acceptors, and causes ethylene desorption to become favored over further dehydrogenation and oxidation of ethane-derived species. The study reveals that IrO 2 (110) exhibits an exceptional ability to promote ethane dehydrogenation to ethylene near room temperature, and provides molecular-level insights for understanding how surface properties influence selectivity toward ethylene production.

Comparison of two-dimensional fast spin echo T2 weighted sequences and three-dimensional volume isotropic T2 weighted fast spin echo (VISTA) MRI in the evaluation of triangular fibrocartilage of the wrist.

PubMed

Park, Hee Jin; Lee, So Yeon; Kang, Kyung A; Kim, Eun Young; Shin, Hun Kyu; Park, Se Jin; Park, Jai Hyung; Kim, Eugene

2018-04-01

To compare image quality of three-dimensional volume isotropic T 2 weighted fast spin echo (3D VISTA) and two-dimensional (2D) T 2 weighted images (T2WI) for evaluation of triangular fibrocartilage (TFC) and to investigate whether 3D VISTA can replace 2D T 2 WI in evaluating TFC injury. This retrospective study included 69 patients who received wrist MRIs using both 2D T 2 WI and 3D VISTA techniques for assessment of wrist pathology, including TFC injury. Two radiologists measured the signal-to-noise ratio (SNR) and the contrast-to-noise ratio (CNR) of the two sequences. The anatomical identification score and diagnostic performance were independently assessed by two interpreters. The diagnostic abilities of 3D VISTA and 2D T 2 WI were analysed by sensitivity, specificity and accuracy for diagnosing TFC injury using surgically or clinically confirmed diagnostic reference standards. 17 cases (25%) were classified as having TFC injury. 2 cases (12%) were diagnosed surgically, and 15 cases (88%) were diagnosed by physical examination. 52 cases (75%) were diagnosed as having intact TFC. 8 of these cases (15%) were surgically confirmed, while the others were diagnosed by physical examination and clinical findings. The 3D VISTA images had significantly higher SNR and CNR values for the TFC than 2D T 2 WI images. The scores of 3D VISTA's total length, full width and sharpness were similar to those of 2D T 2 WI. We were unable to find a significant difference between 3D VISTA and 2D T 2 WI in the ability to diagnose TFC injury. 3D VISTA image quality is similar to that of 2D T 2 WI for TFC evaluation and is also excellent for tissue contrast. 3D VISTA can replace 2D images in TFC injury assessment. Advances in knowledge: 3D VISTA image quality is similar to that of 2D T 2 WI for TFC evaluation and is also excellent for tissue contrast. 3D VISTA can replace 2D images in TFC injury assessment.

Observation sequences and onboard data processing of Planet-C

NASA Astrophysics Data System (ADS)

Suzuki, M.; Imamura, T.; Nakamura, M.; Ishi, N.; Ueno, M.; Hihara, H.; Abe, T.; Yamada, T.

Planet-C or VCO Venus Climate Orbiter will carry 5 cameras IR1 IR 1micrometer camera IR2 IR 2micrometer camera UVI UV Imager LIR Long-IR camera and LAC Lightning and Airglow Camera in the UV-IR region to investigate atmospheric dynamics of Venus During 30 hr orbiting designed to quasi-synchronize to the super rotation of the Venus atmosphere 3 groups of scientific observations will be carried out i image acquisition of 4 cameras IR1 IR2 UVI LIR 20 min in 2 hrs ii LAC operation only when VCO is within Venus shadow and iii radio occultation These observation sequences will define the scientific outputs of VCO program but the sequences must be compromised with command telemetry downlink and thermal power conditions For maximizing science data downlink it must be well compressed and the compression efficiency and image quality have the significant scientific importance in the VCO program Images of 4 cameras IR1 2 and UVI 1Kx1K and LIR 240x240 will be compressed using JPEG2000 J2K standard J2K is selected because of a no block noise b efficiency c both reversible and irreversible d patent loyalty free and e already implemented as academic commercial software ICs and ASIC logic designs Data compression efficiencies of J2K are about 0 3 reversible and 0 1 sim 0 01 irreversible The DE Digital Electronics unit which controls 4 cameras and handles onboard data processing compression is under concept design stage It is concluded that the J2K data compression logics circuits using space

Identification of Genomic Insertion and Flanking Sequence of G2-EPSPS and GAT Transgenes in Soybean Using Whole Genome Sequencing Method.

PubMed

Guo, Bingfu; Guo, Yong; Hong, Huilong; Qiu, Li-Juan

2016-01-01

Molecular characterization of sequence flanking exogenous fragment insertion is essential for safety assessment and labeling of genetically modified organism (GMO). In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS) method. More than 22.4 Gb sequence data (∼21 × coverage) for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundaries of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of genomic insertion sites of G2-EPSPS and GAT transgenes will facilitate the utilization of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS was a cost-effective and rapid method for identifying sites of T-DNA insertions and flanking sequences in soybean.

Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring.

PubMed

Göker, Markus; Spring, Stefan; Scheuner, Carmen; Anderson, Iain; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Rohde, Manfred; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

2014-06-15

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Genome sequence of the Thermotoga thermarum type strain (LA 3 T) from an African solfataric spring

DOE PAGES

Goker, Markus; Spring, Stefan; Scheuner, Carmen; ...

2014-06-15

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum ' Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3 T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significantmore » discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395T (DSM 45146T)

DOE PAGES

Yassin, Atteyet F.; Lapidus, Alla; Han, James; ...

2015-08-05

We report that the Corynebacterium ulceribovis strain IMMIB L-1395T (= DSM 45146T) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395T, together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is partmore » of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.« less

High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395T (DSM 45146T)

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

Yassin, Atteyet F.; Lapidus, Alla; Han, James

We report that the Corynebacterium ulceribovis strain IMMIB L-1395T (= DSM 45146T) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395T, together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is partmore » of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.« less

Magnetic evaluation of hydrogen pressures changes on MHD fluctuations in IR-T1 tokamak plasma

NASA Astrophysics Data System (ADS)

Alipour, Ramin; Ghanbari, Mohamad R.

2018-04-01

Identification of tokamak plasma parameters and investigation on the effects of each parameter on the plasma characteristics is important for the better understanding of magnetohydrodynamic (MHD) activities in the tokamak plasma. The effect of different hydrogen pressures of 1.9, 2.5 and 2.9 Torr on MHD fluctuations of the IR-T1 tokamak plasma was investigated by using of 12 Mirnov coils, singular value decomposition and wavelet analysis. The parameters such as plasma current, loop voltage, power spectrum density, energy percent of poloidal modes, dominant spatial structures and temporal structures of poloidal modes at different plasma pressures are plotted. The results indicate that the MHD activities at the pressure of 2.5 Torr are less than them at other pressures. It also has been shown that in the stable area of plasma and at the pressure of 2.5 Torr, the magnetic force and the force of plasma pressure are in balance with each other and the MHD activities are at their lowest level.

Towards a Molecular Movie: Real Time Observation of Hydrogen Bond Breaking by Transient 2D-IR Spectroscopy in a Cyclic Peptide

NASA Astrophysics Data System (ADS)

Kolano, Christoph; Helbing, Jan; Sander, Wolfram; Hamm, Peter

Transient two-dimensional infrared spectroscopy (T2D-IR) has been used to observe in real time the non-equilibrium structural dynamics of intramolecular hydrogen bond breaking in a small cyclic disulfide-bridged peptide.

Unusual Coexistence of Nickel(II) and Nickel(IV) in the Quadruple Perovskite Ba 4Ni 2Ir 2O 12 Containing Ir 2NiO 12 Mixed-Metal-Cation Trimers

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

Ferreira, Timothy; Heald, Steve M.; Smith, Mark. D.

In this paper, the crystal chemistry and magnetic properties of two hexagonal nickel(IV)-containing perovskites, Ba 4Ni 1.94Ir 2.06O 12 and BaNiO 3, are reported. The 12R perovskite, Ba 4Ni 1.94Ir 2.06O 12, possesses an unexpected coexistence of nickel(II) and nickel(IV). This quadruple perovskite structure contains Ir 2NiO 12 mixed-metal-cation units in which direct metal–metal bonding between nickel(IV) and iridium(V) is inferred. Finally, X-ray absorption near-edge spectroscopy and X-ray photoelectron spectroscopy measurements were conducted to confirm the simultaneous presence of nickel(II) and nickel(IV).

Unusual Coexistence of Nickel(II) and Nickel(IV) in the Quadruple Perovskite Ba 4Ni 2Ir 2O 12 Containing Ir 2NiO 12 Mixed-Metal-Cation Trimers

DOE PAGES

Ferreira, Timothy; Heald, Steve M.; Smith, Mark. D.; ...

2018-03-02

In this paper, the crystal chemistry and magnetic properties of two hexagonal nickel(IV)-containing perovskites, Ba 4Ni 1.94Ir 2.06O 12 and BaNiO 3, are reported. The 12R perovskite, Ba 4Ni 1.94Ir 2.06O 12, possesses an unexpected coexistence of nickel(II) and nickel(IV). This quadruple perovskite structure contains Ir 2NiO 12 mixed-metal-cation units in which direct metal–metal bonding between nickel(IV) and iridium(V) is inferred. Finally, X-ray absorption near-edge spectroscopy and X-ray photoelectron spectroscopy measurements were conducted to confirm the simultaneous presence of nickel(II) and nickel(IV).

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon is a powerful experimental model for the grasses with a large and growing collection of genomic and experimental resources. We have added to these resources by greatly expanding the number of sequence-indexed T-DNA lines. We sequenced 21,165 T-DNA lines, 15,569 of which were ...

Sodium inversion recovery MRI of the knee joint in vivo at 7T.

PubMed

Madelin, Guillaume; Lee, Jae-Seung; Inati, Souheil; Jerschow, Alexej; Regatte, Ravinder R

2010-11-01

The loss of proteoglycans (PG) in the articular cartilage is an early signature of osteoarthritis (OA). The ensuing changes in the fixed charge density in the cartilage can be directly linked to sodium concentration via charge balance. Sodium ions in the knee joint appear in two pools: in the synovial fluids or joint effusion where the ions are in free motion and bound within the cartilage tissue where the Na(+) ions have a restricted motion. The ions in these two compartments have therefore different T₁ and T₂ relaxation times. The purpose of this study is to demonstrate the feasibility of a fluid-suppressed 3D ultrashort TE radial sodium sequence by implementing an inversion recovery (IR) preparation of the magnetization at 7T. This method could allow a more accurate and more sensitive quantification of loss of PG in patients with OA. It is shown that adiabatic pulses offer significantly improved performance in terms of robustness to B₁ and B₀ inhomogeneities when compared to the hard pulse sequence. Power deposition considerations further pose a limit to the RF inversion power, and we demonstrate in simulations and experiments how a practical compromise can be struck between clean suppression of fluid signals and power deposition levels. Two IR sequences with different types of inversion pulses (a rectangular pulse and an adiabatic pulse) were tested on a liquid phantom, ex vivo on a human knee cadaver and then in vivo on five healthy volunteers, with a (Nyquist) resolution of ∼3.6 mm and a signal-to-noise ratio of ∼30 in cartilage without IR and ∼20 with IR. Due to specific absorption rate limitations, the total acquisition time was ∼17 min for the 3D radial sequence without inversion or with the rectangular IR, and 24:30 min for the adiabatic IR sequence. It is shown that the adiabatic IR sequence generates a more uniform fluid suppression over the whole sample than the rectangular IR sequence. Copyright © 2010 Elsevier Inc. All rights

The effect of Liuwei Dihuang decoction on PI3K/Akt signaling pathway in liver of type 2 diabetes mellitus (T2DM) rats with insulin resistance.

PubMed

Dai, Bing; Wu, Qinxuan; Zeng, Chengxi; Zhang, Jiani; Cao, Luting; Xiao, Zizeng; Yang, Menglin

2016-11-04

Liuwei Dihaung decoction (LWDHT) is a well-known classic traditional Chinese medicine formula, consists of six herbs including Rehmannia glutinosa Libosch.(family: Scrophulariaceae), Cornus officinalis Sieb.(family: Cornaceae), Dioscorea opposite Thunb.(family: Dioscoreaceae), Alisma orientale(G. Samuelsson) Juz (family: Alismataceae), Poria cocos (Schw.) Wolf (family: Polyporaceae) and Paeonia suffruticosa Andrews (family: Paeoniaceae). It has been used in the treatment of many types of diseases with signs of deficiency of Yin in the kidneys in China clinically. This study is aimed at investigating the effect of Liuwei dihuang decoction on PI3K/Akt signaling pathway in liver of T2DM rats with insulin resistance. T2DM model was induced in male Sprague-Dawley (SD) rats by high sugar and high fat diets combined with small dose of streptozocin (STZ) injection. The successful T2DM rats were randomly allocated three group--vehicle group, positive control group and Liuwei Dihuang decoction group. After 12-weeks treatment with distilled water, rosiglitazone and LWDHT by intragastric administration respectively, the rats were put to death in batches. The variance of fasting blood glucose (FBG) and fasting insulin (FINS) in serum were determined, the pathological changes of each rats' liver were observed by hematoxylin-eosin (HE) staining, the expression of insulin receptor substrate 2(IRS2), phosphatidylinositol 3-kinase (PI3K) and protein kinas B (Akt) involving the canonical PI3K/Akt signaling pathway were detected by Real-time fluorescent quantitative PCR (RT-PCR), and the expression level of IRS2, PI3K, Akt protein and phosphorylated IRS2, PI3K, Akt protein were evaluated by Western Blot. All the data were analyzed by SPSS 17.0. Four weeks of treatment with LWDHT could significantly decrease the level of FBG and FINS in serum, improve the cellular morphology of liver, kidney, pancreas tissue, and the expression of IRS2, PI3K, Akt mRNA and phosphorylated IRS2, PI3K, Akt

Draft Genome Sequence of Lactobacillus pobuzihii E100301T.

PubMed

Chiu, Chi-Ming; Chang, Chi-Huan; Pan, Shwu-Fen; Wu, Hui-Chung; Li, Shiao-Wen; Chang, Chuan-Hsiung; Lee, Yun-Shien; Chiang, Chih-Ming; Chen, Yi-Sheng

2013-05-09

Lactobacillus pobuzihii E100301(T) is a novel Lactobacillus species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to Lactobacillus acidipiscis, but its phenotypic characteristics can be clearly distinguished from those of L. acidipiscis. We present the draft genome sequence of strain L. pobuzihii E100301(T).

A novel automated method for doing registration and 3D reconstruction from multi-modal RGB/IR image sequences

NASA Astrophysics Data System (ADS)

Kirby, Richard; Whitaker, Ross

2016-09-01

In recent years, the use of multi-modal camera rigs consisting of an RGB sensor and an infrared (IR) sensor have become increasingly popular for use in surveillance and robotics applications. The advantages of using multi-modal camera rigs include improved foreground/background segmentation, wider range of lighting conditions under which the system works, and richer information (e.g. visible light and heat signature) for target identification. However, the traditional computer vision method of mapping pairs of images using pixel intensities or image features is often not possible with an RGB/IR image pair. We introduce a novel method to overcome the lack of common features in RGB/IR image pairs by using a variational methods optimization algorithm to map the optical flow fields computed from different wavelength images. This results in the alignment of the flow fields, which in turn produce correspondences similar to those found in a stereo RGB/RGB camera rig using pixel intensities or image features. In addition to aligning the different wavelength images, these correspondences are used to generate dense disparity and depth maps. We obtain accuracies similar to other multi-modal image alignment methodologies as long as the scene contains sufficient depth variations, although a direct comparison is not possible because of the lack of standard image sets from moving multi-modal camera rigs. We test our method on synthetic optical flow fields and on real image sequences that we created with a multi-modal binocular stereo RGB/IR camera rig. We determine our method's accuracy by comparing against a ground truth.

Complete genome sequence of Staphylothermus hellenicus P8T

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

Anderson, Iain; Wirth, Reinhard; Lucas, Susan

2011-01-01

Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

Formulation of Ames 24E2 IR-black coating

NASA Technical Reports Server (NTRS)

Smith, Sheldon M.

1991-01-01

The formulation of Ames 24E2 IR-black coating and a rationale for the selection of its components are given. The objective was to make a very rough, very thick, and highly absorbing coating to attenuate the specular reflectance of telescope baffles at far-IR wavelengths. Application and curing instructions are also given. Outgassing measurements are quite low following a 24-hour radiative cure.

Draft Genome Sequence of Lactobacillus pobuzihii E100301T

PubMed Central

Chiu, Chi-ming; Chang, Chi-huan; Pan, Shwu-fen; Wu, Hui-chung; Li, Shiao-wen; Chang, Chuan-hsiung; Lee, Yun-shien; Chiang, Chih-ming

2013-01-01

Lactobacillus pobuzihii E100301T is a novel Lactobacillus species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to Lactobacillus acidipiscis, but its phenotypic characteristics can be clearly distinguished from those of L. acidipiscis. We present the draft genome sequence of strain L. pobuzihii E100301T. PMID:23661478

IRS2 silencing increases apoptosis and potentiates the effects of ruxolitinib in JAK2V617F-positive myeloproliferative neoplasms

PubMed Central

de Melo Campos, Paula; Machado-Neto, João A.; Eide, Christopher A.; Savage, Samantha L.; Scopim-Ribeiro, Renata; da Silva Souza Duarte, Adriana; Favaro, Patricia; Lorand-Metze, Irene; Costa, Fernando F.; Tognon, Cristina E.; Druker, Brian J.; Saad, Sara T. Olalla; Traina, Fabiola

2016-01-01

The recurrent V617F mutation in JAK2 (JAK2V617F) has emerged as the primary contributor to the pathogenesis of myeloproliferative neoplasms (MPN). However, the lack of complete response in most patients treated with the JAK1/2 inhibitor, ruxolitinib, indicates the need for identifying pathways that cooperate with JAK2. Activated JAK2 was found to be associated with the insulin receptor substrate 2 (IRS2) in non-hematological cells. We identified JAK2/IRS2 binding in JAK2V617F HEL cells, but not in the JAK2WT U937 cell line. In HEL cells, IRS2 silencing decreased STAT5 phosphorylation, reduced cell viability and increased apoptosis; these effects were enhanced when IRS2 silencing was combined with ruxolitinib. In U937 cells, IRS2 silencing neither reduced cell viability nor induced apoptosis. IRS1/2 pharmacological inhibition in primary MPN samples reduced cell viability in JAK2V617F-positive but not JAK2WT specimens; combination with ruxolitinib had additive effects. IRS2 expression was significantly higher in CD34+ cells from essential thrombocythemia patients compared to healthy donors, and in JAK2V617F MPN patients when compared to JAK2WT. Our data indicate that IRS2 is a binding partner of JAK2V617F in MPN. IRS2 contributes to increased cell viability and reduced apoptosis in JAK2-mutated cells. Combined pharmacological inhibition of IRS2 and JAK2 may have a potential clinical application in MPN. PMID:26755644

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

PubMed

Schleheck, David; Weiss, Michael; Pitluck, Sam; Bruce, David; Land, Miriam L; Han, Shunsheng; Saunders, Elizabeth; Tapia, Roxanne; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Goodwin, Lynne; Pennacchio, Len; Nolan, Matt; Cook, Alasdair M; Kjelleberg, Staffan; Thomas, Torsten

2011-12-31

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

2D IR Spectroscopy using Four-Wave Mixing, Pulse Shaping, and IR Upconversion: A Quantitative Comparison

PubMed Central

Rock, William; Li, Yun-Liang; Pagano, Philip; Cheatum, Christopher M.

2013-01-01

Recent technological advances have led to major changes in the apparatuses used to collect 2D IR spectra. Pulse shaping offers several advantages including rapid data collection, inherent phase stability, and phase cycling capabilities. Visible array detection via upconversion allows the use of visible detectors that are cheaper, faster, more sensitive, and less noisy than IR detectors. However, despite these advantages, many researchers are reluctant to implement these technologies. Here we present a quantitative study of the S/N of 2D IR spectra collected with a traditional four-wave mixing (FWM) apparatus, with a pulse shaping apparatus, and with visible detection via upconversion to address the question of whether or not weak chromophores at low concentrations are still accessible with such an apparatus. We find that the enhanced averaging capability of the pulse shaping apparatus enables the detection of small signals that would be challenging to measure even with the traditional FWM apparatus, and we demonstrate this ability on a sample of cyanylated dihydrofolate reductase (DHFR). PMID:23687988

Physical properties of the Ce 2 M Al 7 Ge 4 heavy-fermion compounds ( M = Co , Ir , Ni , Pd )

DOE PAGES

Ghimire, N. J.; Cary, S. K.; Eley, S.; ...

2016-05-23

Here, we report the synthesis, crystal structure, and characterization by means of single-crystal x-ray diffraction, neutron powder diffraction, and magnetic, thermal, and transport measurements of the new heavy-fermion compounds Ce 2MAl 7Ge 4 (M=Co,Ir,Ni,Pd). These compounds crystallize in a noncentrosymmetric tetragonal space group Pmore » $$\\bar{4}$$2 1m, consisting of layers of square nets of Ce atoms separated by Ge-Al and M-Al-Ge blocks. Ce 2CoAl 7Ge 4,Ce 2IrAl 7Ge 4, and Ce 2NiAl 7Ge 4 order magnetically below TM=1.8, 1.6, and 0.8 K, respectively. There is no evidence of magnetic ordering in Ce 2PdAl 7Ge 4 down to 0.4 K. Furthermore, the small amount of entropy released in the magnetic state of Ce 2MAl 7Ge 4 (M = Co, Ir, Ni) and the reduced specific heat jump at T M suggest a strong Kondo interaction in these materials. Ce 2PdAl 7Ge 4 shows non-Fermi liquid behavior, possibly due to the presence of a nearby quantum critical point.« less

A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences

PubMed Central

Nagano, Yukio; Furuhashi, Hirofumi; Inaba, Takehito; Sasaki, Yukiko

2001-01-01

Complementary DNA encoding a DNA-binding protein, designated PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1), was isolated from peas. The amino acid sequence of the protein is similar to those of other uncharacterized proteins predicted from the genome sequences of higher plants. However, no paralogous sequences have been found outside the plant kingdom. Multiple alignments among these paralogous proteins show that several cysteine and histidine residues are invariant, suggesting that these proteins are a novel class of zinc-dependent DNA-binding proteins with two distantly located regions, C-x2-H-x11-C-x2-C-x(4–5)-C-x2-C-x(3–7)-H-x2-H and C-x2-C-x(10–11)-C-x3-C. In an electrophoretic mobility shift assay, the zinc chelator 1,10-o-phenanthroline inhibited DNA binding, and two distant zinc-binding regions were required for DNA binding. A protein blot with 65ZnCl2 showed that both regions are required for zinc-binding activity. The PLATZ1 protein non-specifically binds to A/T-rich sequences, including the upstream region of the pea GTPase pra2 and plastocyanin petE genes. Expression of the PLATZ1 repressed those of the reporter constructs containing the coding sequence of luciferase gene driven by the cauliflower mosaic virus (CaMV) 35S90 promoter fused to the tandem repeat of the A/T-rich sequences. These results indicate that PLATZ1 is a novel class of plant-specific zinc-dependent DNA-binding protein responsible for A/T-rich sequence-mediated transcriptional repression. PMID:11600698

The relationship between visfatin and HOMA-IR in hypertensive patients, and the effect of antihypertensive drugs on visfatin and HOMA-IR in hypertensive patients with insulin resistance.

PubMed

Lan, Jianjun; Chen, Xiaoni; Chen, Xiaoping; Wang, Si; Zhang, Xin; Wu, Kai; He, Sen; Peng, Yong; Jiang, Lingyun; Li, Longxin; Wan, Liyan

2011-10-01

To investigate the correlation between serum visfatin and insulin resistance (IR) in non-diabetic essential hypertensive (EH) patients with and without IR, and to evaluate the effect of antihypertensive treatment on serum visfatin and IR in these patients. A total of 81 non-diabetic EH patients, including 54 with IR and 27 without IR, were enrolled. After two weeks wash-out, patients with IR were randomly assigned to telmisartan (group T) or amlodipine (group A) for 6 months. Blood samples were taken before and after treatment for measurement of routine biochemical parameters, visfatin and insulin resistance (measured by HOMA-IR). Visfatin was independently correlated with HOMA-IR (r=0.845, P=0.000). After 6 months of treatment, both drugs lowered HOMA-IR, more significantly so in group T than group A (P=0.010). Serum visfatin levels increased in group T but decreased in group A. Serum visfatin levels were higher in non-diabetic EH patients with IR compared with those without IR. Visfatin is independently correlated with HOMA-IR. Telmisartan lowers HOMA-IR to a greater extent than amlodipine. Interestingly, serum visfatin increased with telmisartan yet decreased with amlodipine treatment. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Two-Magnon Raman Scattering and Pseudospin-Lattice Interactions in Sr_{2}IrO_{4} and Sr_{3}Ir_{2}O_{7}.

PubMed

Gretarsson, H; Sung, N H; Höppner, M; Kim, B J; Keimer, B; Le Tacon, M

2016-04-01

We have used Raman scattering to investigate the magnetic excitations and lattice dynamics in the prototypical spin-orbit Mott insulators Sr_{2}IrO_{4} and Sr_{3}Ir_{2}O_{7}. Both compounds exhibit pronounced two-magnon Raman scattering features with different energies, line shapes, and temperature dependencies, which in part reflect the different influence of long-range frustrating exchange interactions. Additionally, we find strong Fano asymmetries in the line shapes of low-energy phonon modes in both compounds, which disappear upon cooling below the antiferromagnetic ordering temperatures. These unusual phonon anomalies indicate that the spin-orbit coupling in Mott-insulating iridates is not sufficiently strong to quench the orbital dynamics in the paramagnetic state.

Epitaxial growth of Al9Ir2 intermetallic compound on Al(100): Mechanism and interface structure

NASA Astrophysics Data System (ADS)

Kadok, J.; Pussi, K.; Šturm, S.; Ambrožič, B.; Gaudry, É.; de Weerd, M.-C.; Fournée, V.; Ledieu, J.

2018-04-01

The adsorption of Ir adatoms on Al(100) has been investigated under various exposures and temperature conditions. The experimental and theoretical results reveal a diffusion of Ir adatoms within the Al(100) surface selvedge already at 300 K. Above 593 K, two domains of a (√{5 }×√{5 }) R 26 .6∘ phase are identified by low energy electron diffraction (LEED) and scanning tunneling microscopy measurements. This phase corresponds to the initial growth of an Al9Ir2 compound at the Al(100) surface. The Al9Ir2 intermetallic domains are terminated by bulklike pure Al layers. The structural stability of Al9Ir2 (001) grown on Al(100) has been analyzed by density functional theory based calculations. Dynamical LEED analysis is consistent with an Ir adsorption leading to the growth of an Al9Ir2 intermetallic compound. We propose that the epitaxial relationship Al9Ir2(001 ) ∥Al (100) and Al9Ir2[100 ] ∥Al [031 ]/[013 ] originates from a matching of Al atomic arrangements present both on Al(100) and on pure Al(001) layers present in the Al9Ir2 compound. Finally, the interface between Al9Ir2 precipitates and the Al matrix has been characterized by transmission electron microscopy measurements. The cross-sectional observations are consistent with the formation of Al9Ir2 (001) compounds. These measurements indicate an important Ir diffusion within Al(100) near the surface region. The coherent interface between Al9Ir2 and the Al matrix is sharp.

Isotropic three-dimensional T2 mapping of knee cartilage: Development and validation.

PubMed

Colotti, Roberto; Omoumi, Patrick; Bonanno, Gabriele; Ledoux, Jean-Baptiste; van Heeswijk, Ruud B

2018-02-01

1) To implement a higher-resolution isotropic 3D T 2 mapping technique that uses sequential T 2 -prepared segmented gradient-recalled echo (Iso3DGRE) images for knee cartilage evaluation, and 2) to validate it both in vitro and in vivo in healthy volunteers and patients with knee osteoarthritis. The Iso3DGRE sequence with an isotropic 0.6 mm spatial resolution was developed on a clinical 3T MR scanner. Numerical simulations were performed to optimize the pulse sequence parameters. A phantom study was performed to validate the T 2 estimation accuracy. The repeatability of the sequence was assessed in healthy volunteers (n = 7). T 2 values were compared with those from a clinical standard 2D multislice multiecho (MSME) T 2 mapping sequence in knees of healthy volunteers (n = 13) and in patients with knee osteoarthritis (OA, n = 5). The numerical simulations resulted in 100 excitations per segment and an optimal radiofrequency (RF) excitation angle of 15°. The phantom study demonstrated a good correlation of the technique with the reference standard (slope 0.9 ± 0.05, intercept 0.2 ± 1.7 msec, R 2 ≥ 0.99). Repeated measurements of cartilage T 2 values in healthy volunteers showed a coefficient of variation of 5.6%. Both Iso3DGRE and MSME techniques found significantly higher cartilage T 2 values (P < 0.03) in OA patients. Iso3DGRE precision was equal to that of the MSME T 2 mapping in healthy volunteers, and significantly higher in OA (P = 0.01). This study successfully demonstrated that high-resolution isotropic 3D T 2 mapping for knee cartilage characterization is feasible, accurate, repeatable, and precise. The technique allows for multiplanar reformatting and thus T 2 quantification in any plane of interest. 1 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:362-371. © 2017 International Society for Magnetic Resonance in Medicine.

The excitation mechanism of btp2 Ir(acac) in CBP host.

PubMed

Xiao-Bo, Zhang; Fu-Xiang, Wei

2017-05-01

Whether bis(2-(2'-benzo[4,5-α]thienyl)pyridinato-N,C3')iridium(acetylacetonate) (btp 2 Ir(acac)) emission comes from carrier trapping and/or energy transfer, when doped in the 4,4'-bis(N-carbazolyl)biphenyl (CBP) host in organic light-emitting devices, is not clear; therefore, the btp 2 Ir(acac) emission in CBP hosts was studied. In the red-doped device, both N,N'-bis(1-naphthyl)-N,N'-diphenyl-1.1'-bipheny1-4-4'-diamine (NPB) and (1,1'-biphenyl-4'-oxy)bis(8-hydroxy-2-methylquinolinato)-aluminum (BAlq) emission appeared, which illustrated that CBP excitons cannot be formed at two emissive layer (EML) interfaces in the device. In the co-doped devices, NPB and BAlq emissions disappear and 1,4-bis[2-(3-N-ethylcarbazoryl)vinyl]benzene (BCzVB) emission appears, illustrating the formation of CBP excitons at two EML interfaces in these devices. The reason for this difference was analyzed and it was found that holes in the NPB layer could be made directly into the CBP host in the EML interface of the red-doped device. In contrast, holes were injected into CBP host via the btp 2 Ir(acac)/BCzVB dopants in the co-doped devices, which facilitated hole injection from the NPB layer to the EML, leading to the formation of CBP excitons at two EML interfaces in the co-doped devices. Therefore, btp 2 Ir(acac) emission was caused by carrier trapping in the red-doped device, while, in the co-doped devices, it resulted from both carrier trapping and energy transfer from the CBP. Furthermore, it was revealed that the carrier trapping mechanism is less efficient than the energy transfer mechanism for btp 2 Ir(acac) excitation in co-doped devices. In summary, our results clarified the excitation mechanism of btp 2 Ir(acac) in the CBP host. Copyright © 2016 John Wiley & Sons, Ltd.

SU-F-T-13: Transit Dose Comparisons for Co-60 and Ir-192 HDR Sources

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

Gimenez-Alventosa, V; Ballester, F; Vijande, J

Purpose: The purpose of this study is to compare the transit dose due to the movement of high dose rate (HDR) Ir-192 and Co-60 sources along the transfer tube. This is performed by evaluating air-kerma differences in the vicinity of the transfer tube when both sources are moved with the same velocity from a HDR brachytherapy afterloader into a patient. Methods: Monte Carlo simulations have been performed using PENELOPE2014. mHDR-v2 and Flexisource sources have been considered. Collisional kerma has been scored. The sources were simulated within a plastic catheter located in an infinite air phantom. The movement of the seedmore » was included by displacing their positions along the connecting catheter from z=−75 cm to z=+75 cm and combining them. Backscatter from the afterloader and the patient was not considered. Since modern afterloaders like Flexitron (Elekta) or Saginova (Bebig) are able to use equally Ir-192 and Co-60 sources it was assumed that both sources are displaced with equal speed. Typical content activity values were provided by the manufacturer (460 GBq for Ir-192 and 75 GBq for Co-60). Results: 2D distributions were obtained with type-A uncertainties (k=2) less than 0.01%. From those, the air kerma ratio Co-60/Ir-192 was evaluated weighted by their corresponding activities. It was found that it varies slowly with distance (less than 10% variation) but strongly in time due to the shorter half-life of the Ir-192 (73.83 days). The maximum ratio is located close to the catheter with a value of 0.57 when both sources are installed by the manufacturer, while increasing up to 1.25 at the end of the recommended working life (90 days) of the Ir-192 source. Conclusion: Air-kerma ratios are almost constant (0.51–0.57) in the vicinity of the source. Nevertheless, air-kerma ratios increase rapidly whenever the Ir-192 is approaching the end of its life.« less

FT-IR SOLUTION SPECTRA OF PROPYL SULFIDE, PROPYL SULFOXIDE, AND PROPYL SULFONE

EPA Science Inventory

FT-IR spectra were obtained of 0.5% volumetric solutions of propyl sulfide, propyl sulfoxide, and propyl sulfone in hexane, CCl4, CS2, and CHCl3 to assist in the assignment of FT-IR-PAS spectra of propyl sulfoxide sorbed within the structure of several peats and onto cellulose. T...

Detection and Tracking of NY-ESO-1-Specific CD8+ T Cells by High-Throughput T Cell Receptor β (TCRB) Gene Rearrangements Sequencing in a Peptide-Vaccinated Patient.

PubMed

Miyai, Manami; Eikawa, Shingo; Hosoi, Akihiro; Iino, Tamaki; Matsushita, Hirokazu; Isobe, Midori; Uenaka, Akiko; Udono, Heiichiro; Nakajima, Jun; Nakayama, Eiichi; Kakimi, Kazuhiro

2015-01-01

Comprehensive immunological evaluation is crucial for monitoring patients undergoing antigen-specific cancer immunotherapy. The identification and quantification of T cell responses is most important for the further development of such therapies. Using well-characterized clinical samples from a high responder patient (TK-f01) in an NY-ESO-1f peptide vaccine study, we performed high-throughput T cell receptor β-chain (TCRB) gene next generation sequencing (NGS) to monitor the frequency of NY-ESO-1-specific CD8+ T cells. We compared these results with those of conventional immunological assays, such as IFN-γ capture, tetramer binding and limiting dilution clonality assays. We sequenced human TCRB complementarity-determining region 3 (CDR3) rearrangements of two NY-ESO-1f-specific CD8+ T cell clones, 6-8L and 2F6, as well as PBMCs over the course of peptide vaccination. Clone 6-8L possessed the TCRB CDR3 gene TCRBV11-03*01 and BJ02-01*01 with amino acid sequence CASSLRGNEQFF, whereas 2F6 possessed TCRBV05-08*01 and BJ02-04*01 (CASSLVGTNIQYF). Using these two sequences as models, we evaluated the frequency of NY-ESO-1-specific CD8+ T cells in PBMCs ex vivo. The 6-8L CDR3 sequence was the second most frequent in PBMC and was present at high frequency (0.7133%) even prior to vaccination, and sustained over the course of vaccination. Despite a marked expansion of NY-ESO-1-specific CD8+ T cells detected from the first through 6th vaccination by tetramer staining and IFN-γ capture assays, as evaluated by CDR3 sequencing the frequency did not increase with increasing rounds of peptide vaccination. By clonal analysis using 12 day in vitro stimulation, the frequency of B*52:01-restricted NY-ESO-1f peptide-specific CD8+ T cells in PBMCs was estimated as only 0.0023%, far below the 0.7133% by NGS sequencing. Thus, assays requiring in vitro stimulation might be underestimating the frequency of clones with lower proliferation potential. High-throughput TCRB sequencing using NGS

Detection and Tracking of NY-ESO-1-Specific CD8+ T Cells by High-Throughput T Cell Receptor β (TCRB) Gene Rearrangements Sequencing in a Peptide-Vaccinated Patient

PubMed Central

Miyai, Manami; Eikawa, Shingo; Hosoi, Akihiro; Iino, Tamaki; Matsushita, Hirokazu; Isobe, Midori; Uenaka, Akiko; Udono, Heiichiro; Nakajima, Jun; Nakayama, Eiichi; Kakimi, Kazuhiro

2015-01-01

Comprehensive immunological evaluation is crucial for monitoring patients undergoing antigen-specific cancer immunotherapy. The identification and quantification of T cell responses is most important for the further development of such therapies. Using well-characterized clinical samples from a high responder patient (TK-f01) in an NY-ESO-1f peptide vaccine study, we performed high-throughput T cell receptor β-chain (TCRB) gene next generation sequencing (NGS) to monitor the frequency of NY-ESO-1-specific CD8+ T cells. We compared these results with those of conventional immunological assays, such as IFN-γ capture, tetramer binding and limiting dilution clonality assays. We sequenced human TCRB complementarity-determining region 3 (CDR3) rearrangements of two NY-ESO-1f-specific CD8+ T cell clones, 6-8L and 2F6, as well as PBMCs over the course of peptide vaccination. Clone 6-8L possessed the TCRB CDR3 gene TCRBV11-03*01 and BJ02-01*01 with amino acid sequence CASSLRGNEQFF, whereas 2F6 possessed TCRBV05-08*01 and BJ02-04*01 (CASSLVGTNIQYF). Using these two sequences as models, we evaluated the frequency of NY-ESO-1-specific CD8+ T cells in PBMCs ex vivo. The 6-8L CDR3 sequence was the second most frequent in PBMC and was present at high frequency (0.7133%) even prior to vaccination, and sustained over the course of vaccination. Despite a marked expansion of NY-ESO-1-specific CD8+ T cells detected from the first through 6th vaccination by tetramer staining and IFN-γ capture assays, as evaluated by CDR3 sequencing the frequency did not increase with increasing rounds of peptide vaccination. By clonal analysis using 12 day in vitro stimulation, the frequency of B*52:01-restricted NY-ESO-1f peptide-specific CD8+ T cells in PBMCs was estimated as only 0.0023%, far below the 0.7133% by NGS sequencing. Thus, assays requiring in vitro stimulation might be underestimating the frequency of clones with lower proliferation potential. High-throughput TCRB sequencing using NGS

High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

DOE PAGES

Laviad, Sivan; Lapidus, Alla; Han, James; ...

2015-05-27

Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. We find the DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins andmore » 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.« less

Whole genome sequence of Enterobacter ludwigii type strain EN-119T, isolated from clinical specimens.

PubMed

Li, Gengmi; Hu, Zonghai; Zeng, Ping; Zhu, Bing; Wu, Lijuan

2015-04-01

Enterobacter ludwigii strain EN-119(T) is the type strain of E. ludwigii, which belongs to the E. cloacae complex (Ecc). This strain was first reported and nominated in 2005 and later been found in many hospitals. In this paper, the whole genome sequencing of this strain was carried out. The total genome size of EN-119(T) is 4952,770 bp with 4578 coding sequences, 88 tRNAs and 10 rRNAs. The genome sequence of EN-119(T) is the first whole genome sequence of E. ludwigii, which will further our understanding of Ecc. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Electronic structure of Rh and Ru doped Sr2IrO4

NASA Astrophysics Data System (ADS)

Chikara, Shalinee; Fabbris, Gilberto; Terzic, Jasminka; Qi, Tongfei; Butrouna, Kamal; Veiga, Larissa; Souza Neto, Narcizo; Cao, Gang; Haskel, Daniel

2014-03-01

Sr2IrO4 is a spin-orbit interaction(SOI) assisted insulator. It has been proposed that the weaker SOI in the 4 d -substituted Sr2Ir1-x(Ru, Rh)xO4 closes the insulating gap, rendering it a paramagnetic metal. Rh(4d5) is isoelectronic to Ir(5d5) whereas Ru(4d4) has one less electron in the 4 d -band. The AFM-I/PM-M transition takes place at lower x for Ru than Rh, presumably due to the effect of hole doping. X-ray absorption near edge structure (XANES) and x-ray magnetic circular dichroism (XMCD) measurements at the Ir L2 , 3 edges show that < L . S > is non-zero and independent of x. This is indicative of a strong local 5 d spin orbit interaction that is rather insensitive to the 4 d doping. In contrast, measurements at the L2 , 3 edges of Ru and Rh show < L . S > ~ 0 for all x. The results point to the importance of local 4 d / 5 d - 2 p hybridization as opposed to 4 d - 5 d band formation in the Rh and Ru doped Sr2IrO4.

The complete mitochondrial genome sequence of the spider habronattus oregonensis reveals rearranged and extremely truncated tRNAs

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

Masta, Susan E.; Boore, Jeffrey L.

2004-01-31

We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TYC arm stem pairings, and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fullymore » paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems in order to allow the tRNAs to function. At least seven tRN As are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunit 2 and 3 genes apparently use UUG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381 bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that post transcriptional RNA editing can likely maintain function of the tRNAs while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome.« less

Multicomponent T2 relaxation studies of the avian egg.

PubMed

Mitsouras, Dimitris; Mulkern, Robert V; Maier, Stephan E

2016-05-01

To investigate the tissue-like multiexponential T2 signal decays in avian eggs. Transverse relaxation studies of raw, soft-boiled and hard-boiled eggs were performed at 3 Tesla using a three-dimensional Carr-Purcell-Meiboom-Gill imaging sequence. Signal decays over a TE range of 11 to 354 ms were fitted assuming single- and multicomponent signal decays with up to three separately decaying components. Fat saturation was used to facilitate spectral assignment of observed decay components. Egg white, yolk and the centrally located latebra all demonstrate nonmonoexponential T2 decays. Specifically, egg white exhibits two-component decays with intermediate and long T2 times. Meanwhile, yolk and latebra are generally best characterized with triexponential decays, with short, intermediate and very long T2 decay times. Fat saturation revealed that the intermediate component of yolk could be attributed to lipids. Cooking of the egg profoundly altered the decay curves. Avian egg T2 decay curves cover a wide range of decay times. Observed T2 components in yolk and latebra as short as 10 ms, may prove valuable for testing clinical sequences designed to measure short T2 components, such as myelin-associated water in the brain. Thus we propose that the egg can be a versatile and widely available MR transverse relaxation phantom. © 2015 Wiley Periodicals, Inc.

The natural logarithm of zinc-α2-glycoprotein/HOMA-IR is a better predictor of insulin sensitivity than the product of triglycerides and glucose and the other lipid ratios.

PubMed

Qu, Chunmei; Zhou, Xiaoxin; Yang, Gangyi; Li, Ling; Liu, Hua; Liang, Zerong

2016-03-01

The euglycemic-hyperinsulinemic clamp (EHC) is not available in most clinical settings and is costly, time consuming and invasive, and requires trained staff. Therefore, an accessible and inexpensive test to identify insulin resistance (IR) is needed. The aim of this study is to assess whether zinc-α2-glycoprotein (ZAG) index [Ln ZAG/homeostasis model assessment of IR (HOMA-IR)] is a better surrogate index for estimating IR or metabolic syndrome (MetS) compared with other surrogate indices. We performed a population-based cross-sectional study. Two hundred healthy subjects, 102 polycystic ovary syndrome (PCOS) patients, 97 newly diagnosed type 2 diabetes mellitus (nT2DM) and 84 impaired glucose tolerance (IGT) subjects were enrolled. The EHC was performed to identify IR. Circulating ZAG and adiponectin levels were determined by ELISA. The ZAG index was significantly lower in participants with IR including IGT, nT2DM and PCOS than in those without IR. In addition, subjects with MetS had lower ZAG indices and higher the product of fasting triglycerides and glucose (TyG) indices than those without MetS. The ZAG index showed a significantly stronger association with M values than the other surrogate indices, whereas the TyG index showed a stronger association with MetS. The optimal cutoff value of the ZAG index for detection of IR was 2.97 with a sensitivity of 88% and a specificity of 91%, whereas the optimal cutoff value of TyG index for detection of MetS was 4.90 with a sensitivity of 82% and a specificity of 86%. The ZAG index is a better marker than the other surrogate indices for identifying IR, whereas the TyG index has high sensitivity and specificity for identifying MetS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Clinical usefulness of the visibility of the transcerebral veins at 3T on T2*-weighted sequence in acute stroke patients.

PubMed

Rosso, Charlotte; Belleville, Martin; Pires, Christine; Dormont, Didier; Crozier, Sophie; Chiras, Jacques; Samson, Yves; Bonneville, Fabrice

2012-06-01

The objective of this work was to investigate the clinical usefulness of the visibility of the transcerebral veins (VTV) in acute ischemic stroke patients at 3T. Sixty consecutive carotid artery territory stroke patients were included retrospectively. Two readers categorized the VTV on T2*-weighted sequence at 3T for each hemisphere, and asymmetry of this sign was assessed between each hemisphere by an asymmetry index (AI) using a three-item scale. The VTV and AI were correlated with clinical and radiological covariates. Particular interest was focused on patients for whom initial diffusion-weighted imaging alone was inconclusive. VTV were detected in the stroke hemisphere in 58.3% (n = 35) and in the contralateral side in 10% (n = 6, p<0.0001). Asymmetry of the VTV between ischemic and contralateral hemispheres was present in 53.3% (n = 32). Intracranial artery occlusion, final infarct volume and symptomatic hemorrhagic transformation were correlated with a higher AI at baseline (ρ = 0.563, ρ = 0.291, and ρ = 0.285, p<0.05, respectively). Three hyperacute stroke patients with subtle DWI high signal intensity at admission demonstrated VTV. The pathological value of the VTV seems to reside in its asymmetry between hemispheres, as it was correlated with important clinical parameters. This study also suggests that the VTV could be a supportive finding in stroke diagnosis, especially when DWI is unreliable. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

In search of the elusive IrB 2: Can mechanochemistry help?

DOE PAGES

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina; ...

2015-10-20

We produced hexagonal ReB 2-type IrB 2 diboride and orthorhombic IrB monoboride phases, that were previously unknown and saw them produced by mechanochemical syntheses. High energy ball milling of elemental Ir and B powder for 30 h, followed by annealing of the powder at 1050 °C for 48 h, resulted in the formation of the desired phases. Both traditional laboratory and high resolution synchrotron X-ray diffraction (XRD) analyses were used for phase identification of the synthesized powder. Additionally, scanning electron microscopy and transmission electron microscopy were employed, along with XRD, to further characterize the microstructure of the phases produced.

In search of the elusive IrB 2: Can mechanochemistry help?

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

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina

We produced hexagonal ReB 2-type IrB 2 diboride and orthorhombic IrB monoboride phases, that were previously unknown and saw them produced by mechanochemical syntheses. High energy ball milling of elemental Ir and B powder for 30 h, followed by annealing of the powder at 1050 °C for 48 h, resulted in the formation of the desired phases. Both traditional laboratory and high resolution synchrotron X-ray diffraction (XRD) analyses were used for phase identification of the synthesized powder. Additionally, scanning electron microscopy and transmission electron microscopy were employed, along with XRD, to further characterize the microstructure of the phases produced.

Metal-Insulator Transition in Epitaxial Pyrochlore Iridates Bi2Ir2O7 thin Films

NASA Astrophysics Data System (ADS)

Chu, Jiun-Haw; Liu, Jian; Yi, Di; Rayan-Serrao, C.; Suresha, S.; Marti, Xavi; Riggs, Scott; Shapiro, Max; Ian, Fisher; Ramesh, R.

2013-03-01

Recently there is a surge of interest in searching for topological order in correlated electronic systems such as transition metal oxides. The strong spin-orbit interaction of 5d electrons and the geometric frustration in the crystal lattice make the pyrochlore iridate(A2Ir2O7) an ideal candidate to achieve this goal. Pioneering experiments on bulk polycrystalline and single crystal samples revealed a temperature dependent metal-insulator transition coupled to a long range magnetic order, and the transition temperature can be tuned by either A-site ionic radius or an external pressure. In this talk we present our efforts to understand and control the metal-insulator transition and the underlying electronic structure of pyrochlore iridates via epitaxial Bi2Ir2O7 thin films. Bulk Bi2Ir2O7 is located at the metallic side of the phase diagram. However as the film's thickness decreases the transport evolves from a metallic to a strongly localized character. Resonant X-ray spectroscopy suggests that the density of states near Fermi level is dominated by the Ir Je ff =1/2 states. Intriguingly, the magnetoresistance shows a linear field dependence over a wide range of fields at low temperatures, which is possibly consistent with the existence of Dirac nodes.

The Yo-Yo IR2 test: physiological response, reliability, and application to elite soccer.

PubMed

Krustrup, Peter; Mohr, Magni; Nybo, Lars; Jensen, Jack Majgaard; Nielsen, Jens Jung; Bangsbo, Jens

2006-09-01

To examine the physiological response, reliability, and validity of the Yo-Yo intermittent recovery level 2 test (Yo-Yo IR2). Thirteen normally trained male subjects carried out four Yo-Yo IR2 tests, an incremental treadmill test (ITT), and various sprint tests. Muscle biopsies and blood samples were obtained, and heart rate was measured before, during, and after the Yo-Yo IR2 test. Additionally, 119 Scandinavian elite soccer players carried out the Yo-Yo IR2 test on two to four occasions. Yo-Yo IR2 performance was 591 +/- 43 (320-920) m or 4.3 (2.6-7.9) min. Test-retest coefficient of variation in distance covered was 9.6% (N = 29). Heart rate (HR) at exhaustion was 191 +/- 3 bpm, or 98 +/- 1% HRmax. Muscle lactate was 41.7 +/- 5.4 and 68.5 +/- 7.6 mmol x kg(-1) d.w. at 85 and 100% of exhaustion time, respectively, with corresponding muscle CP values of 40.4 +/- 5.2 and 29.4 +/- 4.7 mmol x kg(-1) d.w. Peak blood lactate was 13.6 +/- 0.5 mM. Yo-Yo IR2 performance was correlated to ITT performance (r = 0.74, P < 0.05) and VO2max (r = 0.56, P < 0.05) but not to 30- and 50-m sprint performance. Yo-Yo IR2 performance was better (P < 0.05) for international elite soccer players than for moderate elite players (1059 +/- 35 vs 771 +/- 26 m) and better (P < 0.05) for central defenders (N = 21), fullbacks (N = 20), and midfielders (N = 48) than for goalkeepers (N = 6) and attackers (N = 24). Fifteen elite soccer players improved (P < 0.05) Yo-Yo IR2 performance by 42 +/- 8% during 8 wk of preseasonal training. This study demonstrates that the Yo-Yo IR2 test is reproducible and can be used to evaluate an athlete's ability to perform intense intermittent exercise with a high rate of aerobic and anaerobic energy turnover. Specifically, the Yo-Yo IR2 test was shown to be a sensitive tool to differentiate between intermittent exercise performance of soccer players in different seasonal periods and at different competitive levels and playing positions.

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

PubMed Central

Yates, Kathleen B.; Bi, Kevin; Darko, Samuel; Godec, Jernej; Gerdemann, Ulrike; Swadling, Leo; Douek, Daniel C.; Klenerman, Paul; Barnes, Eleanor J.; Sharpe, Arlene H.

2017-01-01

Abstract The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present TRAPeS, a publicly available tool that can efficiently extract TCR sequence information from short-read scRNA-seq libraries. We apply it to investigate heterogeneity in the CD8+ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. Coupling TRAPeS with transcriptome analysis of CD8+ T cells specific for a single epitope from Yellow Fever Virus (YFV), we show that the recently described ‘naive-like’ memory population have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype cells. This suggests that TCR usage is associated with the differentiation state of the CD8+ T cell response to YFV. PMID:28934479

CoRoT-2b: a Tidally Inflated, Young Exoplanet?

NASA Astrophysics Data System (ADS)

Guillot, Tristan; Havel, M.

2009-09-01

CoRoT-2b is among the most anomalously large transiting exoplanet known. Due to its large mass (3.3 Mjup), its large radius ( 1.5 Rjup) cannot be explained by standard evolution models. Recipes that work for other anomalously large exoplanets (e.g. HD209458b), such as invoking kinetic energy transport in the planetary interior or increased opacities, clearly fail for CoRoT-2b. Interestingly, the planet's parent star is an active star with a large fraction (7 to 20%) of spots and a rapid rotation (4.5 days). We first model the star's evolution to accurately constrain the planetary parameters. We find that the stellar activity has little influence on the star's evolution and inferred parameters. However, stellar evolution models point towards two kind of solutions for the star-planet system: (i) a very young system (20-40 Ma) with a star still undergoing pre-main sequence contraction, and a planet which could have a radius as low as 1.4 Rjup, or (ii) a young main-sequence star (40 to 500 Ma) with a planet that is slightly more inflated ( 1.5 Rjup). In either case, planetary evolution models require a significant added internal energy to explain the inferred planet size: from a minimum of 3x1028 erg/s in case (i), to up to 1.5x1029 erg/s in case (ii). We find that evolution models consistently including planet/star tides are able to reproduce the inferred radius but only for a short period of time ( 10 Ma). This points towards a young age for the star/planet system and dissipation by tides due to either circularization or synchronization of the planet. Additional observations of the star (infrared excess due to disk?) and of the planet (precise Rossiter effect, IR secondary eclispe) would be highly valuable to understand the early evolution of star-exoplanet systems.

T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

PubMed Central

Fauzi, Hamid; Agyeman, Akwasi; Hines, Jennifer V.

2008-01-01

Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5′-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation. PMID:19152843

Radiative transfer modeling for analyses with Akatsuki/IR2 images

NASA Astrophysics Data System (ADS)

Sato, Takao M.; Satoh, Takehiko; Hashimoto, George L.; Lee, Yeon Joo; Sagawa, Hideo; Kasaba, Yasumasa

2017-10-01

The 2-micron camera (IR2) onboard Japanese Venus orbiter, Akatsuki had regularly observed Venus with four narrow-band filters (1.735, 2.02, 2.26, and 2.32 micron) from the late of March, 2016 until the electronic device was unable to control IR2 on December 9, 2016. For approximately nine months, we accumulated more than 3,000 dayside and nightside images of Venus. The main purposes of analyzing IR2 data are (i) to study the dynamics in the upper, middle, and lower atmosphere with the cloud-tracked winds, (ii) to derive the cloud top altitude with the 2.02 micron channel which is located in a CO2 absorption band, (iii) to deduce CO distribution, which is thought to be a good tracer of the atmospheric circulation below the massive clouds, by utilizing the 2.26 and 2.32 micron channels, and (iv) to investigate aerosol properties of the lower clouds with the 1.735 and 2.26 micron channels. For purposes (ii)-(iv), we have developed a line-by-line based radiative transfer model for generating synthetic radiance at the IR2 channels. For both solar and thermal radiation cases, adding doubling method (Hovenier et al., 2004; Liu and Weng, 2006) is selected for solving multiple scattering by clouds and molecules. We considered a total of eight molecules (H2O, CO2, CO, SO2, HF, HCl, OCS, and N2) and line parameters of the first three molecules are taken from HITEMP10 and those of the others are from HITRAN12. For all considered molecules, their line shapes are modelled as Voigt function with cutoff of 125 cm-1. For CO2, additional modification is done based on Tonkov et al. (1996). A cloud model consisting of four modal cloud particles with a mixture of 75% H2SO4 and 25% H2O is taken from Haus et al. (2013). This model was tested from near-infrared to mid-infrared ranges for the spectral analyses of Venus Express and Venera 15 data, which is useful for interpreting the very limited spectral information such as Akatsuki data. In this presentation, we will show the detail of

T cell receptor (TCR) structure of autologous melanoma-reactive cytotoxic T lymphocyte (CTL) clones: tumor-infiltrating lymphocytes overexpress in vivo the TCR beta chain sequence used by an HLA-A2- restricted and melanocyte-lineage-specific CTL clone